Absorption correction #649

psavery · 2024-06-21T20:36:26Z

This adds a physics package class along with code to perform absorption corrections due to components of the physics package or components on the detectors.

…ormula and density. Tested and fixed absorption correction for filterpack and sample+window layer.

…nt class

…er correction tested. physics package correction needs to be tested.

…on length

…o test the transmission functions

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

pep8speaks · 2024-06-21T20:36:35Z

Hello @psavery! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file hexrd/constants.py:

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In the file hexrd/instrument/cylindrical_detector.py:

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In the file hexrd/instrument/detector.py:

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In the file hexrd/instrument/planar_detector.py:

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In the file hexrd/material/sample.py:

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In the file hexrd/material/utils.py:

Line 4:1: E122 continuation line missing indentation or outdented
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Comment last updated at 2024-09-06 19:57:48 UTC

Add missing dependency, fix an import, fix attribute name. Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>

codecov · 2024-07-03T16:13:54Z

Codecov Report

Attention: Patch coverage is 38.68613% with 252 lines in your changes missing coverage. Please review.

Please upload report for BASE (master@2534ec5). Learn more about missing BASE report.

Files	Patch %	Lines
hexrd/material/sample.py	51.47%	82 Missing ⚠️
hexrd/instrument/detector.py	38.61%	62 Missing ⚠️
hexrd/material/utils.py	21.66%	47 Missing ⚠️
hexrd/instrument/cylindrical_detector.py	5.40%	35 Missing ⚠️
hexrd/instrument/planar_detector.py	5.26%	18 Missing ⚠️
hexrd/instrument/hedm_instrument.py	11.11%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##             master     #649   +/-   ##
=========================================
  Coverage          ?   30.29%           
=========================================
  Files             ?      141           
  Lines             ?    22947           
  Branches          ?        0           
=========================================
  Hits              ?     6952           
  Misses            ?    15995           
  Partials          ?        0

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psavery · 2024-07-03T17:50:50Z

setup.py

@@ -12,6 +12,7 @@

 install_reqs = [
    'appdirs',
+    'chemparse',


We will need to add chemparse as a conda dependency as well.

Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>

saransh13 and others added 25 commits June 21, 2024 15:32

New packaging for performing absorption corrections

fc0639f

define some properties.

ec99b00

added some description

b10fbf6

start adding code for sample+window absorption correction

34fc55c

add more code. almost done with this code now

89d5dc0

adding final few attributes

9276b7c

filterpack tested. still. need to test sample and window absorptions

f2d606f

functions work, but does not look physical at the moment

810746e

fixed the transformation

12f2466

many more helper routines to compute the absorption length based on f…

59852f7

…ormula and density. Tested and fixed absorption correction for filterpack and sample+window layer.

switching back to the old Anomalous.h5 file.

a634eb6

filter and coating definitions are now on the detector class itself.

8f673cb

fixed the signs and moved all absorption calculations to the instrume…

32d9d50

…nt class

everything in the instrument class now. everything runs. coating+filt…

6212ae9

…er correction tested. physics package correction needs to be tested.

calculate overall transmission

46e741e

add effective pinhole area correction

d3cdc23

added phosphor absorption

da4953c

fix typo

09a59ba

new class for sample, pinhole, filter, coatings etc.

11bbc07

make everything tie back to the abstractlayer class, and add absorpti…

16a5760

…on length

tested code for physics package

aa83308

tested initialization of instrument with default values. Still need t…

4cf305a

…o test the transmission functions

tested transmission functions.

d129c23

remove unnecessary properties and fix the ones that need to be modified

4a4cbd0

Use identity by default for rMat_s in transmission

7210649

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Some minor bug fixes

89c1370

Add missing dependency, fix an import, fix attribute name. Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>

psavery commented Jul 3, 2024

View reviewed changes

Add setters where needed

7792abc

Signed-off-by: Brianna Major <brianna.major@taloid.khq.kitware.com>

bnmajor force-pushed the absorption-correction branch from f628914 to 7792abc Compare September 6, 2024 19:57

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Absorption correction #649

Absorption correction #649

psavery commented Jun 21, 2024

pep8speaks commented Jun 21, 2024 •

edited

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codecov bot commented Jul 3, 2024

psavery Jul 3, 2024

Absorption correction #649

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Absorption correction #649

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psavery commented Jun 21, 2024

pep8speaks commented Jun 21, 2024 • edited Loading

Comment last updated at 2024-09-06 19:57:48 UTC

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pep8speaks commented Jun 21, 2024 •

edited

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