tomwer 2.0.0.dev3__tar.gz → 2.0.0.dev4__tar.gz

{tomwer-2.0.0.dev3/src/tomwer.egg-info → tomwer-2.0.0.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 2.0.0.dev3
+Version: 2.0.0.dev4
 Summary: Tomography workflow tools
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: MIT

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/orangecontrib/tomwer/widgets/cluster/MonitorOW.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import time
+import weakref
 
 from orangewidget import gui
 
@@ -13,7 +14,6 @@ from ewokscore.missing_data import MISSING_DATA
 from ewoksorange.gui.orange_utils.signals import Input
 
 from processview.core.manager import DatasetState, ProcessManager
-from processview.core.superviseprocess import SuperviseProcess
 from silx.gui import qt
 from silx.gui.utils.concurrent import submitToQtMainThread
 
@@ -67,9 +67,11 @@ class MonitorOW(
         # gui
         layout = gui.vBox(self.mainArea, self.name).layout()
         self._widget = FutureTomwerObjectObserverWidget(
-            parent=self, name=self.windowTitle()
+            parent=self,
+            name=self.windowTitle(),
+            process=self,
         )
-        self.set_dynamic_input("process_id", self._widget.process_id)
+        self.set_dynamic_input("process_id", self.process_id)
         layout.addWidget(self._widget)
 
     def handleNewSignals(self) -> None:
@@ -102,17 +104,19 @@ class MonitorOW(
         return super()._output_changed()
 
 
-class FutureTomwerObjectObserverWidget(
-    _FutureTomwerScanObserverWidget, SuperviseProcess
-):
+class FutureTomwerObjectObserverWidget(_FutureTomwerScanObserverWidget):
     """add dataset state notification (ProcessManager) to the original FutureTomwerScanObserverWidget"""
 
     REFRESH_FREQUENCE = 10
     """time between call to updateView"""
 
-    def __init__(self, name, parent=None):
+    def __init__(self, name, process, parent=None):
+        """
+        :param process: Process that 'controls' the futures
+        """
         super().__init__(parent=parent)
         self.name = name
+        self.__master_process = weakref.ref(process)
         self._updateThread = _RefreshThread(
             callback=self.updateView, refresh_frequence=self.REFRESH_FREQUENCE
         )
@@ -168,12 +172,13 @@ class FutureTomwerObjectObserverWidget(
             raise ValueError(
                 f"future scan status '{future_tomo_obj.status}' is not managed, {type(future_tomo_obj.status)}"
             )
-        ProcessManager().notify_dataset_state(
-            dataset=future_tomo_obj.tomo_obj,
-            process=self,
-            state=state,
-            details=details,
-        )
+        if self.__master_process():
+            ProcessManager().notify_dataset_state(
+                dataset=future_tomo_obj.tomo_obj,
+                process=self.__master_process(),
+                state=state,
+                details=details,
+            )
 
     def _updateStatus(self, future_tomo_obj):
         self._updateTomoObjSupervisor(future_tomo_obj)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/orangecontrib/tomwer/widgets/visualization/DataViewerOW.py

@@ -51,6 +51,7 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         self._imagejThreads = []
         # threads used to open frames with image j
         self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self._layout.setContentsMargins(2, 2, 2, 2)
         self.viewer = DataViewer(parent=self)
         self.viewer.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
         self._layout.addWidget(self.viewer)
@@ -61,9 +62,14 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         self._buttons = qt.QDialogButtonBox(self)
         self._buttons.setStandardButtons(types)
         self._buttonOpenImageJ = self._buttons.button(qt.QDialogButtonBox.Apply)
-        self._buttonOpenImageJ.setText("open with ImageJ")
+        self._buttonOpenImageJ.setText("ImageJ")
+        self._buttonOpenImageJ.setToolTip(
+            "Open image(s) using ImageJ. Warning: you might need to do a 'module load fiji' first"
+        )
         self._buttonOpenImageJ.setIcon(icons.getQIcon("Imagej_icon"))
-        self.layout().addWidget(self._buttons)
+        self.viewer.getPlotWidget().getPositionInfoWidget().layout().insertWidget(
+            0, self._buttonOpenImageJ
+        )
 
         # connect signal / slot
         self.viewer.sigConfigChanged.connect(self._updateSettings)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/core/reconstruction/common/NabuBaseReconstructor.py

@@ -41,6 +41,11 @@ from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.utils.slurm import get_slurm_script_name, is_slurm_available
 from tomwer.core.volume.hdf5volume import HDF5VolumeIdentifier
+from tomwer.core.reconstruction.output import (
+    PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+    PROCESS_FOLDER_RECONSTRUCTED_VOLUMES,
+)
+from tomwer.core.reconstruction.common.settings import NABU_CFG_FILE_FOLDER
 
 from . import settings
 
@@ -218,12 +223,16 @@ class NabuBaseReconstructor:
         assert os.path.exists(
             conf_file
         ), "configuration file doesn't exists. Cannot execute it."
+        log_file = self.deduce_log_file_from_config_file(conf_file)
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
 
         command = (
             sys.executable,
             "-m",
             settings.NABU_FULL_FIELD_APP_PATH,
             f"{shlex.quote(conf_file)}",  # adding ' around file name allows to handle config file with spaces
+            "--logfile",
+            f"{shlex.quote(log_file)}",
             "--gpu_mem_fraction",
             str(gpu_mem_fraction),
             "--cpu_mem_fraction",
@@ -308,13 +317,16 @@ class NabuBaseReconstructor:
         # submit job
         script_name = get_slurm_script_name(prefix="nabu")
         conf_file = filter_esrf_mounting_points(conf_file)
+        log_file = self.deduce_log_file_from_config_file(conf_file)
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
+
         # for now force job name
         cluster_config["job_name"] = f"tomwer-nabu {conf_file}"
         act_as_a_login_shell = cluster_config.pop("act_as_login_shell", False)
         job = SBatchScriptJob(
             slurm_config=cluster_config,
             script=(
-                f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} '{conf_file}' --gpu_mem_fraction={gpu_mem_fraction} --cpu_mem_fraction={cpu_mem_fraction}",
+                f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} '{conf_file}' --logfile='{log_file}' --gpu_mem_fraction={gpu_mem_fraction} --cpu_mem_fraction={cpu_mem_fraction}",
             ),
             script_path=filter_esrf_mounting_points(
                 os.path.join(self.scan.resolved_path, "slurm_scripts", script_name)
@@ -448,6 +460,18 @@ class NabuBaseReconstructor:
             finally:
                 self._process = None
 
+    @staticmethod
+    def deduce_log_file_from_config_file(conf_file: str) -> str:
+        dirname = os.path.dirname(conf_file)
+        while os.path.basename(dirname) in (
+            PROCESS_FOLDER_RECONSTRUCTED_VOLUMES,
+            PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+            NABU_CFG_FILE_FOLDER,
+        ):
+            dirname = os.path.dirname(dirname)
+        file_name, _ = os.path.splitext(os.path.basename(conf_file))
+        return os.path.join(dirname, "logs", file_name + "_nabu.log")
+
 
 def dump_normalization_array_for_nabu(
     scan: TomwerScanBase, output_file: str, array: numpy.ndarray | float | int

tomwer-2.0.0.dev4/src/tomwer/core/reconstruction/common/test/test_NabuBaseReconstructor.py

@@ -0,0 +1,16 @@
+from tomwer.core.reconstruction.common.NabuBaseReconstructor import (
+    NabuBaseReconstructor,
+)
+
+
+def test_deduce_log_file_from_config_file():
+    assert NabuBaseReconstructor.deduce_log_file_from_config_file(
+        "/data/dataset/reconstructed_slices/nabu_cfg_files/config.cfg"
+    ) == ("/data/dataset/logs/config_nabu.log")
+    assert NabuBaseReconstructor.deduce_log_file_from_config_file(
+        "/data/dataset/config.cfg"
+    ) == ("/data/dataset/logs/config_nabu.log")
+    assert (
+        NabuBaseReconstructor.deduce_log_file_from_config_file("config.cfg")
+        == "logs/config_nabu.log"
+    )

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/reconstruction/cor/ControlWidget.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import logging
 import numpy
+import qtawesome
 
 from silx.gui import qt
 
@@ -127,6 +128,8 @@ class _PositionInfoWidget(qt.QWidget):
         self._defaultBackgroundColor = None
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
+
+        # relative CoR
         centerLabel = qt.QLabel("center", parent=self)
         centerLabel.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
         font = centerLabel.font()
@@ -144,7 +147,12 @@ class _PositionInfoWidget(qt.QWidget):
         )
         self._relativePositionQLE.setStyleSheet("color: red")
         self.layout().addWidget(self._relativePositionQLE, 0, 2, 1, 1)
+        self._copyRelativeCoRButton = qt.QPushButton(
+            icon=qtawesome.icon("mdi6.content-copy")
+        )
+        self.layout().addWidget(self._copyRelativeCoRButton, 0, 3, 1, 1)
 
+        # relative CoR
         centerLabel = qt.QLabel("center", parent=self)
         centerLabel.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
         font = centerLabel.font()
@@ -160,6 +168,10 @@ class _PositionInfoWidget(qt.QWidget):
         )
         self._absolutePositionQLE.setStyleSheet("color: #ff8c00")
         self.layout().addWidget(self._absolutePositionQLE, 1, 2, 1, 1)
+        self._copyAbsoluteCoRButton = qt.QPushButton(
+            icon=qtawesome.icon("mdi6.content-copy")
+        )
+        self.layout().addWidget(self._copyAbsoluteCoRButton, 1, 3, 1, 1)
 
         if axis:
             self.setAxisParams(axis)
@@ -174,10 +186,11 @@ class _PositionInfoWidget(qt.QWidget):
         self._absolutePositionQLE.textEdited.connect(
             self._userStartEditingAbsolutePosition
         )
-
         self._absolutePositionQLE.editingFinished.connect(
             self._userUpdatedAbsolutePosition
         )
+        self._copyAbsoluteCoRButton.clicked.connect(self._copyAbsoluteCoRToClipBoard)
+        self._copyRelativeCoRButton.clicked.connect(self._copyRelativeCoRToClipBoard)
 
     def _getDefaultBackgroundColor(self):
         if self._defaultBackgroundColor is None:
@@ -284,3 +297,9 @@ class _PositionInfoWidget(qt.QWidget):
                     absolute_pos=abs_value, det_width=width
                 )
                 self._relativePositionQLE.setText(str(rel_value))
+
+    def _copyAbsoluteCoRToClipBoard(self):
+        qt.QApplication.clipboard().setText(self._absolutePositionQLE.text())
+
+    def _copyRelativeCoRToClipBoard(self):
+        qt.QApplication.clipboard().setText(self._relativePositionQLE.text())

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/reconstruction/nabu/nabuconfig/NabuSettingsWidget.py

@@ -8,7 +8,6 @@ from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowArea
 from tomwer.gui.configuration.level import ConfigurationLevel
 from tomwer.gui.utils.flow import FlowDirection
 from tomwer.gui.reconstruction.nabu.nabuconfig.nabuconfig import NabuConfiguration
-from tomwer.gui import icons as tomwer_icons
 
 
 class NabuSettingsWidget(qt.QWidget):
@@ -36,7 +35,7 @@ class NabuSettingsWidget(qt.QWidget):
         for mode in NabuMode:
             self._nabuModeCB.addItem(mode.value)
         self._widget_recons.layout().addWidget(self._nabuModeCB)
-        self.layout().addWidget(self._widget_recons, 0, 1, 1, 2)
+        self.layout().addWidget(self._widget_recons, 0, 2, 1, 2)
 
         # spacer
         spacer = qt.QWidget(self)
@@ -53,9 +52,6 @@ class NabuSettingsWidget(qt.QWidget):
         self._configurationScrollArea.setWidgetResizable(True)
         self._configuration = NabuConfiguration(parent=self)
         self._configurationScrollArea.setWidget(self._configuration)
-        self._configurationScrollArea.setHorizontalScrollBarPolicy(
-            qt.Qt.ScrollBarAlwaysOff
-        )
         self.layout().addWidget(self._configurationScrollArea, 1, 2, 5, 1)
         self._configuration.setSizePolicy(
             qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum
@@ -75,22 +71,16 @@ class NabuSettingsWidget(qt.QWidget):
 
         # set up
         pre_processing = ("pre processing",)
-        roman_one_icon = tomwer_icons.getQIcon("roman_one")
-        self.setPreProcessing(pre_processing, icons=(roman_one_icon,))
+        self.setPreProcessing(pre_processing, icons=(None,))
         phase_processing = ("phase",)
-        roman_two_icon = tomwer_icons.getQIcon("roman_two")
-        phase_icons = (roman_two_icon,)
-        self.setPhaseProcessing(phase_processing, icons=phase_icons)
+        self.setPhaseProcessing(phase_processing, icons=(None,))
         processing = ("reconstruction",)
-        processing_icons = (tomwer_icons.getQIcon("roman_three"),)
-        self.setProcessing(processes=processing, icons=processing_icons)
+        self.setProcessing(processes=processing, icons=(None,))
         post_processing = ("save",)
-        post_processing_icons = (tomwer_icons.getQIcon("roman_four"),)
-        self.setPostProcessing(post_processing, icons=post_processing_icons)
+        self.setPostProcessing(post_processing, icons=(None,))
         index_mode = self._nabuModeCB.findText(NabuMode.AUTO.value)
         assert index_mode >= 0, "full filed should be registered in the widget"
         self._nabuModeCB.setCurrentIndex(index_mode)
-        self._flow.setMaximumWidth(240)
 
         # signal / slot connections
         self._flow.sigConfigurationChanged.connect(self._processSelectionChanged)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/reconstruction/nabu/nabuflow.py

@@ -352,6 +352,7 @@ class NabuFlowArea(qt.QWidget):
             self.layout().addWidget(self._addRmWidget)
 
         # set up
+        self.setMaximumWidth(180)
         # for now hide the add and remove option
         self._addRmWidget.setVisible(False)
 

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/reconstruction/nabu/test/test_cast_volume.py

@@ -11,7 +11,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": None,
         "data_min": None,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": 99.9,
@@ -25,7 +25,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 0.0,
         "data_min": 0.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -41,7 +41,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -54,7 +54,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -67,7 +67,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,
@@ -80,7 +80,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "float32",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,
@@ -93,7 +93,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "float32",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/visualization/dataviewer.py

@@ -131,7 +131,7 @@ class DataViewer(qt.QMainWindow):
             self._scan = None
         # update scan name
         self._viewer.setScan(scan=scan)
-        self._controls.setScanName(str(scan))
+        # self._controls.setScanName(str(scan))
         self._updateDisplay()
         # has the display is post pone we can only set expected dimensions
         # for the viewer
@@ -261,32 +261,23 @@ class DisplayControl(qt.QWidget):
         self.layout().setContentsMargins(0, 0, 0, 0)
         self.layout().setSpacing(0)
 
-        # scan information
-        self._scanLab = qt.QLabel("scan:", self)
-        self._scanLab.setFixedWidth(40)
-        self._scanLab.setAlignment(qt.Qt.AlignRight | qt.Qt.AlignVCenter)
-        self.layout().addWidget(self._scanLab, 0, 0, 1, 1)
-        self._scanQLE = qt.QLineEdit("", self)
-        self._scanQLE.setReadOnly(True)
-        self.layout().addWidget(self._scanQLE, 0, 1, 1, 3)
-
         # display information
         self._displayLab = qt.QLabel("display:", self)
         self._displayLab.setAlignment(qt.Qt.AlignRight | qt.Qt.AlignVCenter)
-        self.layout().addWidget(self._displayLab, 1, 0, 1, 1)
+        self.layout().addWidget(self._displayLab, 0, 0, 1, 1)
         self._displayMode = qt.QComboBox(self)
         for mode in DisplayMode:
             self._displayMode.addItem(mode.value)
-        self.layout().addWidget(self._displayMode, 1, 1, 1, 1)
+        self.layout().addWidget(self._displayMode, 0, 1, 1, 1)
 
         # option information
         self._modeLab = qt.QLabel("mode:", self)
         self._modeLab.setFixedWidth(60)
         self._modeLab.setAlignment(qt.Qt.AlignRight | qt.Qt.AlignVCenter)
-        self.layout().addWidget(self._modeLab, 1, 2, 1, 1)
+        self.layout().addWidget(self._modeLab, 0, 2, 1, 1)
         self._widget_options = qt.QWidget(self)
         self._widget_options.setLayout(qt.QVBoxLayout())
-        self.layout().addWidget(self._widget_options, 1, 3, 1, 1)
+        self.layout().addWidget(self._widget_options, 0, 3, 1, 1)
 
         self._radioMode = qt.QComboBox(self)
         for mode in RadioMode:
@@ -309,10 +300,6 @@ class DisplayControl(qt.QWidget):
         self._radioMode.currentTextChanged.connect(self._updateOptions)
         self._sliceMode.currentTextChanged.connect(self._updateOptions)
 
-    def setScanInfoVisible(self, visible):
-        self._scanLab.setVisible(visible)
-        self._scanQLE.setVisible(visible)
-
     def setDisplayModeVisible(self, visible):
         self._displayLab.setVisible(visible)
         self._displayMode.setVisible(visible)
@@ -366,9 +353,3 @@ class DisplayControl(qt.QWidget):
         if config != self._lastConfig:
             self._lastConfig = config
             self.sigDisplayModeChanged.emit()
-
-    def setScanName(self, scan_name: str):
-        self._scanQLE.setText(scan_name)
-
-    def clear(self):
-        self._scanQLE.clear()

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/visualization/imagestack.py

@@ -67,6 +67,7 @@ class ImageStack(_ImageStack):
         self.setUrlLoaderClass(_TomwerUrlLoader)
         # hide axis to be display
         self._plot.setAxesDisplayed(False)
+        self._plot.getColorBarWidget().setVisible(False)
         self._loadSliceParams = False
         self._resetZoom = True
 
@@ -77,7 +78,9 @@ class ImageStack(_ImageStack):
         self._reconsWidget = ReconstructionParameters(self)
         self._reconsWidgetScrollArea.setWidget(self._reconsWidget)
         self._reconsInfoDockWidget.setWidget(self._reconsWidgetScrollArea)
-        self._reconsInfoDockWidget.setFeatures(qt.QDockWidget.DockWidgetMovable)
+        self._reconsInfoDockWidget.setFeatures(
+            qt.QDockWidget.DockWidgetVerticalTitleBar
+        )
         self.addDockWidget(qt.Qt.RightDockWidgetArea, self._reconsInfoDockWidget)
 
         # add scan overview dock widget
@@ -85,8 +88,11 @@ class ImageStack(_ImageStack):
             self._scanOverviewDockerWidget = qt.QDockWidget(parent=self)
             self._scanOverviewDockerWidget.setMaximumHeight(300)
             self._scanOverviewWidget = ScanOverviewWidget(self)
+            self._scanOverviewWidget.layout().setContentsMargins(2, 2, 2, 2)
             self._scanOverviewDockerWidget.setWidget(self._scanOverviewWidget)
-            self._scanOverviewDockerWidget.setFeatures(qt.QDockWidget.DockWidgetMovable)
+            self._scanOverviewDockerWidget.setFeatures(
+                qt.QDockWidget.DockWidgetVerticalTitleBar
+            )
             self.addDockWidget(
                 qt.Qt.RightDockWidgetArea, self._scanOverviewDockerWidget
             )

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/gui/visualization/scanoverview.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 
+import qtawesome
 import logging
 import weakref
 import pint
@@ -22,7 +23,28 @@ class ScanOverviewWidget(qt.QWidget):
     def __init__(self, parent=None):
         super().__init__(parent)
         self._scan = None
+
         self.setLayout(qt.QVBoxLayout())
+
+        # scan name
+        self._scanWidget = qt.QWidget()
+        self._scanWidget.setLayout(qt.QHBoxLayout())
+        self._scanWidget.layout().setContentsMargins(0, 0, 0, 0)
+        self._scanWidget.layout().setSpacing(0)
+
+        self._scanLabel = qt.QLabel("Scan:")
+        self._scanWidget.layout().addWidget(self._scanLabel)
+        self._scanPath = qt.QLineEdit("")
+        self._scanWidget.layout().addWidget(self._scanPath)
+        self._scanPath.setReadOnly(True)
+        self._scanPathCopyButton = qt.QPushButton(
+            icon=qtawesome.icon("mdi6.content-copy")
+        )
+        self._scanWidget.layout().addWidget(self._scanPathCopyButton)
+        self._scanPathCopyButton.setFlat(True)
+        self.layout().addWidget(self._scanWidget)
+
+        # scan tree
         self._tree = qt.QTreeWidget(self)
         self._tree.setColumnCount(2)
         self._tree.setHeaderLabels(("entry", "value"))
@@ -92,6 +114,9 @@ class ScanOverviewWidget(qt.QWidget):
         self._sample.setExpanded(True)
         self._beam.setExpanded(True)
 
+        # connect signal / slot
+        self._scanPathCopyButton.clicked.connect(self.copyScanPathToClipBoard)
+
     def setScan(self, scan):
         if scan is None:
             self._scan = scan
@@ -101,6 +126,12 @@ class ScanOverviewWidget(qt.QWidget):
             self._scan = weakref.ref(scan)
         if scan is not None:
             self.update_tree(scan=scan)
+            self._scanPath.setText(scan.get_identifier().short_description())
+
+    def copyScanPathToClipBoard(self):
+        scan = self.getScan()
+        if scan:
+            qt.QApplication.clipboard().setText(scan.get_identifier().to_str())
 
     def getScan(self):
         if self._scan is None or self._scan() is None:
@@ -306,6 +337,5 @@ class ScanOverviewWidget(qt.QWidget):
     def _fromTimeStampToHumanReadableTime(timestamp) -> str:
         if timestamp is None:
             return "Unknown"
-        print("time stamp is", timestamp, type(timestamp))
         dt = parser.parse(timestamp)
         return dt.strftime("%B %d, %Y, %H:%M:%S")

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/models/reconstruction/cast_volume.py

@@ -19,7 +19,7 @@ from nabu.io.cast_volume import RESCALE_MAX_PERCENTILE, RESCALE_MIN_PERCENTILE
 from tomoscan.identifier import VolumeIdentifier
 from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 
-CAST_VOLUME_WORKING_SUB_DIRECTORY = "cast_volumes"
+CAST_VOLUME_WORKING_SUB_DIRECTORY = "cast_volume"
 
 
 class InputModel(ProcessInputModel):
@@ -51,7 +51,7 @@ class InputModel(ProcessInputModel):
     )
     output_dir: str | None = Field(
         default="{volume_data_parent_folder}"
-        f"{os.sep}..{os.sep}{CAST_VOLUME_WORKING_SUB_DIRECTORY}",
+        f"{os.sep}{CAST_VOLUME_WORKING_SUB_DIRECTORY}",
         description="Output folder to save the volume.",
     )
     cluster_config: SlurmClusterConfiguration | None = Field(
@@ -146,6 +146,15 @@ class InputModel(ProcessInputModel):
         elif isinstance(value, (VolumeIdentifier, str)):
             return VolumeFactory.create_tomo_object_from_identifier(value)
 
+    @field_validator("output_dir")
+    @classmethod
+    def fallback_on_default(cls, value: str) -> str:
+        if value == "":
+            return InputModel.model_fields[  # pylint: disable=E1136
+                "output_dir"
+            ].default
+        return value
+
 
 class OutputModel(_VolumeModel, BaseOutputModel):
     """OutputModel for volume casting. Inherited Field 'volume' is only the propagation of the input volume"""

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/models/reconstruction/nabu_slices.py

@@ -67,6 +67,15 @@ class InputModel(_DataModel, ProcessInputModel):
     ):
         return {NabuPlane(key): value for key, value in values.items()}
 
+    @field_validator("output_dir")
+    @classmethod
+    def fallback_on_default(cls, value: str) -> str:
+        if value == "":
+            return InputModel.model_fields[  # pylint: disable=E1136
+                "output_dir"
+            ].default
+        return value
+
 
 class OutputModel(_DataModel, BaseOutputModel):
     future_tomo_obj: FutureTomwerObject | None

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/models/reconstruction/nabu_volume.py

@@ -48,6 +48,15 @@ class InputModel(_DataModel, ProcessInputModel):
         check_fields=False,
     )(cast_cluster_config)
 
+    @field_validator("output_dir")
+    @classmethod
+    def fallback_on_default(cls, value: str) -> str:
+        if value == "":
+            return InputModel.model_fields[  # pylint: disable=E1136
+                "output_dir"
+            ].default
+        return value
+
 
 class OutputModel(_DataModel, BaseOutputModel):
     volume: TomwerVolumeBase | None = Field(

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_cast_volumeow.py

@@ -46,7 +46,7 @@ def test_processing(qtapp, hdf5_volume):  # noqa F811
 
     window._process(volume=hdf5_volume, data=None)
     output_folder = os.path.join(
-        os.path.dirname(hdf5_volume.file_path), "..", CAST_VOLUME_WORKING_SUB_DIRECTORY
+        os.path.dirname(hdf5_volume.file_path), CAST_VOLUME_WORKING_SUB_DIRECTORY
     )
     assert not os.path.exists(output_folder)
     wait_for_processing(window)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/tests/test_ewoks/test_workflows.py

@@ -284,9 +284,17 @@ def test_tutorial_cast_volume(tmp_path, hdf5_volume):
         ],
     )
     # check for output volume
-    assert "cast_volumes" in os.listdir(tmp_path)
+    assert "reconstructed_volumes" in os.listdir(tmp_path)
     tiff_files = glob(
-        os.sep.join([str(tmp_path), "cast_volumes", "my_volume", "*.tiff"])
+        os.sep.join(
+            [
+                str(tmp_path),
+                "reconstructed_volumes",
+                "cast_volume",
+                "my_volume",
+                "*.tiff",
+            ]
+        )
     )
     assert len(tiff_files) == 10
 

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4}/src/tomwer/version.py

@@ -79,7 +79,7 @@ MAJOR = 2
 MINOR = 0
 MICRO = 0
 RELEV = "dev"  # <16
-SERIAL = 3  # <16
+SERIAL = 4  # <16
 
 date = __date__
 

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev4/src/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 2.0.0.dev3
+Version: 2.0.0.dev4
 Summary: Tomography workflow tools
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: MIT