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

orangecontrib/tomwer/tutorials/test_cor.ows

@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='utf-8'?>
 <scheme version="2.0" title="" description="">
 	<nodes>
-		<node id="0" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="center of rotation finder" position="(375.0, 146.0)" />
+		<node id="0" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="center of rotation finder" position="(395.0, 173.0)" />
 		<node id="1" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(150.0, 115.0)" />
 	</nodes>
 	<links>
@@ -10,8 +10,8 @@
 	<annotations />
 	<thumbnail />
 	<node_properties>
-		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'sino-coarse-to-fine', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'SINOGRAM_LINE': 'middle', 'SINOGRAM_SUBSAMPLING': 10, 'AXIS_URL_1': '', 'AXIS_URL_2': '', 'LOOK_AT_STDMAX': False, 'NEAR_WX': 5, 'FINE_STEP_X': 0.1, 'SCALE_IMG2_TO_IMG1': False, 'NEAR_POSITION': 'right', 'PADDING_MODE': 'edge', 'FLIP_LR': True, 'COMPOSITE_OPTS': {'theta': 5, 'oversampling': 4, 'n_subsampling_y': 40, 'take_log': True, 'near_width': 40}, 'COR_OPTIONS': '', 'MOTOR_OFFSET': 0.0, 'X_ROTATION_AXIS_PIXEL_POSITION': 0.0}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True, 'y_axis_inverted': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x017\x00\x00\x00\xe5\x00\x00\x06H\x00\x00\x03\xa6\x00\x00\x017\x00\x00\x01\n\x00\x00\x06H\x00\x00\x03\xa6\x00\x00\x00\x00\x00\x00\x00\x00\x07\x80\x00\x00\x017\x00\x00\x01\n\x00\x00\x06H\x00\x00\x03\xa6', '__version__': 1}</properties>
-		<properties node_id="1" format="literal">{'_scanIDs': ['hdf5:scan:/home/payno/Datasets/tomography/bamboo_hercules/bambou_hercules_0001/bambou_hercules_0001_0000.nx?path=/entry0000'], 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06', '__version__': 1}</properties>
+		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'sino-coarse-to-fine', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'SINOGRAM_LINE': 'middle', 'SINOGRAM_SUBSAMPLING': 10, 'AXIS_URL_1': '', 'AXIS_URL_2': '', 'LOOK_AT_STDMAX': False, 'NEAR_WX': 5, 'FINE_STEP_X': 0.1, 'SCALE_IMG2_TO_IMG1': False, 'NEAR_POSITION': 0.0, 'PADDING_MODE': 'edge', 'FLIP_LR': True, 'COMPOSITE_OPTS': {'theta': 5, 'oversampling': 4, 'n_subsampling_y': 40, 'take_log': True, 'near_width': 40}, 'COR_OPTIONS': '', 'MOTOR_OFFSET': 9230.77, 'X_ROTATION_AXIS_PIXEL_POSITION': None}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x01s\x00\x00\x00\xe0\x00\x00\x06\x84\x00\x00\x03\xa1\x00\x00\x01s\x00\x00\x01\x05\x00\x00\x06\x84\x00\x00\x03\xa1\x00\x00\x00\x00\x00\x00\x00\x00\x07\x80\x00\x00\x01s\x00\x00\x01\x05\x00\x00\x06\x84\x00\x00\x03\xa1', '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_scanIDs': ['hdf5:scan:/home/payno/Datasets/tomography/z_series/STYLO/PROCESSED_DATA/SYS01S101_SYS01S101_3scans_0000.nx?path=/entry0000', 'hdf5:scan:/home/payno/Datasets/tomography/z_series/STYLO/PROCESSED_DATA/SYS01S101_SYS01S101_3scans_0001.nx?path=/entry0001'], 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\n\xa0\x00\x00\x01Z\x00\x00\x0b\xcb\x00\x00\x03\x06', '__version__': 1}</properties>
 	</node_properties>
 	<session_state>
 		<window_groups />

orangecontrib/tomwer/widgets/reconstruction/AxisOW.py

@@ -141,6 +141,16 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
 
         self._layout.addWidget(self._widget)
 
+        # expose API
+        self.setMode = self._widget.setMode
+        self.getMode = self._widget.getMode
+        self.getEstimatedCor = self._widget.getEstimatedCor
+        self.setEstimatedCor = self._widget.setEstimatedCor
+        self.getAxisParams = self._widget.getAxisParams
+        self.setValueLock = self._widget.setValueLock
+        self._setModeLockFrmSettings = self._widget._setModeLockFrmSettings
+        self._setValueLockFrmSettings = self._widget._setValueLockFrmSettings
+
         # load settings
         try:
             if "mode_is_lock" in gui_settings:
@@ -160,7 +170,6 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                 "auto_update_estimated_cor", True
             )
             self._widget.setAutoUpdateEstimatedCor(auto_update_estimated_cor)
-            self._widget.setYAxisInverted(gui_settings.get("y_axis_inverted", False))
 
         except Exception as e:
             logger.warning(f"Fail to load settings. Error is {str(e)}")
@@ -175,14 +184,11 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
         self._processingStack.sigComputationEnded.connect(self._scanProcessed)
 
         self._axis_params.sigChanged.connect(self._updateSettingsVals)
-        self._widget._axisWidget._settingsWidget._mainWidget._calculationWidget.sigUpdateXRotAxisPixelPosOnNewScan.connect(
-            self._updateSettingsVals
-        )
         self._widget.sigAxisEditionLocked.connect(self._updateSettingsVals)
         self._widget.sigModeChanged.connect(self._updateSettingsVals)
         self._widget.sigLockModeChanged.connect(self._updateSettingsVals)
 
-        self._widget._axisWidget._settingsWidget._mainWidget._calculationWidget._estimatedCorWidget.sigValueChanged.connect(
+        self._widget._axisWidget._settingsWidget._mainWidget._calculationWidget._nearValueCB.toggled.connect(
             self._updateSettingsVals
         )
 
@@ -347,7 +353,6 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                 "mode_is_lock": self.isModeLocked(),
                 "value_is_lock": self.isValueLock(),
                 "auto_update_estimated_cor": self._widget.getAutoUpdateEstimatedCor(),
-                "y_axis_inverted": self._widget.isYAxisInverted(),
             },
         }
 
@@ -453,6 +458,9 @@ class AxisOW(SuperviseOW, WidgetLongProcessing):
                         "serialize_output_data": False,
                     }
                 )
+                for patch in self._patches:
+                    mode, function = patch
+                    processing_class._CALCULATIONS_METHODS[mode] = function
                 processing_class.run()
             self._updatePosition(scan=self.__scan)
             if self.isModeLocked() or self.isValueLock():

orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -312,10 +312,8 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
                     )
                     drac_processed_datasets.append(icatReconstructedDataset)
 
-            if len(drac_processed_datasets) > 0:
-                self.Outputs.data_portal_processed_datasets.send(
-                    drac_processed_datasets
-                )
+        if len(drac_processed_datasets) > 0:
+            self.Outputs.data_portal_processed_datasets.send(drac_processed_datasets)
 
         if future_tomo_obj is not None:
             self.Outputs.future_out.send(future_tomo_obj)

tomwer/app/axis.py

@@ -169,6 +169,9 @@ def main(argv):
         _logger.setLevel(logging.DEBUG)
 
     axis_params = QAxisRP()
+    axis_params.use_sinogram = options.use_sinogram
+    if scan.dim_2 is not None:
+        axis_params.sinogram_line = scan.dim_2 // 2
 
     window = _AxisProcessGUI(scan=scan, axis_params=axis_params)
     window.setWindowTitle("axis")

tomwer/app/multipag.py

@@ -23,10 +23,6 @@ from tomwer.core.process.reconstruction.darkref.darkrefs import (
 from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
     SADeltaBetaTask,
 )
-from tomwer.core.process.reconstruction.utils.cor import (
-    relative_pos_to_absolute,
-    absolute_pos_to_relative,
-)
 from tomwer.core.process.task import Task
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
@@ -140,17 +136,13 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
 
     def _relativeValueEdited(self):
         old = self._absoluteCORValueQLE.blockSignals(True)
-        value = relative_pos_to_absolute(
-            relative_pos=self._relativeCORValueQLE.value(), det_width=self._imageWidth
-        )
+        value = self._relativeCORValueQLE.value() + (self._imageWidth - 1) / 2.0
         self._absoluteCORValueQLE.setValue(value)
         self._absoluteCORValueQLE.blockSignals(old)
 
-    def _absoluteValueEdited(self):
+    def _absolueValueEdited(self):
         old = self._relativeCORValueQLE.blockSignals(True)
-        value = absolute_pos_to_relative(
-            absolute_pos=self._absoluteCORValueQLE.value(), det_width=self._imageWidth
-        )
+        value = self._absoluteCORValueQLE.value() - (self._imageWidth - 1) / 2.0
         self._relativeCORValueQLE.setValue(value)
         self._relativeCORValueQLE.blockSignals(old)