initial commit

.gitignore

+# Build files
+build
+dist
+ESRF_Orange3_Add_on.egg-info
+Orange/version.py
+doc/build
+*.so
+*.pyd
+*.pyc
+MANIFEST
+
+# Cython generated files
+__pycache__
+
+# Editor files
+.idea
+.idea/*
+*~
+.project
+.pydevproject
+.settings/*
+.DS_Store
+
+# Windows temp files
+Thumbs.db
+
+# PyLint, Coverage reports
+.pylint_cache/*
+htmlcov/*
+
+# Tmp files
+*tmp
+tmp*
+
+*.edf
+*.info
+*.cfg
+*.xml
+*.db
+*.tar.bz2
+
+dataset/
+datasets/
+test10/
+*.egg-info*
+
+
+# notebook checkpoints
+*.ipynb_checkpoints/
+# notebook nbconvert
+*.nbconvert.ipynb
+
+# octave files
+octave-workspace

README.rst

+TODO
\ No newline at end of file

requirements.txt

+silx>=0.9
+lxml
\ No newline at end of file

setup.py

+#!/usr/bin/python
+# coding: utf8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2019 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.
+#
+# ###########################################################################*/
+
+__authors__ = ["Jérôme Kieffer", "Thomas Vincent", "H. Payno"]
+__date__ = "12/02/2019"
+__license__ = "MIT"
+
+
+import sys
+import os
+import platform
+import logging
+import io
+
+logging.basicConfig(level=logging.INFO)
+
+logger = logging.getLogger("tomoscan.setup")
+
+
+from distutils.command.build import build as _build
+try:
+    from setuptools import Command
+    from setuptools.command.build_ext import build_ext
+    from setuptools.command.sdist import sdist
+    logger.info("Use setuptools")
+except ImportError:
+    try:
+        from numpy.distutils.core import Command
+    except ImportError:
+        from distutils.core import Command
+    from distutils.command.build_ext import build_ext
+    from distutils.command.sdist import sdist
+    logger.info("Use distutils")
+
+try:
+    import sphinx
+    import sphinx.util.console
+    sphinx.util.console.color_terminal = lambda: False
+    from sphinx.setup_command import BuildDoc
+except ImportError:
+    sphinx = None
+
+
+PROJECT = "tomoscan"
+
+if "LANG" not in os.environ and sys.platform == "darwin" and sys.version_info[0] > 2:
+    print("""WARNING: the LANG environment variable is not defined,
+an utf-8 LANG is mandatory to use setup.py, you may face unexpected UnicodeError.
+export LANG=en_US.utf-8
+export LC_ALL=en_US.utf-8
+""")
+
+
+def get_version():
+    """Returns current version number from version.py file"""
+    dirname = os.path.dirname(os.path.abspath(__file__))
+    sys.path.insert(0, dirname)
+    import tomoscan.version
+    sys.path = sys.path[1:]
+    return tomoscan.version.strictversion
+
+
+def get_readme():
+    """Returns content of README.rst file"""
+    dirname = os.path.dirname(os.path.abspath(__file__))
+    filename = os.path.join(dirname, "README.rst")
+    with io.open(filename, "r", encoding="utf-8") as fp:
+        long_description = fp.read()
+    return long_description
+
+
+classifiers = ["Development Status :: 4 - Beta",
+               "Environment :: Console",
+               "Environment :: MacOS X",
+               "Environment :: Win32 (MS Windows)",
+               "Intended Audience :: Education",
+               "Intended Audience :: Science/Research",
+               "License :: OSI Approved :: MIT License",
+               "Natural Language :: English",
+               "Operating System :: MacOS",
+               "Operating System :: Microsoft :: Windows",
+               "Operating System :: POSIX",
+               "Programming Language :: Cython",
+               "Programming Language :: Python :: 3.5",
+               "Programming Language :: Python :: 3.6",
+               "Programming Language :: Python :: 3.7",
+               "Programming Language :: Python :: Implementation :: CPython",
+               "Topic :: Scientific/Engineering :: Physics",
+               "Topic :: Software Development :: Libraries :: Python Modules",
+               ]
+
+########
+# Test #
+########
+
+class PyTest(Command):
+    """Command to start tests running the script: run_tests.py"""
+    user_options = []
+
+    description = "Execute the unittests"
+
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        import subprocess
+        errno = subprocess.call([sys.executable, 'run_tests.py'])
+        if errno != 0:
+            raise SystemExit(errno)
+
+
+# ################### #
+# build_doc command   #
+# ################### #
+
+if sphinx is None:
+    class SphinxExpectedCommand(Command):
+        """Command to inform that sphinx is missing"""
+        user_options = []
+
+        def initialize_options(self):
+            pass
+
+        def finalize_options(self):
+            pass
+
+        def run(self):
+            raise RuntimeError(
+                'Sphinx is required to build or test the documentation.\n'
+                'Please install Sphinx (http://www.sphinx-doc.org).')
+
+
+if sphinx is not None:
+    class BuildDocCommand(BuildDoc):
+        """Command to build documentation using sphinx.
+
+        Project should have already be built.
+        """
+
+        def run(self):
+            # make sure the python path is pointing to the newly built
+            # code so that the documentation is built on this and not a
+            # previously installed version
+
+            build = self.get_finalized_command('build')
+            sys.path.insert(0, os.path.abspath(build.build_lib))
+
+            # Build the Users Guide in HTML and TeX format
+            for builder in ['html', 'latex']:
+                self.builder = builder
+                self.builder_target_dir = os.path.join(self.build_dir, builder)
+                self.mkpath(self.builder_target_dir)
+                BuildDoc.run(self)
+            sys.path.pop(0)
+
+else:
+    BuildDocCommand = SphinxExpectedCommand
+
+
+# ############################# #
+# numpy.distutils Configuration #
+# ############################# #
+
+def configuration(parent_package='', top_path=None):
+    """Recursive construction of package info to be used in setup().
+
+    See http://docs.scipy.org/doc/numpy/reference/distutils.html#numpy.distutils.misc_util.Configuration
+    """
+    try:
+        from numpy.distutils.misc_util import Configuration
+    except ImportError:
+        raise ImportError(
+            "To install this package, you must install numpy first\n"
+            "(See https://pypi.python.org/pypi/numpy)")
+    config = Configuration(None, parent_package, top_path)
+    config.set_options(
+        ignore_setup_xxx_py=True,
+        assume_default_configuration=True,
+        delegate_options_to_subpackages=True,
+        quiet=True)
+    config.add_subpackage(PROJECT)
+    return config
+
+# ############## #
+# Compiler flags #
+# ############## #
+
+
+class Build(_build):
+    """Command to support more user options for the build."""
+
+    user_options = [
+        ('no-openmp', None,
+         "do not use OpenMP for compiled extension modules"),
+        ('openmp', None,
+         "use OpenMP for the compiled extension modules"),
+        ('no-cython', None,
+         "do not compile Cython extension modules (use default compiled c-files)"),
+        ('force-cython', None,
+         "recompile all Cython extension modules"),
+    ]
+    user_options.extend(_build.user_options)
+
+    boolean_options = ['no-openmp', 'openmp', 'no-cython', 'force-cython']
+    boolean_options.extend(_build.boolean_options)
+
+    def initialize_options(self):
+        _build.initialize_options(self)
+        self.no_openmp = None
+        self.openmp = None
+        self.no_cython = None
+        self.force_cython = None
+
+    def finalize_options(self):
+        _build.finalize_options(self)
+        self.finalize_cython_options(min_version='0.21.1')
+        self.finalize_openmp_options()
+
+    def _parse_env_as_bool(self, key):
+        content = os.environ.get(key, "")
+        value = content.lower()
+        if value in ["1", "true", "yes", "y"]:
+            return True
+        if value in ["0", "false", "no", "n"]:
+            return False
+        if value in ["none", ""]:
+            return None
+        msg = "Env variable '%s' contains '%s'. But a boolean or an empty \
+            string was expected. Variable ignored."
+        logger.warning(msg, key, content)
+        return None
+
+    def finalize_openmp_options(self):
+        """Check if extensions must be compiled with OpenMP.
+
+        The result is stored into the object.
+        """
+        if self.openmp:
+            use_openmp = True
+        elif self.no_openmp:
+            use_openmp = False
+        else:
+            env_force_cython = self._parse_env_as_bool("WITH_OPENMP")
+            if env_force_cython is not None:
+                use_openmp = env_force_cython
+            else:
+                # Use it by default
+                use_openmp = True
+
+        if use_openmp:
+            if platform.system() == "Darwin":
+                # By default Xcode5 & XCode6 do not support OpenMP, Xcode4 is OK.
+                osx = tuple([int(i) for i in platform.mac_ver()[0].split(".")])
+                if osx >= (10, 8):
+                    logger.warning("OpenMP support ignored. Your platform does not support it.")
+                    use_openmp = False
+
+        # Remove attributes used by distutils parsing
+        # use 'use_openmp' instead
+        del self.no_openmp
+        del self.openmp
+        self.use_openmp = use_openmp
+
+    def finalize_cython_options(self, min_version=None):
+        """
+        Check if cythonization must be used for the extensions.
+
+        The result is stored into the object.
+        """
+
+        if self.force_cython:
+            use_cython = "force"
+        elif self.no_cython:
+            use_cython = "no"
+        else:
+            env_force_cython = self._parse_env_as_bool("FORCE_CYTHON")
+            env_with_cython = self._parse_env_as_bool("WITH_CYTHON")
+            if env_force_cython is True:
+                use_cython = "force"
+            elif env_with_cython is True:
+                use_cython = "yes"
+            elif env_with_cython is False:
+                use_cython = "no"
+            else:
+                # Use it by default
+                use_cython = "yes"
+
+        if use_cython in ["force", "yes"]:
+            try:
+                import Cython.Compiler.Version
+                if min_version and Cython.Compiler.Version.version < min_version:
+                    msg = "Cython version is too old. At least version is %s \
+                        expected. Cythonization is skipped."
+                    logger.warning(msg, str(min_version))
+                    use_cython = "no"
+            except ImportError:
+                msg = "Cython is not available. Cythonization is skipped."
+                logger.warning(msg)
+                use_cython = "no"
+
+        # Remove attribute used by distutils parsing
+        # use 'use_cython' and 'force_cython' instead
+        del self.no_cython
+        self.force_cython = use_cython == "force"
+        self.use_cython = use_cython in ["force", "yes"]
+
+
+################################################################################
+# Debian source tree
+################################################################################
+
+
+class sdist_debian(sdist):
+    """
+    Tailor made sdist for debian
+    * remove auto-generated doc
+    * remove cython generated .c files
+    * remove cython generated .cpp files
+    * remove .bat files
+    * include .l man files
+    """
+
+    description = "Create a source distribution for Debian (tarball, zip file, etc.)"
+
+    @staticmethod
+    def get_debian_name():
+        import version
+        name = "%s_%s" % (PROJECT, version.debianversion)
+        return name
+
+    def prune_file_list(self):
+        sdist.prune_file_list(self)
+        to_remove = ["doc/build", "doc/pdf", "doc/html", "pylint", "epydoc"]
+        print("Removing files for debian")
+        for rm in to_remove:
+            self.filelist.exclude_pattern(pattern="*", anchor=False, prefix=rm)
+
+        # this is for Cython files specifically: remove C & html files
+        search_root = os.path.dirname(os.path.abspath(__file__))
+        for root, _, files in os.walk(search_root):
+            for afile in files:
+                if os.path.splitext(afile)[1].lower() == ".pyx":
+                    base_file = os.path.join(root, afile)[len(search_root) + 1:-4]
+                    self.filelist.exclude_pattern(pattern=base_file + ".c")
+                    self.filelist.exclude_pattern(pattern=base_file + ".cpp")
+                    self.filelist.exclude_pattern(pattern=base_file + ".html")
+
+    def make_distribution(self):
+        self.prune_file_list()
+        sdist.make_distribution(self)
+        dest = self.archive_files[0]
+        dirname, basename = os.path.split(dest)
+        base, ext = os.path.splitext(basename)
+        while ext in [".zip", ".tar", ".bz2", ".gz", ".Z", ".lz", ".orig"]:
+            base, ext = os.path.splitext(base)
+        # if ext:
+        #     dest = "".join((base, ext))
+        # else:
+        #     dest = base
+        # sp = dest.split("-")
+        # base = sp[:-1]
+        # nr = sp[-1]
+        debian_arch = os.path.join(dirname, self.get_debian_name() + ".orig.tar.gz")
+        os.rename(self.archive_files[0], debian_arch)
+        self.archive_files = [debian_arch]
+        print("Building debian .orig.tar.gz in %s" % self.archive_files[0])
+
+
+# ##### #
+# setup #
+# ##### #
+
+def get_project_configuration(dry_run):
+    """Returns project arguments for setup"""
+    install_requires = [
+        # for the script launcher and pkg_resources
+        "setuptools",
+        # for io support
+        "h5py",
+        "fabio>=0.7",
+        ]
+
+    setup_requires = ["setuptools",]
+
+    # extras requirements: target 'full' to install all dependencies at once
+    full_requires = [
+
+    ]
+
+    extras_require = {
+        'full': full_requires,
+    }
+
+    package_data = {
+    }
+
+    entry_points = {
+    }
+
+    cmdclass = dict(
+        build=Build,
+        test=PyTest,
+        build_doc=BuildDocCommand,
+        debian_src=sdist_debian)
+
+    if dry_run:
+        # DRY_RUN implies actions which do not require NumPy
+        #
+        # And they are required to succeed without Numpy for example when
+        # pip is used to install tomoscan when Numpy is not yet present in
+        # the system.
+        setup_kwargs = {}
+    else:
+        config = configuration()
+        setup_kwargs = config.todict()
+
+    setup_kwargs.update(name=PROJECT,
+                        version=get_version(),
+                        url="https://gitlab.esrf.fr/tomotools/tomoscan.git",
+                        author="data analysis unit",
+                        author_email="henri.payno@esrf.fr",
+                        classifiers=classifiers,
+                        description="utilitary to access tomography data at esrf",
+                        long_description=get_readme(),
+                        install_requires=install_requires,
+                        setup_requires=setup_requires,
+                        extras_require=extras_require,
+                        cmdclass=cmdclass,
+                        package_data=package_data,
+                        zip_safe=False,
+                        entry_points=entry_points,
+                        )
+    return setup_kwargs
+
+
+def setup_package():
+    """Run setup(**kwargs)
+
+    Depending on the command, it either runs the complete setup which depends on numpy,
+    or a *dry run* setup with no dependency on numpy.
+    """
+
+    # Check if action requires build/install
+    dry_run = len(sys.argv) == 1 or (len(sys.argv) >= 2 and (
+        '--help' in sys.argv[1:] or
+        sys.argv[1] in ('--help-commands', 'egg_info', '--version',
+                        'clean', '--name')))
+
+    if dry_run:
+        # DRY_RUN implies actions which do not require dependencies, like NumPy
+        try:
+            from setuptools import setup
+            logger.info("Use setuptools.setup")
+        except ImportError:
+            from distutils.core import setup
+            logger.info("Use distutils.core.setup")
+    else:
+        try:
+            from setuptools import setup
+        except ImportError:
+            from numpy.distutils.core import setup
+            logger.info("Use numpy.distutils.setup")
+
+    setup_kwargs = get_project_configuration(dry_run)
+    setup(**setup_kwargs)
+
+
+if __name__ == "__main__":
+    setup_package()

tomoscan/.gitlab-ci.yml

+python -m unittest tomoscan.test.suite -v
\ No newline at end of file

tomoscan/esrf/__init__.py

+# coding: utf-8
+#/*##########################################################################
+# Copyright (C) 2016 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.
+#
+#############################################################################*/
+
+
+__authors__ = ["H.Payno"]
+__license__ = "MIT"
+__date__ = "09/08/2018"
+
+TYPES = ['EDF', 'HDF5']

tomoscan/esrf/hdf5scan.py

+# coding: utf-8
+#/*##########################################################################
+# Copyright (C) 2016 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.
+#
+#############################################################################*/
+
+
+__authors__ = ["H.Payno"]
+__license__ = "MIT"
+__date__ = "09/08/2018"
+
+
+from ..scanbase import TomoScanBase
+import json
+import io
+import os
+import h5py
+import numpy
+from silx.io.url import DataUrl
+from tomoscan.utils import docstring
+import logging