tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/synctools/test/test_scanstages.py

@@ -1,162 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017 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__ = "30/09/2019"
-
-
-import glob
-import os
-import shutil
-import tempfile
-import unittest
-from collections import namedtuple
-
-import pytest
-
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.synctools.utils.scanstages import ScanStages
-from tomwer.tests.utils import UtilsTest, skip_gui_test
-
-if skip_gui_test() is False:
-    from tomwer.synctools.rsyncmanager import RSyncManager
-
-
-_stage_desc = namedtuple(
-    "_stage_desc",
-    [
-        "n_par_file",
-        "n_edf_file",
-        "n_info_file",
-        "n_xml_file",
-        "n_vol",
-        "folder_should_exists",
-    ],
-)  # noqa
-
-
-@pytest.mark.skipif(RSyncManager().has_rsync() is False, reason="Rsync is missing")
-@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
-class TestScanStagesEDF(unittest.TestCase):
-    """
-    test the ScanStages class for edf scans
-    """
-
-    def setUp(self) -> None:
-        self.output_dir = tempfile.mkdtemp()
-        dataset = "D2_H2_T2_h_"
-        self.data_test_dir = UtilsTest.getEDFDataset(dataset)
-        self.target_dir = os.path.join(self.output_dir, dataset)
-        self.scan_stages = ScanStages(
-            scan=ScanFactory.create_scan_object(self.data_test_dir)
-        )
-
-    def tearDown(self) -> None:
-        shutil.rmtree(self.output_dir)
-
-    def testRSyncUntil(self):
-        """test the rsync_until function"""
-        ACQUI_NOT_STARTED = ScanStages.AcquisitionStage.ACQUI_NOT_STARTED
-        # ACQUI_STARTED = ScanStages.AcquisitionStage.ACQUI_STARTED
-        # ACQUI_ON_GOING = ScanStages.AcquisitionStage.ACQUI_ON_GOING
-        # ACQUI_ENDED = ScanStages.AcquisitionStage.ACQUI_ENDED
-        # RECONSTRUCTION_ADDED = ScanStages.AcquisitionStage.RECONSTRUCTION_ADDED
-        # COMPLETE = ScanStages.AcquisitionStage.COMPLETE
-
-        # tomo_n = 3605
-        stage_res = {
-            ACQUI_NOT_STARTED: _stage_desc(
-                n_par_file=0,
-                n_edf_file=0,
-                n_info_file=0,
-                n_xml_file=0,
-                n_vol=0,
-                folder_should_exists=False,
-            ),
-            # comment most of the test because take too long
-            # ACQUI_STARTED: _stage_desc(
-            #     n_par_file=0,
-            #     n_edf_file=0,
-            #     n_info_file=1,
-            #     n_xml_file=0,
-            #     n_vol=0,
-            #     folder_should_exists=True,
-            # ),
-            # ACQUI_ON_GOING: _stage_desc(
-            #     n_par_file=0,
-            #     n_edf_file=tomo_n // 2,
-            #     n_info_file=1,
-            #     n_xml_file=0,
-            #     n_vol=0,
-            #     folder_should_exists=True,
-            # ),
-            # ACQUI_ENDED: _stage_desc(
-            #     n_par_file=0,
-            #     n_edf_file=tomo_n,
-            #     n_info_file=1,
-            #     n_xml_file=1,
-            #     n_vol=0,
-            #     folder_should_exists=True,
-            # ),
-            # RECONSTRUCTION_ADDED: _stage_desc(
-            #     n_par_file=6,
-            #     n_edf_file=tomo_n,
-            #     n_info_file=2,
-            #     n_xml_file=2,
-            #     n_vol=1,
-            #     folder_should_exists=True,
-            # ),
-            # COMPLETE: _stage_desc(
-            #     n_par_file=6,
-            #     n_edf_file=3719,  # there is several ref, darks...
-            #     n_info_file=2,
-            #     n_xml_file=2,
-            #     n_vol=1,
-            #     folder_should_exists=True,
-            # ),
-        }
-        for stage, th_results in stage_res.items():
-            with self.subTest(stage=stage):
-                self.scan_stages.rsync_until(stage=stage, dest_dir=self.output_dir)
-                self.assertEqual(
-                    os.path.exists(self.target_dir), th_results.folder_should_exists
-                )
-                self.assertEqual(
-                    len(glob.glob(os.path.join(self.target_dir, "*.par"))),
-                    th_results.n_par_file,
-                )
-                self.assertEqual(
-                    len(glob.glob(os.path.join(self.target_dir, "*.edf"))),
-                    th_results.n_edf_file,
-                )
-                self.assertEqual(
-                    len(glob.glob(os.path.join(self.target_dir, "*.xml"))),
-                    th_results.n_xml_file,
-                )
-                self.assertEqual(
-                    len(glob.glob(os.path.join(self.target_dir, "*.vol"))),
-                    th_results.n_vol,
-                )

tomwer/tests/utils/__init__.py

@@ -1,247 +0,0 @@
-#!/usr/bin/python
-# coding: utf-8
-#
-#    Project: Azimuthal integration
-#             https://github.com/pyFAI/pyFAI
-#
-#    Copyright (C) 2015 European Synchrotron Radiation Facility, Grenoble, France
-#
-#    Principal author:       Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
-#
-# 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.
-
-
-__doc__ = """test module for pyFAI."""
-__authors__ = ["Jérôme Kieffer", "Valentin Valls", "Henri Payno"]
-__license__ = "MIT"
-__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "07/02/2017"
-
-import fileinput
-import logging
-import os
-import shutil
-
-from tomwer.core.utils import DownloadDataset, url_base
-
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.DEBUG)
-
-
-class UtilsTest(object):
-    """
-    Static class providing useful stuff for preparing tests.
-    """
-
-    timeout = 100  # timeout in seconds for downloading datasets.tar.bz2
-
-    def __init__(self):
-        self.installed = False
-
-    @classmethod
-    def dataDownloaded(cls, archive_folder, archive_file):
-        return cls.dataIsHere(archive_folder=archive_folder) or cls.dataIsDownloaded(
-            archive_file=archive_file
-        )
-
-    @classmethod
-    def dataIsHere(cls, archive_folder):
-        return os.path.isdir(archive_folder)
-
-    @classmethod
-    def dataIsDownloaded(cls, archive_file):
-        return os.path.isfile(archive_file)
-
-    @classmethod
-    def getEDFDataset(cls, folderID):
-        path = os.path.abspath(
-            os.path.join(cls.getDatasets(name="edf_datasets"), folderID)
-        )
-        if os.path.isdir(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing scan %s" % folderID)
-
-    @classmethod
-    def getH5Dataset(cls, folderID):
-        path = os.path.abspath(
-            os.path.join(cls.getDatasets(name="h5_datasets"), folderID)
-        )
-        if os.path.exists(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing scan %s" % folderID)
-
-    @classmethod
-    def getBlissDataset(cls, folderID):
-        path = os.path.abspath(
-            os.path.join(cls.getDatasets(name="bliss_acq"), folderID)
-        )
-        if os.path.exists(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing scan %s" % folderID)
-
-    @classmethod
-    def getRecDatasets(cls):
-        path = os.path.abspath(
-            cls.getDatasets(
-                name="rec_HA-700_45.4_136keV_BM5_burrow_GSA-1-44_021_avg-2_"
-            )
-        )
-        if os.path.exists(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing rec")
-
-    @classmethod
-    def getOrangeTestFile(cls, folderID):
-        path = os.path.abspath(os.path.join(cls.getOrangeTestFiles(), folderID))
-        if os.path.isfile(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing scan %s" % folderID)
-
-    @classmethod
-    def getOrangeTestFiles(cls):
-        return cls.getDatasets(name="orangetestfiles")
-
-    @classmethod
-    def getOrangeExecTestFile(cls, folderID):
-        path = os.path.abspath(os.path.join(cls.getOrangeExecTestFiles(), folderID))
-        if os.path.isfile(path):
-            return path
-        else:
-            raise RuntimeError("Coul'd find folder containing scan %s" % folderID)
-
-    @classmethod
-    def getOrangeExecTestFiles(cls):
-        return cls.getDatasets(name="ows_test_exec")
-
-    @classmethod
-    def getDatasets(cls, name="datasets"):
-        """
-        Downloads the requested image from Forge.EPN-campus.eu
-
-        @param: name of the image.
-        For the RedMine forge, the filename contains a directory name that is removed
-        @return: full path of the locally saved file
-        """
-        archive_file = name + ".tar.bz2"
-        archive_folder = "".join((os.path.dirname(__file__), "/" + name + "/"))
-        archive_file = os.path.join(archive_folder, archive_file)
-
-        # download if needed
-        if not cls.dataDownloaded(
-            archive_folder=archive_folder, archive_file=archive_file
-        ):
-            DownloadDataset(
-                dataset=os.path.basename(archive_file),
-                output_folder=archive_folder,
-                timeout=cls.timeout,
-            )
-
-            if not os.path.isfile(archive_file):
-                raise RuntimeError(
-                    "Could not automatically download test images %s!\n"
-                    "If you are behind a firewall, please set both environment "
-                    "variable http_proxy and https_proxy. "
-                    "This even works under windows ! \n Otherwise please try "
-                    "to download the images manually from \n%s/%s"
-                    % (archive_file, url_base, archive_file)
-                )
-
-        # decompress if needed
-        if os.path.isfile(archive_file):
-            logger.info("decompressing %s." % archive_file)
-            outdir = "".join((os.path.dirname(__file__)))
-            shutil.unpack_archive(archive_file, extract_dir=outdir, format="bztar")
-            os.remove(archive_file)
-        else:
-            logger.info("not trying to decompress it")
-        return archive_folder
-
-    @classmethod
-    def hasInternalTest(cls, dataset):
-        """
-        The id of the internal test is to have some large scan accessible
-        which are stored locally. This should be used only for unit test that
-        can be skipped
-        """
-        if "TOMWER_ADDITIONAL_TESTS_DIR" not in os.environ:
-            return False
-        else:
-            dir_ = os.path.join(os.environ["TOMWER_ADDITIONAL_TESTS_DIR"], dataset)
-        return os.path.isdir(dir_)
-
-    @classmethod
-    def getInternalTestDir(cls, dataset):
-        if cls.hasInternalTest(dataset) is False:
-            return None
-        else:
-            return os.path.join(os.environ["TOMWER_ADDITIONAL_TESTS_DIR"], dataset)
-
-
-def rebaseParFile(filePath, scanOldPath, scanNewPath):
-    """
-    Change some variables on the oar file to rebase it like if it was acquire
-    in scanNewPath and allow pyhst reconstruction.
-    """
-    assert os.path.isfile(filePath)
-
-    with fileinput.FileInput(filePath, inplace=True, backup=".bak") as file:
-        for line in file:
-            print(line.replace(scanOldPath, scanNewPath))
-
-
-def rebaseAcquisition(src, dst):
-    """Copy the acquisition from src to dst by changing the ID of the acquisition
-    on all files and sub-folders"""
-
-    def copyDir(_dirSrc, _dirDst, srcID, dstID):
-        assert os.path.exists(_dirDst) is False
-        os.makedirs(_dirDst)
-        for _file in os.listdir(_dirSrc):
-            _filePath = os.path.join(_dirSrc, _file)
-            if os.path.isdir(_filePath):
-                copyDir(
-                    _dirSrc=_filePath,
-                    _dirDst=os.path.join(_dirDst, _file.replace(srcID, dstID, 1)),
-                    srcID=srcID,
-                    dstID=dstID,
-                )
-            else:
-                shutil.copyfile(
-                    src=_filePath,
-                    dst=os.path.join(_dirDst, _file.replace(srcID, dstID, 1)),
-                )
-
-    # cp folder then copy files
-    assert os.path.isdir(src)
-    srcID = os.path.basename(src)
-    dstID = os.path.basename(dst)
-    copyDir(_dirSrc=src, _dirDst=dst, srcID=srcID, dstID=dstID)
-
-
-def skip_gui_test():
-    return os.environ.get("_TOMWER_NO_GUI_UNIT_TESTS", "False") == "True"
-
-
-def skip_orange_workflows_test():
-    return os.environ.get("_TOMWER_NO_ORANGE_WORKFLOWS_UNIT_TESTS", "False") == "True"

tomwer/tests/utils/utilstest.py

@@ -1,220 +0,0 @@
-# coding: utf-8
-#
-#    Copyright (C) 2012-2016 European Synchrotron Radiation Facility, Grenoble, France
-#
-#    Principal author:       Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
-#
-# 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.
-#
-"bunch of utility function/static classes to handle testing environment"
-
-__author__ = "Jérôme Kieffer"
-__contact__ = "jerome.kieffer@esrf.eu"
-__license__ = "MIT"
-__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "24/01/2018"
-
-import getpass
-import logging
-import os
-import shutil
-import sys
-import tempfile
-import threading
-import unittest
-from argparse import ArgumentParser
-
-from silx.resources import ExternalResources
-
-PACKAGE = "pyFAI"
-DATA_KEY = "PYFAI_DATA"
-
-logger = logging.getLogger(__name__)
-
-TEST_HOME = os.path.dirname(os.path.abspath(__file__))
-
-
-def copy(infile, outfile):
-    "link or copy file according to the OS"
-    if "link" in dir(os):
-        os.link(infile, outfile)
-    else:
-        shutil.copy(infile, outfile)
-
-
-class TestContext(object):
-    """
-    Class providing useful stuff for preparing tests.
-    """
-
-    def __init__(self):
-        self.options = None
-        self.timeout = 60  # timeout in seconds for downloading images
-        self.url_base = "http://ftp.edna-site.org/pyFAI/testimages"
-        self.resources = ExternalResources(
-            PACKAGE, timeout=self.timeout, env_key=DATA_KEY, url_base=self.url_base
-        )
-        self.sem = threading.Semaphore()
-        self.recompiled = False
-        self.reloaded = False
-        self.name = PACKAGE
-        self.script_dir = None
-        self.installed = False
-
-        self.download_images = self.resources.download_all
-        self.getimage = self.resources.getfile
-        self.low_mem = bool(os.environ.get("PYFAI_LOW_MEM"))
-        self.opencl = bool(os.environ.get("PYFAI_OPENCL", True))
-
-        self._tempdir = None
-
-    def forceBuild(self, remove_first=True):
-        """
-        Force the recompilation of pyFAI
-
-        Nonesense, kept for legacy reasons
-        """
-        return
-
-    def get_options(self):
-        """
-        Parse the command line to analyse options ... returns options
-        """
-        if self.options is None:
-            parser = ArgumentParser(usage="Tests for %s" % self.name)
-            parser.add_argument(
-                "-d",
-                "--debug",
-                dest="debug",
-                help="run in debugging mode",
-                default=False,
-                action="store_true",
-            )
-            parser.add_argument(
-                "-i",
-                "--info",
-                dest="info",
-                help="run in more verbose mode ",
-                default=False,
-                action="store_true",
-            )
-            parser.add_argument(
-                "-f",
-                "--force",
-                dest="force",
-                help="force the build of the library",
-                default=False,
-                action="store_true",
-            )
-            parser.add_argument(
-                "-r",
-                "--really-force",
-                dest="remove",
-                help="remove existing build and force the build of the library",
-                default=False,
-                action="store_true",
-            )
-            parser.add_argument(dest="args", type=str, nargs="*")
-            self.options = parser.parse_args([])
-        return self.options
-
-    def get_test_env(self):
-        """
-        Returns an associated environment with a working project.
-        """
-        env = dict((str(k), str(v)) for k, v in os.environ.items())
-        env["PYTHONPATH"] = os.pathsep.join(sys.path)
-        return env
-
-    def script_path(self, script_name, module_name):
-        """Returns the script path according to it's location"""
-        if self.installed:
-            script = self.get_installed_script_path(script_name)
-        else:
-            import importlib
-
-            module = importlib.import_module(module_name)
-            script = module.__file__
-        return script
-
-    def get_installed_script_path(self, script):
-        """
-        Returns the path of the executable and the associated environment
-
-        In Windows, it checks availability of script using .py .bat, and .exe
-        file extensions.
-        """
-        if sys.platform == "win32":
-            available_extensions = [".py", ".bat", ".exe"]
-        else:
-            available_extensions = [""]
-
-        paths = os.environ.get("PATH", "").split(os.pathsep)
-        for base in paths:
-            # clean up extra quotes from paths
-            if base.startswith('"') and base.endswith('"'):
-                base = base[1:-1]
-            for file_extension in available_extensions:
-                script_path = os.path.join(base, script + file_extension)
-                print(script_path)
-                if os.path.exists(script_path):
-                    # script found
-                    return script_path
-        # script not found
-        logger.warning("Script '%s' not found in paths: %s", script, ":".join(paths))
-        script_path = script
-        return script_path
-
-    def _initialize_tmpdir(self):
-        """Initialize the temporary directory"""
-        if not self._tempdir:
-            with self.sem:
-                if not self._tempdir:
-                    self._tempdir = tempfile.mkdtemp(
-                        "_" + getpass.getuser(), self.name + "_"
-                    )
-
-    @property
-    def tempdir(self):
-        if not self._tempdir:
-            self._initialize_tmpdir()
-        return self._tempdir
-
-    def clean_up(self):
-        """Removes the temporary directory (and all its content !)"""
-        with self.sem:
-            if not self._tempdir:
-                return
-            if not os.path.isdir(self._tempdir):
-                return
-            for root, dirs, files in os.walk(self._tempdir, topdown=False):
-                for name in files:
-                    os.remove(os.path.join(root, name))
-                for name in dirs:
-                    os.rmdir(os.path.join(root, name))
-            os.rmdir(self._tempdir)
-            self._tempdir = None
-
-
-UtilsTest = TestContext()
-"""Singleton containing util context of whole the tests"""
-
-
-class ParametricTestCase(unittest.TestCase):
-    pass

tomwer-1.2.1-py3.11-nspkg.pth

@@ -1 +0,0 @@
-import sys, types, os;has_mfs = sys.version_info > (3, 5);p = os.path.join(sys._getframe(1).f_locals['sitedir'], *('orangecontrib',));importlib = has_mfs and __import__('importlib.util');has_mfs and __import__('importlib.machinery');m = has_mfs and sys.modules.setdefault('orangecontrib', importlib.util.module_from_spec(importlib.machinery.PathFinder.find_spec('orangecontrib', [os.path.dirname(p)])));m = m or sys.modules.setdefault('orangecontrib', types.ModuleType('orangecontrib'));mp = (m or []) and m.__dict__.setdefault('__path__',[]);(p not in mp) and mp.append(p)