tomwer 2.0.0.dev6__tar.gz → 2.0.0.dev7__tar.gz

{tomwer-2.0.0.dev6/src/tomwer.egg-info → tomwer-2.0.0.dev7}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 2.0.0.dev6
+Version: 2.0.0.dev7
 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>
+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>
 License: MIT
 Project-URL: Homepage, https://gitlab.esrf.fr/tomotools/tomwer
 Project-URL: Documentation, https://tomotools.gitlab-pages.esrf.fr/tomwer/
@@ -43,7 +43,7 @@ Provides-Extra: full-base
 Requires-Dist: orange-canvas-core; extra == "full-base"
 Requires-Dist: orange-widget-base; extra == "full-base"
 Requires-Dist: ewokscore; extra == "full-base"
-Requires-Dist: ewoksorange>=3.3.0; extra == "full-base"
+Requires-Dist: ewoksorange<5.0,>=3.3.0; extra == "full-base"
 Requires-Dist: fabio; extra == "full-base"
 Requires-Dist: h5py>=3; extra == "full-base"
 Requires-Dist: lxml; extra == "full-base"

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/pyproject.toml

@@ -6,7 +6,6 @@ authors = [
     { name = "Pierre Paleo", email = "pierre.paleo@esrf.fr" },
     { name = "Pierre-Olivier Autran", email = "pierre-olivier.autran@esrf.fr" },
     { name = "Jérôme Lesaint", email = "jerome.lesaint@esrf.fr" },
-    { name = "Alessandro Mirone", email = "mirone@esrf.fr" }
 ]
 description = "Tomography workflow tools"
 readme = { file = "README.rst", content-type = "text/x-rst" }
@@ -49,7 +48,7 @@ full_base = [
     "orange-canvas-core",
     "orange-widget-base",
     "ewokscore",
-    "ewoksorange>=3.3.0",
+    "ewoksorange>=3.3.0,<5.0",
     "fabio",
     "h5py>=3",
     "lxml",

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py

@@ -1,6 +1,9 @@
 from __future__ import annotations
 
+import logging
+
 from orangewidget import gui
+from orangewidget.settings import Setting
 from orangewidget.widget import Input
 
 from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
@@ -17,6 +20,8 @@ from orangecontrib.tomwer.orange.task_widgets.TomwerWidgetWithStack import (
 from orangecontrib.tomwer.orange.ewoks_compatibility import unpack_variable
 from processview.core.manager import DatasetState, ProcessManager
 
+_logger = logging.getLogger(__name__)
+
 
 class CastNabuVolumeOW(
     TomwerWidgetWithStack,
@@ -69,6 +74,8 @@ class CastNabuVolumeOW(
     )
     # Hide input defined by the GUI
 
+    _interactive_mode = Setting(False)
+
     class Inputs:
         data = Input(
             name="data",
@@ -103,16 +110,27 @@ class CastNabuVolumeOW(
         self._layout.addWidget(self._window)
 
         # load default configuration saved
-        self.setConfiguration(
-            filter_missing_data(
-                self.get_default_input_values("cast_volume_params") or {}
-            )
-        )
+        self.setConfiguration(filter_missing_data(self.get_default_input_values()))
         # Store process id to provide task / dataset state
         self.set_dynamic_input("process_id", self.process_id)
 
+        self._pending_data = None
+        """Store a scan arriving"""
+        self._pending_volume = None
+        """Store a volume arriving"""
+
+        self._last_data = None
+        """dataset currently processed"""
+        self._last_volume = None
+        """volume currently processed"""
+
+        # apply saved interactive mode
+        self._window.setInteractive(self._interactive_mode)
+
         # connect signal / slot
         self._window.sigConfigChanged.connect(self._updateConfig)
+        self._window.sigInteractiveModeChanged.connect(self._onInteractiveModeChanged)
+        self._window.sigProcessRequested.connect(self._onProcessRequested)
 
     @Inputs.data
     def process_data(self, data: TomwerScanBase | None, signal_id=None):
@@ -142,6 +160,8 @@ class CastNabuVolumeOW(
     def _process(self, data: TomwerScanBase | None, volume: TomwerVolumeBase | None):
         if data is None and volume is None:
             return
+        self._last_data = data
+        self._last_volume = volume
         # check types
         if data is not None and not isinstance(data, TomwerScanBase):
             raise TypeError(
@@ -153,15 +173,28 @@ class CastNabuVolumeOW(
             )
         if data is None and volume is None:
             raise ValueError("The scan of the volume should be given. Not both")
-        self.set_dynamic_input("volume", volume)
-        self.set_dynamic_input("data", data)
 
-        ProcessManager().notify_dataset_state(
-            dataset=data or volume,
-            process=self,
-            state=DatasetState.PENDING,
-        )
-        self.execute_ewoks_task()
+        if self._window.isInteractive():
+            # handling when in interactive mode
+            self._pending_data = data
+            self._pending_volume = volume
+            if volume is not None:
+                self._window.setVolume(volume)
+            ProcessManager().notify_dataset_state(
+                dataset=data or volume,
+                process=self,
+                state=DatasetState.PENDING,
+            )
+        else:
+            # handling when in automatic mode
+            self.set_dynamic_input("volume", volume)
+            self.set_dynamic_input("data", data)
+            ProcessManager().notify_dataset_state(
+                dataset=data or volume,
+                process=self,
+                state=DatasetState.PENDING,
+            )
+            self.execute_ewoks_task()
 
     def reprocess(self, dataset):
         if isinstance(dataset, TomwerScanBase):
@@ -171,6 +204,27 @@ class CastNabuVolumeOW(
         else:
             raise TypeError("dataset is expected to be an instance of ''")
 
+    def _onInteractiveModeChanged(self, interactive: bool) -> None:
+        self._interactive_mode = interactive
+        if interactive and self._last_volume is not None:
+            # switching from auto → interactive: load histogram and preview for
+            # the volume that was last processed in auto mode
+            self._pending_data = self._last_data
+            self._pending_volume = self._last_volume
+            self._window.setVolume(self._last_volume)
+
+    def _onProcessRequested(self) -> None:
+        if self._pending_data is None and self._pending_volume is None:
+            return
+        self.set_dynamic_input("volume", self._pending_volume)
+        self.set_dynamic_input("data", self._pending_data)
+        ProcessManager().notify_dataset_state(
+            dataset=self._pending_data or self._pending_volume,
+            process=self,
+            state=DatasetState.PENDING,
+        )
+        self.execute_ewoks_task()
+
     def getConfiguration(self) -> dict:
         return self._window.getConfiguration()
 
@@ -180,9 +234,14 @@ class CastNabuVolumeOW(
 
     def _updateConfig(self):
         configuration = self.getConfiguration()
-        for key in configuration.keys():
-            assert key in CastVolumeTask.input_model().model_fields.keys()
-            self.set_default_input(key, configuration[key])
+        valid_keys = CastVolumeTask.input_model().model_fields.keys()
+        for key, value in configuration.items():
+            if key not in valid_keys:
+                _logger.warning(
+                    "cast-volume: ignoring unknown configuration key %r", key
+                )
+                continue
+            self.set_default_input(key, value)
 
     def handleNewSignals(self) -> None:
         """

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/orangecontrib/tomwer/widgets/reconstruction/NabuSlicesOW.py

@@ -238,7 +238,7 @@ class NabuSlicesOW(SuperviseOW, BaseNabuRecOW):
     def getConfiguration(self, allow_no_nabu_config_defined: bool = False):
         """
         :param allow_no_nabu_config_defined: when we save the settings we don't want to raise an error when saving the configuration.
-        But when getting it for reconstructing we want to
+            But when getting it for reconstructing we want to
         """
         slices_config = self._nabuWidget.getConfiguration()
         nabu_param_and_cluster_config = super().getConfiguration()

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -258,7 +258,7 @@ class NabuVolumeOW(SuperviseOW, BaseNabuRecOW):
     def getConfiguration(self, allow_no_nabu_config_defined: bool = False):
         """
         :param allow_no_nabu_config_defined: when we save the settings we don't want to raise an error when saving the configuration.
-        But when getting it for reconstructing we want to
+            But when getting it for reconstructing we want to
         """
         nabu_params_and_slurm_config = super().getConfiguration()
         assert ParametersKeys.SLURM_CLUSTER_KEY in nabu_params_and_slurm_config

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/tomwer/__main__.py

@@ -89,6 +89,11 @@ def main():
         description="Compute center of rotation of a scan or "
         "between two projections",
     )
+    launcher.add_command(
+        "cast-volume",
+        module_name="tomwer.app.cast_volume",
+        description="Cast a nabu volume to a different data type / file format",
+    )
     launcher.add_command(
         "canvas", module_name="tomwer.app.canvas", description="open the orange-canvas"
     )

tomwer-2.0.0.dev7/src/tomwer/app/cast_volume.py

@@ -0,0 +1,173 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""Application to cast a nabu volume to a different data type / file format"""
+
+import argparse
+import logging
+import signal
+import sys
+
+import silx
+from silx.gui import qt
+
+from tomwer.core.utils.resource import increase_max_number_file
+from tomwer.core.volume.volumefactory import VolumeFactory
+from tomwer.gui import icons
+from tomwer.gui.reconstruction.nabu.castvolume import CastVolumeWidget
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
+from tomwer.tasks.reconstruction.castvolume import CastVolumeTask
+from tomoscan.esrf.volume.utils import guess_volumes
+
+logging.basicConfig(level=logging.WARNING)
+_logger = logging.getLogger(__name__)
+
+
+class _CastVolumeMainWindow(qt.QMainWindow):
+    """Standalone window wrapping CastVolumeWidget.
+
+    The widget is always put in interactive mode so the histogram and slice
+    preview are visible from the start.  A toolbar provides Cast / Quit buttons.
+    """
+
+    def __init__(self, volume, parent=None):
+        super().__init__(parent=parent)
+        self._volume = volume
+
+        central = qt.QWidget(self)
+        self.setCentralWidget(central)
+        central.setLayout(qt.QVBoxLayout())
+        central.layout().setContentsMargins(4, 4, 4, 4)
+
+        self._castWidget = CastVolumeWidget(parent=central)
+        central.layout().addWidget(self._castWidget)
+
+        # button row
+        buttonBar = qt.QWidget(central)
+        buttonBar.setLayout(qt.QHBoxLayout())
+        buttonBar.layout().setContentsMargins(0, 4, 0, 0)
+        buttonBar.layout().addStretch()
+        self._castBut = qt.QPushButton("Cast", buttonBar)
+        self._castBut.setToolTip("Run the cast operation with the current settings")
+        buttonBar.layout().addWidget(self._castBut)
+        quitBut = qt.QPushButton("Quit", buttonBar)
+        quitBut.clicked.connect(qt.QApplication.quit)
+        buttonBar.layout().addWidget(quitBut)
+        central.layout().addWidget(buttonBar)
+
+        self._statusBar = self.statusBar()
+
+        # always interactive in the standalone app; hide the toggle controls
+        self._castWidget.setInteractive(True)
+        self._castWidget.setInteractiveControlsVisible(False)
+
+        # load histogram and preview; setVolume starts the background loader
+        self._castWidget.setVolume(volume)
+
+        self._castBut.clicked.connect(self._runCast)
+        self.setWindowIcon(icons.getQIcon("tomwer"))
+
+    def _runCast(self):
+        cfg = self._castWidget.getConfiguration()
+        self._castBut.setEnabled(False)
+        self._statusBar.showMessage("Casting volume – please wait…")
+        qt.QApplication.processEvents()
+        try:
+            task = CastVolumeTask(
+                inputs={
+                    "volume": self._volume,
+                    **cfg,
+                }
+            )
+            task.execute()
+        except Exception as exc:
+            _logger.error("Cast failed: %s", exc, exc_info=True)
+            self._statusBar.showMessage(f"Cast failed: {exc}", 8000)
+        else:
+            self._statusBar.showMessage("Cast completed successfully.", 6000)
+        finally:
+            self._castBut.setEnabled(True)
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        "volume",
+        help="Volume identifier or path (HDF5, TIFF folder, EDF folder, …).",
+    )
+    parser.add_argument(
+        "--debug",
+        action="store_true",
+        default=False,
+        help="Set logging system in debug mode",
+    )
+    parser.add_argument(
+        "--use-opengl-plot",
+        "--opengl-backend",
+        action="store_true",
+        default=False,
+        help="Use OpenGL for plots (instead of matplotlib)",
+    )
+    options = parser.parse_args(argv[1:])
+
+    if options.debug:
+        logging.root.setLevel(logging.DEBUG)
+
+    if options.use_opengl_plot:
+        silx.config.DEFAULT_PLOT_BACKEND = "gl"
+    else:
+        silx.config.DEFAULT_PLOT_BACKEND = "matplotlib"
+
+    increase_max_number_file()
+
+    global app  # QApplication must be global to avoid seg fault on quit
+    app = qt.QApplication.instance() or qt.QApplication(["tomwer"])
+    splash = getMainSplashScreen()
+    qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
+    qt.QApplication.processEvents()
+
+    qt.QLocale.setDefault(qt.QLocale(qt.QLocale.English))
+    qt.QLocale.setDefault(qt.QLocale.c())
+    signal.signal(signal.SIGINT, sigintHandler)
+    sys.excepthook = qt.exceptionHandler
+
+    timer = qt.QTimer()
+    timer.start(500)
+    timer.timeout.connect(lambda: None)
+
+    try:
+        volumes = VolumeFactory.create_tomo_object_from_identifier(options.volume)
+    except Exception:
+        volumes = tuple()
+
+    if not volumes:
+        volumes = guess_volumes(options.volume)
+
+    if not volumes:
+        parser.error(f"No volume found at '{options.volume}'")
+
+    # cast back to tomwer volume in case we get only a tomoscan volume.
+    volume = VolumeFactory.create_tomo_object_from_identifier(
+        volumes[0].get_identifier()
+    )
+
+    window = _CastVolumeMainWindow(volume=volume, parent=None)
+    window.setWindowTitle("tomwer: cast-volume")
+    splash.finish(window)
+    window.show()
+    qt.QApplication.restoreOverrideCursor()
+
+    app.aboutToQuit.connect(window.close)
+    sys.exit(app.exec())
+
+
+def getinputinfo():
+    return "tomwer cast-volume [volume_path]"
+
+
+def sigintHandler(*args):
+    """Handler for the SIGINT signal."""
+    qt.QApplication.quit()
+
+
+if __name__ == "__main__":
+    main(sys.argv)

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/tomwer/core/control/datawatcher/datawatcherprocess.py

@@ -28,8 +28,8 @@ class _DataWatcherProcess:
     DataWatcherProcess is the process managing the observation of acquisition.
     Since we want to loop infinitly on a root folder we have to ignore the
     folder we previously detected. Otherwise if those folders are not removed
-     we will loop infinitly. That is why we now have the ignoredFolders
-     parameter.
+    we will loop infinitly. That is why we now have the ignoredFolders
+    parameter.
 
     :param  dataDir: Root directory containing data
     :param  waitXML: if True then we will be waiting for the XML of

{tomwer-2.0.0.dev6 → tomwer-2.0.0.dev7}/src/tomwer/core/reconstruction/common/test/test_nabu_utils.py

@@ -10,6 +10,12 @@ from tomwer.core.reconstruction.common.utils import (
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 
+from tomwer.core.volume.edfvolume import EDFVolume
+from tomwer.core.volume.hdf5volume import HDF5Volume
+from tomwer.core.reconstruction.common.utils import (
+    get_default_output_volume_for_tiff_3d,
+)
+
 _scans = (
     NXtomoScan(
         scan="/my_scan_file.nx",
@@ -21,7 +27,7 @@ _scans = (
 
 @pytest.mark.parametrize("scan", _scans)
 @pytest.mark.parametrize("axis", ("YZ", "XZ", "XY"))
-def test_get_recons_volume_identifier(scan, axis):
+def test_get_recons_volume_identifier(scan, axis, tmp_path):
     """
     test get_recons_volume_identifier behavior
     """
@@ -31,7 +37,7 @@ def test_get_recons_volume_identifier(scan, axis):
     with pytest.raises(ValueError):
         get_recons_volume_identifier(
             file_prefix="volume_rec",
-            location="/this/is/a/test",
+            location=tmp_path,
             file_format="toto",
             slice_index=1080,
             scan=scan,
@@ -41,7 +47,7 @@ def test_get_recons_volume_identifier(scan, axis):
     # check hdf5 reconstructions
     id_rec_vols = get_recons_volume_identifier(
         file_prefix="volume_rec",
-        location="/this/is/a/test",
+        location=tmp_path,
         file_format="hdf5",
         slice_index="1080",
         scan=scan,
@@ -50,36 +56,32 @@ def test_get_recons_volume_identifier(scan, axis):
     assert len(id_rec_vols) == 1
     assert (
         id_rec_vols[0].to_str()
-        == f"hdf5:volume:/this/is/a/test/volume_rec_plane_{axis}_001080.hdf5?path={entry}/reconstruction"
+        == f"hdf5:volume:{tmp_path}/volume_rec_plane_{axis}_001080.hdf5?path={entry}/reconstruction"
     )
 
     # check edf and jp2k slice reconstructions (are expected to have the same behavior)
     id_rec_vols = get_recons_volume_identifier(
         file_prefix="volume_rec",
-        location="/this/is/a/test",
+        location=tmp_path,
         file_format="edf",
         slice_index="1080",
         scan=scan,
         axis=axis,
     )
     assert len(id_rec_vols) == 1
-    assert (
-        id_rec_vols[0].to_str() == "edf:volume:/this/is/a/test?file_prefix=volume_rec"
-    )
+    assert id_rec_vols[0].to_str() == f"edf:volume:{tmp_path}?file_prefix=volume_rec"
 
     # check tiff slice reconstructions
     id_rec_vols = get_recons_volume_identifier(
-        file_prefix="volume_rec",
-        location="/this/is/a/test",
+        file_prefix="volume_rec2",
+        location=tmp_path,
         file_format="tiff",
         slice_index="1080",
         scan=scan,
         axis=axis,
     )
     assert len(id_rec_vols) == 1
-    assert (
-        id_rec_vols[0].to_str() == "tiff:volume:/this/is/a/test?file_prefix=volume_rec"
-    )
+    assert id_rec_vols[0].to_str() == f"tiff:volume:{tmp_path}?file_prefix=volume_rec2"
 
     # check jp2k
     if not has_minimal_openjpeg:
@@ -87,7 +89,7 @@ def test_get_recons_volume_identifier(scan, axis):
 
     id_rec_vols = get_recons_volume_identifier(
         file_prefix="volume_recslice",
-        location="/this/is/a/test",
+        location=tmp_path,
         file_format="jp2k",
         slice_index="1080",
         scan=scan,
@@ -95,8 +97,7 @@ def test_get_recons_volume_identifier(scan, axis):
     )
     assert len(id_rec_vols) == 1
     assert (
-        id_rec_vols[0].to_str()
-        == "jp2k:volume:/this/is/a/test?file_prefix=volume_recslice"
+        id_rec_vols[0].to_str() == f"jp2k:volume:{tmp_path}?file_prefix=volume_recslice"
     )
 
 
@@ -325,3 +326,30 @@ def test_nabu_std_err_has_error():
         )
         is False
     )
+
+
+def test_get_default_output_volume_for_tiff_3d():
+    """test 'get_default_output_volume_for_tiff_3d' function"""
+    # test from EDF
+    input_edf_volume = EDFVolume(
+        folder="/path/to/my_folder",
+    )
+    assert (
+        get_default_output_volume_for_tiff_3d(
+            input_volume=input_edf_volume,
+            output_dir="/path/to/my_folder",
+        ).data_url.file_path()
+        == "/path/to/my_folder/my_folder.tiff"
+    )
+    # test from hdf5
+    input_hdf5_volume = HDF5Volume(
+        file_path="/path/to/my_file.hdf5",
+        data_path="entry0012",
+    )
+    assert (
+        get_default_output_volume_for_tiff_3d(
+            input_volume=input_hdf5_volume,
+            output_dir="/cast_volume",
+        ).data_url.file_path()
+        == "/cast_volume/my_file.tiff"
+    )