chap_test_20230328: build/bdist.linux-x86_64/egg/CHAP/models/integration.py annotate

annotate build/bdist.linux-x86_64/egg/CHAP/models/integration.py @ 0:cbbe42422d56 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty

author	kls286
date	Tue, 28 Mar 2023 15:07:30 +0000
parents
children

rev	line source
0 cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	1 import copy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	2 from functools import cache, lru_cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	3 import json
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	4 import logging
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	5 import os
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	6 from time import time
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	7 from typing import Literal, Optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	8
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	9 from msnctools.general import input_menu
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	10 from multiprocessing.pool import ThreadPool
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	11 from nexusformat.nexus import (NXdata,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	12 NXdetector,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	13 NXfield,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	14 NXprocess,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	15 NXroot)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	16 import numpy as np
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	17 from pydantic import (BaseModel,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	18 validator,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	19 constr,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	20 conlist,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	21 conint,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	22 confloat,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	23 FilePath)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	24 import pyFAI, pyFAI.multi_geometry, pyFAI.units
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	25 from pyspec.file.tiff import TiffFile
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	26
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	27 from .map import MapConfig, SpecScans
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	28
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	29
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	30 class Detector(BaseModel):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	31 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	32 Detector class to represent a single detector used in the experiment.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	33
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	34 :param prefix: Prefix of the detector in the SPEC file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	35 :type prefix: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	36 :param poni_file: Path to the poni file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	37 :type poni_file: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	38 :param mask_file: Optional path to the mask file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	39 :type mask_file: str, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	40 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	41 prefix: constr(strip_whitespace=True, min_length=1)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	42 poni_file: FilePath
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	43 mask_file: Optional[FilePath]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	44 @validator('poni_file', allow_reuse=True)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	45 def validate_poni_file(cls, poni_file):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	46 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	47 Validate the poni file by checking if it's a valid PONI file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	48
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	49 :param poni_file: Path to the poni file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	50 :type poni_file: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	51 :raises ValueError: If poni_file is not a valid PONI file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	52 :returns: Absolute path to the poni file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	53 :rtype: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	54 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	55 poni_file = os.path.abspath(poni_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	56 try:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	57 ai = azimuthal_integrator(poni_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	58 except:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	59 raise(ValueError(f'{poni_file} is not a valid PONI file'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	60 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	61 return(poni_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	62 @validator('mask_file', allow_reuse=True)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	63 def validate_mask_file(cls, mask_file, values):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	64 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	65 Validate the mask file. If a mask file is provided, it checks if it's a valid TIFF file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	66
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	67 :param mask_file: Path to the mask file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	68 :type mask_file: str or None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	69 :param values: A dictionary of the Detector fields.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	70 :type values: dict
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	71 :raises ValueError: If mask_file is provided and it's not a valid TIFF file.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	72 :raises ValueError: If `'poni_file'` is not provided in `values`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	73 :returns: Absolute path to the mask file or None.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	74 :rtype: str or None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	75 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	76 if mask_file is None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	77 return(mask_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	78 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	79 mask_file = os.path.abspath(mask_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	80 poni_file = values.get('poni_file')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	81 if poni_file is None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	82 raise(ValueError('Cannot validate mask file without a PONI file.'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	83 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	84 try:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	85 mask_array = get_mask_array(mask_file, poni_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	86 except BaseException as e:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	87 raise(ValueError(f'Unable to open {mask_file} as a TIFF file'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	88 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	89 return(mask_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	90 @property
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	91 def azimuthal_integrator(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	92 return(azimuthal_integrator(self.poni_file))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	93 @property
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	94 def mask_array(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	95 return(get_mask_array(self.mask_file, self.poni_file))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	96
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	97 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	98 def azimuthal_integrator(poni_file:str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	99 if not isinstance(poni_file, str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	100 poni_file = str(poni_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	101 return(pyFAI.load(poni_file))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	102 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	103 def get_mask_array(mask_file:str, poni_file:str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	104 if mask_file is not None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	105 if not isinstance(mask_file, str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	106 mask_file = str(mask_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	107 with TiffFile(mask_file) as tiff:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	108 mask_array = tiff.asarray()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	109 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	110 mask_array = np.zeros(azimuthal_integrator(poni_file).detector.shape)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	111 return(mask_array)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	112
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	113 class IntegrationConfig(BaseModel):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	114 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	115 Class representing the configuration for a raw detector data integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	116
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	117 :ivar tool_type: type of integration tool; always set to "integration"
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	118 :type tool_type: str, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	119 :ivar title: title of the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	120 :type title: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	121 :ivar integration_type: type of integration, one of "azimuthal", "radial", or "cake"
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	122 :type integration_type: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	123 :ivar detectors: list of detectors used in the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	124 :type detectors: List[Detector]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	125 :ivar radial_units: radial units for the integration, defaults to `'q_A^-1'`
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	126 :type radial_units: str, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	127 :ivar radial_min: minimum radial value for the integration range
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	128 :type radial_min: float, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	129 :ivar radial_max: maximum radial value for the integration range
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	130 :type radial_max: float, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	131 :ivar radial_npt: number of points in the radial range for the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	132 :type radial_npt: int, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	133 :ivar azimuthal_units: azimuthal units for the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	134 :type azimuthal_units: str, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	135 :ivar azimuthal_min: minimum azimuthal value for the integration range
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	136 :type azimuthal_min: float, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	137 :ivar azimuthal_max: maximum azimuthal value for the integration range
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	138 :type azimuthal_max: float, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	139 :ivar azimuthal_npt: number of points in the azimuthal range for the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	140 :type azimuthal_npt: int, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	141 :ivar error_model: error model for the integration, one of "poisson" or "azimuthal"
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	142 :type error_model: str, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	143 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	144 tool_type: Literal['integration'] = 'integration'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	145 title: constr(strip_whitespace=True, min_length=1)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	146 integration_type: Literal['azimuthal', 'radial', 'cake']
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	147 detectors: conlist(item_type=Detector, min_items=1)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	148 radial_units: str = 'q_A^-1'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	149 radial_min: confloat(ge=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	150 radial_max: confloat(gt=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	151 radial_npt: conint(gt=0) = 1800
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	152 azimuthal_units: str = 'chi_deg'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	153 azimuthal_min: confloat(ge=-180) = -180
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	154 azimuthal_max: confloat(le=360) = 180
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	155 azimuthal_npt: conint(gt=0) = 3600
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	156 error_model: Optional[Literal['poisson', 'azimuthal']]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	157 sequence_index: Optional[conint(gt=0)]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	158 @validator('radial_units', allow_reuse=True)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	159 def validate_radial_units(cls, radial_units):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	160 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	161 Validate the radial units for the integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	162
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	163 :param radial_units: unvalidated radial units for the integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	164 :type radial_units: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	165 :raises ValueError: if radial units are not one of the recognized radial units
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	166 :return: validated radial units
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	167 :rtype: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	168 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	169 if radial_units in pyFAI.units.RADIAL_UNITS.keys():
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	170 return(radial_units)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	171 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	172 raise(ValueError(f'Invalid radial units: {radial_units}. Must be one of {", ".join(pyFAI.units.RADIAL_UNITS.keys())}'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	173 @validator('azimuthal_units', allow_reuse=True)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	174 def validate_azimuthal_units(cls, azimuthal_units):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	175 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	176 Validate that `azimuthal_units` is one of the keys in the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	177 `pyFAI.units.AZIMUTHAL_UNITS` dictionary.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	178
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	179 :param azimuthal_units: The string representing the unit to be validated.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	180 :type azimuthal_units: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	181 :raises ValueError: If `azimuthal_units` is not one of the keys in `pyFAI.units.AZIMUTHAL_UNITS`
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	182 :return: The original supplied value, if is one of the keys in `pyFAI.units.AZIMUTHAL_UNITS`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	183 :rtype: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	184 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	185 if azimuthal_units in pyFAI.units.AZIMUTHAL_UNITS.keys():
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	186 return(azimuthal_units)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	187 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	188 raise(ValueError(f'Invalid azimuthal units: {azimuthal_units}. Must be one of {", ".join(pyFAI.units.AZIMUTHAL_UNITS.keys())}'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	189 def validate_range_max(range_name:str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	190 """Validate the maximum value of an integration range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	191
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	192 :param range_name: The name of the integration range (e.g. radial, azimuthal).
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	193 :type range_name: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	194 :return: The callable that performs the validation.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	195 :rtype: callable
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	196 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	197 def _validate_range_max(cls, range_max, values):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	198 """Check if the maximum value of the integration range is greater than its minimum value.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	199
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	200 :param range_max: The maximum value of the integration range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	201 :type range_max: float
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	202 :param values: The values of the other fields being validated.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	203 :type values: dict
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	204 :raises ValueError: If the maximum value of the integration range is not greater than its minimum value.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	205 :return: The validated maximum range value
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	206 :rtype: float
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	207 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	208 range_min = values.get(f'{range_name}_min')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	209 if range_min < range_max:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	210 return(range_max)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	211 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	212 raise(ValueError(f'Maximum value of integration range must be greater than minimum value of integration range ({range_name}_min={range_min}).'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	213 return(_validate_range_max)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	214 _validate_radial_max = validator('radial_max', allow_reuse=True)(validate_range_max('radial'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	215 _validate_azimuthal_max = validator('azimuthal_max', allow_reuse=True)(validate_range_max('azimuthal'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	216 def validate_for_map_config(self, map_config:MapConfig):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	217 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	218 Validate the existence of the detector data file for all scan points in `map_config`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	219
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	220 :param map_config: The `MapConfig` instance to validate against.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	221 :type map_config: MapConfig
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	222 :raises RuntimeError: If a detector data file could not be found for a scan point occurring in `map_config`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	223 :return: None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	224 :rtype: None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	225 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	226 for detector in self.detectors:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	227 for scans in map_config.spec_scans:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	228 for scan_number in scans.scan_numbers:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	229 scanparser = scans.get_scanparser(scan_number)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	230 for scan_step_index in range(scanparser.spec_scan_npts):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	231 # Make sure the detector data file exists for all scan points
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	232 try:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	233 detector_data_file = scanparser.get_detector_data_file(detector.prefix, scan_step_index)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	234 except:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	235 raise(RuntimeError(f'Could not find data file for detector prefix {detector.prefix} on scan number {scan_number} in spec file {scans.spec_file}'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	236 def get_azimuthal_adjustments(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	237 """To enable a continuous range of integration in the azimuthal direction
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	238 for radial and cake integration, obtain adjusted values for this
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	239 `IntegrationConfig`'s `azimuthal_min` and `azimuthal_max` values, the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	240 angle amount by which those values were adjusted, and the proper location
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	241 of the discontinuity in the azimuthal direction.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	242
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	243 :return: Adjusted chi_min, adjusted chi_max, chi_offset, chi_discontinuity
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	244 :rtype: tuple[float,float,float,float]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	245 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	246 return(get_azimuthal_adjustments(self.azimuthal_min, self.azimuthal_max))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	247 def get_azimuthal_integrators(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	248 """Get a list of `AzimuthalIntegrator`s that correspond to the detector
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	249 configurations in this instance of `IntegrationConfig`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	250
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	251 The returned `AzimuthalIntegrator`s are (if need be) artificially rotated
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	252 in the azimuthal direction to achieve a continuous range of integration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	253 in the azimuthal direction.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	254
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	255 :returns: A list of `AzimuthalIntegrator`s appropriate for use by this
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	256 `IntegrationConfig` tool
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	257 :rtype: list[pyFAI.azimuthalIntegrator.AzimuthalIntegrator]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	258 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	259 chi_min, chi_max, chi_offset, chi_disc = self.get_azimuthal_adjustments()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	260 return(get_azimuthal_integrators(tuple([detector.poni_file for detector in self.detectors]), chi_offset=chi_offset))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	261 def get_multi_geometry_integrator(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	262 """Get a `MultiGeometry` integrator suitable for use by this instance of
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	263 `IntegrationConfig`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	264
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	265 :return: A `MultiGeometry` integrator
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	266 :rtype: pyFAI.multi_geometry.MultiGeometry
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	267 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	268 poni_files = tuple([detector.poni_file for detector in self.detectors])
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	269 radial_range = (self.radial_min, self.radial_max)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	270 azimuthal_range = (self.azimuthal_min, self.azimuthal_max)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	271 return(get_multi_geometry_integrator(poni_files, self.radial_units, radial_range, azimuthal_range))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	272 def get_azimuthally_integrated_data(self, spec_scans:SpecScans, scan_number:int, scan_step_index:int):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	273 """Return azimuthally-integrated data for the scan step specified.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	274
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	275 :param spec_scans: An instance of `SpecScans` containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	276 :type spec_scans: SpecScans
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	277 :param scan_number: The number of the scan containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	278 :type scan_number: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	279 :param scan_step_index: The index of the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	280 :type scan_step_index: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	281 :return: A 1D array of azimuthally-integrated raw detector intensities.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	282 :rtype: np.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	283 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	284 detector_data = spec_scans.get_detector_data(self.detectors, scan_number, scan_step_index)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	285 integrator = self.get_multi_geometry_integrator()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	286 lst_mask = [detector.mask_array for detector in self.detectors]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	287 result = integrator.integrate1d(detector_data, lst_mask=lst_mask, npt=self.radial_npt, error_model=self.error_model)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	288 if result.sigma is None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	289 return(result.intensity)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	290 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	291 return(result.intensity, result.sigma)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	292 def get_radially_integrated_data(self, spec_scans:SpecScans, scan_number:int, scan_step_index:int):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	293 """Return radially-integrated data for the scan step specified.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	294
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	295 :param spec_scans: An instance of `SpecScans` containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	296 :type spec_scans: SpecScans
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	297 :param scan_number: The number of the scan containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	298 :type scan_number: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	299 :param scan_step_index: The index of the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	300 :type scan_step_index: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	301 :return: A 1D array of radially-integrated raw detector intensities.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	302 :rtype: np.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	303 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	304 # Handle idiosyncracies of azimuthal ranges in pyFAI
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	305 # Adjust chi ranges to get a continuous range of iintegrated data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	306 chi_min, chi_max, chi_offset, chi_disc = self.get_azimuthal_adjustments()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	307 # Perform radial integration on a detector-by-detector basis.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	308 I_each_detector = []
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	309 variance_each_detector = []
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	310 integrators = self.get_azimuthal_integrators()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	311 for i,(integrator,detector) in enumerate(zip(integrators,self.detectors)):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	312 detector_data = spec_scans.get_detector_data([detector], scan_number, scan_step_index)[0]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	313 result = integrator.integrate_radial(detector_data, self.azimuthal_npt,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	314 unit=self.azimuthal_units, azimuth_range=(chi_min,chi_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	315 radial_unit=self.radial_units, radial_range=(self.radial_min,self.radial_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	316 mask=detector.mask_array) #, error_model=self.error_model)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	317 I_each_detector.append(result.intensity)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	318 if result.sigma is not None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	319 variance_each_detector.append(result.sigma**2)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	320 # Add the individual detectors' integrated intensities together
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	321 I = np.nansum(I_each_detector, axis=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	322 # Ignore data at values of chi for which there was no data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	323 I = np.where(I==0, np.nan, I)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	324 if len(I_each_detector) != len(variance_each_detector):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	325 return(I)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	326 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	327 # Get the standard deviation of the summed detectors' intensities
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	328 sigma = np.sqrt(np.nansum(variance_each_detector, axis=0))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	329 return(I, sigma)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	330 def get_cake_integrated_data(self, spec_scans:SpecScans, scan_number:int, scan_step_index:int):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	331 """Return cake-integrated data for the scan step specified.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	332
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	333 :param spec_scans: An instance of `SpecScans` containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	334 :type spec_scans: SpecScans
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	335 :param scan_number: The number of the scan containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	336 :type scan_number: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	337 :param scan_step_index: The index of the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	338 :type scan_step_index: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	339 :return: A 2D array of cake-integrated raw detector intensities.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	340 :rtype: np.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	341 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	342 detector_data = spec_scans.get_detector_data(self.detectors, scan_number, scan_step_index)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	343 integrator = self.get_multi_geometry_integrator()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	344 lst_mask = [detector.mask_array for detector in self.detectors]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	345 result = integrator.integrate2d(detector_data, lst_mask=lst_mask,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	346 npt_rad=self.radial_npt, npt_azim=self.azimuthal_npt,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	347 method='bbox',
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	348 error_model=self.error_model)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	349 if result.sigma is None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	350 return(result.intensity)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	351 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	352 return(result.intensity, result.sigma)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	353 def get_integrated_data(self, spec_scans:SpecScans, scan_number:int, scan_step_index:int):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	354 """Return integrated data for the scan step specified.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	355
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	356 :param spec_scans: An instance of `SpecScans` containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	357 :type spec_scans: SpecScans
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	358 :param scan_number: The number of the scan containing the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	359 :type scan_number: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	360 :param scan_step_index: The index of the scan step requested.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	361 :type scan_step_index: int
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	362 :return: An array of integrated raw detector intensities.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	363 :rtype: np.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	364 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	365 if self.integration_type == 'azimuthal':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	366 return(self.get_azimuthally_integrated_data(spec_scans, scan_number, scan_step_index))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	367 elif self.integration_type == 'radial':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	368 return(self.get_radially_integrated_data(spec_scans, scan_number, scan_step_index))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	369 elif self.integration_type == 'cake':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	370 return(self.get_cake_integrated_data(spec_scans, scan_number, scan_step_index))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	371
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	372 @property
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	373 def integrated_data_coordinates(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	374 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	375 Return a dictionary of coordinate arrays for navigating the dimension(s)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	376 of the integrated data produced by this instance of `IntegrationConfig`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	377
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	378 :return: A dictionary with either one or two keys: 'azimuthal' and/or
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	379 'radial', each of which points to a 1-D `numpy` array of coordinate
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	380 values.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	381 :rtype: dict[str,np.ndarray]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	382 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	383 if self.integration_type == 'azimuthal':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	384 return(get_integrated_data_coordinates(radial_range=(self.radial_min,self.radial_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	385 radial_npt=self.radial_npt))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	386 elif self.integration_type == 'radial':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	387 return(get_integrated_data_coordinates(azimuthal_range=(self.azimuthal_min,self.azimuthal_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	388 azimuthal_npt=self.azimuthal_npt))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	389 elif self.integration_type == 'cake':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	390 return(get_integrated_data_coordinates(radial_range=(self.radial_min,self.radial_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	391 radial_npt=self.radial_npt,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	392 azimuthal_range=(self.azimuthal_min,self.azimuthal_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	393 azimuthal_npt=self.azimuthal_npt))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	394 @property
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	395 def integrated_data_dims(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	396 """Return a tuple of the coordinate labels for the integrated data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	397 produced by this instance of `IntegrationConfig`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	398 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	399 directions = list(self.integrated_data_coordinates.keys())
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	400 dim_names = [getattr(self, f'{direction}_units') for direction in directions]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	401 return(dim_names)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	402 @property
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	403 def integrated_data_shape(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	404 """Return a tuple representing the shape of the integrated data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	405 produced by this instance of `IntegrationConfig` for a single scan step.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	406 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	407 return(tuple([len(coordinate_values) for coordinate_name,coordinate_values in self.integrated_data_coordinates.items()]))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	408
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	409 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	410 def get_azimuthal_adjustments(chi_min:float, chi_max:float):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	411 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	412 Fix chi discontinuity at 180 degrees and return the adjusted chi range,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	413 offset, and discontinuty.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	414
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	415 If the discontinuity is crossed, obtain the offset to artificially rotate
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	416 detectors to achieve a continuous azimuthal integration range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	417
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	418 :param chi_min: The minimum value of the azimuthal range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	419 :type chi_min: float
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	420 :param chi_max: The maximum value of the azimuthal range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	421 :type chi_max: float
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	422 :return: The following four values: the adjusted minimum value of the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	423 azimuthal range, the adjusted maximum value of the azimuthal range, the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	424 value by which the chi angle was adjusted, the position of the chi
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	425 discontinuity.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	426 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	427 # Fix chi discontinuity at 180 degrees for now.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	428 chi_disc = 180
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	429 # If the discontinuity is crossed, artificially rotate the detectors to
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	430 # achieve a continuous azimuthal integration range
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	431 if chi_min < chi_disc and chi_max > chi_disc:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	432 chi_offset = chi_max - chi_disc
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	433 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	434 chi_offset = 0
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	435 return(chi_min-chi_offset, chi_max-chi_offset, chi_offset, chi_disc)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	436 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	437 def get_azimuthal_integrators(poni_files:tuple, chi_offset=0):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	438 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	439 Return a list of `AzimuthalIntegrator` objects generated from PONI files.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	440
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	441 :param poni_files: Tuple of strings, each string being a path to a PONI file. : tuple
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	442 :type poni_files: tuple
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	443 :param chi_offset: The angle in degrees by which the `AzimuthalIntegrator` objects will be rotated, defaults to 0.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	444 :type chi_offset: float, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	445 :return: List of `AzimuthalIntegrator` objects
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	446 :rtype: list[pyFAI.azimuthalIntegrator.AzimuthalIntegrator]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	447 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	448 ais = []
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	449 for poni_file in poni_files:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	450 ai = copy.deepcopy(azimuthal_integrator(poni_file))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	451 ai.rot3 += chi_offset * np.pi/180
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	452 ais.append(ai)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	453 return(ais)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	454 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	455 def get_multi_geometry_integrator(poni_files:tuple, radial_unit:str, radial_range:tuple, azimuthal_range:tuple):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	456 """Return a `MultiGeometry` instance that can be used for azimuthal or cake
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	457 integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	458
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	459 :param poni_files: Tuple of PONI files that describe the detectors to be
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	460 integrated.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	461 :type poni_files: tuple
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	462 :param radial_unit: Unit to use for radial integration range.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	463 :type radial_unit: str
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	464 :param radial_range: Tuple describing the range for radial integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	465 :type radial_range: tuple[float,float]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	466 :param azimuthal_range:Tuple describing the range for azimuthal integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	467 :type azimuthal_range: tuple[float,float]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	468 :return: `MultiGeometry` instance that can be used for azimuthal or cake
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	469 integration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	470 :rtype: pyFAI.multi_geometry.MultiGeometry
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	471 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	472 chi_min, chi_max, chi_offset, chi_disc = get_azimuthal_adjustments(*azimuthal_range)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	473 ais = copy.deepcopy(get_azimuthal_integrators(poni_files, chi_offset=chi_offset))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	474 multi_geometry = pyFAI.multi_geometry.MultiGeometry(ais,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	475 unit=radial_unit,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	476 radial_range=radial_range,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	477 azimuth_range=(chi_min,chi_max),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	478 wavelength=sum([ai.wavelength for ai in ais])/len(ais),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	479 chi_disc=chi_disc)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	480 return(multi_geometry)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	481 @cache
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	482 def get_integrated_data_coordinates(azimuthal_range:tuple=None, azimuthal_npt:int=None, radial_range:tuple=None, radial_npt:int=None):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	483 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	484 Return a dictionary of coordinate arrays for the specified radial and/or
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	485 azimuthal integration ranges.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	486
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	487 :param azimuthal_range: Tuple specifying the range of azimuthal angles over
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	488 which to generate coordinates, in the format (min, max), defaults to
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	489 None.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	490 :type azimuthal_range: tuple[float,float], optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	491 :param azimuthal_npt: Number of azimuthal coordinate points to generate,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	492 defaults to None.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	493 :type azimuthal_npt: int, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	494 :param radial_range: Tuple specifying the range of radial distances over
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	495 which to generate coordinates, in the format (min, max), defaults to
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	496 None.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	497 :type radial_range: tuple[float,float], optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	498 :param radial_npt: Number of radial coordinate points to generate, defaults
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	499 to None.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	500 :type radial_npt: int, optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	501 :return: A dictionary with either one or two keys: 'azimuthal' and/or
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	502 'radial', each of which points to a 1-D `numpy` array of coordinate
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	503 values.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	504 :rtype: dict[str,np.ndarray]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	505 """
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	506 integrated_data_coordinates = {}
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	507 if azimuthal_range is not None and azimuthal_npt is not None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	508 integrated_data_coordinates['azimuthal'] = np.linspace(*azimuthal_range, azimuthal_npt)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	509 if radial_range is not None and radial_npt is not None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	510 integrated_data_coordinates['radial'] = np.linspace(*radial_range, radial_npt)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty kls286 parents: diff changeset	511 return(integrated_data_coordinates)

Mercurial > repos > kls286 > chap_test_20230328

annotate build/bdist.linux-x86_64/egg/CHAP/models/integration.py @ 0:cbbe42422d56 draft