tomwer 1.1.0rc7__tar.gz → 1.1.1__tar.gz

{tomwer-1.1.0rc7/tomwer.egg-info → tomwer-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.1.0rc7
+Version: 1.1.1
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.1.0rc7 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -190,7 +190,8 @@ class SAAxisWindow(_SAAxisWindow):
         if scan is None:
             return
         assert isinstance(scan, TomwerScanBase)
-        selected_cor_value = self.getCurrentCorValue()
+        selected_cor_value = self.getCurrentCorValue() or scan.saaxis_params.autofocus
+        # if validate is done manually then pick current cor value; else we are in 'auto mode' and get it from the autofocus.
         details = ProcessManager().get_dataset_details(
             dataset_id=scan.get_identifier(), process=self._processing_stack
         )
@@ -453,9 +454,9 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
             "data": None,
             "sa_axis_params": self._widget.getConfiguration(),
         }
-        self._ewoks_default_inputs["sa_axis_params"][
-            "autofocus_lock"
-        ] = self._widget.isAutoFocusLock()
+        self._ewoks_default_inputs["sa_axis_params"]["workflow"] = {
+            "autofocus_lock": self._widget.isAutoFocusLock(),
+        }
 
     def _raiseResults(self):
         if not self.isAutoFocusLock():

{tomwer-1.1.0rc7 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -125,7 +125,9 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
         if scan is None:
             return
         assert isinstance(scan, TomwerScanBase)
-        selected_db_value = self.getCurrentDeltaBetaValue()
+        selected_db_value = (
+            self.getCurrentDeltaBetaValue() or scan.sa_delta_beta_params.autofocus
+        )
         if selected_db_value is None:
             infos = "no selected delta / beta value. {} skip SADeltaBetaParams".format(
                 scan

{tomwer-1.1.0rc7 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/utils.py

@@ -413,6 +413,7 @@ def nabu_std_err_has_error(errs: typing.Optional[bytes]):
         return (
             "warning" in line
             or "Warning" in line
+            or "deprecated" in line
             or line.replace(" ", "") == ""
             or "unable to load" in line
         )

{tomwer-1.1.0rc7 → tomwer-1.1.1}/tomwer/version.py

@@ -77,8 +77,8 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 1
-MICRO = 0
-RELEV = "rc"  # <16
+MICRO = 1
+RELEV = "final"  # <16
 SERIAL = 7  # <16
 
 date = __date__

{tomwer-1.1.0rc7 → tomwer-1.1.1/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.1.0rc7
+Version: 1.1.1
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.1.0rc7 → tomwer-1.1.1}/tomwer.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ orangecontrib/tomwer/state_summary.py
 orangecontrib/tomwer/orange/__init__.py
 orangecontrib/tomwer/orange/managedprocess.py
 orangecontrib/tomwer/orange/settings.py
-orangecontrib/tomwer/test/TestAcquisition.py
 orangecontrib/tomwer/tutorials/EBS_tomo_listener.ows
 orangecontrib/tomwer/tutorials/__init__.py
 orangecontrib/tomwer/tutorials/cast_volume.ows
@@ -76,7 +75,6 @@ orangecontrib/tomwer/widgets/control/icons/volumeselector.png
 orangecontrib/tomwer/widgets/control/icons/volumeselector.svg
 orangecontrib/tomwer/widgets/control/icons/volumesymlink.png
 orangecontrib/tomwer/widgets/control/icons/volumesymlink.svg
-orangecontrib/tomwer/widgets/control/test/test_datalistener.py
 orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py
 orangecontrib/tomwer/widgets/debugtools/ObjectInspectorOW.py
 orangecontrib/tomwer/widgets/debugtools/__init__.py
@@ -157,12 +155,6 @@ orangecontrib/tomwer/widgets/reconstruction/icons/sadeltabeta.png
 orangecontrib/tomwer/widgets/reconstruction/icons/sadeltabeta.svg
 orangecontrib/tomwer/widgets/reconstruction/icons/tomogui.png
 orangecontrib/tomwer/widgets/reconstruction/icons/tomwer.png
-orangecontrib/tomwer/widgets/reconstruction/test/test_axis.py
-orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_widget.py
-orangecontrib/tomwer/widgets/reconstruction/test/test_saaxis.py
-orangecontrib/tomwer/widgets/test/test_conditions.py
-orangecontrib/tomwer/widgets/test/test_darkref.py
-orangecontrib/tomwer/widgets/test/test_foldertransfert.py
 orangecontrib/tomwer/widgets/visualization/DataViewerOW.py
 orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py
 orangecontrib/tomwer/widgets/visualization/LivesliceOW.py

tomwer-1.1.0rc7/orangecontrib/tomwer/test/TestAcquisition.py

@@ -1,246 +0,0 @@
-# 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.tests.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()

tomwer-1.1.0rc7/orangecontrib/tomwer/widgets/control/test/test_datalistener.py

@@ -1,135 +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__ = "28/04/2020"
-
-
-import os
-import gc
-import time
-import shutil
-import pytest
-import pickle
-import tempfile
-from glob import glob
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-from tomwer.core import settings
-from tomwer.tests.utils import skip_gui_test
-from tomwer.core.utils.scanutils import MockBlissAcquisition
-from tomwer.core.process.control.datalistener.rpcserver import BlissAcquisition
-from orangecanvas.scheme.readwrite import literal_dumps
-from orangecontrib.tomwer.widgets.control.DataListenerOW import DataListenerOW
-
-try:
-    from tomwer.synctools.rsyncmanager import RSyncManager  # noqa F401
-except ImportError:
-    has_rsync = False
-else:
-    has_rsync = RSyncManager().has_rsync()
-
-
-@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
-class TestDataListenerSynchronization(TestCaseQt):
-    """Insure synchronization is working with the orangecontrib widget"""
-
-    def setUp(self):
-        super().setUp()
-        self._src_dir = tempfile.mkdtemp()
-        self._dst_dir = tempfile.mkdtemp()
-        # mock lbsram
-        settings.mock_lsbram(True)
-        settings._set_lbsram_path(self._src_dir)
-        settings._set_dest_path(self._dst_dir)
-
-        scan_path = os.path.join(self._src_dir, "scan0000")
-        self.mock_scan = MockBlissAcquisition(
-            n_sample=1,
-            n_sequence=1,
-            n_scan_per_sequence=3,
-            n_darks=2,
-            n_flats=2,
-            output_dir=scan_path,
-        )
-
-        self.bliss_acquisition = BlissAcquisition(
-            file_path=self.mock_scan.samples[0].sample_file,
-            proposal_file=self.mock_scan.proposal_file,
-            sample_file=self.mock_scan.samples[0].sample_file,
-            entry_name="self.entry = '/1'",
-            start_time=time.ctime(),
-        )
-
-        self.widget = DataListenerOW()
-
-    def tearDown(self):
-        self.mock_scan = None
-        self.bliss_acquisition = None
-        # self.widget.activate(False)
-        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self.widget.close()
-        self.widget = None
-        shutil.rmtree(self._src_dir)
-        shutil.rmtree(self._dst_dir)
-        gc.collect()
-
-    @pytest.mark.skipif(not has_rsync, reason="rsync not installed")
-    def testSynchronization(self):
-        """Make sure the datalistener will launch a synchronization on the
-        data dir when receive it"""
-        self.assertEqual(len(os.listdir(self._dst_dir)), 0)
-        self.widget.activate(True)
-
-        self.widget.get_listening_thread()._rpc_sequence_started(
-            saving_file=self.bliss_acquisition.sample_file,
-            scan_title="toto",
-            sequence_scan_number="1",
-            proposal_file=self.bliss_acquisition.proposal_file,
-            sample_file=self.bliss_acquisition.sample_file,
-        )
-        time.sleep(1.0)
-        self.assertEqual(self.widget._get_n_scan_observe(), 1)
-        self.assertEqual(len(os.listdir(self._dst_dir)), 1)
-        self.widget.get_listening_thread()._rpc_sequence_ended(
-            saving_file=self.bliss_acquisition.sample_file,
-            sequence_scan_number="1",
-            success=True,
-        )
-        nx_pattern = os.path.join(self.mock_scan.samples[0].sample_directory, "*.nx")
-        self.assertEqual(len(glob(nx_pattern)), 0)
-        for i in range(8):
-            self.qapp.processEvents()
-            time.sleep(1.0)
-        # check .nx file has been created
-        #
-        self.assertEqual(len(glob(nx_pattern)), 1)
-
-    def testSerialization(self):
-        pickle.dumps(self.widget.get_configuration())
-
-    def testLiteralDumps(self):
-        literal_dumps(self.widget.get_configuration())