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Merge commit '5a62732fc740ff73fb4d52e192c4e36b22f0369f' as 'third-party/fisx'
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‎third-party/fisx/.gitignore

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# Compiled Object files
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*.slo
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*.lo
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*.o
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# Compiled Dynamic libraries
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*.so
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*.dylib
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# Compiled Static libraries
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*.lai
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*.la
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*.a
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#vim
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*.swp
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*~
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# Python .gitignore template follows
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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#cython generated files added (line commented)
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#python/cython/*.cpp
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# Distribution / packaging
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#bin/
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build/
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develop-eggs/
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dist/
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eggs/
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lib/
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lib64/
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#parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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.tox/
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.coverage
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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*.mo
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Rope
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.ropeproject
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# Django stuff:
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*.log
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*.pot
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# Sphinx documentation
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docs/_build/
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‎third-party/fisx/LICENSE

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The MIT License (MIT)
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Copyright (c) 2014 V. Armando Sole
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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the Software, and to permit persons to whom the Software is furnished to do so,
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subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

‎third-party/fisx/MANIFEST.in

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include MANIFEST.in
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include LICENSE
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include changelog.txt
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include README.md
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include README
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include TODO
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recursive-include fisx_data *.dat
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recursive-include python *.py *.pyx *.pxd *.cpp
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recursive-include src *.h *.cpp

‎third-party/fisx/README

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fisx
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====
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C++ port (with enhancements) of the PyMca Physics routines.
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This library allows to calculate the expected X-ray fluorescence intensities measured by a detection system.
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Account for scondary excitation is made via the reference:
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D.K.G. de Boer, X-Ray Spectrometry 19 (1990) 145-154
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with the correction mentioned in:
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D.K.G. de Boer et al, X-Ray Spectrometry 22 (1993) 33-28
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Tertiary excitation is accounted for with an appproximation.
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The accuracy of the corrections has been tested against experimental data and Monte Carlo simulations.

‎third-party/fisx/README.md

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fisx
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====
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This software library implements formulas to calculate, given an experimental setup, the expected x-ray fluorescence intensities. The library accounts for secondary and tertiary excitation, K, L and M shell emission lines and de-excitation cascade effects. The basic implementation is written in C++ and a Python binding is provided.
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License
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-------
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This code is relased under the MIT license as detailed in the LICENSE file.
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Installation
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------------
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To build the library for python use, just use the "python setup.py install" approach. It is convenient (but not mandatory) to have cython >= 0.17 installed.
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Example
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-------
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This piece of Python code shows how the library can be used via its python binding.
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```python
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from fisx import Elements
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from fisx import Material
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from fisx import Detector
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from fisx import XRF
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elementsInstance = Elements()
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elementsInstance.initializeAsPyMca()
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# After the slow initialization (to be made once), the rest is fairly fast.
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xrf = XRF()
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xrf.setBeam(16.0) # set incident beam as a single photon energy of 16 keV
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xrf.setBeamFilters([["Al1", 2.72, 0.11, 1.0]]) # Incident beam filters
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# Steel composition of Schoonjans et al, 2012 used to generate table I
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steel = {"C": 0.0445,
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"N": 0.04,
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"Si": 0.5093,
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"P": 0.02,
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"S": 0.0175,
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"V": 0.05,
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"Cr":18.37,
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"Mn": 1.619,
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"Fe":64.314, # calculated by subtracting the sum of all other elements
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"Co": 0.109,
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"Ni":12.35,
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"Cu": 0.175,
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"As": 0.010670,
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"Mo": 2.26,
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"W": 0.11,
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"Pb": 0.001}
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SRM_1155 = Material("SRM_1155", 1.0, 1.0)
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SRM_1155.setComposition(steel)
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elementsInstance.addMaterial(SRM_1155)
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xrf.setSample([["SRM_1155", 1.0, 1.0]]) # Sample, density and thickness
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xrf.setGeometry(45., 45.) # Incident and fluorescent beam angles
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detector = Detector("Si1", 2.33, 0.035) # Detector Material, density, thickness
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detector.setActiveArea(0.50) # Area and distance in consistent units
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detector.setDistance(2.1) # expected cm2 and cm.
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xrf.setDetector(detector)
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Air = Material("Air", 0.0012048, 1.0)
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Air.setCompositionFromLists(["C1", "N1", "O1", "Ar1", "Kr1"],
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[0.0012048, 0.75527, 0.23178, 0.012827, 3.2e-06])
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elementsInstance.addMaterial(Air)
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xrf.setAttenuators([["Air", 0.0012048, 5.0, 1.0],
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["Be1", 1.848, 0.002, 1.0]]) # Attenuators
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fluo = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"],
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elementsInstance,
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secondary=2,
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useMassFractions=1)
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print("Element Peak Energy Rate Secondary Tertiary")
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for key in fluo:
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for layer in fluo[key]:
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peakList = list(fluo[key][layer].keys())
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peakList.sort()
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for peak in peakList:
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# energy of the peak
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energy = fluo[key][layer][peak]["energy"]
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# expected measured rate
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rate = fluo[key][layer][peak]["rate"]
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# primary photons (no attenuation and no detector considered)
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primary = fluo[key][layer][peak]["primary"]
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# secondary photons (no attenuation and no detector considered)
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secondary = fluo[key][layer][peak]["secondary"]
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# tertiary photons (no attenuation and no detector considered)
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tertiary = fluo[key][layer][peak].get("tertiary", 0.0)
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# correction due to secondary excitation
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enhancement2 = (primary + secondary) / primary
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enhancement3 = (primary + secondary + tertiary) / primary
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print("%s %s %.4f %.3g %.5g %.5g" % \
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(key, peak + (13 - len(peak)) * " ", energy,
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rate, enhancement2, enhancement3))
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```

‎third-party/fisx/TODO

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- Add doc strings based on the C++ doxygen information to the python binding.
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- Possibility to save and to load the configuration in own fisx format.

‎third-party/fisx/changelog.txt

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VERSION 1.0.2
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Give correct weight to elastic scattering contribution.
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VERSION 1.0.1
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Add conda recipe
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Correct test suite
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Correct bug reading PyMca configuration files
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VERSION 1.0.0
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First release.
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Secondary excitation due to fluorescence and elastic scattering considered.
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Tertiary implemented via an approximation method.

‎third-party/fisx/conda.recipe/bld.bat

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%PYTHON% setup.py install
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if errorlevel 1 exit 1

‎third-party/fisx/conda.recipe/build.sh

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$PYTHON setup.py install

‎third-party/fisx/conda.recipe/meta.yaml

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package:
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name: fisx
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version: {{ environ.get('GIT_DESCRIBE_TAG', '')[1:] }}
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source:
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git_url: ../
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git_tag: master # change to branch or tag name, as needed
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build:
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number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
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requirements:
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build:
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- python
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- cython
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- numpy
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run:
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- python
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- numpy
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- pymca
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test:
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requires:
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- pymca
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imports:
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- fisx
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about:
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license: MIT
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home: http://pymca.sourceforge.net
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summary: Resources for synchrotron data analysis

‎third-party/fisx/conda.recipe/run_test.py

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#/*##########################################################################
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#
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# The fisx library for X-Ray Fluorescence
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#
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# Copyright (c) 2014 V. Armando Sole
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#
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# This file is part of the fisx X-ray developed by V.A. Sole
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#
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# This file is a contribution from Darren Dale
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# in the Software without restriction, including without limitation the rights
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# copies of the Software, and to permit persons to whom the Software is
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# furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in
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# all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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# THE SOFTWARE.
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#
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#############################################################################*/
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__author__ = "Darren Dale - CHESS"
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import os
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import sys
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if sys.version.startswith('2.6') or sys.version.startswith('3.1'):
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import unittest2 as unittest
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else:
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import unittest
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suite = unittest.TestLoader().discover('fisx')
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unittest.TextTestRunner(verbosity=1).run(suite)

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