tomwer 0.5.2b4__tar.gz → 0.5.4__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==0.5.2b4','console_scripts','tomwer'
-__requires__ = 'tomwer==0.5.2b4'
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.4','console_scripts','tomwer'
+__requires__ = 'tomwer==0.5.4'
 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==0.5.2b4', 'console_scripts', 'tomwer')()
+        load_entry_point('tomwer==0.5.4', 'console_scripts', 'tomwer')()
     )

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

@@ -74,7 +74,7 @@ class DataListOW(widget.OWWidget, OWClient):
         :param parent: the parent widget
         """
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, logger)
+        OWClient.__init__(self)
         self.widget = GenericDataListDialog(parent=self)
         self.widget.setScanIDs(self._scanIDs)
         layout = gui.vBox(self.mainArea, self.name).layout()

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

@@ -82,7 +82,7 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
 
     def __init__(self, parent=None):
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, (logger, ))
+        OWClient.__init__(self)
         WidgetLongProcessing.__init__(self)
         DataListener.__init__(self)
         self._widget = DataListenerWidget(parent=self)
@@ -125,6 +125,27 @@ class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing,
 
     @docstring(DataListener.activate)
     def activate(self, activate=True):
+        if activate and not self.is_port_available():
+            old = self._widget.blockSignals(True)
+            self._widget.activate(activate=False)
+            self._widget.blockSignals(old)
+            err = (
+                "port ({port}) of {host} already in use. Maybe an "
+                'other instance of "datalistener" is running in this '
+                "session or another tomwer session. As this widget is "
+                "connecting with bliss we enforce it to be unique. "
+                "If necessary you can hard kill server process ()"
+                "".format(port=self.port, host=self.host)
+            )
+            logger.warning(err)
+            mess = qt.QMessageBox(self)
+            mess.setIcon(qt.QMessageBox.Warning)
+            mess.setText(err)
+            mess.setModal(False)
+            mess.setWindowTitle("Unable to launch two listener in parallel")
+            mess.show()
+            return
+
         old = self._widget.blockSignals(True)
         self.set_configuration(self._widget.getBlissServerConfiguration())
         self._widget.activate(activate=activate)

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

@@ -61,7 +61,7 @@ class DataSelectorOW(widget.OWWidget, OWClient):
         """
         """
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, (logger))
+        OWClient.__init__(self)
 
         self.widget = ScanSelectorWidget(parent=self)
         self.widget.sigSelectionChanged.connect(self.changeSelection)

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

@@ -85,7 +85,7 @@ class DataTransfertOW(widget.OWWidget, FolderTransfert, OWClient):
     def __init__(self, parent=None):
         FolderTransfert.__init__(self)
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, (logger, FTLogger))
+        OWClient.__init__(self)
 
         # define GUI
         self._widget = DataTransfertSelector(parent=self,

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

@@ -84,7 +84,7 @@ class DataWatcherOW(widget.OWWidget, OWClient, WidgetLongProcessing):
         :param parent: the parent widget
         """
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, (logger, TDLogger))
+        OWClient.__init__(self)
         WidgetLongProcessing.__init__(self)
         self._widget = DataWatcherWidget(parent=self)
         self._widget.setFolderObserved(self.folderObserved)

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

@@ -65,7 +65,7 @@ class NameFilterOW(widget.OWWidget, OWClient):
         """
         """
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, (logger))
+        OWClient.__init__(self)
 
         self.widget = FileNameFilterWidget(parent=self)
         self.widget.setContentsMargins(0, 0, 0, 0)

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

@@ -91,7 +91,7 @@ class NXTomomillOW(widget.OWWidget, OWClient):
 
     def __init__(self, parent=None):
         widget.OWWidget.__init__(self, parent)
-        OWClient.__init__(self, logger)
+        OWClient.__init__(self)
         self.widget = HDF5DataListDialog(parent=self)
         self.widget.setScanIDs(self._scans)
         layout = gui.vBox(self.mainArea, self.name).layout()
@@ -118,6 +118,8 @@ class NXTomomillOW(widget.OWWidget, OWClient):
     def _sendList(self):
         """Send a signal for each list to the next widget"""
         for bliss_url in self.widget.datalist.items:
+            logger.processStarted(
+                'Start translate {} to NXTomo'.format(str(bliss_url)))
 
             entry, file_path = bliss_url.split('@')
             bliss_scan = BlissScan(master_file=file_path, entry=entry,
@@ -137,20 +139,20 @@ class NXTomomillOW(widget.OWWidget, OWClient):
                                                      file_extension='.nx',
                                                      input_callback=_nxtomomill_input_callback)
             except Exception as e:
-                logger.error(
-                    'Fail to convert from bliss file: %s to NXTomo.'
+                logger.processFailed(
+                    'Fail to convert from bliss file: %s to NXTomo. '
                     'Conversion error is: %s' % (bliss_url, e))
             else:
                 if len(conv) != 1:
-                    logger.error(
-                        'Something went wrong during file conversion. Unable to process the file.')
+                    logger.processFailed(
+                        'Something went wrong during file conversion. '
+                        'Unable to process the file.')
                 else:
                     conv_file, conv_entry = conv[0]
                     scan_converted = HDF5TomoScan(scan=conv_file, entry=conv_entry)
-                    mess = "sending one scan %s" % bliss_url
-                    logger.debug(mess,
-                                 extra={logconfig.DOC_TITLE: self.widget._scheme_title,
-                                        logconfig.SCAN_ID: bliss_url})
+                    mess = '{} has been translated to {}' \
+                           ''.format(str(bliss_scan), str(scan_converted))
+                    logger.processSucceed(mess)
                     self.Outputs.data_out.send(scan_converted)
 
     def _userAgreeForOverwrite(self, file_path):

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

@@ -108,7 +108,7 @@ class OldDataValidatorOW(widget.OWWidget, ScanValidator):
         """
         widget.OWWidget.__init__(self, parent)
         ScanValidator.__init__(self, memoryReleaser=QWaiterThread(memReleaserWaitLoop))
-        OWClient.__init__(self, (logger, SVLogger))
+        OWClient.__init__(self)
 
         self._buildGUI(ftserie)
 

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

@@ -33,11 +33,11 @@ from Orange.widgets.settings import Setting
 from Orange.widgets.widget import Input, Output
 from tomwer.core.process.timer import Timer
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.log import TomwerLogger
+import logging
 
 import functools
 
-_logger = TomwerLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 class _TimerWidget(qt.QWidget):

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

@@ -0,0 +1,140 @@
+# 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__ = "28/09/2020"
+
+from silx.gui import qt
+from Orange.widgets import widget, gui
+from Orange.widgets.widget import Output
+from tomwer.gui.debugtools.datasetgenerator import DatasetGeneratorDialog
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.utils.scanutils import MockEDF
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.core.utils.scanutils import MockBlissAcquisition
+import os
+import uuid
+
+
+class DatasetGeneratorOW(widget.OWWidget):
+    """
+    A simple widget to generate on the fly and 'continuously' datasets
+    """
+
+    name = "random data generator"
+    id = "orangecontrib.tomwer.widgets.debugtools.datasetgeneratorow"
+    description = "create on the fly dataset"
+    icon = "icons/hammer.png"
+    priority = 250
+    category = "esrfWidgets"
+    keywords = ["tomography", "file", "tomwer", "dataset", "debug"]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    class Outputs:
+        data_out = Output(name="data", type=object)
+
+    def __init__(self, parent=None):
+        widget.OWWidget.__init__(self, parent=parent)
+        self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self.generatorGUI = DatasetGeneratorDialog(parent=self)
+        self._layout.addWidget(self.generatorGUI)
+
+        # connect signal / slot
+        self.generatorGUI.sigGenerationStopped.connect(self._stop)
+        self.generatorGUI.sigGenerationStarted.connect(self._start)
+        self.generatorGUI.sigConfigChanged.connect(self._reset)
+        self.generatorGUI.sigCreateOne.connect(self._generate)
+
+    def _start(self):
+        return
+        self._displayTimer = qt.QTimer()
+        self._displayTimer.timeout.connect(self._generate)
+        self._displayTimer.start(self.generatorGUI.getTimeout())
+
+    def _stop(self):
+        return
+        self._displayTimer.stop()
+        self._displayTimer.timeout.disconnect(self._generate)
+        self._displayTimer = None
+
+    def _reset(self):
+        if self.isRunning():
+            self._stop()
+            self._start()
+
+    def isRunning(self):
+        raise NotImplementedError()
+
+    def _timerCallback(self):
+        self._reset()
+        self._generate()
+
+    def _generate(self):
+        type_to_generate = self.generatorGUI.getTypeToGenerate()
+        scan_path = os.path.join(
+            self.generatorGUI.getRootDir(),
+            str(uuid.uuid4()),
+        )
+        n_proj = self.generatorGUI.getNProj()
+        create_ini_dark = self.generatorGUI.isDarkNeededAtBeginning()
+        create_ini_flat = self.generatorGUI.isFlatNeededAtBeginning()
+        dims = self.generatorGUI.getFrameDims()
+        if type_to_generate == EDFTomoScan.__name__:
+            scan = MockEDF.mockScan(scanID=scan_path, nRadio=n_proj, dim=dims[0])
+        elif type_to_generate == HDF5TomoScan.__name__:
+            scan = MockHDF5(
+                scan_path=scan_path,
+                n_proj=n_proj,
+                n_ini_proj=n_proj,
+                create_ini_dark=create_ini_dark,
+                create_ini_ref=create_ini_flat,
+                dim=dims[0],
+            ).scan
+        elif type_to_generate == BlissScan.__name__:
+            n_darks = 10 if create_ini_dark else 0
+            n_flats = 10 if create_ini_flat else 0
+            mock = MockBlissAcquisition(
+                n_sample=1,
+                n_sequence=1,
+                n_scan_per_sequence=1,
+                n_darks=n_darks,
+                n_flats=n_flats,
+                output_dir=scan_path,
+            )
+            scan = mock.create_bliss_scan()
+        else:
+            raise ValueError(
+                "type to generate {} not recognized".format(type_to_generate)
+            )
+
+        self.Outputs.data_out.send(scan)

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

@@ -0,0 +1,67 @@
+# 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__ = "30/09/2020"
+
+from silx.gui import qt
+from Orange.widgets import widget, gui
+from tomwer.gui.debugtools.datasetgenerator import DatasetGeneratorDialog
+from tomwer.gui.debugtools.objectinspector import ObjectInspector
+from Orange.widgets.widget import Input
+
+
+class ObjectInspectorOW(widget.OWWidget):
+    """
+    A simple widget to browse a TomwerScanBase object
+    """
+
+    name = "tomwer object browser"
+    id = "orangecontrib.tomwer.widgets.debugtools.tomwerscanbasebrowser"
+    description = "create on the fly dataset"
+    icon = "icons/inspector.png"
+    priority = 255
+    category = "esrfWidgets"
+    keywords = ["tomography", "file", "tomwer", "dataset", "debug"]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    class Inputs:
+        data_in = Input(name="object", type=object)
+
+    def __init__(self, parent=None):
+        widget.OWWidget.__init__(self, parent=parent)
+        self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self.inspector = ObjectInspector(parent=self)
+        self._layout.addWidget(self.inspector)
+
+    @Inputs.data_in
+    def setObject(self, obj):
+        self.inspector.setObject(obj)

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

@@ -0,0 +1,37 @@
+# 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.
+#
+#############################################################################
+
+NAME = "debug tools"
+
+ID = "orangecontrib.tomwer.widgets.debugtools"
+
+DESCRIPTION = "some widgets to help debugging"
+
+LONG_DESCRIPTION = "some widgets to help debugging"
+
+ICON = "../../widgets/icons/tomwer_debug_tools.png"
+
+BACKGROUND = "#C0CCFF"
+
+PRIORITY = 20

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/debugtools/icons/hammer.svg

@@ -0,0 +1,83 @@
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