tomwer 1.3.12__py3-none-any.whl → 1.3.26__py3-none-any.whl

tomwer/gui/cluster/test/test_cluster.py

@@ -63,7 +63,6 @@ class TestSlurmWidget(TestCaseQt):
             "job_name": "tomwer_{scan}_-_{process}_-_{info}",
             "n_jobs": 1,
             "modules": ("tomotools/stable",),
-            "walltime": "01:00:00",
             "sbatch_extra_params": {
                 "export": "NONE",
                 "gpu_card": None,

tomwer/gui/control/selectorwidgetbase.py

@@ -156,7 +156,9 @@ class _SelectorWidget(qt.QMainWindow):
 
     def removeSelectedDatasets(self):
         sItem = self.dataList.selectedItems()
-        selection = [_item.text().get_identifier().to_str() for _item in sItem]
+        selection = [
+            _item.data(qt.Qt.UserRole).get_identifier().to_str() for _item in sItem
+        ]
 
         with block_signals(self):
             # make sure sigUpdated is called only once.

tomwer/gui/edit/nxtomoeditor.py

@@ -574,28 +574,36 @@ class NXtomoEditor(qt.QWidget):
                 ),
                 solve_empty_dependency=True,
             )
-            detector_transformation_path = "/".join(
-                (
-                    nexus_paths.INSTRUMENT_PATH,
-                    nexus_paths.nx_instrument_paths.DETECTOR_PATH,
-                    nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS,
-                ),
-            )
-            if detector_transformation_path in entry:
-                del entry[detector_transformation_path]
-
-            detector_transformation_path = "/".join(
-                (scan.entry, detector_transformation_path)
+            if nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS is not None:
+                # old NXtomo are not handling NX_TRANSFORMATIONS
+                detector_transformation_path = "/".join(
+                    (
+                        nexus_paths.INSTRUMENT_PATH,
+                        nexus_paths.nx_instrument_paths.DETECTOR_PATH,
+                        nexus_paths.nx_detector_paths.NX_TRANSFORMATIONS,
+                    ),
+                )
+                if detector_transformation_path in entry:
+                    del entry[detector_transformation_path]
+
+                detector_transformation_path = "/".join(
+                    (scan.entry, detector_transformation_path)
+                )
+            else:
+                _logger.debug(
+                    "Old version of NXtomo found. No information about transformation will be saved"
+                )
+                detector_transformation_path = None
+
+        if detector_transformation_path is not None:
+            dicttonx(
+                nx_dict,
+                h5file=scan.master_file,
+                h5path=detector_transformation_path,
+                update_mode="replace",
+                mode="a",
             )
 
-        dicttonx(
-            nx_dict,
-            h5file=scan.master_file,
-            h5path=detector_transformation_path,
-            update_mode="replace",
-            mode="a",
-        )
-
         # clear caches to make sure all modifications will be considered
         scan.clear_caches()
         scan.clear_frames_caches()

tomwer/gui/edit/test/test_nx_editor.py

@@ -1,4 +1,5 @@
 import os
+import h5py
 
 import numpy
 import pytest
@@ -252,7 +253,7 @@ def test_nx_editor_lock(
     # 3.0 save the nxtomo
     widget.overwriteNXtomo()
 
-    # 4.0 check save went twell
+    # 4.0 check save went well
     overwrite_nx_tomo = NXtomo().load(
         file_path=file_path,
         data_path=entry,
@@ -305,3 +306,59 @@ def test_nx_editor_lock(
         "instrument.detector.x_flipped": (False, False),
         "instrument.detector.y_flipped": (True, False),
     }
+
+
+def test_nxtomo_editor_with_missing_paths(
+    tmp_path,
+    qtapp,  # noqa F811
+):
+    """
+    test widget behavior in the case some nxtomo path don't exist
+    """
+
+    # create nx tomo with raw data
+    nx_tomo = NXtomo()
+    nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
+    nx_tomo.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
+    nx_tomo.sample.rotation_angle = numpy.linspace(0, 20, num=12)
+
+    file_path = os.path.join(tmp_path, "nxtomo.nx")
+    entry = "entry0000"
+    nx_tomo.save(
+        file_path=file_path,
+        data_path=entry,
+    )
+    # delete some path that can be missing in some case
+    with h5py.File(file_path, mode="a") as h5f:
+        assert "entry0000" in h5f
+        assert "entry0000/beam" not in h5f
+        assert "entry0000/instrument/beam" not in h5f
+        assert "entry0000/instrument/detector/distance" not in h5f
+        assert "entry0000/instrument/detector/x_pixel_size" not in h5f
+        assert "entry0000/instrument/detector/y_pixel_size" not in h5f
+        assert "entry0000/instrument/detector/transformations" not in h5f
+
+    scan = NXtomoScan(file_path, entry)
+
+    # create the widget and do the edition
+    widget = NXtomoEditor()
+
+    widget.setScan(scan=scan)
+
+    widget._distanceMetricEntry.setValue(0.05)
+    widget._energyEntry.setValue(50)
+    widget._xPixelSizeMetricEntry.setValue(0.02)
+    widget._yPixelSizeMetricEntry.setValue(0.03)
+
+    # overwrite the NXtomo
+    widget.overwriteNXtomo()
+
+    # check save went well
+    overwrite_nx_tomo = NXtomo().load(
+        file_path=file_path,
+        data_path=entry,
+    )
+    assert overwrite_nx_tomo.instrument.detector.x_pixel_size.value == 0.02
+    assert overwrite_nx_tomo.instrument.detector.y_pixel_size.value == 0.03
+    assert overwrite_nx_tomo.energy.value == 50
+    assert overwrite_nx_tomo.instrument.detector.distance.value == 0.05

tomwer/gui/reconstruction/axis/axis.py

@@ -31,6 +31,7 @@ __license__ = "MIT"
 __date__ = "14/10/2019"
 
 
+import numpy
 import logging
 from typing import Optional
 
@@ -272,6 +273,7 @@ class _AxisWidget(qt.QMainWindow):
                 self._axis_params.relative_cor_value,
                 self._axis_params.absolute_cor_value,
             )
+        self._controlWidget._positionInfo.setAxis(self._axis_params)
 
         # connect signal / slots
         self._controlWidget.sigComputationRequest.connect(self.sigComputationRequested)
@@ -663,7 +665,13 @@ class _PositionInfoWidget(qt.QWidget):
         if self._relativePositionQLE.text().startswith((".", "?")):
             return
         else:
-            self.sigRelativeValueSet.emit(float(self._relativePositionQLE.text()))
+            value = float(self._relativePositionQLE.text())
+            # make sure we only emit the signal if the value changed (and when the Qline has been edited).
+            if self._axis.relative_cor_value is None or (
+                self._axis is not None
+                and not numpy.isclose(value, self._axis.relative_cor_value, atol=1e-3)
+            ):
+                self.sigRelativeValueSet.emit(value)
 
     def _userUpdatedAbsolutePosition(self, *args, **kwargs):
         palette = self.palette()
@@ -675,24 +683,19 @@ class _PositionInfoWidget(qt.QWidget):
         if self._absolutePositionQLE.text().startswith((".", "?")):
             return
         else:
-            self.sigAbsolueValueSet.emit(float(self._absolutePositionQLE.text()))
+            value = float(self._absolutePositionQLE.text())
+            # make sure we only emit the signal if the value changed (and when the Qline has been edited).
+            if self._axis.absolute_cor_value is None or (
+                self._axis is not None
+                and not numpy.isclose(value, self._axis.absolute_cor_value, atol=1e-3)
+            ):
+                self.sigAbsolueValueSet.emit(value)
 
     def setAxis(self, axis):
         assert isinstance(axis, QAxisRP)
         if axis == self._axis:
             return
-        if self._axis is not None:
-            self._axis.sigChanged.disconnect(self._updatePosition)
         self._axis = axis
-        self._axis.sigChanged.connect(self._updatePosition)
-        self._updatePosition()
-
-    def _updatePosition(self):
-        if self._axis:
-            self.setPosition(
-                relative_cor=self._axis.relative_cor_value,
-                abs_cor=self._axis.absolute_cor_value,
-            )
 
     def getPosition(self):
         return float(self._relativePositionQLE.text())

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/gui/reconstruction/darkref/darkrefcopywidget.py

@@ -54,6 +54,7 @@ class DarkRefAndCopyWidget(DarkRefWidget):
     """Signal emitted when the mode auto change"""
     sigCopyActivationChanged = qt.Signal()
     """Signal emitted when the copy is activated or deactivated"""
+    sigClearCache = qt.Signal()
 
     def __init__(self, save_dir: str, parent=None, reconsparams=None, process_id=None):
         DarkRefWidget.__init__(
@@ -79,6 +80,7 @@ class DarkRefAndCopyWidget(DarkRefWidget):
         self._refCopyWidget.sigCopyActivationChanged.connect(
             self._triggerCopyActivation
         )
+        self._refCopyWidget.sigClearCache.connect(self.sigClearCache)
 
     def setRefSetBy(self, scan_id: str):
         self._refCopyWidget._statusBar.showMessage(f"ref set from {scan_id}")
@@ -155,6 +157,8 @@ class RefCopyWidget(qt.QGroupBox):
     """Signal emitted when the mode auto change"""
     sigCopyActivationChanged = qt.Signal()
     """Signal emitted when the copy is activated or deactivated"""
+    sigClearCache = qt.Signal()
+    """Signal when the cache needs to be cleared"""
 
     _DEFAULT_DIRECTORY = "/lbsram/data/visitor"
     """Default directory used when the user need to set path to references"""
@@ -190,6 +194,12 @@ class RefCopyWidget(qt.QGroupBox):
         spacer = qt.QWidget(self)
         spacer.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Expanding)
         self.layout().addWidget(spacer)
+        self._removeCacheFile = qt.QPushButton("clear cache")
+        self._removeCacheFile.setToolTip(
+            "Remove the file used for cacheing reduce dark / flat."
+        )
+        self.layout().addWidget(self._removeCacheFile)
+
         self.layout().addWidget(self.__createStatusBarGUI())
 
         self.setModeAuto(True)
@@ -201,6 +211,7 @@ class RefCopyWidget(qt.QGroupBox):
         # connect signal / slot
         self.toggled.connect(self._triggerCopyActivated)
         self._qcbAutoMode.toggled.connect(self._triggerModeAutoChanged)
+        self._removeCacheFile.released.connect(self.sigClearCache)
 
     def _triggerCopyActivated(self, *args, **kwargs):
         self.sigCopyActivationChanged.emit()

tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -188,13 +188,14 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
 
         # option dedicated to Helical
         ## process file
-        self._processFileQLE = qt.QLabel("file containing weights maps", self)
+        self._processFileLabel = qt.QLabel("file containing weights maps", self)
+        self.registerWidget(self._processFileLabel, "advanced")
+        self.layout().addWidget(self._processFileLabel, 20, 0, 1, 1)
+        self._processFileQLE = qt.QLineEdit("", self)
+        self.registerWidget(self._processFileQLE, "advanced")
         self._processFileQLE.setToolTip(
             "also know as 'process_file'. If you don't have this file it can be created from the 'helical-prepare-weights' widget"
         )
-        self.layout().addWidget(self._processFileQLE, 20, 0, 1, 1)
-        self._processFileQLE = qt.QLineEdit("", self)
-        self.registerWidget(self._processFileQLE, "advanced")
         self.layout().addWidget(self._processFileQLE, 20, 1, 1, 3)
 
         # style

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]:
@@ -859,6 +860,10 @@ class ZStitchingWindow(qt.QMainWindow):
             level >= ConfigurationLevel.ADVANCED
         )
 
+    def close(self):
+        shutil.rmtree(self._previewFolder, ignore_errors=True)
+        super().close()
+
 
 def concatenate_dict(dict_1, dict_2) -> dict:
     """update dict which has dict as values. And we want concatenate those values to"""

tomwer/gui/visualization/dataviewer.py

@@ -34,7 +34,6 @@ from silx.gui import qt
 from silx.gui.dialog.ColormapDialog import DisplayMode
 from silx.gui.plot.ImageStack import ImageStack as _ImageStack
 from silx.gui.plot.ImageStack import UrlLoader
-from silx.gui.utils.signal import SignalProxy
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
 
@@ -86,17 +85,6 @@ class DataViewer(qt.QMainWindow):
         self._viewer.getPlotWidget().setKeepDataAspectRatio(True)
         self.setCentralWidget(self._viewer)
 
-        # signal / slot
-        # add a signal proxy on the QSlider
-        self._viewer._slider.sigCurrentUrlIndexChanged.disconnect(
-            self._viewer.setCurrentUrlIndex
-        )
-        self._proxySig = SignalProxy(
-            self._viewer._slider.sigCurrentUrlIndexChanged,
-            delay=0.3,
-            slot=self._urlIndexDelayed,
-        )
-
         # display control
         self._controls = DisplayControl(parent=self)
         self._controlsDW = qt.QDockWidget(self)
@@ -110,6 +98,33 @@ class DataViewer(qt.QMainWindow):
         self._controls.sigDisplayModeChanged.connect(self._updateDisplay)
         self._controls.sigDisplayModeChanged.connect(self.sigConfigChanged)
 
+        # upgrade of the slider (see details in '__sliderPressed' docstring).
+        horizontal_slider = self._viewer._slider
+        horizontal_slider._slider.sliderReleased.connect(self.__sliderReleased)
+        horizontal_slider._slider.sliderPressed.connect(self.__sliderPressed)
+
+    def __sliderPressed(self):
+        """
+        today each time the slider value is modified it will load the frame and display it
+        but in our case we cannot afford it as it will take too much memory.
+        So we will disconnect the callback (self._viewer.setCurrentUrlIndex) until the slider is active
+        and reactivate it afterwards
+        """
+        self._viewer._slider.sigCurrentUrlIndexChanged.disconnect(
+            self._viewer.setCurrentUrlIndex
+        )
+
+    def __sliderReleased(self):
+        """
+        See details in '__sliderPressed'
+        """
+        horizontal_slider = self._viewer._slider
+        self._viewer._slider.sigCurrentUrlIndexChanged.connect(
+            self._viewer.setCurrentUrlIndex
+        )
+        # set the url with the latest value to display the requested frame
+        self._viewer.setCurrentUrlIndex(horizontal_slider.value())
+
     def getPlotWidget(self):
         return self._viewer.getPlotWidget()
 
@@ -134,9 +149,6 @@ class DataViewer(qt.QMainWindow):
         self._viewer = None
         super().close()
 
-    def _urlIndexDelayed(self, *args, **kwargs):
-        self._viewer.setCurrentUrlIndex(args[0][0])
-
     def getScan(self):
         if self._scan:
             return self._scan()

tomwer/gui/visualization/diffviewer/diffviewer.py

@@ -25,6 +25,7 @@
 """
 contains gui relative frame difference display
 """
+from __future__ import annotations
 
 __authors__ = ["H. Payno"]
 __license__ = "MIT"
@@ -148,7 +149,7 @@ class _FrameSelector(qt.QWidget):
             return
 
         urls = []
-        angles = []
+        urls_to_angles: dict[str, float] = {}
         self._currentFrameUrlsText.clear()
         self._frameUrlCB.clear()
         if type_selected == self.FrameType.DARKS:
@@ -162,7 +163,7 @@ class _FrameSelector(qt.QWidget):
                 angles_and_urls = self._scan.get_proj_angle_url(with_alignment=False)
                 for angle, url in angles_and_urls.items():
                     urls.append(url)
-                    angles.append(angle)
+                    urls_to_angles[url.path()] = angle
             else:
                 urls = self._scan.projections.values()
         elif type_selected == self.FrameType.ALIGN_PROJ:
@@ -174,14 +175,14 @@ class _FrameSelector(qt.QWidget):
             raise ValueError(f"Type {type_selected} not managed")
         urls = sorted(urls, key=lambda url: url.path())
 
-        # if thre is some angles missing, avoiding setting any angle because they are probably wrong
+        # if there is some angles missing, avoiding setting any angle because they are probably wrong
         # this will probably fail with EDF but this is legacy
-        if len(angles) != len(urls):
-            angles = []
+        if len(urls_to_angles) != len(urls):
+            urls_to_angles.clear()
 
-        for i_url, url in enumerate(urls):
-            if len(angles) > 0:
-                text = f"angle={angles[i_url]}&"
+        for url in urls:
+            if len(urls_to_angles) > 0:
+                text = f"angle={urls_to_angles[url.path()]}&"
             else:
                 text = ""
             if url.data_slice() is not None:

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -30,6 +30,7 @@ import functools
 import logging
 import shutil
 import tempfile
+import os
 
 from processview.core.manager import DatasetState, ProcessManager
 from processview.core.superviseprocess import SuperviseProcess
@@ -132,6 +133,15 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
     def _create_processing_thread(self, process_id=None) -> qt.QThread:
         return _ProcessingThread(process_id=process_id, save_dir=self._save_dir)
 
+    def clear_cache(self):
+        """
+        remove the file used to cache the reduced darks / flats.
+        This can be used in the case it contain unrelevant data. Like frame with another shape...
+        """
+        cache_file = DarkRefsCopy.get_save_file(self._save_dir)
+        if os.path.exists(cache_file):
+            os.remove(cache_file)
+
 
 class _ProcessingThread(ProcessingThread, SuperviseProcess):
     """

tomwer/tests/datasets.py

@@ -1,5 +1,9 @@
 import os
-from tomoscan.test.datasets import GitlabProject
+
+try:
+    from tomoscan.test.datasets import GitlabProject
+except ImportError:
+    from tomoscan.tests.datasets import GitlabProject
 
 TomwerCIDatasets = GitlabProject(
     branch_name="tomwer",

tomwer/utils.py

@@ -81,10 +81,7 @@ class LauncherCommand(_LauncherCommand):
     """Description of a command"""
 
     def get_module(self):
-        """Returns the python module to execute. If any.
-
-        :rtype: module
-        """
+        """Returns the python module to execute. If any."""
         try:
             module = importlib.import_module(self.module_name)
             return module

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 12
+MICRO = 26
 RELEV = "final"  # <16
 SERIAL = 0  # <16