tomwer 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

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

@@ -33,6 +33,7 @@ from tomwer.utils import docstring
 from silx.gui import qt
 from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
 from tomwer.gui.reconstruction.nabu.nabuconfig import base
+from tomwer.gui.reconstruction.nabu.nabuconfig.ctf import CTFConfig
 from tomwer.gui.utils.inputwidget import SelectionLineEdit
 from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 from tomwer.core.process.reconstruction.nabu.utils import _NabuStages, _NabuPhaseMethod
@@ -75,11 +76,15 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
         self._methodCB = QComboBox(parent=self, scrollArea=scrollArea)
         for method in _NabuPhaseMethod:
             self._methodCB.addItem(method.value)
+        idx_ctf = self._methodCB.findText(_NabuPhaseMethod.CTF.value)
+        self._methodCB.setItemData(
+            idx_ctf, "Contrast Transfert Function", qt.Qt.ToolTipRole
+        )
         self.layout().addWidget(self._methodCB, 1, 1, 1, 3)
         self.registerWidget(self._methodLabel, "required")
         self.registerWidget(self._methodCB, "required")
 
-        # paganin options
+        # paganin & ctf options
         self._paganinOpts = NabuPaganinConfig(parent=self, scrollArea=scrollArea)
         self.layout().addWidget(self._paganinOpts, 2, 0, 3, 3)
 
@@ -87,6 +92,11 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
         self._unsharpOpts = NabuUnsharpConfig(parent=self)
         self.layout().addWidget(self._unsharpOpts, 6, 0, 3, 3)
 
+        # ctf options
+        self._ctfOpts = CTFConfig(parent=self)
+        self.layout().addWidget(self._ctfOpts, 9, 0, 3, 4)
+        self.registerWidget(self._ctfOpts, "advanced")
+
         # spacer for style
         spacer = qt.QWidget(self)
         spacer.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Expanding)
@@ -101,12 +111,15 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
         self._methodCB.currentIndexChanged.connect(self._methodChanged)
         self._paganinOpts.sigConfChanged.connect(self._signalConfChanged)
         self._unsharpOpts.sigConfChanged.connect(self._signalConfChanged)
+        self._ctfOpts.sigConfChanged.connect(self._signalConfChanged)
 
         # set up
         self._paganinOpts.setEnabled(self.getMethod() is not _NabuPhaseMethod.NONE)
+        self._ctfOpts.setEnabled(self.getMethod() is _NabuPhaseMethod.CTF)
 
     def _methodChanged(self, *args, **kwargs):
         self._paganinOpts.setEnabled(self.getMethod() is not _NabuPhaseMethod.NONE)
+        self._ctfOpts.setEnabled(self.getMethod() is _NabuPhaseMethod.CTF)
         self._signalConfChanged("method")
 
     def _signalConfChanged(self, param):
@@ -129,13 +142,15 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
             else:
                 _logger.warning("unable to find method {method}")
         self._unsharpOpts.setConfiguration(config)
+        self._ctfOpts.setConfiguration(config)
 
     @docstring(base._NabuStageConfigBase)
     def getConfiguration(self) -> dict:
         configuration = {"method": self.getMethod().value}
-        if self.getMethod() is _NabuPhaseMethod.PAGANIN:
+        if self.getMethod() in (_NabuPhaseMethod.PAGANIN, _NabuPhaseMethod.CTF):
             configuration.update(self._paganinOpts.getConfiguration())
         configuration.update(self._unsharpOpts.getConfiguration())
+        configuration.update(self._ctfOpts.getConfiguration())
         return configuration
 
     def setConfigurationLevel(self, level):
@@ -169,22 +184,6 @@ class NabuPaganinConfig(qt.QWidget, base._NabuStageConfigBase):
         self.registerWidget(self._db_label, "required")
         self.registerWidget(self._deltaBetaQLE, "required")
 
-        # paganin lmicron
-        # we skip this paramter, only used for compatibility
-
-        # paganin margin
-        # note: hide for now margin as it is not connected at nabu side
-        # self.layout().addWidget(qt.QLabel("margin"), 1, 0, 1, 1)
-        # self._margeQSB = qt.QSpinBox(self)
-        # self._margeQSB.setMinimum(0)
-        # self._margeQSB.setMaximum(9999)
-        # self._margeQSB.setToolTip(
-        #     "Marge (in pixels) in the Paganin filtering "
-        #     "to avoid local tomography artefacts"
-        # )
-        # self.layout().addWidget(self._margeQSB, 1, 1, 1, 1)
-        # self.registerWidget(self._margeQSB, "optional")
-
         # paganin padding_type
         self._paddingLabel = qt.QLabel("padding", self)
         self.layout().addWidget(self._paddingLabel, 2, 0, 1, 1)
@@ -192,7 +191,7 @@ class NabuPaganinConfig(qt.QWidget, base._NabuStageConfigBase):
         self._paddingTypeCB.setToolTip(
             "Padding type for the filtering step " "in Paganin/CTR."
         )
-        for padding_type in (PaddingMode.ZEROS, PaddingMode.ZEROS.EDGE):
+        for padding_type in (PaddingMode.ZEROS, PaddingMode.EDGE):
             self._paddingTypeCB.addItem(padding_type.value)
         self.layout().addWidget(self._paddingTypeCB, 2, 1, 1, 3)
         self.registerWidget(self._paddingLabel, "advanced")

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):
@@ -675,7 +696,6 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
 
 
 class _SubRegionEditor(qt.QObject):
-
     sigConfChanged = qt.Signal(str)
     """Signal emitted each type a parameter is edited"""
 
@@ -897,7 +917,6 @@ class _NabuReconstructionSubRegion(qt.QGroupBox, _NabuStageConfigBase):
 
 
 class _BinSubSampling(qt.QGroupBox):
-
     binningChanged = qt.Signal()
     """signal emitted when binning change"""
 
@@ -960,11 +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

@@ -202,7 +202,6 @@ class NabuDialog(qt.QDialog):
 
 
 class NabuWindow(qt.QMainWindow):
-
     sigConfigChanged = qt.Signal()
     """Signal emitted when the configuration change"""
 
@@ -317,7 +316,6 @@ class NabuWindow(qt.QMainWindow):
             self.setConfigurationLevel(level=configuration_level)
 
     def _saveParameters(self):
-
         from nabu.pipeline.config import generate_nabu_configfile
         from tomwer.core.process.reconstruction.nabu.nabuslices import (
             interpret_tomwer_configuration,
@@ -363,9 +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

@@ -54,7 +54,6 @@ import typing
 
 
 class SinoNormWindow(qt.QMainWindow):
-
     sigConfigurationChanged = qt.Signal()
     """signal emit when the configuration change"""
 
@@ -411,7 +410,6 @@ class SinogramViewer(_SinogramViewer):
 
 
 class _NormIntensityOptions(qt.QWidget):
-
     sigValueCanBeLocked = qt.Signal(bool)
 
     sigProcessingRequested = qt.Signal()
@@ -715,7 +713,6 @@ class _NormIntensityControl(ControlWidget):
 
 
 class _NormIntensityScalarValue(qt.QWidget):
-
     sigValueChanged = qt.Signal(float)
 
     def __init__(self, parent=None):
@@ -740,7 +737,6 @@ class _NormIntensityScalarValue(qt.QWidget):
 
 
 class _NormIntensityDatasetWidget(qt.QWidget):
-
     _FILE_PATH_LOCAL_VALUE = "scan master file"
 
     sigConfigurationChanged = qt.Signal()
@@ -870,7 +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 = [
@@ -206,14 +210,13 @@ class SinogramViewer(_SinogramViewer):
 
 
 class _ReconstructionModeGB(qt.QGroupBox):
-
     reconstructionModeChanged = qt.Signal(str)
 
     reconstructionSliceChanged = qt.Signal()
 
     _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)
@@ -263,9 +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")
@@ -310,7 +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)
@@ -399,7 +402,6 @@ class _ReconstructionModeGB(qt.QGroupBox):
 
 
 class _DetectionAccuracyGB(qt.QGroupBox):
-
     detectionAccuracyChanged = qt.Signal()
     """signal emitted when the value change"""
 
@@ -469,7 +471,6 @@ class _DetectionAccuracyGB(qt.QGroupBox):
 
 
 class _EstimatedCorWidget(qt.QGroupBox):
-
     _MIDDLE_COR_TXT = "middle"
     _OTHER_COR_TXT = "other"
 
@@ -826,31 +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
@@ -138,7 +139,6 @@ class NabuAutoCorDiag(qt.QDialog):
 
 
 class _SAAxisTabWidget(qt.QTabWidget):
-
     sigConfigurationChanged = qt.Signal()
     """signal emitted each time the 'input' configuration changed.
     like slice to reconstruct, number of reconstruction, research width,
@@ -183,7 +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
@@ -201,6 +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
@@ -319,8 +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)
@@ -356,7 +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
@@ -409,6 +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)
 
@@ -451,9 +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()