Mercurial > repos > kls286 > chap_test_20230328

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
1 from msnctools.general import create_mask
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
2 from msnctools.material import Material
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
3 from msnctools.scanparsers import SMBMCAScanParser as ScanParser
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
4 import numpy as np
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
5 from pathlib import PosixPath
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
6 from pydantic import (BaseModel,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
7 confloat,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
8 conint,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
9 conlist,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
10 constr,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
11 FilePath,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
12 validator)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
13 from scipy.interpolate import interp1d
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
14 from typing import Optional
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
15
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
16
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
17 class MCACeriaCalibrationConfig(BaseModel):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
18 '''Class representing metadata required to perform a Ceria calibration for an
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
19 MCA detector.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
20
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
21 :ivar spec_file: Path to the SPEC file containing the CeO2 scan
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
22 :ivar scan_number: Number of the CeO2 scan in `spec_file`
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
23 :ivar scan_step_index: Index of the scan step to use for calibration,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
24 optional. If not specified, the calibration routine will be performed on
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
25 the average of all MCA spectra for the scan.
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 :ivar flux_file: csv file containing station beam energy in eV (column 0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
28 and flux (column 1)
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 :ivar detector_name: name of the MCA to calibrate
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
31 :ivar num_bins: number of channels on the MCA to calibrate
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
32 :ivar max_energy_kev: maximum channel energy of the MCA in keV
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 :ivar hexrd_h5_material_file: path to a HEXRD materials.h5 file containing an
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
35 entry for the material properties.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
36 :ivar hexrd_h5_material_name: Name of the material entry in
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
37 `hexrd_h5_material_file`, defaults to `'CeO2'`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
38 :ivar lattice_parameter_angstrom: lattice spacing in angstrom to use for
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
39 the cubic CeO2 crystal, defaults to `5.41153`.
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 :ivar tth_max: detector rotation about hutch x axis, defaults to `90`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
42 :ivar hkl_tth_tol: minimum resolvable difference in 2&theta between two
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
43 unique HKL peaks, defaults to `0.15`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
44
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
45 :ivar fit_include_bin_ranges: list of MCA channel index ranges whose data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
46 will be included in the calibration routine
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
47 :ivar fit_hkls: list of unique HKL indices to fit peaks for in the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
48 calibration routine
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
49
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
50 :ivar tth_initial_guess: initial guess for 2&theta
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
51 :ivar slope_initial_guess: initial guess for detector channel energy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
52 correction linear slope, defaults to `1.0`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
53 :ivar intercept_initial_guess: initial guess for detector channel energy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
54 correction y-intercept, defaults to `0.0`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
55
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
56 :ivar tth_calibrated: calibrated value for 2&theta, defaults to None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
57 :ivar slope_calibrated: calibrated value for detector channel energy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
58 correction linear slope, defaults to `None`
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
59 :ivar intercept_calibrated: calibrated value for detector channel energy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
60 correction y-intercept, defaluts to None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
61
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
62 :ivar max_iter: maximum number of iterations of the calibration routine,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
63 defaults to `10`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
64 :ivar tune_tth_tol: stop iteratively tuning 2&theta when an iteration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
65 produces a change in the tuned value of 2&theta that is smaller than this
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
66 value, defaults to `1e-8`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
67 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
68
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
69 spec_file: FilePath
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
70 scan_number: conint(gt=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
71 scan_step_index: Optional[conint(ge=0)]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
72
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
73 flux_file: FilePath
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
74
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
75 detector_name: 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
76 num_bins: conint(gt=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
77 max_energy_kev: confloat(gt=0)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
78
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
79 hexrd_h5_material_file: FilePath
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
80 hexrd_h5_material_name: constr(strip_whitespace=True, min_length=1) = 'CeO2'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
81 lattice_parameter_angstrom: confloat(gt=0) = 5.41153
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
82
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
83 tth_max: confloat(gt=0, allow_inf_nan=False) = 90.0
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
84 hkl_tth_tol: confloat(gt=0, allow_inf_nan=False) = 0.15
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
85
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
86 fit_include_bin_ranges: conlist(min_items=1,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
87 item_type=conlist(item_type=conint(ge=0),
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
88 min_items=2,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
89 max_items=2))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
90 fit_hkls: conlist(item_type=conint(ge=0), min_items=1)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
91
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
92 tth_initial_guess: confloat(gt=0, le=tth_max, allow_inf_nan=False)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
93 slope_initial_guess: float = 1.0
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
94 intercept_initial_guess: float = 0.0
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
95 tth_calibrated: Optional[confloat(gt=0, allow_inf_nan=False)]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
96 slope_calibrated: Optional[confloat(allow_inf_nan=False)]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
97 intercept_calibrated: Optional[confloat(allow_inf_nan=False)]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
98
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
99 max_iter: conint(gt=0) = 10
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
100 tune_tth_tol: confloat(ge=0) = 1e-8
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
101
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
102 @validator('fit_include_bin_ranges', each_item=True)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
103 def validate_include_bin_range(cls, value, values):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
104 '''Ensure no bin ranges are outside the boundary of the detector'''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
105
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
106 num_bins = values.get('num_bins')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
107 value[1] = min(value[1], num_bins)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
108 return(value)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
109
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
110 def mca_data(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
111 '''Get the 1D array of MCA data to use for calibration.
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 :return: MCA data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
114 :rtype: np.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
115 '''
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 scanparser = ScanParser(self.spec_file, self.scan_number)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
118 if self.scan_step_index is None:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
119 data = scanparser.get_all_detector_data(self.detector_name)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
120 if scanparser.spec_scan_npts > 1:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
121 data = np.average(data, axis=1)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
122 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
123 data = data[0]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
124 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
125 data = scanparser.get_detector_data(self.detector_name, self.scan_step_index)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
126
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
127 return(np.array(data))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
128
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
129 def mca_mask(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
130 '''Get a boolean mask array to use on MCA data before fitting.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
131
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
132 :return: boolean mask array
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
133 :rtype: numpy.ndarray
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
134 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
135
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
136 mask = None
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
137 bin_indices = np.arange(self.num_bins)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
138 for bin_range in self.fit_include_bin_ranges:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
139 mask = create_mask(bin_indices,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
140 bounds=bin_range,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
141 exclude_bounds=False,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
142 current_mask=mask)
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 return(mask)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
145
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
146 def flux_correction_interpolation_function(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
147 '''Get an interpolation function to correct MCA data for relative energy
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
148 flux of the incident beam.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
149
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
150 :return: energy flux correction interpolation function
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
151 :rtype: scipy.interpolate._polyint._Interpolator1D
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
152 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
153
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
154 flux = np.loadtxt(self.flux_file)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
155 energies = flux[:,0]/1.e3
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
156 relative_intensities = flux[:,1]/np.max(flux[:,1])
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
157 interpolation_function = interp1d(energies, relative_intensities)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
158 return(interpolation_function)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
159
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
160 def material(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
161 '''Get CeO2 as a `msnctools.materials.Material` object.
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 :return: CeO2 material
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
164 :rtype: msnctools.material.Material
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
165 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
166
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
167 material = Material(material_name=self.hexrd_h5_material_name,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
168 material_file=self.hexrd_h5_material_file,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
169 lattice_parameters_angstroms=self.lattice_parameter_angstrom)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
170 # The following kwargs will be needed if we allow the material to be
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
171 # built using xrayutilities (for now, we only allow hexrd to make the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
172 # material):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
173 # sgnum=225,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
174 # atoms=['Ce4p', 'O2mdot'],
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
175 # pos=[(0.,0.,0.), (0.25,0.75,0.75)],
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
176 # enrgy=50000.) # Why do we need to specify an energy to get HKLs when using xrayutilities?
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
177 return(material)
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 def unique_ds(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
180 '''Get a list of unique HKLs and their lattice spacings
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
181
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
182 :return: unique HKLs and their lattice spacings in angstroms
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
183 :rtype: np.ndarray, np.ndarray
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
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
186 unique_hkls, unique_ds = self.material().get_unique_ds(tth_tol=self.hkl_tth_tol, tth_max=self.tth_max)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
187
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
188 return(unique_hkls, unique_ds)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
189
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
190 def fit_ds(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
191 '''Get a list of HKLs and their lattice spacings that will be fit in the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
192 calibration routine
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
193
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
194 :return: HKLs to fit and their lattice spacings in angstroms
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
195 :rtype: np.ndarray, np.ndarray
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
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
198 unique_hkls, unique_ds = self.unique_ds()
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 fit_hkls = np.array([unique_hkls[i] for i in self.fit_hkls])
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
201 fit_ds = np.array([unique_ds[i] for i in self.fit_hkls])
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
202
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
203 return(fit_hkls, fit_ds)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
204
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
205 def dict(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
206 '''Return a representation of this configuration in a dictionary that is
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
207 suitable for dumping to a YAML file (one that converts all instances of
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
208 fields with type `PosixPath` to `str`).
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
209
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
210 :return: dictionary representation of the configuration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
211 :rtype: dict
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
212 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
213
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
214 d = super().dict()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
215 for k,v in d.items():
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
216 if isinstance(v, PosixPath):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
217 d[k] = str(v)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
218 return(d)