tomo: workflow/run_tomo.py annotate

annotate workflow/run_tomo.py @ 71:1cf15b61cd83 draft

planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213

author	rv43
date	Mon, 20 Mar 2023 13:56:57 +0000
parents	fba792d5f83b
children	d5e1d4ea2b7e

rev	line source
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1 #!/usr/bin/env python3
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	3 import logging
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	4 logger = logging.getLogger(__name__)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	5
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	6 import numpy as np
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	7 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	8 import numexpr as ne
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	9 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	10 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	11 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	12 import scipy.ndimage as spi
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	13 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	14 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	16 from multiprocessing import cpu_count
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	17 from nexusformat.nexus import *
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	18 from os import mkdir
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	19 from os import path as os_path
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	20 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	21 from skimage.transform import iradon
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	22 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	23 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	24 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	25 from skimage.restoration import denoise_tv_chambolle
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	26 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	27 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	28 from time import time
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	29 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	30 import tomopy
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	31 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	32 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	33 from yaml import safe_load, safe_dump
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	34
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	35 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	36 from msnctools.fit import Fit
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	37 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	38 from fit import Fit
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	39 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	40 from msnctools.general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	41 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	42 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	43 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	44 from general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	45 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	46 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	47
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	48 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	49 from workflow.models import import_scanparser, FlatField, TomoField, TomoWorkflow
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	50 from workflow.__version__ import __version__
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	51 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	52 pass
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	53
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	54 num_core_tomopy_limit = 24
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	55
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	56 def nxcopy(nxobject:NXobject, exclude_nxpaths:list[str]=[], nxpath_prefix:str='') -> NXobject:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	57 '''Function that returns a copy of a nexus object, optionally exluding certain child items.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	58
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	59 :param nxobject: the original nexus object to return a "copy" of
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	60 :type nxobject: nexusformat.nexus.NXobject
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	61 :param exlude_nxpaths: a list of paths to child nexus objects that
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	62 should be exluded from the returned "copy", defaults to `[]`
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	63 :type exclude_nxpaths: list[str], optional
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	64 :param nxpath_prefix: For use in recursive calls from inside this
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	65 function only!
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	66 :type nxpath_prefix: str
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	67 :return: a copy of `nxobject` with some children optionally exluded.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	68 :rtype: NXobject
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	69 '''
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	70
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	71 nxobject_copy = nxobject.__class__()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	72 if not len(nxpath_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	73 if 'default' in nxobject.attrs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	74 nxobject_copy.attrs['default'] = nxobject.attrs['default']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	75 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	76 for k, v in nxobject.attrs.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	77 nxobject_copy.attrs[k] = v
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	78
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	79 for k, v in nxobject.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	80 nxpath = os_path.join(nxpath_prefix, k)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	81
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	82 if nxpath in exclude_nxpaths:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	83 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	84
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	85 if isinstance(v, NXgroup):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	86 nxobject_copy[k] = nxcopy(v, exclude_nxpaths=exclude_nxpaths,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	87 nxpath_prefix=os_path.join(nxpath_prefix, k))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	88 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	89 nxobject_copy[k] = v
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	90
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	91 return(nxobject_copy)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	92
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	93 class set_numexpr_threads:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	94
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	95 def __init__(self, num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	96 if num_core is None or num_core < 1 or num_core > cpu_count():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	97 self.num_core = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	98 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	99 self.num_core = num_core
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	100
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	101 def __enter__(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	102 self.num_core_org = ne.set_num_threads(self.num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	103
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	104 def __exit__(self, exc_type, exc_value, traceback):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	105 ne.set_num_threads(self.num_core_org)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	106
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	107 class Tomo:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	108 """Processing tomography data with misalignment.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	109 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	110 def __init__(self, galaxy_flag=False, num_core=-1, output_folder='.', save_figs=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	111 test_mode=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	112 """Initialize with optional config input file or dictionary
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	113 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	114 if not isinstance(galaxy_flag, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	115 raise ValueError(f'Invalid parameter galaxy_flag ({galaxy_flag})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	116 self.galaxy_flag = galaxy_flag
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	117 self.num_core = num_core
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	118 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	119 if output_folder != '.':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	120 logger.warning('Ignoring output_folder in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	121 self.output_folder = '.'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	122 if test_mode != False:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	123 logger.warning('Ignoring test_mode in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	124 self.test_mode = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	125 if save_figs is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	126 logger.warning('Ignoring save_figs in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	127 save_figs = 'only'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	128 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	129 self.output_folder = os_path.abspath(output_folder)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	130 if not os_path.isdir(output_folder):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	131 mkdir(os_path.abspath(output_folder))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	132 if not isinstance(test_mode, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	133 raise ValueError(f'Invalid parameter test_mode ({test_mode})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	134 self.test_mode = test_mode
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	135 if save_figs is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	136 save_figs = 'no'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	137 self.test_config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	138 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	139 if save_figs != 'only':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	140 logger.warning('Ignoring save_figs in test mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	141 save_figs = 'only'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	142 if save_figs == 'only':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	143 self.save_only = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	144 self.save_figs = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	145 elif save_figs == 'yes':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	146 self.save_only = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	147 self.save_figs = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	148 elif save_figs == 'no':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	149 self.save_only = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	150 self.save_figs = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	151 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	152 raise ValueError(f'Invalid parameter save_figs ({save_figs})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	153 if self.save_only:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	154 self.block = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	155 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	156 self.block = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	157 if self.num_core == -1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	158 self.num_core = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	159 if not is_int(self.num_core, gt=0, log=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	160 raise ValueError(f'Invalid parameter num_core ({num_core})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	161 if self.num_core > cpu_count():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	162 logger.warning(f'num_core = {self.num_core} is larger than the number of available '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	163 f'processors and reduced to {cpu_count()}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	164 self.num_core= cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	165
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	166 def read(self, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	167 extension = os_path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	168 if extension == '.yml' or extension == '.yaml':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	169 with open(filename, 'r') as f:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	170 config = safe_load(f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	171 # if len(config) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	172 # raise ValueError(f'Multiple root entries in {filename} not yet implemented')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	173 # if len(list(config.values())[0]) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	174 # raise ValueError(f'Multiple sample maps in {filename} not yet implemented')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	175 return(config)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	176 elif extension == '.nxs':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	177 with NXFile(filename, mode='r') as nxfile:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	178 nxroot = nxfile.readfile()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	179 return(nxroot)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	180 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	181 raise ValueError(f'Invalid filename extension ({extension})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	182
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	183 def write(self, data, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	184 extension = os_path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	185 if extension == '.yml' or extension == '.yaml':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	186 with open(filename, 'w') as f:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	187 safe_dump(data, f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	188 elif extension == '.nxs':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	189 data.save(filename, mode='w')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	190 elif extension == '.nc':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	191 data.to_netcdf(os_path=filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	192 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	193 raise ValueError(f'Invalid filename extension ({extension})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	194
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	195 def gen_reduced_data(self, data, img_x_bounds=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	196 """Generate the reduced tomography images.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	197 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	198 logger.info('Generate the reduced tomography images')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	199
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	200 # Create plot galaxy path directory if needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	201 if self.galaxy_flag and not os_path.exists('tomo_reduce_plots'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	202 mkdir('tomo_reduce_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	203
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	204 if isinstance(data, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	205 # Create Nexus format object from input dictionary
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	206 wf = TomoWorkflow(**data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	207 if len(wf.sample_maps) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	208 raise ValueError(f'Multiple sample maps not yet implemented')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	209 # print(f'\nwf:\n{wf}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	210 nxroot = NXroot()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	211 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	212 for sample_map in wf.sample_maps:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	213 logger.info(f'Start constructing the {sample_map.title} map.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	214 import_scanparser(sample_map.station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	215 sample_map.construct_nxentry(nxroot, include_raw_data=False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	216 logger.info(f'Constructed all sample maps in {time()-t0:.2f} seconds.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	217 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	218 # Get test mode configuration info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	219 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	220 self.test_config = data['sample_maps'][0]['test_mode']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	221 elif isinstance(data, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	222 nxentry = data[data.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	223 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	224 raise ValueError(f'Invalid parameter data ({data})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	225
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	226 # Create an NXprocess to store data reduction (meta)data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	227 reduced_data = NXprocess()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	228
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	229 # Generate dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	230 if 'dark_field' in nxentry['spec_scans']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	231 reduced_data = self._gen_dark(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	232
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	233 # Generate bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	234 reduced_data = self._gen_bright(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	235
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	236 # Set vertical detector bounds for image stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	237 img_x_bounds = self._set_detector_bounds(nxentry, reduced_data, img_x_bounds=img_x_bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	238 logger.info(f'img_x_bounds = {img_x_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	239 reduced_data['img_x_bounds'] = img_x_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	240
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	241 # Set zoom and/or theta skip to reduce memory the requirement
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	242 zoom_perc, num_theta_skip = self._set_zoom_or_skip()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	243 if zoom_perc is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	244 reduced_data.attrs['zoom_perc'] = zoom_perc
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	245 if num_theta_skip is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	246 reduced_data.attrs['num_theta_skip'] = num_theta_skip
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	247
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	248 # Generate reduced tomography fields
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	249 reduced_data = self._gen_tomo(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	250
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	251 # Create a copy of the input Nexus object and remove raw and any existing reduced data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	252 if isinstance(data, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	253 exclude_items = [f'{nxentry._name}/reduced_data/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	254 f'{nxentry._name}/instrument/detector/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	255 f'{nxentry._name}/instrument/detector/image_key',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	256 f'{nxentry._name}/instrument/detector/sequence_number',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	257 f'{nxentry._name}/sample/rotation_angle',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	258 f'{nxentry._name}/sample/x_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	259 f'{nxentry._name}/sample/z_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	260 f'{nxentry._name}/data/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	261 f'{nxentry._name}/data/image_key',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	262 f'{nxentry._name}/data/rotation_angle',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	263 f'{nxentry._name}/data/x_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	264 f'{nxentry._name}/data/z_translation']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	265 nxroot = nxcopy(data, exclude_nxpaths=exclude_items)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	266 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	267
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	268 # Add the reduced data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	269 nxentry.reduced_data = reduced_data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	270
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	271 if 'data' not in nxentry:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	272 nxentry.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	273 nxentry.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	274 nxentry.data.makelink(nxentry.reduced_data.data.tomo_fields, name='reduced_data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	275 nxentry.data.makelink(nxentry.reduced_data.rotation_angle, name='rotation_angle')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	276 nxentry.data.attrs['signal'] = 'reduced_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	277
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	278 return(nxroot)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	279
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	280 def find_centers(self, nxroot, center_rows=None, center_stack_index=None):
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	281 """Find the calibrated center axis info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	282 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	283 logger.info('Find the calibrated center axis info')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	284
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	285 if not isinstance(nxroot, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	286 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	287 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	288 if not isinstance(nxentry, NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	289 raise ValueError(f'Invalid nxentry ({nxentry})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	290 if self.galaxy_flag:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	291 if center_rows is not None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	292 center_rows = tuple(center_rows)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	293 if not is_int_pair(center_rows):
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	294 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	295 elif center_rows is not None:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	296 logger.warning(f'Ignoring parameter center_rows ({center_rows})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	297 center_rows = None
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	298 if self.galaxy_flag:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	299 if center_stack_index is not None and not is_int(center_stack_index, ge=0):
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	300 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	301 elif center_stack_index is not None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	302 logger.warning(f'Ignoring parameter center_stack_index ({center_stack_index})')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	303 center_stack_index = None
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	304
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	305 # Create plot galaxy path directory and path if needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	306 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	307 if not os_path.exists('tomo_find_centers_plots'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	308 mkdir('tomo_find_centers_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	309 path = 'tomo_find_centers_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	310 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	311 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	312
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	313 # Check if reduced data is available
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	314 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	315 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	316
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	317 # Select the image stack to calibrate the center axis
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	318 # reduced data axes order: stack,theta,row,column
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	319 # Note: Nexus cannot follow a link if the data it points to is too big,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	320 # so get the data from the actual place, not from nxentry.data
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	321 tomo_fields_shape = nxentry.reduced_data.data.tomo_fields.shape
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	322 if len(tomo_fields_shape) != 4 or any(True for dim in tomo_fields_shape if not dim):
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	323 raise KeyError('Unable to load the required reduced tomography stack')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	324 num_tomo_stacks = tomo_fields_shape[0]
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	325 if num_tomo_stacks == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	326 center_stack_index = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	327 default = 'n'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	328 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	329 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	330 center_stack_index = self.test_config['center_stack_index']-1 # make offset 0
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	331 elif self.galaxy_flag:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	332 if center_stack_index is None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	333 center_stack_index = int(num_tomo_stacks/2)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	334 if center_stack_index >= num_tomo_stacks:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	335 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	336 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	337 center_stack_index = input_int('\nEnter tomography stack index to calibrate the '
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	338 'center axis', ge=1, le=num_tomo_stacks, default=int(1+num_tomo_stacks/2))
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	339 center_stack_index -= 1
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	340 default = 'y'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	341
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	342 # Get thetas (in degrees)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	343 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	344
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	345 # Get effective pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	346 if 'zoom_perc' in nxentry.reduced_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	347 eff_pixel_size = 100.*(nxentry.instrument.detector.x_pixel_size/
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	348 nxentry.reduced_data.attrs['zoom_perc'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	349 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	350 eff_pixel_size = nxentry.instrument.detector.x_pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	351
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	352 # Get cross sectional diameter
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	353 cross_sectional_dim = tomo_fields_shape[3]*eff_pixel_size
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	354 logger.debug(f'cross_sectional_dim = {cross_sectional_dim}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	355
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	356 # Determine center offset at sample row boundaries
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	357 logger.info('Determine center offset at sample row boundaries')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	358
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	359 # Lower row center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	360 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	361 lower_row = self.test_config['lower_row']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	362 elif self.galaxy_flag:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	363 if center_rows is None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	364 lower_row = 0
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	365 else:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	366 lower_row = min(center_rows)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	367 if not 0 <= lower_row < tomo_fields_shape[2]-1:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	368 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	369 else:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	370 lower_row = select_one_image_bound(
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	371 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, bound=0,
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	372 title=f'theta={round(thetas[0], 2)+0}',
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	373 bound_name='row index to find lower center', default=default, raise_error=True)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	374 logger.debug('Finding center...')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	375 t0 = time()
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	376 lower_center_offset = self._find_center_one_plane(
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	377 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:]),
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	378 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:],
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	379 lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	380 num_core=self.num_core)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	381 logger.debug(f'... done in {time()-t0:.2f} seconds')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	382 logger.debug(f'lower_row = {lower_row:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	383 logger.debug(f'lower_center_offset = {lower_center_offset:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	384
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	385 # Upper row center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	386 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	387 upper_row = self.test_config['upper_row']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	388 elif self.galaxy_flag:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	389 if center_rows is None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	390 upper_row = tomo_fields_shape[2]-1
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	391 else:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	392 upper_row = max(center_rows)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	393 if not lower_row < upper_row < tomo_fields_shape[2]:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	394 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	395 else:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	396 upper_row = select_one_image_bound(
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	397 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0,
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	398 bound=tomo_fields_shape[2]-1, title=f'theta={round(thetas[0], 2)+0}',
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	399 bound_name='row index to find upper center', default=default, raise_error=True)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	400 logger.debug('Finding center...')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	401 t0 = time()
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	402 upper_center_offset = self._find_center_one_plane(
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	403 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:]),
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	404 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:],
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	405 upper_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	406 num_core=self.num_core)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	407 logger.debug(f'... done in {time()-t0:.2f} seconds')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	408 logger.debug(f'upper_row = {upper_row:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	409 logger.debug(f'upper_center_offset = {upper_center_offset:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	410
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	411 center_config = {'lower_row': lower_row, 'lower_center_offset': lower_center_offset,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	412 'upper_row': upper_row, 'upper_center_offset': upper_center_offset}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	413 if num_tomo_stacks > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	414 center_config['center_stack_index'] = center_stack_index+1 # save as offset 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	415
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	416 # Save test data to file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	417 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	418 with open(f'{self.output_folder}/center_config.yaml', 'w') as f:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	419 safe_dump(center_config, f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	420
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	421 return(center_config)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	422
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	423 def reconstruct_data(self, nxroot, center_info, x_bounds=None, y_bounds=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	424 """Reconstruct the tomography data.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	425 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	426 logger.info('Reconstruct the tomography data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	427
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	428 if not isinstance(nxroot, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	429 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	430 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	431 if not isinstance(nxentry, NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	432 raise ValueError(f'Invalid nxentry ({nxentry})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	433 if not isinstance(center_info, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	434 raise ValueError(f'Invalid parameter center_info ({center_info})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	435
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	436 # Create plot galaxy path directory and path if needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	437 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	438 if not os_path.exists('tomo_reconstruct_plots'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	439 mkdir('tomo_reconstruct_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	440 path = 'tomo_reconstruct_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	441 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	442 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	443
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	444 # Check if reduced data is available
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	445 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	446 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	447
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	448 # Create an NXprocess to store image reconstruction (meta)data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	449 nxprocess = NXprocess()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	450
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	451 # Get rotation axis rows and centers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	452 lower_row = center_info.get('lower_row')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	453 lower_center_offset = center_info.get('lower_center_offset')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	454 upper_row = center_info.get('upper_row')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	455 upper_center_offset = center_info.get('upper_center_offset')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	456 if (lower_row is None or lower_center_offset is None or upper_row is None or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	457 upper_center_offset is None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	458 raise KeyError(f'Unable to find valid calibrated center axis info in {center_info}.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	459 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	460
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	461 # Get thetas (in degrees)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	462 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	463
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	464 # Reconstruct tomography data
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	465 # reduced data axes order: stack,theta,row,column
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	466 # reconstructed data order in each stack: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	467 # Note: Nexus cannot follow a link if the data it points to is too big,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	468 # so get the data from the actual place, not from nxentry.data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	469 if 'zoom_perc' in nxentry.reduced_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	470 res_title = f'{nxentry.reduced_data.attrs["zoom_perc"]}p'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	471 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	472 res_title = 'fullres'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	473 load_error = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	474 num_tomo_stacks = nxentry.reduced_data.data.tomo_fields.shape[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	475 tomo_recon_stacks = num_tomo_stacks*[np.array([])]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	476 for i in range(num_tomo_stacks):
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	477 # Convert reduced data stack from theta,row,column to row,theta,column
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	478 logger.debug(f'Reading reduced data stack {i+1}...')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	479 t0 = time()
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	480 tomo_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[i])
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	481 logger.debug(f'... done in {time()-t0:.2f} seconds')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	482 if len(tomo_stack.shape) != 3 or any(True for dim in tomo_stack.shape if not dim):
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	483 raise ValueError(f'Unable to load tomography stack {i+1} for reconstruction')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	484 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	485 assert(len(thetas) == tomo_stack.shape[1])
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	486 assert(0 <= lower_row < upper_row < tomo_stack.shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	487 center_offsets = [lower_center_offset-lower_row*center_slope,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	488 upper_center_offset+(tomo_stack.shape[0]-1-upper_row)*center_slope]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	489 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	490 logger.debug(f'Running _reconstruct_one_tomo_stack on {self.num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	491 tomo_recon_stack = self._reconstruct_one_tomo_stack(tomo_stack, thetas,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	492 center_offsets=center_offsets, num_core=self.num_core, algorithm='gridrec')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	493 logger.debug(f'... done in {time()-t0:.2f} seconds')
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	494 logger.info(f'Reconstruction of stack {i+1} took {time()-t0:.2f} seconds')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	495
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	496 # Combine stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	497 tomo_recon_stacks[i] = tomo_recon_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	498
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	499 # Resize the reconstructed tomography data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	500 # reconstructed data order in each stack: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	501 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	502 x_bounds = self.test_config.get('x_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	503 y_bounds = self.test_config.get('y_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	504 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	505 elif self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	506 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	507 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	508 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	509 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	510 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	511 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	512 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	513 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	514 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	515 if x_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	516 x_range = (0, tomo_recon_stacks[0].shape[1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	517 x_slice = int(x_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	518 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	519 x_range = (min(x_bounds), max(x_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	520 x_slice = int((x_bounds[0]+x_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	521 if y_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	522 y_range = (0, tomo_recon_stacks[0].shape[2])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	523 y_slice = int(y_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	524 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	525 y_range = (min(y_bounds), max(y_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	526 y_slice = int((y_bounds[0]+y_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	527 if z_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	528 z_range = (0, tomo_recon_stacks[0].shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	529 z_slice = int(z_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	530 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	531 z_range = (min(z_bounds), max(z_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	532 z_slice = int((z_bounds[0]+z_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	533
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	534 # Plot a few reconstructed image slices
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	535 if num_tomo_stacks == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	536 basetitle = 'recon'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	537 else:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	538 basetitle = f'recon stack {i+1}'
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	539 for i, stack in enumerate(tomo_recon_stacks):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	540 title = f'{basetitle} {res_title} xslice{x_slice}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	541 quick_imshow(stack[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	542 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	543 block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	544 title = f'{basetitle} {res_title} yslice{y_slice}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	545 quick_imshow(stack[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	546 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	547 block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	548 title = f'{basetitle} {res_title} zslice{z_slice}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	549 quick_imshow(stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	550 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	551 block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	552
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	553 # Save test data to file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	554 # reconstructed data order in each stack: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	555 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	556 for i, stack in enumerate(tomo_recon_stacks):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	557 np.savetxt(f'{self.output_folder}/recon_stack_{i+1}.txt',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	558 stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	559
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	560 # Add image reconstruction to reconstructed data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	561 # reconstructed data order in each stack: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	562 nxprocess.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	563 nxprocess.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	564 for k, v in center_info.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	565 nxprocess[k] = v
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	566 if x_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	567 nxprocess.x_bounds = x_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	568 if y_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	569 nxprocess.y_bounds = y_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	570 if z_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	571 nxprocess.z_bounds = z_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	572 nxprocess.data['reconstructed_data'] = np.asarray([stack[z_range[0]:z_range[1],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	573 x_range[0]:x_range[1],y_range[0]:y_range[1]] for stack in tomo_recon_stacks])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	574 nxprocess.data.attrs['signal'] = 'reconstructed_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	575
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	576 # Create a copy of the input Nexus object and remove reduced data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	577 exclude_items = [f'{nxentry._name}/reduced_data/data', f'{nxentry._name}/data/reduced_data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	578 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	579
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	580 # Add the reconstructed data NXprocess to the new Nexus object
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	581 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	582 nxentry_copy.reconstructed_data = nxprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	583 if 'data' not in nxentry_copy:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	584 nxentry_copy.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	585 nxentry_copy.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	586 nxentry_copy.data.makelink(nxprocess.data.reconstructed_data, name='reconstructed_data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	587 nxentry_copy.data.attrs['signal'] = 'reconstructed_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	588
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	589 return(nxroot_copy)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	590
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	591 def combine_data(self, nxroot, x_bounds=None, y_bounds=None):
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	592 """Combine the reconstructed tomography stacks.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	593 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	594 logger.info('Combine the reconstructed tomography stacks')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	595
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	596 if not isinstance(nxroot, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	597 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	598 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	599 if not isinstance(nxentry, NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	600 raise ValueError(f'Invalid nxentry ({nxentry})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	601
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	602 # Create plot galaxy path directory and path if needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	603 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	604 if not os_path.exists('tomo_combine_plots'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	605 mkdir('tomo_combine_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	606 path = 'tomo_combine_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	607 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	608 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	609
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	610 # Check if reconstructed image data is available
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	611 if ('reconstructed_data' not in nxentry or 'reconstructed_data' not in nxentry.data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	612 raise KeyError(f'Unable to find valid reconstructed image data in {nxentry}.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	613
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	614 # Create an NXprocess to store combined image reconstruction (meta)data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	615 nxprocess = NXprocess()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	616
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	617 # Get the reconstructed data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	618 # reconstructed data order: stack,row(z),x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	619 # Note: Nexus cannot follow a link if the data it points to is too big,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	620 # so get the data from the actual place, not from nxentry.data
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	621 num_tomo_stacks = nxentry.reconstructed_data.data.reconstructed_data.shape[0]
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	622 if num_tomo_stacks == 1:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	623 logger.info('Only one stack available: leaving combine_data')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	624 return(None)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	625
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	626 # Combine the reconstructed stacks
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	627 # (load one stack at a time to reduce risk of hitting Nexus data access limit)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	628 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	629 logger.debug(f'Combining the reconstructed stacks ...')
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	630 tomo_recon_combined = np.asarray(nxentry.reconstructed_data.data.reconstructed_data[0])
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	631 if num_tomo_stacks > 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	632 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	633 [nxentry.reconstructed_data.data.reconstructed_data[i]
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	634 for i in range(1, num_tomo_stacks-1)])
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	635 if num_tomo_stacks > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	636 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	637 [nxentry.reconstructed_data.data.reconstructed_data[num_tomo_stacks-1]])
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	638 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	639 logger.info(f'Combining the reconstructed stacks took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	640
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	641 # Resize the combined tomography data stacks
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	642 # combined data order: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	643 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	644 x_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	645 y_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	646 z_bounds = self.test_config.get('z_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	647 elif self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	648 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	649 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	650 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	651 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	652 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	653 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	654 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	655 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	656 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_combined,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	657 z_only=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	658 if x_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	659 x_range = (0, tomo_recon_combined.shape[1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	660 x_slice = int(x_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	661 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	662 x_range = x_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	663 x_slice = int((x_bounds[0]+x_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	664 if y_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	665 y_range = (0, tomo_recon_combined.shape[2])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	666 y_slice = int(y_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	667 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	668 y_range = y_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	669 y_slice = int((y_bounds[0]+y_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	670 if z_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	671 z_range = (0, tomo_recon_combined.shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	672 z_slice = int(z_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	673 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	674 z_range = z_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	675 z_slice = int((z_bounds[0]+z_bounds[1])/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	676
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	677 # Plot a few combined image slices
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	678 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	679 title=f'recon combined xslice{x_slice}', path=path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	680 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	681 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	682 title=f'recon combined yslice{y_slice}', path=path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	683 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	684 quick_imshow(tomo_recon_combined[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	685 title=f'recon combined zslice{z_slice}', path=path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	686 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	687
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	688 # Save test data to file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	689 # combined data order: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	690 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	691 np.savetxt(f'{self.output_folder}/recon_combined.txt', tomo_recon_combined[
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	692 z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	693
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	694 # Add image reconstruction to reconstructed data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	695 # combined data order: row/z,x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	696 nxprocess.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	697 nxprocess.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	698 if x_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	699 nxprocess.x_bounds = x_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	700 if y_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	701 nxprocess.y_bounds = y_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	702 if z_bounds is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	703 nxprocess.z_bounds = z_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	704 nxprocess.data['combined_data'] = tomo_recon_combined
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	705 nxprocess.data.attrs['signal'] = 'combined_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	706
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	707 # Create a copy of the input Nexus object and remove reconstructed data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	708 exclude_items = [f'{nxentry._name}/reconstructed_data/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	709 f'{nxentry._name}/data/reconstructed_data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	710 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	711
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	712 # Add the combined data NXprocess to the new Nexus object
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	713 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	714 nxentry_copy.combined_data = nxprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	715 if 'data' not in nxentry_copy:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	716 nxentry_copy.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	717 nxentry_copy.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	718 nxentry_copy.data.makelink(nxprocess.data.combined_data, name='combined_data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	719 nxentry_copy.data.attrs['signal'] = 'combined_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	720
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	721 return(nxroot_copy)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	722
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	723 def _gen_dark(self, nxentry, reduced_data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	724 """Generate dark field.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	725 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	726 # Get the dark field images
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	727 image_key = nxentry.instrument.detector.get('image_key', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	728 if image_key and 'data' in nxentry.instrument.detector:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	729 field_indices = [index for index, key in enumerate(image_key) if key == 2]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	730 tdf_stack = nxentry.instrument.detector.data[field_indices,:,:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	731 # RV the default NXtomo form does not accomodate bright or dark field stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	732 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	733 dark_field_scans = nxentry.spec_scans.dark_field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	734 dark_field = FlatField.construct_from_nxcollection(dark_field_scans)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	735 prefix = str(nxentry.instrument.detector.local_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	736 tdf_stack = dark_field.get_detector_data(prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	737 if isinstance(tdf_stack, list):
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	738 assert(len(tdf_stack) == 1) # TODO
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	739 tdf_stack = tdf_stack[0]
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	740
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	741 # Take median
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	742 if tdf_stack.ndim == 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	743 tdf = tdf_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	744 elif tdf_stack.ndim == 3:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	745 tdf = np.median(tdf_stack, axis=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	746 del tdf_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	747 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	748 raise ValueError(f'Invalid tdf_stack shape ({tdf_stack.shape})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	749
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	750 # Remove dark field intensities above the cutoff
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	751 #RV tdf_cutoff = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	752 tdf_cutoff = tdf.min()+2*(np.median(tdf)-tdf.min())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	753 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	754 if tdf_cutoff is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	755 if not is_num(tdf_cutoff, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	756 logger.warning(f'Ignoring illegal value of tdf_cutoff {tdf_cutoff}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	757 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	758 tdf[tdf > tdf_cutoff] = np.nan
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	759 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	760
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	761 # Remove nans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	762 tdf_mean = np.nanmean(tdf)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	763 logger.debug(f'tdf_mean = {tdf_mean}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	764 np.nan_to_num(tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	765
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	766 # Plot dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	767 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	768 quick_imshow(tdf, title='dark field', path='tomo_reduce_plots', save_fig=self.save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	769 save_only=self.save_only)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	770 elif not self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	771 quick_imshow(tdf, title='dark field', path=self.output_folder, save_fig=self.save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	772 save_only=self.save_only)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	773 clear_imshow('dark field')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	774 # quick_imshow(tdf, title='dark field', block=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	775
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	776 # Add dark field to reduced data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	777 reduced_data.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	778 reduced_data.data['dark_field'] = tdf
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	779
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	780 return(reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	781
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	782 def _gen_bright(self, nxentry, reduced_data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	783 """Generate bright field.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	784 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	785 # Get the bright field images
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	786 image_key = nxentry.instrument.detector.get('image_key', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	787 if image_key and 'data' in nxentry.instrument.detector:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	788 field_indices = [index for index, key in enumerate(image_key) if key == 1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	789 tbf_stack = nxentry.instrument.detector.data[field_indices,:,:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	790 # RV the default NXtomo form does not accomodate bright or dark field stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	791 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	792 bright_field_scans = nxentry.spec_scans.bright_field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	793 bright_field = FlatField.construct_from_nxcollection(bright_field_scans)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	794 prefix = str(nxentry.instrument.detector.local_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	795 tbf_stack = bright_field.get_detector_data(prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	796 if isinstance(tbf_stack, list):
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	797 assert(len(tbf_stack) == 1) # TODO
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	798 tbf_stack = tbf_stack[0]
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	799
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	800 # Take median if more than one image
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	801 """Median or mean: It may be best to try the median because of some image
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	802 artifacts that arise due to crinkles in the upstream kapton tape windows
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	803 causing some phase contrast images to appear on the detector.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	804 One thing that also may be useful in a future implementation is to do a
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	805 brightfield adjustment on EACH frame of the tomo based on a ROI in the
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	806 corner of the frame where there is no sample but there is the direct X-ray
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	807 beam because there is frame to frame fluctuations from the incoming beam.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	808 We don’t typically account for them but potentially could.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	809 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	810 if tbf_stack.ndim == 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	811 tbf = tbf_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	812 elif tbf_stack.ndim == 3:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	813 tbf = np.median(tbf_stack, axis=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	814 del tbf_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	815 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	816 raise ValueError(f'Invalid tbf_stack shape ({tbf_stacks.shape})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	817
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	818 # Subtract dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	819 if 'data' in reduced_data and 'dark_field' in reduced_data.data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	820 tbf -= reduced_data.data.dark_field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	821 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	822 logger.warning('Dark field unavailable')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	823
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	824 # Set any non-positive values to one
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	825 # (avoid negative bright field values for spikes in dark field)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	826 tbf[tbf < 1] = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	827
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	828 # Plot bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	829 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	830 quick_imshow(tbf, title='bright field', path='tomo_reduce_plots',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	831 save_fig=self.save_figs, save_only=self.save_only)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	832 elif not self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	833 quick_imshow(tbf, title='bright field', path=self.output_folder,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	834 save_fig=self.save_figs, save_only=self.save_only)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	835 clear_imshow('bright field')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	836 # quick_imshow(tbf, title='bright field', block=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	837
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	838 # Add bright field to reduced data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	839 if 'data' not in reduced_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	840 reduced_data.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	841 reduced_data.data['bright_field'] = tbf
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	842
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	843 return(reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	844
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	845 def _set_detector_bounds(self, nxentry, reduced_data, img_x_bounds=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	846 """Set vertical detector bounds for each image stack.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	847 Right now the range is the same for each set in the image stack.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	848 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	849 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	850 return(tuple(self.test_config['img_x_bounds']))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	851
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	852 # Get the first tomography image and the reference heights
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	853 image_key = nxentry.instrument.detector.get('image_key', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	854 if image_key and 'data' in nxentry.instrument.detector:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	855 field_indices = [index for index, key in enumerate(image_key) if key == 0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	856 first_image = np.asarray(nxentry.instrument.detector.data[field_indices[0],:,:])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	857 theta = float(nxentry.sample.rotation_angle[field_indices[0]])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	858 z_translation_all = nxentry.sample.z_translation[field_indices]
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	859 vertical_shifts = sorted(list(set(z_translation_all)))
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	860 num_tomo_stacks = len(vertical_shifts)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	861 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	862 tomo_field_scans = nxentry.spec_scans.tomo_fields
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	863 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	864 vertical_shifts = tomo_fields.get_vertical_shifts()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	865 if not isinstance(vertical_shifts, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	866 vertical_shifts = [vertical_shifts]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	867 prefix = str(nxentry.instrument.detector.local_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	868 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	869 first_image = tomo_fields.get_detector_data(prefix, tomo_fields.scan_numbers[0], 0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	870 logger.debug(f'Getting first image took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	871 num_tomo_stacks = len(tomo_fields.scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	872 theta = tomo_fields.theta_range['start']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	873
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	874 # Select image bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	875 title = f'tomography image at theta={round(theta, 2)+0}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	876 if (img_x_bounds is not None and not is_index_range(img_x_bounds, ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	877 le=first_image.shape[0])):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	878 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	879 if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	880 pixel_size = nxentry.instrument.detector.x_pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	881 # Try to get a fit from the bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	882 tbf = np.asarray(reduced_data.data.bright_field)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	883 tbf_shape = tbf.shape
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	884 x_sum = np.sum(tbf, 1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	885 x_sum_min = x_sum.min()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	886 x_sum_max = x_sum.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	887 fit = Fit.fit_data(x_sum, 'rectangle', x=np.array(range(len(x_sum))), form='atan',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	888 guess=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	889 parameters = fit.best_values
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	890 x_low_fit = parameters.get('center1', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	891 x_upp_fit = parameters.get('center2', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	892 sig_low = parameters.get('sigma1', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	893 sig_upp = parameters.get('sigma2', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	894 have_fit = fit.success and x_low_fit is not None and x_upp_fit is not None and \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	895 sig_low is not None and sig_upp is not None and \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	896 0 <= x_low_fit < x_upp_fit <= x_sum.size and \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	897 (sig_low+sig_upp)/(x_upp_fit-x_low_fit) < 0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	898 if have_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	899 # Set a 5% margin on each side
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	900 margin = 0.05*(x_upp_fit-x_low_fit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	901 x_low_fit = max(0, x_low_fit-margin)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	902 x_upp_fit = min(tbf_shape[0], x_upp_fit+margin)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	903 if num_tomo_stacks == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	904 if have_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	905 # Set the default range to enclose the full fitted window
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	906 x_low = int(x_low_fit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	907 x_upp = int(x_upp_fit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	908 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	909 # Center a default range of 1 mm (RV: can we get this from the slits?)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	910 num_x_min = int((1.0-0.5*pixel_size)/pixel_size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	911 x_low = int(0.5*(tbf_shape[0]-num_x_min))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	912 x_upp = x_low+num_x_min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	913 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	914 # Get the default range from the reference heights
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	915 delta_z = vertical_shifts[1]-vertical_shifts[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	916 for i in range(2, num_tomo_stacks):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	917 delta_z = min(delta_z, vertical_shifts[i]-vertical_shifts[i-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	918 logger.debug(f'delta_z = {delta_z}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	919 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	920 logger.debug(f'num_x_min = {num_x_min}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	921 if num_x_min > tbf_shape[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	922 logger.warning('Image bounds and pixel size prevent seamless stacking')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	923 if have_fit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	924 # Center the default range relative to the fitted window
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	925 x_low = int(0.5*(x_low_fit+x_upp_fit-num_x_min))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	926 x_upp = x_low+num_x_min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	927 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	928 # Center the default range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	929 x_low = int(0.5*(tbf_shape[0]-num_x_min))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	930 x_upp = x_low+num_x_min
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	931 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	932 img_x_bounds = (x_low, x_upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	933 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	934 tmp = np.copy(tbf)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	935 tmp_max = tmp.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	936 tmp[x_low,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	937 tmp[x_upp-1,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	938 quick_imshow(tmp, title='bright field')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	939 tmp = np.copy(first_image)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	940 tmp_max = tmp.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	941 tmp[x_low,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	942 tmp[x_upp-1,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	943 quick_imshow(tmp, title=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	944 del tmp
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	945 quick_plot((range(x_sum.size), x_sum),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	946 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	947 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	948 title='sum over theta and y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	949 print(f'lower bound = {x_low} (inclusive)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	950 print(f'upper bound = {x_upp} (exclusive)]')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	951 accept = input_yesno('Accept these bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	952 clear_imshow('bright field')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	953 clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	954 clear_plot('sum over theta and y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	955 if accept:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	956 img_x_bounds = (x_low, x_upp)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	957 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	958 while True:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	959 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	960 legend='sum over theta and y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	961 if len(img_x_bounds) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	962 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	963 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	964 print(f'Choose a single connected data range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	965 img_x_bounds = tuple(img_x_bounds[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	966 if (num_tomo_stacks > 1 and img_x_bounds[1]-img_x_bounds[0]+1 <
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	967 int((delta_z-0.5*pixel_size)/pixel_size)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	968 logger.warning('Image bounds and pixel size prevent seamless stacking')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	969 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	970 if num_tomo_stacks > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	971 raise NotImplementedError('Selecting image bounds for multiple stacks on FMB')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	972 # For FMB: use the first tomography image to select range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	973 # RV: revisit if they do tomography with multiple stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	974 x_sum = np.sum(first_image, 1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	975 x_sum_min = x_sum.min()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	976 x_sum_max = x_sum.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	977 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	978 if img_x_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	979 img_x_bounds = (0, first_image.shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	980 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	981 quick_imshow(first_image, title=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	982 print('Select vertical data reduction range from first tomography image')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	983 img_x_bounds = select_image_bounds(first_image, 0, title=title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	984 clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	985 if img_x_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	986 raise ValueError('Unable to select image bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	987
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	988 # Plot results
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	989 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	990 path = 'tomo_reduce_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	991 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	992 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	993 x_low = img_x_bounds[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	994 x_upp = img_x_bounds[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	995 tmp = np.copy(first_image)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	996 tmp_max = tmp.max()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	997 tmp[x_low,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	998 tmp[x_upp-1,:] = tmp_max
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	999 quick_imshow(tmp, title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1000 block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1001 del tmp
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1002 quick_plot((range(x_sum.size), x_sum),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1003 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1004 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1005 title='sum over theta and y', path=path, save_fig=self.save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1006 save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1007
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1008 return(img_x_bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1009
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1010 def _set_zoom_or_skip(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1011 """Set zoom and/or theta skip to reduce memory the requirement for the analysis.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1012 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1013 # if input_yesno('\nDo you want to zoom in to reduce memory requirement (y/n)?', 'n'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1014 # zoom_perc = input_int(' Enter zoom percentage', ge=1, le=100)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1015 # else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1016 # zoom_perc = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1017 zoom_perc = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1018 # if input_yesno('Do you want to skip thetas to reduce memory requirement (y/n)?', 'n'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1019 # num_theta_skip = input_int(' Enter the number skip theta interval', ge=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1020 # lt=num_theta)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1021 # else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1022 # num_theta_skip = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1023 num_theta_skip = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1024 logger.debug(f'zoom_perc = {zoom_perc}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1025 logger.debug(f'num_theta_skip = {num_theta_skip}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1026
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1027 return(zoom_perc, num_theta_skip)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1028
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1029 def _gen_tomo(self, nxentry, reduced_data):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1030 """Generate tomography fields.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1031 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1032 # Get full bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1033 tbf = np.asarray(reduced_data.data.bright_field)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1034 tbf_shape = tbf.shape
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1035
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1036 # Get image bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1037 img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0])))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1038 img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1])))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1039
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1040 # Get resized dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1041 # if 'dark_field' in data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1042 # tbf = np.asarray(reduced_data.data.dark_field[
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1043 # img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1044 # else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1045 # logger.warning('Dark field unavailable')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1046 # tdf = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1047 tdf = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1048
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1049 # Resize bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1050 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1051 tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1052
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1053 # Get the tomography images
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1054 image_key = nxentry.instrument.detector.get('image_key', None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1055 if image_key and 'data' in nxentry.instrument.detector:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1056 field_indices_all = [index for index, key in enumerate(image_key) if key == 0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1057 z_translation_all = nxentry.sample.z_translation[field_indices_all]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1058 z_translation_levels = sorted(list(set(z_translation_all)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1059 num_tomo_stacks = len(z_translation_levels)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1060 tomo_stacks = num_tomo_stacks*[np.array([])]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1061 horizontal_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1062 vertical_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1063 thetas = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1064 tomo_stacks = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1065 for i, z_translation in enumerate(z_translation_levels):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1066 field_indices = [field_indices_all[index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1067 for index, z in enumerate(z_translation_all) if z == z_translation]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1068 horizontal_shift = list(set(nxentry.sample.x_translation[field_indices]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1069 assert(len(horizontal_shift) == 1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1070 horizontal_shifts += horizontal_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1071 vertical_shift = list(set(nxentry.sample.z_translation[field_indices]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1072 assert(len(vertical_shift) == 1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1073 vertical_shifts += vertical_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1074 sequence_numbers = nxentry.instrument.detector.sequence_number[field_indices]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1075 if thetas is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1076 thetas = np.asarray(nxentry.sample.rotation_angle[field_indices]) \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1077 [sequence_numbers]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1078 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1079 assert(all(thetas[i] == nxentry.sample.rotation_angle[field_indices[index]]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1080 for i, index in enumerate(sequence_numbers)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1081 assert(list(set(sequence_numbers)) == [i for i in range(len(sequence_numbers))])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1082 if list(sequence_numbers) == [i for i in range(len(sequence_numbers))]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1083 tomo_stack = np.asarray(nxentry.instrument.detector.data[field_indices])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1084 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1085 raise ValueError('Unable to load the tomography images')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1086 tomo_stacks.append(tomo_stack)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1087 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1088 tomo_field_scans = nxentry.spec_scans.tomo_fields
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1089 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1090 horizontal_shifts = tomo_fields.get_horizontal_shifts()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1091 vertical_shifts = tomo_fields.get_vertical_shifts()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1092 prefix = str(nxentry.instrument.detector.local_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1093 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1094 tomo_stacks = tomo_fields.get_detector_data(prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1095 logger.debug(f'Getting tomography images took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1096 logger.debug(f'Getting all images took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1097 thetas = np.linspace(tomo_fields.theta_range['start'], tomo_fields.theta_range['end'],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1098 tomo_fields.theta_range['num'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1099 if not isinstance(tomo_stacks, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1100 horizontal_shifts = [horizontal_shifts]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1101 vertical_shifts = [vertical_shifts]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1102 tomo_stacks = [tomo_stacks]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1103
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1104 reduced_tomo_stacks = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1105 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1106 path = 'tomo_reduce_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1107 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1108 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1109 for i, tomo_stack in enumerate(tomo_stacks):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1110 # Resize the tomography images
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1111 # Right now the range is the same for each set in the image stack.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1112 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1113 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1114 tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1115 img_y_bounds[0]:img_y_bounds[1]].astype('float64')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1116 logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1117
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1118 # Subtract dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1119 if tdf is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1120 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1121 with set_numexpr_threads(self.num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1122 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1123 logger.debug(f'Subtracting dark field took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1124
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1125 # Normalize
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1126 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1127 with set_numexpr_threads(self.num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1128 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1129 logger.debug(f'Normalizing took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1130
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1131 # Remove non-positive values and linearize data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1132 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1133 cutoff = 1.e-6
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1134 with set_numexpr_threads(self.num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1135 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1136 with set_numexpr_threads(self.num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1137 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1138 logger.debug('Removing non-positive values and linearizing data took '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1139 f'{time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1140
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1141 # Get rid of nans/infs that may be introduced by normalization
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1142 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1143 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1144 logger.debug(f'Remove nans/infs took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1145
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1146 # Downsize tomography stack to smaller size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1147 # TODO use theta_skip as well
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1148 tomo_stack = tomo_stack.astype('float32')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1149 if not self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1150 if len(tomo_stacks) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1151 title = f'red fullres theta {round(thetas[0], 2)+0}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1152 else:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1153 title = f'red stack {i+1} fullres theta {round(thetas[0], 2)+0}'
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1154 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1155 save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1156 # if not self.block:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1157 # clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1158 if False and zoom_perc != 100:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1159 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1160 logger.debug(f'Zooming in ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1161 tomo_zoom_list = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1162 for j in range(tomo_stack.shape[0]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1163 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1164 tomo_zoom_list.append(tomo_zoom)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1165 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1166 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1167 logger.info(f'Zooming in took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1168 del tomo_zoom_list
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1169 if not self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1170 title = f'red stack {zoom_perc}p theta {round(thetas[0], 2)+0}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1171 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1172 save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1173 # if not self.block:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1174 # clear_imshow(title)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1175
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1176 # Save test data to file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1177 if self.test_mode:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1178 # row_index = int(tomo_stack.shape[0]/2)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1179 # np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[row_index,:,:],
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1180 # fmt='%.6e')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1181 row_index = int(tomo_stack.shape[1]/2)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1182 np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[:,row_index,:],
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1183 fmt='%.6e')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1184
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1185 # Combine resized stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1186 reduced_tomo_stacks.append(tomo_stack)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1187
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1188 # Add tomo field info to reduced data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1189 reduced_data['rotation_angle'] = thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1190 reduced_data['x_translation'] = np.asarray(horizontal_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1191 reduced_data['z_translation'] = np.asarray(vertical_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1192 reduced_data.data['tomo_fields'] = np.asarray(reduced_tomo_stacks)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1193
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1194 if tdf is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1195 del tdf
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1196 del tbf
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1197
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1198 return(reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1199
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1200 def _find_center_one_plane(self, sinogram, row, thetas, eff_pixel_size, cross_sectional_dim,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1201 path=None, tol=0.1, num_core=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1202 """Find center for a single tomography plane.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1203 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1204 # Try automatic center finding routines for initial value
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1205 # sinogram index order: theta,column
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1206 # need column,theta for iradon, so take transpose
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1207 sinogram = np.asarray(sinogram)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1208 sinogram_T = sinogram.T
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1209 center = sinogram.shape[1]/2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1210
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1211 # Try using Nghia Vo’s method
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1212 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1213 if num_core > num_core_tomopy_limit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1214 logger.debug(f'Running find_center_vo on {num_core_tomopy_limit} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1215 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1216 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1217 logger.debug(f'Running find_center_vo on {num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1218 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1219 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1220 logger.info(f'Finding the center using Nghia Vo’s method took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1221 center_offset_vo = tomo_center-center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1222 logger.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1223 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1224 logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1225 recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1226 eff_pixel_size, cross_sectional_dim, False, num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1227 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1228 logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1229
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1230 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1231 self._plot_edges_one_plane(recon_plane, title, path=path)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1232
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1233 # Try using phase correlation method
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1234 # if input_yesno('Try finding center using phase correlation (y/n)?', 'n'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1235 # t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1236 # logger.debug(f'Running find_center_pc ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1237 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, rotc_guess=tomo_center)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1238 # error = 1.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1239 # while error > tol:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1240 # prev = tomo_center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1241 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1242 # rotc_guess=tomo_center)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1243 # error = np.abs(tomo_center-prev)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1244 # logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1245 # logger.info('Finding the center using the phase correlation method took '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1246 # f'{time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1247 # center_offset = tomo_center-center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1248 # print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1249 # t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1250 # logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1251 # recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1252 # eff_pixel_size, cross_sectional_dim, False, num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1253 # logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1254 # logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1255 #
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1256 # title = f'edges row{row} center_offset{center_offset:.2f} PC'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1257 # self._plot_edges_one_plane(recon_plane, title, path=path)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1258
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1259 # Select center location
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1260 # if input_yesno('Accept a center location (y) or continue search (n)?', 'y'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1261 if True:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1262 # center_offset = input_num(' Enter chosen center offset', ge=-center, le=center,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1263 # default=center_offset_vo)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1264 center_offset = center_offset_vo
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1265 del sinogram_T
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1266 del recon_plane
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1267 return float(center_offset)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1268
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1269 # perform center finding search
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1270 while True:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1271 center_offset_low = input_int('\nEnter lower bound for center offset', ge=-center,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1272 le=center)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1273 center_offset_upp = input_int('Enter upper bound for center offset',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1274 ge=center_offset_low, le=center)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1275 if center_offset_upp == center_offset_low:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1276 center_offset_step = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1277 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1278 center_offset_step = input_int('Enter step size for center offset search', ge=1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1279 le=center_offset_upp-center_offset_low)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1280 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1281 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1282 for center_offset in center_offsets:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1283 if center_offset == center_offset_vo:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1284 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1285 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1286 logger.debug(f'Running _reconstruct_one_plane on {num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1287 recon_plane = self._reconstruct_one_plane(sinogram_T, center_offset+center, thetas,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1288 eff_pixel_size, cross_sectional_dim, False, num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1289 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1290 logger.info(f'Reconstructing center_offset {center_offset} took '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1291 f'{time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1292 title = f'edges row{row} center_offset{center_offset:.2f}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1293 self._plot_edges_one_plane(recon_plane, title, path=path)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1294 if input_int('\nContinue (0) or end the search (1)', ge=0, le=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1295 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1296
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1297 del sinogram_T
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1298 del recon_plane
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1299 center_offset = input_num(' Enter chosen center offset', ge=-center, le=center)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1300 return float(center_offset)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1301
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1302 def _reconstruct_one_plane(self, tomo_plane_T, center, thetas, eff_pixel_size,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1303 cross_sectional_dim, plot_sinogram=True, num_core=1):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1304 """Invert the sinogram for a single tomography plane.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1305 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1306 # tomo_plane_T index order: column,theta
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1307 assert(0 <= center < tomo_plane_T.shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1308 center_offset = center-tomo_plane_T.shape[0]/2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1309 two_offset = 2*int(np.round(center_offset))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1310 two_offset_abs = np.abs(two_offset)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1311 max_rad = int(0.55*(cross_sectional_dim/eff_pixel_size)) # 10% slack to avoid edge effects
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1312 if max_rad > 0.5*tomo_plane_T.shape[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1313 max_rad = 0.5*tomo_plane_T.shape[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1314 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1315 if two_offset >= 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1316 logger.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1317 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1318 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1319 logger.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1320 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1321 if not self.galaxy_flag and plot_sinogram:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1322 quick_imshow(sinogram.T, f'sinogram center offset{center_offset:.2f}', aspect='auto',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1323 path=self.output_folder, save_fig=self.save_figs, save_only=self.save_only,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1324 block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1325
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1326 # Inverting sinogram
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1327 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1328 recon_sinogram = iradon(sinogram, theta=thetas, circle=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1329 logger.debug(f'Inverting sinogram took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1330 del sinogram
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1331
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1332 # Performing Gaussian filtering and removing ring artifacts
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1333 recon_parameters = None#self.config.get('recon_parameters')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1334 if recon_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1335 sigma = 1.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1336 ring_width = 15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1337 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1338 sigma = recon_parameters.get('gaussian_sigma', 1.0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1339 if not is_num(sigma, ge=0.0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1340 logger.warning(f'Invalid gaussian_sigma ({sigma}) in _reconstruct_one_plane, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1341 'set to a default value of 1.0')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1342 sigma = 1.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1343 ring_width = recon_parameters.get('ring_width', 15)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1344 if not is_int(ring_width, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1345 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1346 'set to a default value of 15')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1347 ring_width = 15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1348 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1349 recon_sinogram = spi.gaussian_filter(recon_sinogram, sigma, mode='nearest')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1350 recon_clean = np.expand_dims(recon_sinogram, axis=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1351 del recon_sinogram
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1352 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=ring_width, ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1353 logger.debug(f'Filtering and removing ring artifacts took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1354
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1355 return recon_clean
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1356
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1357 def _plot_edges_one_plane(self, recon_plane, title, path=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1358 vis_parameters = None#self.config.get('vis_parameters')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1359 if vis_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1360 weight = 0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1361 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1362 weight = vis_parameters.get('denoise_weight', 0.1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1363 if not is_num(weight, ge=0.0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1364 logger.warning(f'Invalid weight ({weight}) in _plot_edges_one_plane, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1365 'set to a default value of 0.1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1366 weight = 0.1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1367 edges = denoise_tv_chambolle(recon_plane, weight=weight)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1368 vmax = np.max(edges[0,:,:])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1369 vmin = -vmax
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1370 if path is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1371 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1372 quick_imshow(edges[0,:,:], f'{title} coolwarm', path=path, cmap='coolwarm',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1373 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1374 quick_imshow(edges[0,:,:], f'{title} gray', path=path, cmap='gray', vmin=vmin, vmax=vmax,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1375 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1376 del edges
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1377
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1378 def _reconstruct_one_tomo_stack(self, tomo_stack, thetas, center_offsets=[], num_core=1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1379 algorithm='gridrec'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1380 """Reconstruct a single tomography stack.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1381 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1382 # tomo_stack order: row,theta,column
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1383 # input thetas must be in degrees
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1384 # centers_offset: tomography axis shift in pixels relative to column center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1385 # RV should we remove stripes?
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1386 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1387 # RV should we remove rings?
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1388 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1389 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1390 if not len(center_offsets):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1391 centers = np.zeros((tomo_stack.shape[0]))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1392 elif len(center_offsets) == 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1393 centers = np.linspace(center_offsets[0], center_offsets[1], tomo_stack.shape[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1394 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1395 if center_offsets.size != tomo_stack.shape[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1396 raise ValueError('center_offsets dimension mismatch in reconstruct_one_tomo_stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1397 centers = center_offsets
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1398 centers += tomo_stack.shape[2]/2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1399
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1400 # Get reconstruction parameters
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1401 recon_parameters = None#self.config.get('recon_parameters')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1402 if recon_parameters is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1403 sigma = 2.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1404 secondary_iters = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1405 ring_width = 15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1406 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1407 sigma = recon_parameters.get('stripe_fw_sigma', 2.0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1408 if not is_num(sigma, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1409 logger.warning(f'Invalid stripe_fw_sigma ({sigma}) in '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1410 '_reconstruct_one_tomo_stack, set to a default value of 2.0')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1411 ring_width = 15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1412 secondary_iters = recon_parameters.get('secondary_iters', 0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1413 if not is_int(secondary_iters, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1414 logger.warning(f'Invalid secondary_iters ({secondary_iters}) in '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1415 '_reconstruct_one_tomo_stack, set to a default value of 0 (skip them)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1416 ring_width = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1417 ring_width = recon_parameters.get('ring_width', 15)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1418 if not is_int(ring_width, ge=0):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1419 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1420 'set to a default value of 15')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1421 ring_width = 15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1422
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1423 # Remove horizontal stripe
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1424 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1425 if num_core > num_core_tomopy_limit:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1426 logger.debug('Running remove_stripe_fw on {num_core_tomopy_limit} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1427 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1428 ncore=num_core_tomopy_limit)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1429 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1430 logger.debug(f'Running remove_stripe_fw on {num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1431 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1432 ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1433 logger.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1434
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1435 # Perform initial image reconstruction
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1436 logger.debug('Performing initial image reconstruction')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1437 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1438 logger.debug(f'Running recon on {num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1439 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1440 sinogram_order=True, algorithm=algorithm, ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1441 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1442 logger.info(f'Performing initial image reconstruction took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1443
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1444 # Run optional secondary iterations
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1445 if secondary_iters > 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1446 logger.debug(f'Running {secondary_iters} secondary iterations')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1447 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iters}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1448 #RV: doesn't work for me:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1449 #"Error: CUDA error 803: system has unsupported display driver/cuda driver combination."
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1450 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iters}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1451 #SIRT did not finish while running overnight
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1452 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iters}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1453 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1454 'num_iter':secondary_iters}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1455 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1456 logger.debug(f'Running recon on {num_core} cores ...')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1457 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1458 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1459 algorithm=tomopy.astra, ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1460 logger.debug(f'... done in {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1461 logger.info(f'Performing secondary iterations took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1462
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1463 # Remove ring artifacts
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1464 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1465 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=ring_width, out=tomo_recon_stack,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1466 ncore=num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1467 logger.debug(f'Removing ring artifacts took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1468
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1469 return tomo_recon_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1470
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1471 def _resize_reconstructed_data(self, data, z_only=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1472 """Resize the reconstructed tomography data.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1473 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1474 # Data order: row(z),x,y or stack,row(z),x,y
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1475 if isinstance(data, list):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1476 for stack in data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1477 assert(stack.ndim == 3)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1478 num_tomo_stacks = len(data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1479 tomo_recon_stacks = data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1480 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1481 assert(data.ndim == 3)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1482 num_tomo_stacks = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1483 tomo_recon_stacks = [data]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1484
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1485 if z_only:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1486 x_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1487 y_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1488 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1489 # Selecting x bounds (in yz-plane)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1490 tomosum = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1491 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,2))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1492 for i in range(num_tomo_stacks)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1493 select_x_bounds = input_yesno('\nDo you want to change the image x-bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1494 if not select_x_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1495 x_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1496 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1497 accept = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1498 index_ranges = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1499 while not accept:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1500 mask, x_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1501 title='select x data range', legend='recon stack sum yz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1502 while len(x_bounds) != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1503 print('Please select exactly one continuous range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1504 mask, x_bounds = draw_mask_1d(tomosum, title='select x data range',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1505 legend='recon stack sum yz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1506 x_bounds = x_bounds[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1507 # quick_plot(tomosum, vlines=x_bounds, title='recon stack sum yz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1508 # print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1509 # 'exclusive)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1510 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1511 accept = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1512 logger.debug(f'x_bounds = {x_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1513
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1514 # Selecting y bounds (in xz-plane)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1515 tomosum = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1516 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,1))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1517 for i in range(num_tomo_stacks)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1518 select_y_bounds = input_yesno('\nDo you want to change the image y-bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1519 if not select_y_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1520 y_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1521 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1522 accept = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1523 index_ranges = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1524 while not accept:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1525 mask, y_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1526 title='select x data range', legend='recon stack sum xz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1527 while len(y_bounds) != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1528 print('Please select exactly one continuous range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1529 mask, y_bounds = draw_mask_1d(tomosum, title='select x data range',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1530 legend='recon stack sum xz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1531 y_bounds = y_bounds[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1532 # quick_plot(tomosum, vlines=y_bounds, title='recon stack sum xz')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1533 # print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1534 # 'exclusive)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1535 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1536 accept = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1537 logger.debug(f'y_bounds = {y_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1538
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1539 # Selecting z bounds (in xy-plane) (only valid for a single image stack)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1540 if num_tomo_stacks != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1541 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1542 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1543 tomosum = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1544 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(1,2))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1545 for i in range(num_tomo_stacks)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1546 select_z_bounds = input_yesno('Do you want to change the image z-bounds (y/n)?', 'n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1547 if not select_z_bounds:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1548 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1549 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1550 accept = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1551 index_ranges = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1552 while not accept:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1553 mask, z_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1554 title='select x data range', legend='recon stack sum xy')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1555 while len(z_bounds) != 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1556 print('Please select exactly one continuous range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1557 mask, z_bounds = draw_mask_1d(tomosum, title='select x data range',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1558 legend='recon stack sum xy')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1559 z_bounds = z_bounds[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1560 # quick_plot(tomosum, vlines=z_bounds, title='recon stack sum xy')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1561 # print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1562 # 'exclusive)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1563 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1564 accept = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1565 logger.debug(f'z_bounds = {z_bounds}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1566
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1567 return(x_bounds, y_bounds, z_bounds)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1568
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1569
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1570 def run_tomo(input_file:str, output_file:str, modes:list[str], center_file=None, num_core=-1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1571 output_folder='.', save_figs='no', test_mode=False) -> None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1572
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1573 if test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1574 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1575 level = logging.getLevelName('INFO')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1576 logging.basicConfig(filename=f'{output_folder}/tomo.log', filemode='w',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1577 format=logging_format, level=level, force=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1578 logger.info(f'input_file = {input_file}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1579 logger.info(f'center_file = {center_file}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1580 logger.info(f'output_file = {output_file}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1581 logger.debug(f'modes= {modes}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1582 logger.debug(f'num_core= {num_core}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1583 logger.info(f'output_folder = {output_folder}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1584 logger.info(f'save_figs = {save_figs}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1585 logger.info(f'test_mode = {test_mode}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1586
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1587 # Check for correction modes
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1588 legal_modes = ['reduce_data', 'find_center', 'reconstruct_data', 'combine_data', 'all']
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1589 if modes is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1590 modes = ['all']
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1591 if not all(True if mode in legal_modes else False for mode in modes):
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1592 raise ValueError(f'Invalid parameter modes ({modes})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1593
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1594 # Instantiate Tomo object
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1595 tomo = Tomo(num_core=num_core, output_folder=output_folder, save_figs=save_figs,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1596 test_mode=test_mode)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1597
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1598 # Read input file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1599 data = tomo.read(input_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1600
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1601 # Generate reduced tomography images
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1602 if 'reduce_data' in modes or 'all' in modes:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1603 data = tomo.gen_reduced_data(data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1604
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1605 # Find rotation axis centers for the tomography stacks.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1606 center_data = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1607 if 'find_center' in modes or 'all' in modes:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1608 center_data = tomo.find_centers(data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1609
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1610 # Reconstruct tomography stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1611 if 'reconstruct_data' in modes or 'all' in modes:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1612 if center_data is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1613 # Read input file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1614 center_data = tomo.read(center_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1615 data = tomo.reconstruct_data(data, center_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1616 center_data = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1617
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1618 # Combine reconstructed tomography stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1619 if 'combine_data' in modes or 'all' in modes:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1620 data = tomo.combine_data(data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1621
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1622 # Write output file
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1623 if data is not None and not test_mode:
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1624 if center_data is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1625 data = tomo.write(data, output_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1626 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1627 data = tomo.write(center_data, output_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1628
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1629 logger.info(f'Completed modes: {modes}')

Mercurial > repos > rv43 > tomo

annotate workflow/run_tomo.py @ 71:1cf15b61cd83 draft