PyMca5 5.9.7rc2__tar.gz → 5.9.7rc3__tar.gz

pymca5-5.9.7rc3/PKG-INFO

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+Metadata-Version: 2.4
+Name: PyMca5
+Version: 5.9.7rc3
+Summary: Mapping and X-Ray Fluorescence Analysis
+Author: V. Armando Sole
+Author-email: sole@esrf.fr
+License: MIT
+Platform: any
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+License-File: LICENSE
+License-File: LICENSE.GPL
+License-File: LICENSE.LGPL
+License-File: LICENSE.MIT
+Requires-Dist: numpy
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: fisx>=1.1.6
+Requires-Dist: h5py
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: summary
+
+Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided

pymca5-5.9.7rc3/doc/source/recipes/recipescode/GenerateHDF5Stack.py

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+#/*##########################################################################
+#
+# Copyright (c) 2018 European Synchrotron Radiation Facility
+#
+# 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__ = "V.A. Sole - ESRF Data Analysis"
+__contact__ = "sole@esrf.fr"
+__license__ = "MIT"
+__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+__doc__ = """
+Script writing a stack of XRF data with calibration and live_time information
+"""
+
+import os
+import numpy
+import h5py
+
+# use a dummy 3D array generated using data supplied with PyMca
+from PyMca5 import PyMcaDataDir
+from PyMca5.PyMcaIO import specfilewrapper as specfile
+from PyMca5.PyMcaIO import ConfigDict
+
+dataDir = PyMcaDataDir.PYMCA_DATA_DIR
+spe = os.path.join(dataDir, "Steel.spe")
+cfg = os.path.join(dataDir, "Steel.cfg")
+sf = specfile.Specfile(spe)
+y = counts = sf[0].mca(1)
+x = channels = numpy.arange(y.size).astype(numpy.float64)
+configuration = ConfigDict.ConfigDict()
+configuration.read(cfg)
+calibration = configuration["detector"]["zero"], \
+              configuration["detector"]["gain"], 0.0
+initialTime = configuration["concentrations"]["time"]
+
+# create the data
+nRows = 5
+nColumns = 10
+nTimes = 3
+data = numpy.zeros((nRows, nColumns, counts.size), dtype = numpy.float64)
+live_time = numpy.zeros((nRows * nColumns), dtype=numpy.float64)
+
+mcaIndex = 0
+for i in range(nRows):
+    for j in range(nColumns):
+        factor = (1 + mcaIndex % nTimes)
+        data[i, j] = counts * factor
+        live_time[i * nColumns + j] = initialTime * factor
+        mcaIndex += 1
+
+# now we have a 3D array containing the spectra in data (mandatory)
+# we have the channels (not mandatory)
+# we have the associated calibration (not mandatory)
+# we have the live_time (not mandatory)
+# and we are going to create an HDF5 with that information
+#
+# Just writing those data as a dataset in an HDF5 file would be enough for
+# using it in PyMca, but we can create a container group in order to associate
+# additional information (channels, live_time, calibration)
+# "instrument" can be replaced by, for instance, the beamline name
+# "detector" can be replaced by, for instance, "mca_0"
+#
+h5File = "Steel.h5"
+if os.path.exists(h5File):
+    os.remove(h5File)
+h5 = h5py.File(h5File, "w")
+h5["/entry/instrument/detector/calibration"] = calibration
+h5["/entry/instrument/detector/channels"] = channels
+h5["/entry/instrument/detector/data"] = data
+h5["/entry/instrument/detector/live_time"] = live_time
+
+# add nexus conventions (not needed)
+h5["/entry/title"] = u"Dummy generated map"
+h5["/entry"].attrs["NX_class"] = u"NXentry"
+h5["/entry/instrument"].attrs["NX_class"] = u"NXinstrument"
+h5["/entry/instrument/detector/"].attrs["NX_class"] = u"NXdetector"
+h5["/entry/instrument/detector/data"].attrs["interpretation"] = \
+                                                      u"spectrum"
+# implement a default plot named measurement (not needed)
+h5["/entry/measurement/data"] = \
+                    h5py.SoftLink("/entry/instrument/detector/data")
+h5["/entry/measurement"].attrs["NX_class"] = u"NXdata"
+h5["/entry/measurement"].attrs["signal"] = u"data"
+h5["/entry"].attrs["default"] = u"measurement"
+
+h5.flush()
+h5.close()
+h5 = None

pymca5-5.9.7rc3/package/py2app/py2app_setup.py

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+#
+# These Python modules have been developed by V.A. Sole, from the European
+# Synchrotron Radiation Facility (ESRF) to build a frozen version of PyMca.
+# Given the nature of this work, these module can be considered public domain.
+# Therefore redistribution and use in source and binary forms, with or without
+# modification, are permitted provided the following disclaimer is accepted:
+#
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR(S) AND THE ESRF ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE AUTHOR(S) AND/OR THE ESRF BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+"""
+Script for building the PyMca bundle.
+For a distributable application Platypus is needed
+
+Usage:
+    python py2app_setup.py py2app
+"""
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+import py2app
+import os
+import sys
+
+#force a clean build
+os.system("/bin/rm -rf dist")
+os.system("/bin/rm -rf build")
+os.system("/bin/rm -rf *.pyc")
+
+BUNDLE_ICON = os.path.join(os.path.abspath('icons'), 'PyMca.icns')
+
+#obtain the current PyMca version from the source file
+ffile = open(os.path.join('src', 'PyMca5', '__init__.py'), 'r').readlines()
+for line in ffile:
+    if line.startswith('__version__'):
+        #remove spaces and split
+        __version__ = "%s" % line.replace(' ','').split("=")[-1][:-1]
+        #remove " or ' present
+        __version__ = __version__[1:-1]
+        break
+
+PyMcaInstallationDir = os.path.abspath("build")
+PyMcaDir = os.path.join(PyMcaInstallationDir, "PyMca5")
+#make sure PyMca is freshly built
+cmd = "setup.py install --distutils --install-lib %s --install-data %s --install-scripts /tmp/scripts" % \
+                          (PyMcaInstallationDir, PyMcaInstallationDir)
+cmd = sys.executable + " " + cmd
+if os.system(cmd):
+    print("Error building PyMca")
+    sys.exit(1)
+
+# awful workaround because py2app picks PyMca form the source directory
+os.chdir(PyMcaInstallationDir)
+sys.path.insert(0, PyMcaInstallationDir)
+pymcapath = PyMcaDir
+application=os.path.join(pymcapath, 'PyMcaGui','pymca', "PyMcaMain.py")
+
+#The options below are equivalent to running from the command line
+#python py2app_setup.py py2app --packages=matplotlib,ctypes,h5py,Object3D
+#probably matplotlib and PyOpenGL are properly detected by py2app
+PACKAGES = ['fisx', 'OpenGL','ctypes','matplotlib', 'h5py','hdf5plugin','logging', 'PyMca5']
+PACKAGES.append("PyQt5")
+
+import silx
+PACKAGES.append("silx")
+SILX = True
+
+try:
+   import IPython
+   import pygments
+   PACKAGES.append("IPython")
+   PACKAGES.append("pygments")
+except:
+   pass
+
+try:
+    import fabio
+    PACKAGES.append("fabio")
+except:
+    pass
+
+try:
+    import mdp
+    PACKAGES.append('mdp')
+except:
+    pass
+try:
+    import pyopencl
+    PACKAGES.append('pyopencl')
+    PYOPENCL = True
+except:
+    PYOPENCL = False
+
+try:
+    import tomogui
+    PACKAGES.append('tomogui')
+    try:
+       import freeart
+       PACKAGES.append('freeart')
+    except:
+       pass
+except:
+    pass
+
+PY2APP_OPTIONS = {'packages':PACKAGES}
+if "PyQt5" in PACKAGES:
+    PY2APP_OPTIONS['qt_plugins'] = ["cocoa"]
+
+if os.path.exists(BUNDLE_ICON):
+    PY2APP_OPTIONS['iconfile'] = BUNDLE_ICON
+else:
+    BUNDLE_ICON = None
+PY2APP_OPTIONS["excludes"] = ["scipy"]
+
+if sys.version.startswith("2"):
+    PY2APP_OPTIONS["excludes"].append("PyQt4.uic.port_v3")
+    PY2APP_OPTIONS["excludes"].append("PyQt5.uic.port_v3")
+
+setup(
+    app=[application],
+    options={'py2app':PY2APP_OPTIONS}
+)
+
+# move to the proper place
+os.system("mv -f ./dist ../dist")
+os.chdir(os.path.dirname(PyMcaInstallationDir))
+
+# patch problematic modules
+patching_dir = os.path.join(os.getcwd(),
+                    "dist/PyMcaMain.app/Contents/Resources/lib/python%s/" % \
+                            sys.version[:3])
+if SILX:
+    # silx gui._qt module needs to be patched to get rid of uic
+    initFile = os.path.join(patching_dir, "silx", "gui", "qt", "_qt.py")
+    print("###################################################################")
+    print("Patching silx file")
+    print(initFile)
+    print("###################################################################")
+    f = open(initFile, "r")
+    content = f.readlines()
+    f.close()
+    f = open(initFile, "w")
+    for line in content:
+        if ("PyQt4.uic" in line) or ("PyQt5.uic" in line):
+            continue
+        f.write(line)
+    f.close()
+
+if PYOPENCL:
+    # pyopencl __init__.py needs to be patched
+    initFile = os.path.join(patching_dir, "pyopencl", "__init__.py")
+    print("###################################################################")
+    print("Patching pyopencl file")
+    print(initFile)
+    print("###################################################################")
+    f = open(initFile, "r")
+    content = f.readlines()
+    f.close()
+    i = 0
+    i0 = 0
+    for line in content:
+        if "def _find_pyopencl_include_path():" in line:
+            i0 = i - 1
+        elif (i0 != 0) and ("}}}" in line):
+            i1 = i
+            break
+        i += 1
+    f = open(initFile, "w")
+    for i in range(0, i0):
+        f.write(content[i])
+    txt ='\n'
+    txt +='def _find_pyopencl_include_path():\n'
+    txt +='     from os.path import dirname, join, realpath\n'
+    txt +="     return '\"%s\"' % join(realpath(dirname(__file__)), \"cl\")"
+    txt +="\n"
+    txt +="\n"
+    f.write(txt)
+    for line in content[i1:]:
+        f.write(line)
+    f.close()
+
+#Command line call to Platypus ...
+platypusFile = '/usr/local/bin/platypus'
+if os.path.exists(platypusFile):
+    import subprocess
+    args = [platypusFile,
+            '-R',
+            '-a',
+            'PyMca%s' % __version__,
+            '-o',
+            'Progress Bar',
+            '-p',
+            '/bin/bash',
+            '-V',
+            '%s' % __version__,
+            '-I',
+            'ESRF.sole.PyMca%s' % __version__,
+            '-y', #force overwrite
+            '-f',
+            os.path.join(os.getcwd(),'dist', 'PyMcaMain.app')]
+    if BUNDLE_ICON is not None:
+        args.append('-i')
+        args.append(BUNDLE_ICON)
+    args.append(os.path.join(os.getcwd(), 'PlatypusScript'))
+    process = subprocess.call(args)
+    py2app_bundle = os.path.join(os.getcwd(), 'PyMca%s.app' % __version__, "Contents", "Resources", "PyMcaMain.app")
+    if not os.path.exists(py2app_bundle):
+        print("Forcing copy")
+        os.system("cp -R ./dist/PyMcaMain.app "+ os.path.dirname(py2app_bundle)) 

pymca5-5.9.7rc3/requirements.txt

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+# List all dependencies of PyMca for GUI functionality and not just
+# command line XRF analysis
+# Requires pip >= 8.0
+
+--trusted-host www.silx.org
+--find-links http://www.silx.org/pub/wheelhouse/
+--only-binary numpy,h5py,PyQt5,PySide2
+
+numpy >= 1.8
+fisx >= 1.1.6
+PyOpenGL                  # For PyMca5.Object3D module 
+h5py                      # For HDF5 file format support
+matplotlib >= 3.5         # For visualization
+qtconsole                 # For interactive console plugin
+
+# PyQt5 or PySide2 or PySide6  # For PyMca5.PyMcaGui
+# Try to install a Qt binding from a wheel
+# This is no available for all configurations
+
+# Require PyQt when wheel is available
+PyQt5; python_version >= '3.5'
+PySide2; sys_platform == 'darwin' and python_version == '2.7'