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

orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py

@@ -1,169 +1,184 @@
-# import logging
-
-# from orangewidget import gui
-# from orangewidget.settings import Setting
-# from orangewidget.widget import Input, Output
-# from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
-# from silx.gui import qt
-# from typing import Optional
-
-# from tomwer.core.futureobject import FutureTomwerObject
-# from tomwer.core.scan.scanbase import TomwerScanBase
-# from tomwer.gui.reconstruction.nabu.helical import HelicalPrepareWeightsDouble
-# from tomwer.core.process.reconstruction.nabu.helical import (
-#     NabuHelicalPrepareWeightsDouble,
-# )
-# from tomwer.core.scan.hdf5scan import HDF5TomoScan
-
-# _logger = logging.getLogger(__name__)
-
-
-# class NabuHelicalPrepareWeightsDoubleOW(
-#     TomwerWithStackStack,
-#     ewokstaskclass=NabuHelicalPrepareWeightsDouble,
-# ):
-#     """
-#     widget used to call the `nabu-helical-prepare-weights-double` application on a dedicated thread. It define weights map and double flat field.
-
-#     :param parent: the parent widget
-#     """
-
-#     # note of this widget should be the one registered on the documentation
-#     name = "helical prerate weights double"
-#     id = "orangecontrib.tomwer.widgets.reconstruction.NabuHelicalPrepareWeightsDoubleOW.NabuHelicalPrepareWeightsDoubleOW"
-#     description = "compute map of weights requested for nabu helical reconstruction"
-#     icon = "icons/nabu_prepare_weights_double.svg"
-#     priority = 199
-#     keywords = [
-#         "tomography",
-#         "nabu",
-#         "reconstruction",
-#         "nabu-helical",
-#         "helical",
-#         "weights",
-#         "prepare",
-#     ]
-
-#     want_main_area = True
-#     want_control_area = False
-#     resizing_enabled = True
-
-#     _ewoks_default_inputs = Setting(
-#         {
-#             "data": None,
-#             "transition_width": 50,
-#             "processes_file": "",
-#         }
-#     )
-
-#     sigScanReady = qt.Signal(TomwerScanBase)
-#     "Signal emitted when a scan is ended"
-
-#     TIMEOUT = 30
-
-#     class Inputs:
-#         data = Input(
-#             name="data",
-#             type=TomwerScanBase,
-#             doc="one scan to be process",
-#             default=True,
-#             multiple=False,
-#         )
-
-#     class Outputs:
-#         data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
-#         future_tomo_obj = Output(
-#             name="future_tomo_obj",
-#             type=FutureTomwerObject,
-#             doc="future object (process remotely)",
-#         )
-
-#     LOGGER = _logger
-
-#     def __init__(self, parent=None):
-#         super().__init__(parent)
-#         self.__scan = None
-
-#         # gui definition
-#         _layout = gui.vBox(self.mainArea, self.name).layout()
-#         self.widget = HelicalPrepareWeightsDouble(parent=self)
-#         _layout.addWidget(self.widget)
-
-#         ## connect signal / slot
-#         self.widget.sigConfigChanged.connect(self._updateSettings)
-
-#         self.task_output_changed_callbacks.add(self._notify_state)
-
-#         ## handle settings
-#         self._loadSettings()
-#         self.task_executor_queue.sigComputationStarted.connect(self._newTaskStarted)
-
-#     def _updateSettings(self):
-#         config = self.widget.getConfiguration()
-#         for key in ("transition_width", "processes_file"):
-#             self._ewoks_default_inputs[key] = config[key]  # pylint: disable=E1137
-
-#     @property
-#     def request_input(self):
-#         return self.__request_input
-
-#     @request_input.setter
-#     def request_input(self, request):
-#         self.__request_input = request
-
-#     def get_task_inputs(self):
-#         assert self.__scan is not None
-#         return {
-#             "data": self.__scan,
-#             "transition_width": self.widget.getConfiguration()["transition_width"],
-#             "processes_file": self.widget.getConfiguration()["processes_file"],
-#         }
-
-#     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
-#         data = super().get_task_inputs().get("data", None)
-#         if data is not None:
-#             if not isinstance(data, HDF5TomoScan):
-#                 raise TypeError(
-#                     f"data is expected to be an instance of HDF5TomoScan. {type(data)} are not handled"
-#                 )
-#             self.add(data.path)
-
-#     def _loadSettings(self):
-#         self.widget.setConfiguration(self._ewoks_default_inputs)
-
-#     def _newTaskStarted(self):
-#         try:
-#             task_executor = self.sender()
-#             scan = task_executor.current_task.inputs.data
-#             self.notify_on_going(scan)
-#         except Exception:
-#             pass
-
-#     def _notify_state(self):
-#         try:
-#             task_executor = self.sender()
-#             task_suceeded = task_executor.succeeded
-#             scan = task_executor.current_task.outputs.data
-#             if task_suceeded:
-#                 self.notify_succeed(scan=scan)
-#             else:
-#                 self.notify_failed(scan=scan)
-#         except Exception as e:
-#             _logger.error(f"failed to handle task finished callback. Raiseon is {e}")
-
-#     @Inputs.data
-#     def process_data(self, scan: Optional[TomwerScanBase]):
-#         if scan is None:
-#             return
-#         else:
-#             self.__scan = scan
-#             self.notify_pending(scan=scan)
-#             self.execute_ewoks_task()
-
-#     def sizeHint(self) -> qt.QSize:
-#         return qt.QSize(650, 60)
+import logging
+
+from orangewidget import gui
+from orangewidget.settings import Setting
+from orangewidget.widget import Input, Output
+from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
+from silx.gui import qt
+from typing import Optional
+
+from tomwer.core.futureobject import FutureTomwerObject
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.gui.reconstruction.nabu.helical import HelicalPrepareWeightsDouble
+from tomwer.core.process.reconstruction.nabu.helical import (
+    NabuHelicalPrepareWeightsDouble,
+)
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+
+_logger = logging.getLogger(__name__)
+
+
+class NabuHelicalPrepareWeightsDoubleOW(
+    TomwerWithStackStack,
+    ewokstaskclass=NabuHelicalPrepareWeightsDouble,
+):
+    """
+    widget used to call the `nabu-helical-prepare-weights-double` application on a dedicated thread. It define weights map and double flat field.
+
+    :param parent: the parent widget
+    """
+
+    # note of this widget should be the one registered on the documentation
+    name = "helical prerate weights double"
+    id = "orangecontrib.tomwer.widgets.reconstruction.NabuHelicalPrepareWeightsDoubleOW.NabuHelicalPrepareWeightsDoubleOW"
+    description = "compute map of weights requested for nabu helical reconstruction"
+    icon = "icons/nabu_prepare_weights_double.svg"
+    priority = 199
+    keywords = [
+        "tomography",
+        "nabu",
+        "reconstruction",
+        "nabu-helical",
+        "helical",
+        "weights",
+        "prepare",
+    ]
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    _ewoks_default_inputs = Setting(
+        {
+            "data": None,
+            "transition_width_vertical": 50,
+            "transition_width_horizontal": 50,
+            "processes_file": "",
+            "rotation_axis_position": 0,
+        }
+    )
+
+    _ewoks_inputs_to_hide_from_orange = (
+        "progress",
+        "processes_file",
+        "transition_width_vertical",
+        "transition_width_horizontal",
+        "rotation_axis_position",
+    )
+
+    sigScanReady = qt.Signal(TomwerScanBase)
+    "Signal emitted when a scan is ended"
+
+    TIMEOUT = 30
+
+    class Inputs:
+        data = Input(
+            name="data",
+            type=TomwerScanBase,
+            doc="one scan to be process",
+            default=True,
+            multiple=False,
+        )
+
+    class Outputs:
+        data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
+        future_tomo_obj = Output(
+            name="future_tomo_obj",
+            type=FutureTomwerObject,
+            doc="future object (process remotely)",
+        )
+
+    LOGGER = _logger
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.__scan = None
+
+        # gui definition
+        _layout = gui.vBox(self.mainArea, self.name).layout()
+        self.widget = HelicalPrepareWeightsDouble(parent=self)
+        _layout.addWidget(self.widget)
+
+        ## connect signal / slot
+        self.widget.sigConfigChanged.connect(self._updateSettings)
+
+        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()
+        self.task_executor_queue.sigComputationStarted.connect(self._newTaskStarted)
+
+    def _updateSettings(self):
+        config = self.widget.getConfiguration()
+        for key in ("transition_width", "processes_file"):
+            self._ewoks_default_inputs[key] = config[key]  # pylint: disable=E1137
+
+    @property
+    def request_input(self):
+        return self.__request_input
+
+    @request_input.setter
+    def request_input(self, request):
+        self.__request_input = request
+
+    def get_task_inputs(self):
+        assert self.__scan is not None
+        return {
+            "data": self.__scan,
+            "transition_width": self.widget.getConfiguration()["transition_width"],
+            "processes_file": self.widget.getConfiguration()["processes_file"],
+        }
+
+    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
+        data = super().get_task_inputs().get("data", None)
+        if data is not None:
+            if not isinstance(data, NXtomoScan):
+                raise TypeError(
+                    f"data is expected to be an instance of NXtomoScan. {type(data)} are not handled"
+                )
+            self.add(data.path)
+
+    def _loadSettings(self):
+        self.widget.setConfiguration(self._ewoks_default_inputs)
+
+    def _newTaskStarted(self):
+        try:
+            task_executor = self.sender()
+            scan = task_executor.current_task.inputs.data
+            self.notify_on_going(scan)
+        except Exception:
+            pass
+
+    def _notify_state(self):
+        try:
+            task_executor = self.sender()
+            task_suceeded = task_executor.succeeded
+            scan = task_executor.current_task.outputs.data
+            if task_suceeded:
+                self.notify_succeed(scan=scan)
+            else:
+                self.notify_failed(scan=scan)
+        except Exception as e:
+            _logger.error(f"failed to handle task finished callback. Raiseon is {e}")
+
+    @Inputs.data
+    def process_data(self, scan: Optional[TomwerScanBase]):
+        if scan is None:
+            return
+        else:
+            self.__scan = scan
+            self.notify_pending(scan=scan)
+            self.execute_ewoks_task()
+
+    def sizeHint(self) -> qt.QSize:
+        return qt.QSize(650, 60)

orangecontrib/tomwer/widgets/reconstruction/NabuOW.py

@@ -28,6 +28,7 @@ __license__ = "MIT"
 __date__ = "14/02/2020"
 
 
+import os
 import copy
 import logging
 from contextlib import AbstractContextManager
@@ -44,6 +45,10 @@ from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSlicesTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.core.volume.volumefactory import VolumeFactory
+from tomwer.core.process.icat.gallery import (
+    IcatScreenshots,
+    deduce_dataset_gallery_location,
+)
 from tomwer.gui.reconstruction.nabu.slices import NabuWindow
 from tomwer.synctools.stacks.reconstruction.nabu import NabuSliceProcessStack
 
@@ -109,6 +114,12 @@ class NabuOW(WidgetLongProcessing, SuperviseOW):
 
         slice_urls = Output(name="slice urls", type=tuple, doc="tuple of urls created")
 
+        screenshots = Output(
+            name="screenshots",
+            type=IcatScreenshots,
+            doc="screenshots that can be saved",
+        )
+
     class DialogCM(AbstractContextManager):
         """Simple context manager to hide / show button dialogs"""
 
@@ -262,7 +273,19 @@ class NabuOW(WidgetLongProcessing, SuperviseOW):
                 )
             if len(slice_urls) > 0:
                 slice_urls = tuple(slice_urls)
+                # provide list of reconstructed slices
                 self.Outputs.slice_urls.send(slice_urls)
+                # provide list of screenshots
+                self.Outputs.screenshots.send(
+                    IcatScreenshots(
+                        data_dir=deduce_dataset_gallery_location(scan),
+                        screenshots={
+                            os.path.splitext(os.path.basename(url.file_path()))[0]: url
+                            for url in slice_urls
+                        },
+                        scan=scan,
+                    )
+                )
 
             self.sigScanReady.emit(scan)
         if future_tomo_obj is not None:

orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -45,6 +45,11 @@ from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 from tomwer.core import settings
 from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
+from tomwer.core.process.icat.gallery import (
+    IcatScreenshots,
+    deduce_dataset_gallery_location,
+    select_screenshot_from_volume,
+)
 from tomwer.core.process.reconstruction.nabu import utils as nabu_utils
 from tomwer.core.process.reconstruction.nabu.nabuvolume import NabuVolumeTask
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -123,6 +128,11 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
         volume_urls = Output(
             name="volume urls", type=tuple, doc="url of the volume(s) reconstructed"
         )
+        screenshots = Output(
+            name="screenshots",
+            type=IcatScreenshots,
+            doc="screenshots that can be saved",
+        )
 
     class DialogCM(AbstractContextManager):
         """Simple context manager to hida / show button dialogs"""
@@ -172,7 +182,7 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
 
         if nabu_volume_params not in (dict(), None):
             try:
-                self._nabuWidget.setConfiguration(nabu_volume_params)
+                self.setConfiguration(nabu_volume_params)
             except Exception:
                 _logger.warning("fail to load reconstruction settings")
 
@@ -213,14 +223,19 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
         config = scan.nabu_recons_params
         # update output format if requested
         if self._nabuWidget._mainWidget.redefineNabuFileFormat():
-            config.get("output")[
+            config["output"][
                 "file_format"
             ] = self._nabuWidget._mainWidget.getNabuFileFormat()
         # update output location if requested
         if self._nabuWidget._mainWidget.redefineOutputLocation():
-            config.get("output")["location"] = format_output_location(
-                location=self._nabuWidget._mainWidget.getNabuOutputLocation(),
-                scan=scan,
+            location = self._nabuWidget._mainWidget.getNabuOutputLocation()
+            if location is not None:
+                location = format_output_location(location=location, scan=scan)
+            config["output"]["location"] = location
+            config["output"][
+                "output_dir_mode"
+            ] = (
+                self._nabuWidget._mainWidget._outputLocationWidget.getOutputDirMode().value
             )
 
         if "phase" in config and "delta_beta" in config["phase"]:
@@ -314,7 +329,26 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
                 assert isinstance(volume_id, VolumeIdentifier)
                 volume_urls.extend(VolumeFactory.from_identifier_to_vol_urls(volume_id))
             if len(volume_urls) > 0:
+                # send list of reconcstructed volume
                 self.Outputs.volume_urls.send(tuple(volume_urls))
+                # send list of screenshots
+                screenshots = {}
+                [
+                    screenshots.update(
+                        select_screenshot_from_volume(
+                            VolumeFactory.create_tomo_object_from_identifier(volume_id)
+                        )
+                    )
+                    for volume_id in scan.latest_vol_reconstructions
+                ]
+                self.Outputs.screenshots.send(
+                    IcatScreenshots(
+                        data_dir=deduce_dataset_gallery_location(scan),
+                        screenshots=screenshots,
+                        scan=scan,
+                    ),
+                )
+
             # send volume identifier(s)  # only one expected
             n_rec_volumes = len(scan.latest_vol_reconstructions)
             if n_rec_volumes > 0:

orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -43,9 +43,9 @@ from silx.gui import qt
 import tomwer.core.process.reconstruction.saaxis.saaxis
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
-from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.axis import AxisTask
 from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
@@ -270,12 +270,14 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     Details about :ref:`saaxis score calculation`
     """
 
-    name = "semi-automated center of rotation"
+    name = "multi-cor (sa-axis)"
     id = "orange.widgets.tomwer.sa_axis"
-    description = "use to compute the center of rotation semi automatic way"
+    description = "Reconstruct a slice with different center of rotation (cor) values"
     icon = "icons/saaxis.png"
     priority = 21
     keywords = [
+        "multi",
+        "multi-cor",
         "tomography",
         "semi automatic",
         "half automatic",
@@ -322,12 +324,6 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     class Outputs:
         data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
 
-        future_out = Output(
-            name="future_tomo_obj",
-            type=FutureTomwerObject,
-            doc="data with some remote processing",
-        )
-
     def __init__(self, parent=None):
         """
 
@@ -347,7 +343,6 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
 
         # connect signal / slot
         self._widget.sigConfigurationChanged.connect(self._updateSettings)
-        self.destroyed.connect(self._widget.stop)
         self._widget._processing_stack.sigComputationStarted.connect(
             self._startProcessing
         )
@@ -358,6 +353,17 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
         # expose API
         self.wait_processing = self._widget.wait_processing
 
+    def getWaitingOverlay(self):
+        return self._widget._tabWidget._resultsViewer._plot.getWaiterOverlay()
+
+    def _startProcessing(self, *args, **kwargs):
+        self.getWaitingOverlay().show()
+        super()._startProcessing()
+
+    def _endProcessing(self, *args, **kwargs):
+        self.getWaitingOverlay().hide()
+        super()._endProcessing()
+
     def __new__(cls, *args, **kwargs):
         # ensure backward compatibility with 'static_input'
         static_input = kwargs.get("stored_settings", {}).get("static_input", None)
@@ -404,9 +410,7 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
             scan.saaxis_params = QSAAxisParams()
         self._skipCurrentScan(new_scan=scan)
 
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             self.notify_skip(
                 scan=scan,
                 details=f"saaxis has been skiped for {scan} because of low space in lbsram",
@@ -484,13 +488,5 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
             self.show()
             self._widget.showResults()
 
-    def stop(self):
-        self._widget.stop()
-
-    def close(self):
-        self.stop()
-        self._widget = None
-        super().close()
-
     def getConfiguration(self):
         return self._widget.getConfiguration()