Merge commit '5a62732fc740ff73fb4d52e192c4e36b22f0369f' as 'third-par…

…ty/fisx'

third-party/fisx/.gitignore

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

third-party/fisx/LICENSE

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

third-party/fisx/README

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+fisx
+====
+
+C++ port (with enhancements) of the PyMca Physics routines.
+
+This library allows to calculate the expected X-ray fluorescence intensities measured by a detection system.
+
+Account for scondary excitation is made via the reference:
+
+D.K.G. de Boer, X-Ray Spectrometry 19 (1990) 145-154
+
+with the correction mentioned in:
+
+D.K.G. de Boer et al, X-Ray Spectrometry 22 (1993) 33-28
+
+Tertiary excitation is accounted for with an appproximation.
+
+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
+====
+
+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.
+
+License
+-------
+
+This code is relased under the MIT license as detailed in the LICENSE file.
+
+Installation
+------------
+
+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.
+
+
+Example
+-------
+
+This piece of Python code shows how the library can be used via its python binding.
+
+```python
+from fisx import Elements
+from fisx import Material
+from fisx import Detector
+from fisx import XRF
+elementsInstance = Elements()
+elementsInstance.initializeAsPyMca()
+# After the slow initialization (to be made once), the rest is fairly fast.
+xrf = XRF()
+xrf.setBeam(16.0) # set incident beam as a single photon energy of 16 keV
+xrf.setBeamFilters([["Al1", 2.72, 0.11, 1.0]]) # Incident beam filters
+# Steel composition of Schoonjans et al, 2012 used to generate table I
+steel = {"C":  0.0445, 
+         "N":  0.04,
+         "Si": 0.5093,
+         "P":  0.02,
+         "S":  0.0175,
+         "V":  0.05,
+         "Cr":18.37,
+         "Mn": 1.619,
+         "Fe":64.314, # calculated by subtracting the sum of all other elements
+         "Co": 0.109,
+         "Ni":12.35,
+         "Cu": 0.175,
+         "As": 0.010670,
+         "Mo": 2.26,
+         "W":  0.11,
+         "Pb": 0.001}
+SRM_1155 = Material("SRM_1155", 1.0, 1.0)
+SRM_1155.setComposition(steel)
+elementsInstance.addMaterial(SRM_1155)
+xrf.setSample([["SRM_1155", 1.0, 1.0]]) # Sample, density and thickness
+xrf.setGeometry(45., 45.)               # Incident and fluorescent beam angles
+detector = Detector("Si1", 2.33, 0.035) # Detector Material, density, thickness
+detector.setActiveArea(0.50)            # Area and distance in consistent units
+detector.setDistance(2.1)               # expected cm2 and cm.
+xrf.setDetector(detector)
+Air = Material("Air", 0.0012048, 1.0)
+Air.setCompositionFromLists(["C1", "N1", "O1", "Ar1", "Kr1"],
+                            [0.0012048, 0.75527, 0.23178, 0.012827, 3.2e-06])
+elementsInstance.addMaterial(Air)
+xrf.setAttenuators([["Air", 0.0012048, 5.0, 1.0],
+                    ["Be1", 1.848, 0.002, 1.0]]) # Attenuators
+fluo = xrf.getMultilayerFluorescence(["Cr K", "Fe K", "Ni K"],
+                                     elementsInstance,
+                                     secondary=2,
+                                     useMassFractions=1)
+print("Element   Peak          Energy       Rate      Secondary  Tertiary")
+for key in fluo:
+    for layer in fluo[key]:
+        peakList = list(fluo[key][layer].keys())
+        peakList.sort()
+        for peak in peakList:
+            # energy of the peak
+            energy = fluo[key][layer][peak]["energy"]
+            # expected measured rate
+            rate = fluo[key][layer][peak]["rate"]
+            # primary photons (no attenuation and no detector considered)
+            primary = fluo[key][layer][peak]["primary"]
+            # secondary photons (no attenuation and no detector considered)
+            secondary = fluo[key][layer][peak]["secondary"]
+            # tertiary photons (no attenuation and no detector considered)
+            tertiary = fluo[key][layer][peak].get("tertiary", 0.0)
+            # correction due to secondary excitation
+            enhancement2 = (primary + secondary) / primary
+            enhancement3 = (primary + secondary + tertiary) / primary
+            print("%s   %s    %.4f     %.3g     %.5g    %.5g" % \
+                               (key, peak + (13 - len(peak)) * " ", energy,
+                               rate, enhancement2, enhancement3))
+```

third-party/fisx/TODO

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+- Add doc strings based on the C++ doxygen information to the python binding.
+- 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
+
+Give correct weight to elastic scattering contribution.
+
+VERSION 1.0.1
+
+Add conda recipe
+
+Correct test suite
+
+Correct bug reading PyMca configuration files
+
+VERSION 1.0.0
+
+First release.
+
+Secondary excitation due to fluorescence and elastic scattering considered.
+
+Tertiary implemented via an approximation method.

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

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

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

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