tomwer 1.3.10__tar.gz → 1.3.16__tar.gz

{tomwer-1.3.10/tomwer.egg-info → tomwer-1.3.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.10
+Version: 1.3.16
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -18,8 +18,8 @@ Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: setuptools
@@ -30,7 +30,7 @@ Requires-Dist: nxtomo>=1.2.3rc1
 Requires-Dist: nxtomomill>=1.0dev
 Requires-Dist: processview>=1.3
 Requires-Dist: ewoks>=0.1.1
-Requires-Dist: ewoksorange==0.6
+Requires-Dist: ewoksorange<0.7,>=0.6
 Requires-Dist: sluurp>=0.3.3
 Requires-Dist: packaging
 Requires-Dist: flufl-lock

{tomwer-1.3.10 → tomwer-1.3.16}/orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py

@@ -152,6 +152,7 @@ class DarkRefAndCopyOW(SuperviseOW, WidgetLongProcessing):
         self.widget.recons_params.sigChanged.connect(self._updateSettingsVals)
         self.widget.sigModeAutoChanged.connect(self._updateSettingsVals)
         self.widget.sigCopyActivationChanged.connect(self._updateSettingsVals)
+        self.widget.sigClearCache.connect(self._processing_stack.clear_cache)
         self._processing_stack.sigComputationStarted.connect(self._startProcessing)
         self._processing_stack.sigComputationEnded.connect(self._endProcessing)
         self._processing_stack.sigRefSetted.connect(self.widget.setRefSetBy)

{tomwer-1.3.10 → tomwer-1.3.16}/setup.cfg

@@ -5,7 +5,7 @@ author = data analysis unit
 author_email = henri.payno@esrf.fr
 description = "tomography workflow tools"
 long_description = file: README.rst
-long_description_content_type = text/markdown
+long_description_content_type = text/x-rst
 license = MIT
 url = https://gitlab.esrf.fr/tomotools/tomwer
 project_urls = 
@@ -26,7 +26,7 @@ keywords =
 
 [options]
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.8
 install_requires = 
 	numpy
 	setuptools
@@ -37,7 +37,7 @@ install_requires =
 	nxtomomill>=1.0dev
 	processview>=1.3
 	ewoks>=0.1.1
-	ewoksorange==0.6
+	ewoksorange >=0.6, <0.7
 	sluurp>=0.3.3
 	packaging
 	flufl-lock

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/control/datawatcher/edfdwprocess.py

@@ -50,15 +50,6 @@ except ImportError:
     has_rsync = True
 
 
-def get_info_val(lines, key):
-    r = range(len(lines))
-    key = key + "="
-    for i in r:
-        if key in lines[i]:
-            val = float(lines[i].split("=")[1])
-    return val
-
-
 class _DataWatcherEDFProcess(_DataWatcherProcess):
     """
     Base class for edf acquisition observation

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/darkref/darkrefscopy.py

@@ -34,6 +34,7 @@ __date__ = "17/08/2021"
 
 import logging
 import os
+import h5py
 import tempfile
 from typing import Union
 
@@ -198,10 +199,37 @@ class DarkRefsCopy(DarkRefsTask):
             update_mode="replace",
         )
 
+    def clear_cache(self):
+        """
+        remove the file used to cache the reduced darks / flats.
+        This can be used in the case it contain unrelevant data. Like frame with another shape...
+        """
+        cache_file = DarkRefsCopy.get_save_file(self._savedir)
+        if os.path.exists(cache_file):
+            os.remove(cache_file)
+
+    def _clear_cache_data_path(self, file_path: str, data_path: str):
+        if not os.path.exists(file_path):
+            return
+        with h5py.File(file_path, mode="a") as h5f:
+            if data_path in h5f:
+                del h5f[data_path]
+
     def set_darks_and_flats_from_scan(self, scan: TomwerScanBase) -> bool:
-        if scan.reduced_flats in (None, {}):
+        has_flats = scan.reduced_flats not in (None, {})
+        has_darks = scan.reduced_darks not in (None, {})
+        if has_flats and has_darks:
+            # if the scan has darks and flats remove directly the cache file
+            # else in append mode HDF5 is not removing the dataset and
+            # the cache size will continue to increase
+            self.clear_cache()
+        if not has_flats:
             logger.warning(f"No flat found for {scan}. Unable to copy them")
         else:
+            self._clear_cache_data_path(
+                file_path=self._flats_url.file_path(),
+                data_path=self._flats_url.data_path(),
+            )
             dicttoh5(
                 scan.reduced_flats,
                 h5file=self._flats_url.file_path(),
@@ -209,9 +237,13 @@ class DarkRefsCopy(DarkRefsTask):
                 mode="a",
                 update_mode="replace",
             )
-        if scan.reduced_darks in (None, {}):
+        if not has_darks:
             logger.warning(f"No dark found for {scan}. Unable to copy them")
         else:
+            self._clear_cache_data_path(
+                file_path=self._darks_url.file_path(),
+                data_path=self._darks_url.data_path(),
+            )
             dicttoh5(
                 scan.reduced_darks,
                 h5file=self._darks_url.file_path(),
@@ -247,10 +279,6 @@ class DarkRefsCopy(DarkRefsTask):
                 overwrite=True,
             )
 
-    def clean_save_files(self):
-        if os.path.exists(self._save_file):
-            os.remove(self._save_file)
-
     def run(self):
         """
         This is function triggered when a new scan / data is received.

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/nabu/nabuscores.py

@@ -211,6 +211,7 @@ def run_nabu_multicor(
         recons_urls = {}
         std_outs = []
         std_errs = []
+        future_tomo_obj = None
 
         success = result.success
         if isinstance(result, ResultsWithStd):

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/nabu/nabuslices.py

@@ -962,6 +962,8 @@ class NabuSliceMode(_Enum):
                     n_slice = scan.dim_2 or 2048
                 elif axis in (NabuPlane.YZ, NabuPlane.XZ):
                     n_slice = scan.dim_1 or 2048
+                else:
+                    raise NotImplementedError(f"unknow axis {axis}")
                 res.append(n_slice // 2)
             else:
                 raise ValueError(

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/nabu/utils.py

@@ -171,6 +171,8 @@ def get_recons_volume_identifier(
             entry = scan.entry
         elif isinstance(scan, EDFTomoScan):
             entry = "entry"
+        else:
+            raise NotImplementedError(f"unrecognized scan type ({type(scan)})")
 
         volumes = (
             HDF5Volume(

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/saaxis/saaxis.py

@@ -536,6 +536,8 @@ class SAAxisTask(
                     mess = "sa-axis computation succeeded"
             else:
                 cors_res = {}
+                state = DatasetState.FAILED
+                mess = "couldn't find 'compute_scores'"
 
         if self._cancelled:
             state = DatasetState.CANCELLED

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py

@@ -341,6 +341,8 @@ class SADeltaBetaTask(
                     mess = "sa-delta-beta computation succeeded"
             else:
                 dbs_res = {}
+                state = DatasetState.FAILED
+                mess = "couldn't find 'compute_scores'"
 
         if self._cancelled:
             state = DatasetState.CANCELLED

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/core/process/task.py

@@ -383,6 +383,7 @@ class BaseProcessInfo:
                     root = h5f[list(h5f.keys())[0]]
                 else:
                     _logger.warning("no process find")
+                    return []
             else:
                 root = h5f[entry]
 

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/control/selectorwidgetbase.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/edit/nxtomoeditor.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/edit/test/test_nx_editor.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/qfolderdialog.py

@@ -544,6 +544,10 @@ class QVolumeDialog(qt.QDialog):
                 constructor = TIFFVolume
             elif file_extension in self._JP2K_EXTENSIONS:
                 constructor = JP2KVolume
+            else:
+                raise NotImplementedError(
+                    f"unhandled file extension ({file_extension})"
+                )
             volume = constructor(
                 folder=file_path,
                 volume_basename=None if basename in ("", None) else basename,

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/reconstruction/axis/axis.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/reconstruction/axis/radioaxis.py

@@ -1647,6 +1647,9 @@ class _CalculationWidget(qt.QWidget):
     def setEstimatedCorValue(self, value):
         if value is not None:
             self._qleNearPosQLE.setText(str(value))
+            # note: keep self._axis_params up to date.
+            if self._axis_params:
+                self._axis_params.estimated_cor = value
 
     def getEstimatedCor(self):
         try:

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/reconstruction/darkref/darkrefcopywidget.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -40,6 +40,7 @@ from tomwer.core.process.reconstruction.nabu.utils import (
 from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
 from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
 from tomwer.gui.utils.scrollarea import QDoubleSpinBoxIgnoreWheel as QDoubleSpinBox
+from tomwer.gui.utils.scrollarea import QSpinBoxIgnoreWheel as QSpinBox
 from tomwer.utils import docstring
 
 _logger = logging.getLogger(__name__)
@@ -104,7 +105,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self.layout().addWidget(self._sinoRingCorrectionMthd, 2, 2, 1, 1)
         self.registerWidget(self._sinoRingCorrectionMthd, "required")
 
-        self._sinoRingsOpts = SinoRingsOptions(parent=self)
+        self._sinoRingsOpts = SinoRingsOptions(parent=self, scrollArea=scrollArea)
         self.layout().addWidget(self._sinoRingsOpts, 3, 1, 1, 3)
 
         ## ccd filter
@@ -187,13 +188,14 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
 
         # option dedicated to Helical
         ## process file
-        self._processFileQLE = qt.QLabel("file containing weights maps", self)
+        self._processFileLabel = qt.QLabel("file containing weights maps", self)
+        self.registerWidget(self._processFileLabel, "advanced")
+        self.layout().addWidget(self._processFileLabel, 20, 0, 1, 1)
+        self._processFileQLE = qt.QLineEdit("", self)
+        self.registerWidget(self._processFileQLE, "advanced")
         self._processFileQLE.setToolTip(
             "also know as 'process_file'. If you don't have this file it can be created from the 'helical-prepare-weights' widget"
         )
-        self.layout().addWidget(self._processFileQLE, 20, 0, 1, 1)
-        self._processFileQLE = qt.QLineEdit("", self)
-        self.registerWidget(self._processFileQLE, "advanced")
         self.layout().addWidget(self._processFileQLE, 20, 1, 1, 3)
 
         # style
@@ -443,7 +445,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
 class SinoRingsOptions(qt.QWidget):
     _VO_DIMS = ("horizontaly", "horizontaly and vertically")
 
-    def __init__(self, parent=None, *args, **kwargs):
+    def __init__(self, parent=None, scrollArea=None, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
         self._method = None
         self.setLayout(qt.QFormLayout())
@@ -451,12 +453,12 @@ class SinoRingsOptions(qt.QWidget):
         self.layout().setSpacing(0)
         # munch parameters
         self._sigmaMunchLabel = qt.QLabel("sigma", self)
-        self._sigmaMunch = qt.QDoubleSpinBox(self)
+        self._sigmaMunch = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._sigmaMunch.setRange(0.0, 2147483647)
         self.layout().addRow(self._sigmaMunchLabel, self._sigmaMunch)
 
         self._levelsMunchLabel = qt.QLabel("levels", self)
-        self._levelsMunch = qt.QSpinBox(self)
+        self._levelsMunch = QSpinBox(self, scrollArea=scrollArea)
         self._levelsMunch.setRange(0, 2147483647)
         self.layout().addRow(self._levelsMunchLabel, self._levelsMunch)
 
@@ -465,7 +467,7 @@ class SinoRingsOptions(qt.QWidget):
 
         # vo parameters
         self._snrVOLabel = qt.QLabel("snr", self)
-        self._snrVO = qt.QDoubleSpinBox(self)
+        self._snrVO = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._snrVO.setMinimum(0.0)
         tooltip = "Ratio used to locate large stripes. Greater is less sensitive."
         self._snrVO.setToolTip(tooltip)
@@ -473,7 +475,7 @@ class SinoRingsOptions(qt.QWidget):
         self.layout().addRow(self._snrVOLabel, self._snrVO)
 
         self._laSizeVOLabel = qt.QLabel("la_size", self)
-        self._laSizeVO = qt.QSpinBox(self)
+        self._laSizeVO = QSpinBox(self, scrollArea=scrollArea)
         self._laSizeVO.setMinimum(0)
         tooltip = "Window size of the median filter to remove large stripes."
         self._laSizeVO.setToolTip(tooltip)
@@ -481,7 +483,7 @@ class SinoRingsOptions(qt.QWidget):
         self.layout().addRow(self._laSizeVOLabel, self._laSizeVO)
 
         self._smSizeVOLabel = qt.QLabel("sm_size", self)
-        self._smSizeVO = qt.QSpinBox(self)
+        self._smSizeVO = QSpinBox(self, scrollArea=scrollArea)
         self._smSizeVO.setMinimum(0)
         tooltip = "Window size of the median filter to remove small-to-medium stripes."
         self._laSizeVO.setToolTip(tooltip)
@@ -489,18 +491,18 @@ class SinoRingsOptions(qt.QWidget):
         self.layout().addRow(self._smSizeVOLabel, self._smSizeVO)
 
         self._dimVOLabel = qt.QLabel("dimension", self)
-        self._dimVO = qt.QComboBox(self)
+        self._dimVO = QComboBox(self, scrollArea=scrollArea)
         self._dimVO.addItems(self._VO_DIMS)
         self.layout().addRow(self._dimVOLabel, self._dimVO)
 
         # sino mean deringer
         self._sigmaLowLabel = qt.QLabel("signal low", self)
-        self._sigmaLow = qt.QDoubleSpinBox(self)
+        self._sigmaLow = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._sigmaLow.setMinimum(0.0)
         self._sigmaHighLabel = qt.QLabel("signal high", self)
         self.layout().addRow(self._sigmaLowLabel, self._sigmaLow)
 
-        self._sigmaHigh = qt.QDoubleSpinBox(self)
+        self._sigmaHigh = QDoubleSpinBox(self, scrollArea=scrollArea)
         self._sigmaHigh.setMinimum(0.0)
         tooltip = (
             "sigma low and sigma high values are defining the standard deviation of "

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/gui/reconstruction/saaxis/saaxis.py

@@ -66,14 +66,14 @@ class ScorePlot(_ScorePlot, constructor=CorSelection):
 
     def _updateScores(self):
         scan = self.__scan() if self.__scan else None
+        img_width = None
         if scan is not None:
             if scan.saaxis_params:
                 scan.saaxis_params.score_method = self.getScoreMethod()
                 img_width = scan.dim_1
                 # update autofocus
                 SAAxisTask.autofocus(scan)
-        else:
-            img_width = None
+
         self.setVarScores(
             scores=self._scores,
             score_method=self.getScoreMethod(),

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/synctools/stacks/reconstruction/dkrefcopy.py

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

{tomwer-1.3.10 → tomwer-1.3.16}/tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 10
+MICRO = 16
 RELEV = "final"  # <16
 SERIAL = 0  # <16