tomo: workflow/models.py annotate

annotate workflow/models.py @ 75:d5e1d4ea2b7e draft default tip

planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69

author	rv43
date	Thu, 23 Mar 2023 13:39:14 +0000
parents	1cf15b61cd83
children

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 logging
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	7
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	8 import numpy as np
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	9 import os
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	10 import yaml
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	11
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	12 from functools import cache
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	13 from pathlib import PosixPath
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	14 from pydantic import BaseModel as PydanticBaseModel
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	15 from pydantic import validator, ValidationError, conint, confloat, constr, conlist, FilePath, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	16 PrivateAttr
69 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 time import time
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	19 from typing import Optional, Literal
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	20 from typing_extensions import TypedDict
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	21 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	22 from pyspec.file.spec import FileSpec
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	23 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	24 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	25
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	26 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	27 from msnctools.general import is_int, is_num, input_int, input_int_list, input_num, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	28 input_yesno, input_menu, index_nearest, string_to_list, file_exists_and_readable
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	29 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	30 from general import is_int, is_num, input_int, input_int_list, input_num, \
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	31 input_yesno, input_menu, index_nearest, string_to_list, file_exists_and_readable
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	32
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	33
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	34 def import_scanparser(station):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	35 if station in ('id1a3', 'id3a'):
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	36 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	37 from msnctools.scanparsers import SMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	38 globals()['ScanParser'] = SMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	39 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	40 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	41 from scanparsers import SMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	42 globals()['ScanParser'] = SMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	43 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	44 pass
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	45 elif station in ('id3b'):
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	46 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	47 from msnctools.scanparsers import FMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	48 globals()['ScanParser'] = FMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	49 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	50 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	51 from scanparsers import FMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	52 globals()['ScanParser'] = FMBRotationScanParser
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	53 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	54 pass
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	55 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	56 raise RuntimeError(f'Invalid station: {station}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	57
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	58 @cache
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	59 def get_available_scan_numbers(spec_file:str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	60 scans = FileSpec(spec_file).scans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	61 scan_numbers = list(scans.keys())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	62 for scan_number in scan_numbers.copy():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	63 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	64 parser = ScanParser(spec_file, scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	65 try:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	66 scan_type = parser.scan_type
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	67 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	68 scan_type = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	69 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	70 scan_numbers.remove(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	71 return(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	72
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	73 @cache
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	74 def get_scanparser(spec_file:str, scan_number:int):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	75 if scan_number not in get_available_scan_numbers(spec_file):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	76 return(None)
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 return(ScanParser(spec_file, scan_number))
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
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	81 class BaseModel(PydanticBaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	82 class Config:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	83 validate_assignment = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	84 arbitrary_types_allowed = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	85
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	86 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	87 def construct_from_cli(cls):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	88 obj = cls.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	89 obj.cli()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	90 return(obj)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	91
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	92 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	93 def construct_from_yaml(cls, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	94 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	95 with open(filename, 'r') as infile:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	96 indict = yaml.load(infile, Loader=yaml.CLoader)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	97 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	98 raise ValueError(f'Could not load a dictionary from {filename}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	99 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	100 obj = cls(**indict)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	101 return(obj)
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 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	104 def construct_from_file(cls, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	105 file_exists_and_readable(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	106 filename = os.path.abspath(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	107 fileformat = os.path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	108 yaml_extensions = ('.yaml','.yml')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	109 nexus_extensions = ('.nxs','.nx5','.h5','.hdf5')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	110 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	111 if fileformat.lower() in yaml_extensions:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	112 obj = cls.construct_from_yaml(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	113 logger.info(f'Constructed a model from {filename} in {time()-t0:.2f} seconds.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	114 return(obj)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	115 elif fileformat.lower() in nexus_extensions:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	116 obj = cls.construct_from_nexus(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	117 logger.info(f'Constructed a model from {filename} in {time()-t0:.2f} seconds.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	118 return(obj)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	119 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	120 logger.error(f'Unsupported file extension for constructing a model: {fileformat}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	121 raise TypeError(f'Unrecognized file extension: {fileformat}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	122
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	123 def dict_for_yaml(self, exclude_fields=[]):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	124 yaml_dict = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	125 for field_name in self.__fields__:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	126 if field_name in exclude_fields:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	127 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	128 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	129 field_value = getattr(self, field_name, None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	130 if field_value is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	131 if isinstance(field_value, BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	132 yaml_dict[field_name] = field_value.dict_for_yaml()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	133 elif isinstance(field_value,list) and all(isinstance(item,BaseModel)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	134 for item in field_value):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	135 yaml_dict[field_name] = [item.dict_for_yaml() for item in field_value]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	136 elif isinstance(field_value, PosixPath):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	137 yaml_dict[field_name] = str(field_value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	138 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	139 yaml_dict[field_name] = field_value
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 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	142 return(yaml_dict)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	143
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	144 def write_to_yaml(self, filename=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	145 yaml_dict = self.dict_for_yaml()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	146 if filename is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	147 logger.info('Printing yaml representation here:\n'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	148 f'{yaml.dump(yaml_dict, sort_keys=False)}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	149 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	150 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	151 with open(filename, 'w') as outfile:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	152 yaml.dump(yaml_dict, outfile, sort_keys=False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	153 logger.info(f'Successfully wrote this model to {filename}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	154 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	155 logger.error(f'Unknown error -- could not write to {filename} in yaml format.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	156 logger.info('Printing yaml representation here:\n'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	157 f'{yaml.dump(yaml_dict, sort_keys=False)}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	158
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	159 def write_to_file(self, filename, force_overwrite=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	160 file_writeable, fileformat = self.output_file_valid(filename,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	161 force_overwrite=force_overwrite)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	162 if fileformat == 'yaml':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	163 if file_writeable:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	164 self.write_to_yaml(filename=filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	165 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	166 self.write_to_yaml()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	167 elif fileformat == 'nexus':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	168 if file_writeable:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	169 self.write_to_nexus(filename=filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	170
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	171 def output_file_valid(self, filename, force_overwrite=False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	172 filename = os.path.abspath(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	173 fileformat = os.path.splitext(filename)[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	174 yaml_extensions = ('.yaml','.yml')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	175 nexus_extensions = ('.nxs','.nx5','.h5','.hdf5')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	176 if fileformat.lower() not in (yaml_extensions, nexus_extensions):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	177 return(False, None) # Only yaml and NeXus files allowed for output now.
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	178 elif fileformat.lower() in yaml_extensions:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	179 fileformat = 'yaml'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	180 elif fileformat.lower() in nexus_extensions:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	181 fileformat = 'nexus'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	182 if os.path.isfile(filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	183 if os.access(filename, os.W_OK):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	184 if not force_overwrite:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	185 logger.error(f'{filename} will not be overwritten.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	186 return(False, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	187 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	188 logger.error(f'Cannot access {filename} for writing.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	189 return(False, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	190 if os.path.isdir(os.path.dirname(filename)):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	191 if os.access(os.path.dirname(filename), os.W_OK):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	192 return(True, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	193 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	194 logger.error(f'Cannot access {os.path.dirname(filename)} for writing.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	195 return(False, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	196 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	197 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	198 os.makedirs(os.path.dirname(filename))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	199 return(True, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	200 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	201 logger.error(f'Cannot create {os.path.dirname(filename)} for output.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	202 return(False, fileformat)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	203
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	204 def set_single_attr_cli(self, attr_name, attr_desc='unknown attribute', list_flag=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	205 **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	206 if cli_kwargs.get('chain_attr_desc', False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	207 cli_kwargs['attr_desc'] = attr_desc
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	208 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	209 attr = getattr(self, attr_name, None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	210 if attr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	211 attr = self.__fields__[attr_name].type_.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	212 if cli_kwargs.get('chain_attr_desc', False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	213 cli_kwargs['attr_desc'] = attr_desc
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	214 input_accepted = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	215 while not input_accepted:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	216 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	217 attr.cli(**cli_kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	218 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	219 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	220 print(f'Removing {attr_desc} configuration')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	221 attr = self.__fields__[attr_name].type_.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	222 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	223 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	224 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	225 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	226 print(f'{type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	227 print(f'Removing {attr_desc} configuration')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	228 attr = self.__fields__[attr_name].type_.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	229 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	230 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	231 setattr(self, attr_name, attr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	232 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	233 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	234 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	235 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	236 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	237 print(f'{type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	238 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	239 input_accepted = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	240 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	241 input_accepted = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	242 while not input_accepted:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	243 attr = getattr(self, attr_name, None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	244 if attr is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	245 input_value = input(f'Type and enter a value for {attr_desc}: ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	246 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	247 input_value = input(f'Type and enter a new value for {attr_desc} or press '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	248 f'enter to keep the current one ({attr}): ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	249 if list_flag:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	250 input_value = string_to_list(input_value, remove_duplicates=False, sort=False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	251 if len(input_value) == 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	252 input_value = getattr(self, attr_name, None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	253 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	254 setattr(self, attr_name, input_value)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	255 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	256 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	257 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	258 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	259 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	260 print(f'Unexpected {type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	261 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	262 input_accepted = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	263
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	264 def set_list_attr_cli(self, attr_name, attr_desc='unknown attribute', **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	265 if cli_kwargs.get('chain_attr_desc', False):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	266 cli_kwargs['attr_desc'] = attr_desc
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	267 attr = getattr(self, attr_name, None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	268 if attr is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	269 # Check existing items
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	270 for item in attr:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	271 item_accepted = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	272 while not item_accepted:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	273 item.cli(**cli_kwargs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	274 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	275 setattr(self, attr_name, attr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	276 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	277 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	278 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	279 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	280 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	281 print(f'{type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	282 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	283 item_accepted = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	284 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	285 # Initialize list for new attribute & starting item
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	286 attr = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	287 item = self.__fields__[attr_name].type_.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	288 # Append (optional) additional items
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	289 append = input_yesno(f'Add a {attr_desc} configuration? (y/n)', 'n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	290 while append:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	291 attr.append(item.__class__.construct_from_cli())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	292 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	293 setattr(self, attr_name, attr)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	294 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	295 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	296 print(f'Removing last {attr_desc} configuration from the list')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	297 attr.pop()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	298 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	299 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	300 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	301 print(f'{type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	302 print(f'Removing last {attr_desc} configuration from the list')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	303 attr.pop()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	304 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	305 append = input_yesno(f'Add another {attr_desc} configuration? (y/n)', 'n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	306
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	307
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	308 class Detector(BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	309 prefix: constr(strip_whitespace=True, min_length=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	310 rows: conint(gt=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	311 columns: conint(gt=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	312 pixel_size: conlist(item_type=confloat(gt=0), min_items=1, max_items=2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	313 lens_magnification: confloat(gt=0) = 1.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	314
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	315 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	316 def get_pixel_size(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	317 return(list(np.asarray(self.pixel_size)/self.lens_magnification))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	318
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	319 def construct_from_yaml(self, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	320 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	321 with open(filename, 'r') as infile:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	322 indict = yaml.load(infile, Loader=yaml.CLoader)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	323 detector = indict['detector']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	324 self.prefix = detector['id']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	325 pixels = detector['pixels']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	326 self.rows = pixels['rows']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	327 self.columns = pixels['columns']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	328 self.pixel_size = pixels['size']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	329 self.lens_magnification = indict['lens_magnification']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	330 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	331 logging.warning(f'Could not load a dictionary from {filename}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	332 return(False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	333 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	334 return(True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	335
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	336 def cli(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	337 print('\n -- Configure the detector -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	338 self.set_single_attr_cli('prefix', 'detector ID')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	339 self.set_single_attr_cli('rows', 'number of pixel rows')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	340 self.set_single_attr_cli('columns', 'number of pixel columns')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	341 self.set_single_attr_cli('pixel_size', 'pixel size in mm (enter either a single value for '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	342 'square pixels or a pair of values for the size in the respective row and column '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	343 'directions)', list_flag=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	344 self.set_single_attr_cli('lens_magnification', 'lens magnification')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	345
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	346 def construct_nxdetector(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	347 nxdetector = NXdetector()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	348 nxdetector.local_name = self.prefix
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	349 pixel_size = self.get_pixel_size
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	350 if len(pixel_size) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	351 nxdetector.x_pixel_size = pixel_size[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	352 nxdetector.y_pixel_size = pixel_size[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	353 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	354 nxdetector.x_pixel_size = pixel_size[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	355 nxdetector.y_pixel_size = pixel_size[1]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	356 nxdetector.x_pixel_size.attrs['units'] = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	357 nxdetector.y_pixel_size.attrs['units'] = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	358 return(nxdetector)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	359
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	360
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	361 class ScanInfo(TypedDict):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	362 scan_number: int
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	363 starting_image_offset: conint(ge=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	364 num_image: conint(gt=0)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	365 ref_x: float
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	366 ref_z: float
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	367
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	368 class SpecScans(BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	369 spec_file: FilePath
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	370 scan_numbers: conlist(item_type=conint(gt=0), min_items=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	371 stack_info: conlist(item_type=ScanInfo, min_items=1) = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	372
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	373 @validator('spec_file')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	374 def validate_spec_file(cls, spec_file):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	375 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	376 spec_file = os.path.abspath(spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	377 sspec_file = FileSpec(spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	378 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	379 raise ValueError(f'Invalid SPEC file {spec_file}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	380 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	381 return(spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	382
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	383 @validator('scan_numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	384 def validate_scan_numbers(cls, scan_numbers, values):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	385 spec_file = values.get('spec_file')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	386 if spec_file is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	387 spec_scans = FileSpec(spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	388 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	389 scan = spec_scans.get_scan_by_number(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	390 if scan is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	391 raise ValueError(f'There is no scan number {scan_number} in {spec_file}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	392 return(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	393
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	394 @validator('stack_info')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	395 def validate_stack_info(cls, stack_info, values):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	396 scan_numbers = values.get('scan_numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	397 assert(len(scan_numbers) == len(stack_info))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	398 for scan_info in stack_info:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	399 assert(scan_info['scan_number'] in scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	400 is_int(scan_info['starting_image_offset'], ge=0, lt=scan_info['num_image'],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	401 raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	402 return(stack_info)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	403
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	404 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	405 def construct_from_nxcollection(cls, nxcollection:NXcollection):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	406 config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	407 config['spec_file'] = nxcollection.attrs['spec_file']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	408 scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	409 stack_info = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	410 for nxsubentry_name, nxsubentry in nxcollection.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	411 scan_number = int(nxsubentry_name.split('_')[-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	412 scan_numbers.append(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	413 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	414 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	415 'num_image': len(nxsubentry.sample.rotation_angle),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	416 'ref_x': float(nxsubentry.sample.x_translation),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	417 'ref_z': float(nxsubentry.sample.z_translation)})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	418 config['scan_numbers'] = sorted(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	419 config['stack_info'] = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	420 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	421
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	422 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	423 def available_scan_numbers(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	424 return(get_available_scan_numbers(self.spec_file))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	425
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	426 def set_from_nxcollection(self, nxcollection:NXcollection):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	427 self.spec_file = nxcollection.attrs['spec_file']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	428 scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	429 stack_info = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	430 for nxsubentry_name, nxsubentry in nxcollection.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	431 scan_number = int(nxsubentry_name.split('_')[-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	432 scan_numbers.append(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	433 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	434 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	435 'num_image': len(nxsubentry.sample.rotation_angle),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	436 'ref_x': float(nxsubentry.sample.x_translation),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	437 'ref_z': float(nxsubentry.sample.z_translation)})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	438 self.scan_numbers = sorted(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	439 self.stack_info = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	440
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	441 def get_scan_index(self, scan_number):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	442 scan_index = [scan_index for scan_index, scan_info in enumerate(self.stack_info)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	443 if scan_info['scan_number'] == scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	444 if len(scan_index) > 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	445 raise ValueError('Duplicate scan_numbers in image stack')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	446 elif len(scan_index) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	447 return(scan_index[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	448 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	449 return(None)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	450
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	451 def get_scanparser(self, scan_number):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	452 return(get_scanparser(self.spec_file, scan_number))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	453
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	454 def get_detector_data(self, detector_prefix, scan_number=None, scan_step_index=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	455 image_stacks = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	456 if scan_number is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	457 scan_numbers = self.scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	458 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	459 scan_numbers = [scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	460 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	461 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	462 scan_info = self.stack_info[self.get_scan_index(scan_number)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	463 image_offset = scan_info['starting_image_offset']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	464 if scan_step_index is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	465 num_image = scan_info['num_image']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	466 image_stacks.append(parser.get_detector_data(detector_prefix,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	467 (image_offset, image_offset+num_image)))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	468 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	469 image_stacks.append(parser.get_detector_data(detector_prefix,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	470 image_offset+scan_step_index))
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	471 if scan_number is not None and scan_step_index is not None:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	472 # Return a single image for a specific scan_number and scan_step_index request
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	473 return(image_stacks[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	474 else:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	475 # Return a list otherwise
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	476 return(image_stacks)
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	477 return(image_stacks)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	478
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	479 def scan_numbers_cli(self, attr_desc, **kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	480 available_scan_numbers = self.available_scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	481 station = kwargs.get('station')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	482 if (station is not None and station in ('id1a3', 'id3a') and
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	483 'scan_type' in kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	484 scan_type = kwargs['scan_type']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	485 if scan_type == 'ts1':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	486 available_scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	487 for scan_number in self.available_scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	488 parser = self.get_scanparser(scan_number)
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	489 try:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	490 if parser.scan_type == scan_type:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	491 available_scan_numbers.append(scan_number)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	492 except:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	493 pass
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	494 elif scan_type == 'df1':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	495 tomo_scan_numbers = kwargs['tomo_scan_numbers']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	496 available_scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	497 for scan_number in tomo_scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	498 parser = self.get_scanparser(scan_number-2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	499 assert(parser.scan_type == scan_type)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	500 available_scan_numbers.append(scan_number-2)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	501 elif scan_type == 'bf1':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	502 tomo_scan_numbers = kwargs['tomo_scan_numbers']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	503 available_scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	504 for scan_number in tomo_scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	505 parser = self.get_scanparser(scan_number-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	506 assert(parser.scan_type == scan_type)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	507 available_scan_numbers.append(scan_number-1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	508 if len(available_scan_numbers) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	509 input_mode = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	510 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	511 if hasattr(self, 'scan_numbers'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	512 print(f'Currently selected {attr_desc}scan numbers are: {self.scan_numbers}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	513 menu_options = [f'Select a subset of the available {attr_desc}scan numbers',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	514 f'Use all available {attr_desc}scan numbers in {self.spec_file}',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	515 f'Keep the currently selected {attr_desc}scan numbers']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	516 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	517 menu_options = [f'Select a subset of the available {attr_desc}scan numbers',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	518 f'Use all available {attr_desc}scan numbers in {self.spec_file}']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	519 print(f'Available scan numbers in {self.spec_file} are: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	520 f'{available_scan_numbers}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	521 input_mode = input_menu(menu_options, header='Choose one of the following options '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	522 'for selecting scan numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	523 if input_mode == 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	524 accept_scan_numbers = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	525 while not accept_scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	526 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	527 self.scan_numbers = \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	528 input_int_list(f'Enter a series of {attr_desc}scan numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	529 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	530 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	531 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	532 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	533 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	534 print(f'Unexpected {type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	535 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	536 accept_scan_numbers = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	537 elif input_mode == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	538 self.scan_numbers = available_scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	539 elif input_mode == 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	540 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	541
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	542 def cli(self, **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	543 if cli_kwargs.get('attr_desc') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	544 attr_desc = f'{cli_kwargs["attr_desc"]} '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	545 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	546 attr_desc = ''
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	547 print(f'\n -- Configure which scans to use from a single {attr_desc}SPEC file')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	548 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	549 self.scan_numbers_cli(attr_desc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	550
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	551 def construct_nxcollection(self, image_key, thetas, detector):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	552 nxcollection = NXcollection()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	553 nxcollection.attrs['spec_file'] = str(self.spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	554 parser = self.get_scanparser(self.scan_numbers[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	555 nxcollection.attrs['date'] = parser.spec_scan.file_date
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	556 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	557 # Get scan info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	558 scan_info = self.stack_info[self.get_scan_index(scan_number)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	559 # Add an NXsubentry to the NXcollection for each scan
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	560 entry_name = f'scan_{scan_number}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	561 nxsubentry = NXsubentry()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	562 nxcollection[entry_name] = nxsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	563 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	564 nxsubentry.start_time = parser.spec_scan.date
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	565 nxsubentry.spec_command = parser.spec_command
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	566 # Add an NXdata for independent dimensions to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	567 num_image = scan_info['num_image']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	568 if thetas is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	569 thetas = num_image*[0.0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	570 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	571 assert(num_image == len(thetas))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	572 # nxsubentry.independent_dimensions = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	573 # nxsubentry.independent_dimensions.rotation_angle = thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	574 # nxsubentry.independent_dimensions.rotation_angle.units = 'degrees'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	575 # Add an NXinstrument to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	576 nxsubentry.instrument = NXinstrument()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	577 # Add an NXdetector to the NXinstrument to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	578 nxsubentry.instrument.detector = detector.construct_nxdetector()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	579 nxsubentry.instrument.detector.frame_start_number = scan_info['starting_image_offset']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	580 nxsubentry.instrument.detector.image_key = image_key
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	581 # Add an NXsample to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	582 nxsubentry.sample = NXsample()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	583 nxsubentry.sample.rotation_angle = thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	584 nxsubentry.sample.rotation_angle.units = 'degrees'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	585 nxsubentry.sample.x_translation = scan_info['ref_x']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	586 nxsubentry.sample.x_translation.units = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	587 nxsubentry.sample.z_translation = scan_info['ref_z']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	588 nxsubentry.sample.z_translation.units = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	589 return(nxcollection)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	590
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	591
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	592 class FlatField(SpecScans):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	593
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	594 def image_range_cli(self, attr_desc, detector_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	595 stack_info = self.stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	596 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	597 # Parse the available image range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	598 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	599 image_offset = parser.starting_image_offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	600 num_image = parser.get_num_image(detector_prefix.upper())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	601 scan_index = self.get_scan_index(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	602
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	603 # Select the image set
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	604 last_image_index = image_offset+num_image
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	605 print(f'Available good image set index range: [{image_offset}, {last_image_index})')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	606 image_set_approved = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	607 if scan_index is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	608 scan_info = stack_info[scan_index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	609 print(f'Current starting image offset and number of images: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	610 f'{scan_info["starting_image_offset"]} and {scan_info["num_image"]}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	611 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	612 if not image_set_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	613 print(f'Default starting image offset and number of images: '+
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	614 f'{image_offset} and {num_image}')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	615 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	616 if image_set_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	617 offset = image_offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	618 num = last_image_index-offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	619 while not image_set_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	620 offset = input_int(f'Enter the starting image offset', ge=image_offset,
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	621 lt=last_image_index)#, default=image_offset)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	622 num = input_int(f'Enter the number of images', ge=1,
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	623 le=last_image_index-offset)#, default=last_image_index-offset)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	624 print(f'Current starting image offset and number of images: {offset} and {num}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	625 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	626 if scan_index is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	627 scan_info['starting_image_offset'] = offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	628 scan_info['num_image'] = num
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	629 scan_info['ref_x'] = parser.horizontal_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	630 scan_info['ref_z'] = parser.vertical_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	631 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	632 stack_info.append({'scan_number': scan_number, 'starting_image_offset': offset,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	633 'num_image': num, 'ref_x': parser.horizontal_shift,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	634 'ref_z': parser.vertical_shift})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	635 self.stack_info = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	636
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	637 def cli(self, **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	638 if cli_kwargs.get('attr_desc') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	639 attr_desc = f'{cli_kwargs["attr_desc"]} '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	640 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	641 attr_desc = ''
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	642 station = cli_kwargs.get('station')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	643 detector = cli_kwargs.get('detector')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	644 print(f'\n -- Configure the location of the {attr_desc}scan data -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	645 if station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	646 self.spec_file = cli_kwargs['spec_file']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	647 tomo_scan_numbers = cli_kwargs['tomo_scan_numbers']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	648 scan_type = cli_kwargs['scan_type']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	649 self.scan_numbers_cli(attr_desc, station=station, tomo_scan_numbers=tomo_scan_numbers,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	650 scan_type=scan_type)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	651 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	652 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	653 self.scan_numbers_cli(attr_desc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	654 self.image_range_cli(attr_desc, detector.prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	655
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	656
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	657 class TomoField(SpecScans):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	658 theta_range: dict = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	659
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	660 @validator('theta_range')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	661 def validate_theta_range(cls, theta_range):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	662 if len(theta_range) != 3 and len(theta_range) != 4:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	663 raise ValueError(f'Invalid theta range {theta_range}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	664 is_num(theta_range['start'], raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	665 is_num(theta_range['end'], raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	666 is_int(theta_range['num'], gt=1, raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	667 if theta_range['end'] <= theta_range['start']:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	668 raise ValueError(f'Invalid theta range {theta_range}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	669 if 'start_index' in theta_range:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	670 is_int(theta_range['start_index'], ge=0, raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	671 return(theta_range)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	672
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	673 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	674 def construct_from_nxcollection(cls, nxcollection:NXcollection):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	675 #RV Can I derive this from the same classfunction for SpecScans by adding theta_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	676 config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	677 config['spec_file'] = nxcollection.attrs['spec_file']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	678 scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	679 stack_info = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	680 for nxsubentry_name, nxsubentry in nxcollection.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	681 scan_number = int(nxsubentry_name.split('_')[-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	682 scan_numbers.append(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	683 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	684 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	685 'num_image': len(nxsubentry.sample.rotation_angle),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	686 'ref_x': float(nxsubentry.sample.x_translation),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	687 'ref_z': float(nxsubentry.sample.z_translation)})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	688 config['scan_numbers'] = sorted(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	689 config['stack_info'] = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	690 for name in nxcollection.entries:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	691 if 'scan_' in name:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	692 thetas = np.asarray(nxcollection[name].sample.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	693 config['theta_range'] = {'start': thetas[0], 'end': thetas[-1], 'num': thetas.size}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	694 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	695 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	696
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	697 def get_horizontal_shifts(self, scan_number=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	698 horizontal_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	699 if scan_number is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	700 scan_numbers = self.scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	701 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	702 scan_numbers = [scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	703 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	704 parser = self.get_scanparser(scan_number)
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	705 horizontal_shifts.append(parser.horizontal_shift)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	706 if len(horizontal_shifts) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	707 return(horizontal_shifts[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	708 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	709 return(horizontal_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	710
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	711 def get_vertical_shifts(self, scan_number=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	712 vertical_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	713 if scan_number is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	714 scan_numbers = self.scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	715 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	716 scan_numbers = [scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	717 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	718 parser = self.get_scanparser(scan_number)
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	719 vertical_shifts.append(parser.vertical_shift)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	720 if len(vertical_shifts) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	721 return(vertical_shifts[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	722 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	723 return(vertical_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	724
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	725 def theta_range_cli(self, scan_number, attr_desc, station):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	726 # Parse the available theta range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	727 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	728 theta_vals = parser.theta_vals
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	729 spec_theta_start = theta_vals.get('start')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	730 spec_theta_end = theta_vals.get('end')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	731 spec_num_theta = theta_vals.get('num')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	732
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	733 # Check for consistency of theta ranges between scans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	734 if scan_number != self.scan_numbers[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	735 parser = self.get_scanparser(self.scan_numbers[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	736 if (parser.theta_vals.get('start') != spec_theta_start or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	737 parser.theta_vals.get('end') != spec_theta_end or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	738 parser.theta_vals.get('num') != spec_num_theta):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	739 raise ValueError(f'Incompatible theta ranges between {attr_desc}scans:'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	740 f'\n\tScan {scan_number}: {theta_vals}'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	741 f'\n\tScan {self.scan_numbers[0]}: {parser.theta_vals}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	742 return
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	743
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	744 # Select the theta range for the tomo reconstruction from the first scan
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	745 theta_range_approved = False
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	746 thetas = np.linspace(spec_theta_start, spec_theta_end, spec_num_theta)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	747 delta_theta = thetas[1]-thetas[0]
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	748 print(f'Theta range obtained from SPEC data: [{spec_theta_start}, {spec_theta_end}]')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	749 print(f'Theta step size = {delta_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	750 print(f'Number of theta values: {spec_num_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	751 default_start = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	752 default_end = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	753 if station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	754 theta_range_approved = input_yesno(f'Accept this theta range (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	755 if theta_range_approved:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	756 self.theta_range = {'start': float(spec_theta_start), 'end': float(spec_theta_end),
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	757 'num': int(spec_num_theta), 'start_index': 0}
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	758 return
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	759 elif station in ('id3b'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	760 if spec_theta_start <= 0.0 and spec_theta_end >= 180.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	761 default_start = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	762 default_end = 180
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	763 elif spec_theta_end-spec_theta_start == 180:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	764 default_start = spec_theta_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	765 default_end = spec_theta_end
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	766 while not theta_range_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	767 theta_start = input_num(f'Enter the first theta (included)', ge=spec_theta_start,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	768 lt=spec_theta_end, default=default_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	769 theta_index_start = index_nearest(thetas, theta_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	770 theta_start = thetas[theta_index_start]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	771 theta_end = input_num(f'Enter the last theta (excluded)',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	772 ge=theta_start+delta_theta, le=spec_theta_end, default=default_end)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	773 theta_index_end = index_nearest(thetas, theta_end)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	774 theta_end = thetas[theta_index_end]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	775 num_theta = theta_index_end-theta_index_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	776 print(f'Selected theta range: [{theta_start}, {theta_start+delta_theta}, ..., '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	777 f'{theta_end})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	778 print(f'Number of theta values: {num_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	779 theta_range_approved = input_yesno(f'Accept this theta range (y/n)?', 'y')
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	780 self.theta_range = {'start': float(theta_start), 'end': float(theta_end),
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	781 'num': int(num_theta), 'start_index': int(theta_index_start)}
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	782
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	783 def image_range_cli(self, attr_desc, detector_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	784 stack_info = self.stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	785 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	786 # Parse the available image range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	787 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	788 image_offset = parser.starting_image_offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	789 num_image = parser.get_num_image(detector_prefix.upper())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	790 scan_index = self.get_scan_index(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	791
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	792 # Select the image set matching the theta range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	793 num_theta = self.theta_range['num']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	794 theta_index_start = self.theta_range['start_index']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	795 if num_theta > num_image-theta_index_start:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	796 raise ValueError(f'Available {attr_desc}image indices incompatible with thetas:'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	797 f'\n\tNumber of thetas and offset = {num_theta} and {theta_index_start}'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	798 f'\n\tNumber of available images {num_image}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	799 if scan_index is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	800 scan_info = stack_info[scan_index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	801 scan_info['starting_image_offset'] = image_offset+theta_index_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	802 scan_info['num_image'] = num_theta
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	803 scan_info['ref_x'] = parser.horizontal_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	804 scan_info['ref_z'] = parser.vertical_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	805 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	806 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	807 'starting_image_offset': image_offset+theta_index_start,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	808 'num_image': num_theta, 'ref_x': parser.horizontal_shift,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	809 'ref_z': parser.vertical_shift})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	810 self.stack_info = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	811
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	812 def cli(self, **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	813 if cli_kwargs.get('attr_desc') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	814 attr_desc = f'{cli_kwargs["attr_desc"]} '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	815 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	816 attr_desc = ''
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	817 cycle = cli_kwargs.get('cycle')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	818 btr = cli_kwargs.get('btr')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	819 station = cli_kwargs.get('station')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	820 detector = cli_kwargs.get('detector')
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	821 sample_name = cli_kwargs.get('sample_name')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	822 print(f'\n -- Configure the location of the {attr_desc}scan data -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	823 if station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	824 basedir = f'/nfs/chess/{station}/{cycle}/{btr}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	825 runs = [d for d in os.listdir(basedir) if os.path.isdir(os.path.join(basedir, d))]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	826 #RV index = 15-1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	827 #RV index = 7-1
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	828 if sample_name is not None and sample_name in runs:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	829 index = runs.index(sample_name)
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	830 else:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	831 index = input_menu(runs, header='Choose a sample directory')
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	832 self.spec_file = f'{basedir}/{runs[index]}/spec.log'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	833 self.scan_numbers_cli(attr_desc, station=station, scan_type='ts1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	834 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	835 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	836 self.scan_numbers_cli(attr_desc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	837 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	838 self.theta_range_cli(scan_number, attr_desc, station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	839 self.image_range_cli(attr_desc, detector.prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	840
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	841
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	842 class Sample(BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	843 name: constr(min_length=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	844 description: Optional[str]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	845 rotation_angles: Optional[list]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	846 x_translations: Optional[list]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	847 z_translations: Optional[list]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	848
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	849 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	850 def construct_from_nxsample(cls, nxsample:NXsample):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	851 config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	852 config['name'] = nxsample.name.nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	853 if 'description' in nxsample:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	854 config['description'] = nxsample.description.nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	855 if 'rotation_angle' in nxsample:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	856 config['rotation_angle'] = nxsample.rotation_angle.nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	857 if 'x_translation' in nxsample:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	858 config['x_translation'] = nxsample.x_translation.nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	859 if 'z_translation' in nxsample:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	860 config['z_translation'] = nxsample.z_translation.nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	861 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	862
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	863 def cli(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	864 print('\n -- Configure the sample metadata -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	865 #RV self.name = 'sobhani-3249-A'
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	866 #RV self.name = 'tenstom_1304r-1'
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	867 self.set_single_attr_cli('name', 'the sample name')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	868 #RV self.description = 'test sample'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	869 self.set_single_attr_cli('description', 'a description of the sample (optional)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	870
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	871
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	872 class MapConfig(BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	873 cycle: constr(strip_whitespace=True, min_length=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	874 btr: constr(strip_whitespace=True, min_length=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	875 title: constr(strip_whitespace=True, min_length=1)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	876 station: Literal['id1a3', 'id3a', 'id3b'] = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	877 sample: Sample
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	878 detector: Detector = Detector.construct()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	879 tomo_fields: TomoField
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	880 dark_field: Optional[FlatField]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	881 bright_field: FlatField
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	882 _thetas: list[float] = PrivateAttr()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	883 _field_types = ({'name': 'dark_field', 'image_key': 2}, {'name': 'bright_field',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	884 'image_key': 1}, {'name': 'tomo_fields', 'image_key': 0})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	885
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	886 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	887 def construct_from_nxentry(cls, nxentry:NXentry):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	888 config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	889 config['cycle'] = nxentry.instrument.source.attrs['cycle']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	890 config['btr'] = nxentry.instrument.source.attrs['btr']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	891 config['title'] = nxentry.nxname
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	892 config['station'] = nxentry.instrument.source.attrs['station']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	893 config['sample'] = Sample.construct_from_nxsample(nxentry['sample'])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	894 for nxobject_name, nxobject in nxentry.spec_scans.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	895 if isinstance(nxobject, NXcollection):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	896 config[nxobject_name] = SpecScans.construct_from_nxcollection(nxobject)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	897 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	898
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	899 #FIX cache?
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	900 @property
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	901 def thetas(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	902 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	903 return(self._thetas)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	904 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	905 theta_range = self.tomo_fields.theta_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	906 self._thetas = list(np.linspace(theta_range['start'], theta_range['end'],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	907 theta_range['num']))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	908 return(self._thetas)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	909
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	910 def cli(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	911 print('\n -- Configure a map from a set of SPEC scans (dark, bright, and tomo), '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	912 'and / or detector data -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	913 #RV self.cycle = '2021-3'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	914 #RV self.cycle = '2022-2'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	915 #RV self.cycle = '2023-1'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	916 self.set_single_attr_cli('cycle', 'beam cycle')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	917 #RV self.btr = 'z-3234-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	918 #RV self.btr = 'sobhani-3249-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	919 #RV self.btr = 'przybyla-3606-a'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	920 self.set_single_attr_cli('btr', 'BTR')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	921 #RV self.title = 'z-3234-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	922 #RV self.title = 'tomo7C'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	923 #RV self.title = 'cmc-test-dwell-1'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	924 self.set_single_attr_cli('title', 'title for the map entry')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	925 #RV self.station = 'id3a'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	926 #RV self.station = 'id3b'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	927 #RV self.station = 'id1a3'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	928 self.set_single_attr_cli('station', 'name of the station at which scans were collected '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	929 '(currently choose from: id1a3, id3a, id3b)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	930 import_scanparser(self.station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	931 self.set_single_attr_cli('sample')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	932 use_detector_config = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	933 if hasattr(self.detector, 'prefix') and len(self.detector.prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	934 use_detector_config = input_yesno(f'Current detector settings:\n{self.detector}\n'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	935 f'Keep these settings? (y/n)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	936 if not use_detector_config:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	937 menu_options = ['not listed', 'andor2', 'manta', 'retiga']
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	938 input_mode = input_menu(menu_options, header='Choose one of the following detector '+
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	939 'configuration options')
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	940 if input_mode:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	941 detector_config_file = f'{menu_options[input_mode]}.yaml'
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	942 have_detector_config = self.detector.construct_from_yaml(detector_config_file)
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	943 else:
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	944 have_detector_config = False
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	945 if not have_detector_config:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	946 self.set_single_attr_cli('detector', 'detector')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	947 self.set_single_attr_cli('tomo_fields', 'Tomo field', chain_attr_desc=True,
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	948 cycle=self.cycle, btr=self.btr, station=self.station, detector=self.detector,
1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	949 sample_name=self.sample.name)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	950 if self.station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	951 have_dark_field = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	952 tomo_spec_file = self.tomo_fields.spec_file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	953 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	954 have_dark_field = input_yesno(f'Are Dark field images available? (y/n)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	955 tomo_spec_file = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	956 if have_dark_field:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	957 self.set_single_attr_cli('dark_field', 'Dark field', chain_attr_desc=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	958 station=self.station, detector=self.detector, spec_file=tomo_spec_file,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	959 tomo_scan_numbers=self.tomo_fields.scan_numbers, scan_type='df1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	960 self.set_single_attr_cli('bright_field', 'Bright field', chain_attr_desc=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	961 station=self.station, detector=self.detector, spec_file=tomo_spec_file,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	962 tomo_scan_numbers=self.tomo_fields.scan_numbers, scan_type='bf1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	963
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	964 def construct_nxentry(self, nxroot, include_raw_data=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	965 # Construct base NXentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	966 nxentry = NXentry()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	967
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	968 # Add an NXentry to the NXroot
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	969 nxroot[self.title] = nxentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	970 nxroot.attrs['default'] = self.title
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	971 nxentry.definition = 'NXtomo'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	972 # nxentry.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	973
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	974 # Add an NXinstrument to the NXentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	975 nxinstrument = NXinstrument()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	976 nxentry.instrument = nxinstrument
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	977
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	978 # Add an NXsource to the NXinstrument
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	979 nxsource = NXsource()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	980 nxinstrument.source = nxsource
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	981 nxsource.type = 'Synchrotron X-ray Source'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	982 nxsource.name = 'CHESS'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	983 nxsource.probe = 'x-ray'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	984
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	985 # Tag the NXsource with the runinfo (as an attribute)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	986 nxsource.attrs['cycle'] = self.cycle
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	987 nxsource.attrs['btr'] = self.btr
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	988 nxsource.attrs['station'] = self.station
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	989
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	990 # Add an NXdetector to the NXinstrument (don't fill in data fields yet)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	991 nxinstrument.detector = self.detector.construct_nxdetector()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	992
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	993 # Add an NXsample to NXentry (don't fill in data fields yet)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	994 nxsample = NXsample()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	995 nxentry.sample = nxsample
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	996 nxsample.name = self.sample.name
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	997 nxsample.description = self.sample.description
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	998
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	999 # Add an NXcollection to the base NXentry to hold metadata about the spec scans in the map
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1000 # Also obtain the data fields in NXsample and NXdetector
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1001 nxspec_scans = NXcollection()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1002 nxentry.spec_scans = nxspec_scans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1003 image_keys = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1004 sequence_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1005 image_stacks = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1006 rotation_angles = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1007 x_translations = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1008 z_translations = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1009 for field_type in self._field_types:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1010 field_name = field_type['name']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1011 field = getattr(self, field_name)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1012 if field is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1013 continue
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1014 image_key = field_type['image_key']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1015 if field_type['name'] == 'tomo_fields':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1016 thetas = self.thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1017 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1018 thetas = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1019 # Add the scans in a single spec file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1020 nxspec_scans[field_name] = field.construct_nxcollection(image_key, thetas,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1021 self.detector)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1022 if include_raw_data:
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	1023 image_stacks += field.get_detector_data(self.detector.prefix)
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1024 for scan_number in field.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1025 parser = field.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1026 scan_info = field.stack_info[field.get_scan_index(scan_number)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1027 num_image = scan_info['num_image']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1028 image_keys += num_image*[image_key]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1029 sequence_numbers += [i for i in range(num_image)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1030 if thetas is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1031 rotation_angles += scan_info['num_image']*[0.0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1032 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1033 assert(num_image == len(thetas))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1034 rotation_angles += thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1035 x_translations += scan_info['num_image']*[scan_info['ref_x']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1036 z_translations += scan_info['num_image']*[scan_info['ref_z']]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1037
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1038 if include_raw_data:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1039 # Add image data to NXdetector
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1040 nxinstrument.detector.image_key = image_keys
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1041 nxinstrument.detector.sequence_number = sequence_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1042 nxinstrument.detector.data = np.concatenate([image for image in image_stacks])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1043
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1044 # Add image data to NXsample
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1045 nxsample.rotation_angle = rotation_angles
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1046 nxsample.rotation_angle.attrs['units'] = 'degrees'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1047 nxsample.x_translation = x_translations
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1048 nxsample.x_translation.attrs['units'] = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1049 nxsample.z_translation = z_translations
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1050 nxsample.z_translation.attrs['units'] = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1051
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1052 # Add an NXdata to NXentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1053 nxdata = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1054 nxentry.data = nxdata
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1055 nxdata.makelink(nxentry.instrument.detector.data, name='data')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1056 nxdata.makelink(nxentry.instrument.detector.image_key)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1057 nxdata.makelink(nxentry.sample.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1058 nxdata.makelink(nxentry.sample.x_translation)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1059 nxdata.makelink(nxentry.sample.z_translation)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1060 # nxdata.attrs['axes'] = ['field', 'row', 'column']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1061 # nxdata.attrs['field_indices'] = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1062 # nxdata.attrs['row_indices'] = 1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1063 # nxdata.attrs['column_indices'] = 2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1064
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1065
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1066 class TomoWorkflow(BaseModel):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1067 sample_maps: conlist(item_type=MapConfig, min_items=1) = [MapConfig.construct()]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1068
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1069 @classmethod
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1070 def construct_from_nexus(cls, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1071 nxroot = nxload(filename)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1072 sample_maps = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1073 config = {'sample_maps': sample_maps}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1074 for nxentry_name, nxentry in nxroot.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1075 sample_maps.append(MapConfig.construct_from_nxentry(nxentry))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1076 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1077
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1078 def cli(self):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1079 print('\n -- Configure a map -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1080 self.set_list_attr_cli('sample_maps', 'sample map')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1081
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1082 def construct_nxfile(self, filename, mode='w-'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1083 nxroot = NXroot()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1084 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1085 for sample_map in self.sample_maps:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1086 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	1087 import_scanparser(sample_map.station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1088 sample_map.construct_nxentry(nxroot)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1089 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	1090 logger.info(f'Start saving all sample maps to {filename}.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1091 nxroot.save(filename, mode=mode)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1092
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1093 def write_to_nexus(self, filename):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1094 t0 = time()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1095 self.construct_nxfile(filename, mode='w')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1096 logger.info(f'Saved all sample maps to {filename} in {time()-t0:.2f} seconds.')

Mercurial > repos > rv43 > tomo

annotate workflow/models.py @ 75:d5e1d4ea2b7e draft default tip