tomwer 1.4.19__py3-none-any.whl → 1.5.2rc0__py3-none-any.whl

orangecontrib/tomwer/tutorials/simple_volume_local_reconstruction.ows

@@ -3,19 +3,21 @@
 	<nodes>
 		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(150, 150)" />
 		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(324.0, 183.0)" />
-		<node id="2" name="default center of rotation" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="default center of rotation" position="(490.0, 218.0)" />
+		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="default center of rotation" position="(490.0, 218.0)" />
 		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(649.0, 261.0)" />
 		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(818.0, 248.0)" />
 		<node id="5" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(812.0, 391.0)" />
 		<node id="6" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(978.0, 424.0)" />
+		<node id="7" name="Data Portal Publishing" qualified_name="orangecontrib.tomwer.widgets.dataportal.PublishProcessedDataOW.PublishProcessedDataOW" project_name="tomwer" version="" title="Data Portal Publishing" position="(980.0, 580.0)" />
 	</nodes>
 	<links>
-		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" />
-		<link id="1" source_node_id="1" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" />
-		<link id="2" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" />
-		<link id="3" source_node_id="3" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" />
-		<link id="4" source_node_id="3" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" />
-		<link id="5" source_node_id="5" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" />
+		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="1" source_node_id="1" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="2" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="3" source_node_id="3" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="4" source_node_id="3" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="5" source_node_id="5" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="6" source_node_id="5" sink_node_id="7" source_channel="data_portal_processed_datasets" sink_channel="data_portal_processed_datasets" enabled="true" source_channel_id="data_portal_processed_datasets" sink_channel_id="data_portal_processed_datasets" />
 	</links>
 	<annotations>
 		<arrow id="0" start="(267.0, 56.0)" end="(194.0, 105.0)" fill="#C1272D" />
@@ -37,11 +39,12 @@
 	<node_properties>
 		<properties node_id="0" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'USE_SINOGRAM': False, 'SINOGRAM_LINE': '', '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': 10, 'n_subsampling_y': 10, 'oversampling': 4, 'take_log': True, 'near_pos': 0, 'near_width': 20}, 'SIDE': 'all', 'COR_OPTIONS': ''}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'SINOGRAM_LINE': '', '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': 10, 'oversampling': 4, 'n_subsampling_y': 10, 'take_log': True, 'near_width': 20}, 'COR_OPTIONS': '', 'MOTOR_OFFSET': 0.0, 'X_ROTATION_AXIS_PIXEL_POSITION': None}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True, 'y_axis_inverted': False}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="3" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="4" format="literal">{'_viewer_config': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="5" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_volume_params': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="6" format="literal">{'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 	</node_properties>
 	<session_state>
 		<window_groups />

orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows

@@ -7,22 +7,24 @@
 		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(649.0, 261.0)" />
 		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(930.222222222222, 248.00000000000003)" />
 		<node id="5" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(926.4444444444445, 404.3333333333334)" />
-		<node id="6" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(1186.7500000000002, 547.4722222222222)" />
+		<node id="6" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(1199.75, 482.4722222222222)" />
 		<node id="7" name="slurm cluster" qualified_name="orangecontrib.tomwer.widgets.cluster.SlurmClusterOW.SlurmClusterOW" project_name="tomwer" version="" title="slurm cluster" position="(475.0, 502.5)" />
 		<node id="8" name="future supervisor" qualified_name="orangecontrib.tomwer.widgets.cluster.FutureSupervisorOW.FutureSupervisorOW" project_name="tomwer" version="" title="future supervisor" position="(1060.2222222222224, 489.9722222222221)" />
 		<node id="9" name="future supervisor" qualified_name="orangecontrib.tomwer.widgets.cluster.FutureSupervisorOW.FutureSupervisorOW" project_name="tomwer" version="" title="future supervisor (1)" position="(800.4999999999997, 329.3333333333333)" />
+		<node id="10" name="Data Portal Publishing" qualified_name="orangecontrib.tomwer.widgets.dataportal.PublishProcessedDataOW.PublishProcessedDataOW" project_name="tomwer" version="" title="Data Portal Publishing" position="(1203.0, 707.0)" />
 	</nodes>
 	<links>
 		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="1" source_node_id="1" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="2" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="3" source_node_id="7" sink_node_id="5" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="config_out" sink_channel_id="cluster_in" />
-		<link id="4" source_node_id="5" sink_node_id="8" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_tomo_obj" />
+		<link id="4" source_node_id="5" sink_node_id="8" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_in" />
 		<link id="5" source_node_id="8" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="6" source_node_id="7" sink_node_id="3" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="config_out" sink_channel_id="cluster_in" />
-		<link id="7" source_node_id="3" sink_node_id="9" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_tomo_obj" />
+		<link id="7" source_node_id="3" sink_node_id="9" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_in" />
 		<link id="8" source_node_id="9" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
 		<link id="9" source_node_id="9" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="10" source_node_id="8" sink_node_id="10" source_channel="data_portal_processed_datasets" sink_channel="data_portal_processed_datasets" enabled="true" source_channel_id="data_portal_processed_datasets" sink_channel_id="data_portal_processed_datasets" />
 	</links>
 	<annotations>
 		<arrow id="0" start="(267.0, 56.0)" end="(194.0, 105.0)" fill="#C1272D" />
@@ -36,8 +38,8 @@
 		<text id="8" type="text/plain" rect="(648.75, 45.75, 150.0, 69.0)" font-family="Ubuntu" font-size="16">define one or several slice to be reconstructed</text>
 		<text id="9" type="text/plain" rect="(1022.3333333333333, 124.33333333333331, 150.0, 88.0)" font-family="Ubuntu" font-size="16">display reconstructed slices and browse dataset</text>
 		<arrow id="10" start="(782.5555555555552, 528.5277777777778)" end="(858.8333333333331, 466.111111111111)" fill="#C1272D" />
-		<arrow id="11" start="(1220.75, 472.0)" end="(1183.75, 510.0)" fill="#C1272D" />
-		<text id="12" type="text/plain" rect="(1244.75, 439.0, 150.0, 67.0)" font-family="Ubuntu" font-size="16">browse reconstructed volume</text>
+		<arrow id="11" start="(1253.75, 396.0)" end="(1216.75, 434.0)" fill="#C1272D" />
+		<text id="12" type="text/plain" rect="(1263.75, 361.0, 150.0, 69.0)" font-family="Ubuntu" font-size="16">browse reconstructed volume</text>
 		<text id="13" type="text/plain" rect="(680.4166666666672, 542.5833333333333, 150.0, 50.0)" font-family="Ubuntu" font-size="16">reconstruct volume</text>
 		<arrow id="14" start="(394.75, 594.75)" end="(438.5, 529.75)" fill="#C1272D" />
 		<arrow id="15" start="(987.5000000000002, 316.9444444444446)" end="(888.7500000000002, 332.63888888888914)" fill="#C1272D" />
@@ -49,14 +51,15 @@
 	<node_properties>
 		<properties node_id="0" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'USE_SINOGRAM': False, 'SINOGRAM_LINE': '', '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': 10, 'n_subsampling_y': 10, 'oversampling': 4, 'take_log': True, 'near_pos': 0, 'near_width': 20}, 'SIDE': 'all', 'COR_OPTIONS': ''}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'SINOGRAM_LINE': '', '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': 10, 'oversampling': 4, 'n_subsampling_y': 10, 'take_log': True, 'near_width': 20}, 'COR_OPTIONS': '', 'MOTOR_OFFSET': 0.0, 'X_ROTATION_AXIS_PIXEL_POSITION': None}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True, 'y_axis_inverted': False}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="3" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="4" format="literal">{'_viewer_config': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="5" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_volume_params': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 		<properties node_id="6" format="literal">{'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="8" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="9" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, 'slurm_mode_name': 'GENERIC', '__version__': 1}</properties>
+		<properties node_id="8" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="9" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="10" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
 	</node_properties>
 	<session_state>
 		<window_groups />

orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py

@@ -165,7 +165,7 @@ class _DiscoverThread(qt.QThread):
 
     def setConfiguration(self, config: dict):
         self._root_dir = config.get("start_folder", None)
-        self._research_type = ScanType.from_value(config["scan_type_searched"])
+        self._research_type = ScanType(config["scan_type_searched"])
         self._file_filter = config.get("file_filter", None)
         self._look_for_hdf5 = self._research_type in (
             ScanType.BLISS,

orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py

@@ -58,18 +58,29 @@ class NXTomomillMixIn:
                 keyword: self.CONFIG_CLS().to_dict(),  # pylint: disable=E1102
             }
 
-        # hack: try to upgrade x_pixel_keys and y_pixels keys to list.
+        # hack: try to upgrade sample|detector_x|y_pixel_keys
         # otherwise has they have the same values and are tuples they have the same id and orange raises an
         # dump_literals raise a ValueError - check_relaxed - is a recursive structure
-        try:
-            default_inputs[keyword]["KEYS_SECTION"]["x_pixel_keys"] = list(
-                default_inputs[keyword]["KEYS_SECTION"]["x_pixel_keys"]
-            )
-            default_inputs[keyword]["KEYS_SECTION"]["y_pixel_keys"] = list(
-                default_inputs[keyword]["KEYS_SECTION"]["y_pixel_keys"]
-            )
-        except KeyError:
-            pass
+        default_inputs_keys_section = default_inputs.get(keyword, {}).get(
+            "KEYS_SECTION", {}
+        )
+        for key in (
+            "sample_x_detector_keys",
+            "sample_y_detector_keys",
+            "detector_x_detector_keys",
+            "detector_y_detector_keys",
+            "sample_detector_distance",
+            "detector_x_pixel_size_keys",
+            "detector_y_pixel_size_keys",
+            "sample_x_pixel_size_keys",
+            "sample_y_pixel_size_keys",
+        ):
+            try:
+                default_inputs_keys_section[key] = list(
+                    default_inputs_keys_section[key]
+                )
+            except KeyError:
+                pass
 
         self.update_default_inputs(
             **default_inputs,

tomwer/app/axis.py

@@ -104,7 +104,7 @@ def main(argv):
     parser.add_argument(
         "--mode",
         default=None,
-        help=f"Use a specific mode. Available modes are {AxisMode.values()}",
+        help=f"Use a specific mode. Available modes are {[item.value for item in AxisMode]}",
     )
     parser.add_argument(
         "--full-image",

tomwer/app/reducedarkflat.py

@@ -179,8 +179,8 @@ def main(argv):
 
     scan = ScanFactory.create_scan_object(options.scan_path, entry=options.entry)
 
-    dark_method = ReduceMethod.from_value(options.dark_method)
-    flat_method = ReduceMethod.from_value(options.flat_method)
+    dark_method = ReduceMethod(options.dark_method)
+    flat_method = ReduceMethod(options.flat_method)
 
     if options.run:
         exit(

tomwer/core/process/control/datalistener/rpcserver.py

@@ -1,6 +1,7 @@
 # coding: utf-8
 from __future__ import annotations
 
+from enum import Enum as _Enum
 import getpass
 import logging
 import socket
@@ -10,7 +11,6 @@ from multiprocessing import Process
 
 from jsonrpc import JSONRPCResponseManager, dispatcher
 from psutil import process_iter
-from silx.utils.enum import Enum as _Enum
 from werkzeug.serving import run_simple
 from werkzeug.wrappers import Request, Response
 
@@ -26,12 +26,6 @@ class TangoAcquisitionStatus(_Enum):
     ENDED = "ended"
 
 
-class _TangoState:
-    MOVING = "moving"
-    ON = "on"
-    FAULT = "fault"
-
-
 class BlissAcquisition:
     """Define an acquisition made with bliss / tango"""
 
@@ -59,7 +53,7 @@ class BlissAcquisition:
         self.scan_numbers.append(scan_number)
 
     def set_status(self, status):
-        self.status = TangoAcquisitionStatus.from_value(status)
+        self.status = TangoAcquisitionStatus(status)
 
     def end(self, end_time, succeed: bool, error: str | None):
         if succeed is True:

tomwer/core/process/drac/binning.py

@@ -1,5 +1,5 @@
 import numpy
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class Binning(_Enum):
@@ -18,7 +18,7 @@ class Binning(_Enum):
             raise TypeError("data should be a numpy array")
         if not data.ndim == 2:
             raise ValueError("data is expected to be 2d")
-        binning = Binning.from_value(binning)
+        binning = Binning(binning)
         if binning is Binning.ONE_BY_ONE:
             return data
         elif binning is Binning.TWO_BY_TWO:

tomwer/core/process/drac/output.py

@@ -1,4 +1,4 @@
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 PROPOSAL_GALLERY_DIR_NAME = "GALLERY"

tomwer/core/process/edit/imagekeyeditor.py

@@ -49,9 +49,7 @@ def change_image_key_control(scan: NXtomoScan, config: dict) -> TomwerScanBase:
             modifications = {}
 
     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:
         frame_indexes_dict = dict(
             filter(lambda item: item[1] is image_key_type, modifications.items())
@@ -65,7 +63,7 @@ def change_image_key_control(scan: NXtomoScan, config: dict) -> TomwerScanBase:
             image_key_control_value=image_key_type.value,
             logger=_logger,
         )
-    scan.clear_frames_caches()
+    scan.clear_frames_cache()
     return scan
 
 
@@ -181,8 +179,8 @@ class ImageKeyUpgraderTask(
         """
         retrieve frame indices to be updated
         """
-        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)
 
         config = {}
         for i_frame, frame in enumerate(scan.frames):

tomwer/core/process/edit/nxtomoeditor.py

@@ -33,9 +33,13 @@ class NXtomoEditorKeys:
     """namespace to store all keys used by the nxtomo editor"""
 
     ENERGY = "instrument.beam.energy"
-    X_PIXEL_SIZE = "instrument.detector.x_pixel_size"
-    Y_PIXEL_SIZE = "instrument.detector.y_pixel_size"
+    DETECTOR_X_PIXEL_SIZE = "instrument.detector.x_pixel_size"
+    DETECTOR_Y_PIXEL_SIZE = "instrument.detector.y_pixel_size"
     SAMPLE_DETECTOR_DISTANCE = "instrument.detector.distance"
+    SAMPLE_SOURCE_DISTANCE = "instrument.source.distance"
+    SAMPLE_X_PIXEL_SIZE = "sample.x_pixel_size"
+    SAMPLE_Y_PIXEL_SIZE = "sample.y_pixel_size"
+    PROPAGATION_DISTANCE = "sample.propagation_distance"
     FIELD_OF_VIEW = "instrument.detector.field_of_view"
     X_FLIPPED = "instrument.detector.x_flipped"
     Y_FLIPPED = "instrument.detector.y_flipped"
@@ -125,8 +129,8 @@ class NXtomoEditorTask(
                 overwrite=True,
             )
         # clear caches to make sure all modifications will be considered
-        scan.clear_caches()
-        scan.clear_frames_caches()
+        scan.clear_cache()
+        scan.clear_frames_cache()
         self.outputs.data = scan
 
     @staticmethod
@@ -239,7 +243,7 @@ class NXtomoEditorTask(
         """
         nexus_paths = get_nexus_paths(nexus_version)
 
-        return {
+        mapping = {
             # energy
             NXtomoEditorKeys.ENERGY: _EditorFieldInfo(
                 nexus_path=nexus_paths.ENERGY_PATH,
@@ -248,25 +252,17 @@ class NXtomoEditorTask(
                 name="energy",
                 n_value=1,
             ),
-            # x pixel size
-            NXtomoEditorKeys.X_PIXEL_SIZE: _EditorFieldInfo(
-                nexus_path=nexus_paths.X_PIXEL_SIZE_PATH,
+            # sample / detector distance
+            NXtomoEditorKeys.SAMPLE_DETECTOR_DISTANCE: _EditorFieldInfo(
+                nexus_path=nexus_paths.SAMPLE_DETECTOR_DISTANCE_PATH,
                 expected_type=float,
                 units="m",
-                name="x pixel size",
+                name="sample detector distance",
                 n_value=1,
             ),
-            # y pixel size
-            NXtomoEditorKeys.Y_PIXEL_SIZE: _EditorFieldInfo(
-                nexus_path=nexus_paths.Y_PIXEL_SIZE_PATH,
-                expected_type=float,
-                units="m",
-                name="y pixel size",
-                n_value=1,
-            ),
-            # sample / detector distance
-            NXtomoEditorKeys.SAMPLE_DETECTOR_DISTANCE: _EditorFieldInfo(
-                nexus_path=nexus_paths.DISTANCE_PATH,
+            # sample / source distance
+            NXtomoEditorKeys.SAMPLE_SOURCE_DISTANCE: _EditorFieldInfo(
+                nexus_path=nexus_paths.SAMPLE_SOURCE_DISTANCE_PATH,
                 expected_type=float,
                 units="m",
                 name="sample detector distance",
@@ -304,4 +300,46 @@ class NXtomoEditorTask(
                 name="z translation",
                 n_value=n_frames,
             ),
+            # detector x pixel size
+            NXtomoEditorKeys.DETECTOR_X_PIXEL_SIZE: _EditorFieldInfo(
+                nexus_path=nexus_paths.DETECTOR_X_PIXEL_SIZE_PATH,
+                expected_type=float,
+                units="m",
+                name="detector x pixel size",
+                n_value=1,
+            ),
+            # detector y pixel size
+            NXtomoEditorKeys.DETECTOR_Y_PIXEL_SIZE: _EditorFieldInfo(
+                nexus_path=nexus_paths.DETECTOR_Y_PIXEL_SIZE_PATH,
+                expected_type=float,
+                units="m",
+                name="detector y pixel size",
+                n_value=1,
+            ),
+            # sample x pixel size
+            NXtomoEditorKeys.SAMPLE_X_PIXEL_SIZE: _EditorFieldInfo(
+                nexus_path=nexus_paths.SAMPLE_X_PIXEL_SIZE_PATH,
+                expected_type=float,
+                units="m",
+                name="sample x pixel size",
+                n_value=1,
+            ),
+            # sample y pixel size
+            NXtomoEditorKeys.SAMPLE_Y_PIXEL_SIZE: _EditorFieldInfo(
+                nexus_path=nexus_paths.SAMPLE_Y_PIXEL_SIZE_PATH,
+                expected_type=float,
+                units="m",
+                name="sample y pixel size",
+                n_value=1,
+            ),
+            # propagation distance
+            NXtomoEditorKeys.PROPAGATION_DISTANCE: _EditorFieldInfo(
+                nexus_path=nexus_paths.PROPAGATION_DISTANCE,
+                expected_type=float,
+                units="m",
+                name="propagation distance",
+                n_value=1,
+            ),
         }
+
+        return mapping

tomwer/core/process/output.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
+
 import os
+from enum import Enum
 import warnings
-from silx.utils.enum import Enum as _Enum
 
 
-class ProcessDataOutputDirMode(_Enum):
+class ProcessDataOutputDirMode(Enum):
     IN_SCAN_FOLDER = "same folder as scan"
     PROCESSED_DATA_FOLDER = "PROCESSED_DATA folder"
     OTHER = "other"
@@ -25,10 +26,10 @@ class ProcessDataOutputDirMode(_Enum):
                 stacklevel=2,
             )
             return cls.PROCESSED_DATA_FOLDER
-        return super().from_value(value)
+        return ProcessDataOutputDirMode(value)
 
 
-class NabuOutputFileFormat(_Enum):
+class NabuOutputFileFormat(Enum):
     TIFF = "tiff"
     HDF5 = "hdf5"
     JP2K = "jp2"
@@ -39,7 +40,7 @@ class NabuOutputFileFormat(_Enum):
     def from_value(cls, value):
         if isinstance(value, str):
             value = value.lstrip(".")
-        return super().from_value(value)
+        return NabuOutputFileFormat(value)
 
 
 def get_file_format(file_str):

tomwer/core/process/reconstruction/axis/anglemode.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class CorAngleMode(_Enum):
@@ -18,4 +18,4 @@ class CorAngleMode(_Enum):
         elif value == 2:
             return CorAngleMode.manual_selection
         else:
-            return super().from_value(value=value)
+            return CorAngleMode(value=value)

tomwer/core/process/reconstruction/axis/axis.py

@@ -65,6 +65,7 @@ def adapt_tomwer_scan_to_nabu(scan: TomwerScanBase, do_flatfield: bool):
             update_dataset_info_flats_darks(
                 dataset_infos,
                 flatfield_mode=do_flatfield,
+                loading_mode="load_if_present",
             )
         except ValueError as exception:
             # nabu raise an error if no darks / flats set. But this can make sense at this stage if the NXtomo has no

tomwer/core/process/reconstruction/axis/mode.py

@@ -1,6 +1,6 @@
 import logging
 
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 from tomwer.core.process.reconstruction.axis.side import Side
 
 _logger = logging.getLogger(__name__)
@@ -120,7 +120,7 @@ class AxisMode(_Enum):
         elif value in ("read", "read from estimated cor"):
             value = AxisMode.read
 
-        return super().from_value(value=value)
+        return AxisMode(value)
 
     def requires_radio_indices(self) -> bool:
         return self in (

tomwer/core/process/reconstruction/axis/params.py

@@ -5,7 +5,7 @@ from collections import namedtuple
 
 import numpy
 from silx.io.url import DataUrl
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 from tomoscan.esrf.scan.utils import get_data
 
 from tomwer.core.process.reconstruction.utils.cor import relative_pos_to_absolute
@@ -60,8 +60,8 @@ class AxisCalculationInput(_Enum):
         if type(value) is str and len(value.split("_")) == 2:
             proj_type, pag = value.split("_")
             value_pag = True if pag == _WITH_PAG else False
-            value_proj = ProjectionType.from_value(proj_type)
-            return cls.from_value(_calculation_conf(value_proj, value_pag))
+            value_proj = ProjectionType(proj_type)
+            return cls(_calculation_conf(value_proj, value_pag))
         elif isinstance(value, cls):
             return value
         else:
@@ -348,7 +348,7 @@ class AxisRP:
     @estimated_cor.setter
     def estimated_cor(self, value: Side | float | None):
         try:
-            value = Side.from_value(value)
+            value = Side(value)
         except ValueError:
             pass
         if self.__estimated_cor != value:

tomwer/core/process/reconstruction/axis/projectiontype.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 class ProjectionType(_Enum):

tomwer/core/process/reconstruction/axis/side.py

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

tomwer/core/process/reconstruction/darkref/darkrefs.py

@@ -341,13 +341,13 @@ class DarkRefsTask(
             return REDUCER_TARGET.FLATS
         elif target == "dark":
             return REDUCER_TARGET.DARKS
-        return REDUCER_TARGET.from_value(target)
+        return REDUCER_TARGET(target)
 
     def compute(
         self, scan, target: REDUCER_TARGET, method: ReduceMethod, overwrite: bool
     ):
         target = self._target_to_reducer_target(target)
-        method = ReduceMethod.from_value(method)
+        method = ReduceMethod(method)
         if target is REDUCER_TARGET.DARKS:
             reduced_darks, metadata = scan.compute_reduced_darks(
                 reduced_method=method,

tomwer/core/process/reconstruction/darkref/darkrefscopy.py

@@ -115,7 +115,7 @@ class DarkRefsCopy(DarkRefsTask):
                                            is provided instead of the 'darks' or 'flats' one.
         :return: tuple as (data, metadata)
         """
-        reduced_target = REDUCER_TARGET.from_value(reduced_target)
+        reduced_target = REDUCER_TARGET(reduced_target)
 
         with cwd_context(url.file_path()):
             try:

tomwer/core/process/reconstruction/darkref/params.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 
 import enum
 
-from silx.utils.enum import Enum as _Enum
 from tomoscan.framereducer.method import ReduceMethod
 
 from tomwer.core.process.reconstruction.darkref.settings import (
@@ -17,7 +16,7 @@ from tomwer.core.utils.deprecation import deprecated
 # TODO: those classes (when, method) should be linked / embedded in the DarkRef
 # method
 @enum.unique
-class When(_Enum):
+class When(enum.Enum):
     never = (0,)
     before = (1,)
     after = (2,)
@@ -35,7 +34,7 @@ def _from_value_reduce_method_backward_compatibility(value) -> ReduceMethod:
     elif value in ("last", 11, (11,)):
         return ReduceMethod.FIRST
     else:
-        return ReduceMethod.from_value(value)
+        return ReduceMethod(value)
 
 
 class DKRFRP(_ReconsParam):

tomwer/core/process/reconstruction/nabu/castvolume.py

@@ -129,6 +129,7 @@ class CastVolumeTask(
 
         # build output volume object
         overwrite = configuration.get("overwrite", False)
+        remove_input_volume = configuration.get("remove_input_volume", False)
         output_volume.overwrite = overwrite
         cratios = configuration.get("compression_ratios", None)
         if cratios is not None:
@@ -161,6 +162,7 @@ class CastVolumeTask(
                     rescale_max_percentile=rescale_max_percentile,
                     save=True,
                     store=False,
+                    remove_input_volume=remove_input_volume,
                 )
             except Exception as e:
                 mess = f"volume cast of {str(input_volume)} failed. Reason is {str(e)}"
@@ -203,7 +205,8 @@ class CastVolumeTask(
                     command += f" --rescale_min_percentile={rescale_min_percentile}"
                 if rescale_max_percentile is not None:
                     command += f" --rescale_max_percentile={rescale_max_percentile}"
-
+                if remove_input_volume:
+                    command += " --remove-input-volume"
                 return command
 
             script_name = get_slurm_script_name(prefix="nabu_cast")

tomwer/core/process/reconstruction/nabu/helical.py

@@ -34,7 +34,9 @@ class NabuHelicalPrepareWeightsDouble(
             scan.master_file,
             extra_options={"h5_entry": scan.entry},
         )
-        update_dataset_info_flats_darks(dataset_info, flatfield_mode=1)
+        update_dataset_info_flats_darks(
+            dataset_info, flatfield_mode=1, loading_mode="load_if_present"
+        )
 
         mappe = 0
         my_flats = load_images_from_dataurl_dict(dataset_info.flats)