tomwer 1.3.0.dev2__py3-none-any.whl → 1.3.0rc10__py3-none-any.whl

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"
 
@@ -33,13 +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.icat",
         "orangecontrib.tomwer.widgets.reconstruction",
         # "orangecontrib.tomwer.widgets.stitching",
         "orangecontrib.tomwer.widgets.visualization",
@@ -54,11 +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/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/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/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

@@ -42,6 +42,7 @@ from tomwer.core.scan.blissscan import BlissScan
 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
 
 
@@ -137,9 +138,10 @@ class NXTomomillOW(
                 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):
@@ -161,11 +163,11 @@ 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 NXtomoScan")
-            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: str):
         """

orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py

@@ -147,9 +147,9 @@ class SingleTomoObjOW(OWBaseWidget, openclass=True):
                         reduced_frames=data.reduced_darks, scan=data
                     )
                 )
-                reduced_darks[
-                    "reduce_frames_name"
-                ] = f"darks from {data.get_identifier().short_description()}"
+                reduced_darks["reduce_frames_name"] = (
+                    f"darks from {data.get_identifier().short_description()}"
+                )
                 self.Outputs.relative_reduced_darks.send(reduced_darks)
 
             if data.reduced_flats not in (None, {}):
@@ -162,7 +162,7 @@ class SingleTomoObjOW(OWBaseWidget, openclass=True):
                         reduced_frames=data.reduced_flats, scan=data
                     )
                 )
-                reduced_flats[
-                    "reduce_frames_name"
-                ] = f"flats from {data.get_identifier().short_description()}"
+                reduced_flats["reduce_frames_name"] = (
+                    f"flats from {data.get_identifier().short_description()}"
+                )
                 self.Outputs.relative_reduced_flats.send(reduced_flats)

orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py

@@ -156,7 +156,7 @@ class _DatasetGeneratorThread(threading.Thread):
                 n_proj=self.n_proj,
                 n_ini_proj=self.n_proj,
                 create_ini_dark=self.create_ini_dark,
-                create_ini_ref=self.create_ini_flat,
+                create_ini_flat=self.create_ini_flat,
                 dim=self.dims[0],
             ).scan
         elif self.type_to_generate == BlissScan.__name__:

orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py

@@ -1,98 +1,98 @@
-from orangewidget import gui
-from orangewidget.settings import Setting
-
-from silx.gui import qt
-import weakref
-from ewoksorange.bindings.owwidgets import OWEwoksWidgetOneThreadPerRun
-
-import tomwer.core.process.icat.createscreenshots
-from tomwer.gui.icat.createscreenshots import CreateRawDataScreenshotsWidget
-from processview.core.superviseprocess import SuperviseProcess
-
-
-class RawDataScreenshotCreatorOW(
-    OWEwoksWidgetOneThreadPerRun,
-    SuperviseProcess,
-    ewokstaskclass=tomwer.core.process.icat.createscreenshots.CreateRawDataScreenshotsTask,
-):
-    """
-    This widget can receive 'data' (scan) and but some screenshot to be pushed on GALLERY.
-    """
-
-    name = "Create raw data screenshots"
-    id = "orangecontrib.widgets.tomwer.icat.RawDataScreenshotCreatorOW.RawDataScreenshotCreatorOW"
-    description = "Create screenshot of the raw data from user wishes. \n"
-    icon = "icons/raw_screenshots.svg"
-    priority = 63
-    keywords = [
-        "tomography",
-        "tomwer",
-        "tomo_obj",
-        "screenshot",
-        "raw data",
-    ]
-
-    want_main_area = True
-    want_control_area = False
-    resizing_enabled = True
-
-    _ewoks_default_inputs = Setting(
-        {
-            "raw_projections_required": True,
-            "raw_projections_each": 90,
-            "raw_darks_required": True,
-            "raw_flats_required": True,
-        }
-    )
-
-    _ewoks_inputs_to_hide_from_orange = (
-        "__process__",
-        "raw_projections_required",
-        "raw_projections_each",
-        "raw_darks_required",
-        "raw_flats_required",
-    )
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        SuperviseProcess.__init__(self)
-        self._widget = CreateRawDataScreenshotsWidget(parent=self)
-
-        self._box = gui.vBox(self.mainArea, self.name)
-        layout = self._box.layout()
-        layout.addWidget(self._widget)
-
-        # 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 handleNewSignals(self) -> None:
-        """Invoked by the workflow signal propagation manager after all
-        signals handlers have been called.
-        """
-        # for now we want to avoid propagation any processing.
-        # task will be executed only when the user validates the dialog
-        if self.get_task_input_value("data", None) is None:
-            return
-        else:
-            super().handleNewSignals()
-
-    def get_task_inputs(self):
-        task_inputs = super().get_task_inputs()
-        configuration = self._widget.getConfiguration()
-        task_inputs["raw_projections_required"] = configuration[
-            "raw_projections_required"
-        ]
-        task_inputs["raw_projections_each"] = configuration["raw_projections_each"]
-        task_inputs["raw_darks_required"] = configuration["raw_darks_required"]
-        task_inputs["raw_flats_required"] = configuration["raw_flats_required"]
-        task_inputs["__process__"] = weakref.ref(self)
-        return task_inputs
-
-    def sizeHint(self):
-        return qt.QSize(500, 200)
+# from orangewidget import gui
+# from orangewidget.settings import Setting
+
+# from silx.gui import qt
+# import weakref
+# from ewoksorange.bindings.owwidgets import OWEwoksWidgetOneThreadPerRun
+
+# import tomwer.core.process.icat.createscreenshots
+# from tomwer.gui.icat.createscreenshots import CreateRawDataScreenshotsWidget
+# from processview.core.superviseprocess import SuperviseProcess
+
+
+# class RawDataScreenshotCreatorOW(
+#     OWEwoksWidgetOneThreadPerRun,
+#     SuperviseProcess,
+#     ewokstaskclass=tomwer.core.process.icat.createscreenshots.CreateRawDataScreenshotsTask,
+# ):
+#     """
+#     This widget can receive 'data' (scan) and but some screenshot to be pushed on GALLERY.
+#     """
+
+#     name = "Create raw data screenshots"
+#     id = "orangecontrib.widgets.tomwer.icat.RawDataScreenshotCreatorOW.RawDataScreenshotCreatorOW"
+#     description = "Create screenshot of the raw data from user wishes. \n"
+#     icon = "icons/raw_screenshots.svg"
+#     priority = 63
+#     keywords = [
+#         "tomography",
+#         "tomwer",
+#         "tomo_obj",
+#         "screenshot",
+#         "raw data",
+#     ]
+
+#     want_main_area = True
+#     want_control_area = False
+#     resizing_enabled = True
+
+#     _ewoks_default_inputs = Setting(
+#         {
+#             "raw_projections_required": True,
+#             "raw_projections_each": 90,
+#             "raw_darks_required": True,
+#             "raw_flats_required": True,
+#         }
+#     )
+
+#     _ewoks_inputs_to_hide_from_orange = (
+#         "__process__",
+#         "raw_projections_required",
+#         "raw_projections_each",
+#         "raw_darks_required",
+#         "raw_flats_required",
+#     )
+
+#     def __init__(self, *args, **kwargs):
+#         super().__init__(*args, **kwargs)
+#         SuperviseProcess.__init__(self)
+#         self._widget = CreateRawDataScreenshotsWidget(parent=self)
+
+#         self._box = gui.vBox(self.mainArea, self.name)
+#         layout = self._box.layout()
+#         layout.addWidget(self._widget)
+
+#         # 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 handleNewSignals(self) -> None:
+#         """Invoked by the workflow signal propagation manager after all
+#         signals handlers have been called.
+#         """
+#         # for now we want to avoid propagation any processing.
+#         # task will be executed only when the user validates the dialog
+#         if self.get_task_input_value("data", None) is None:
+#             return
+#         else:
+#             super().handleNewSignals()
+
+#     def get_task_inputs(self):
+#         task_inputs = super().get_task_inputs()
+#         configuration = self._widget.getConfiguration()
+#         task_inputs["raw_projections_required"] = configuration[
+#             "raw_projections_required"
+#         ]
+#         task_inputs["raw_projections_each"] = configuration["raw_projections_each"]
+#         task_inputs["raw_darks_required"] = configuration["raw_darks_required"]
+#         task_inputs["raw_flats_required"] = configuration["raw_flats_required"]
+#         task_inputs["__process__"] = weakref.ref(self)
+#         return task_inputs
+
+#     def sizeHint(self):
+#         return qt.QSize(500, 200)

orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py

@@ -1,129 +1,129 @@
-from typing import Optional
-from orangewidget import gui
-from orangewidget.settings import Setting
-
-from silx.gui import qt
-import weakref
-from ewoksorange.bindings.owwidgets import OWEwoksWidgetOneThreadPerRun
-
-from tomwer.core.scan.scanbase import TomwerScanBase
-import tomwer.core.process.icat.gallery
-from tomwer.gui.icat.gallery import GalleryWidget, _GalleryOutputDir
-from processview.core.superviseprocess import SuperviseProcess
-
-
-class SaveToGalleryAndPublishOW(
-    OWEwoksWidgetOneThreadPerRun,
-    SuperviseProcess,
-    ewokstaskclass=tomwer.core.process.icat.gallery.SaveToGalleryAndPublishTask,
-):
-    """
-    This widget can receive 'screenshots' signal (expected as a tuple (source, screenshots_dict)
-    source is the tomo obj associated (so we can automate deduction of the output dir)
-    screenshots_dict is a dict of str: DataUrl
-    """
-
-    name = "Save to gallery and publish"
-    id = "orangecontrib.widgets.tomwer.icat.MoveToGalleryOW.SaveToGalleryAndPublishOW"
-    description = "This widget will save screenshot of reconstruction to a specific location (acquisition gallery as the default end point) \n"
-    icon = "icons/add_gallery.svg"
-    priority = 63
-    keywords = [
-        "tomography",
-        "tomwer",
-        "tomo_obj",
-        "screenshot",
-        "acquisition",
-        "gallery",
-    ]
-
-    want_main_area = True
-    want_control_area = False
-    resizing_enabled = True
-
-    _ewoks_default_inputs = Setting(
-        {
-            "format": "png",
-            "output_location_mode": "default",
-            "custom_output": None,
-            "screenshots": None,
-            "overwrite": False,
-        }
-    )
-
-    _ewoks_inputs_to_hide_from_orange = (
-        "proposal",
-        "dataset",
-        "beamline",
-        "dry_run",
-        "__process__",
-    )
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        SuperviseProcess.__init__(self)
-        self._scan = None
-        self._widget = GalleryWidget(parent=self)
-
-        self._box = gui.vBox(self.mainArea, self.name)
-        layout = self._box.layout()
-        layout.addWidget(self._widget)
-
-        # 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._publishConfig.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...)
-        screenshots = self.get_task_input_value("screenshots", None)
-        if screenshots is None:
-            return
-        else:
-            scan = screenshots.scan
-            if scan != self.getScan():
-                self.setScan(scan)
-
-        if self.get_task_input_value("screenshots", None) is None:
-            return
-        else:
-            super().handleNewSignals()
-
-    def get_task_inputs(self):
-        task_inputs = super().get_task_inputs()
-        configuration = self._widget.getConfiguration()
-
-        use_custom_output_dir = _GalleryOutputDir.OutputDirMode.from_value(
-            configuration.get("output_location_mode", "default")
-        )
-        # if user requested to overwrite the output directory
-        if use_custom_output_dir is _GalleryOutputDir.OutputDirMode.PROPOSAL_GALLERY:
-            task_inputs["screenshots"]["output_dir"] = configuration["custom_output"]
-
-        task_inputs["overwrite"] = configuration["overwrite"]
-        task_inputs["format"] = configuration["output_format"]
-        task_inputs["beamline"] = configuration["beamline"]
-        task_inputs["dataset"] = configuration["dataset"]
-        task_inputs["proposal"] = configuration["proposal"]
-        task_inputs["__process__"] = weakref.ref(self)
-        return task_inputs
-
-    def sizeHint(self):
-        return qt.QSize(500, 200)
+# from typing import Optional
+# from orangewidget import gui
+# from orangewidget.settings import Setting
+
+# from silx.gui import qt
+# import weakref
+# from ewoksorange.bindings.owwidgets import OWEwoksWidgetOneThreadPerRun
+
+# from tomwer.core.scan.scanbase import TomwerScanBase
+# import tomwer.core.process.icat.gallery
+# from tomwer.gui.icat.gallery import GalleryWidget, _GalleryOutputDir
+# from processview.core.superviseprocess import SuperviseProcess
+
+
+# class SaveToGalleryAndPublishOW(
+#     OWEwoksWidgetOneThreadPerRun,
+#     SuperviseProcess,
+#     ewokstaskclass=tomwer.core.process.icat.gallery.SaveToGalleryAndPublishTask,
+# ):
+#     """
+#     This widget can receive 'screenshots' signal (expected as a tuple (source, screenshots_dict)
+#     source is the tomo obj associated (so we can automate deduction of the output dir)
+#     screenshots_dict is a dict of str: DataUrl
+#     """
+
+#     name = "Save to gallery and publish"
+#     id = "orangecontrib.widgets.tomwer.icat.MoveToGalleryOW.SaveToGalleryAndPublishOW"
+#     description = "This widget will save screenshot of reconstruction to a specific location (acquisition gallery as the default end point) \n"
+#     icon = "icons/add_gallery.svg"
+#     priority = 63
+#     keywords = [
+#         "tomography",
+#         "tomwer",
+#         "tomo_obj",
+#         "screenshot",
+#         "acquisition",
+#         "gallery",
+#     ]
+
+#     want_main_area = True
+#     want_control_area = False
+#     resizing_enabled = True
+
+#     _ewoks_default_inputs = Setting(
+#         {
+#             "format": "png",
+#             "output_location_mode": "default",
+#             "custom_output": None,
+#             "screenshots": None,
+#             "overwrite": False,
+#         }
+#     )
+
+#     _ewoks_inputs_to_hide_from_orange = (
+#         "proposal",
+#         "dataset",
+#         "beamline",
+#         "dry_run",
+#         "__process__",
+#     )
+
+#     def __init__(self, *args, **kwargs):
+#         super().__init__(*args, **kwargs)
+#         SuperviseProcess.__init__(self)
+#         self._scan = None
+#         self._widget = GalleryWidget(parent=self)
+
+#         self._box = gui.vBox(self.mainArea, self.name)
+#         layout = self._box.layout()
+#         layout.addWidget(self._widget)
+
+#         # 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._publishConfig.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...)
+#         screenshots = self.get_task_input_value("screenshots", None)
+#         if screenshots is None:
+#             return
+#         else:
+#             scan = screenshots.scan
+#             if scan != self.getScan():
+#                 self.setScan(scan)
+
+#         if self.get_task_input_value("screenshots", None) is None:
+#             return
+#         else:
+#             super().handleNewSignals()
+
+#     def get_task_inputs(self):
+#         task_inputs = super().get_task_inputs()
+#         configuration = self._widget.getConfiguration()
+
+#         use_custom_output_dir = _GalleryOutputDir.OutputDirMode.from_value(
+#             configuration.get("output_location_mode", "default")
+#         )
+#         # if user requested to overwrite the output directory
+#         if use_custom_output_dir is _GalleryOutputDir.OutputDirMode.PROPOSAL_GALLERY:
+#             task_inputs["screenshots"]["output_dir"] = configuration["custom_output"]
+
+#         task_inputs["overwrite"] = configuration["overwrite"]
+#         task_inputs["format"] = configuration["output_format"]
+#         task_inputs["beamline"] = configuration["beamline"]
+#         task_inputs["dataset"] = configuration["dataset"]
+#         task_inputs["proposal"] = configuration["proposal"]
+#         task_inputs["__process__"] = weakref.ref(self)
+#         return task_inputs
+
+#     def sizeHint(self):
+#         return qt.QSize(500, 200)