tomwer 2.0.0.dev2__py3-none-any.whl → 2.0.0.dev3__py3-none-any.whl

orangecontrib/tomwer/state_summary.py

@@ -1,6 +1,6 @@
 from orangewidget.utils.signals import PartialSummary, summarize
 
-from tomwer.core.cluster import SlurmClusterConfiguration
+from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.scanbase import TomwerScanBase

orangecontrib/tomwer/tutorials/EBS_tomo_listener.ows

@@ -4,7 +4,7 @@
 		<node id="0" name="bliss-data listener" qualified_name="orangecontrib.tomwer.widgets.control.BlissDataListenerOW.BlissDataListenerOW" project_name="tomwer" version="" title="scan listener" position="(150, 150)" />
 		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(296.13186813186815, 180.10989010989013)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(619.0, 258.0)" />
-		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(766.0, 292.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(766.0, 292.0)" />
 		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(931.0, 329.0)" />
 		<node id="5" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(605.0, 400.0)" />
 		<node id="6" name="copy reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CopyReducedDarkAndFlatOW.CopyReducedDarkAndFlatOW" project_name="tomwer" version="" title="copy reduced darks and flats" position="(439.8461538461538, 210.30769230769235)" />

orangecontrib/tomwer/tutorials/complete_on_the_fly.ows

@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="compete on the fly" description="Workflow that goes from scan listener to the final converted volume.">
+	<nodes>
+		<node id="0" name="Blissdata Listener" qualified_name="orangecontrib.tomwer.widgets.control.BlissDataListenerOW.BlissDataListenerOW" project_name="tomwer" version="" title="scan listener" position="(120.0, 247.0)" />
+		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(275.13186813186815, 247.1098901098901)" />
+		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(594.0, 248.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(766.0, 292.0)" />
+		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(932.0, 285.0)" />
+		<node id="5" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(596.0, 390.0)" />
+		<node id="6" name="copy reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CopyReducedDarkAndFlatOW.CopyReducedDarkAndFlatOW" project_name="tomwer" version="" title="copy reduced darks and flats" position="(433.8461538461538, 246.30769230769238)" />
+		<node id="7" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(947.0, 395.0)" />
+		<node id="8" name="cast volume" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CastNabuVolumeOW.CastNabuVolumeOW" project_name="tomwer" version="" title="cast volume" position="(1280.0, 413.0)" />
+		<node id="9" name="Cluster Configuration" qualified_name="orangecontrib.tomwer.widgets.cluster.SlurmClusterOW.SlurmClusterOW" project_name="tomwer" version="" title="Cluster Configuration Volume reconstruction" position="(784.0, 555.0)" />
+		<node id="10" name="Cluster monitor" qualified_name="orangecontrib.tomwer.widgets.cluster.MonitorOW.MonitorOW" project_name="tomwer" version="" title="Cluster monitor" position="(1111.0, 403.5)" />
+		<node id="11" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(1098.0, 279.0)" />
+		<node id="12" name="Cluster Configuration" qualified_name="orangecontrib.tomwer.widgets.cluster.SlurmClusterOW.SlurmClusterOW" project_name="tomwer" version="" title="Cluster configuration cast volume" position="(1116.0, 559.0)" />
+		<node id="13" name="Cluster monitor" qualified_name="orangecontrib.tomwer.widgets.cluster.MonitorOW.MonitorOW" project_name="tomwer" version="" title="Cluster monitor (1)" position="(1445.0, 411.0)" />
+	</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="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="2" 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="3" source_node_id="5" sink_node_id="3" source_channel="nabu_params" sink_channel="nabu_params" enabled="true" source_channel_id="nabu_params" sink_channel_id="nabu_params" />
+		<link id="4" source_node_id="1" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="5" source_node_id="6" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="6" source_node_id="3" sink_node_id="7" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="7" source_node_id="5" sink_node_id="7" source_channel="nabu_params" sink_channel="nabu_params" enabled="true" source_channel_id="nabu_params" sink_channel_id="nabu_params" />
+		<link id="8" source_node_id="9" sink_node_id="7" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="config_out" sink_channel_id="cluster_config" />
+		<link id="9" source_node_id="7" sink_node_id="10" 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="10" source_node_id="10" sink_node_id="8" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="11" source_node_id="7" sink_node_id="11" source_channel="volume" sink_channel="volume" enabled="true" source_channel_id="volume" sink_channel_id="volume" />
+		<link id="12" source_node_id="12" sink_node_id="8" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="config_out" sink_channel_id="cluster_config" />
+		<link id="13" source_node_id="8" sink_node_id="13" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_tomo_obj" sink_channel_id="future_tomo_obj" />
+	</links>
+	<annotations>
+		<arrow id="0" start="(83.53846153846158, 360.61538461538464)" end="(86.07692307692312, 310.5384615384615)" fill="#C1272D" />
+		<text id="1" type="text/plain" rect="(29.999999999999943, 369.2307692307693, 202.0, 76.0)" font-family="Ubuntu" font-size="16">wait for bliss scan and create NXtomo</text>
+		<arrow id="2" start="(298.9230769230769, 143.0769230769231)" end="(290.0769230769231, 207.30769230769232)" fill="#C1272D" />
+		<text id="3" type="text/plain" rect="(287.30769230769226, 55.0, 135.0, 69.0)" font-family="Ubuntu" font-size="16">compute reduced darks and flats</text>
+		<text id="4" type="text/plain" rect="(536.0, 76.0, 114.0, 50.0)" font-family="Ubuntu" font-size="16">compute CoR</text>
+		<arrow id="5" start="(589.0, 136.0)" end="(587.0, 194.99999999999997)" fill="#C1272D" />
+		<arrow id="6" start="(758.9999999999999, 195.0)" end="(760.0, 254.0)" fill="#C1272D" />
+		<text id="7" type="text/plain" rect="(680.0, 151.0, 150.0, 31.0)" font-family="Ubuntu" font-size="16">compute slice</text>
+		<text id="8" type="text/plain" rect="(897.0, 76.0, 128.0, 89.0)" font-family="Ubuntu" font-size="16">browse dataset and reconstructed slice(s)</text>
+		<arrow id="9" start="(941.0, 175.0)" end="(933.0, 237.0)" fill="#C1272D" />
+		<arrow id="10" start="(563.0, 536.0)" end="(594.0, 463.0)" fill="#C1272D" />
+		<text id="11" type="text/plain" rect="(493.0, 513.0, 150.0, 69.0)" font-family="Sans Serif" font-size="16">define reconstruction settings</text>
+		<text id="12" type="text/plain" rect="(296.7692307692307, 382.46153846153845, 150.0, 50.0)" font-family="Sans Serif" font-size="16">copy reduced darks and flats</text>
+		<arrow id="13" start="(379.0, 371.0)" end="(403.99999999999994, 319.0)" fill="#C1272D" />
+		<text id="14" type="text/plain" rect="(1180.0, 124.0, 150.0, 27.0)" font-family="Cantarell" font-size="16">View reconstructed volume</text>
+		<arrow id="15" start="(1162.0, 167.0)" end="(1115.0, 241.0)" fill="#C1272D" />
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_blissConfiguration': {}, '_nxtomo_cfg_file': '', '_static_input': {'nxtomomill_cfg_file': ''}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\nu\x00\x00\x013\x00\x00\x0b\xf6\x00\x00\x02\x8f\x00\x00\nu\x00\x00\x01X\x00\x00\x0b\xf6\x00\x00\x02\x8f\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\nu\x00\x00\x01X\x00\x00\x0b\xf6\x00\x00\x02\x8f', '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'cor_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': 5, 'oversampling': 4, 'n_subsampling_y': 40, 'take_log': True, 'near_width': 40}, '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}, 'relative_value': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x01k\x00\x00\x00\xac\x00\x00\x06\x01\x00\x00\x03\x8e\x00\x00\x01k\x00\x00\x00\xd1\x00\x00\x06\x01\x00\x00\x03\x8e\x00\x00\x00\x00\x00\x00\x00\x00\x07\x80\x00\x00\x01k\x00\x00\x00\xd1\x00\x00\x06\x01\x00\x00\x03\x8e', '__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': {'nabu_params': {'preproc': {'flatfield': 1, 'double_flatfield': 0, 'dff_sigma': 0.0, 'ccd_filter_enabled': 0, 'ccd_filter_threshold': 0.04, 'take_logarithm': True, 'log_min_clip': 1e-06, 'log_max_clip': 10.0, 'sino_rings_correction': 'None', 'sino_rings_options': 'sigma=1.0 ; levels=10 ; padding=False', 'tilt_correction': '', 'autotilt_options': '', 'normalize_srcurrent': 1, 'rotate_projections_center': ''}, 'reconstruction': {'method': 'FBP', 'angles_file': '', 'axis_correction_file': '', 'angle_offset': 0.0, 'fbp_filter_type': 'ramlak', 'padding_type': 'edges', 'iterations': 200, 'optim_algorithm': 'chambolle-pock', 'regularization_weight': 0.0, 'preconditioning_filter': 1, 'positivity_constraint': 1, 'rotation_axis_position': '', 'translation_movements_file': '', 'clip_outer_circle': 1, 'centered_axis': 1, 'start_x': 0, 'end_x': -1, 'start_y': 0, 'end_y': -1, 'start_z': 0, 'end_z': -1, 'enable_halftomo': 'auto'}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1, 'exclude_projections': ''}, 'output': {'file_format': 'hdf5'}, 'phase': {'method': 'None', 'unsharp_coeff': 0, 'unsharp_sigma': 0, 'ctf_geometry': ' z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True', 'beam_shape': 'parallel', 'ctf_advanced_params': ' length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True'}, 'configuration_level': 'optional'}}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="6" format="literal">{'_auto_mode': True, '_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\n\\\x00\x00\x01k\x00\x00\x0c\x0f\x00\x00\x02}\x00\x00\n\\\x00\x00\x01k\x00\x00\x0c\x0f\x00\x00\x02}\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\n\\\x00\x00\x01k\x00\x00\x0c\x0f\x00\x00\x02}', '__version__': 1}</properties>
+		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': {}, 'slurm_settings': {}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="8" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="9" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\n\x84\x00\x00\x00\xb1\x00\x00\x0b\xe7\x00\x00\x03\x11\x00\x00\n\x84\x00\x00\x00\xd6\x00\x00\x0b\xe7\x00\x00\x03\x11\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\n\x84\x00\x00\x00\xd6\x00\x00\x0b\xe7\x00\x00\x03\x11', '__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>
+		<properties node_id="11" format="literal">{'_ewoks_default_inputs': {'load_volume': False}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="12" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\n\x84\x00\x00\x00\xd6\x00\x00\x0b\xe7\x00\x00\x03\x11\x00\x00\n\x84\x00\x00\x00\xd6\x00\x00\x0b\xe7\x00\x00\x03\x11\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\n\x84\x00\x00\x00\xd6\x00\x00\x0b\xe7\x00\x00\x03\x11', '__version__': 1}</properties>
+		<properties node_id="13" 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 />
+	</session_state>
+</scheme>

orangecontrib/tomwer/tutorials/default_cor_search.ows

@@ -4,7 +4,7 @@
 		<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.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(319.0, 189.0)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(469.0, 237.0)" />
-		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(659.0, 325.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(659.0, 325.0)" />
 		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(818.0, 362.0)" />
 		<node id="5" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(515.0, 427.0)" />
 	</nodes>

orangecontrib/tomwer/tutorials/drac_publication.ows

@@ -4,7 +4,7 @@
 		<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.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(324.0, 183.0)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" 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="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" 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="(986.75, 383.25)" />

orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows

@@ -2,7 +2,7 @@
 <scheme version="2.0" title="full volume" description="">
 	<nodes>
 		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(157.0, 160.0)" />
-		<node id="1" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(350.0, 152.0)" />
+		<node id="1" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(350.0, 152.0)" />
 		<node id="2" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(505.0, 151.0)" />
 		<node id="3" name="tone notifier" qualified_name="orangecontrib.ewoksnotify.ToneNotifierOW.ToneNotifierOW" project_name="ewoksnotify" version="" title="tone notifier" position="(693.0, 151.0)" />
 		<node id="4" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(238.0, 62.0)" />

orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows

@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='utf-8'?>
 <scheme version="2.0" title="insitu" description="">
 	<nodes>
-		<node id="0" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(757.6666666666667, 415.66666666666663)" />
+		<node id="0" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(757.6666666666667, 415.66666666666663)" />
 		<node id="1" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(625.6666666666667, 415.3333333333335)" />
 		<node id="2" name="Python Script" qualified_name="orangecontrib.tomwer.widgets.other.PythonScriptOW.OWPythonScript" project_name="tomwer" version="" title="create volfloat symlink" position="(1048.5555555555557, 553.3333333333333)" />
 		<node id="3" name="Python Script" qualified_name="orangecontrib.tomwer.widgets.other.PythonScriptOW.OWPythonScript" project_name="tomwer" version="" title="Python Script (old)" position="(358.6666666666667, 240.5)" />

orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows

@@ -4,7 +4,7 @@
 		<node id="0" name="scan watcher" qualified_name="orangecontrib.tomwer.widgets.control.BlissDataListenerOW.BlissDataListenerOW" project_name="tomwer" version="" title="scan watcher" position="(45.0, 221.0)" />
 		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="dark and flat field construction" position="(338.0, 228.0)" />
 		<node id="2" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(84.0, 57.0)" />
-		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(581.0, 344.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(581.0, 344.0)" />
 		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(1078.0, 475.0)" />
 		<node id="5" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(460.0, 307.0)" />
 		<node id="6" name="Python Script" qualified_name="orangecontrib.tomwer.widgets.other.PythonScriptOW.OWPythonScript" project_name="tomwer" version="" title="create volfloat symlink" position="(1053.0, 615.0)" />

orangecontrib/tomwer/tutorials/simple_slice_reconstruction.ows

@@ -4,7 +4,7 @@
 		<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.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(324.0, 183.0)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" 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="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" 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="(820.0, 307.0)" />
 		<node id="5" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(426.0, 355.0)" />
 	</nodes>

orangecontrib/tomwer/tutorials/simple_slice_reconstruction_on_slurm.ows

@@ -4,7 +4,7 @@
 		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(99.99999999999997, 255.71428571428572)" />
 		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(261.1428571428571, 254.42857142857142)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(384.2857142857143, 255.1428571428571)" />
-		<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="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" 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="(946.4285714285714, 255.1428571428571)" />
 		<node id="5" name="slurm cluster" qualified_name="orangecontrib.tomwer.widgets.cluster.SlurmClusterOW.SlurmClusterOW" project_name="tomwer" version="" title="slurm cluster" position="(480.57142857142856, 369.8571428571429)" />
 		<node id="6" name="Cluster monitor" qualified_name="orangecontrib.tomwer.widgets.cluster.MonitorOW.MonitorOW" project_name="tomwer" version="" title="cluster monitor" position="(794.9285714285714, 258.3571428571429)" />

orangecontrib/tomwer/tutorials/using_multicor_to_find_cor.ows

@@ -5,7 +5,7 @@
 		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.ComputeReduceDarkAndFlatOW.ComputeReduceDarkAndFlatOW" project_name="tomwer" version="" title="reduced darks and flats" position="(319.0, 189.0)" />
 		<node id="2" name="center of rotation finder" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CoROW.CoROW" project_name="tomwer" version="" title="default center of rotation" position="(469.0, 237.0)" />
 		<node id="3" name="multi-cor (sa-axis)" qualified_name="orangecontrib.tomwer.widgets.reconstruction.MultiCoROW.MultiCoROW" project_name="tomwer" version="" title="semi-automated center of rotation" position="(605.0, 288.0)" />
-		<node id="4" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(772.0, 340.0)" />
+		<node id="4" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSlicesOW.NabuSlicesOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(772.0, 340.0)" />
 		<node id="5" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(931.0, 377.0)" />
 		<node id="6" name="nabu settings" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuSettingsOW.NabuSettingsOW" project_name="tomwer" version="" title="nabu settings" position="(450.0, 373.0)" />
 	</nodes>

orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py

@@ -8,8 +8,8 @@ from orangewidget import gui
 from orangewidget.settings import Setting
 from orangewidget.widget import Output, OWBaseWidget
 
+from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 from tomwer.core.settings import ParametersKeys
-from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.gui.cluster.slurm import SlurmSettingsWindow
 
 _logger = logging.getLogger(__name__)

orangecontrib/tomwer/widgets/other/PythonScriptOW.py

@@ -19,8 +19,8 @@ from silx.gui import qt
 from tomoscan.series import Series
 
 import tomwer.tasks.script.python
+from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 from tomwer.core.settings import ParametersKeys
-from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.volume.volumebase import TomwerVolumeBase

orangecontrib/tomwer/widgets/reconstruction/BaseNabuRecOW.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from tomwer.core.cluster import SlurmClusterConfiguration
+from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 from tomwer.core.settings import ParametersKeys
 
 
@@ -37,3 +37,6 @@ class BaseNabuRecOW:
     def setNabuParams(self, config: dict) -> None:
         assert config is None or isinstance(config, dict)
         self._nabu_params = config
+
+    def getNabuParams(self) -> dict:
+        return self._nabu_params

orangecontrib/tomwer/widgets/reconstruction/CastNabuVolumeOW.py

@@ -3,14 +3,14 @@ from __future__ import annotations
 from orangewidget import gui
 from orangewidget.widget import Input
 
-from tomwer.core.cluster.cluster import SlurmClusterConfiguration
+from tomwer.models.cluster.slurm_cluster import SlurmClusterConfiguration
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import ParametersKeys
 from tomwer.core.utils.ewoks import filter_missing_data
 from tomwer.core.volume.volumebase import TomwerVolumeBase
 from tomwer.gui.reconstruction.nabu.castvolume import CastVolumeWidget
 from tomwer.gui.utils.qt_utils import block_signals
-from tomwer.tasks.reconstruction.nabu.castvolume import CastVolumeTask
+from tomwer.tasks.reconstruction.castvolume import CastVolumeTask
 from orangecontrib.tomwer.orange.task_widgets.TomwerWidgetWithStack import (
     TomwerWidgetWithStack,
 )

orangecontrib/tomwer/widgets/reconstruction/MultiCoROW.py

@@ -11,19 +11,20 @@ from orangecontrib.tomwer.orange.task_widgets.TomwerWidgetWithStack import (
 
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
 
-import tomwer.tasks.reconstruction.nabu.multicor
+import tomwer.tasks.reconstruction.multicor
 from tomwer.tasks.reconstruction.cor import CoRTask
 from tomwer.core.reconstruction.params_cache import (
     save_reconstruction_parameters_to_cache,
 )
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.reconstruction.multi.multicor.multicor import _is_margin_too_large
-from tomwer.core.reconstruction.nabu.phase import NabuPhaseMethod
+from tomwer.core.reconstruction.common.phase import NabuPhaseMethod
 from tomwer.core.settings import ParametersKeys
 from tomwer.gui.reconstruction.cor.QCoRParams import QCoRParams as _QCoRParams
 from tomwer.gui.reconstruction.multicor.QMultiCoRParams import (
     QMultiCoRParams as _QMultiCoRParams,
 )
+from tomwer.gui.utils.reconstruction import check_nabu_params_are_provided
 from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 
 from processview.core.manager import ProcessManager, DatasetState
@@ -31,6 +32,7 @@ from processview.core import helpers as pv_helpers
 from processview.core.superviseprocess import SuperviseProcess
 
 from tomwer.gui.reconstruction.multicor.MultiCoRWindow import MultiCoRWindow
+from ewoksorange.gui.orange_utils.signals import Input
 
 _logger = logging.getLogger(__name__)
 
@@ -38,7 +40,7 @@ _logger = logging.getLogger(__name__)
 class MultiCoROW(
     TomwerWidgetWithStack,
     SuperviseProcess,
-    ewokstaskclass=tomwer.tasks.reconstruction.nabu.multicor.MultiCoRTask,
+    ewokstaskclass=tomwer.tasks.reconstruction.multicor.MultiCoRTask,
     openclass=True,
 ):
     """
@@ -107,9 +109,19 @@ class MultiCoROW(
         "pool_size",
         "platform_resources",
         "process_id",
+        "invalid_slice_callback",
     )
     _MARGIN_LIMIT_WARNING = 100
 
+    class Inputs:
+        data = Input(
+            name="data",
+            type=TomwerScanBase,
+            doc="one scan to be process",
+            default=True,
+            multiple=True,
+        )
+
     def __init__(self, parent=None):
         """
 
@@ -130,7 +142,7 @@ class MultiCoROW(
         self._widget.sigValidated.connect(self.validate)
         self._widget.sigValidated.connect(self.accept)
         self._widget._multicorControl.sigComputationRequest.connect(
-            self._computationTriggered
+            self.execute_ewoks_task_without_propagation
         )
         self._widget._multicorControl.sigComputationRequest.connect(
             self._widget.showResults
@@ -154,13 +166,13 @@ class MultiCoROW(
             }
         )
 
-    def _computationTriggered(self):
+    def execute_ewoks_task_without_propagation(self):
         if self._checkCancelProcessingForMargins():
             _logger.info(
                 "Multi-cor reconstruction cancelled by the user because of phasing / margins warning"
             )
             return
-        self.execute_ewoks_task_without_propagation()  # propagation is handle once processing is done to handle interactive of auto modes
+        super().execute_ewoks_task_without_propagation()  # propagation is handle once processing is done to handle interactive of auto modes
 
     def _updateSettings(self):
         self.set_default_input(
@@ -186,6 +198,10 @@ class MultiCoROW(
     def setConfiguration(self, configuration):
         self._widget.setConfiguration(configuration)
 
+    @Inputs.data
+    def _scanReceived(self, scan):
+        self.process(scan=scan)
+
     def process(self, scan):
         """
         call when a new scan is received
@@ -196,6 +212,12 @@ class MultiCoROW(
             scan.cor_params = _QCoRParams()
         if scan.multicor_params is None:
             scan.multicor_params = _QMultiCoRParams()
+        if not check_nabu_params_are_provided(
+            nabu_params=self.get_task_input_value("nabu_params"),
+            process=self,
+            tomo_obj=scan,
+        ):
+            return
         # clear interface
         self._widget.clearResults()
         self.set_dynamic_input("data", scan)
@@ -391,11 +413,6 @@ class MultiCoROW(
             self.show()
             self._widget.showResults()
 
-    def handleNewSignals(self):
-        scan = self.get_task_input_value("data", None)
-        if scan is not None:
-            self.process(scan)
-
     def _output_changed(self):
         self._updateAccordingToResult()
         return super()._output_changed()
@@ -419,3 +436,13 @@ class MultiCoROW(
 
     def isAutoFocusLock(self):
         return self._widget.isAutoFocusLock()
+
+    def handleNewSignals(self) -> None:
+        """
+        in order to handle https://gitlab.esrf.fr/workflow/ewoks/ewoksorange/-/issues/60
+        we need to overwrite the Inputs.data and overwrite the 'handleNewSignals' function.
+
+        The Inputs.data is used to make sure the task is executed each time the value of a link is changed.
+        The overwrite of `handleNewSignals` is to make sure we won't trigger one extra time the widget.
+        """
+        pass