tomwer 1.2.8__py3-none-any.whl → 1.3.0a0__py3-none-any.whl

orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py

@@ -1,182 +1,182 @@
-# 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__ = "16/11/2020"
-
-
-import logging
-
-from orangewidget import gui
-from orangewidget.settings import Setting
-from orangewidget.widget import Input, Output
-from processview.core.manager import DatasetState, ProcessManager
-from silx.gui import qt
-
-import tomwer.core.process.control.volumesymlink
-from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
-from tomwer.core.process.control.volumesymlink import (
-    OutputType,
-    VolumeSymbolicLinkTask,
-)
-from tomwer.core.scan.scanbase import TomwerScanBase
-
-_logger = logging.getLogger(__name__)
-
-
-class VolumeSymLinkOW(SuperviseOW):
-    """
-    link volume reconstructed at proposal file if possible else under
-    the given folder
-    """
-
-    name = "volume symbolic link"
-    id = "orange.widgets.tomwer.control.VolumeSymLinkOW.VolumeSymLinkOW"
-    description = (
-        "create a symbolic link for the latest volume reconstructed on a "
-        "given folder"
-    )
-    icon = "icons/volumesymlink.svg"
-    priority = 200
-    keywords = [
-        "hdf5",
-        "tomwer",
-        "folder",
-        "volume",
-        "symlink",
-        "tomography",
-        "symbolic link",
-    ]
-
-    want_main_area = True
-    resizing_enabled = True
-
-    ewokstaskclass = tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkTask
-
-    _scans = Setting(list())
-
-    class Inputs:
-        data = Input(name="data", type=TomwerScanBase, doc="scan to be process")
-
-    class Outputs:
-        data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
-
-    def __init__(self, parent=None):
-        super().__init__(parent)
-        self._mainWidget = _OutputDir(parent=self)
-        layout = gui.vBox(self.mainArea, self.name).layout()
-        layout.addWidget(self._mainWidget)
-
-    @Inputs.data
-    def process(self, scan):
-        if scan is None:
-            return
-        symlink_process = VolumeSymbolicLinkTask(
-            inputs={
-                "data": scan,
-                "output_type": self._mainWidget.getOutputType(),
-                "output_folder": self._mainWidget.getOutputFolder(),
-                "serialize_output_data": False,
-            }
-        )
-        ProcessManager().notify_dataset_state(
-            dataset=self.scan,
-            process=self,
-            state=DatasetState.ON_GOING,
-        )
-        try:
-            symlink_process.run()
-        except Exception:
-            mess = f"Failed to create symbolic link for {scan}"
-            _logger.processFailed(mess)
-            ProcessManager().notify_dataset_state(
-                dataset=self.scan, process=self, state=DatasetState.FAILED, details=mess
-            )
-        else:
-            mess = f"Create symbolic link for {scan}"
-            _logger.processSucceed(mess)
-            ProcessManager().notify_dataset_state(
-                dataset=self.scan,
-                process=self,
-                state=DatasetState.SUCCEED,
-                details=mess,
-            )
-        self.Outputs.data.send(scan)
-
-    def reprocess(self, dataset):
-        self.process(dataset)
-
-
-class _OutputDir(qt.QGroupBox):
-    def __init__(self, parent):
-        qt.QGroupBox.__init__(self, parent)
-        self._button_grp = qt.QButtonGroup(self)
-        self._button_grp.setExclusive(True)
-        self.setLayout(qt.QGridLayout())
-        self._oneLevelCB = qt.QRadioButton(OutputType.ONE_LEVEL_UPPER.value, self)
-        self._button_grp.addButton(self._oneLevelCB)
-        self.layout().addWidget(self._oneLevelCB, 1, 0, 1, 3)
-        self._staticOpt = qt.QRadioButton("", self)
-        self._button_grp.addButton(self._staticOpt)
-        self.layout().addWidget(self._staticOpt, 2, 0, 1, 1)
-        self._qleFolder = qt.QLineEdit("", self)
-        self.layout().addWidget(self._qleFolder, 2, 1, 1, 1)
-        self._selectPB = qt.QPushButton("select", self)
-        self.layout().addWidget(self._selectPB, 2, 2, 1, 1)
-
-        # connect signal / slot
-        self._selectPB.released.connect(self._selectFolder)
-        self._qleFolder.editingFinished.connect(self._activeStaticOpt)
-
-        # set up
-        self._oneLevelCB.setChecked(True)
-
-    def _activeStaticOpt(self, *args, **kwargs):
-        self._staticOpt.setChecked(True)
-
-    def _selectFolder(self):  # pragma: no cover
-        dialog = qt.QFileDialog(self)
-        dialog.setWindowTitle("Select destination folder for symbolic link")
-        dialog.setModal(1)
-        dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
-
-        if not dialog.exec_():
-            dialog.close()
-            return None
-
-        dest_folder = dialog.selectedFiles()[0]
-        self._qleFolder.setText(dest_folder)
-
-    def getOutputType(self) -> OutputType:
-        if self._oneLevelCB.isChecked():
-            return OutputType.ONE_LEVEL_UPPER
-        elif self._staticOpt.isChecked():
-            return OutputType.STATIC
-        else:
-            raise TypeError("Not managed")
-
-    def getOutputFolder(self):
-        return self._qleFolder.text()
+# # 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__ = "16/11/2020"
+
+
+# import logging
+
+# from orangewidget import gui
+# from orangewidget.settings import Setting
+# from orangewidget.widget import Input, Output
+# from processview.core.manager import DatasetState, ProcessManager
+# from silx.gui import qt
+
+# import tomwer.core.process.control.volumesymlink
+# from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
+# from tomwer.core.process.control.volumesymlink import (
+#     OutputType,
+#     VolumeSymbolicLinkTask,
+# )
+# from tomwer.core.scan.scanbase import TomwerScanBase
+
+# _logger = logging.getLogger(__name__)
+
+
+# class VolumeSymLinkOW(SuperviseOW):
+#     """
+#     link volume reconstructed at proposal file if possible else under
+#     the given folder
+#     """
+
+#     name = "volume symbolic link"
+#     id = "orange.widgets.tomwer.control.VolumeSymLinkOW.VolumeSymLinkOW"
+#     description = (
+#         "create a symbolic link for the latest volume reconstructed on a "
+#         "given folder"
+#     )
+#     icon = "icons/volumesymlink.svg"
+#     priority = 200
+#     keywords = [
+#         "hdf5",
+#         "tomwer",
+#         "folder",
+#         "volume",
+#         "symlink",
+#         "tomography",
+#         "symbolic link",
+#     ]
+
+#     want_main_area = True
+#     resizing_enabled = True
+
+#     ewokstaskclass = tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkTask
+
+#     _scans = Setting(list())
+
+#     class Inputs:
+#         data = Input(name="data", type=TomwerScanBase, doc="scan to be process")
+
+#     class Outputs:
+#         data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
+
+#     def __init__(self, parent=None):
+#         super().__init__(parent)
+#         self._mainWidget = _OutputDir(parent=self)
+#         layout = gui.vBox(self.mainArea, self.name).layout()
+#         layout.addWidget(self._mainWidget)
+
+#     @Inputs.data
+#     def process(self, scan):
+#         if scan is None:
+#             return
+#         symlink_process = VolumeSymbolicLinkTask(
+#             inputs={
+#                 "data": scan,
+#                 "output_type": self._mainWidget.getOutputType(),
+#                 "output_folder": self._mainWidget.getOutputFolder(),
+#                 "serialize_output_data": False,
+#             }
+#         )
+#         ProcessManager().notify_dataset_state(
+#             dataset=self.scan,
+#             process=self,
+#             state=DatasetState.ON_GOING,
+#         )
+#         try:
+#             symlink_process.run()
+#         except Exception:
+#             mess = f"Failed to create symbolic link for {scan}"
+#             _logger.processFailed(mess)
+#             ProcessManager().notify_dataset_state(
+#                 dataset=self.scan, process=self, state=DatasetState.FAILED, details=mess
+#             )
+#         else:
+#             mess = f"Create symbolic link for {scan}"
+#             _logger.processSucceed(mess)
+#             ProcessManager().notify_dataset_state(
+#                 dataset=self.scan,
+#                 process=self,
+#                 state=DatasetState.SUCCEED,
+#                 details=mess,
+#             )
+#         self.Outputs.data.send(scan)
+
+#     def reprocess(self, dataset):
+#         self.process(dataset)
+
+
+# class _OutputDir(qt.QGroupBox):
+#     def __init__(self, parent):
+#         qt.QGroupBox.__init__(self, parent)
+#         self._button_grp = qt.QButtonGroup(self)
+#         self._button_grp.setExclusive(True)
+#         self.setLayout(qt.QGridLayout())
+#         self._oneLevelCB = qt.QRadioButton(OutputType.ONE_LEVEL_UPPER.value, self)
+#         self._button_grp.addButton(self._oneLevelCB)
+#         self.layout().addWidget(self._oneLevelCB, 1, 0, 1, 3)
+#         self._staticOpt = qt.QRadioButton("", self)
+#         self._button_grp.addButton(self._staticOpt)
+#         self.layout().addWidget(self._staticOpt, 2, 0, 1, 1)
+#         self._qleFolder = qt.QLineEdit("", self)
+#         self.layout().addWidget(self._qleFolder, 2, 1, 1, 1)
+#         self._selectPB = qt.QPushButton("select", self)
+#         self.layout().addWidget(self._selectPB, 2, 2, 1, 1)
+
+#         # connect signal / slot
+#         self._selectPB.released.connect(self._selectFolder)
+#         self._qleFolder.editingFinished.connect(self._activeStaticOpt)
+
+#         # set up
+#         self._oneLevelCB.setChecked(True)
+
+#     def _activeStaticOpt(self, *args, **kwargs):
+#         self._staticOpt.setChecked(True)
+
+#     def _selectFolder(self):  # pragma: no cover
+#         dialog = qt.QFileDialog(self)
+#         dialog.setWindowTitle("Select destination folder for symbolic link")
+#         dialog.setModal(1)
+#         dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
+
+#         if not dialog.exec_():
+#             dialog.close()
+#             return None
+
+#         dest_folder = dialog.selectedFiles()[0]
+#         self._qleFolder.setText(dest_folder)
+
+#     def getOutputType(self) -> OutputType:
+#         if self._oneLevelCB.isChecked():
+#             return OutputType.ONE_LEVEL_UPPER
+#         elif self._staticOpt.isChecked():
+#             return OutputType.STATIC
+#         else:
+#             raise TypeError("Not managed")
+
+#     def getOutputFolder(self):
+#         return self._qleFolder.text()

orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py

@@ -41,8 +41,8 @@ from silx.gui.utils import concurrent
 
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomwer.core.utils.scanutils import MockBlissAcquisition, MockEDF, MockHDF5
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import MockBlissAcquisition, MockEDF, MockNXtomo
 from tomwer.gui.debugtools.datasetgenerator import DatasetGeneratorDialog
 
 
@@ -150,8 +150,8 @@ class _DatasetGeneratorThread(threading.Thread):
             scan = MockEDF.mockScan(
                 scanID=self.scan_path, nRadio=self.n_proj, dim=self.dims[0]
             )
-        elif self.type_to_generate == HDF5TomoScan.__name__:
-            scan = MockHDF5(
+        elif self.type_to_generate == NXtomoScan.__name__:
+            scan = MockNXtomo(
                 scan_path=self.scan_path,
                 n_proj=self.n_proj,
                 n_ini_proj=self.n_proj,

orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py

@@ -38,7 +38,7 @@ from orangewidget.widget import Input, Output
 from silx.io.url import DataUrl
 
 import tomwer.core.process.edit.darkflatpatch
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.edit.dkrfpatch import DarkRefPatchWidget
 from tomwer.synctools.stacks.edit.darkflatpatch import DarkFlatPatchProcessStack
@@ -52,7 +52,7 @@ _logger = logging.getLogger(__name__)
 
 class DarkFlatPatchOW(WidgetLongProcessing, SuperviseOW):
     """
-    Widget to define on the fly the image_key of a HDF5TomoScan
+    Widget to define on the fly the image_key of a NXtomoScan
     """
 
     name = "dark-flat-patch"
@@ -110,8 +110,8 @@ class DarkFlatPatchOW(WidgetLongProcessing, SuperviseOW):
     def process(self, scan):
         if scan is None:
             return
-        elif not isinstance(scan, HDF5TomoScan):
-            _logger.error("We can only patch dark and flat for HDF5TomoScan")
+        elif not isinstance(scan, NXtomoScan):
+            _logger.error("We can only patch dark and flat for NXtomoScan")
         else:
             self._processingStack.add(scan, self.getConfiguration())
 

orangecontrib/tomwer/widgets/edit/ImageKeyEditorOW.py

@@ -35,7 +35,7 @@ from orangewidget import gui
 from orangewidget.widget import Input, Output
 
 import tomwer.core.process.edit.imagekeyeditor
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.edit.imagekeyeditor import ImageKeyDialog
 from tomwer.synctools.stacks.edit.imagekeyeditor import ImageKeyEditorProcessStack
@@ -49,7 +49,7 @@ _logger = logging.getLogger(__name__)
 
 class ImageKeyEditorOW(SuperviseOW, WidgetLongProcessing):
     """
-    Widget to define on the fly the image_key of a HDF5TomoScan
+    Widget to define on the fly the image_key of a NXtomoScan
     """
 
     name = "image-key-editor"
@@ -103,7 +103,7 @@ class ImageKeyEditorOW(SuperviseOW, WidgetLongProcessing):
     def process(self, scan):
         if scan is None:
             return
-        elif not isinstance(scan, HDF5TomoScan):
+        elif not isinstance(scan, NXtomoScan):
             _logger.error("You can only edit image keys for the HDF5 scans")
         else:
             self._scan = scan

orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py

@@ -71,6 +71,8 @@ class ImageKeyUpgraderOW(
     want_main_area = True
     resizing_enabled = True
 
+    _ewoks_inputs_to_hide_from_orange = ("operations", "serialize_output_data")
+
     def __init__(self, parent=None, *args, **kwargs):
         super().__init__(parent=parent, *args, **kwargs)
 

orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py

@@ -5,7 +5,7 @@ from orangewidget.settings import Setting
 from orangewidget.widget import Input, Output
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.edit.nxtomoeditor import NXtomoEditorDialog as _NXtomoEditorDialog
 
@@ -104,9 +104,9 @@ class NXtomoEditorOW(SuperviseOW):
     def _setScan(self, scan):
         if scan is None:
             pass
-        elif not isinstance(scan, HDF5TomoScan):
+        elif not isinstance(scan, NXtomoScan):
             raise TypeError(
-                f"expect to have an instance of {HDF5TomoScan}. {type(scan)} provided."
+                f"expect to have an instance of {NXtomoScan}. {type(scan)} provided."
             )
         else:
             self.widget.setScan(scan)

orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py

@@ -9,10 +9,10 @@ from nxtomomill.nexus.nxtomo import NXtomo
 from orangecanvas.scheme.readwrite import literal_dumps
 from silx.gui import qt
 from silx.gui.utils.testutils import SignalListener, TestCaseQt
-from tomoscan.esrf.scan.hdf5scan import ImageKey
+from nxtomo.nxobject.nxdetector import ImageKey
 
 from orangecontrib.tomwer.widgets.edit.NXtomoEditorOW import NXtomoEditorOW
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.tests.utils import skip_gui_test
 
 
@@ -100,7 +100,7 @@ class TestNXtomoEditorOW(TestCaseQt):
                 data_path=entry,
             )
             # 2.0 set scan to the nxtomo-editor
-            scan = HDF5TomoScan(file_path, entry)
+            scan = NXtomoScan(file_path, entry)
             self._window._setScan(scan=scan)
             self.qapp.processEvents()
             # 3.0 check results are as expected

orangecontrib/tomwer/widgets/icat/PublishProcessedDataOW.py

@@ -0,0 +1,115 @@
+import weakref
+from typing import Optional
+from silx.gui import qt
+from ewoksorange.bindings.owwidgets import OWEwoksWidgetOneThreadPerRun
+from orangewidget import gui
+from orangewidget.settings import Setting
+
+import tomwer.core.process.icat.publish
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.gui.icat.publish import PublishProcessedDataWidget
+
+from processview.core.superviseprocess import SuperviseProcess
+
+
+class PublishProcessedDataOW(
+    OWEwoksWidgetOneThreadPerRun,
+    SuperviseProcess,
+    ewokstaskclass=tomwer.core.process.icat.publish.PublishReconstructedVolumeFromScanTask,
+):
+    """
+    This widget can receive 'data' (scan) and but some screenshot to be pushed on GALLERY.
+    """
+
+    name = "Publish processed data to icat"
+    id = "orangecontrib.widgets.tomwer.icat.PublishProcessedDataOW.PublishProcessedDataOW"
+    description = "Publish processed data to icat. \n For now we expect processed data to be reconstructed volume"
+    icon = "icons/publish.svg"
+    priority = 64
+    keywords = [
+        "tomography",
+        "tomwer",
+        "tomo_obj",
+        "processed data",
+        "PROCESSED_DATA",
+        "publish",
+        "icat",
+        "icatplus",
+        "pyicatplus",
+        "pyicat-plus",
+    ]
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    _ewoks_default_inputs = Setting({})
+
+    _ewoks_inputs_to_hide_from_orange = (
+        "__process__",
+        "beamline",
+        "proposal",
+        "dataset",
+        "dry_run",
+        "path",
+    )
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        SuperviseProcess.__init__(self)
+        self._widget = PublishProcessedDataWidget(parent=self)
+        layout = gui.vBox(self.mainArea, self.name).layout()
+        layout.addWidget(self._widget)
+        self._scan = None
+
+        # load settings
+        self._widget.setConfiguration(self._ewoks_default_inputs)
+
+        # connect signal / slot
+        self._widget.sigConfigChanged.connect(self._updateSettings)
+
+    def _updateSettings(self):
+        self._ewoks_default_inputs = self._widget.getConfiguration()
+
+    def setScan(self, scan: TomwerScanBase):
+        self._scan = weakref.ref(scan)
+        self._widget.setScan(scan=scan)
+
+    def getScan(self) -> Optional[TomwerScanBase]:
+        if self._scan is None:
+            return None
+        else:
+            return self._scan()
+
+    def handleNewSignals(self) -> None:
+        """Invoked by the workflow signal propagation manager after all
+        signals handlers have been called.
+        """
+        # update the widget when receive the scan (proposal, dataset...)
+        scan = self.get_task_input_value("data", None)
+        if scan is None:
+            return
+        elif scan != self.getScan():
+            self._widget.setScan(scan)
+            super().handleNewSignals()
+        else:
+            super().handleNewSignals()
+
+    def get_task_inputs(self):
+        task_inputs = super().get_task_inputs()
+        configuration = self._widget.getConfiguration()
+
+        task_inputs["beamline"] = configuration["beamline"]
+        task_inputs["proposal"] = configuration["proposal"]
+        task_inputs["dataset"] = configuration["dataset"]
+        task_inputs["__process__"] = weakref.ref(self)
+
+        print("get task inputs")
+        from pprint import pprint
+
+        pprint(task_inputs)
+
+        return task_inputs
+
+    def sizeHint(self):
+        return qt.QSize(500, 200)