tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

orangecontrib/tomwer/tutorials/icat_publication.ows

@@ -0,0 +1,58 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="Reconstruction of a volume and publication to icat" description="">
+	<nodes>
+		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(150, 150)" />
+		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(324.0, 183.0)" />
+		<node id="2" name="default center of rotation" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="default center of rotation" position="(490.0, 218.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(649.0, 261.0)" />
+		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(818.0, 248.0)" />
+		<node id="5" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(812.0, 391.0)" />
+		<node id="6" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(986.75, 383.25)" />
+		<node id="7" name="create raw data screenshots" qualified_name="orangecontrib.tomwer.widgets.icat.RawDataScreenshotCreatorOW.RawDataScreenshotCreatorOW" project_name="tomwer" version="" title="create raw data screenshots" position="(321.0, 509.0)" />
+		<node id="8" name="save to gallery and publish" qualified_name="orangecontrib.tomwer.widgets.icat.SaveToGalleryAndPublishOW.SaveToGalleryAndPublishOW" project_name="tomwer" version="" title="save to gallery and publish" position="(506.0, 510.0)" />
+		<node id="9" name="save to gallery and publish" qualified_name="orangecontrib.tomwer.widgets.icat.SaveToGalleryAndPublishOW.SaveToGalleryAndPublishOW" project_name="tomwer" version="" title="save to gallery and publish (1)" position="(731.0, 514.0)" />
+		<node id="10" name="Publish processed data to icat" qualified_name="orangecontrib.tomwer.widgets.icat.PublishProcessedDataOW.PublishProcessedDataOW" project_name="tomwer" version="" title="Publish processed data to icat" position="(990.0, 514.0)" />
+	</nodes>
+	<links>
+		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="1" source_node_id="1" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="2" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="3" source_node_id="3" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="4" source_node_id="3" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="5" source_node_id="5" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="6" source_node_id="0" sink_node_id="7" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="7" source_node_id="7" sink_node_id="8" source_channel="screenshots" sink_channel="screenshots" enabled="true" source_channel_id="screenshots" sink_channel_id="screenshots" />
+		<link id="8" source_node_id="3" sink_node_id="9" source_channel="screenshots" sink_channel="screenshots" enabled="true" source_channel_id="screenshots" sink_channel_id="screenshots" />
+		<link id="9" source_node_id="5" sink_node_id="10" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<arrow id="0" start="(267.0, 56.0)" end="(194.0, 105.0)" fill="#C1272D" />
+		<text id="1" type="text/plain" rect="(276.25, 17.75, 150.0, 31.0)" font-family="Ubuntu" font-size="16">provide dataset</text>
+		<text id="2" type="text/plain" rect="(146.0, 597.0, 168.0, 89.0)" font-family="Cantarell" font-size="16">create screenshot for raw projection, raw falt and raw dark</text>
+		<text id="3" type="text/plain" rect="(413.0, 612.0, 215.0, 62.0)" font-family="Cantarell" font-size="16">save screenshot to the gallry and publish to icat</text>
+		<arrow id="4" start="(630.0, 605.0)" end="(674.0, 573.0)" fill="#C1272D" />
+		<arrow id="5" start="(475.99999999999994, 612.0)" end="(477.99999999999994, 568.0)" fill="#C1272D" />
+		<arrow id="6" start="(607.0, 387.0)" end="(671.0, 395.0)" fill="#C1272D" />
+		<text id="7" type="text/plain" rect="(449.0, 350.0, 150.0, 51.0)" font-family="Cantarell" font-size="16">screenshot of the reconstructed slice</text>
+		<arrow id="8" start="(235.0, 592.0)" end="(281.0, 521.0)" fill="#C1272D" />
+		<text id="9" type="text/plain" rect="(901.0, 618.0, 179.0, 70.0)" font-family="Cantarell" font-size="16">publish reconstructed volume to icat</text>
+		<arrow id="10" start="(980.0, 621.0)" end="(981.0, 579.0)" fill="#C1272D" />
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'USE_SINOGRAM': False, 'SINOGRAM_LINE': '', 'SINOGRAM_SUBSAMPLING': 10, 'AXIS_URL_1': '', 'AXIS_URL_2': '', 'LOOK_AT_STDMAX': False, 'NEAR_WX': 5, 'FINE_STEP_X': 0.1, 'SCALE_IMG2_TO_IMG1': False, 'NEAR_POSITION': 0.0, 'PADDING_MODE': 'edge', 'FLIP_LR': True, 'COMPOSITE_OPTS': {'theta': 10, 'n_subsampling_y': 10, 'oversampling': 4, 'take_log': True, 'near_pos': 0, 'near_width': 20}, 'SIDE': 'all', 'COR_OPTIONS': ''}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="4" format="literal">{'_viewer_config': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="5" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_volume_params': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="6" format="literal">{'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="8" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="9" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="10" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

orangecontrib/tomwer/widgets/__init__.py

@@ -22,9 +22,10 @@
 #
 #############################################################################
 
-import sysconfig
-
-import pkg_resources
+try:
+    from orangecanvas.utils.pkgmeta import get_distribution
+except ImportError:
+    from pkg_resources import get_distribution
 
 ICON = "../widgets/icons/tomwer.png"
 
@@ -33,12 +34,13 @@ BACKGROUND = "#C0CCFF"
 
 # Entry point for main Orange categories/widgets discovery
 def widget_discovery(discovery):
-    dist = pkg_resources.get_distribution("tomwer")
+    dist = get_distribution("tomwer")
     pkgs = [
         "orangecontrib.tomwer.widgets.cluster",
         "orangecontrib.tomwer.widgets.control",
         "orangecontrib.tomwer.widgets.debugtools",
         "orangecontrib.tomwer.widgets.edit",
+        # "orangecontrib.tomwer.widgets.icat",
         "orangecontrib.tomwer.widgets.reconstruction",
         # "orangecontrib.tomwer.widgets.stitching",
         "orangecontrib.tomwer.widgets.visualization",
@@ -53,11 +55,9 @@ WIDGET_HELP_PATH = (
     # You still need to build help pages using
     # make htmlhelp
     # inside doc folder
-    ("/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.
-    (f"{sysconfig.get_path('data')}/help/tomwer/index.html", None),
-    ("http://www.silx.org/pub/doc/tomwer/htmlhelp/0.9/", None),
+    # (
+    #     "/home/payno/Documents/dev/tomography/tomwer/build/html/canvas/widgets/widgets.html",
+    #     None,
+    # ),
+    ("https://tomwer.readthedocs.io/en/latest/canvas/widgets/widgets.html", None),
 )

orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py

@@ -13,7 +13,7 @@ import tomwer.core.process.control.datadiscovery
 from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.scan.scantype import ScanType
@@ -217,7 +217,7 @@ class _DiscoverThread(qt.QThread):
                 ):
                     self.sigDataFound.emit(scan)
                 elif (
-                    isinstance(scan, HDF5TomoScan)
+                    isinstance(scan, NXtomoScan)
                     and self._research_type is ScanType.NX_TOMO
                 ):
                     self.sigDataFound.emit(scan)

orangecontrib/tomwer/widgets/control/DataListOW.py

@@ -35,9 +35,9 @@ from orangewidget.widget import Input, Output, OWBaseWidget
 from silx.gui import qt
 
 import tomwer.core.process.control.scanlist
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.gui.control.datalist import GenericScanListDialog
+from tomwer.gui.control.datalist import GenericScanListWindow
 
 logger = logging.getLogger(__name__)
 
@@ -73,19 +73,21 @@ class DataListOW(OWBaseWidget, openclass=True):
         :param parent: the parent widget
         """
         super().__init__(parent)
-        self.widget = GenericScanListDialog(parent=self)
+
+        self.widget = GenericScanListWindow(parent=self)
+        self.widget.setWindowFlags(qt.Qt.Widget)
         self.widget.sigUpdated.connect(self._updateSettings)
         self._loadSettings()
         layout = gui.vBox(self.mainArea, self.name).layout()
         layout.addWidget(self.widget)
-        self.widget._sendButton.clicked.connect(self._sendList)
+        self.widget._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
+        self.clear = self.widget._widget.clear
 
     def _sendList(self):
         """Send a signal for each list to the next widget"""
@@ -107,8 +109,8 @@ class DataListOW(OWBaseWidget, openclass=True):
             # kept for backward compatibility since 0.11. To be removed on the future version.
             if "@" in scan:
                 entry, file_path = scan.split("@")
-                hdf5_tomo_scan = HDF5TomoScan(entry=entry, scan=file_path)
-                self.add(hdf5_tomo_scan)
+                nxtomo_scan = NXtomoScan(entry=entry, scan=file_path)
+                self.add(nxtomo_scan)
             else:
                 self.add(scan)
 

orangecontrib/tomwer/widgets/control/DataListenerOW.py

@@ -258,12 +258,12 @@ class DataListenerOW(
 
     def _jsonRPCConfigChanged(self):
         self._blissConfiguration = self._widget.getBlissServerConfiguration()
-        self._static_input[  # pylint: disable=E1137
-            "bliss_server_configuration"
-        ] = self._widget.getBlissServerConfiguration()
-        self._static_input[  # pylint: disable=E1137
-            "output_dir"
-        ] = self._widget.getOutputFolder()
+        self._static_input["bliss_server_configuration"] = (  # pylint: disable=E1137
+            self._widget.getBlissServerConfiguration()
+        )
+        self._static_input["output_dir"] = (  # pylint: disable=E1137
+            self._widget.getOutputFolder()
+        )
         if self.is_active():
             self.activate(False)
             self.activate(True)

orangecontrib/tomwer/widgets/control/DataSelectorOW.py

@@ -35,7 +35,7 @@ from orangewidget.widget import Input, Output, OWBaseWidget
 from silx.gui import qt
 
 import tomwer.core.process.control.scanselector
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.control.scanselectorwidget import ScanSelectorWidget
 
@@ -72,22 +72,21 @@ class DataSelectorOW(OWBaseWidget, openclass=True):
         super().__init__(parent)
 
         self.widget = ScanSelectorWidget(parent=self)
+        self.widget.setWindowFlags(qt.Qt.Widget)
         self._loadSettings()
 
         self.widget.sigUpdated.connect(self._updateSettings)
         self.widget.sigSelectionChanged.connect(self.changeSelection)
         layout = gui.vBox(self.mainArea, self.name).layout()
         layout.addWidget(self.widget)
-        # expose API
-        self.setActiveScan = self.widget.setActiveData
-        self.selectAll = self.widget.selectAll
-        self.n_scan = self.widget.n_scan
-        self.add = self.widget.add
 
     @Inputs.data
     def addScan(self, scan, *args, **kwargs):
+        self.add(scan)
+
+    def add(self, scan):
         if scan is not None:
-            self.widget.add(scan)
+            self.widget.add(scan=scan)
 
     def changeSelection(self, list_objs):
         if list_objs is None:
@@ -105,7 +104,9 @@ class DataSelectorOW(OWBaseWidget, openclass=True):
         """send output signals for each selected items"""
         sItem = self.widget.dataList.selectedItems()
         if sItem and len(sItem) >= 1:
-            selection = [_item.text() for _item in sItem]
+            selection = [
+                _item.data(qt.Qt.UserRole).get_identifier().to_str() for _item in sItem
+            ]
             self.changeSelection(list_objs=selection)
 
     def _loadSettings(self):
@@ -114,8 +115,8 @@ class DataSelectorOW(OWBaseWidget, openclass=True):
             # kept for backward compatibility since 0.11. To be removed on the future version.
             if "@" in scan:
                 entry, file_path = scan.split("@")
-                hdf5_tomo_scan = HDF5TomoScan(entry=entry, scan=file_path)
-                self.addScan(hdf5_tomo_scan)
+                nxtomo_scan = NXtomoScan(entry=entry, scan=file_path)
+                self.addScan(nxtomo_scan)
             else:
                 self.addScan(scan)
 
@@ -132,3 +133,13 @@ class DataSelectorOW(OWBaseWidget, openclass=True):
             self.widget.removeSelectedDatasets()
         else:
             super().keyPressEvent(event)
+
+    # expose API
+    def setActiveScan(self, data):
+        self.widget.setActiveData(data=data)
+
+    def selectAll(self):
+        return self.widget.selectAll()
+
+    def n_scan(self):
+        return self.widget.n_scan()

orangecontrib/tomwer/widgets/control/DataValidatorOW.py

@@ -166,12 +166,12 @@ class DataValidatorOW(SuperviseOW):
     def _updateSettings(self):
         viewer = self._widget._centralWidget
         self._viewer_config["mode"] = viewer.getDisplayMode()  # pylint: disable=E1137
-        self._viewer_config[  # pylint: disable=E1137
-            "slice_opt"
-        ] = viewer.getSliceOption()
-        self._viewer_config[  # pylint: disable=E1137
-            "radio_opt"
-        ] = viewer.getRadioOption()
+        self._viewer_config["slice_opt"] = (  # pylint: disable=E1137
+            viewer.getSliceOption()
+        )
+        self._viewer_config["radio_opt"] = (  # pylint: disable=E1137
+            viewer.getRadioOption()
+        )
 
     def _setSettings(self, settings):
         viewer = self._widget._centralWidget

orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py

@@ -38,7 +38,7 @@ from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
 from orangecontrib.tomwer.widgets.control.NXTomomillMixIn import NXTomomillMixIn
 from tomwer.core.process.control.nxtomomill import EDFToNxProcess
 from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.gui.control.datalist import EDFDataListMainWindow
 
 logger = logging.getLogger(__name__)
@@ -54,7 +54,7 @@ class EDF2NXOW(
     to HDF5scan.
     """
 
-    name = "edf2nx-nxtomomill"
+    name = "nxtomomill - edf2nx (Spec-EDF)"
     id = "orange.widgets.tomwer.control.NXTomomillOW.EDF2NXOW"
     description = "Convert folders with .edf to .nx"
     icon = "icons/edf2nx.svg"
@@ -79,6 +79,12 @@ class EDF2NXOW(
 
     LOGGER = logger
 
+    _ewoks_inputs_to_hide_from_orange = (
+        "edf_to_nx_configuration",
+        "progress",
+        "serialize_output_data",
+    )
+
     def __init__(self, parent=None):
         self.__configuration_cache = None
         # cache updated for each folder in order to match `_execute_ewoks_task` design
@@ -89,7 +95,7 @@ class EDF2NXOW(
         self.widget = EDFDataListMainWindow(parent=self)
         _layout.addWidget(self.widget)
         # for edf default output path is still the 'near to input file'
-        self.widget._dialog._nxTomomillOutputWidget._closeToBlissFileRB.setChecked(True)
+        self.widget._dialog._nxTomomillOutputWidget._inScanFolder.setChecked(True)
         # add 'convert auto' check box
         self._convertAutoCB = qt.QCheckBox(
             "convert automatically when edf scan send through 'edf scan' channel", self
@@ -109,7 +115,12 @@ class EDF2NXOW(
             edf_to_nx_configuration=EDFConfig().to_dict(),
         )
 
-        self.task_output_changed_callbacks.add(self._notify_state)
+        if isinstance(self.task_output_changed_callbacks, set):
+            self.task_output_changed_callbacks.add(self._notify_state)
+        elif isinstance(self.task_output_changed_callbacks, list):
+            self.task_output_changed_callbacks.append(self._notify_state)
+        else:
+            raise NotImplementedError
 
         # handle settings
         self._loadSettings()
@@ -175,8 +186,14 @@ class EDF2NXOW(
             edf_to_nx_configuration=self.__configuration_cache.to_dict()
         )
 
-        self.notify_on_going(scan=HDF5TomoScan(output_file, output_entry))
-        self._execute_ewoks_task(propagate=True)
+        self.notify_on_going(scan=NXtomoScan(output_file, output_entry))
+        try:
+            self._execute_ewoks_task(  # pylint: disable=E1123
+                propagate=True,
+                log_missing_inputs=False,
+            )
+        except Exception:
+            self._execute_ewoks_task(propagate=True)  # pylint: disable=E1123
 
     def get_task_inputs(self):
         return {
@@ -204,7 +221,7 @@ class EDF2NXOW(
             task_suceeded = task_executor.succeeded
             config = task_executor.current_task.inputs.edf_to_nx_configuration
             config = EDFConfig.from_dict(config)
-            scan = HDF5TomoScan(
+            scan = NXtomoScan(
                 config.output_file,
                 "entry",
             )

orangecontrib/tomwer/widgets/control/EmailOW.py

@@ -4,14 +4,14 @@ from orangewidget.settings import Setting
 from silx.gui import qt
 from ewoksorange.bindings.owwidgets import OWEwoksWidgetNoThread
 
-import tomwer.core.process.control.email
-from tomwer.gui.control.email import Emailwidget
-from tomwer.core.utils import concatenate_dict
+import tomwer.core.process.control.emailnotifier
+from tomwer.gui.control.emailnotifier import Emailwidget
+from tomwer.core.utils.dictutils import concatenate_dict
 
 
 class EmailOW(
     OWEwoksWidgetNoThread,
-    ewokstaskclass=tomwer.core.process.control.email.TomoEmailTask,
+    ewokstaskclass=tomwer.core.process.control.emailnotifier.TomoEmailTask,
 ):
     """
     This widget will browse a folder and sub folder to find valid tomo scan project.

orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py

@@ -36,9 +36,9 @@ class NXTomomillMixIn:
         assert (
             self.CONFIG_CLS is not None
         ), "inheriting classes are expected to redefine CONFIG_CLS"
-        self._ewoks_default_inputs[
-            "nxtomomill_cfg_file"
-        ] = cfg_file  # pylint: disable=E1137
+        self._ewoks_default_inputs["nxtomomill_cfg_file"] = (
+            cfg_file  # pylint: disable=E1137
+        )
 
         if os.path.exists(cfg_file):
             try:

orangecontrib/tomwer/widgets/control/NXTomomillOW.py

@@ -39,9 +39,12 @@ from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
 from orangecontrib.tomwer.widgets.control.NXTomomillMixIn import NXTomomillMixIn
 from tomwer.core.process.control.nxtomomill import H5ToNxProcess
 from tomwer.core.scan.blissscan import BlissScan
-from tomwer.core.scan.hdf5scan import HDF5TomoScan, HDF5TomoScanIdentifier
+from tomwer.core.scan.nxtomoscan import NXtomoScan, NXtomoScanIdentifier
 from tomwer.gui.control.datalist import BlissHDF5DataListMainWindow
 from tomwer.gui.control.nxtomomill import NXTomomillInput, OverwriteMessage
+from tomwer.core.process.output import ProcessDataOutputDirMode
+from ewoksorange.bindings.owwidgets import invalid_data
+
 
 logger = logging.getLogger(__name__)
 
@@ -56,7 +59,7 @@ class NXTomomillOW(
     to HDF5scan.
     """
 
-    name = "bliss(HDF5)-nxtomomill"
+    name = "nxtomomill h52nx (bliss-HDF5)"
     id = "orange.widgets.tomwer.control.NXTomomillOW.NXTomomillOW"
     description = (
         "Read a bliss .h5 file and extract from it all possible"
@@ -74,6 +77,7 @@ class NXTomomillOW(
         "NXTomo",
         "tomography",
         "nxtomomill",
+        "h52nx",
     ]
 
     want_main_area = True
@@ -84,6 +88,12 @@ class NXTomomillOW(
 
     LOGGER = logger
 
+    _ewoks_inputs_to_hide_from_orange = (
+        "h5_to_nx_configuration",
+        "progress",
+        "serialize_output_data",
+    )
+
     def __init__(self, parent=None):
         TomwerWithStackStack.__init__(self, parent=parent)
         NXTomomillMixIn.__init__(self)
@@ -113,7 +123,12 @@ class NXTomomillOW(
         self.update_default_inputs(
             h5_to_nx_configuration=HDF5Config().to_dict(),
         )
-        self.task_output_changed_callbacks.add(self._notify_state)
+        if isinstance(self.task_output_changed_callbacks, set):
+            self.task_output_changed_callbacks.add(self._notify_state)
+        elif isinstance(self.task_output_changed_callbacks, list):
+            self.task_output_changed_callbacks.append(self._notify_state)
+        else:
+            raise NotImplementedError
 
         # handle settings
         self._loadSettings()
@@ -124,13 +139,14 @@ class NXTomomillOW(
             # kept for backward compatibility since 0.11. To be removed on the future version.
             if "@" in scan:
                 entry, file_path = scan.split("@")
-                hdf5_tomo_scan = HDF5TomoScan(entry=entry, scan=file_path)
-                self.add(hdf5_tomo_scan)
+                nxtomo_scan = NXtomoScan(entry=entry, scan=file_path)
+                self.add(nxtomo_scan)
             else:
                 self._scans.append(scan)
-        self._ewoks_default_inputs[  # pylint: disable=E1137
-            "output_dir"
-        ] = self.widget.getOutputFolder()
+        output_dir = self.widget.getOutputFolder()
+        if isinstance(output_dir, ProcessDataOutputDirMode):
+            output_dir = output_dir.value
+        self._ewoks_default_inputs["output_dir"] = output_dir  # pylint: disable=E1137
 
     @property
     def request_input(self):
@@ -152,15 +168,13 @@ class NXTomomillOW(
         """
         # for now we want to avoid propagation any processing.
         # task will be executed only when the user validates the dialog
-        h5_scan = super().get_task_inputs().get("hdf5_scan", None)
-        if h5_scan is not None:
-            if not isinstance(h5_scan, H5ToNxProcess):
-                raise TypeError(
-                    "hdf5_scan is expected to be an instance of HDF5TomoScan"
-                )
-            self.add(h5_scan.path)
+        bliss_scan = super().get_task_inputs().get("bliss_scan", None)
+        if bliss_scan is not None:
+            if not isinstance(bliss_scan, BlissScan):
+                raise TypeError("bliss_scan is expected to be an instance of BlissScan")
+            self.add(bliss_scan.master_file)
 
-    def _convertAndSend(self, bliss_url):
+    def _convertAndSend(self, bliss_url: str):
         """
 
         :param str bliss_url: string at entry@file format
@@ -170,7 +184,7 @@ class NXTomomillOW(
             copy(self.get_default_input_values()["h5_to_nx_configuration"])
         )
 
-        identifier = HDF5TomoScanIdentifier.from_str(bliss_url)
+        identifier = NXtomoScanIdentifier.from_str(bliss_url)
         bliss_scan = BlissScan(
             master_file=identifier.file_path,
             entry=identifier.data_path,
@@ -235,7 +249,13 @@ class NXTomomillOW(
         self.update_default_inputs(
             h5_to_nx_configuration=self.__configuration_cache.to_dict()
         )
-        self._execute_ewoks_task(propagate=True)
+        try:
+            self._execute_ewoks_task(  # pylint: disable=E1123
+                propagate=True,
+                log_missing_inputs=False,
+            )
+        except Exception:
+            self._execute_ewoks_task(propagate=True)  # pylint: disable=E1123
 
     def _loadSettings(self):
         for scan in self._scans:
@@ -279,23 +299,27 @@ class NXTomomillOW(
         # reset the GUI for input (reset all the cache for answers)
         self._canOverwriteOutputs = False
         for bliss_url in self.widget.datalist.selectedItems():
-            identifier = HDF5TomoScanIdentifier.from_str(bliss_url.text())
+            data = bliss_url.data(qt.Qt.UserRole)
+            assert isinstance(data, NXtomoScan)
+            identifier = data.get_identifier()
             self._inputGUI.setBlissScan(
                 entry=identifier.data_path, file_path=identifier.file_path
             )
-            self._convertAndSend(bliss_url.text())
+            self._convertAndSend(identifier.to_str())
 
     def _sendAll(self):
         """Send a signal for each scan found to the next widget"""
         self._inputGUI = NXTomomillInput()
         # reset the GUI for input (reset all the cache for answers)
         self._canOverwriteOutputs = False
-        for bliss_url in self.widget.datalist.selectedItems():
-            identifier = HDF5TomoScanIdentifier.from_str(bliss_url.text())
+        for bliss_url in self.widget.datalist._myitems.values():
+            data = bliss_url.data(qt.Qt.UserRole)
+            identifier = data.get_identifier()
+            assert isinstance(data, NXtomoScan)
             self._inputGUI.setBlissScan(
                 entry=identifier.data_path, file_path=identifier.file_path
             )
-            self._convertAndSend(bliss_url.text())
+            self._convertAndSend(identifier.to_str())
 
     def _notify_state(self):
         try:
@@ -310,3 +334,20 @@ class NXTomomillOW(
                 self.notify_failed(scan=scan)
         except Exception as e:
             logger.error(f"failed to handle task finished callback. Raiseon is {e}")
+
+    def trigger_downstream(self) -> None:
+        for ewoksname, var in self.get_task_outputs().items():
+            # note: for now we want to trigger 'data' for each items of 'datas'
+            if ewoksname == "serie" and not (
+                invalid_data.is_invalid_data(var.value) or var.value is None
+            ):
+                for data in var.value:
+                    data_channel = self._get_output_signal("data")
+                    data_channel.send(data)
+                serie_channel = self._get_output_signal("serie")
+                # then send the list of value / serie (also know as datas)
+                serie_channel.send(var.value)
+            elif ewoksname == "data" and not (
+                invalid_data.is_invalid_data(var.value) or var.value is None
+            ):
+                pass  # handle by 'serie' in this case