tomwer 0.2.0a1__tar.gz → 0.5.0__tar.gz

home/payno/.local/share/virtualenvs/tomwer_venv/bin/tomwer

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+#!/home/payno/.local/share/virtualenvs/tomwer_venv/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.0','console_scripts','tomwer'
+__requires__ = 'tomwer==0.5.0'
+import re
+import sys
+from pkg_resources import load_entry_point
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit(
+        load_entry_point('tomwer==0.5.0', 'console_scripts', 'tomwer')()
+    )

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/__init__.py

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+import logging
+
+# orange_logger = logging.getLogger('Orange.canvas')
+
+fabio_logger = logging.getLogger('fabio.edfimage')
+fabio_logger.setLevel(logging.WARNING)

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/orange/settings.py

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+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 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__ = "26/10/2018"
+
+from Orange.widgets import settings
+
+
+class CallbackSettingsHandler(settings.SettingsHandler):
+    """
+    Settings handler used to call some callback before packing data (so before)
+    saving orange :class:`Setting`
+    """
+    def __init__(self):
+        super(CallbackSettingsHandler, self).__init__()
+        self.__callbacks = []
+
+    def addCallback(self, _callback):
+        self.__callbacks.append(_callback)
+
+    def removeCallback(self, callback):
+        self.__callbacks.remove(callback)
+    
+    def pack_data(self, widget):
+        for callback in self.__callbacks:
+            callback()
+        return super(CallbackSettingsHandler, self).pack_data(widget)

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/setup.py

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+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 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__ = "05/07/2017"
+
+
+from numpy.distutils.misc_util import Configuration
+
+
+def configuration(parent_package='', top_path=None):
+    config = Configuration('tomwer', parent_package, top_path)
+    config.add_subpackage('widgets')
+    config.add_subpackage('test')
+
+    return config
+
+
+if __name__ == "__main__":
+    from numpy.distutils.core import setup
+    setup(configuration=configuration)

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/test/TestAcquisition.py

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+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2016 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.
+#
+# ###########################################################################*/
+"""Full tomwer test suite.
+
+"""
+
+__authors__ = ["H.Payno"]
+__license__ = "MIT"
+__date__ = "19/01/2017"
+
+import logging
+import os
+import shutil
+
+from tomwer.core.scan.edfscan import EDFTomoScan
+from silx.gui import qt
+
+from tomwer.test.utils import UtilsTest
+
+logger = logging.getLogger(__name__)
+
+
+class Simulation(qt.QThread):
+    """Simulation is a simple class able to simulate an acquisition by copying
+    files on a targetted directory.
+
+    :param str: targetdir the folder where the acquisition is stored
+    :param str: manipulationId the id of the simulation we want to simulate
+    :param str: finalState when launched, the state to reach before stopping
+
+    :warning: the targetted directory won't be removed or cleaned during class
+        destruction. This is to be managed by callers.
+    """
+
+    advancement = {
+        'not started': -1,
+        'starting-s0': 0,
+        'starting-s1': 1,
+        'acquisitionRunning': 2,
+        'acquisitionDone': 3,
+        'reconstructionLaunched': 4}
+    sigAdvancementChanged = qt.Signal(int)
+
+    __definedDataset = ['test01', 'test10']
+
+    def __init__(self, targetdir, manipulationId, finalState=4):
+        assert(type(manipulationId) is str)
+        assert(type(targetdir) is str)
+        assert(manipulationId in self.__definedDataset)
+        super(Simulation, self).__init__()
+
+        self.targetdir = targetdir
+        self.outputFolder = os.path.sep.join((targetdir, manipulationId))
+        self.finalState = finalState
+        self.currentState = 'not started'
+        self._createFinalXML = False
+        self.originalFolder, self.nbSlices, self.manipulationId = \
+            self.__getOriginalDataSet(manipulationId)
+        self.stopFileCreationForRunningState = int(self.nbSlices/2)
+        self.srcPattern = None
+        self.destPattern = None
+
+    def __getOriginalDataSet(self, dataSetID):
+        """Return paths to the requested scan
+        """
+        assert(dataSetID in self.__definedDataset)
+        dataDir = UtilsTest.getEDFDataset(dataSetID)
+
+        assert(os.path.isdir(dataDir))
+        assert(os.path.isfile(os.path.join(dataDir, dataSetID + ".info")))
+        slices = EDFTomoScan(dataDir).projections
+        nbSlices = len(slices)
+        manipulationID = dataSetID
+
+        return dataDir, nbSlices, manipulationID
+
+    def advanceTo(self, state):
+        """Reset the new advancement targetted
+
+        :param str state: the new state to reach when run will be executed
+        """
+        assert(state in Simulation.advancement)
+        assert(type(state) is str)
+        self.finalState = Simulation.advancement[state]
+
+    def setSrcDestPatterns(self, srcPattern, destPattern):
+        """
+        If setted, will set the .info and .xml files into a different folder
+        """
+        self.srcPattern = srcPattern
+        self.destPattern = destPattern
+        if srcPattern is not None or destPattern is not None:
+            assert(os.path.isdir(srcPattern))
+            assert(os.path.isdir(destPattern))
+            targettedFolder = self.outputFolder.replace(self.srcPattern, self.destPattern, 1)
+            if not os.path.isdir(targettedFolder):
+                os.mkdir(targettedFolder)
+
+    def __shouldExecStep(self, step):
+        """Return True if the thread should exec this step to advance taking
+        into consideration is current state and his final state
+        """
+        return self.finalState >= self.advancement[step] and \
+            (Simulation.advancement[self.currentState] +1 == self.advancement[step])
+
+    def run(self):
+        """Main function, run the acquisition through all states until
+        finalState is reached
+        """
+        if self.__shouldExecStep('starting-s0') is True:
+            logger.info('starting-s0')
+            self._startAcquisition()
+            self.currentState = 'starting-s0'
+            self.signalCurrentState()
+
+        if self.__shouldExecStep('starting-s1') is True:
+            self.copyInitialFiles()
+            logger.info('starting-s1')
+            self.currentState = 'starting-s1'
+            self.signalCurrentState()
+
+        if self.__shouldExecStep('acquisitionRunning') is True:
+            self._copyScans((0,
+                             self.stopFileCreationForRunningState))
+            logger.info('acquisitionRunning')
+            self.currentState = 'acquisitionRunning'
+            self.signalCurrentState()
+
+        if self.__shouldExecStep('acquisitionDone') is True:
+            self._copyScans((self.stopFileCreationForRunningState,
+                             self.nbSlices))
+            if self._createFinalXML is True:
+                inputXMLFile = os.path.join(self.originalFolder, self.manipulationId + '.xml')
+                assert(os.path.isfile(inputXMLFile))
+                ouputXMLFile = os.path.join(self.outputFolder, self.manipulationId + '.xml')
+                shutil.copyfile(inputXMLFile, ouputXMLFile)
+
+            logger.info('acquisitionDone')
+            self.currentState = 'acquisitionDone'
+            self.signalCurrentState()
+
+    def signalCurrentState(self):
+        """Signal the actual state of the simulation
+        """
+        self.sigAdvancementChanged.emit(self.currentState)
+
+    def _startAcquisition(self):
+        """create needed data dir
+        """
+        for newFolder in (self.targetdir, self.outputFolder):
+            if not os.path.exists(self.outputFolder):
+                os.makedirs(self.outputFolder)
+
+    def _copyScans(self, _slicesRange):
+        """copy the .edf file from the original directory to the outputFolder
+
+        :_slicesRange tuple: the _range of slices data we want to copy
+        """
+        logger.info('copying files from %s to %s' % (_slicesRange[0], _slicesRange[1]))
+        for iSlice in list(range(_slicesRange[0], _slicesRange[1])):
+            filename = "".join((self.manipulationId, format(iSlice, '04d'), '.edf'))
+            srcFile = os.path.join(self.originalFolder, filename)
+            outputFile = os.path.join(self.outputFolder, filename)
+            assert(os.path.isfile(srcFile))
+            assert(os.path.isdir(self.outputFolder))
+            shutil.copyfile(srcFile, outputFile)
+
+    def copyInitialFiles(self):
+        """copy the .info file
+        """
+        assert(os.path.isdir(self.originalFolder))
+        logger.info('copying initial files (.info, .xml...) from %s to %s' % (self.originalFolder, self.manipulationId))
+        for extension in ('.info', '.db', '.cfg'):
+            filename = "".join((self.manipulationId, extension))
+            srcFile = os.path.join(self.originalFolder, filename)
+
+            targettedFolder = self.outputFolder
+            if self.srcPattern is not None or self.destPattern is not None:
+                targettedFolder = self.outputFolder.replace(self.srcPattern, self.destPattern, 1)
+            assert(os.path.isfile(srcFile))
+            assert(os.path.isdir(targettedFolder))
+            assert (os.path.isdir(self.originalFolder))
+            shutil.copy2(srcFile, targettedFolder)
+
+    def createFinalXML(self, val):
+        """If activated, once all the file will be copied, this will create
+        an .xml file into the output directory
+        """
+        self._createFinalXML = val
+
+    def createParFile(self):
+        pass
+
+    def createReconstructedFile(self):
+        pass
+
+    def createOARJob(self):
+        pass
+
+    def createDark(self):
+        pass
+
+    def createJPG(self):
+        pass
+
+    def createVolfloat(self):
+        pass
+
+    def createVolraw(self):
+        pass
+
+    def __createFileTo(self, filePath):
+        assert(type(filePath) is str)
+        open(filePath, 'a').close()
+
+
+def main():
+    import time
+    _qapp = qt.QApplication.instance() or qt.QApplication([])
+
+    inputdir = '/tmp'
+    manipulationId = 'test10'
+    s = Simulation(inputdir, manipulationId, finalState=Simulation.advancement['acquisitionRunning'])
+    s.start()
+    while(not s.isFinished()):
+        _qapp.processEvents()
+        time.sleep(1)
+
+
+if __name__ == '__main__':
+    main()

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/test/__init__.py

@@ -0,0 +1,59 @@
+# 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__ = "15/05/2017"
+
+import unittest
+from . import test_axis_reconstruction
+from . import test_scanlist_samplemoved
+from . import test_scanlist_ftserie
+from . import test_dark_flat_field
+from . import test_lamino
+from . import test_nabu
+from . import test_owidgets
+from . import test_dump_widget_canvas
+from . import test_folder_transfert
+from ..widgets import test as test_widgets
+
+
+def suite(loader=None, pattern='test*.py'):
+    test_suite = unittest.TestSuite()
+    test_suite.addTest(test_axis_reconstruction.suite())
+    test_suite.addTest(test_widgets.suite())
+    test_suite.addTest(test_scanlist_ftserie.suite())
+    test_suite.addTest(test_dark_flat_field.suite())
+    test_suite.addTest(test_lamino.suite())
+    test_suite.addTest(test_nabu.suite())
+    test_suite.addTest(test_scanlist_samplemoved.suite())
+    test_suite.addTest(test_owidgets.suite())
+    test_suite.addTest(test_dump_widget_canvas.suite())
+    test_suite.addTests(test_folder_transfert.suite())
+    return test_suite
+
+
+if __name__ == '__main__':
+    unittest.main(defaultTest='suite')