tomwer 1.4.18__py3-none-any.whl → 1.5.0__py3-none-any.whl

tomwer/core/scan/nxtomoscan.py

@@ -178,9 +178,9 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         else:
             return os.path.exists(master_file + ".h5")
 
-    def clear_caches(self):
-        _tsNXtomoScan.clear_caches(self)
-        TomwerScanBase.clear_caches(self)
+    def clear_cache(self):
+        _tsNXtomoScan.clear_cache(self)
+        TomwerScanBase.clear_cache(self)
 
     def is_abort(self, src_pattern, dest_pattern):
         """

tomwer/core/scan/scanbase.py

@@ -10,7 +10,7 @@ from typing import Iterable
 
 import numpy
 from silx.io.url import DataUrl
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 from tomoscan.identifier import VolumeIdentifier
 from tomoscan.normalization import IntensityNormalization
@@ -92,10 +92,10 @@ class TomwerScanBase(TomwerObject):
         """
         raise NotImplementedError("Base class")
 
-    def clear_caches(self):
+    def clear_cache(self):
         self._cache_proj_urls = None
         self._notify_ffc_rsc_missing = True
-        super().clear_caches()
+        super().clear_cache()
 
     def _flat_field_correction(
         self,

tomwer/core/scan/scantype.py

@@ -1,4 +1,4 @@
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class ScanType(_Enum):

tomwer/core/settings.py

@@ -1,5 +1,5 @@
 import os
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 __LBSRAM_PATH = "/lbsram"

tomwer/core/tomwer_object.py

@@ -19,7 +19,7 @@ class TomwerObject(Dataset):
         """util function to clear some heavy object from the cache"""
         raise NotImplementedError()
 
-    def clear_caches(self):
+    def clear_cache(self):
         pass
 
     @property

tomwer/core/utils/nxtomoutils.py

@@ -11,12 +11,12 @@ def get_n_series(image_key_values: tuple | list, image_key_type: ImageKey) -> in
 
     :param image_key_values: list or tuple of image_keys to consider. Can be integers or tomoscan.esrf.scan.hdf5scan.ImageKey
     """
-    image_key_type = ImageKey.from_value(image_key_type)
+    image_key_type = ImageKey(image_key_type)
     if image_key_type is ImageKey.INVALID:
         raise ValueError(
             "we can't count Invalid image keys series because those are ignored from tomoscan"
         )
-    image_key_values = [ImageKey.from_value(img_key) for img_key in image_key_values]
+    image_key_values = [ImageKey(img_key) for img_key in image_key_values]
 
     # remove invalid frames
     image_key_values = numpy.array(

tomwer/core/utils/spec.py

@@ -3,14 +3,17 @@ from __future__ import annotations
 import fileinput
 import logging
 import os
+import pint
+
+import fabio
 
-import fabio.edfimage
 from lxml import etree
-from pyunitsystem.metricsystem import MetricSystem
 
 
 _logger = logging.getLogger(__name__)
 
+_ureg = pint.get_application_registry()
+
 
 def _getInformation(scan, refFile, information, _type, aliases=None):
     """
@@ -258,6 +261,6 @@ def getPixelSize(scan) -> float | None:
                 value = float(ddict["IMAGE_PIXEL_SIZE_1".lower()])
     # for now pixel size are stored in microns. We want to return them in meter
     if value is not None:
-        return value * MetricSystem.MICROMETER.value
+        return (value * _ureg.micrometer).to_base_units().magnitude
     else:
         return None

tomwer/gui/cluster/slurm.py

@@ -94,7 +94,7 @@ class SlurmSettingsWindow(qt.QMainWindow):
 
         self._modeCombox = qt.QComboBox(self)
         self._mainWidget.layout().addRow("configuration: ", self._modeCombox)
-        self._modeCombox.addItems(SlurmSettingsMode.values())
+        self._modeCombox.addItems([item.value for item in SlurmSettingsMode])
         self._modeCombox.setCurrentText(SlurmSettingsMode.GENERIC.value)
 
         self._settingsWidget = SlurmSettingsWidget(self, jobLimitation=None)
@@ -110,6 +110,7 @@ class SlurmSettingsWindow(qt.QMainWindow):
         # connect signal / slot
         self._modeCombox.currentIndexChanged.connect(self._reloadPredefinedSettings)
         self._settingsWidget.sigConfigChanged.connect(self._configChanged)
+        self._modeCombox.currentIndexChanged.connect(self.sigConfigChanged)
         # when the settings widget is edited them we automatically move to 'manual' settings. To notify visually the user
         self._settingsWidget.sigConfigChanged.connect(self._switchToManual)
 
@@ -154,12 +155,20 @@ class SlurmSettingsWindow(qt.QMainWindow):
         self._modeCombox.setCurrentText(SlurmSettingsMode.MANUAL.value)
 
     def getCurrentSettingsMode(self) -> SlurmSettingsMode:
-        return SlurmSettingsMode.from_value(self._modeCombox.currentText())
+        return SlurmSettingsMode(self._modeCombox.currentText())
 
     def setCurrentSettingsMode(self, mode: SlurmSettingsMode) -> SlurmSettingsMode:
-        mode = SlurmSettingsMode.from_value(mode)
+        mode = SlurmSettingsMode(mode)
         self._modeCombox.setCurrentText(mode.value)
 
+    def setMode(self, mode: SlurmSettingsMode) -> None:
+        """Alias for setCurrentSettingsMode(), used by SlurmClusterOW."""
+        self.setCurrentSettingsMode(mode)
+
+    def mode(self) -> SlurmSettingsMode:
+        """Alias for getCurrentSettingsMode(), used by SlurmClusterOW."""
+        return self.getCurrentSettingsMode()
+
     # expose API
     def getConfiguration(self) -> dict:
         return self._settingsWidget.getConfiguration()

tomwer/gui/configuration/level.py

@@ -1,4 +1,4 @@
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class ConfigurationLevel(_Enum):

tomwer/gui/control/actions.py

@@ -86,7 +86,7 @@ class TomoObjDisplayModeToolButton(qt.QToolButton):
         urlDescAction.triggered.connect(partial(self.setDisplayMode, DisplayMode.URL))
 
     def setDisplayMode(self, mode: DisplayMode):
-        mode = DisplayMode.from_value(mode)
+        mode = DisplayMode(mode)
         if mode is DisplayMode.SHORT:
             self.setIcon(self._shortDescIcon)
             self.setToolTip(self._SHORT_DESC_TOOLTIP)

tomwer/gui/control/datadiscovery.py

@@ -44,7 +44,7 @@ class ScanDiscoveryConfigWidget(qt.QGroupBox):
             raise NotImplementedError
 
     def setScanType(self, mode: ScanType):
-        mode = ScanType.from_value(mode)
+        mode = ScanType(mode)
         if mode is ScanType.SPEC:
             self._specQRB.setChecked(True)
         elif mode is ScanType.BLISS:

tomwer/gui/control/datalist.py

@@ -616,7 +616,7 @@ class _TomwerObjectList(qt.QTableWidget):
         self.setDisplayMode(DisplayMode.SHORT)
 
     def setDisplayMode(self, mode: DisplayMode) -> None:
-        self._displayMode = DisplayMode.from_value(mode)
+        self._displayMode = DisplayMode(mode)
         self._update()
 
     def n_data(self):

tomwer/gui/control/reducedarkflatselector.py

@@ -287,11 +287,11 @@ class ReduceDarkFlatSelectorTableWidget(qt.QWidget):
                 h5file=url.file_path(),
                 path=url.data_path(),
             )
-            for target in REDUCER_TARGET.values():
-                if target in reduced_info_dict:
-                    reduced_frames = reduced_info_dict[target]
+            for target in REDUCER_TARGET:
+                if target.value in reduced_info_dict:
+                    reduced_frames = reduced_info_dict[target.value]
                     reduced_frames["reduce_frames_name"] = (
-                        f"{target} from {url.data_path()}@{os.path.basename(url.file_path())}"
+                        f"{target.value} from {url.data_path()}@{os.path.basename(url.file_path())}"
                     )
                     result.append(reduced_frames)
 

tomwer/gui/control/series/seriescreator.py

@@ -6,7 +6,7 @@ from typing import Iterable
 
 from silx.gui import qt
 from silx.gui.utils import blockSignals
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 from tomoscan.series import Series
 
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -144,8 +144,8 @@ class SeriesDefinition(qt.QWidget):
         self.layout().addWidget(self._modeLabel, 0, 0, 1, 1)
 
         self._modeCB = qt.QComboBox(self)
-        for mode in _SeriesDefinitionMode.values():
-            self._modeCB.addItem(mode)
+        for mode in _SeriesDefinitionMode:
+            self._modeCB.addItem(mode.value)
         self.layout().addWidget(self._modeCB, 0, 1, 1, 1)
 
         self._manualDefWidget = SeriesManualFromTomoObj(parent=self)
@@ -169,10 +169,10 @@ class SeriesDefinition(qt.QWidget):
             raise ValueError(f"mode {self.getMode()} is not handled yet")
 
     def getMode(self) -> str:
-        return _SeriesDefinitionMode.from_value(self._modeCB.currentText())
+        return _SeriesDefinitionMode(self._modeCB.currentText())
 
     def setMode(self, mode: str):
-        mode = _SeriesDefinitionMode.from_value(mode)
+        mode = _SeriesDefinitionMode(mode)
         idx = self._modeCB.findText(mode.value)
         self._modeCB.setCurrentIndex(idx)
 

tomwer/gui/control/tomoobjdisplaymode.py

@@ -1,4 +1,4 @@
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class DisplayMode(_Enum):

tomwer/gui/dataportal/gallery.py

@@ -29,7 +29,7 @@ class GalleryWidget(qt.QWidget):
         self.layout().addRow("precision", self._precisionQCB)
         # binning
         self._binningQCB = qt.QComboBox(self)
-        self._binningQCB.addItems(Binning.values())
+        self._binningQCB.addItems([item.value for item in Binning])
         self.layout().addRow("binning", self._binningQCB)
         self._binningQCB.setCurrentText(Binning.SIXTEEN_BY_SIXTEEN.value)
         self._binningQCB.setToolTip(
@@ -37,7 +37,7 @@ class GalleryWidget(qt.QWidget):
         )  # recommended size: 5ko for the entire gallery
         # output format
         self._outputFormat = qt.QComboBox(self)
-        self._outputFormat.addItems(OutputFormat.values())
+        self._outputFormat.addItems([item.value for item in OutputFormat])
         self.layout().addRow("output format", self._outputFormat)
         # overwrite
         self._overwriteCB = qt.QCheckBox("overwrite", self)
@@ -49,17 +49,17 @@ class GalleryWidget(qt.QWidget):
         self._binningQCB.currentIndexChanged.connect(self._configChanged)
 
     def getOutputFormat(self) -> OutputFormat:
-        return OutputFormat.from_value(self._outputFormat.currentText())
+        return OutputFormat(self._outputFormat.currentText())
 
     def setOutputFormat(self, format: OutputFormat):
-        format = OutputFormat.from_value(format)
+        format = OutputFormat(format)
         self._outputFormat.setCurrentText(format.value)
 
     def getBinning(self) -> Binning:
-        return Binning.from_value(self._binningQCB.currentText())
+        return Binning(self._binningQCB.currentText())
 
     def setBinning(self, binning: Binning):
-        binning = Binning.from_value(binning)
+        binning = Binning(binning)
         self._binningQCB.setCurrentText(binning.value)
 
     def overwrite(self) -> bool:

tomwer/gui/edit/imagekeyeditor.py

@@ -112,9 +112,7 @@ class ImageKeyWindow(qt.QMainWindow):
     def setModifications(self, modifications):
         self._mainWindow.clearModifcations()
         image_keys_set = set(modifications.values())
-        image_keys_set = set(
-            [_ImageKey.from_value(image_key) for image_key in image_keys_set]
-        )
+        image_keys_set = set([_ImageKey(image_key) for image_key in image_keys_set])
         for image_key_type in image_keys_set:
             self._mainWindow.applyModifications(
                 modifications=modifications, new_image_key=image_key_type
@@ -432,7 +430,7 @@ class _ImageKeyList(qt.QTableWidget):
             self.setItem(i_frame, 0, _item)
 
             # current image key
-            current_image_key = _ImageKey.from_value(frame.image_key)
+            current_image_key = _ImageKey(frame.image_key)
             current_image_key = self._IMAGE_KEYS_INV[current_image_key]
             currentImgKeyItem = qt.QLabel(current_image_key, self)
             self.setCellWidget(i_frame, 1, currentImgKeyItem)
@@ -442,7 +440,7 @@ class _ImageKeyList(qt.QTableWidget):
                 new_image_key = frames_new_keys[frame.index]
             else:
                 new_image_key = frame.image_key
-            new_image_key = _ImageKey.from_value(new_image_key)
+            new_image_key = _ImageKey(new_image_key)
             new_image_key = self._IMAGE_KEYS_INV[new_image_key]
             newImgKeyItem = _ImageKeyComboBox(parent=self, image_key=new_image_key)
             self._imageKeyComboboxes[index] = newImgKeyItem
@@ -694,16 +692,16 @@ class ImageKeyUpgraderList(qt.QTableWidget):
             self.setCellWidget(i_operation, 1, remove_button)
 
     def addOperation(self, from_image_key: _ImageKey, to_image_key: _ImageKey):
-        from_image_key = _ImageKey.from_value(from_image_key)
-        to_image_key = _ImageKey.from_value(to_image_key)
+        from_image_key = _ImageKey(from_image_key)
+        to_image_key = _ImageKey(to_image_key)
 
         self._operations[from_image_key] = to_image_key
         self._update()
         self.sigOperationsChanged.emit()
 
     def removeOperation(self, from_image_key: _ImageKey, to_image_key: _ImageKey):
-        from_image_key = _ImageKey.from_value(from_image_key)
-        to_image_key = _ImageKey.from_value(to_image_key)
+        from_image_key = _ImageKey(from_image_key)
+        to_image_key = _ImageKey(to_image_key)
         if (
             from_image_key not in self._operations
             or self._operations[from_image_key] != to_image_key