tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

tomwer/gui/reconstruction/darkref/darkrefcopywidget.py

@@ -1,36 +1,7 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["C. Nemoz", "H. Payno"]
-__license__ = "MIT"
-__date__ = "13/08/2021"
-
+from __future__ import annotations
 
 import logging
 import shutil
-from typing import Union
 
 from silx.gui import qt
 from silx.gui.dialog.DataFileDialog import DataFileDialog
@@ -169,7 +140,7 @@ class RefCopyWidget(qt.QGroupBox):
         """
 
         :param parent: Qt parent
-        :param str save_dir: where the dark and flats 'references' are stored
+        :param save_dir: where the dark and flats 'references' are stored
         """
         qt.QGroupBox.__init__(self, "activate", parent)
         self.__save_dir = save_dir
@@ -180,7 +151,7 @@ class RefCopyWidget(qt.QGroupBox):
             """
             The copy action happen after the reduced (computed) darks and flats. It can be activate or not. \n\n
             Reduced darks and / or flats can be registered and then copy to scan without darks or flat. \n
-            You can set manually Darks and flat (button displayed when the mode auto is unchcked.) \n
+            You can set manually Darks and flat (button displayed when the mode auto is unchecked.) \n
             Otherwise if the mode 'auto' is activated then each time he meets scan with dark and / or flat it will register those as the one to be copied. \n
 
             Then each time the copy action meets scan without reduced dark and / or flat it will copy them. \n
@@ -306,8 +277,8 @@ class RefCopyWidget(qt.QGroupBox):
         """
         return self.isChecked()
 
-    def save_darks_to_be_copied(self, darks: Union[DataUrl, dict]):
+    def save_darks_to_be_copied(self, darks: DataUrl | dict):
         DarkRefsCopy.save_darks_to_be_copied(data=darks, save_dir=self.__save_dir)
 
-    def save_flats_to_be_copied(self, flats: Union[DataUrl, dict]):
+    def save_flats_to_be_copied(self, flats: DataUrl | dict):
         DarkRefsCopy.save_flats_to_be_copied(data=flats, save_dir=self.__save_dir)

tomwer/gui/reconstruction/darkref/darkrefwidget.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "10/01/2018"
+from __future__ import annotations
 
 
 import logging

tomwer/gui/reconstruction/nabu/castvolume.py

@@ -1,35 +1,6 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "15/12/2021"
-
+from __future__ import annotations
 
 import logging
-from typing import Optional
 
 from silx.gui import qt
 from silx.gui.utils import blockSignals
@@ -90,9 +61,9 @@ class CastVolumeWidget(qt.QWidget):
         )
         self.layout().addWidget(self._minMaxAuto, 2, 1, 1, 1)
 
-        self._minPixValue = qt.QLineEdit("", self)
+        self._minPixValue = qt.QLineEdit("0.0", self)
         self._minPixValue.setPlaceholderText("min")
-        self._maxPixValue = qt.QLineEdit("", self)
+        self._maxPixValue = qt.QLineEdit("0.0", self)
         self._maxPixValue.setPlaceholderText("max")
         validator = qt.QDoubleValidator(self)
         validator.setNotation(qt.QDoubleValidator.ScientificNotation)
@@ -181,6 +152,10 @@ class CastVolumeWidget(qt.QWidget):
         self._useDefaultSaveDirQCB.toggled.connect(self._updateOutputDirVis)
         self._minMaxAuto.toggled.connect(self._configChanged)
         self._minMaxAuto.toggled.connect(self._updatePixMinMaxVis)
+        self._minPixValue.textChanged.connect(self._configChanged)
+        self._maxPixValue.textChanged.connect(self._configChanged)
+        self._lowPercentileQSB.valueChanged.connect(self._configChanged)
+        self._highPercentileQSB.valueChanged.connect(self._configChanged)
 
     def _updateCRatiosVis(self, *args, **kwargs):
         self._cRatiosLabel.setVisible(
@@ -225,7 +200,7 @@ class CastVolumeWidget(qt.QWidget):
     def setOverwrite(self, remove) -> None:
         self._overwriteCB.setChecked(remove)
 
-    def getDataMin(self) -> Optional[float]:
+    def getDataMin(self) -> float | None:
         if (
             self._minMaxAuto.isChecked()
             or self._minPixValue.text().replace(" ", "") == ""
@@ -234,14 +209,15 @@ class CastVolumeWidget(qt.QWidget):
         else:
             return float(self._minPixValue.text())
 
-    def setDataMin(self, value: Optional[float]) -> None:
+    def setDataMin(self, value: float | None) -> None:
         with blockSignals(self._minMaxAuto):
             self._minMaxAuto.setChecked(value is None)
         if value is not None:
             with blockSignals(self._minPixValue):
                 self._minPixValue.setText(str(value))
+        self._updatePixMinMaxVis()
 
-    def getDataMax(self) -> Optional[float]:
+    def getDataMax(self) -> float | None:
         if (
             self._minMaxAuto.isChecked()
             or self._maxPixValue.text().replace(" ", "") == ""
@@ -250,14 +226,15 @@ class CastVolumeWidget(qt.QWidget):
         else:
             return float(self._maxPixValue.text())
 
-    def setDataMax(self, value: Optional[float]) -> None:
+    def setDataMax(self, value: float | None) -> None:
         with blockSignals(self._minMaxAuto):
             self._minMaxAuto.setChecked(value is None)
         if value is not None:
             with blockSignals(self._maxPixValue):
                 self._maxPixValue.setText(str(value))
+        self._updatePixMinMaxVis()
 
-    def setCompressionRatios(self, c_ratios: Optional[list]):
+    def setCompressionRatios(self, c_ratios: list | None):
         if c_ratios in (None, tuple(), list()):
             c_ratios = ""
         self._cRatiosQLE.setText(str(c_ratios))
@@ -271,29 +248,41 @@ class CastVolumeWidget(qt.QWidget):
         else:
             return None
 
+    def getRescalePercentiles(self) -> tuple[int | None, int | None]:
+        if self._minMaxAuto.isChecked():
+            return self._lowPercentileQSB.value(), self._highPercentileQSB.value()
+        else:
+            return None, None
+
+    def setRescalePercentiles(self, low: int | None, high: int | None) -> tuple:
+        if low is not None:
+            with blockSignals(self._minMaxAuto):
+                self._minMaxAuto.setChecked(True)
+                self._lowPercentileQSB.setValue(low)
+        if high is not None:
+            with blockSignals(self._minMaxAuto):
+                self._minMaxAuto.setChecked(True)
+                self._highPercentileQSB.setValue(high)
+        self._updatePixMinMaxVis()
+
     def getConfiguration(self) -> dict:
         rescale_min_percentile, rescale_max_percentile = self.getRescalePercentiles()
+        if (rescale_min_percentile, rescale_max_percentile) == (None, None):
+            data_min, data_max = self.getDataMin(), self.getDataMax()
+        else:
+            data_min, data_max = None, None
         return {
             "output_data_type": self.getOutputDataType(),
-            "output_type": self.getOutputFileFormat().value,
+            "output_file_format": self.getOutputFileFormat().value,
             "output_dir": self.getOutputDir(),
             "overwrite": self.getOverwrite(),
             "rescale_min_percentile": rescale_min_percentile,
             "rescale_max_percentile": rescale_max_percentile,
-            "data_min": self.getDataMin(),
-            "data_max": self.getDataMax(),
+            "data_min": data_min,
+            "data_max": data_max,
             "compression_ratios": self.getCompressionRatios(),
         }
 
-    def getRescalePercentiles(self) -> tuple:
-        return self._lowPercentileQSB.value(), self._highPercentileQSB.value()
-
-    def setRescalePercentiles(self, low, high) -> tuple:
-        if low is not None:
-            self._lowPercentileQSB.setValue(low)
-        if high is not None:
-            self._highPercentileQSB.setValue(high)
-
     def setConfiguration(self, config: dict) -> None:
         output_data_type = config.get("output_data_type", None)
         if output_data_type is not None:
@@ -307,16 +296,8 @@ class CastVolumeWidget(qt.QWidget):
         overwrite = config.get("overwrite", None)
         if overwrite is not None:
             self.setOverwrite(overwrite)
-        if "rescale_percentiles" in config:
-            rescale_min_percentile, rescale_max_percentile = config[
-                "rescale_percentiles"
-            ]
-            _logger.warning(
-                "'rescale_percentiles' is deprecated. Please use 'rescale_min_percentile' and 'rescale_max_percentile' instead"
-            )
-        else:
-            rescale_min_percentile = config.get("rescale_min_percentile", None)
-            rescale_max_percentile = config.get("rescale_max_percentile", None)
+        rescale_min_percentile = config.get("rescale_min_percentile", None)
+        rescale_max_percentile = config.get("rescale_max_percentile", None)
 
         self.setRescalePercentiles(rescale_min_percentile, rescale_max_percentile)
         if "data_min" in config:

tomwer/gui/reconstruction/nabu/check.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "02/12/2021"
+from __future__ import annotations
 
 
 from silx.gui import qt
@@ -39,12 +13,12 @@ def check_dark_series(scan: NXtomoScan, logger=None, user_input: bool = True) ->
     """
     check:
         - if scan has computed_dark attached. If there is more than one then ask confirmation to the user to process the dataset
-        - else if the NXTomo has more than one serie of dark. Otherwise ask confirmation to the user to process the dataset
+        - else if the NXTomo has more than one series of dark. Otherwise ask confirmation to the user to process the dataset
 
     ask confirmation for processing is done by a pop up dialog.
 
-    :param NXtomoScan scan: scan to check
-    :param bool user_input: if True and if n series of flat is invalid then ask the user to confirm the processing. Else print a warning and refuse processing
+    :param scan: scan to check
+    :param user_input: if True and if n series of flat is invalid then ask the user to confirm the processing. Else print a warning and refuse processing
 
     :return: True if processing can be done else False
     :note: user can 'force' the processing to be done
@@ -62,9 +36,9 @@ def check_dark_series(scan: NXtomoScan, logger=None, user_input: bool = True) ->
         image_key_values=image_keys, image_key_type=ImageKey.DARK_FIELD
     )
     if n_series != 1:
-        text = f"{n_series} serie(s) of dark found when one expected. Nabu won't be able to run reconstruction (flat field will fail)."
+        text = f"{n_series} series of dark found when one expected. Nabu won't be able to run reconstruction (flat field will fail)."
         if n_series > 1:
-            text += "\nYou can edit image_keys from the `image-key-editor` to ignore a serie (invalid all keys of series you want to ignore)."
+            text += "\nYou can edit image_keys from the `image-key-editor` to ignore a series (invalid all keys of series you want to ignore)."
         if user_input is False:
             text += "\n skip processing"
             if logger is not None:
@@ -84,7 +58,7 @@ def check_dark_series(scan: NXtomoScan, logger=None, user_input: bool = True) ->
 
 def check_flat_series(scan: NXtomoScan, logger, user_input: bool = True) -> bool:
     """
-    Insure the scan contains at least one serie of flat. Otherwise warn the user nabu will not be able to process
+    Insure the scan contains at least one series of flat. Otherwise warn the user nabu will not be able to process
     """
     if not isinstance(scan, NXtomoScan):
         raise TypeError(

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

@@ -1,34 +1,4 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "11/02/2020"
-
-
-from typing import Union
+from __future__ import annotations
 
 from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 from tomwer.gui.configuration.level import ConfigurationLevel
@@ -64,8 +34,11 @@ class _NabuStageConfigBase:
     (or a part of the stage configuration)
     """
 
-    def __init__(self, stage: Union[_NabuStages, str]):
-        self.__stage = _NabuStages.from_value(stage)
+    def __init__(self, stage: _NabuStages | str | None):
+        if stage is None:
+            self.__stage = None
+        else:
+            self.__stage = _NabuStages.from_value(stage)
         self._registeredWidgets = {}
         # list required widgets. Key is widget, value is the configuration
         # level
@@ -87,7 +60,7 @@ class _NabuStageConfigBase:
     def setConfiguration(self, config) -> None:
         raise NotImplementedError("Base class")
 
-    def getStage(self) -> _NabuStages:
+    def getStage(self) -> _NabuStages | None:
         return self.__stage
 
     def setConfigurationLevel(self, level):

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

@@ -1,4 +1,4 @@
-from typing import Optional, Union
+from __future__ import annotations
 
 from silx.gui import qt
 from silx.gui.utils import blockSignals
@@ -7,6 +7,7 @@ from silx.utils.enum import Enum as _Enum
 from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 from tomwer.gui.reconstruction.nabu.nabuconfig import base
 from tomwer.gui.utils.illustrations import _IllustrationWidget
+from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel
 
 from .reconstruction import AnglesFileWidget as Filewidget
 
@@ -69,13 +70,13 @@ class OptionalDouble(qt.QWidget):
     def _changed(self, *args, **kwargs):
         self.sigChanged.emit()
 
-    def value(self) -> Optional[float]:
+    def value(self) -> float | None:
         if self._cb.isChecked():
             return self._dsb.value()
         else:
             return None
 
-    def setValue(self, value: Optional[float]):
+    def setValue(self, value: float | None):
         if value in (None, "None"):
             self._cb.setChecked(False)
         else:
@@ -157,7 +158,7 @@ class CTFGeometry(qt.QGroupBox):
     def __init__(self, parent=None, title="ctf-geometry") -> None:
         super().__init__(parent, title=title)
         self.setLayout(qt.QFormLayout())
-        self._beamShapeCB = qt.QComboBox(self)
+        self._beamShapeCB = QComboBoxIgnoreWheel(self)
         for shape in _BeamShape.values():
             self._beamShapeCB.addItem(shape)
         self.layout().addRow("shape", self._beamShapeCB)
@@ -189,7 +190,7 @@ class CTFGeometry(qt.QGroupBox):
     def getBeamShape(self):
         return _BeamShape.from_value(self._beamShapeCB.currentText())
 
-    def setBeamShape(self, shape: Union[str, _BeamShape]):
+    def setBeamShape(self, shape: str | _BeamShape):
         shape = _BeamShape.from_value(shape)
         self._beamShapeCB.setCurrentText(shape.value)
 

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

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "11/02/2020"
+from __future__ import annotations
 
 
 from silx.gui import qt
@@ -51,7 +25,7 @@ class NabuConfiguration(qt.QWidget):
     (stage, index option modified)
     """
 
-    def __init__(self, parent, scrollArea):
+    def __init__(self, parent):
         qt.QWidget.__init__(self, parent=parent)
         self._stageHided = []
         # list of hided stage. Not taking into account the filter
@@ -62,9 +36,7 @@ class NabuConfiguration(qt.QWidget):
         self._preProcessingGB = qt.QGroupBox("pre processing", self)
         self._preProcessingGB.setLayout(qt.QVBoxLayout())
 
-        self._preProcessingWidget = _NabuPreProcessingConfig(
-            parent=self, scrollArea=scrollArea
-        )
+        self._preProcessingWidget = _NabuPreProcessingConfig(parent=self)
         self._preProcessingGB.layout().addWidget(self._preProcessingWidget)
         self.layout().addWidget(self._preProcessingGB)
 
@@ -72,18 +44,15 @@ class NabuConfiguration(qt.QWidget):
         self._phaseGB = qt.QGroupBox("phase", self)
         self._phaseGB.setLayout(qt.QVBoxLayout())
 
-        self._phaseWidget = _NabuPhaseConfig(parent=self, scrollArea=scrollArea)
+        self._phaseWidget = _NabuPhaseConfig(parent=self)
         self._phaseGB.layout().addWidget(self._phaseWidget)
-        self._phaseGB.setCheckable(True)
         self.layout().addWidget(self._phaseGB)
 
         # reconstruction opts
         self._reconstructionGB = qt.QGroupBox("reconstruction", self)
         self._reconstructionGB.setLayout(qt.QVBoxLayout())
 
-        self._reconstructionWidget = _NabuReconstructionConfig(
-            parent=self, scrollArea=scrollArea
-        )
+        self._reconstructionWidget = _NabuReconstructionConfig(parent=self)
         self._reconstructionGB.layout().addWidget(self._reconstructionWidget)
         self.layout().addWidget(self._reconstructionGB)
 
@@ -95,14 +64,10 @@ class NabuConfiguration(qt.QWidget):
         self._outputGB.layout().addWidget(self._outputWidget)
         self.layout().addWidget(self._outputGB)
 
-        # set up
-        self._phaseGB.setChecked(True)
-
         # connect signal / slot
         self._preProcessingWidget.sigConfChanged.connect(
             self._signalConfChangedPreProcessing
         )
-        self._phaseGB.toggled.connect(self._signalPhaseActivationChanged)
         self._phaseWidget.sigConfChanged.connect(self._signalConfChangedPhase)
         self._reconstructionWidget.sigConfChanged.connect(
             self._signalConfChangedReconstruction
@@ -123,9 +88,6 @@ class NabuConfiguration(qt.QWidget):
         self._stageHided.append(self._phaseGB)
         self._phaseGB.hide()
 
-    def _signalPhaseActivationChanged(self, *args, **kwargs):
-        self.sigConfChanged.emit(self._phaseWidget.getStage().value, "method")
-
     def _signalConfChangedPhase(self, param):
         self.sigConfChanged.emit(self._phaseWidget.getStage().value, param)
 
@@ -147,8 +109,6 @@ class NabuConfiguration(qt.QWidget):
             "output": self._outputWidget.getConfiguration(),
             "phase": self._phaseWidget.getConfiguration(),
         }
-        if not self._phaseGB.isChecked():
-            config["phase"]["method"] = ""
         return config
 
     def setConfiguration(self, config):
@@ -156,13 +116,6 @@ class NabuConfiguration(qt.QWidget):
             self._preProcessingWidget.setConfiguration(config["preproc"])
         if "phase" in config:
             self._phaseWidget.setConfiguration(config["phase"])
-            paganin = config["phase"].get("method", "")
-            if paganin == "":
-                self._phaseGB.setChecked(False)
-            else:
-                self._phaseGB.setChecked(True)
-        else:
-            self._phaseGB.setChecked(False)
         if "reconstruction" in config:
             self._reconstructionWidget.setConfiguration(config["reconstruction"])
         if "tomwer_slices" in config:
@@ -219,37 +172,29 @@ class NabuConfigurationTab(qt.QTabWidget):
     (stage, index option modified)
     """
 
-    def __init__(self, parent, scrollArea):
+    def __init__(self, parent):
         qt.QTabWidget.__init__(self, parent=parent)
 
         # pre processing options
-        self._preProcessingWidget = _NabuPreProcessingConfig(
-            parent=self, scrollArea=scrollArea
-        )
+        self._preProcessingWidget = _NabuPreProcessingConfig(parent=self)
         self.addTab(self._preProcessingWidget, "pre processing")
 
         # phase options
         self._phaseGB = qt.QGroupBox("apply phase", self)
         self._phaseGB.setLayout(qt.QVBoxLayout())
 
-        self._phaseWidget = _NabuPhaseConfig(parent=self, scrollArea=scrollArea)
+        self._phaseWidget = _NabuPhaseConfig(parent=self)
         self._phaseGB.layout().addWidget(self._phaseWidget)
-        self._phaseGB.setCheckable(True)
         self.addTab(self._phaseGB, "phase")
 
         # reconstruction opts
-        self._reconstructionWidget = _NabuReconstructionConfig(
-            parent=self, scrollArea=scrollArea
-        )
+        self._reconstructionWidget = _NabuReconstructionConfig(parent=self)
         self.addTab(self._reconstructionWidget, "reconstruction")
 
         # output information
         self._outputWidget = _NabuOutputConfig(parent=self)
         self.addTab(self._outputWidget, "output")
 
-        # set up
-        self._phaseGB.setChecked(True)
-
         # connect signal / slot
         self._preProcessingWidget.sigConfChanged.connect(
             self._signalConfChangedPreProcessing
@@ -279,8 +224,7 @@ class NabuConfigurationTab(qt.QTabWidget):
             "tomwer_slices": self.getSlices(),
             "output": self._outputWidget.getConfiguration(),
         }
-        if self._phaseGB.isChecked():
-            config["phase"] = self._phaseWidget.getConfiguration()
+        config["phase"] = self._phaseWidget.getConfiguration()
         return config
 
     def setConfiguration(self, config):
@@ -288,9 +232,6 @@ class NabuConfigurationTab(qt.QTabWidget):
             self._preProcessingWidget.setConfiguration(config["preproc"])
         if "phase" in config:
             self._phaseWidget.setConfiguration(config["phase"])
-            self._phaseGB.setChecked(True)
-        else:
-            self._phaseGB.setChecked(False)
         if "reconstruction" in config:
             self._reconstructionWidget.setConfiguration(config["reconstruction"])
         if "tomwer_slices" in config: