tomwer 1.3.25__tar.gz → 1.3.27__tar.gz

{tomwer-1.3.25/tomwer.egg-info → tomwer-1.3.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.25
+Version: 1.3.27
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

tomwer-1.3.27/orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py

@@ -0,0 +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.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)

{tomwer-1.3.25 → tomwer-1.3.27}/tomwer/core/process/reconstruction/nabu/utils.py

@@ -304,7 +304,7 @@ def get_multi_cor_recons_volume_identifiers(
 class _NabuMode(_Enum):
     FULL_FIELD = "standard acquisition"
     HALF_ACQ = "half acquisition"
-    HELICAL = "helical acquisition"
+    # HELICAL = "helical acquisition"
 
 
 class _NabuStages(_Enum):

{tomwer-1.3.25 → tomwer-1.3.27}/tomwer/gui/reconstruction/axis/radioaxis.py

@@ -1148,7 +1148,6 @@ class _ShiftInformation(qt.QWidget):
             self.setPalette(palette)
 
         def _userEndEditing(self, *args, **kwargs):
-            print("user end editing")
             palette = self.palette()
             palette.setColor(
                 self.backgroundRole(),

{tomwer-1.3.25 → tomwer-1.3.27}/tomwer/gui/stitching/stitching.py

@@ -1,5 +1,6 @@
 import logging
 import os
+import shutil
 import tempfile
 import functools
 
@@ -399,7 +400,7 @@ class ZStitchingWindow(qt.QMainWindow):
         # separator
         toolbar.addSeparator()
 
-        # configuraiton level / mode
+        # configuration level / mode
         self.__configurationModesAction = qt.QAction(self)
         self.__configurationModesAction.setCheckable(False)
         menu = qt.QMenu(self)
@@ -602,6 +603,8 @@ class ZStitchingWindow(qt.QMainWindow):
         self._callbackToSetSlurmConfig = callback
 
     def close(self):
+        # remove folder used for preview
+        shutil.rmtree(self._previewFolder, ignore_errors=True)
         self._widget.close()
         # requested for the waiting plot update
         super().close()
@@ -618,7 +621,6 @@ class ZStitchingWindow(qt.QMainWindow):
 
     def getPreviewFolder(self):
         if self._previewFolder is None:
-            # TODO: improve management of file: must be removed when the widget is closed...
             self._previewFolder = tempfile.mkdtemp(prefix="tomwer_stitcher_preview")
         return self._previewFolder
 
@@ -782,7 +784,6 @@ class ZStitchingWindow(qt.QMainWindow):
                 tomo_obj = existing_tomo_obj.get(tomo_obj_id, None)
                 if tomo_obj is None:
                     continue
-                # TODO: recuperer le tomo obj a partir de l'identifiant
                 if update_requested[0]:
                     tomo_obj.stitching_metadata.setPxPos(int(new_axis_0_pos), 0)
                 if update_requested[2]:

{tomwer-1.3.25 → tomwer-1.3.27}/tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 25
+MICRO = 27
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.3.25 → tomwer-1.3.27/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.25
+Version: 1.3.27
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

tomwer-1.3.25/orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py

@@ -1,184 +0,0 @@
-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)