tomwer 0.6.0__tar.gz → 0.6.0b0__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==0.6.0b0','console_scripts','tomwer'
+__requires__ = 'tomwer==0.6.0b0'
+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==0.6.0b0', 'console_scripts', 'tomwer')()
+    )

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/orangecontrib/tomwer/widgets/control/DataListOW.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__ = ["C. Nemoz", "H. Payno"]
+__license__ = "MIT"
+__date__ = "01/12/2016"
+
+from Orange.widgets import widget, gui
+from silx.gui import qt
+from tomwer.core.utils import logconfig
+from tomwer.gui.control.datalist import GenericDataListDialog
+from tomwer.core.process.scanlist import _ScanList
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.web.client import OWClient
+from tomwer.core.scan.scanbase import TomwerScanBase
+from Orange.widgets.settings import Setting
+from Orange.widgets.widget import Output, Input
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+class DataListOW(widget.OWWidget, OWClient):
+    name = "data list"
+    id = "orange.widgets.tomwer.scanlist"
+    description = "List path to reconstructions/scans. Those path will be send to the next box once validated."
+    icon = "icons/scanlist.svg"
+    priority = 50
+    category = "esrfWidgets"
+    keywords = ["tomography", "file", "tomwer", "folder"]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    _scanIDs = Setting(list())
+
+    assert len(_ScanList.outputs) == 1
+
+    class Outputs:
+        data_out = Output(
+            name=_ScanList.outputs[0].name,
+            type=_ScanList.outputs[0].type,
+            doc=_ScanList.outputs[0].doc,
+        )
+
+    class Inputs:
+        data_in = Input(name="data", type=TomwerScanBase)
+
+    def __init__(self, parent=None):
+        """A simple annuary which register all folder containing completed scan
+
+        .. warning: the widget won't check for scan validity and will only
+            emit the path to folders to the next widgets
+
+        :param parent: the parent widget
+        """
+        widget.OWWidget.__init__(self, parent)
+        OWClient.__init__(self)
+        self.widget = GenericDataListDialog(parent=self)
+        self.widget.setScanIDs(self._scanIDs)
+        layout = gui.vBox(self.mainArea, self.name).layout()
+        layout.addWidget(self.widget)
+        self.widget._sendButton.clicked.connect(self._sendList)
+
+        # expose API
+        self.n_scan = self.widget.n_scan
+
+        # alias used for the 'simple workflow' for now
+        self.start = self._sendList
+        self.clear = self.widget.clear
+
+    def _sendList(self):
+        """Send a signal for each list to the next widget"""
+
+        def send(scan_):
+            mess = "sending one scan %s" % d
+            logger.debug(
+                mess,
+                extra={
+                    logconfig.DOC_TITLE: self.widget._scheme_title,
+                    logconfig.SCAN_ID: str(scan_),
+                },
+            )
+            self.Outputs.data_out.send(scan_)
+
+        for d in self.widget.datalist.items:
+            if d in self.widget.datalist._scanIDs:
+                send(scan_=self.widget.datalist._scanIDs[d])
+            else:
+                logger.error("unable to retrieve scan {}".format(d))
+
+    @Inputs.data_in
+    def add(self, scan):
+        if scan is None:
+            return
+
+        self.widget.add(scan)
+
+
+def main():
+    app = qt.QApplication([])
+    s = DataListOW()
+    s.show()
+    app.exec_()
+
+
+if __name__ == "__main__":
+    main()

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

@@ -0,0 +1,261 @@
+# 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__ = "06/03/2020"
+
+
+from silx.gui import qt
+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
+from tomwer.core.process.datalistener import DataListener
+from tomwer.utils import docstring
+from tomwer.synctools.datalistener import DataListenerQThread
+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__)
+
+
+class DataListenerOW(widget.OWWidget, OWClient, WidgetLongProcessing, DataListener):
+    """
+    This widget is used to listen to a server notifying the widget when an
+    acquisition is finished.
+    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 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
+    category = "tomwer"
+    keywords = [
+        "tomography",
+        "file",
+        "tomwer",
+        "listener",
+        "datalistener",
+        "hdf5",
+        "NXtomo",
+    ]
+
+    allows_cycle = True
+    compress_signal = False
+
+    want_main_area = True
+    resizing_enabled = True
+
+    _blissConfiguration = settings.Setting(dict())
+
+    class Outputs:
+        data_out = Output(
+            name="data", type=TomwerScanBase, doc="one scan to be process"
+        )
+
+    def __init__(self, parent=None):
+        widget.OWWidget.__init__(self, parent)
+        OWClient.__init__(self)
+        WidgetLongProcessing.__init__(self)
+        DataListener.__init__(self)
+        self._widget = DataListenerWidget(parent=self)
+        self._mock = False
+
+        self._box = gui.vBox(self.mainArea, self.name)
+        layout = self._box.layout()
+        layout.addWidget(self._widget)
+
+        # signal / slot connection
+        self._widget.sigActivate.connect(self._activated)
+        self._widget.sigDeactivate.connect(self._deactivated)
+        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, 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)
+
+    def _deactivated(self):
+        self.activate(False)
+
+    @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)
+        DataListener.activate(self, activate=activate)
+        self.processing_state(activate, info="listener active")
+        self._widget.blockSignals(old)
+
+    def _signal_scan_ready(self, scan):
+        assert isinstance(scan, TomwerScanBase)
+        self.Outputs.data_out.send(scan)
+
+    def _ask_user_for_overwritting(self, file_path):
+        msg = qt.QMessageBox(self)
+        msg.setIcon(qt.QMessageBox.Question)
+        types = qt.QMessageBox.Ok | qt.QMessageBox.Cancel
+        msg.setStandardButtons(types)
+
+        text = "NXtomomill will overwrite: \n %s. Do you agree ?" % file_path
+        msg.setText(text)
+        return msg.exec_() == qt.QMessageBox.Ok
+
+    def _jsonRPCConfigChanged(self):
+        self._blissConfiguration = self._widget.getBlissServerConfiguration()
+        if self.is_active():
+            self.activate(False)
+            self.activate(True)
+
+    def setMock(self, mock, acquisitions):
+        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(
+                host=self.getHost(),
+                port=self.getPort(),
+                acquisitions=None,
+                mock_acquisitions=self._mock_acquisitions,
+            )
+        else:
+            thread = DataListenerQThread(
+                host=self.getHost(), port=self.getPort(), acquisitions=None
+            )
+        # connect thread
+        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)
+    def delete_listening_thread(self):
+        self._listening_thread.sigAcquisitionStarted.disconnect(
+            self._widget._acquisitionStarted
+        )
+        self._listening_thread.sigAcquisitionEnded.disconnect(
+            self._widget._acquisitionEnded
+        )
+        self._listening_thread.sigScanAdded.disconnect(self._widget._acquisitionUpdated)
+        DataListener.delete_listening_thread(self)
+
+    def _stopServerBeforeclosing(self):
+        self.activate(False)
+
+    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

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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__ = ["C. Nemoz", "H. Payno"]
+__license__ = "MIT"
+__date__ = "07/12/2016"
+
+import logging
+from Orange.widgets import widget, gui
+from Orange.widgets import settings
+from Orange.widgets.widget import Output, Input
+from silx.gui import qt
+from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
+from tomwer.core.process.datatransfert import FolderTransfert, logger as FTLogger
+from tomwer.web.client import OWClient
+from tomwer.gui.control.datatransfert import DataTransfertSelector
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.scan.scanbase import TomwerScanBase
+
+logger = logging.getLogger(__name__)
+
+
+class DataTransfertOW(widget.OWWidget, FolderTransfert, OWClient):
+    """
+    A simple widget managing the copy of an incoming folder to an other one
+
+    :param parent: the parent widget
+    """
+
+    name = "data transfert"
+    id = "orange.widgets.tomwer.foldertransfert"
+    description = "This widget insure data transfert of the received data "
+    description += "to the given directory"
+    icon = "icons/folder-transfert.svg"
+    priority = 30
+    category = "esrfWidgets"
+    keywords = [
+        "tomography",
+        "transfert",
+        "cp",
+        "copy",
+        "move",
+        "file",
+        "tomwer",
+        "folder",
+    ]
+
+    settingsHandler = CallbackSettingsHandler()
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    dest_dir = settings.Setting(str())
+    """Parameters directly editabled from the TOFU interface"""
+
+    scanready = qt.Signal(TomwerScanBase)
+
+    assert len(FolderTransfert.inputs) == 1
+
+    class Inputs:
+        data_in = Input(
+            name=FolderTransfert.inputs[0].name,
+            type=FolderTransfert.inputs[0].type,
+            doc=FolderTransfert.inputs[0].doc,
+        )
+
+    assert len(FolderTransfert.outputs) == 1
+
+    class Outputs:
+        data_out = Output(
+            name=FolderTransfert.outputs[0].name,
+            type=FolderTransfert.outputs[0].type,
+            doc=FolderTransfert.outputs[0].doc,
+        )
+
+    def __init__(self, parent=None):
+        FolderTransfert.__init__(self)
+        widget.OWWidget.__init__(self, parent)
+        OWClient.__init__(self)
+
+        # define GUI
+        self._widget = DataTransfertSelector(
+            parent=self,
+            rnice_option=True,
+            default_root_folder=self._getDefaultOutputDir(),
+        )
+        self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self._layout.addWidget(self._widget)
+
+        # signal / SLOT connection
+        self.settingsHandler.addCallback(self._updateSettingsVals)
+
+        # setting configuration
+        if self.dest_dir != "":
+            self._widget.setFolder(self.dest_dir)
+
+    def _requestFolder(self):
+        """Launch a QFileDialog to ask the user the output directory"""
+        dialog = qt.QFileDialog(self)
+        dialog.setWindowTitle("Destination folder")
+        dialog.setModal(1)
+        dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
+
+        if not dialog.exec_():
+            dialog.close()
+            return None
+
+        return dialog.selectedFiles()[0]
+
+    def signalTransfertOk(self, input_scan, output_scan):
+        if output_scan is None:
+            return
+        assert isinstance(output_scan, TomwerScanBase)
+        self.Outputs.data_out.send(output_scan)
+        self.scanready.emit(output_scan)
+
+    def _updateSettingsVals(self):
+        """function used to update the settings values"""
+        self.dest_dir = self._destDir
+
+    @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
+        )