tomwer 1.0.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

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

@@ -131,21 +131,29 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             self.registerWidget(self._ccdThreshold, "optional"),
         ]
 
+        # sr current normalization
+        self._normalizeCurrent = qt.QCheckBox("normalize with current", self)
+        self._normalizeCurrent.setToolTip(
+            "Whether to normalize frames with Synchrotron Current. This can correct the effect of a beam refill not taken into account by flats."
+        )
+        self.layout().addWidget(self._normalizeCurrent, 6, 0, 1, 2)
+        self.registerWidget(self._normalizeCurrent, "required")
+
         # take logarithm
         self._takeLogarithmCB = qt.QCheckBox("take logarithm", self)
-        self.layout().addWidget(self._takeLogarithmCB, 6, 0, 1, 2)
-        self.registerWidget(self._takeLogarithmCB, "required")
+        self.layout().addWidget(self._takeLogarithmCB, 7, 0, 1, 2)
+        self.registerWidget(self._takeLogarithmCB, "advanced")
 
         # log min clip value
         self._clipMinLogValueLabel = qt.QLabel("log min clip value:", self)
         self._clipMinLogValueLabel.setAlignment(qt.Qt.AlignRight)
-        self.layout().addWidget(self._clipMinLogValueLabel, 7, 2, 1, 1)
+        self.layout().addWidget(self._clipMinLogValueLabel, 8, 2, 1, 1)
         self._clipMinLogValue = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._clipMinLogValue.setMinimum(0.0)
         self._clipMinLogValue.setMaximum(9999999)
         self._clipMinLogValue.setSingleStep(0.01)
         self._clipMinLogValue.setDecimals(6)
-        self.layout().addWidget(self._clipMinLogValue, 7, 3, 1, 1)
+        self.layout().addWidget(self._clipMinLogValue, 8, 3, 1, 1)
         self._takeLogOpt = [
             self.registerWidget(self._clipMinLogValueLabel, "optional"),
             self.registerWidget(self._clipMinLogValue, "optional"),
@@ -154,13 +162,13 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         # log max clip value
         self._clipMaxLogValueLabel = qt.QLabel("log max clip value:", self)
         self._clipMaxLogValueLabel.setAlignment(qt.Qt.AlignRight)
-        self.layout().addWidget(self._clipMaxLogValueLabel, 8, 2, 1, 1)
+        self.layout().addWidget(self._clipMaxLogValueLabel, 9, 2, 1, 1)
         self._clipMaxLogValue = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._clipMaxLogValue.setMinimum(0.0)
         self._clipMaxLogValue.setMaximum(9999999)
         self._clipMaxLogValue.setSingleStep(0.01)
         self._clipMaxLogValue.setDecimals(6)
-        self.layout().addWidget(self._clipMaxLogValue, 8, 3, 1, 1)
+        self.layout().addWidget(self._clipMaxLogValue, 9, 3, 1, 1)
         self._takeLogOpt.extend(
             [
                 self.registerWidget(self._clipMaxLogValueLabel, "optional"),
@@ -171,7 +179,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         # tilt correction
         self._tiltCorrection = TiltCorrection("tilt correction", self)
         self.registerWidget(self._tiltCorrection, "advanced")
-        self.layout().addWidget(self._tiltCorrection, 9, 0, 1, 4)
+        self.layout().addWidget(self._tiltCorrection, 10, 0, 1, 4)
 
         # spacer for style
         spacer = qt.QWidget(self)
@@ -183,6 +191,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self.setDFFOptVisible(False)
 
         self._ccdFilterCB.setChecked(False)
+        self._normalizeCurrent.setChecked(False)
         self._ccdThreshold.setValue(0.04)
 
         self._clipMinLogValue.setValue(1e-6)
@@ -201,6 +210,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self._dffCB.toggled.connect(self.setDFFOptVisible)
         self._dffSigmaQDSB.valueChanged.connect(self._dffSigmaChanged)
         self._ccdFilterCB.toggled.connect(self._ccdFilterChanged)
+        self._normalizeCurrent.toggled.connect(self._normalizeCurrentChanged)
         self._ccdThreshold.editingFinished.connect(self._ccdFilterThresholdChanged)
         self._clipMinLogValue.editingFinished.connect(self._logMinClipChanged)
         self._clipMaxLogValue.editingFinished.connect(self._logMaxClipChanged)
@@ -226,6 +236,9 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
     def _ccdFilterChanged(self, *args, **kwargs):
         self._signalConfChanged("ccd_filter_enabled")
 
+    def _normalizeCurrentChanged(self, *args, **kwargs):
+        self._signalConfChanged("normalize_srcurrent")
+
     def _ccdFilterThresholdChanged(self, *args, **kwargs):
         self._signalConfChanged("ccd_filter_threshold")
 
@@ -284,6 +297,12 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
     def getCCDThreshold(self) -> float:
         return float(self._ccdThreshold.text())
 
+    def getNormalizeCurrent(self) -> bool:
+        return self._normalizeCurrent.isChecked()
+
+    def setNormalizeCurrent(self, normalize: bool) -> None:
+        self._normalizeCurrent.setChecked(normalize)
+
     def getLogMinClipValue(self) -> float:
         return float(self._clipMinLogValue.text())
 
@@ -329,6 +348,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             "sino_rings_options": self.getSinoRingcorrectionOptions(),
             "tilt_correction": tilt_correction,
             "autotilt_options": autotilt_opts,
+            "normalize_srcurrent": int(self.getNormalizeCurrent()),
         }
 
     @docstring(_NabuStageConfigBase)
@@ -359,6 +379,9 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             ccd_filter_threshold = conf["ccd_filter_threshold"]
             if ccd_filter_threshold not in (None, "", "none"):
                 self._ccdThreshold.setValue(float(ccd_filter_threshold))
+        normalize_srcurrent = conf.get("normalize_srcurrent", None)
+        if normalize_srcurrent is not None:
+            self.setNormalizeCurrent(bool(normalize_srcurrent))
         if "take_logarithm" in conf:
             take_logarithm = conf["take_logarithm"]
             if take_logarithm not in (None, "", "none"):

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

@@ -194,7 +194,7 @@ class TranslationMvtFileWidget(qt.QWidget):
         else:
             return dialog.selectedUrl()
 
-    def _selectTextFile(self):
+    def _selectTextFile(self):  # pragma: no cover
         dialog = qt.QFileDialog(self)
         dialog.setFileMode(qt.QFileDialog.ExistingFile)
 
@@ -256,7 +256,7 @@ class AnglesFileWidget(qt.QWidget):
     def setFile(self, file_path):
         self._qle.setText(file_path)
 
-    def _selectFile(self) -> str:
+    def _selectFile(self) -> str:  # pragma: no cover
         dialog = qt.QFileDialog()
         dialog.setFileMode(qt.QFileDialog.ExistingFile)
         dialog.setNameFilters(
@@ -401,6 +401,13 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
             "Whether to set to zero voxels falling outside of the reconstruction region"
         )
         self.layout().addWidget(self._clipOuterCircleCB, 11, 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.registerWidget(self._centeredAxisCB, "optional")
 
         # translation movement file
         self._transMvtFileLabel = qt.QLabel("translation movement file", self)
@@ -437,6 +444,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._preconditioningFilter.setChecked(True)
         self._positivityConstraintCB.setChecked(True)
         self._clipOuterCircleCB.setChecked(False)
+        self._centeredAxisCB.setChecked(False)
 
         # connect signal / slot
         self._methodQCB.currentIndexChanged.connect(self._methodChanged)
@@ -454,6 +462,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         self._binSubSamplingGB.binningChanged.connect(self._binningChanged)
         self._anglesFileWidget._qle.textChanged.connect(self._anglesFilechanged)
         self._clipOuterCircleCB.toggled.connect(self._clipOuterCircleChanged)
+        self._centeredAxisCB.toggled.connect(self._centeredAxisChanged)
 
     def getSlices(self):
         return self._slicesWidget.getSlices()
@@ -501,6 +510,9 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
     def _clipOuterCircleChanged(self, *args, **kwargs):
         self._signalConfChanged("clip_outer_circle")
 
+    def _centeredAxisChanged(self, *args, **kwargs):
+        self._signalConfChanged("centered_axis")
+
     def _binningChanged(self, *args, **kwargs):
         self._signalConfChanged("binning")
         self._signalConfChanged("binning_z")
@@ -590,7 +602,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         return self._binSubSamplingGB.getVerticalBinning()
 
     def setVerticalBinning(self, binning):
-        return self._binSubSamplingGB.getVerticalBinning(binning=binning)
+        return self._binSubSamplingGB.setVerticalBinning(binning=binning)
 
     def getProjSubsampling(self):
         return self._binSubSamplingGB.getProjSubsampling()
@@ -607,8 +619,14 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
     def getClipOuterCircle(self) -> bool:
         return self._clipOuterCircleCB.isChecked()
 
-    def setClipOuterCircle(self, checked) -> bool:
-        return self._clipOuterCircleCB.setChecked(checked)
+    def setClipOuterCircle(self, checked: bool) -> None:
+        self._clipOuterCircleCB.setChecked(checked)
+
+    def getCenteredAxis(self) -> bool:
+        return self._centeredAxisCB.isChecked()
+
+    def setCenteredAxis(self, checked: bool):
+        self._centeredAxisCB.setChecked(checked)
 
     @docstring(_NabuStageConfigBase)
     def getConfiguration(self) -> dict:
@@ -632,6 +650,7 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
             "rotation_axis_position": "",
             "translation_movements_file": self.getTranslationMvtFile() or "",
             "clip_outer_circle": int(self.getClipOuterCircle()),
+            "centered_axis": int(self.getCenteredAxis()),
         }
         config.update(self._subRegionSelector.getConfiguration())
         return config
@@ -668,6 +687,8 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
             self.setTranslationMvtFile(config["translation_movements_file"])
         if "clip_outer_circle" in config:
             self.setClipOuterCircle(bool(config["clip_outer_circle"]))
+        if "centered_axis" in config:
+            self.setCenteredAxis(bool(config["centered_axis"]))
         self._subRegionSelector.setConfiguration(config=config)
 
     def _signalConfChanged(self, param):
@@ -958,11 +979,3 @@ class _BinSubSampling(qt.QGroupBox):
 
     def _valueUpdated(self, *args, **kwargs):
         self.binningChanged.emit()
-
-
-if __name__ == "__main__":
-    app = qt.QApplication([])
-    widget = _NabuReconstructionConfig(None, None)
-    widget.show()
-    print(widget.getConfiguration())
-    app.exec_()

tomwer/gui/reconstruction/nabu/slices.py

@@ -361,9 +361,17 @@ class NabuWindow(qt.QMainWindow):
             config = parse_nabu_config_file(inputFile)
             self.setConfiguration(config)
 
-    def askForNabuconfigFile(self, acceptMode=qt.QFileDialog.AcceptSave):
+    def askForNabuconfigFile(  # pragma: no cover
+        self, acceptMode=qt.QFileDialog.AcceptSave
+    ):
         dialog = qt.QFileDialog(self)
-        dialog.setNameFilters(["*.cfg"])
+        dialog.setNameFilters(
+            [
+                "Configuration files (*.cfg *.conf *.config)",
+                "Any files (*)",
+            ]
+        )
+
         dialog.setAcceptMode(acceptMode)
         dialog.setFileMode(qt.QFileDialog.AnyFile)
 

tomwer/gui/reconstruction/nabu/slurm.py

@@ -117,7 +117,7 @@ class SlurmSettingsWidget(qt.QWidget):
         self._nCores.setValue(SlurmSettings.N_CORES_PER_TASK)
         self._nWorkers.setValue(SlurmSettings.N_TASKS)
         self._memory.setValue(SlurmSettings.MEMORY_PER_WORKER)
-        self._queue.setText(SlurmSettings.PARTIION)
+        self._queue.setText(SlurmSettings.PARTITION)
         self._nGpu.setValue(SlurmSettings.N_GPUS_PER_WORKER)
 
         # connect signal / slot

tomwer/gui/reconstruction/nabu/volume.py

@@ -435,13 +435,6 @@ class NabuVolumeWindow(qt.QMainWindow):
         menu.addAction(self._expertConfiguration)
         self.__configurationModesGroup.addAction(self._expertConfiguration)
 
-        # expose API
-        self.getConfiguration = self._mainWidget.getConfiguration
-        self.setConfiguration = self._mainWidget.setConfiguration
-        self.setConfigurationLevel = self._mainWidget.setConfigurationLevel
-        self.getConfigurationLevel = self._mainWidget.getConfigurationLevel
-        self.setScan = self._mainWidget.setScan
-
         # set up
         self._basicConfigAction.setChecked(True)
         self._userModeChanged(action=self._basicConfigAction)
@@ -463,5 +456,18 @@ class NabuVolumeWindow(qt.QMainWindow):
             raise ValueError("unknow configuration level")
         self._mainWidget.setConfigurationLevel(level)
 
+    # expose API
     def getConfigurationLevel(self):
         self._mainWidget.getConfigurationLevel()
+
+    def setConfigurationLevel(self, level):
+        self._mainWidget.setConfigurationLevel(level=level)
+
+    def getConfiguration(self):
+        return self._mainWidget.getConfiguration()
+
+    def setConfiguration(self, config):
+        return self._mainWidget.setConfiguration(config=config)
+
+    def setScan(self, scan):
+        return self._mainWidget.setScan(scan=scan)

tomwer/gui/reconstruction/normalization/intensity.py

@@ -866,7 +866,7 @@ class _NormIntensityDatasetWidget(qt.QWidget):
             if self._lastGlobalPath is not None:
                 self.setGlobalFilePath(self._lastGlobalPath)
 
-    def _selectFile(self):
+    def _selectFile(self):  # pragma: no cover
         dialog = qt.QFileDialog(self)
         dialog.setNameFilters(["HDF5 file *.h5 *.hdf5 *.nx *.nxs *.nexus"])
 

tomwer/gui/reconstruction/saaxis/corrangeselector.py

@@ -150,9 +150,13 @@ class SinogramViewer(_SinogramViewer):
         if self._corMarker is not None:
             self._corMarker.sigDragFinished.disconnect(self._middleMarkerMoved)
         if self._fromMarker is not None:
-            self._fromMarker.sigDragFinished.disconnect(self._fromCallback)
+            self._fromMarker.sigDragFinished.disconnect(
+                self._fromCallback  # pylint: disable=E0203
+            )
         if self._toMarker is not None:
-            self._toMarker.sigDragFinished.disconnect(self._toCallback)
+            self._toMarker.sigDragFinished.disconnect(
+                self._toCallback  # pylint: disable=E0203
+            )
 
         # clear existing markers
         markers = [
@@ -212,7 +216,7 @@ class _ReconstructionModeGB(qt.QGroupBox):
 
     _DEFAULT_VERTICAL_SLICE_MODE = ("middle", "other")
 
-    def __init__(self, parent=None, title="Slice reconstruction mode"):
+    def __init__(self, parent=None, title="Slice to be reconstructed"):
         self.__scan = None
         qt.QGroupBox.__init__(self, parent)
         self.setTitle(title)
@@ -262,9 +266,9 @@ class _ReconstructionModeGB(qt.QGroupBox):
         self.blockSignals(True)
         self.setCurrentMode("vertical", "middle")
         self.blockSignals(False)
-        # for now we don't have the tilt correction mode
-        # self._sliceTiltCorrQSB.hide()
         self._tiltCorrectionRB.hide()
+        # as for now only the Vertical mode is handled hide it to avoid confusing user
+        self._verticalRB.hide()
 
     def setCurrentMode(self, mode, slices):
         valid_modes = ("vertical", "horizontal")
@@ -309,7 +313,7 @@ class _ReconstructionModeGB(qt.QGroupBox):
                 index_radio = list(projections.keys())[len(projections) // 2]
                 data = get_data(projections[index_radio])
             except Exception as e:
-                _logger.error("Fail to load radio data:", str(e))
+                _logger.error(f"Fail to load radio data: {str(e)}")
                 return
 
         lineSelection.setData(data)
@@ -823,31 +827,3 @@ class SliceAndCorWidget(qt.QMainWindow):
         self._sinogramViewer.close()
         self._sinogramViewer = None
         super().close()
-
-
-if __name__ == "__main__":
-    import tempfile
-    import shutil
-    from tomwer.core.utils.scanutils import MockHDF5
-
-    app = qt.QApplication([])
-    window = SliceAndCorWidget()
-
-    img_width = 216
-    slices_folder = tempfile.mkdtemp()
-
-    scan = MockHDF5(
-        scan_path=slices_folder,
-        n_proj=60,
-        n_ini_proj=60,
-        create_ini_dark=False,
-        create_ini_ref=False,
-        dim=img_width,
-    ).scan
-
-    window.setScan(scan)
-    window.setWindowTitle("cor and slice selection")
-    window.show()
-    app.exec_()
-
-    shutil.rmtree(slices_folder)

tomwer/gui/reconstruction/saaxis/saaxis.py

@@ -48,6 +48,7 @@ from tomwer.gui.utils.buttons import TabBrowsersButtons
 from tomwer.gui.reconstruction.scores.control import ControlWidget
 from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisProcess
 from tomwer.core.process.reconstruction.axis import mode as axis_mode
+from tomwer.gui.utils.scandescription import ScanNameLabelAndShape
 import numpy
 from typing import Union
 import logging
@@ -182,7 +183,6 @@ class _SAAxisTabWidget(qt.QTabWidget):
         self.setVolumeSize = self._resultsViewer.setVolumeSize
         self.setCurrentCorValue = self._resultsViewer.setCurrentVarValue
         self.getCurrentCorValue = self._resultsViewer.getCurrentVarValue
-        self.getScoreMethod = self._resultsViewer.getScoreMethod
         self.getEstimatedCorPosition = self._sliceAndCorWidget.getEstimatedCorPosition
         self.setEstimatedCorPosition = self._sliceAndCorWidget.setEstimatedCorPosition
         self.getNReconstruction = self._sliceAndCorWidget.getNReconstruction
@@ -200,6 +200,7 @@ class _SAAxisTabWidget(qt.QTabWidget):
         self.getSlicesRange = self._sliceAndCorWidget.getSlicesRange
         self.setSlicesRange = self._sliceAndCorWidget.setSlicesRange
         self.loadSinogram = self._sliceAndCorWidget.loadSinogram
+        self.saveReconstructedSlicesTo = self._resultsViewer.saveReconstructedSlicesTo
         # expose signals
         self.sigStartSinogramLoad = self._sliceAndCorWidget.sigStartSinogramLoad
         self.sigEndSinogramLoad = self._sliceAndCorWidget.sigEndSinogramLoad
@@ -318,8 +319,14 @@ class SAAxisWindow(qt.QMainWindow):
         self._qaxis_rp = QAxisRP()
         self.setWindowFlags(qt.Qt.Widget)
         # central widget
+        self._mainWidget = qt.QWidget(self)
+        self._mainWidget.setLayout(qt.QVBoxLayout())
+
+        self._scanInfo = ScanNameLabelAndShape(self)
+        self._mainWidget.layout().addWidget(self._scanInfo)
         self._tabWidget = _SAAxisTabWidget(self)
-        self.setCentralWidget(self._tabWidget)
+        self._mainWidget.layout().addWidget(self._tabWidget)
+        self.setCentralWidget(self._mainWidget)
         # next and previous buttons for browsing the tab widget
         self._browserButtons = TabBrowsersButtons(self)
         self._dockWidgetBrwButtons = qt.QDockWidget(self)
@@ -355,7 +362,7 @@ class SAAxisWindow(qt.QMainWindow):
         self.getCors = self._tabWidget.getCors
         self.getMode = self._tabWidget.getReconstructionMode
         self.loadSinogram = self._tabWidget.loadSinogram
-        self.isAutoFocusLock = self._tabWidget.isAutoFocusLock
+        self.saveReconstructedSlicesTo = self._tabWidget.saveReconstructedSlicesTo
         # expose signals
         self.sigValidated = self._saaxisControl.sigValidateRequest
         self.sigStartSinogramLoad = self._tabWidget.sigStartSinogramLoad
@@ -408,6 +415,7 @@ class SAAxisWindow(qt.QMainWindow):
     def setScan(self, scan):
         self._scan = scan
         self._tabWidget.setScan(scan)
+        self._scanInfo.setScan(scan)
         self._updateSinogramLine()
         self._loadEstimatedCorFromScan(scan)
 
@@ -450,9 +458,6 @@ class SAAxisWindow(qt.QMainWindow):
             line = list(r_slice.values())[0]
         self._tabWidget.getSinogramViewer().setLine(line)
 
-    def setEstimatedCorPosition(self, value):
-        self.setEstimatedCorPosition(value=value)
-
     def _autoCorRequested(self):
         window = self.getAutomaticCorWindow()
         window.activateWindow()

tomwer/gui/reconstruction/saaxis/sliceselector.py

@@ -63,14 +63,6 @@ class SliceSelector(qt.QWidget):
         self._volumeView = _SliceSelectorFrmVolume(self, invert_y_axis=invert_y_axis)
         self.layout().addWidget(self._volumeView)
 
-        # expose API
-        self.getSlicesValue = self._volumeView.getSlicesValue
-        self.getSlicesRange = self._volumeView.getSlicesRange
-        self.setSliceValue = self._volumeView.setSliceValue
-
-    def getSlicesRange(self) -> tuple:
-        return self._volumeView.getSlicesRange()
-
     def setSlicesRange(self, min_index, max_index):
         self._volumeView.setSlicesRange(min_index, max_index)
         for widget in self._slicesQSB:
@@ -136,6 +128,16 @@ class SliceSelector(qt.QWidget):
             position = self._volumeView.plotSpaceToValue(marker.getPosition()[1])
             sb.setValue(position)
 
+    # expose API
+    def getSlicesValue(self) -> dict:
+        return self._volumeView.getSlicesValue()
+
+    def setSliceValue(self, name: str, value: float):
+        self._volumeView.setSliceValue(name=name, value=value)
+
+    def getSlicesRange(self) -> tuple:
+        return self._volumeView.getSlicesRange()
+
 
 class _SliceSelectorFrmVolume(PlotWidget):
     """
@@ -252,7 +254,7 @@ class _SliceSelectorFrmVolume(PlotWidget):
         )
         if self._yAxisInverted:
             res = self._slicesRange[1] - res
-        return res
+        return int(res)
 
     def _updatePlane(self, y, curve_name, color):
         anchor_shift = 0.2
@@ -334,20 +336,3 @@ class _SliceSelectorFrmVolume(PlotWidget):
         marker = self._getMarker(self.getMarkerName(name))
         marker.setPosition(0, self.valueToPlotSpace(float(value)))
         marker.sigDragFinished.emit()
-
-
-class _SliceSB(qt.QWidget):
-    def __init__(self, parent):
-        qt.QWidget.__init__(self, parent)
-
-
-if __name__ == "__main__":
-    app = qt.QApplication([])
-    window = SliceSelector(insert=False)
-    window.setSlicesRange(0, 100)
-    window.addSlice(value=0, name="slice0", color="blue")
-    window.addSlice(value=25, name="slice1", color="green")
-    window.addSlice(value=70, name="slice2", color="cyan")
-    window.addSlice(value=100, name="slice3", color="red")
-    window.show()
-    app.exec_()

tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py

@@ -43,6 +43,7 @@ from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
 from tomwer.synctools.sadeltabeta import QSADeltaBetaParams
 from tomwer.gui.utils.buttons import TabBrowsersButtons
 from tomwer.gui.reconstruction.nabu.slices import NabuWindow
+from tomwer.gui.utils.scandescription import ScanNameLabelAndShape
 from tomwer.gui.reconstruction.scores.scoreplot import ScorePlot as _ScorePlot
 from tomwer.gui.reconstruction.scores.scoreplot import DelaBetaSelection
 from tomwer.core.process.reconstruction.nabu.utils import _NabuMode
@@ -120,6 +121,7 @@ class _SADeltaBetaTabWidget(qt.QTabWidget):
         # expose function API
         self.setNabuReconsParams = self._nabuSettings.setConfiguration
         self.getNabuReconsParams = self._nabuSettings.getConfiguration
+        self.saveReconstructedSlicesTo = self._resultsViewer.saveReconstructedSlicesTo
 
     def setDeltaBetaScores(self, *args, **kwargs):
         self._resultsViewer.setVarScores(*args, **kwargs)
@@ -239,8 +241,13 @@ class SADeltaBetaWindow(qt.QMainWindow):
         self._qdeltabeta_rp = QSADeltaBetaParams()
         self.setWindowFlags(qt.Qt.Widget)
         # central widget
+        self._mainWidget = qt.QWidget(self)
+        self._mainWidget.setLayout(qt.QVBoxLayout())
+        self._scanInfo = ScanNameLabelAndShape(self)
+        self._mainWidget.layout().addWidget(self._scanInfo)
         self._tabWidget = _SADeltaBetaTabWidget(self)
-        self.setCentralWidget(self._tabWidget)
+        self._mainWidget.layout().addWidget(self._tabWidget)
+        self.setCentralWidget(self._mainWidget)
         # next and previous buttons for browsing the tab widget
         self._browserButtons = TabBrowsersButtons(self)
         self._dockWidgetBrwButtons = qt.QDockWidget(self)
@@ -283,6 +290,7 @@ class SADeltaBetaWindow(qt.QMainWindow):
     def setScan(self, scan):
         self._scan = scan
         self._tabWidget.setScan(scan)
+        self._scanInfo.setScan(scan)
 
     def getScan(self):
         return self._scan
@@ -358,6 +366,9 @@ class SADeltaBetaWindow(qt.QMainWindow):
     def setSlicesRange(self, min_, max_):
         self._tabWidget.setSliceRange(min_, max_)
 
+    def saveReconstructedSlicesTo(self, output_folder):
+        self._tabWidget.saveReconstructedSlicesTo(output_folder=output_folder)
+
 
 class DeltaBetaSelectionWidget(qt.QWidget):
     """Widget used to select the range of delta / beta to use"""
@@ -396,6 +407,7 @@ class DeltaBetaSelectionWidget(qt.QWidget):
         self._paganinGB.setLayout(qt.QVBoxLayout())
         self._mainWindow = _NabuPhaseConfig(self, scrollArea=None)
         self._mainWindow.setConfigurationLevel(ConfigurationLevel.ADVANCED)
+        self._mainWindow._ctfOpts.hide()
         self._paganinGB.layout().addWidget(self._mainWindow)
         self._mainWindow._methodCB.hide()
         self._mainWindow._methodLabel.hide()
@@ -489,10 +501,3 @@ class DeltaBetaSelectionWidget(qt.QWidget):
                     from_=values.min(), to_=values.max(), step_=step
                 )
             )
-
-
-if __name__ == "__main__":
-    qapp = qt.QApplication([])
-    widget = SADeltaBetaWindow(parent=None)
-    widget.show()
-    qapp.exec_()