tomo: workflow/run_tomo.py annotate

author	rv43
date	Fri, 10 Mar 2023 16:02:04 +0000
parents
children	1cf15b61cd83

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
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	35 from msnctools.fit import Fit
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	36 from msnctools.general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	37 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	38 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	39
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	40 from workflow.models import import_scanparser, FlatField, TomoField, TomoWorkflow
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	41 from workflow.__version__ import __version__
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	42
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	43 num_core_tomopy_limit = 24
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	44
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	45 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	46 '''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	47
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	48 :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	49 :type nxobject: nexusformat.nexus.NXobject
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	50 :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	51 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	52 :type exclude_nxpaths: list[str], optional
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	53 :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	54 function only!
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	55 :type nxpath_prefix: str
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	56 :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	57 :rtype: NXobject
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
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	60 nxobject_copy = nxobject.__class__()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	61 if not len(nxpath_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	62 if 'default' in nxobject.attrs:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	63 nxobject_copy.attrs['default'] = nxobject.attrs['default']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	64 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	65 for k, v in nxobject.attrs.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	66 nxobject_copy.attrs[k] = v
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	67
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	68 for k, v in nxobject.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	69 nxpath = os_path.join(nxpath_prefix, k)
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 if nxpath in exclude_nxpaths:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	72 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	73
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	74 if isinstance(v, NXgroup):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	75 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	76 nxpath_prefix=os_path.join(nxpath_prefix, k))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	77 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	78 nxobject_copy[k] = v
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	79
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	80 return(nxobject_copy)
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 class set_numexpr_threads:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	83
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	84 def __init__(self, num_core):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	85 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	86 self.num_core = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	87 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	88 self.num_core = num_core
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	89
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	90 def __enter__(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	91 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	92
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	93 def __exit__(self, exc_type, exc_value, traceback):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	94 ne.set_num_threads(self.num_core_org)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	95
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	96 class Tomo:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	97 """Processing tomography data with misalignment.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	98 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	99 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	100 test_mode=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	101 """Initialize with optional config input file or dictionary
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	102 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	103 if not isinstance(galaxy_flag, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	104 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	105 self.galaxy_flag = galaxy_flag
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	106 self.num_core = num_core
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	107 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	108 if output_folder != '.':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	109 logger.warning('Ignoring output_folder in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	110 self.output_folder = '.'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	111 if test_mode != False:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	112 logger.warning('Ignoring test_mode in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	113 self.test_mode = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	114 if save_figs is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	115 logger.warning('Ignoring save_figs in galaxy mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	116 save_figs = 'only'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	117 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	118 self.output_folder = os_path.abspath(output_folder)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	119 if not os_path.isdir(output_folder):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	120 mkdir(os_path.abspath(output_folder))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	121 if not isinstance(test_mode, bool):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	122 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	123 self.test_mode = test_mode
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	124 if save_figs is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	125 save_figs = 'no'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	126 self.test_config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	127 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	128 if save_figs != 'only':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	129 logger.warning('Ignoring save_figs in test mode')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	130 save_figs = 'only'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	131 if save_figs == 'only':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	132 self.save_only = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	133 self.save_figs = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	134 elif save_figs == 'yes':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	135 self.save_only = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	136 self.save_figs = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	137 elif save_figs == 'no':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	138 self.save_only = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	139 self.save_figs = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	140 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	141 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	142 if self.save_only:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	143 self.block = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	144 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	145 self.block = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	146 if self.num_core == -1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	147 self.num_core = cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	148 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	149 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	150 if self.num_core > cpu_count():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	151 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	152 f'processors and reduced to {cpu_count()}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	153 self.num_core= cpu_count()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	154
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	155 def read(self, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	156 extension = os_path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	157 if extension == '.yml' or extension == '.yaml':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	158 with open(filename, 'r') as f:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	159 config = safe_load(f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	160 # if len(config) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	161 # 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	162 # if len(list(config.values())[0]) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	163 # 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	164 return(config)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	165 elif extension == '.nxs':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	166 with NXFile(filename, mode='r') as nxfile:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	167 nxroot = nxfile.readfile()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	168 return(nxroot)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	169 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	170 raise ValueError(f'Invalid filename extension ({extension})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	171
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	172 def write(self, data, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	173 extension = os_path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	174 if extension == '.yml' or extension == '.yaml':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	175 with open(filename, 'w') as f:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	176 safe_dump(data, f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	177 elif extension == '.nxs':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	178 data.save(filename, mode='w')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	179 elif extension == '.nc':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	180 data.to_netcdf(os_path=filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	181 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	182 raise ValueError(f'Invalid filename extension ({extension})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	183
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	184 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	185 """Generate the reduced tomography images.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	186 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	187 logger.info('Generate the reduced tomography images')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	188
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	189 # Create plot galaxy path directory if needed
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	190 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	191 mkdir('tomo_reduce_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	192
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	193 if isinstance(data, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	194 # Create Nexus format object from input dictionary
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	195 wf = TomoWorkflow(**data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	196 if len(wf.sample_maps) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	197 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	198 # print(f'\nwf:\n{wf}\n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	199 nxroot = NXroot()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	200 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	201 for sample_map in wf.sample_maps:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	202 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	203 import_scanparser(sample_map.station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	204 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	205 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	206 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	207 # Get test mode configuration info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	208 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	209 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	210 elif isinstance(data, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	211 nxentry = data[data.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	212 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	213 raise ValueError(f'Invalid parameter data ({data})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	214
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	215 # 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	216 reduced_data = NXprocess()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	217
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	218 # Generate dark field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	219 if 'dark_field' in nxentry['spec_scans']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	220 reduced_data = self._gen_dark(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	221
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	222 # Generate bright field
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	223 reduced_data = self._gen_bright(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	224
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	225 # Set vertical detector bounds for image stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	226 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	227 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	228 reduced_data['img_x_bounds'] = img_x_bounds
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	229
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	230 # 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	231 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	232 if zoom_perc is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	233 reduced_data.attrs['zoom_perc'] = zoom_perc
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	234 if num_theta_skip is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	235 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	236
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	237 # Generate reduced tomography fields
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	238 reduced_data = self._gen_tomo(nxentry, reduced_data)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	239
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	240 # 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	241 if isinstance(data, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	242 exclude_items = [f'{nxentry._name}/reduced_data/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	243 f'{nxentry._name}/instrument/detector/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	244 f'{nxentry._name}/instrument/detector/image_key',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	245 f'{nxentry._name}/instrument/detector/sequence_number',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	246 f'{nxentry._name}/sample/rotation_angle',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	247 f'{nxentry._name}/sample/x_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	248 f'{nxentry._name}/sample/z_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	249 f'{nxentry._name}/data/data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	250 f'{nxentry._name}/data/image_key',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	251 f'{nxentry._name}/data/rotation_angle',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	252 f'{nxentry._name}/data/x_translation',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	253 f'{nxentry._name}/data/z_translation']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	254 nxroot = nxcopy(data, exclude_nxpaths=exclude_items)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	255 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	256
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	257 # Add the reduced data NXprocess
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	258 nxentry.reduced_data = reduced_data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	259
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	260 if 'data' not in nxentry:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	261 nxentry.data = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	262 nxentry.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	263 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	264 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	265 nxentry.data.attrs['signal'] = 'reduced_data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	266
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	267 return(nxroot)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	268
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	269 def find_centers(self, nxroot, center_rows=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	270 """Find the calibrated center axis info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	271 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	272 logger.info('Find the calibrated center axis info')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	273
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	274 if not isinstance(nxroot, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	275 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	276 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	277 if not isinstance(nxentry, NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	278 raise ValueError(f'Invalid nxentry ({nxentry})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	279 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	280 if center_rows is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	281 raise ValueError(f'Missing parameter center_rows ({center_rows})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	282 if not is_int_pair(center_rows):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	283 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	284 elif center_rows is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	285 logging.warning(f'Ignoring parameter center_rows ({center_rows})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	286 center_rows = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	287
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	288 # 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	289 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	290 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	291 mkdir('tomo_find_centers_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	292 path = 'tomo_find_centers_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	293 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	294 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	295
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	296 # Check if reduced data is available
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	297 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	298 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	299
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	300 # Select the image stack to calibrate the center axis
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	301 # reduced data axes order: stack,row,theta,column
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	302 # 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	303 # 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	304 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	305 if num_tomo_stacks == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	306 center_stack_index = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	307 center_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	308 if not center_stack.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	309 raise KeyError('Unable to load the required reduced tomography stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	310 default = 'n'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	311 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	312 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	313 center_stack_index = self.test_config['center_stack_index']-1 # make offset 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	314 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	315 center_stack_index = input_int('\nEnter tomography stack index to calibrate the '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	316 'center axis', ge=0, le=num_tomo_stacks-1, default=int(num_tomo_stacks/2))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	317 center_stack = \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	318 np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	319 if not center_stack.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	320 raise KeyError('Unable to load the required reduced tomography stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	321 default = 'y'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	322
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	323 # Get thetas (in degrees)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	324 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	325
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	326 # Get effective pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	327 if 'zoom_perc' in nxentry.reduced_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	328 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	329 nxentry.reduced_data.attrs['zoom_perc'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	330 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	331 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	332
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	333 # Get cross sectional diameter
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	334 cross_sectional_dim = center_stack.shape[2]*eff_pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	335 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	336
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	337 # Determine center offset at sample row boundaries
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	338 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	339
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	340 # Lower row center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	341 # center_stack order: row,theta,column
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	342 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	343 lower_row = self.test_config['lower_row']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	344 elif self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	345 lower_row = min(center_rows)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	346 if not 0 <= lower_row < center_stack.shape[0]-1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	347 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	348 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	349 lower_row = select_one_image_bound(center_stack[:,0,:], 0, bound=0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	350 title=f'theta={round(thetas[0], 2)+0}',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	351 bound_name='row index to find lower center', default=default)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	352 lower_center_offset = self._find_center_one_plane(center_stack[lower_row,:,:], lower_row,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	353 thetas, eff_pixel_size, cross_sectional_dim, path=path, num_core=self.num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	354 logger.debug(f'lower_row = {lower_row:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	355 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	356
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	357 # Upper row center
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	358 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	359 upper_row = self.test_config['upper_row']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	360 elif self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	361 upper_row = max(center_rows)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	362 if not lower_row < upper_row < center_stack.shape[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	363 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	364 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	365 upper_row = select_one_image_bound(center_stack[:,0,:], 0,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	366 bound=center_stack.shape[0]-1, title=f'theta={round(thetas[0], 2)+0}',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	367 bound_name='row index to find upper center', default=default)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	368 upper_center_offset = self._find_center_one_plane(center_stack[upper_row,:,:], upper_row,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	369 thetas, eff_pixel_size, cross_sectional_dim, path=path, num_core=self.num_core)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	370 logger.debug(f'upper_row = {upper_row:.2f}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	371 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	372 del center_stack
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	373
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	374 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	375 '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	376 if num_tomo_stacks > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	377 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	378
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	379 # Save test data to file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	380 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	381 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	382 safe_dump(center_config, f)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	383
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	384 return(center_config)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	385
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	386 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	387 """Reconstruct the tomography data.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	388 """
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	389 logger.info('Reconstruct the tomography data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	390
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	391 if not isinstance(nxroot, NXroot):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	392 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	393 nxentry = nxroot[nxroot.attrs['default']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	394 if not isinstance(nxentry, NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	395 raise ValueError(f'Invalid nxentry ({nxentry})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	396 if not isinstance(center_info, dict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	397 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	398
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	399 # 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	400 if self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	401 if not os_path.exists('tomo_reconstruct_plots'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	402 mkdir('tomo_reconstruct_plots')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	403 path = 'tomo_reconstruct_plots'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	404 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	405 path = self.output_folder
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	406
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	407 # Check if reduced data is available
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	408 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	409 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	410
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	411 # 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	412 # if 'reconstructed_data' in nxentry:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	413 # logger.warning(f'Existing reconstructed data in {nxentry} will be overwritten.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	414 # del nxentry['reconstructed_data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	415 # if 'data' in nxentry and 'reconstructed_data' in nxentry.data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	416 # del nxentry.data['reconstructed_data']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	417 nxprocess = NXprocess()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	418
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	419 # Get rotation axis rows and centers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	420 lower_row = center_info.get('lower_row')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	421 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	422 upper_row = center_info.get('upper_row')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	423 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	424 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	425 upper_center_offset is None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	426 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	427 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	428
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	429 # Get thetas (in degrees)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	430 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	431
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	432 # Reconstruct tomography data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	433 # reduced data axes order: stack,row,theta,column
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	434 # 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	435 # 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	436 # 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	437 if 'zoom_perc' in nxentry.reduced_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	438 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	439 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	440 res_title = 'fullres'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	441 load_error = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	442 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	443 tomo_recon_stacks = num_tomo_stacks*[np.array([])]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	444 for i in range(num_tomo_stacks):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	445 tomo_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[i])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	446 if not tomo_stack.size:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	447 raise KeyError(f'Unable to load tomography stack {i} for reconstruction')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	448 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	449 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	450 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	451 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	452 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	453 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	454 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	455 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	456 logger.info(f'Reconstruction of stack {i} took {time()-t0:.2f} seconds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	457
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	458 # Combine stacks
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	459 tomo_recon_stacks[i] = tomo_recon_stack
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 # Resize the reconstructed tomography data
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	462 # 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	463 if self.test_mode:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	464 x_bounds = self.test_config.get('x_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	465 y_bounds = self.test_config.get('y_bounds')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	466 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	467 elif self.galaxy_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	468 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	469 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	470 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	471 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	472 lt=tomo_recon_stacks[0].shape[1]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	473 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	474 z_bounds = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	475 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	476 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	477 if x_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	478 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	479 x_slice = int(x_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	480 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	481 x_range = (min(x_bounds), max(x_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	482 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	483 if y_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	484 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	485 y_slice = int(y_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	486 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	487 y_range = (min(y_bounds), max(y_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	488 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	489 if z_bounds is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	490 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	491 z_slice = int(z_range[1]/2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	492 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	493 z_range = (min(z_bounds), max(z_bounds))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	494 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	495
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	496 # Plot a few reconstructed image slices
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	497 if num_tomo_stacks == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	498 basetitle = 'recon'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	499 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	500 basetitle = f'recon stack {i}'

69

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1 #!/usr/bin/env python3

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2

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3 import logging

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4 logger = logging.getLogger(__name__)

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5

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6 import numpy as np

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7 try:

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8 import numexpr as ne

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9 except:

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10 pass

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11 try:

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12 import scipy.ndimage as spi

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13 except:

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14 pass

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15

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16 from multiprocessing import cpu_count

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17 from nexusformat.nexus import *

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18 from os import mkdir

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19 from os import path as os_path

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20 try:

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21 from skimage.transform import iradon

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22 except:

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23 pass

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24 try:

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25 from skimage.restoration import denoise_tv_chambolle

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26 except:

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27 pass

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28 from time import time

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29 try:

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30 import tomopy

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31 except:

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32 pass

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33 from yaml import safe_load, safe_dump

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34

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35 from msnctools.fit import Fit

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36 from msnctools.general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \

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37 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \

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38 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot

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39

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40 from workflow.models import import_scanparser, FlatField, TomoField, TomoWorkflow

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41 from workflow.__version__ import __version__

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42

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43 num_core_tomopy_limit = 24

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44

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45 def nxcopy(nxobject:NXobject, exclude_nxpaths:list[str]=[], nxpath_prefix:str='') -> NXobject:

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46 '''Function that returns a copy of a nexus object, optionally exluding certain child items.

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47

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48 :param nxobject: the original nexus object to return a "copy" of

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49 :type nxobject: nexusformat.nexus.NXobject

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50 :param exlude_nxpaths: a list of paths to child nexus objects that

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51 should be exluded from the returned "copy", defaults to `[]`

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52 :type exclude_nxpaths: list[str], optional

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53 :param nxpath_prefix: For use in recursive calls from inside this

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54 function only!

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55 :type nxpath_prefix: str

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56 :return: a copy of `nxobject` with some children optionally exluded.

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57 :rtype: NXobject

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58 '''

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59

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60 nxobject_copy = nxobject.__class__()

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61 if not len(nxpath_prefix):

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62 if 'default' in nxobject.attrs:

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63 nxobject_copy.attrs['default'] = nxobject.attrs['default']

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64 else:

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65 for k, v in nxobject.attrs.items():

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66 nxobject_copy.attrs[k] = v

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67

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68 for k, v in nxobject.items():

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69 nxpath = os_path.join(nxpath_prefix, k)

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70

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71 if nxpath in exclude_nxpaths:

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72 continue

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73

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74 if isinstance(v, NXgroup):

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75 nxobject_copy[k] = nxcopy(v, exclude_nxpaths=exclude_nxpaths,

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76 nxpath_prefix=os_path.join(nxpath_prefix, k))

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77 else:

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78 nxobject_copy[k] = v

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79

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80 return(nxobject_copy)

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81

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82 class set_numexpr_threads:

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83

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84 def __init__(self, num_core):

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85 if num_core is None or num_core < 1 or num_core > cpu_count():

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86 self.num_core = cpu_count()

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87 else:

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88 self.num_core = num_core

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89

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90 def __enter__(self):

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91 self.num_core_org = ne.set_num_threads(self.num_core)

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92

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93 def __exit__(self, exc_type, exc_value, traceback):

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94 ne.set_num_threads(self.num_core_org)

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95

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96 class Tomo:

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97 """Processing tomography data with misalignment.

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98 """

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99 def __init__(self, galaxy_flag=False, num_core=-1, output_folder='.', save_figs=None,

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100 test_mode=False):

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101 """Initialize with optional config input file or dictionary

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102 """

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103 if not isinstance(galaxy_flag, bool):

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104 raise ValueError(f'Invalid parameter galaxy_flag ({galaxy_flag})')

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105 self.galaxy_flag = galaxy_flag

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106 self.num_core = num_core

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107 if self.galaxy_flag:

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108 if output_folder != '.':

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109 logger.warning('Ignoring output_folder in galaxy mode')

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110 self.output_folder = '.'

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111 if test_mode != False:

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112 logger.warning('Ignoring test_mode in galaxy mode')

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113 self.test_mode = False

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114 if save_figs is not None:

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115 logger.warning('Ignoring save_figs in galaxy mode')

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116 save_figs = 'only'

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117 else:

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118 self.output_folder = os_path.abspath(output_folder)

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119 if not os_path.isdir(output_folder):

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120 mkdir(os_path.abspath(output_folder))

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121 if not isinstance(test_mode, bool):

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122 raise ValueError(f'Invalid parameter test_mode ({test_mode})')

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123 self.test_mode = test_mode

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124 if save_figs is None:

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125 save_figs = 'no'

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126 self.test_config = {}

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127 if self.test_mode:

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128 if save_figs != 'only':

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129 logger.warning('Ignoring save_figs in test mode')

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130 save_figs = 'only'

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131 if save_figs == 'only':

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132 self.save_only = True

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133 self.save_figs = True

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134 elif save_figs == 'yes':

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135 self.save_only = False

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136 self.save_figs = True

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137 elif save_figs == 'no':

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138 self.save_only = False

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139 self.save_figs = False

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140 else:

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141 raise ValueError(f'Invalid parameter save_figs ({save_figs})')

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142 if self.save_only:

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143 self.block = False

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144 else:

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145 self.block = True

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146 if self.num_core == -1:

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147 self.num_core = cpu_count()

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148 if not is_int(self.num_core, gt=0, log=False):

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149 raise ValueError(f'Invalid parameter num_core ({num_core})')

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150 if self.num_core > cpu_count():

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151 logger.warning(f'num_core = {self.num_core} is larger than the number of available '

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152 f'processors and reduced to {cpu_count()}')

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153 self.num_core= cpu_count()

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154

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155 def read(self, filename):

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156 extension = os_path.splitext(filename)[1]

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157 if extension == '.yml' or extension == '.yaml':

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158 with open(filename, 'r') as f:

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159 config = safe_load(f)

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160 # if len(config) > 1:

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161 # raise ValueError(f'Multiple root entries in {filename} not yet implemented')

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162 # if len(list(config.values())[0]) > 1:

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163 # raise ValueError(f'Multiple sample maps in {filename} not yet implemented')

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164 return(config)

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165 elif extension == '.nxs':

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166 with NXFile(filename, mode='r') as nxfile:

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167 nxroot = nxfile.readfile()

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168 return(nxroot)

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169 else:

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170 raise ValueError(f'Invalid filename extension ({extension})')

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171

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172 def write(self, data, filename):

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173 extension = os_path.splitext(filename)[1]

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174 if extension == '.yml' or extension == '.yaml':

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175 with open(filename, 'w') as f:

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176 safe_dump(data, f)

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177 elif extension == '.nxs':

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178 data.save(filename, mode='w')

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179 elif extension == '.nc':

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180 data.to_netcdf(os_path=filename)

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181 else:

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182 raise ValueError(f'Invalid filename extension ({extension})')

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183

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184 def gen_reduced_data(self, data, img_x_bounds=None):

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185 """Generate the reduced tomography images.

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186 """

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187 logger.info('Generate the reduced tomography images')

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188

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189 # Create plot galaxy path directory if needed

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190 if self.galaxy_flag and not os_path.exists('tomo_reduce_plots'):

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191 mkdir('tomo_reduce_plots')

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192

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193 if isinstance(data, dict):

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194 # Create Nexus format object from input dictionary

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195 wf = TomoWorkflow(**data)

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196 if len(wf.sample_maps) > 1:

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197 raise ValueError(f'Multiple sample maps not yet implemented')

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198 # print(f'\nwf:\n{wf}\n')

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199 nxroot = NXroot()

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200 t0 = time()

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201 for sample_map in wf.sample_maps:

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202 logger.info(f'Start constructing the {sample_map.title} map.')

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203 import_scanparser(sample_map.station)

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204 sample_map.construct_nxentry(nxroot, include_raw_data=False)

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205 logger.info(f'Constructed all sample maps in {time()-t0:.2f} seconds.')

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206 nxentry = nxroot[nxroot.attrs['default']]

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207 # Get test mode configuration info

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208 if self.test_mode:

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209 self.test_config = data['sample_maps'][0]['test_mode']

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210 elif isinstance(data, NXroot):

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211 nxentry = data[data.attrs['default']]

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212 else:

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213 raise ValueError(f'Invalid parameter data ({data})')

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214

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215 # Create an NXprocess to store data reduction (meta)data

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216 reduced_data = NXprocess()

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217

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218 # Generate dark field

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219 if 'dark_field' in nxentry['spec_scans']:

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220 reduced_data = self._gen_dark(nxentry, reduced_data)

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221

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222 # Generate bright field

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223 reduced_data = self._gen_bright(nxentry, reduced_data)

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224

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225 # Set vertical detector bounds for image stack

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226 img_x_bounds = self._set_detector_bounds(nxentry, reduced_data, img_x_bounds=img_x_bounds)

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227 logger.info(f'img_x_bounds = {img_x_bounds}')

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228 reduced_data['img_x_bounds'] = img_x_bounds

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229

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230 # Set zoom and/or theta skip to reduce memory the requirement

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231 zoom_perc, num_theta_skip = self._set_zoom_or_skip()

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232 if zoom_perc is not None:

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233 reduced_data.attrs['zoom_perc'] = zoom_perc

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234 if num_theta_skip is not None:

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235 reduced_data.attrs['num_theta_skip'] = num_theta_skip

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236

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237 # Generate reduced tomography fields

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238 reduced_data = self._gen_tomo(nxentry, reduced_data)

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239

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240 # Create a copy of the input Nexus object and remove raw and any existing reduced data

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241 if isinstance(data, NXroot):

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242 exclude_items = [f'{nxentry._name}/reduced_data/data',

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243 f'{nxentry._name}/instrument/detector/data',

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244 f'{nxentry._name}/instrument/detector/image_key',

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245 f'{nxentry._name}/instrument/detector/sequence_number',

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246 f'{nxentry._name}/sample/rotation_angle',

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247 f'{nxentry._name}/sample/x_translation',

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248 f'{nxentry._name}/sample/z_translation',

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249 f'{nxentry._name}/data/data',

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250 f'{nxentry._name}/data/image_key',

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251 f'{nxentry._name}/data/rotation_angle',

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252 f'{nxentry._name}/data/x_translation',

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253 f'{nxentry._name}/data/z_translation']

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254 nxroot = nxcopy(data, exclude_nxpaths=exclude_items)

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255 nxentry = nxroot[nxroot.attrs['default']]

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256

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257 # Add the reduced data NXprocess

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258 nxentry.reduced_data = reduced_data

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259

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260 if 'data' not in nxentry:

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261 nxentry.data = NXdata()

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262 nxentry.attrs['default'] = 'data'

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263 nxentry.data.makelink(nxentry.reduced_data.data.tomo_fields, name='reduced_data')

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264 nxentry.data.makelink(nxentry.reduced_data.rotation_angle, name='rotation_angle')

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265 nxentry.data.attrs['signal'] = 'reduced_data'

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266

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267 return(nxroot)

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268

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269 def find_centers(self, nxroot, center_rows=None):

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270 """Find the calibrated center axis info

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271 """

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272 logger.info('Find the calibrated center axis info')

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273

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274 if not isinstance(nxroot, NXroot):

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275 raise ValueError(f'Invalid parameter nxroot ({nxroot})')

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276 nxentry = nxroot[nxroot.attrs['default']]

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277 if not isinstance(nxentry, NXentry):

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278 raise ValueError(f'Invalid nxentry ({nxentry})')

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279 if self.galaxy_flag:

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280 if center_rows is None:

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281 raise ValueError(f'Missing parameter center_rows ({center_rows})')

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282 if not is_int_pair(center_rows):

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283 raise ValueError(f'Invalid parameter center_rows ({center_rows})')

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284 elif center_rows is not None:

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285 logging.warning(f'Ignoring parameter center_rows ({center_rows})')

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286 center_rows = None

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287

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288 # Create plot galaxy path directory and path if needed

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289 if self.galaxy_flag:

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290 if not os_path.exists('tomo_find_centers_plots'):

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291 mkdir('tomo_find_centers_plots')

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292 path = 'tomo_find_centers_plots'

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293 else:

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294 path = self.output_folder

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295

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296 # Check if reduced data is available

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297 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):

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298 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')

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299

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300 # Select the image stack to calibrate the center axis

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301 # reduced data axes order: stack,row,theta,column

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302 # Note: Nexus cannot follow a link if the data it points to is too big,

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303 # so get the data from the actual place, not from nxentry.data

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304 num_tomo_stacks = nxentry.reduced_data.data.tomo_fields.shape[0]

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305 if num_tomo_stacks == 1:

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306 center_stack_index = 0

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307 center_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[0])

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308 if not center_stack.size:

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309 raise KeyError('Unable to load the required reduced tomography stack')

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310 default = 'n'

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311 else:

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312 if self.test_mode:

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313 center_stack_index = self.test_config['center_stack_index']-1 # make offset 0

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314 else:

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315 center_stack_index = input_int('\nEnter tomography stack index to calibrate the '

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316 'center axis', ge=0, le=num_tomo_stacks-1, default=int(num_tomo_stacks/2))

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317 center_stack = \

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318 np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index])

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319 if not center_stack.size:

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320 raise KeyError('Unable to load the required reduced tomography stack')

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321 default = 'y'

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322

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323 # Get thetas (in degrees)

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324 thetas = np.asarray(nxentry.reduced_data.rotation_angle)

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325

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326 # Get effective pixel_size

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327 if 'zoom_perc' in nxentry.reduced_data:

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328 eff_pixel_size = 100.*(nxentry.instrument.detector.x_pixel_size/

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329 nxentry.reduced_data.attrs['zoom_perc'])

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330 else:

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331 eff_pixel_size = nxentry.instrument.detector.x_pixel_size

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332

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333 # Get cross sectional diameter

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334 cross_sectional_dim = center_stack.shape[2]*eff_pixel_size

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335 logger.debug(f'cross_sectional_dim = {cross_sectional_dim}')

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336

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337 # Determine center offset at sample row boundaries

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338 logger.info('Determine center offset at sample row boundaries')

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339

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340 # Lower row center

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341 # center_stack order: row,theta,column

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342 if self.test_mode:

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343 lower_row = self.test_config['lower_row']

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344 elif self.galaxy_flag:

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345 lower_row = min(center_rows)

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346 if not 0 <= lower_row < center_stack.shape[0]-1:

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347 raise ValueError(f'Invalid parameter center_rows ({center_rows})')

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348 else:

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349 lower_row = select_one_image_bound(center_stack[:,0,:], 0, bound=0,

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350 title=f'theta={round(thetas[0], 2)+0}',

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351 bound_name='row index to find lower center', default=default)

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352 lower_center_offset = self._find_center_one_plane(center_stack[lower_row,:,:], lower_row,

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353 thetas, eff_pixel_size, cross_sectional_dim, path=path, num_core=self.num_core)

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354 logger.debug(f'lower_row = {lower_row:.2f}')

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355 logger.debug(f'lower_center_offset = {lower_center_offset:.2f}')

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356

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357 # Upper row center

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358 if self.test_mode:

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359 upper_row = self.test_config['upper_row']

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360 elif self.galaxy_flag:

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361 upper_row = max(center_rows)

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362 if not lower_row < upper_row < center_stack.shape[0]:

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363 raise ValueError(f'Invalid parameter center_rows ({center_rows})')

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364 else:

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365 upper_row = select_one_image_bound(center_stack[:,0,:], 0,

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366 bound=center_stack.shape[0]-1, title=f'theta={round(thetas[0], 2)+0}',

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367 bound_name='row index to find upper center', default=default)

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368 upper_center_offset = self._find_center_one_plane(center_stack[upper_row,:,:], upper_row,

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369 thetas, eff_pixel_size, cross_sectional_dim, path=path, num_core=self.num_core)

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370 logger.debug(f'upper_row = {upper_row:.2f}')

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371 logger.debug(f'upper_center_offset = {upper_center_offset:.2f}')

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372 del center_stack

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373

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374 center_config = {'lower_row': lower_row, 'lower_center_offset': lower_center_offset,

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375 'upper_row': upper_row, 'upper_center_offset': upper_center_offset}

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376 if num_tomo_stacks > 1:

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377 center_config['center_stack_index'] = center_stack_index+1 # save as offset 1

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378

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379 # Save test data to file

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380 if self.test_mode:

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381 with open(f'{self.output_folder}/center_config.yaml', 'w') as f:

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382 safe_dump(center_config, f)

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383

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384 return(center_config)

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385

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386 def reconstruct_data(self, nxroot, center_info, x_bounds=None, y_bounds=None):

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387 """Reconstruct the tomography data.

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388 """

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389 logger.info('Reconstruct the tomography data')

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390

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391 if not isinstance(nxroot, NXroot):

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392 raise ValueError(f'Invalid parameter nxroot ({nxroot})')

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393 nxentry = nxroot[nxroot.attrs['default']]

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394 if not isinstance(nxentry, NXentry):

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395 raise ValueError(f'Invalid nxentry ({nxentry})')

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396 if not isinstance(center_info, dict):

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397 raise ValueError(f'Invalid parameter center_info ({center_info})')

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398

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399 # Create plot galaxy path directory and path if needed

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400 if self.galaxy_flag:

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401 if not os_path.exists('tomo_reconstruct_plots'):

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402 mkdir('tomo_reconstruct_plots')

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403 path = 'tomo_reconstruct_plots'

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404 else:

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405 path = self.output_folder

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406

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407 # Check if reduced data is available

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408 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):

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409 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')

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410

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411 # Create an NXprocess to store image reconstruction (meta)data

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412 # if 'reconstructed_data' in nxentry:

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413 # logger.warning(f'Existing reconstructed data in {nxentry} will be overwritten.')

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414 # del nxentry['reconstructed_data']

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415 # if 'data' in nxentry and 'reconstructed_data' in nxentry.data:

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416 # del nxentry.data['reconstructed_data']

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417 nxprocess = NXprocess()

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418

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419 # Get rotation axis rows and centers

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420 lower_row = center_info.get('lower_row')

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421 lower_center_offset = center_info.get('lower_center_offset')

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422 upper_row = center_info.get('upper_row')

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423 upper_center_offset = center_info.get('upper_center_offset')

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424 if (lower_row is None or lower_center_offset is None or upper_row is None or

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425 upper_center_offset is None):

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426 raise KeyError(f'Unable to find valid calibrated center axis info in {center_info}.')

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427 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)

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428

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429 # Get thetas (in degrees)

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430 thetas = np.asarray(nxentry.reduced_data.rotation_angle)

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431

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432 # Reconstruct tomography data

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433 # reduced data axes order: stack,row,theta,column

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434 # reconstructed data order in each stack: row/z,x,y

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435 # Note: Nexus cannot follow a link if the data it points to is too big,

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436 # so get the data from the actual place, not from nxentry.data

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437 if 'zoom_perc' in nxentry.reduced_data:

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438 res_title = f'{nxentry.reduced_data.attrs["zoom_perc"]}p'

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439 else:

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440 res_title = 'fullres'

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441 load_error = False

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442 num_tomo_stacks = nxentry.reduced_data.data.tomo_fields.shape[0]

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443 tomo_recon_stacks = num_tomo_stacks*[np.array([])]

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444 for i in range(num_tomo_stacks):

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445 tomo_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[i])

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446 if not tomo_stack.size:

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447 raise KeyError(f'Unable to load tomography stack {i} for reconstruction')

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448 assert(0 <= lower_row < upper_row < tomo_stack.shape[0])

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449 center_offsets = [lower_center_offset-lower_row*center_slope,

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450 upper_center_offset+(tomo_stack.shape[0]-1-upper_row)*center_slope]

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451 t0 = time()

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452 logger.debug(f'Running _reconstruct_one_tomo_stack on {self.num_core} cores ...')

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453 tomo_recon_stack = self._reconstruct_one_tomo_stack(tomo_stack, thetas,

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454 center_offsets=center_offsets, num_core=self.num_core, algorithm='gridrec')

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455 logger.debug(f'... done in {time()-t0:.2f} seconds')

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456 logger.info(f'Reconstruction of stack {i} took {time()-t0:.2f} seconds')

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457

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458 # Combine stacks

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459 tomo_recon_stacks[i] = tomo_recon_stack

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460

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461 # Resize the reconstructed tomography data

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462 # reconstructed data order in each stack: row/z,x,y

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463 if self.test_mode:

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464 x_bounds = self.test_config.get('x_bounds')

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465 y_bounds = self.test_config.get('y_bounds')

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466 z_bounds = None

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467 elif self.galaxy_flag:

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468 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,

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469 lt=tomo_recon_stacks[0].shape[1]):

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470 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')

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471 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,

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472 lt=tomo_recon_stacks[0].shape[1]):

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473 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')

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474 z_bounds = None

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475 else:

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476 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks)

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477 if x_bounds is None:

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478 x_range = (0, tomo_recon_stacks[0].shape[1])

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479 x_slice = int(x_range[1]/2)

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480 else:

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481 x_range = (min(x_bounds), max(x_bounds))

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482 x_slice = int((x_bounds[0]+x_bounds[1])/2)

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483 if y_bounds is None:

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484 y_range = (0, tomo_recon_stacks[0].shape[2])

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485 y_slice = int(y_range[1]/2)

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486 else:

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487 y_range = (min(y_bounds), max(y_bounds))

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488 y_slice = int((y_bounds[0]+y_bounds[1])/2)

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489 if z_bounds is None:

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490 z_range = (0, tomo_recon_stacks[0].shape[0])

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491 z_slice = int(z_range[1]/2)

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492 else:

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493 z_range = (min(z_bounds), max(z_bounds))

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494 z_slice = int((z_bounds[0]+z_bounds[1])/2)

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495

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496 # Plot a few reconstructed image slices

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497 if num_tomo_stacks == 1:

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498 basetitle = 'recon'

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499 else:

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500 basetitle = f'recon stack {i}'

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501 for i, stack in enumerate(tomo_recon_stacks):

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502 title = f'{basetitle} {res_title} xslice{x_slice}'

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503 quick_imshow(stack[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],

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504 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,

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505 block=self.block)

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506 title = f'{basetitle} {res_title} yslice{y_slice}'

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507 quick_imshow(stack[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],

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508 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,

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509 block=self.block)

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510 title = f'{basetitle} {res_title} zslice{z_slice}'

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511 quick_imshow(stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],

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512 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,

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513 block=self.block)

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514

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515 # Save test data to file

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516 # reconstructed data order in each stack: row/z,x,y

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517 if self.test_mode:

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518 for i, stack in enumerate(tomo_recon_stacks):

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519 np.savetxt(f'{self.output_folder}/recon_stack_{i+1}.txt',

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520 stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')

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521

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522 # Add image reconstruction to reconstructed data NXprocess

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523 # reconstructed data order in each stack: row/z,x,y

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524 nxprocess.data = NXdata()

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525 nxprocess.attrs['default'] = 'data'

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526 for k, v in center_info.items():

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527 nxprocess[k] = v

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528 if x_bounds is not None:

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529 nxprocess.x_bounds = x_bounds

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530 if y_bounds is not None:

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531 nxprocess.y_bounds = y_bounds

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532 if z_bounds is not None:

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533 nxprocess.z_bounds = z_bounds

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534 nxprocess.data['reconstructed_data'] = np.asarray([stack[z_range[0]:z_range[1],

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535 x_range[0]:x_range[1],y_range[0]:y_range[1]] for stack in tomo_recon_stacks])

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536 nxprocess.data.attrs['signal'] = 'reconstructed_data'

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537

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538 # Create a copy of the input Nexus object and remove reduced data

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539 exclude_items = [f'{nxentry._name}/reduced_data/data', f'{nxentry._name}/data/reduced_data']

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540 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)

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541

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542 # Add the reconstructed data NXprocess to the new Nexus object

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543 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]

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544 nxentry_copy.reconstructed_data = nxprocess

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545 if 'data' not in nxentry_copy:

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546 nxentry_copy.data = NXdata()

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547 nxentry_copy.attrs['default'] = 'data'

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548 nxentry_copy.data.makelink(nxprocess.data.reconstructed_data, name='reconstructed_data')

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549 nxentry_copy.data.attrs['signal'] = 'reconstructed_data'

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550

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551 return(nxroot_copy)

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552

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553 def combine_data(self, nxroot):

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554 """Combine the reconstructed tomography stacks.

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555 """

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556 logger.info('Combine the reconstructed tomography stacks')

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557

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558 if not isinstance(nxroot, NXroot):

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559 raise ValueError(f'Invalid parameter nxroot ({nxroot})')

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560 nxentry = nxroot[nxroot.attrs['default']]

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561 if not isinstance(nxentry, NXentry):

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562 raise ValueError(f'Invalid nxentry ({nxentry})')

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563

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564 # Create plot galaxy path directory and path if needed

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565 if self.galaxy_flag:

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566 if not os_path.exists('tomo_combine_plots'):

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567 mkdir('tomo_combine_plots')

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568 path = 'tomo_combine_plots'

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569 else:

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570 path = self.output_folder

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571

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572 # Check if reconstructed image data is available

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573 if ('reconstructed_data' not in nxentry or 'reconstructed_data' not in nxentry.data):

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574 raise KeyError(f'Unable to find valid reconstructed image data in {nxentry}.')

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575

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576 # Create an NXprocess to store combined image reconstruction (meta)data

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577 # if 'combined_data' in nxentry:

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578 # logger.warning(f'Existing combined data in {nxentry} will be overwritten.')

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579 # del nxentry['combined_data']

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580 # if 'data' in nxentry 'combined_data' in nxentry.data:

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581 # del nxentry.data['combined_data']

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582 nxprocess = NXprocess()

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583

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584 # Get the reconstructed data

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585 # reconstructed data order: stack,row(z),x,y

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586 # Note: Nexus cannot follow a link if the data it points to is too big,

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587 # so get the data from the actual place, not from nxentry.data

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588 tomo_recon_stacks = np.asarray(nxentry.reconstructed_data.data.reconstructed_data)

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589 num_tomo_stacks = tomo_recon_stacks.shape[0]

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590 if num_tomo_stacks == 1:

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591 return(nxroot)

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592 t0 = time()

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593 logger.debug(f'Combining the reconstructed stacks ...')

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594 tomo_recon_combined = tomo_recon_stacks[0,:,:,:]

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595 if num_tomo_stacks > 2:

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596 tomo_recon_combined = np.concatenate([tomo_recon_combined]+

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597 [tomo_recon_stacks[i,:,:,:] for i in range(1, num_tomo_stacks-1)])

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598 if num_tomo_stacks > 1:

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599 tomo_recon_combined = np.concatenate([tomo_recon_combined]+

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600 [tomo_recon_stacks[num_tomo_stacks-1,:,:,:]])

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601 logger.debug(f'... done in {time()-t0:.2f} seconds')

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602 logger.info(f'Combining the reconstructed stacks took {time()-t0:.2f} seconds')

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603

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604 # Resize the combined tomography data set

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605 # combined data order: row/z,x,y

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606 if self.test_mode:

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607 x_bounds = None

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608 y_bounds = None

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609 z_bounds = self.test_config.get('z_bounds')

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610 elif self.galaxy_flag:

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611 exit('TODO')

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612 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,

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613 lt=tomo_recon_stacks[0].shape[1]):

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614 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')

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615 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,

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616 lt=tomo_recon_stacks[0].shape[1]):

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617 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')

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618 z_bounds = None

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619 else:

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620 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_combined,

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621 z_only=True)

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622 if x_bounds is None:

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623 x_range = (0, tomo_recon_combined.shape[1])

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624 x_slice = int(x_range[1]/2)

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625 else:

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626 x_range = x_bounds

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627 x_slice = int((x_bounds[0]+x_bounds[1])/2)

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628 if y_bounds is None:

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629 y_range = (0, tomo_recon_combined.shape[2])

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630 y_slice = int(y_range[1]/2)

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631 else:

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632 y_range = y_bounds

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633 y_slice = int((y_bounds[0]+y_bounds[1])/2)

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634 if z_bounds is None:

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635 z_range = (0, tomo_recon_combined.shape[0])

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636 z_slice = int(z_range[1]/2)

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637 else:

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638 z_range = z_bounds

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diff changeset

639 z_slice = int((z_bounds[0]+z_bounds[1])/2)

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diff changeset

640

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diff changeset

641 # Plot a few combined image slices

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642 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],

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643 title=f'recon combined xslice{x_slice}', path=path,

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644 save_fig=self.save_figs, save_only=self.save_only, block=self.block)

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645 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],

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646 title=f'recon combined yslice{y_slice}', path=path,

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647 save_fig=self.save_figs, save_only=self.save_only, block=self.block)

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648 quick_imshow(tomo_recon_combined[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],

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649 title=f'recon combined zslice{z_slice}', path=path,

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650 save_fig=self.save_figs, save_only=self.save_only, block=self.block)

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651

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652 # Save test data to file

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653 # combined data order: row/z,x,y

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654 if self.test_mode:

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655 np.savetxt(f'{self.output_folder}/recon_combined.txt', tomo_recon_combined[

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656 z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')

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diff changeset

657

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diff changeset

658 # Add image reconstruction to reconstructed data NXprocess

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659 # combined data order: row/z,x,y

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660 nxprocess.data = NXdata()

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661 nxprocess.attrs['default'] = 'data'

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662 if x_bounds is not None:

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663 nxprocess.x_bounds = x_bounds

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664 if y_bounds is not None:

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665 nxprocess.y_bounds = y_bounds

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666 if z_bounds is not None:

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667 nxprocess.z_bounds = z_bounds

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668 nxprocess.data['combined_data'] = tomo_recon_combined

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669 nxprocess.data.attrs['signal'] = 'combined_data'

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diff changeset

670

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diff changeset

671 # Create a copy of the input Nexus object and remove reconstructed data

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672 exclude_items = [f'{nxentry._name}/reconstructed_data/data',

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673 f'{nxentry._name}/data/reconstructed_data']

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674 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)

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diff changeset

675

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676 # Add the combined data NXprocess to the new Nexus object

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677 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]

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678 nxentry_copy.combined_data = nxprocess

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679 if 'data' not in nxentry_copy:

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680 nxentry_copy.data = NXdata()

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681 nxentry_copy.attrs['default'] = 'data'

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682 nxentry_copy.data.makelink(nxprocess.data.combined_data, name='combined_data')

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683 nxentry_copy.data.attrs['signal'] = 'combined_data'

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diff changeset

684

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diff changeset

685 return(nxroot_copy)

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686

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687 def _gen_dark(self, nxentry, reduced_data):

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688 """Generate dark field.

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689 """

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690 # Get the dark field images

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691 image_key = nxentry.instrument.detector.get('image_key', None)

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692 if image_key and 'data' in nxentry.instrument.detector:

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693 field_indices = [index for index, key in enumerate(image_key) if key == 2]

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694 tdf_stack = nxentry.instrument.detector.data[field_indices,:,:]

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695 # RV the default NXtomo form does not accomodate bright or dark field stacks

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696 else:

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697 dark_field_scans = nxentry.spec_scans.dark_field

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698 dark_field = FlatField.construct_from_nxcollection(dark_field_scans)

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699 prefix = str(nxentry.instrument.detector.local_name)

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700 tdf_stack = dark_field.get_detector_data(prefix)

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701 if isinstance(tdf_stack, list):

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702 exit('TODO')

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703

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diff changeset

704 # Take median

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705 if tdf_stack.ndim == 2:

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706 tdf = tdf_stack

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707 elif tdf_stack.ndim == 3:

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708 tdf = np.median(tdf_stack, axis=0)

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diff changeset

709 del tdf_stack

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710 else:

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711 raise ValueError(f'Invalid tdf_stack shape ({tdf_stack.shape})')

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diff changeset

712

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713 # Remove dark field intensities above the cutoff

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714 #RV tdf_cutoff = None

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715 tdf_cutoff = tdf.min()+2*(np.median(tdf)-tdf.min())

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716 logger.debug(f'tdf_cutoff = {tdf_cutoff}')

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717 if tdf_cutoff is not None:

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718 if not is_num(tdf_cutoff, ge=0):

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diff changeset

719 logger.warning(f'Ignoring illegal value of tdf_cutoff {tdf_cutoff}')

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720 else:

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diff changeset

721 tdf[tdf > tdf_cutoff] = np.nan

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diff changeset

722 logger.debug(f'tdf_cutoff = {tdf_cutoff}')

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diff changeset

723

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diff changeset

724 # Remove nans

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725 tdf_mean = np.nanmean(tdf)

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diff changeset

726 logger.debug(f'tdf_mean = {tdf_mean}')

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727 np.nan_to_num(tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)

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diff changeset

728

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diff changeset

729 # Plot dark field

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730 if self.galaxy_flag:

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731 quick_imshow(tdf, title='dark field', path='tomo_reduce_plots', save_fig=self.save_figs,

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732 save_only=self.save_only)

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733 elif not self.test_mode:

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734 quick_imshow(tdf, title='dark field', path=self.output_folder, save_fig=self.save_figs,

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735 save_only=self.save_only)

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736 clear_imshow('dark field')

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737 # quick_imshow(tdf, title='dark field', block=True)

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738

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739 # Add dark field to reduced data NXprocess

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740 reduced_data.data = NXdata()

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741 reduced_data.data['dark_field'] = tdf

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742

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743 return(reduced_data)

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744

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745 def _gen_bright(self, nxentry, reduced_data):

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746 """Generate bright field.

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747 """

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diff changeset

748 # Get the bright field images

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749 image_key = nxentry.instrument.detector.get('image_key', None)

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750 if image_key and 'data' in nxentry.instrument.detector:

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751 field_indices = [index for index, key in enumerate(image_key) if key == 1]

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752 tbf_stack = nxentry.instrument.detector.data[field_indices,:,:]

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753 # RV the default NXtomo form does not accomodate bright or dark field stacks

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754 else:

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755 bright_field_scans = nxentry.spec_scans.bright_field

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756 bright_field = FlatField.construct_from_nxcollection(bright_field_scans)

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757 prefix = str(nxentry.instrument.detector.local_name)

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758 tbf_stack = bright_field.get_detector_data(prefix)

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759 if isinstance(tbf_stack, list):

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760 exit('TODO')

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761

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762 # Take median if more than one image

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763 """Median or mean: It may be best to try the median because of some image

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764 artifacts that arise due to crinkles in the upstream kapton tape windows

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765 causing some phase contrast images to appear on the detector.

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766 One thing that also may be useful in a future implementation is to do a

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767 brightfield adjustment on EACH frame of the tomo based on a ROI in the

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768 corner of the frame where there is no sample but there is the direct X-ray

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diff changeset

769 beam because there is frame to frame fluctuations from the incoming beam.

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770 We don’t typically account for them but potentially could.

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771 """

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diff changeset

772 if tbf_stack.ndim == 2:

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773 tbf = tbf_stack

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774 elif tbf_stack.ndim == 3:

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diff changeset

775 tbf = np.median(tbf_stack, axis=0)

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diff changeset

776 del tbf_stack

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777 else:

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778 raise ValueError(f'Invalid tbf_stack shape ({tbf_stacks.shape})')

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diff changeset

779

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diff changeset

780 # Subtract dark field

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781 if 'data' in reduced_data and 'dark_field' in reduced_data.data:

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782 tbf -= reduced_data.data.dark_field

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diff changeset

783 else:

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diff changeset

784 logger.warning('Dark field unavailable')

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diff changeset

785

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diff changeset

786 # Set any non-positive values to one

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787 # (avoid negative bright field values for spikes in dark field)

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diff changeset

788 tbf[tbf < 1] = 1

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diff changeset

789

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diff changeset

790 # Plot bright field

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791 if self.galaxy_flag:

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792 quick_imshow(tbf, title='bright field', path='tomo_reduce_plots',

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793 save_fig=self.save_figs, save_only=self.save_only)

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794 elif not self.test_mode:

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795 quick_imshow(tbf, title='bright field', path=self.output_folder,

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796 save_fig=self.save_figs, save_only=self.save_only)

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diff changeset

797 clear_imshow('bright field')

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798 # quick_imshow(tbf, title='bright field', block=True)

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799

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800 # Add bright field to reduced data NXprocess

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801 if 'data' not in reduced_data:

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802 reduced_data.data = NXdata()

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803 reduced_data.data['bright_field'] = tbf

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diff changeset

804

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diff changeset

805 return(reduced_data)

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806

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807 def _set_detector_bounds(self, nxentry, reduced_data, img_x_bounds=None):

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808 """Set vertical detector bounds for each image stack.

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809 Right now the range is the same for each set in the image stack.

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diff changeset

810 """

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diff changeset

811 if self.test_mode:

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812 return(tuple(self.test_config['img_x_bounds']))

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diff changeset

813

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814 # Get the first tomography image and the reference heights

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815 image_key = nxentry.instrument.detector.get('image_key', None)

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816 if image_key and 'data' in nxentry.instrument.detector:

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817 field_indices = [index for index, key in enumerate(image_key) if key == 0]

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diff changeset

818 first_image = np.asarray(nxentry.instrument.detector.data[field_indices[0],:,:])

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diff changeset

819 theta = float(nxentry.sample.rotation_angle[field_indices[0]])

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

820 z_translation_all = nxentry.sample.z_translation[field_indices]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

821 z_translation_levels = sorted(list(set(z_translation_all)))

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

822 num_tomo_stacks = len(z_translation_levels)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

823 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

824 tomo_field_scans = nxentry.spec_scans.tomo_fields

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

825 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

826 vertical_shifts = tomo_fields.get_vertical_shifts()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

827 if not isinstance(vertical_shifts, list):

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

828 vertical_shifts = [vertical_shifts]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

829 prefix = str(nxentry.instrument.detector.local_name)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

830 t0 = time()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

831 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

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diff changeset

832 logger.debug(f'Getting first image took {time()-t0:.2f} seconds')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

833 num_tomo_stacks = len(tomo_fields.scan_numbers)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

834 theta = tomo_fields.theta_range['start']

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

835

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

836 # Select image bounds

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

837 title = f'tomography image at theta={round(theta, 2)+0}'

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

838 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

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diff changeset

839 le=first_image.shape[0])):

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

840 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

841 if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

842 pixel_size = nxentry.instrument.detector.x_pixel_size

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

843 # Try to get a fit from the bright field

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

844 tbf = np.asarray(reduced_data.data.bright_field)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

845 tbf_shape = tbf.shape

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

846 x_sum = np.sum(tbf, 1)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

847 x_sum_min = x_sum.min()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

848 x_sum_max = x_sum.max()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

849 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

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diff changeset

850 guess=True)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

851 parameters = fit.best_values

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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852 x_low_fit = parameters.get('center1', None)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

853 x_upp_fit = parameters.get('center2', None)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

854 sig_low = parameters.get('sigma1', None)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

855 sig_upp = parameters.get('sigma2', None)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

856 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

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diff changeset

857 sig_low is not None and sig_upp is not None and \

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

858 0 <= x_low_fit < x_upp_fit <= x_sum.size and \

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

859 (sig_low+sig_upp)/(x_upp_fit-x_low_fit) < 0.1

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

860 if have_fit:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

861 # Set a 5% margin on each side

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

862 margin = 0.05*(x_upp_fit-x_low_fit)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

863 x_low_fit = max(0, x_low_fit-margin)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

864 x_upp_fit = min(tbf_shape[0], x_upp_fit+margin)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

865 if num_tomo_stacks == 1:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

866 if have_fit:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

867 # Set the default range to enclose the full fitted window

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

868 x_low = int(x_low_fit)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

869 x_upp = int(x_upp_fit)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

870 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

871 # 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

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diff changeset

872 num_x_min = int((1.0-0.5*pixel_size)/pixel_size)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

873 x_low = int(0.5*(tbf_shape[0]-num_x_min))

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

874 x_upp = x_low+num_x_min

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

875 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

876 # Get the default range from the reference heights

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

877 delta_z = vertical_shifts[1]-vertical_shifts[0]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

878 for i in range(2, num_tomo_stacks):

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

879 delta_z = min(delta_z, vertical_shifts[i]-vertical_shifts[i-1])

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

880 logger.debug(f'delta_z = {delta_z}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

881 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

882 logger.debug(f'num_x_min = {num_x_min}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

883 if num_x_min > tbf_shape[0]:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

884 logger.warning('Image bounds and pixel size prevent seamless stacking')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

885 if have_fit:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

886 # Center the default range relative to the fitted window

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

887 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

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diff changeset

888 x_upp = x_low+num_x_min

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

889 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

890 # Center the default range

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

891 x_low = int(0.5*(tbf_shape[0]-num_x_min))

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

892 x_upp = x_low+num_x_min

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

893 if self.galaxy_flag:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

894 img_x_bounds = (x_low, x_upp)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

895 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

896 tmp = np.copy(tbf)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

897 tmp_max = tmp.max()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

898 tmp[x_low,:] = tmp_max

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

899 tmp[x_upp-1,:] = tmp_max

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

900 quick_imshow(tmp, title='bright field')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

901 tmp = np.copy(first_image)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

902 tmp_max = tmp.max()

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

903 tmp[x_low,:] = tmp_max

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

904 tmp[x_upp-1,:] = tmp_max

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

905 quick_imshow(tmp, title=title)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

906 del tmp

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

907 quick_plot((range(x_sum.size), x_sum),

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

908 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

909 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

910 title='sum over theta and y')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

911 print(f'lower bound = {x_low} (inclusive)')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

912 print(f'upper bound = {x_upp} (exclusive)]')

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diff changeset

913 accept = input_yesno('Accept these bounds (y/n)?', 'y')

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diff changeset

914 clear_imshow('bright field')

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diff changeset

915 clear_imshow(title)

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diff changeset

916 clear_plot('sum over theta and y')

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diff changeset

917 if accept:

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diff changeset

918 img_x_bounds = (x_low, x_upp)

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diff changeset

919 else:

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diff changeset

920 while True:

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diff changeset

921 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',

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diff changeset

922 legend='sum over theta and y')

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diff changeset

923 if len(img_x_bounds) == 1:

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diff changeset

924 break

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diff changeset

925 else:

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diff changeset

926 print(f'Choose a single connected data range')

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diff changeset

927 img_x_bounds = tuple(img_x_bounds[0])

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diff changeset

928 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

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diff changeset

929 int((delta_z-0.5*pixel_size)/pixel_size)):

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diff changeset

930 logger.warning('Image bounds and pixel size prevent seamless stacking')

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diff changeset

931 else:

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diff changeset

932 if num_tomo_stacks > 1:

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diff changeset

933 raise NotImplementedError('Selecting image bounds for multiple stacks on FMB')

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diff changeset

934 # For FMB: use the first tomography image to select range

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diff changeset

935 # RV: revisit if they do tomography with multiple stacks

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diff changeset

936 x_sum = np.sum(first_image, 1)

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diff changeset

937 x_sum_min = x_sum.min()

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diff changeset

938 x_sum_max = x_sum.max()

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diff changeset

939 if self.galaxy_flag:

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diff changeset

940 if img_x_bounds is None:

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diff changeset

941 img_x_bounds = (0, first_image.shape[0])

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diff changeset

942 else:

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diff changeset

943 quick_imshow(first_image, title=title)

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diff changeset

944 print('Select vertical data reduction range from first tomography image')

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diff changeset

945 img_x_bounds = select_image_bounds(first_image, 0, title=title)

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diff changeset

946 clear_imshow(title)

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diff changeset

947 if img_x_bounds is None:

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diff changeset

948 raise ValueError('Unable to select image bounds')

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diff changeset

949

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diff changeset

950 # Plot results

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diff changeset

951 if self.galaxy_flag:

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diff changeset

952 path = 'tomo_reduce_plots'

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diff changeset

953 else:

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diff changeset

954 path = self.output_folder

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diff changeset

955 x_low = img_x_bounds[0]

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diff changeset

956 x_upp = img_x_bounds[1]

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diff changeset

957 tmp = np.copy(first_image)

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diff changeset

958 tmp_max = tmp.max()

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diff changeset

959 tmp[x_low,:] = tmp_max

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diff changeset

960 tmp[x_upp-1,:] = tmp_max

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diff changeset

961 quick_imshow(tmp, title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,

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diff changeset

962 block=self.block)

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diff changeset

963 del tmp

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diff changeset

964 quick_plot((range(x_sum.size), x_sum),

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

965 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),

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diff changeset

966 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),

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diff changeset

967 title='sum over theta and y', path=path, save_fig=self.save_figs,

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diff changeset

968 save_only=self.save_only, block=self.block)

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diff changeset

969

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diff changeset

970 return(img_x_bounds)

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diff changeset

971

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diff changeset

972 def _set_zoom_or_skip(self):

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973 """Set zoom and/or theta skip to reduce memory the requirement for the analysis.

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diff changeset

974 """

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diff changeset

975 # if input_yesno('\nDo you want to zoom in to reduce memory requirement (y/n)?', 'n'):

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diff changeset

976 # zoom_perc = input_int(' Enter zoom percentage', ge=1, le=100)

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diff changeset

977 # else:

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diff changeset

978 # zoom_perc = None

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diff changeset

979 zoom_perc = None

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980 # if input_yesno('Do you want to skip thetas to reduce memory requirement (y/n)?', 'n'):

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diff changeset

981 # num_theta_skip = input_int(' Enter the number skip theta interval', ge=0,

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diff changeset

982 # lt=num_theta)

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diff changeset

983 # else:

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diff changeset

984 # num_theta_skip = None

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diff changeset

985 num_theta_skip = None

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diff changeset

986 logger.debug(f'zoom_perc = {zoom_perc}')

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diff changeset

987 logger.debug(f'num_theta_skip = {num_theta_skip}')

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diff changeset

988

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diff changeset

989 return(zoom_perc, num_theta_skip)

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diff changeset

990

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diff changeset

991 def _gen_tomo(self, nxentry, reduced_data):

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diff changeset

992 """Generate tomography fields.

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993 """

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diff changeset

994 # Get full bright field

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diff changeset

995 tbf = np.asarray(reduced_data.data.bright_field)

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diff changeset

996 tbf_shape = tbf.shape

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diff changeset

997

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998 # Get image bounds

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diff changeset

999 img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0])))

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1000 img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1])))

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diff changeset

1001

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diff changeset

1002 # Get resized dark field

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diff changeset

1003 # if 'dark_field' in data:

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diff changeset

1004 # tbf = np.asarray(reduced_data.data.dark_field[

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diff changeset

1005 # img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])

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diff changeset

1006 # else:

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1007 # logger.warning('Dark field unavailable')

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1008 # tdf = None

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diff changeset

1009 tdf = None

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diff changeset

1010

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1011 # Resize bright field

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1012 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):

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1013 tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]

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1014

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1015 # Get the tomography images

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1016 image_key = nxentry.instrument.detector.get('image_key', None)

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1017 if image_key and 'data' in nxentry.instrument.detector:

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1018 field_indices_all = [index for index, key in enumerate(image_key) if key == 0]

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1019 z_translation_all = nxentry.sample.z_translation[field_indices_all]

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1020 z_translation_levels = sorted(list(set(z_translation_all)))

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1021 num_tomo_stacks = len(z_translation_levels)

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1022 tomo_stacks = num_tomo_stacks*[np.array([])]

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1023 horizontal_shifts = []

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1024 vertical_shifts = []

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1025 thetas = None

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1026 tomo_stacks = []

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1027 for i, z_translation in enumerate(z_translation_levels):

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1028 field_indices = [field_indices_all[index]

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1029 for index, z in enumerate(z_translation_all) if z == z_translation]

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1030 horizontal_shift = list(set(nxentry.sample.x_translation[field_indices]))

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1031 assert(len(horizontal_shift) == 1)

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1032 horizontal_shifts += horizontal_shift

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1033 vertical_shift = list(set(nxentry.sample.z_translation[field_indices]))

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1034 assert(len(vertical_shift) == 1)

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1035 vertical_shifts += vertical_shift

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1036 sequence_numbers = nxentry.instrument.detector.sequence_number[field_indices]

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1037 if thetas is None:

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1038 thetas = np.asarray(nxentry.sample.rotation_angle[field_indices]) \

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1039 [sequence_numbers]

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1040 else:

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1041 assert(all(thetas[i] == nxentry.sample.rotation_angle[field_indices[index]]

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1042 for i, index in enumerate(sequence_numbers)))

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1043 assert(list(set(sequence_numbers)) == [i for i in range(len(sequence_numbers))])

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1044 if list(sequence_numbers) == [i for i in range(len(sequence_numbers))]:

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1045 tomo_stack = np.asarray(nxentry.instrument.detector.data[field_indices])

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1046 else:

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1047 raise ValueError('Unable to load the tomography images')

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1048 tomo_stacks.append(tomo_stack)

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1049 else:

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1050 tomo_field_scans = nxentry.spec_scans.tomo_fields

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1051 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)

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1052 horizontal_shifts = tomo_fields.get_horizontal_shifts()

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1053 vertical_shifts = tomo_fields.get_vertical_shifts()

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1054 prefix = str(nxentry.instrument.detector.local_name)

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1055 t0 = time()

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1056 tomo_stacks = tomo_fields.get_detector_data(prefix)

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1057 logger.debug(f'Getting tomography images took {time()-t0:.2f} seconds')

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1058 logger.debug(f'Getting all images took {time()-t0:.2f} seconds')

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1059 thetas = np.linspace(tomo_fields.theta_range['start'], tomo_fields.theta_range['end'],

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1060 tomo_fields.theta_range['num'])

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1061 if not isinstance(tomo_stacks, list):

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1062 horizontal_shifts = [horizontal_shifts]

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1063 vertical_shifts = [vertical_shifts]

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1064 tomo_stacks = [tomo_stacks]

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1065

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1066 reduced_tomo_stacks = []

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1067 if self.galaxy_flag:

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1068 path = 'tomo_reduce_plots'

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1069 else:

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1070 path = self.output_folder

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1071 for i, tomo_stack in enumerate(tomo_stacks):

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1072 # Resize the tomography images

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1073 # Right now the range is the same for each set in the image stack.

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1074 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):

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1075 t0 = time()

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1076 tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1],

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1077 img_y_bounds[0]:img_y_bounds[1]].astype('float64')

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1078 logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds')

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1079

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1080 # Subtract dark field

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1081 if tdf is not None:

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1082 t0 = time()

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1083 with set_numexpr_threads(self.num_core):

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1084 ne.evaluate('tomo_stack-tdf', out=tomo_stack)

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1085 logger.debug(f'Subtracting dark field took {time()-t0:.2f} seconds')

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1086

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1087 # Normalize

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1088 t0 = time()

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1089 with set_numexpr_threads(self.num_core):

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1090 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)

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1091 logger.debug(f'Normalizing took {time()-t0:.2f} seconds')

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1092

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1093 # Remove non-positive values and linearize data

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1094 t0 = time()

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1095 cutoff = 1.e-6

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1096 with set_numexpr_threads(self.num_core):

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1097 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)

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1098 with set_numexpr_threads(self.num_core):

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1099 ne.evaluate('-log(tomo_stack)', out=tomo_stack)

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1100 logger.debug('Removing non-positive values and linearizing data took '+

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1101 f'{time()-t0:.2f} seconds')

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1102

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1103 # Get rid of nans/infs that may be introduced by normalization

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1104 t0 = time()

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diff changeset

1105 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)

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1106 logger.debug(f'Remove nans/infs took {time()-t0:.2f} seconds')

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1107

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1108 # Downsize tomography stack to smaller size

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1109 # TODO use theta_skip as well

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1110 tomo_stack = tomo_stack.astype('float32')

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1111 if not self.test_mode:

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1112 if len(tomo_stacks) == 1:

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1113 title = f'red fullres theta {round(thetas[0], 2)+0}'

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1114 else:

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1115 title = f'red stack {i} fullres theta {round(thetas[0], 2)+0}'

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1116 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,

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1117 save_only=self.save_only, block=self.block)

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1118 # if not self.block:

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1119 # clear_imshow(title)

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1120 if False and zoom_perc != 100:

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1121 t0 = time()

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1122 logger.debug(f'Zooming in ...')

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1123 tomo_zoom_list = []

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1124 for j in range(tomo_stack.shape[0]):

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1125 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)

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1126 tomo_zoom_list.append(tomo_zoom)

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1127 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])

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1128 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1129 logger.info(f'Zooming in took {time()-t0:.2f} seconds')

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1130 del tomo_zoom_list

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1131 if not self.test_mode:

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1132 title = f'red stack {zoom_perc}p theta {round(thetas[0], 2)+0}'

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1133 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,

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1134 save_only=self.save_only, block=self.block)

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1135 # if not self.block:

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1136 # clear_imshow(title)

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1137

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1138 # Convert tomography stack from theta,row,column to row,theta,column

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1139 t0 = time()

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1140 tomo_stack = np.swapaxes(tomo_stack, 0, 1)

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1141 logger.debug(f'Converting coordinate order took {time()-t0:.2f} seconds')

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1142

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1143 # Save test data to file

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1144 if self.test_mode:

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1145 row_index = int(tomo_stack.shape[0]/2)

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1146 np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[row_index,:,:],

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1147 fmt='%.6e')

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1148

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1149 # Combine resized stacks

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1150 reduced_tomo_stacks.append(tomo_stack)

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1151

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1152 # Add tomo field info to reduced data NXprocess

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1153 reduced_data['rotation_angle'] = thetas

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1154 reduced_data['x_translation'] = np.asarray(horizontal_shifts)

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1155 reduced_data['z_translation'] = np.asarray(vertical_shifts)

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1156 reduced_data.data['tomo_fields'] = np.asarray(reduced_tomo_stacks)

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1157

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1158 if tdf is not None:

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1159 del tdf

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1160 del tbf

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1161

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1162 return(reduced_data)

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1163

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1164 def _find_center_one_plane(self, sinogram, row, thetas, eff_pixel_size, cross_sectional_dim,

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1165 path=None, tol=0.1, num_core=1):

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1166 """Find center for a single tomography plane.

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1167 """

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1168 # Try automatic center finding routines for initial value

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1169 # sinogram index order: theta,column

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1170 # need column,theta for iradon, so take transpose

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1171 sinogram_T = sinogram.T

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1172 center = sinogram.shape[1]/2

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1173

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1174 # Try using Nghia Vo’s method

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1175 t0 = time()

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1176 if num_core > num_core_tomopy_limit:

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1177 logger.debug(f'Running find_center_vo on {num_core_tomopy_limit} cores ...')

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1178 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)

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1179 else:

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1180 logger.debug(f'Running find_center_vo on {num_core} cores ...')

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1181 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)

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1182 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1183 logger.info(f'Finding the center using Nghia Vo’s method took {time()-t0:.2f} seconds')

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1184 center_offset_vo = tomo_center-center

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1185 logger.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')

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1186 t0 = time()

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1187 logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')

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1188 recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,

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1189 eff_pixel_size, cross_sectional_dim, False, num_core)

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1190 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1191 logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')

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1192

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1193 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'

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1194 self._plot_edges_one_plane(recon_plane, title, path=path)

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1195

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1196 # Try using phase correlation method

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1197 # if input_yesno('Try finding center using phase correlation (y/n)?', 'n'):

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1198 # t0 = time()

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1199 # logger.debug(f'Running find_center_pc ...')

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1200 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, rotc_guess=tomo_center)

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1201 # error = 1.

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1202 # while error > tol:

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1203 # prev = tomo_center

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1204 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,

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1205 # rotc_guess=tomo_center)

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1206 # error = np.abs(tomo_center-prev)

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1207 # logger.debug(f'... done in {time()-t0:.2f} seconds')

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1208 # logger.info('Finding the center using the phase correlation method took '+

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1209 # f'{time()-t0:.2f} seconds')

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1210 # center_offset = tomo_center-center

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1211 # print(f'Center at row {row} using phase correlation = {center_offset:.2f}')

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1212 # t0 = time()

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1213 # logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')

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1214 # recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,

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1215 # eff_pixel_size, cross_sectional_dim, False, num_core)

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1216 # logger.debug(f'... done in {time()-t0:.2f} seconds')

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1217 # logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')

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1218 #

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1219 # title = f'edges row{row} center_offset{center_offset:.2f} PC'

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1220 # self._plot_edges_one_plane(recon_plane, title, path=path)

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1221

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1222 # Select center location

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1223 # if input_yesno('Accept a center location (y) or continue search (n)?', 'y'):

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1224 if True:

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1225 # center_offset = input_num(' Enter chosen center offset', ge=-center, le=center,

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1226 # default=center_offset_vo)

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1227 center_offset = center_offset_vo

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1228 del sinogram_T

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diff changeset

1229 del recon_plane

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1230 return float(center_offset)

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1231

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1232 # perform center finding search

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1233 while True:

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1234 center_offset_low = input_int('\nEnter lower bound for center offset', ge=-center,

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diff changeset

1235 le=center)

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1236 center_offset_upp = input_int('Enter upper bound for center offset',

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1237 ge=center_offset_low, le=center)

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1238 if center_offset_upp == center_offset_low:

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1239 center_offset_step = 1

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1240 else:

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1241 center_offset_step = input_int('Enter step size for center offset search', ge=1,

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1242 le=center_offset_upp-center_offset_low)

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1243 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)

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1244 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)

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1245 for center_offset in center_offsets:

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1246 if center_offset == center_offset_vo:

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diff changeset

1247 continue

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1248 t0 = time()

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1249 logger.debug(f'Running _reconstruct_one_plane on {num_core} cores ...')

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diff changeset

1250 recon_plane = self._reconstruct_one_plane(sinogram_T, center_offset+center, thetas,

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1251 eff_pixel_size, cross_sectional_dim, False, num_core)

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1252 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1253 logger.info(f'Reconstructing center_offset {center_offset} took '+

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1254 f'{time()-t0:.2f} seconds')

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1255 title = f'edges row{row} center_offset{center_offset:.2f}'

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diff changeset

1256 self._plot_edges_one_plane(recon_plane, title, path=path)

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1257 if input_int('\nContinue (0) or end the search (1)', ge=0, le=1):

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diff changeset

1258 break

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diff changeset

1259

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diff changeset

1260 del sinogram_T

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diff changeset

1261 del recon_plane

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diff changeset

1262 center_offset = input_num(' Enter chosen center offset', ge=-center, le=center)

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diff changeset

1263 return float(center_offset)

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diff changeset

1264

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1265 def _reconstruct_one_plane(self, tomo_plane_T, center, thetas, eff_pixel_size,

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diff changeset

1266 cross_sectional_dim, plot_sinogram=True, num_core=1):

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1267 """Invert the sinogram for a single tomography plane.

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1268 """

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diff changeset

1269 # tomo_plane_T index order: column,theta

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1270 assert(0 <= center < tomo_plane_T.shape[0])

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1271 center_offset = center-tomo_plane_T.shape[0]/2

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1272 two_offset = 2*int(np.round(center_offset))

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diff changeset

1273 two_offset_abs = np.abs(two_offset)

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1274 max_rad = int(0.55*(cross_sectional_dim/eff_pixel_size)) # 10% slack to avoid edge effects

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1275 if max_rad > 0.5*tomo_plane_T.shape[0]:

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1276 max_rad = 0.5*tomo_plane_T.shape[0]

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1277 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))

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diff changeset

1278 if two_offset >= 0:

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1279 logger.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')

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1280 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]

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1281 else:

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1282 logger.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')

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1283 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]

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1284 if not self.galaxy_flag and plot_sinogram:

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1285 quick_imshow(sinogram.T, f'sinogram center offset{center_offset:.2f}', aspect='auto',

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1286 path=self.output_folder, save_fig=self.save_figs, save_only=self.save_only,

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1287 block=self.block)

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1288

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1289 # Inverting sinogram

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1290 t0 = time()

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1291 recon_sinogram = iradon(sinogram, theta=thetas, circle=True)

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1292 logger.debug(f'Inverting sinogram took {time()-t0:.2f} seconds')

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diff changeset

1293 del sinogram

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diff changeset

1294

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1295 # Performing Gaussian filtering and removing ring artifacts

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1296 recon_parameters = None#self.config.get('recon_parameters')

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diff changeset

1297 if recon_parameters is None:

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diff changeset

1298 sigma = 1.0

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1299 ring_width = 15

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1300 else:

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1301 sigma = recon_parameters.get('gaussian_sigma', 1.0)

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1302 if not is_num(sigma, ge=0.0):

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1303 logger.warning(f'Invalid gaussian_sigma ({sigma}) in _reconstruct_one_plane, '+

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diff changeset

1304 'set to a default value of 1.0')

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diff changeset

1305 sigma = 1.0

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1306 ring_width = recon_parameters.get('ring_width', 15)

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1307 if not is_int(ring_width, ge=0):

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1308 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+

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diff changeset

1309 'set to a default value of 15')

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diff changeset

1310 ring_width = 15

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1311 t0 = time()

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diff changeset

1312 recon_sinogram = spi.gaussian_filter(recon_sinogram, sigma, mode='nearest')

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diff changeset

1313 recon_clean = np.expand_dims(recon_sinogram, axis=0)

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1314 del recon_sinogram

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1315 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=ring_width, ncore=num_core)

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1316 logger.debug(f'Filtering and removing ring artifacts took {time()-t0:.2f} seconds')

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1317

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1318 return recon_clean

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1319

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1320 def _plot_edges_one_plane(self, recon_plane, title, path=None):

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1321 vis_parameters = None#self.config.get('vis_parameters')

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1322 if vis_parameters is None:

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diff changeset

1323 weight = 0.1

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1324 else:

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1325 weight = vis_parameters.get('denoise_weight', 0.1)

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1326 if not is_num(weight, ge=0.0):

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1327 logger.warning(f'Invalid weight ({weight}) in _plot_edges_one_plane, '+

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diff changeset

1328 'set to a default value of 0.1')

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diff changeset

1329 weight = 0.1

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1330 edges = denoise_tv_chambolle(recon_plane, weight=weight)

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1331 vmax = np.max(edges[0,:,:])

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1332 vmin = -vmax

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1333 if path is None:

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1334 path = self.output_folder

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1335 quick_imshow(edges[0,:,:], f'{title} coolwarm', path=path, cmap='coolwarm',

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diff changeset

1336 save_fig=self.save_figs, save_only=self.save_only, block=self.block)

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diff changeset

1337 quick_imshow(edges[0,:,:], f'{title} gray', path=path, cmap='gray', vmin=vmin, vmax=vmax,

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diff changeset

1338 save_fig=self.save_figs, save_only=self.save_only, block=self.block)

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diff changeset

1339 del edges

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diff changeset

1340

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diff changeset

1341 def _reconstruct_one_tomo_stack(self, tomo_stack, thetas, center_offsets=[], num_core=1,

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diff changeset

1342 algorithm='gridrec'):

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diff changeset

1343 """Reconstruct a single tomography stack.

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1344 """

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diff changeset

1345 # tomo_stack order: row,theta,column

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diff changeset

1346 # input thetas must be in degrees

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diff changeset

1347 # centers_offset: tomography axis shift in pixels relative to column center

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1348 # RV should we remove stripes?

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diff changeset

1349 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html

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diff changeset

1350 # RV should we remove rings?

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diff changeset

1351 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html

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diff changeset

1352 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?

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diff changeset

1353 if not len(center_offsets):

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diff changeset

1354 centers = np.zeros((tomo_stack.shape[0]))

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diff changeset

1355 elif len(center_offsets) == 2:

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diff changeset

1356 centers = np.linspace(center_offsets[0], center_offsets[1], tomo_stack.shape[0])

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1357 else:

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diff changeset

1358 if center_offsets.size != tomo_stack.shape[0]:

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diff changeset

1359 raise ValueError('center_offsets dimension mismatch in reconstruct_one_tomo_stack')

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diff changeset

1360 centers = center_offsets

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1361 centers += tomo_stack.shape[2]/2

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diff changeset

1362

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diff changeset

1363 # Get reconstruction parameters

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diff changeset

1364 recon_parameters = None#self.config.get('recon_parameters')

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1365 if recon_parameters is None:

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diff changeset

1366 sigma = 2.0

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diff changeset

1367 secondary_iters = 0

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diff changeset

1368 ring_width = 15

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diff changeset

1369 else:

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diff changeset

1370 sigma = recon_parameters.get('stripe_fw_sigma', 2.0)

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diff changeset

1371 if not is_num(sigma, ge=0):

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diff changeset

1372 logger.warning(f'Invalid stripe_fw_sigma ({sigma}) in '+

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diff changeset

1373 '_reconstruct_one_tomo_stack, set to a default value of 2.0')

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diff changeset

1374 ring_width = 15

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diff changeset

1375 secondary_iters = recon_parameters.get('secondary_iters', 0)

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diff changeset

1376 if not is_int(secondary_iters, ge=0):

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diff changeset

1377 logger.warning(f'Invalid secondary_iters ({secondary_iters}) in '+

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diff changeset

1378 '_reconstruct_one_tomo_stack, set to a default value of 0 (skip them)')

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diff changeset

1379 ring_width = 0

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diff changeset

1380 ring_width = recon_parameters.get('ring_width', 15)

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diff changeset

1381 if not is_int(ring_width, ge=0):

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diff changeset

1382 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+

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diff changeset

1383 'set to a default value of 15')

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diff changeset

1384 ring_width = 15

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diff changeset

1385

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diff changeset

1386 # Remove horizontal stripe

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diff changeset

1387 t0 = time()

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1388 if num_core > num_core_tomopy_limit:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1389 logger.debug('Running remove_stripe_fw on {num_core_tomopy_limit} cores ...')

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diff changeset

1390 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,

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1391 ncore=num_core_tomopy_limit)

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1392 else:

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1393 logger.debug(f'Running remove_stripe_fw on {num_core} cores ...')

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1394 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,

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1395 ncore=num_core)

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1396 logger.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds')

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1397

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1398 # Perform initial image reconstruction

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1399 logger.debug('Performing initial image reconstruction')

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1400 t0 = time()

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1401 logger.debug(f'Running recon on {num_core} cores ...')

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1402 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,

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1403 sinogram_order=True, algorithm=algorithm, ncore=num_core)

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1404 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1405 logger.info(f'Performing initial image reconstruction took {time()-t0:.2f} seconds')

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1406

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1407 # Run optional secondary iterations

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1408 if secondary_iters > 0:

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1409 logger.debug(f'Running {secondary_iters} secondary iterations')

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1410 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iters}

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1411 #RV: doesn't work for me:

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1412 #"Error: CUDA error 803: system has unsupported display driver/cuda driver combination."

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1413 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iters}

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1414 #SIRT did not finish while running overnight

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1415 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iters}

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1416 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,

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1417 'num_iter':secondary_iters}

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1418 t0 = time()

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1419 logger.debug(f'Running recon on {num_core} cores ...')

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1420 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,

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1421 init_recon=tomo_recon_stack, options=options, sinogram_order=True,

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1422 algorithm=tomopy.astra, ncore=num_core)

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1423 logger.debug(f'... done in {time()-t0:.2f} seconds')

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1424 logger.info(f'Performing secondary iterations took {time()-t0:.2f} seconds')

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1425

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1426 # Remove ring artifacts

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1427 t0 = time()

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1428 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=ring_width, out=tomo_recon_stack,

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1429 ncore=num_core)

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1430 logger.debug(f'Removing ring artifacts took {time()-t0:.2f} seconds')

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diff changeset

1431

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diff changeset

1432 return tomo_recon_stack

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1433

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diff changeset

1434 def _resize_reconstructed_data(self, data, z_only=False):

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diff changeset

1435 """Resize the reconstructed tomography data.

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1436 """

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diff changeset

1437 # Data order: row(z),x,y or stack,row(z),x,y

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diff changeset

1438 if isinstance(data, list):

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1439 for stack in data:

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diff changeset

1440 assert(stack.ndim == 3)

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diff changeset

1441 num_tomo_stacks = len(data)

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diff changeset

1442 tomo_recon_stacks = data

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1443 else:

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diff changeset

1444 assert(data.ndim == 3)

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diff changeset

1445 num_tomo_stacks = 1

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diff changeset

1446 tomo_recon_stacks = [data]

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diff changeset

1447

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diff changeset

1448 if z_only:

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diff changeset

1449 x_bounds = None

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diff changeset

1450 y_bounds = None

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diff changeset

1451 else:

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diff changeset

1452 # Selecting x bounds (in yz-plane)

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diff changeset

1453 tomosum = 0

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diff changeset

1454 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,2))

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diff changeset

1455 for i in range(num_tomo_stacks)]

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diff changeset

1456 select_x_bounds = input_yesno('\nDo you want to change the image x-bounds (y/n)?', 'y')

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diff changeset

1457 if not select_x_bounds:

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diff changeset

1458 x_bounds = None

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diff changeset

1459 else:

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diff changeset

1460 accept = False

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diff changeset

1461 index_ranges = None

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diff changeset

1462 while not accept:

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diff changeset

1463 mask, x_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,

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diff changeset

1464 title='select x data range', legend='recon stack sum yz')

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diff changeset

1465 while len(x_bounds) != 1:

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diff changeset

1466 print('Please select exactly one continuous range')

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diff changeset

1467 mask, x_bounds = draw_mask_1d(tomosum, title='select x data range',

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diff changeset

1468 legend='recon stack sum yz')

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diff changeset

1469 x_bounds = x_bounds[0]

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diff changeset

1470 # quick_plot(tomosum, vlines=x_bounds, title='recon stack sum yz')

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diff changeset

1471 # print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+

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diff changeset

1472 # 'exclusive)')

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diff changeset

1473 # accept = input_yesno('Accept these bounds (y/n)?', 'y')

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diff changeset

1474 accept = True

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diff changeset

1475 logger.debug(f'x_bounds = {x_bounds}')

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diff changeset

1476

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diff changeset

1477 # Selecting y bounds (in xz-plane)

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diff changeset

1478 tomosum = 0

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diff changeset

1479 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,1))

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diff changeset

1480 for i in range(num_tomo_stacks)]

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diff changeset

1481 select_y_bounds = input_yesno('\nDo you want to change the image y-bounds (y/n)?', 'y')

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diff changeset

1482 if not select_y_bounds:

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diff changeset

1483 y_bounds = None

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diff changeset

1484 else:

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diff changeset

1485 accept = False

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diff changeset

1486 index_ranges = None

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diff changeset

1487 while not accept:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1488 mask, y_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1489 title='select x data range', legend='recon stack sum xz')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1490 while len(y_bounds) != 1:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1491 print('Please select exactly one continuous range')

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diff changeset

1492 mask, y_bounds = draw_mask_1d(tomosum, title='select x data range',

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1493 legend='recon stack sum xz')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1494 y_bounds = y_bounds[0]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1495 # quick_plot(tomosum, vlines=y_bounds, title='recon stack sum xz')

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diff changeset

1496 # print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1497 # 'exclusive)')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1498 # accept = input_yesno('Accept these bounds (y/n)?', 'y')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1499 accept = True

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diff changeset

1500 logger.debug(f'y_bounds = {y_bounds}')

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diff changeset

1501

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1502 # Selecting z bounds (in xy-plane) (only valid for a single image set)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1503 if num_tomo_stacks != 1:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1504 z_bounds = None

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1505 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1506 tomosum = 0

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1507 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(1,2))

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1508 for i in range(num_tomo_stacks)]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1509 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

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diff changeset

1510 if not select_z_bounds:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1511 z_bounds = None

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diff changeset

1512 else:

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parents:

diff changeset

1513 accept = False

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parents:

diff changeset

1514 index_ranges = None

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1515 while not accept:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1516 mask, z_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1517 title='select x data range', legend='recon stack sum xy')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1518 while len(z_bounds) != 1:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1519 print('Please select exactly one continuous range')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1520 mask, z_bounds = draw_mask_1d(tomosum, title='select x data range',

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1521 legend='recon stack sum xy')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1522 z_bounds = z_bounds[0]

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1523 # quick_plot(tomosum, vlines=z_bounds, title='recon stack sum xy')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1524 # print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1525 # 'exclusive)')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1526 # accept = input_yesno('Accept these bounds (y/n)?', 'y')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1527 accept = True

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1528 logger.debug(f'z_bounds = {z_bounds}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1529

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1530 return(x_bounds, y_bounds, z_bounds)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1531

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parents:

diff changeset

1532

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diff changeset

1533 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

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diff changeset

1534 output_folder='.', save_figs='no', test_mode=False) -> None:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1535

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1536 if test_mode:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1537 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1538 level = logging.getLevelName('INFO')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1539 logging.basicConfig(filename=f'{output_folder}/tomo.log', filemode='w',

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1540 format=logging_format, level=level, force=True)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1541 logger.info(f'input_file = {input_file}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1542 logger.info(f'center_file = {center_file}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1543 logger.info(f'output_file = {output_file}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1544 logger.debug(f'modes= {modes}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1545 logger.debug(f'num_core= {num_core}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1546 logger.info(f'output_folder = {output_folder}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1547 logger.info(f'save_figs = {save_figs}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1548 logger.info(f'test_mode = {test_mode}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1549

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1550 # Check for correction modes

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1551 if modes is None:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1552 modes = ['all']

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1553 logger.debug(f'modes {type(modes)} = {modes}')

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1554

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1555 # Instantiate Tomo object

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1556 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

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parents:

diff changeset

1557 test_mode=test_mode)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1558

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parents:

diff changeset

1559 # Read input file

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1560 data = tomo.read(input_file)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1561

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1562 # Generate reduced tomography images

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1563 if 'reduce_data' in modes or 'all' in modes:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1564 data = tomo.gen_reduced_data(data)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1565

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diff changeset

1566 # Find rotation axis centers for the tomography stacks.

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1567 center_data = None

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1568 if 'find_center' in modes or 'all' in modes:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1569 center_data = tomo.find_centers(data)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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diff changeset

1570

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1571 # Reconstruct tomography stacks

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1572 if 'reconstruct_data' in modes or 'all' in modes:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1573 if center_data is None:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1574 # Read input file

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1575 center_data = tomo.read(center_file)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1576 data = tomo.reconstruct_data(data, center_data)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1577 center_data = None

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1578

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1579 # Combine reconstructed tomography stacks

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1580 if 'combine_data' in modes or 'all' in modes:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1581 data = tomo.combine_data(data)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1582

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1583 # Write output file

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

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parents:

diff changeset

1584 if not test_mode:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

rv43

parents:

diff changeset

1585 if center_data is None:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

rv43

parents:

diff changeset

1586 data = tomo.write(data, output_file)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

rv43

parents:

diff changeset

1587 else:

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

rv43

parents:

diff changeset

1588 data = tomo.write(center_data, output_file)

fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1

rv43

parents:

diff changeset

1589

Mercurial > repos > rv43 > tomo

annotate workflow/run_tomo.py @ 69:fba792d5f83b draft