tomwer 0.6.0b1__tar.gz → 0.7.0__tar.gz

home/payno/.local/share/virtualenvs/test_tomwer_0_7/bin/tomwer

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+#!/home/payno/.local/share/virtualenvs/test_tomwer_0_7/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.7.0','console_scripts','tomwer'
+__requires__ = 'tomwer==0.7.0'
+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==0.7.0', 'console_scripts', 'tomwer')()
+    )

home/payno/.local/share/virtualenvs/test_tomwer_0_7/lib/python3.7/site-packages/orangecontrib/tomwer/orange/managedprocess.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__ = "22/20/2020"
+
+
+from Orange.widgets import widget
+from processview.core.superviseprocess import SuperviseProcess
+import functools
+from processview.core.manager import ProcessManager, DatasetState
+from processview.core import helpers
+
+
+class SuperviseOW(widget.OWWidget, SuperviseProcess):
+    """
+    A basic OWWidget but registered on the process manager
+    """
+
+    def __init__(self, parent, process_id=None):
+        widget.OWWidget.__init__(self, parent, process_id=process_id)
+        SuperviseProcess.__init__(self, process_id=process_id)
+        self.destroyed.connect(functools.partial(ProcessManager().unregister, self))
+
+    def setCaption(self, caption):
+        widget.OWWidget.setCaption(self, caption)
+        self.name = caption
+
+    def notify_skip(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.SKIPPED, details=details
+        )
+
+    def notify_pending(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.PENDING, details=details
+        )
+
+    def notify_succeed(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.SUCCEED, details=details
+        )
+
+    def notify_failed(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.FAILED, details=details
+        )

home/payno/.local/share/virtualenvs/test_tomwer_0_7/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.makedirs(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()