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

orangecontrib/tomwer/widgets/reconstruction/AxisOW.py

@@ -495,18 +495,19 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
             cor = self._axis_params.relative_cor_value
             scan.axis_params.set_relative_value(cor)
             scan._axis_params.mode = "manual"
-            try:
-                AxisTask._register_process(
-                    process_file=scan.process_file,
-                    entry=entry,
-                    process=AxisTask,
-                    results={"center_of_rotation": cor if cor is not None else "-"},
-                    configuration=self._axis_params.to_dict(),
-                    process_index=scan.pop_process_index(),
-                    overwrite=True,
-                )
-            except Exception as e:
-                logger.warning(f"Fail to register Axis process. Error is {e}")
+            with scan.acquire_process_file_lock():
+                try:
+                    AxisTask._register_process(
+                        process_file=scan.process_file,
+                        entry=entry,
+                        process=AxisTask,
+                        results={"center_of_rotation": cor if cor is not None else "-"},
+                        configuration=self._axis_params.to_dict(),
+                        process_index=scan.pop_process_index(),
+                        overwrite=True,
+                    )
+                except Exception as e:
+                    logger.warning(f"Fail to register Axis process. Error is {e}")
             ProcessManager().notify_dataset_state(
                 dataset=scan,
                 process=AxisTask(

orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -343,7 +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
         )
@@ -354,6 +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)
@@ -478,13 +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()

orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -277,7 +277,6 @@ class SADeltaBetaOW(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
         )
@@ -383,14 +382,6 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             "autofocus_lock": self._widget.isAutoFocusLock(),
         }
 
-    def close(self):
-        self.stop()
-        self._widget = None
-        super().close()
-
-    def stop(self):
-        self._widget.stop()
-
     def getConfiguration(self):
         return self._widget.getConfiguration()
 
@@ -408,3 +399,14 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             # if possible process next
             if self._widget._processing_stack.can_process_next():
                 self._widget._processing_stack._process_next()
+
+    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()

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

@@ -164,7 +164,6 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
 
         # connect signal / slot
         self._window.sigConfigurationChanged.connect(self._updateSettings)
-        self.destroyed.connect(self._window.stop)
         self._window._processing_stack.sigComputationStarted.connect(
             self._startProcessing
         )
@@ -218,17 +217,18 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
         tomwer_processing_res_code = extra_infos.pop(
             "tomwer_processing_res_code", "unprocessed"
         )
-        SinoNormalizationTask._register_process(
-            process_file=scan.process_file,
-            process=SinoNormalizationTask,
-            entry=scan.entry,
-            configuration=self.getConfiguration(),
-            results={
-                "method": scan.intensity_normalization.method.value,
-                "extra_infos": extra_infos,
-            },
-            process_index=scan.pop_process_index(),
-        )
+        with scan.acquire_process_file_lock():
+            SinoNormalizationTask._register_process(
+                process_file=scan.process_file,
+                process=SinoNormalizationTask,
+                entry=scan.entry,
+                configuration=self.getConfiguration(),
+                results={
+                    "method": scan.intensity_normalization.method.value,
+                    "extra_infos": extra_infos,
+                },
+                process_index=scan.pop_process_index(),
+            )
         if tomwer_processing_res_code is True:
             # if defined by manual scalar we need to set the value
             if extra_infos.get("source", None) == _ValueSource.MANUAL_SCALAR.value:
@@ -292,9 +292,6 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
     def getConfiguration(self):
         return self._window.getConfiguration()
 
-    def stop(self):
-        self._window.stop()
-
     def _updateSettings(self):
         self._ewoks_default_inputs = self._window.getConfiguration()
         self._ewoks_default_inputs["__lock__"] = self.isLocked()

orangecontrib/tomwer/widgets/visualization/DataViewerOW.py

@@ -120,15 +120,15 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         return qt.QSize(400, 500)
 
     def _updateSettings(self):
-        self._viewer_config[  # pylint: disable=E1137
-            "mode"
-        ] = self.viewer.getDisplayMode().value
-        self._viewer_config[  # pylint: disable=E1137
-            "slice_opt"
-        ] = self.viewer.getSliceOption().value
-        self._viewer_config[  # pylint: disable=E1137
-            "radio_opt"
-        ] = self.viewer.getRadioOption().value
+        self._viewer_config["mode"] = (  # pylint: disable=E1137
+            self.viewer.getDisplayMode().value
+        )
+        self._viewer_config["slice_opt"] = (  # pylint: disable=E1137
+            self.viewer.getSliceOption().value
+        )
+        self._viewer_config["radio_opt"] = (  # pylint: disable=E1137
+            self.viewer.getRadioOption().value
+        )
 
     def _setSettings(self, settings):
         old_state = self.viewer.blockSignals(True)

orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py

@@ -47,7 +47,7 @@ class DiffViewerOW(widget.OWBaseWidget, openclass=True):
     Allows to compare two random frame.
     """
 
-    name = "diff viewer"
+    name = "diff frame viewer"
     id = "orangecontrib.tomwer.widgets.visualization.diffviewerow"
     description = "Allows comparison between two random frame from a scan"
     icon = "icons/diff.png"

orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py

@@ -79,7 +79,6 @@ class SinogramViewerOW(WidgetLongProcessing, widget.OWBaseWidget, openclass=True
         # connect signal / slot
         self._viewer.sigSinoLoadStarted.connect(self._startProcessing)
         self._viewer.sigSinoLoadEnded.connect(self._endProcessing)
-        self.destroyed.connect(self._viewer._stopAnimationThread)
 
     @Inputs.data
     def addLeafScan(self, scanID):

tomwer/__main__.py

@@ -168,16 +168,6 @@ def main():
         module_name="tomwer.app.intensitynormalization",
         description="Tool to compute intensity normalization.",
     )
-    launcher.add_command(
-        "lamino",
-        module_name="tomwer.app.lamino",
-        description="Run laminography reconstruction using tofu",
-    )
-    launcher.add_command(
-        "liveslice",
-        module_name="tomwer.app.liveslice",
-        description="Run liveslice application",
-    )
     launcher.add_command(
         "multi-cor",
         module_name="tomwer.app.multicor",

tomwer/app/canvas_launcher/config.py

@@ -112,9 +112,9 @@ class TomwerConfig(config.Config):
 
         all_eps = sorted(
             all_eps,
-            key=lambda ep: 0
-            if ep.dist.project_name.lower() in ("orange3", "tomwer")
-            else 1,
+            key=lambda ep: (
+                0 if ep.dist.project_name.lower() in ("orange3", "tomwer") else 1
+            ),
         )
         return iter(all_eps)
 

tomwer/app/canvas_launcher/environ.py

@@ -40,6 +40,7 @@ orangerc.cfg
     canvas_settings_dir = %(prefix)s/config/%(name)s/canvas
 
 """
+
 import configparser
 import os
 import sys

tomwer/app/intensitynormalization.py

@@ -72,17 +72,18 @@ class NormIntensityWindow(_SinoNormWindow):
     def _validated(self):
         scan = self.getScan()
         if scan is not None:
-            SinoNormalizationTask._register_process(
-                process_file=scan.process_file,
-                process=SinoNormalizationTask,
-                entry=scan.entry,
-                configuration=self.getConfiguration(),
-                results={
-                    "method": scan.intensity_normalization.method.value,
-                    "extra_infos": scan.intensity_normalization.get_extra_infos(),
-                },
-                process_index=scan.pop_process_index(),
-            )
+            with scan.acquire_process_file_lock():
+                SinoNormalizationTask._register_process(
+                    process_file=scan.process_file,
+                    process=SinoNormalizationTask,
+                    entry=scan.entry,
+                    configuration=self.getConfiguration(),
+                    results={
+                        "method": scan.intensity_normalization.method.value,
+                        "extra_infos": scan.intensity_normalization.get_extra_infos(),
+                    },
+                    process_index=scan.pop_process_index(),
+                )
         self.close()
 
     def _launchProcessing(self):

tomwer/app/nabuapp.py

@@ -44,12 +44,6 @@ class DataViewer(_DataViewer):
         if event.key() is qt.Qt.Key_F5:
             self._updateDisplay()
 
-    def event(self, event) -> bool:
-        if event.type() == qt.QEvent.DeferredDelete:
-            self.cleanBeforeQuit()
-            self.closed.emit()
-        return super().event(event)
-
 
 class NabuProcessingThread(qt.QThread):
     def init(self, data, config, dry_run=False):
@@ -185,10 +179,6 @@ class NabuWindow(NabuDialog):
             self._dataViewer.close()
             self._dataViewer = None
 
-    def _aboutToQuit(self):
-        if self._dataViewer is not None:
-            self._dataViewer.cleanBeforeQuit()
-
 
 def main(argv):
     import os
@@ -248,7 +238,6 @@ def main(argv):
     widget.setWindowIcon(icons.getQIcon("tomwer"))
     splash.finish(widget)
     widget.show()
-    qt.QApplication.instance().aboutToQuit.connect(widget._aboutToQuit)
 
     app.exec_()
 

tomwer/app/zstitching.py

@@ -21,6 +21,7 @@ from tomwer.gui.utils.splashscreen import getMainSplashScreen
 from tomwer.gui.stitching.stitching import ZStitchingWindow as _ZStitchingWindow
 from tomwer.gui.stitching import action as stitching_action
 from tomwer.gui.cluster.slurm import SlurmSettingsWidget
+from tomwer.core.scan.scanbase import TomwerScanBase
 
 logging.basicConfig(level=logging.WARNING)
 
@@ -296,7 +297,12 @@ def main(argv):
         action="store_true",
         default=False,
     )
-
+    parser.add_argument(
+        "--check-scans",
+        help="If True will check scans before adding them. This check scan validity (virtual dataset contains data...)",
+        action="store_true",
+        default=False,
+    )
     options = parser.parse_args(argv[1:])
 
     if options.use_opengl_plot:
@@ -342,6 +348,10 @@ def main(argv):
 
     tomo_objs, (has_scans, has_vols) = get_tomo_objs_instances(options.tomo_objs)
     for tomo_obj in tomo_objs:
+        if isinstance(tomo_obj, TomwerScanBase):
+            tomo_obj.set_check_behavior(
+                run_check=options.check_scans
+            )  # speed up processing
         window.addTomoObj(tomo_obj=tomo_obj)
     if has_scans and has_vols:
         _logger.warning(

tomwer/core/process/control/datalistener/datalistener.py

@@ -102,6 +102,11 @@ class DataListener(BaseProcessInfo):
     TIMOUT_READ_FILE = 30
     "When the event 'scan_ended' is received all data might not have been write" " yet"
 
+    SWMR_MODE = None
+    """The bliss writer is not using the swmr mode. This class has independant behavior regarding the tomoscan / nxotmo get_swmr_mode which is
+    dedicated to the internal tomotools behavior
+    """
+
     def __init__(self):
         super().__init__()
         self._host = settings.JSON_RPC_HOST
@@ -224,7 +229,7 @@ class DataListener(BaseProcessInfo):
         """Return the list of scans dir for this bliss_file / entry"""
 
         def get_scan_indexes():
-            with HDF5File(bliss_file, "r", swmr=True) as h5f:
+            with HDF5File(bliss_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                 entry_node = h5f[entry]
                 if _SCAN_NUMBER_PATH in entry_node:
                     return h5py_read_dataset(entry_node[_SCAN_NUMBER_PATH])
@@ -249,7 +254,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=True) as h5f:
+            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -264,7 +269,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=True) as h5f:
+        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -306,7 +311,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=True) as h5f:
+            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -321,7 +326,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=True) as h5f:
+        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -355,7 +360,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=True) as h5f:
+            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -370,7 +375,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=True) as h5f:
+        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -405,7 +410,7 @@ class DataListener(BaseProcessInfo):
         specific sequence data
         """
         if entry is None:
-            with HDF5File(process_file, "r", swmr=True) as h5f:
+            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -420,7 +425,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=True) as h5f:
+        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -498,7 +503,7 @@ class DataListener(BaseProcessInfo):
         # write
         def sequence_is_finished():
             try:
-                with HDF5File(bliss_file, "r", swmr=True) as h5f:
+                with HDF5File(bliss_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
                     end_scan_path = "/".join((entry, "end_time"))
                     return end_scan_path in h5f
             except Exception:

tomwer/core/process/control/nxtomomill.py

@@ -57,7 +57,7 @@ class H5ToNxProcess(
     input_names=("h5_to_nx_configuration",),
     optional_input_names=(
         "progress",
-        "hdf5_scan",
+        "bliss_scan",
         "serialize_output_data",
     ),
     output_names=("data", "serie"),

tomwer/core/process/control/scantransfer.py

@@ -1,33 +1,3 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "05/07/2017"
-
-
 import fnmatch
 import logging
 import os
@@ -48,6 +18,12 @@ from tomwer.core.utils import logconfig
 from tomwer.core.utils.spec import rebaseParFile
 from tomwer.core.utils.scanutils import data_identifier_to_scan
 from tomwer.io.utils import get_linked_files_with_entry
+from tomwer.core.process.reconstruction.saaxis.saaxis import (
+    DEFAULT_RECONS_FOLDER as MULTI_COR_DEFAULT_FOLDER,
+)
+from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
+    DEFAULT_RECONS_FOLDER as MULTI_DB_DEFAULT_FOLDER,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -398,8 +374,8 @@ class ScanTransferTask(
         patterns = [
             NABU_CFG_FILE_FOLDER,
             "*slice*",
-            "saaxis_results",
-            "sadeltabeta_results",
+            MULTI_COR_DEFAULT_FOLDER,
+            MULTI_DB_DEFAULT_FOLDER,
             "steps_file_basename_nabu_sinogram_save_step",
         ]
         for folder_ in os.listdir(dir_name):

tomwer/core/process/edit/darkflatpatch.py

@@ -95,15 +95,14 @@ class DarkFlatPatchTask(
             if isinstance(value, DataUrl):
                 config[key] = value.path()
 
-        with scan.acquire_process_file_lock():
-            self.register_process(
-                process_file=scan.process_file,
-                entry=scan.entry,
-                configuration=config,
-                results={},
-                process_index=scan.pop_process_index(),
-                overwrite=True,
-            )
+        self.register_process(
+            process_file=scan.process_file,
+            entry=scan.entry,
+            configuration=config,
+            results={},
+            process_index=scan.pop_process_index(),
+            overwrite=True,
+        )
         if self.get_input_value("serialize_output_data", True):
             self.outputs.data = scan.to_dict()
         else:

tomwer/core/process/edit/imagekeyeditor.py

@@ -83,7 +83,7 @@ def change_image_key_control(scan: NXtomoScan, config: dict) -> TomwerScanBase:
             filter(lambda item: item[1] is image_key_type, modifications.items())
         )
         frame_indexes = tuple(frame_indexes_dict.keys())
-        _logger.warning(f"will modify {frame_indexes} to {image_key_type}")
+        _logger.info(f"will modify {frame_indexes} to {image_key_type}")
         _change_image_key_control(
             file_path=scan.master_file,
             entry=scan.entry,
@@ -137,15 +137,14 @@ class ImageKeyEditorTask(
             value = config["modifications"][key]
             config["modifications"][str(key)] = value
         config["modifications"] = new_modif
-        with scan.acquire_process_file_lock():
-            self.register_process(
-                process_file=scan.process_file,
-                entry=scan.entry,
-                configuration=config,
-                results={},
-                process_index=scan.pop_process_index(),
-                overwrite=True,
-            )
+        self.register_process(
+            process_file=scan.process_file,
+            entry=scan.entry,
+            configuration=config,
+            results={},
+            process_index=scan.pop_process_index(),
+            overwrite=True,
+        )
         if self.get_input_value("serialize_output_data", True):
             self.outputs.data = scan.to_dict()
         else:
@@ -198,18 +197,17 @@ class ImageKeyUpgraderTask(
 
         # apply modification using tomoscan
         change_image_key_control(scan=scan, config=configuration)
-        with scan.acquire_process_file_lock():
-            self.register_process(
-                process_file=scan.process_file,
-                entry=scan.entry,
-                configuration={
-                    ImageKey.from_value(key).value: ImageKey.from_value(value).value
-                    for key, value in operations.items()
-                },
-                results={},
-                process_index=scan.pop_process_index(),
-                overwrite=True,
-            )
+        self.register_process(
+            process_file=scan.process_file,
+            entry=scan.entry,
+            configuration={
+                ImageKey.from_value(key).value: ImageKey.from_value(value).value
+                for key, value in operations.items()
+            },
+            results={},
+            process_index=scan.pop_process_index(),
+            overwrite=True,
+        )
         if self.get_input_value("serialize_output_data", True):
             self.outputs.data = scan.to_dict()
         else:

tomwer/core/process/icat/screenshots.py

@@ -1,5 +1,6 @@
 """utils around screenshots.
 """
+
 from .icatbase import IcatProcessedDataBase
 from tomwer.core.scan.scanbase import TomwerScanBase