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

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

@@ -35,6 +35,7 @@ from silx.gui import qt
 from silx.gui.dialog.DataFileDialog import DataFileDialog
 from silx.utils.enum import Enum as _Enum
 
+from tomwer.core.process.reconstruction.nabu.plane import NabuPlane
 from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSliceMode
 from tomwer.core.process.reconstruction.nabu.utils import (
     _NabuFBPFilterType,
@@ -300,55 +301,74 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         # come with an issue as we are on a scroll area
         self._slicesWidget.setFocusPolicy(qt.Qt.FocusPolicy.NoFocus)
 
+        # axis
+        self._axisLabel = qt.QLabel("reconstruction plane", self)
+        self._axisLabel.setToolTip("Over which axis the slice must be picked")
+        self.layout().addWidget(self._axisLabel)
+        self._axisQCB = qt.QComboBox(self)
+        axis_tooltips = {
+            NabuPlane.YZ.value: "along axis x (aka axis 2 - expected to be slow)",
+            NabuPlane.XZ.value: "along axis y (aka axis 1 - expected to be slow)",
+            NabuPlane.XY.value: "along axis Z (aka axis 0 - fastest)",
+        }
+        for item, tooltip in axis_tooltips.items():
+            self._axisQCB.addItem(item)
+            self._axisQCB.setItemData(
+                self._axisQCB.findText(item),
+                tooltip,
+                qt.Qt.ToolTipRole,
+            )
+        self.layout().addWidget(self._axisQCB, 1, 1, 1, 1)
+
         # method
         self._methodLabel = qt.QLabel("method", self)
-        self.layout().addWidget(self._methodLabel, 1, 0, 1, 1)
+        self.layout().addWidget(self._methodLabel, 2, 0, 1, 1)
         self._methodQCB = QComboBoxIgnoreWheel(parent=self, scrollArea=scrollArea)
         for method in _NabuReconstructionMethods:
             self._methodQCB.addItem(method.value)
-        self.layout().addWidget(self._methodQCB, 1, 1, 1, 1)
+        self.layout().addWidget(self._methodQCB, 2, 1, 1, 1)
         self.registerWidget(self._methodLabel, "required")
         self.registerWidget(self._methodQCB, "required")
 
         # angle_offset
         self._labelOffsetLabel = qt.QLabel("angle offset (in degree)", self)
-        self.layout().addWidget(self._labelOffsetLabel, 2, 0, 1, 1)
+        self.layout().addWidget(self._labelOffsetLabel, 3, 0, 1, 1)
         self._angleOffsetQDSB = QDoubleSpinBoxIgnoreWheel(self, scrollArea)
         self._angleOffsetQDSB.setMaximum(-180)
         self._angleOffsetQDSB.setMaximum(180)
-        self.layout().addWidget(self._angleOffsetQDSB, 2, 1, 1, 1)
+        self.layout().addWidget(self._angleOffsetQDSB, 3, 1, 1, 1)
         self.registerWidget(self._labelOffsetLabel, "advanced")
         self.registerWidget(self._angleOffsetQDSB, "advanced")
 
         # fbp filter type
         self._fbpFilterCB = qt.QCheckBox("fbp filter", self)
-        self.layout().addWidget(self._fbpFilterCB, 3, 0, 1, 1)
+        self.layout().addWidget(self._fbpFilterCB, 4, 0, 1, 1)
         self._fbpFilterType = QComboBoxIgnoreWheel(self, scrollArea)
         for filter_type in _NabuFBPFilterType:
             self._fbpFilterType.addItem(filter_type.value)
-        self.layout().addWidget(self._fbpFilterType, 3, 1, 1, 1)
+        self.layout().addWidget(self._fbpFilterType, 4, 1, 1, 1)
         self.registerWidget(self._fbpFilterCB, "advanced")
         self.registerWidget(self._fbpFilterType, "advanced")
 
         # padding type
         self._paddingTypeLabel = qt.QLabel("padding type", self)
-        self.layout().addWidget(self._paddingTypeLabel, 4, 0, 1, 1)
+        self.layout().addWidget(self._paddingTypeLabel, 5, 0, 1, 1)
         self._paddingType = QComboBoxIgnoreWheel(self, scrollArea)
         for fbp_padding_type in _NabuPaddingType:
             self._paddingType.addItem(fbp_padding_type.value)
-        self.layout().addWidget(self._paddingType, 4, 1, 1, 1)
+        self.layout().addWidget(self._paddingType, 5, 1, 1, 1)
         self.registerWidget(self._paddingTypeLabel, "optional")
         self.registerWidget(self._paddingType, "optional")
 
         # sub region
         self._subRegionSelector = _NabuReconstructionSubRegion(parent=self)
-        self.layout().addWidget(self._subRegionSelector, 6, 0, 1, 2)
+        self.layout().addWidget(self._subRegionSelector, 7, 0, 1, 2)
 
         # iterations
         self._iterationsLabel = qt.QLabel("iterations", self)
-        self.layout().addWidget(self._iterationsLabel, 7, 0, 1, 1)
+        self.layout().addWidget(self._iterationsLabel, 8, 0, 1, 1)
         self._iterationSB = qt.QSpinBox(parent=self)
-        self.layout().addWidget(self._iterationSB, 7, 1, 1, 1)
+        self.layout().addWidget(self._iterationSB, 8, 1, 1, 1)
         self._iterationSB.setMinimum(1)
         self._iterationSB.setMaximum(9999)
         # not supported for now so hidden
@@ -359,14 +379,14 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._binSubSamplingGB = _BinSubSampling(
             "binning and subsampling", parent=self, scrollArea=scrollArea
         )
-        self.layout().addWidget(self._binSubSamplingGB, 8, 0, 1, 2)
+        self.layout().addWidget(self._binSubSamplingGB, 9, 0, 1, 2)
 
         # optimization algorithm:
         # set has default value for now, because has only one at the moment
 
         # weight total variation
         self._tvLabel = qt.QLabel("total variation weight", self)
-        self.layout().addWidget(self._tvLabel, 9, 0, 1, 1)
+        self.layout().addWidget(self._tvLabel, 10, 0, 1, 1)
         self._totalVariationWeight = qt.QDoubleSpinBox(self)
         self._totalVariationWeight.setMinimum(0.0)
         self._totalVariationWeight.setMaximum(1.0)
@@ -382,7 +402,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._preconditioningFilter.setToolTip(
             'Whether to enable "filter ' 'preconditioning" for iterative' " methods"
         )
-        self.layout().addWidget(self._preconditioningFilter, 9, 0, 1, 2)
+        self.layout().addWidget(self._preconditioningFilter, 10, 0, 1, 2)
         # not supported for now so hidden
         self._preconditioningFilter.hide()
 
@@ -391,7 +411,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._positivityConstraintCB.setToolTip(
             "Whether to enforce a " "positivity constraint in the " "reconstruction."
         )
-        self.layout().addWidget(self._positivityConstraintCB, 10, 0, 1, 2)
+        self.layout().addWidget(self._positivityConstraintCB, 11, 0, 1, 2)
         # not supported for now so hidden
         self._positivityConstraintCB.hide()
 
@@ -400,28 +420,28 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._clipOuterCircleCB.setToolTip(
             "Whether to set to zero voxels falling outside of the reconstruction region"
         )
-        self.layout().addWidget(self._clipOuterCircleCB, 11, 0, 1, 2)
+        self.layout().addWidget(self._clipOuterCircleCB, 12, 0, 1, 2)
         self.registerWidget(self._clipOuterCircleCB, "optional")
 
         # centered axis option
         self._centeredAxisCB = qt.QCheckBox("centered axis", self)
         self._centeredAxisCB.setToolTip("")
-        self.layout().addWidget(self._centeredAxisCB, 12, 0, 1, 2)
+        self.layout().addWidget(self._centeredAxisCB, 13, 0, 1, 2)
         self.registerWidget(self._centeredAxisCB, "optional")
 
         # translation movement file
         self._transMvtFileLabel = qt.QLabel("translation movement file", self)
-        self.layout().addWidget(self._transMvtFileLabel, 21, 0, 1, 1)
+        self.layout().addWidget(self._transMvtFileLabel, 22, 0, 1, 1)
         self._transMvtFileWidget = TranslationMvtFileWidget(self)
-        self.layout().addWidget(self._transMvtFileWidget, 21, 1, 1, 1)
+        self.layout().addWidget(self._transMvtFileWidget, 22, 1, 1, 1)
         self.registerWidget(self._transMvtFileLabel, "advanced")
         self.registerWidget(self._transMvtFileWidget, "advanced")
 
         # angle files (if the user want's to overwrite rotation angles)
         self._angleFileLabel = qt.QLabel("angles file", self)
-        self.layout().addWidget(self._angleFileLabel, 22, 0, 1, 1)
+        self.layout().addWidget(self._angleFileLabel, 23, 0, 1, 1)
         self._anglesFileWidget = AnglesFileWidget(self)
-        self.layout().addWidget(self._anglesFileWidget, 22, 1, 1, 1)
+        self.layout().addWidget(self._anglesFileWidget, 23, 1, 1, 1)
         self.registerWidget(self._angleFileLabel, "advanced")
         self.registerWidget(self._anglesFileWidget, "advanced")
 
@@ -431,6 +451,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self.layout().addWidget(spacer, 200, 1, 1, 1)
 
         # set up
+        self.setNabuPlane("XY")
         self._fbpFilterCB.setChecked(True)
         fbp_item = self._methodQCB.findText(_NabuReconstructionMethods.FBP.value)
         self._methodQCB.setCurrentIndex(fbp_item)
@@ -447,6 +468,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._centeredAxisCB.setChecked(False)
 
         # connect signal / slot
+        self._axisQCB.currentIndexChanged.connect(self._slicesChanged)
         self._methodQCB.currentIndexChanged.connect(self._methodChanged)
         self._angleOffsetQDSB.editingFinished.connect(self._angleOffsetChanged)
         self._fbpFilterCB.toggled.connect(self._FBPFilterTypeChanged)
@@ -628,6 +650,14 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
     def setCenteredAxis(self, checked: bool):
         self._centeredAxisCB.setChecked(checked)
 
+    def getNabuPlane(self) -> NabuPlane:
+        """return over which axis we expect to do the reconstruction"""
+        return NabuPlane.from_value(self._axisQCB.currentText())
+
+    def setNabuPlane(self, axis: typing.Union[str, NabuPlane]):
+        axis = NabuPlane.from_value(axis)
+        self._axisQCB.setCurrentText(axis.value)
+
     @docstring(_NabuStageConfigBase)
     def getConfiguration(self) -> dict:
         fbp_filter_type = self.getFBPFilterType()
@@ -637,6 +667,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
             fbp_filter_type = fbp_filter_type.value
         config = {
             "method": self.getMethod().value,
+            "slice_plane": self.getNabuPlane().value,
             "angles_file": self.getAnglesFile(),
             "axis_correction_file": "",  # not managed for now
             "angle_offset": self.getAngleOffset(),
@@ -689,6 +720,8 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
             self.setClipOuterCircle(bool(config["clip_outer_circle"]))
         if "centered_axis" in config:
             self.setCenteredAxis(bool(config["centered_axis"]))
+        if "slice_plane" in config:
+            self.setNabuPlane(config["slice_plane"])
         self._subRegionSelector.setConfiguration(config=config)
 
     def _signalConfChanged(self, param):

tomwer/gui/reconstruction/normalization/intensity.py

@@ -96,11 +96,6 @@ class SinoNormWindow(qt.QMainWindow):
         self._centralWidget._updateSinogramROI()
         self._modeChanged()
 
-    def close(self):
-        self._centralWidget.stop()
-        self._centralWidget = None
-        super().close()
-
     def _hideLockButton(self):
         self._optsWidget._hideLockButton()
 
@@ -165,11 +160,6 @@ class SinoNormWindow(qt.QMainWindow):
         self._centralWidget.setScan(scan=scan)
         self._optsWidget.setScan(scan=scan)
 
-    def stop(self):
-        if self._centralWidget is not None:
-            self._centralWidget.stop()
-            self._centralWidget = None
-
     def getExtraArgs(self) -> dict:
         return self._optsWidget.getExtraInfos()
 
@@ -246,12 +236,6 @@ class _Viewer(qt.QTabWidget):
         self._projView.setManualROIVisible(visible=visible)
         self._sinoView.setROIVisible(visible=visible)
 
-    def stop(self):
-        self._projView.stop()
-        self._projView = None
-        self._sinoView.stop()
-        self._sinoView = None
-
     def getROI(self):
         return self._projView.getROI()
 
@@ -341,9 +325,6 @@ class _ProjPlotWithROI(DataViewer):
         super().clear()
         self.getPlotWidget().removeMarker("sinogram_line")
 
-    def stop(self):
-        self._viewer._plot.stopUpdateThread()
-
 
 class SinogramViewer(_SinogramViewer):
     """ "Sinogram viewer but adapated for Intensity normalization"""
@@ -397,14 +378,11 @@ class SinogramViewer(_SinogramViewer):
                     self.getPlotWidget().addItem(item)
 
     def getPlotWidget(self):
-        return self._plot.getPlotWidget()
+        return self._plot
 
     def _updatePlot(self, sinogram):
-        self._plot.getPlotWidget().addImage(data=sinogram)
-        self._plot.getPlotWidget().replot()
-
-    def stop(self):
-        self._plot.stopUpdateThread()
+        self.getPlotWidget().addImage(data=sinogram)
+        self.getPlotWidget().replot()
 
 
 class _NormIntensityOptions(qt.QWidget):

tomwer/gui/reconstruction/saaxis/corrangeselector.py

@@ -148,7 +148,7 @@ class SinogramViewer(_SinogramViewer):
         self._estimated_cor = estimated_cor
         self._other_cors = other_cors if other_cors is not None else tuple()
 
-        plot = self._plot.getPlotWidget()
+        plot = self._plot
 
         if self._corMarker is not None:
             self._corMarker.sigDragFinished.disconnect(self._middleMarkerMoved)

tomwer/gui/reconstruction/saaxis/saaxis.py

@@ -303,10 +303,6 @@ class _SAAxisTabWidget(qt.QTabWidget):
         self._nabuSettings = None
         super().close()
 
-    def _stopAnimationThread(self):
-        self._resultsViewer._stopAnimationThread()
-        self._sliceAndCorWidget._sinogramViewer._stopAnimationThread()
-
 
 class SAAxisWindow(qt.QMainWindow):
     """
@@ -381,9 +377,6 @@ class SAAxisWindow(qt.QMainWindow):
         self._saaxisControl.sigComputationRequest.connect(self._launchReconstructions)
         self._saaxisControl.sigValidateRequest.connect(self._validate)
 
-    def stop(self):
-        self._stopAnimationThread()
-
     def showResults(self):
         self._tabWidget.showResults()
 
@@ -451,7 +444,7 @@ class SAAxisWindow(qt.QMainWindow):
     def _updateSinogramLine(self):
         r_slice = self.getReconstructionSlices()
         if r_slice == "middle":
-            line = slice_index_to_int(slice_index="middle", scan=self._scan)
+            line = slice_index_to_int(slice_index="middle", scan=self._scan, axis="XY")
         else:
             line = list(r_slice.values())[0]
         self._tabWidget.getSinogramViewer().setLine(line)
@@ -507,9 +500,6 @@ class SAAxisWindow(qt.QMainWindow):
         if idx >= 0:
             self._tabWidget.setCurrentIndex(idx)
 
-    def _stopAnimationThread(self):
-        self._tabWidget._stopAnimationThread()
-
     def close(self):
         self._tabWidget.close()
         self._tabWidget = None

tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py

@@ -239,7 +239,6 @@ class _SADeltaBetaTabWidget(qt.QTabWidget):
         self._resultsViewer.setScoreMethod(method)
 
     def close(self):
-        self._stopAnimationThread()
         self._resultsViewer.close()
         self._resultsViewer = None
         self._deltaBetaSelectionWidget.close()
@@ -248,9 +247,6 @@ class _SADeltaBetaTabWidget(qt.QTabWidget):
         self._nabuSettings = None
         super().close()
 
-    def _stopAnimationThread(self):
-        self._resultsViewer._stopAnimationThread()
-
     def setSliceRange(self, min_, max_):
         self._deltaBetaSelectionWidget.setSliceRange(min_, max_)
 
@@ -357,12 +353,6 @@ class SADeltaBetaWindow(qt.QMainWindow):
         self._tabWidget = None
         super().close()
 
-    def stop(self):
-        self._stopAnimationThread()
-
-    def _stopAnimationThread(self):
-        self._tabWidget._stopAnimationThread()
-
     def setDBScores(
         self,
         scores: dict,

tomwer/gui/reconstruction/scores/scoreplot.py

@@ -612,12 +612,7 @@ class ScorePlot(qt.QWidget):
         self.sigConfigurationChanged.emit()
 
     def getPlotWidget(self):
-        return self._plot.getPlotWidget()
-
-    def _stopAnimationThread(self):
-        self._plot._freeLoadingThreads()
-        if self._plot._plot.updateThread.is_alive():
-            self._plot._plot.updateThread.stop()
+        return self._plot
 
     def close(self):
         self._plot.close()

tomwer/gui/reconstruction/test/test_axis.py

@@ -74,19 +74,33 @@ class TestWindowAxis(TestCaseQt):
     def testSetImagesNumpyArray(self):
         """Test the setImages function"""
         radio_axis = self._window._axisWidget._radioAxis
-        self.assertEqual(radio_axis.getPlot().getPlot().getActiveImage(), None)
+        radio_axis_plot = self._window._axisWidget._radioAxis.getPlot()
+        numpy.testing.assert_array_equal(
+            radio_axis_plot.getPlot().getActiveImage().getData(), numpy.empty((0, 0, 4))
+        )
         imgA = numpy.random.random((100, 100))
         imgB = numpy.random.random((100, 100))
         radio_axis.setImages(imgA=imgA, imgB=imgB, flipB=True)
         self.qapp.processEvents()
-        self.assertNotEqual(radio_axis.getPlot().getPlot().getActiveImage(), None)
+        # make sur the image has been set
+        assert radio_axis_plot.getPlot().getImage(legend="image1").getData().shape == (
+            100,
+            100,
+        )
 
     def testSetScan(self):
         """Test the setScan function"""
         radio_axis_plot = self._window._axisWidget._radioAxis.getPlot()
-        self.assertEqual(radio_axis_plot.getPlot().getActiveImage(), None)
+        numpy.testing.assert_array_equal(
+            radio_axis_plot.getPlot().getActiveImage().getData(), numpy.empty((0, 0, 4))
+        )
         self._window.setScan(self.scan)
-        self.assertNotEqual(radio_axis_plot.getPlot().getActiveImage(), None)
+        self.qapp.processEvents()
+        # make sur the image has been set
+        assert radio_axis_plot.getPlot().getImage(legend="image1").getData().shape == (
+            20,
+            20,
+        )
 
     def testShiftButtons(self):
         """Test that the 'left', 'right', ... buttons and the shift steps are

tomwer/gui/reconstruction/test/test_nabu.py

@@ -219,6 +219,7 @@ class TestNabuReconstructionConfig(TestCaseQt):
         """Test that the get configuration is working"""
         ini_conf = {
             "method": "FBP",
+            "slice_plane": "XY",
             "angles_file": "",
             "axis_correction_file": "",
             "angle_offset": 0.0,
@@ -246,6 +247,7 @@ class TestNabuReconstructionConfig(TestCaseQt):
         """Test that the set configuration is working"""
         ini_conf = {
             "method": "FBP",
+            "slice_plane": "XZ",
             "angles_file": "",
             "axis_correction_file": "",
             "angle_offset": 12.5,
@@ -284,6 +286,7 @@ class TestNabuReconstructionConfig(TestCaseQt):
         self.assertFalse(self.nabuWidget._preconditioningFilter.isChecked())
         self.assertTrue(self.nabuWidget._clipOuterCircleCB.isChecked())
         self.assertTrue(self.nabuWidget._centeredAxisCB.isChecked())
+        assert self.nabuWidget._axisQCB.currentText() == ini_conf["slice_plane"]
 
         # check the generated configuration
         self.assertEqual(self.nabuWidget.getConfiguration(), ini_conf)

tomwer/gui/stitching/stitching.py

@@ -727,7 +727,7 @@ class ZStitchingWindow(qt.QMainWindow):
 
         # clean current preview to notify some calculation is going on
         preview_plot = self._widget._mainWidget._previewPlot
-        preview_plot.setWaiting(True)
+        preview_plot._waitingOverlay.show()
 
         # start sitching on a thread
         self._previewThread = PreviewThread(stitching_config=config)
@@ -749,7 +749,7 @@ class ZStitchingWindow(qt.QMainWindow):
         output_obj_identifier = sender.output_identifier
 
         preview_plot = self._widget._mainWidget._previewPlot
-        preview_plot.setWaiting(False)
+        preview_plot._waitingOverlay.hide()
 
         self._previewThread.finished.disconnect(self._previewCalculationFinished)
         self._previewThread = None

tomwer/gui/stitching/stitching_preview.py

@@ -14,14 +14,9 @@ from tomwer.core.volume.volumefactory import VolumeFactory
 from tomwer.gui import icons as tomwer_icons
 from tomwer.gui import settings
 from tomwer.gui.stitching.stitchandbackground import StitchAndBackgroundAlphaMixIn
-from silx.gui.plot import Plot2D, items
 
-try:
-    from silx.gui.plot.ImageStack import (  # noqa F401
-        PlotWithWaitingLabel as _PlotWithWaitingLabel,
-    )
-except ImportError:
-    from silx.gui.plot.ImageStack import _PlotWithWaitingLabel  # noqa F401
+from silx.gui.plot import Plot2D, items
+from silx.gui.widgets.WaitingOverlay import WaitingOverlay
 
 _logger = logging.getLogger(__name__)
 
@@ -62,22 +57,23 @@ class _PreviewPlot2D(Plot2D):
         return "-"  # No image picked
 
 
-class PreviewStitchingPlot(_PlotWithWaitingLabel, StitchAndBackgroundAlphaMixIn):
+class PreviewStitchingPlot(Plot2D, StitchAndBackgroundAlphaMixIn):
     DEFAULT_STITCHED_IMG_ALPHA = 0.95
     DEFAULT_BACKGROUND_IMG_ALPHA = 0.20
 
     def __init__(self, parent=None) -> None:
         super().__init__(parent=parent)  # pylint: disable=E1123
+        self._waitingOverlay = WaitingOverlay(self)
+        self._waitingOverlay.setIconSize(qt.QSize(30, 30))
         self._stitched_image = None
         self._composition_background = None
 
         # replace the simple Plot2D by a `_PreviewPlot2D` (to filter overlay image value to be displayed)
-        self.layout().removeWidget(self._plot)
         self._plot = _PreviewPlot2D(parent=self)
         self.layout().addWidget(self._plot)
 
         # tune plot
-        self.getPlotWidget().setYAxisInverted(settings.Y_AXIS_DOWNWARD)
+        self.setYAxisInverted(settings.Y_AXIS_DOWNWARD)
         # by default we want to have a full screen display
         self.setAxesDisplayed(False)
 
@@ -110,7 +106,7 @@ class PreviewStitchingPlot(_PlotWithWaitingLabel, StitchAndBackgroundAlphaMixIn)
         # set up
         self.setAlphaBackgroundImg(value=self.DEFAULT_BACKGROUND_IMG_ALPHA)
         self.setAlphaStitchedImg(value=self.DEFAULT_STITCHED_IMG_ALPHA)
-        self.setWaiting(False)
+        self._waitingOverlay.hide()
 
         # connect signal / slot
         self._backGroundAction.toggled.connect(self._update)
@@ -249,48 +245,6 @@ class PreviewStitchingPlot(_PlotWithWaitingLabel, StitchAndBackgroundAlphaMixIn)
     def stitched_image(self):
         return self._stitched_image
 
-    # expose API
-    def getImage(self, *args, **kwargs):
-        return self.getPlotWidget().getImage(*args, **kwargs)
-
-    def addImage(self, *args, **kwargs):
-        self.getPlotWidget().addImage(*args, **kwargs)
-
-    def removeImage(self, *args, **kwargs):
-        self.getPlotWidget().removeImage(*args, **kwargs)
-
-    def toolBar(self, *args, **kwargs):
-        return self.getPlotWidget().toolBar(*args, **kwargs)
-
-    def setKeepDataAspectRatio(self, *args, **kwargs):
-        return self.getPlotWidget().setKeepDataAspectRatio(*args, **kwargs)
-
-    def getColorBarWidget(self, *args, **kwargs):
-        return self.getPlotWidget().getColorBarWidget(*args, **kwargs)
-
-    def getMaskAction(self, *args, **kwargs):
-        return self.getPlotWidget().getMaskAction(*args, **kwargs)
-
-    def getCopyAction(self, *args, **kwargs):
-        return self.getPlotWidget().getCopyAction(*args, **kwargs)
-
-    def addToolBar(self, *args, **kwargs):
-        return self.getPlotWidget().addToolBar(*args, **kwargs)
-
-    def setActiveImage(self, *args, **kwargs):
-        return self.getPlotWidget().setActiveImage(*args, **kwargs)
-
-    def setAxesDisplayed(self, *args, **kwargs):
-        plotWidget = self.getPlotWidget()
-        if hasattr(plotWidget, "setAxesDisplayed"):
-            plotWidget.setAxesDisplayed(*args, **kwargs)
-
-    def getDefaultColormap(self, *args, **kwargs):
-        return self.getPlotWidget().getDefaultColormap()
-
-    def setDefaultColormap(self, *args, **kwargs):
-        return self.getPlotWidget().setDefaultColormap(*args, **kwargs)
-
     def setPixelSize(self, pixel_size: Union[tuple, float]):
         """set the pixel size to be used by the ruler"""
         self._tapeMeasureButton.setPixelSize(pixel_size_m=pixel_size)

tomwer/gui/stitching/stitching_raw.py

@@ -189,9 +189,9 @@ class RawStitchingPlot(PlotWindow):
 
         self._alphaValuesWidget.addTomoObj(tomo_obj)
         if isinstance(tomo_obj, TomwerScanBase):
-            self._scan_reading_order[
-                tomo_obj.get_identifier().to_str()
-            ] = self.getRotationAngleDirection(tomo_obj)
+            self._scan_reading_order[tomo_obj.get_identifier().to_str()] = (
+                self.getRotationAngleDirection(tomo_obj)
+            )
             if first_tomo_obj_id != tuple(self._tomo_objs.keys())[0]:
                 # if the order of scans might have change we need to update the full stack (to handle reading order)
                 self._updateImages()

tomwer/gui/utils/inputwidget.py

@@ -360,9 +360,9 @@ class NXTomomillOutputDirSelector(qt.QWidget):
             self._manualRB.setChecked(True)
         else:
             if default_output is ProcessDataOutputDirMode.IN_SCAN_FOLDER:
-                self._processedDataFolderRB.setChecked(True)
-            elif default_output is ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER:
                 self._inScanFolder.setChecked(True)
+            elif default_output is ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER:
+                self._processedDataFolderRB.setChecked(True)
             elif default_output is ProcessDataOutputDirMode.RAW_DATA_FOLDER:
                 self._rawDataFolderRB.setChecked(True)
             else:
@@ -524,6 +524,11 @@ class OutputVolumeDefinition(qt.QWidget):
             os.environ["TOMWER_DEFAULT_INPUT_DIR"]
         ):
             dialog.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
+        elif dialog.directory() != os.getcwd() or str(dialog.directory()).startswith(
+            "/data"
+        ):
+            # if the directory as already been set by the user. Avoid redefining it
+            pass
         elif os.path.isdir("/data"):
             dialog.setDirectory("/data")
 
@@ -540,6 +545,11 @@ class OutputVolumeDefinition(qt.QWidget):
             os.environ["TOMWER_DEFAULT_INPUT_DIR"]
         ):
             dialog.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
+        elif dialog.directory() != os.getcwd() or str(dialog.directory()).startswith(
+            "/data"
+        ):
+            # if the directory as already been set by the user. Avoid redefining it
+            pass
         elif os.path.isdir("/data"):
             dialog.setDirectory("/data")
 

tomwer/gui/utils/lineselector/lineselector.py

@@ -219,7 +219,7 @@ class QLineSelector(qt.QWidget):
         """
         legend = self._getLegend(row_n=row)
         if legend in self.__selection:
-            self._plot.removeItem(legend)
+            self._plot.remove(legend=legend, kind="item")
             del self.__selection[legend]
 
     def _plotDrawEvent(self, event):