tomwer 0.5.0b1__tar.gz → 0.5.2__tar.gz

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

@@ -1,6 +1,6 @@
 #!/home/payno/.local/share/virtualenvs/tomwer_venv/bin/python
-# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.0b1','console_scripts','tomwer'
-__requires__ = 'tomwer==0.5.0b1'
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.2','console_scripts','tomwer'
+__requires__ = 'tomwer==0.5.2'
 import re
 import sys
 from pkg_resources import load_entry_point
@@ -8,5 +8,5 @@ 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==0.5.0b1', 'console_scripts', 'tomwer')()
+        load_entry_point('tomwer==0.5.2', 'console_scripts', 'tomwer')()
     )

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

@@ -37,6 +37,7 @@ from . import test_nabu
 from . import test_owidgets
 from . import test_dump_widget_canvas
 from . import test_folder_transfert
+from . import test_workflow_volume
 from ..widgets import test as test_widgets
 
 
@@ -52,6 +53,7 @@ def suite(loader=None, pattern='test*.py'):
     test_suite.addTest(test_owidgets.suite())
     test_suite.addTest(test_dump_widget_canvas.suite())
     test_suite.addTests(test_folder_transfert.suite())
+    test_suite.addTests(test_widgets.suite())
     return test_suite
 
 

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

@@ -37,7 +37,7 @@ from tomwer.core.utils.scanutils import MockHDF5, MockEDF
 from silx.gui.utils.testutils import SignalListener
 from tomwer.core.process.reconstruction.darkref.darkrefs import DarkRefs
 from tomwer.core.process.reconstruction.axis.axis import AxisProcess
-from tomwer.core.process.reconstruction.nabu import Nabu
+from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSlices
 import tempfile
 import shutil
 import time
@@ -440,8 +440,8 @@ class TestAxisFtseriesHDF5(OrangeWorflowTest):
 
         # 4.2 make sure Nabu process has been registered in tomwer_processes.h5
         for scan in self.scans:
-            nabu_proc_rec = Nabu.get_process_frm_process_file(process_file=scan.process_file,
-                                                              entry=scan.entry)
+            nabu_proc_rec = NabuSlices.get_process_frm_process_file(process_file=scan.process_file,
+                                                                    entry=scan.entry)
             self.assertTrue(nabu_proc_rec is not None)
 
 

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

@@ -159,16 +159,7 @@ class TestCopyNFolder(OrangeWorflowTest):
             time.sleep(0.2)
 
         self.assertTrue(self.dataHasBeenCopied())
-
-        signal_manager = self.canvas_window.current_document().scheme().signal_manager
-        timeout = self.TIMEOUT_TEST
-        while timeout > 0 and self.app.hasPendingEvents():
-            timeout = timeout - 0.2
-            self.app.processEvents()
-            print('blocking_nodes:', signal_manager.pending_nodes())
-            time.sleep(0.2)
-        if timeout <= 0.0:
-            raise TimeoutError('Loop infinitely on some qt event...')
+        self.app.processEvents()
 
     def outpudirIsEmpty(self):
         return len(os.listdir(self.outputdir)) == 0

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

@@ -0,0 +1,96 @@
+# 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__ = "13/08/2020"
+
+import logging
+import unittest
+from tomwer.test.utils import skip_gui_test
+from orangecontrib.tomwer.test.utils import OrangeWorflowTest
+
+logging.disable(logging.INFO)
+
+
+@unittest.skipIf(skip_gui_test(), reason='skip gui test')
+class TestVolumeWidget(OrangeWorflowTest):
+    """Insure connection of the following widgets:
+
+    - NabuOW
+    - NabuVolumeOW
+    - VolumeViewerOW
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        OrangeWorflowTest.setUpClass()
+        # create widgets
+        cls.nabuSlice = cls.addWidget(cls,
+                                      'orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW')
+        cls.nabuVolume = cls.addWidget(cls,
+                                      'orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW')
+        cls.volumeViewer = cls.addWidget(cls,
+                                         'orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW')
+
+        # Let Orange process events (node creations)
+        cls.processOrangeEvents(cls)
+
+        # linking the workflow
+        cls.link(cls, cls.nabuSlice, "data", cls.nabuVolume, "data")
+        cls.link(cls, cls.nabuVolume, "data", cls.volumeViewer, "data")
+
+        # Let Orange process events (node creations)
+        cls.processOrangeEvents(cls)
+
+        # getting the widgets
+        cls.nabuSliceWidget = cls.getWidgetForNode(cls, cls.nabuSlice)
+        cls.nabuVolumeWidget = cls.getWidgetForNode(cls, cls.nabuVolume)
+        cls.volumeViewerWidget = cls.getWidgetForNode(cls, cls.volumeViewer)
+
+    @classmethod
+    def tearDownClass(cls):
+        for node in (cls.nabuSlice, cls.nabuVolume, cls.volumeViewer):
+            cls.removeNode(cls, node)
+        del cls.nabuSlice
+        del cls.nabuVolume
+        del cls.volumeViewer
+        OrangeWorflowTest.tearDownClass()
+
+    def testWorkflow(self):
+        """Test construction is possible (in fact test is on the setUpClass
+        part for now)"""
+        pass
+
+
+def suite():
+    test_suite = unittest.TestSuite()
+    for ui in (TestVolumeWidget,):
+        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
+    return test_suite
+
+
+if __name__ == '__main__':
+    unittest.main(defaultTest="suite")

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

@@ -312,7 +312,8 @@ class OrangeWorkflowMixIn:
         self.canvas_window.closeEvent = self.closeEventMonkeyPatch
         self.canvas_window.close()
         self.app.removePostedEvents(signal_manager)
-        del self.canvas_window
+        if hasattr(self, 'canvas_window'):
+            del self.canvas_window
         gc.collect()
         self.app.quit()
 

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

@@ -37,6 +37,7 @@ def widget_discovery(discovery):
         "orangecontrib.tomwer.widgets.control",
         "orangecontrib.tomwer.widgets.reconstruction",
         "orangecontrib.tomwer.widgets.visualization",
+        "orangecontrib.tomwer.widgets.other",
     ]
     for pkg in pkgs:
         discovery.process_category_package(pkg, distribution=dist)
@@ -47,21 +48,20 @@ WIDGET_HELP_PATH = (
     # You still need to build help pages using
     # make htmlhelp
     # inside doc folder
-    ("{DEVELOP_ROOT}/build/sphinx/htmlhelp/index.html", None),
+    ("/build/sphinx/htmlhelp/index.html", None),
     #
     # Documentation included in wheel
     # Correct DATA_FILES entry is needed in setup.py and documentation has to be built
     # # before the wheel is created.
     ("{}/help/tomwer/index.html".format(sysconfig.get_path("data")), None),
 
-    ("http://www.silx.org/pub/doc/tomwer/.htmlhelp/0.4/", ""),
+    ("http://www.silx.org/pub/doc/tomwer/htmlhelp/0.5/", ""),
 )
 
 
-
-
 import unittest
 
+
 def suite():
 
     test_suite = unittest.TestSuite()

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

@@ -82,7 +82,7 @@ class DataListOW(widget.OWWidget, OWClient):
         self.widget._sendButton.clicked.connect(self._sendList)
 
         # expose API
-        self.size = self.widget.size
+        self.n_scan = self.widget.n_scan
 
         # alias used for the 'simple workflow' for now
         self.start = self._sendList
@@ -98,19 +98,10 @@ class DataListOW(widget.OWWidget, OWClient):
             self.Outputs.data_out.send(scan_)
 
         for d in self.widget.datalist.items:
-            if '@' in d:
-                entry, scan_file_or_dir = d.split('@')
+            if d in self.widget.datalist._scanIDs:
+                send(scan_=self.widget.datalist._scanIDs[d])
             else:
-                entry = None,
-                scan_file_or_dir = d
-            try:
-                scan = ScanFactory.create_scan_object(scan_file_or_dir,
-                                                      entry=entry)
-            except Exception as e:
-                logger.error("Fail to create an instance of TomoBase from %s." \
-                             " Reason is %s" % (d, str(e)))
-            else:
-                send(scan_=scan)
+                logger.error('unable to retrieve scan {}'.format(d))
 
     @Inputs.data_in
     def add(self, scan):

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

@@ -29,7 +29,7 @@ __date__ = "06/03/2020"
 
 
 from silx.gui import qt
-from ..utils import WidgetLongProcessing
+from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 from Orange.widgets import widget, gui
 from Orange.widgets.widget import Output
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -40,7 +40,10 @@ from tomwer.gui.control.datalistener import DataListenerWidget
 from tomwer.synctools.datalistener import MockDataListenerQThread
 from tomwer.web.client import OWClient
 from Orange.widgets import settings
+import functools
 import logging
+import signal
+import sys
 
 logger = logging.getLogger(__name__)
 
@@ -50,13 +53,13 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
     """
     This widget is used to listen to a server notifying the widget when an
     acquisition is finished.
-    Then the tango file will be converted to .nx file, NXtomo compliant.
+    Then the bliss file will be converted to .nx file, NXtomo compliant.
     """
     name = "data listener"
     id = "orangecontrib.widgets.tomwer.control.DataListenerOW.DataListenerOW"
-    description = "The widget will listen to (hdf5) tango acquisition and " \
-                  "wait for acquisition to be finished. Once finished it " \
-                  "will call nxtomomill to convert from tango .hdf5 to " \
+    description = "The widget will receive information from bliss acquisition " \
+                  "and wait for acquisition to be finished. Once finished it " \
+                  "will call nxtomomill to convert from bliss .hdf5 to " \
                   "NXtomo compliant .nx file"
     icon = "icons/datalistener.svg"
     priority = 2
@@ -92,18 +95,27 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
         # signal / slot connection
         self._widget.sigActivate.connect(self._activated)
         self._widget.sigDeactivate.connect(self._deactivated)
-        self._widget.sigConfigurationChanged.connect(self._tangoDeviceChanged)
+        self._widget.sigConfigurationChanged.connect(self._jsonRPCConfigChanged)
         self._widget.sigAcquisitionEnded.connect(self._process_bliss_file_frm_tuple)
 
+        # manange server stop when delete directly the widget or stop by Ctr+C
+        signal.signal(signal.SIGINT, self.handleSigTerm)
+        onDestroy = functools.partial(self._stopServerBeforeclosing)
+        self.destroyed.connect(onDestroy)
+
         # set up
         if self._blissConfiguration != {}:
             self._widget.setBlissServerConfiguation(self._blissConfiguration)
 
     def _process_bliss_file_frm_tuple(self, t):
-        master_file, entry, proposal_file = t
-        return self.process_bliss_file(bliss_file=master_file,
-                                       entry=entry,
-                                       proposal_file=proposal_file)
+        master_file, entry, proposal_file, saving_file = t
+        try:
+            self.process_sample_file(sample_file=master_file,
+                                     entry=str(entry) + '.1',
+                                     proposal_file=proposal_file,
+                                     master_sample_file=saving_file)
+        except Exception as e:
+            logger.error(e)
 
     def _activated(self):
         self.activate(True)
@@ -134,7 +146,7 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
         msg.setText(text)
         return msg.exec_() == qt.QMessageBox.Ok
 
-    def _tangoDeviceChanged(self):
+    def _jsonRPCConfigChanged(self):
         self._blissConfiguration = self._widget.getBlissServerConfiguration()
         if self.is_active():
             self.activate(False)
@@ -144,18 +156,32 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
         self._mock = mock
         self._mock_acquisitions = acquisitions
 
+    @docstring(DataListenerWidget.getHost)
+    def getHost(self):
+        return self._widget.getHost()
+
+    @docstring(DataListenerWidget.getPort)
+    def getPort(self):
+        return self._widget.getPort()
+
     @docstring(DataListener.create_listening_thread)
     def create_listening_thread(self):
         if self._mock is True:
-            thread = MockDataListenerQThread(acquisitions=None,
+            thread = MockDataListenerQThread(host=self.getHost(),
+                                             port=self.getPort(),
+                                             acquisitions=None,
                                              mock_acquisitions=self._mock_acquisitions)
         else:
-            thread = DataListenerQThread(device=self.session_name,
+            thread = DataListenerQThread(host=self.getHost(),
+                                         port=self.getPort(),
                                          acquisitions=None)
         # connect thread
-        thread.sigAcquisitionStarted.connect(self._widget._acquisitionStarted)
-        thread.sigAcquisitionEnded.connect(self._widget._acquisitionEnded)
-        thread.sigScanAdded.connect(self._widget._acquisitionUpdated)
+        thread.sigAcquisitionStarted.connect(self._widget._acquisitionStarted,
+                                             qt.Qt.DirectConnection)
+        thread.sigAcquisitionEnded.connect(self._widget._acquisitionEnded,
+                                           qt.Qt.DirectConnection)
+        thread.sigScanAdded.connect(self._widget._acquisitionUpdated,
+                                    qt.Qt.DirectConnection)
         return thread
 
     @docstring(DataListener.delete_listening_thread)
@@ -165,12 +191,28 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
         self._listening_thread.sigScanAdded.disconnect(self._widget._acquisitionUpdated)
         DataListener.delete_listening_thread(self)
 
-    def close(self):
+    def _stopServerBeforeclosing(self):
         self.activate(False)
-        widget.OWWidget.close(self)
+
+    def handleSigTerm(self, signo, *args, **kwargs):
+        if signo == signal.SIGINT:
+            self._stopServerBeforeclosing()
+            sys.exit()
 
     def _get_n_scan_observe(self):
         return self._widget._observationWidget.observationTable.model().rowCount()
 
     def _get_n_scan_finished(self):
         return self._widget._historyWindow.scanHistory.model().rowCount()
+def start_app():
+    listener = DataListenerOW()
+    listener.activate()
+    listener.show()
+
+
+if __name__ == '__main__':
+    app = qt.QApplication([])
+
+    start_app()
+
+    exit(app.exec_())

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

@@ -95,7 +95,6 @@ class DataTransfertOW(widget.OWWidget, FolderTransfert, OWClient):
         self._layout.addWidget(self._widget)
 
         # signal / SLOT connection
-        # self._widget.sigSelectionChanged.connect(self.setDestDir)
         self.settingsHandler.addCallback(self._updateSettingsVals)
 
         # setting configuration
@@ -128,5 +127,7 @@ class DataTransfertOW(widget.OWWidget, FolderTransfert, OWClient):
 
     @Inputs.data_in
     def process(self, scan, move=False, force=True, noRsync=False):
+        if scan is None:
+            return
         FolderTransfert.process(self, scan=scan, move=move, force=force,
                                 noRsync=noRsync)