tomwer 1.5.0rc3__py3-none-any.whl → 1.5.2__py3-none-any.whl

orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows

@@ -31,7 +31,7 @@
 	<thumbnail />
 	<node_properties>
 		<properties node_id="0" format="literal">{'_muted': False, 'controlAreaVisible': False, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x04n\x00\x00\x01\xfe\x00\x00\x05\xc1\x00\x00\x03-\x00\x00\x04n\x00\x00\x02#\x00\x00\x05\xc1\x00\x00\x03-\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x04n\x00\x00\x02#\x00\x00\x05\xc1\x00\x00\x03-', '__version__': 1}</properties>
-		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': {'preproc': {'flatfield': 1, 'double_flatfield_enabled': 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}, 'reconstruction': {'method': 'FBP', 'slice_plane': 'XY', 'angles_file': '', 'axis_correction_file': '', 'angle_offset': 0.0, 'fbp_filter_type': 'ramlak', 'padding_type': 'edges', 'iterations': 200, 'optim_algorithm': 'chambolle-pock', 'weight_tv': 0.01, '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': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1}, 'tomwer_slices': 'middle', 'output': {'file_format': 'vol', 'location': '', 'output_dir_mode': 'same folder as scan'}, 'phase': {'method': 'Paganin', 'delta_beta': '180', 'padding_type': 'edge', 'unsharp_coeff': 3.0, 'unsharp_sigma': 0.8, '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', 'ctf_translations_file': ''}, 'configuration_level': 'optional', 'mode_locked': True, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12', '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, '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}, 'reconstruction': {'method': 'FBP', 'slice_plane': 'XY', 'angles_file': '', 'axis_correction_file': '', 'angle_offset': 0.0, 'fbp_filter_type': 'ramlak', 'padding_type': 'edges', 'iterations': 200, 'optim_algorithm': 'chambolle-pock', 'weight_tv': 0.01, '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': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1}, 'tomwer_slices': 'middle', 'output': {'file_format': 'vol', 'location': '', 'output_dir_mode': 'same folder as scan'}, 'phase': {'method': 'Paganin', 'delta_beta': '180', 'padding_type': 'edge', 'unsharp_coeff': 3.0, 'unsharp_sigma': 0.8, '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', 'ctf_translations_file': ''}, 'configuration_level': 'optional', 'mode_locked': True, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x02\xaa\x00\x00\x00\xb4\x00\x00\x083\x00\x00\x04\x12', '__version__': 1}</properties>
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orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows

@@ -33,7 +33,7 @@
 		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': {'DOWHEN': 'before', 'DARKCAL': 'Average', 'DARKOVE': 1, 'DARKRMV': 0, 'DKFILE': 'darkend[0-9]{3,4}', 'REFSCAL': 'Median', 'REFSOVE': 1, 'REFSRMV': 0, 'RFFILE': 'ref*.*[0-9]{3,4}_[0-9]{3,4}'}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x00H\x00\x00\x00\x1b\x00\x00\x03\xef\x00\x00\x02\x1f\x00\x00\x00H\x00\x00\x00@\x00\x00\x03\xef\x00\x00\x02\x1f\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x00H\x00\x00\x00@\x00\x00\x03\xef\x00\x00\x02\x1f', '__version__': 1}</properties>
 		<properties node_id="2" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x02\x80\x00\x00\x01C\x00\x00\x04\xff\x00\x00\x03G\x00\x00\x02\x80\x00\x00\x01h\x00\x00\x04\xff\x00\x00\x03G\x00\x00\x00\x00\x00\x00\x00\x00\x07\x80\x00\x00\x02\x80\x00\x00\x01h\x00\x00\x04\xff\x00\x00\x03G', '__version__': 1}</properties>
 		<properties node_id="3" format="literal">{'_muted': False, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
-		<properties node_id="4" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': {'preproc': {'flatfield': 1, 'double_flatfield_enabled': 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', 'tilt_correction': '', 'autotilt_options': ''}, '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', 'weight_tv': 0.01, 'preconditioning_filter': 1, 'positivity_constraint': 1, 'rotation_axis_position': '', 'translation_movements_file': '', 'clip_outer_circle': 1, 'start_x': 0, 'end_x': -1, 'start_y': 0, 'end_y': -1, 'start_z': 0, 'end_z': -1, 'enable_halftomo': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1}, 'tomwer_slices': 'middle', 'output': {'file_format': 'vol', 'location': ''}, 'phase': {'method': 'Paganin', 'delta_beta': '500', 'padding_type': 'edge', 'unsharp_coeff': 3.0, 'unsharp_sigma': 0.65}, 'configuration_level': 'optional', 'mode_locked': False, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e', '__version__': 1}</properties>
+		<properties node_id="4" format="literal">{'_ewoks_default_inputs': {'data': None, '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', 'tilt_correction': '', 'autotilt_options': ''}, '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', 'weight_tv': 0.01, 'preconditioning_filter': 1, 'positivity_constraint': 1, 'rotation_axis_position': '', 'translation_movements_file': '', 'clip_outer_circle': 1, 'start_x': 0, 'end_x': -1, 'start_y': 0, 'end_y': -1, 'start_z': 0, 'end_z': -1, 'enable_halftomo': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1}, 'tomwer_slices': 'middle', 'output': {'file_format': 'vol', 'location': ''}, 'phase': {'method': 'Paganin', 'delta_beta': '500', 'padding_type': 'edge', 'unsharp_coeff': 3.0, 'unsharp_sigma': 0.65}, 'configuration_level': 'optional', 'mode_locked': False, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e\x00\x00\x00\x00\x00\x00\x00\x00\n\x00\x00\x00\x00H\x00\x00\x00@\x00\x00\x05\xd1\x00\x00\x03\x9e', '__version__': 1}</properties>
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 ZGWUk5SMBlNMSUNFU5SGlFKUjAlzbGljZV9vcHSUaAZoB4wKX1NsaWNlTW9kZZSTlIwGTEFURVNU

orangecontrib/tomwer/tutorials/untitled.ows

@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="" 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="(234.0, 102.0)" />
+	</nodes>
+	<links />
+	<annotations />
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'data': None, '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': '', 'flat_distortion_correction_enabled': True, 'flat_distortion_params': "tile_size=100; interpolation_kind='linear'; padding_mode='edge'; correction_spike_threshold=None", 'detector_distortion_correction': False, 'detector_distortion_correction_options': {'map_x': '', 'map_z': ''}}, 'reconstruction': {'method': 'FBP', 'slice_plane': 'XY', 'angles_file': '', 'axis_correction_file': '', 'angle_offset': 0.0, 'fbp_filter_type': 'ramlak', 'padding_type': 'edges', 'iterations': 200, 'optim_algorithm': 'chambolle-pock', 'weight_tv': 0.01, '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': 0}, 'dataset': {'binning': 1, 'binning_z': 1, 'projections_subsampling': 1, 'exclude_projections': ''}, 'tomwer_slices': 'middle', 'output': {'file_format': 'hdf5', 'location': '', 'output_dir_mode': 'same folder as scan'}, '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'}, 'gpu_mem_fraction': 0.9, 'cpu_mem_fraction': 0.9, 'configuration_level': 'advanced', 'mode_locked': False, 'cluster_config': None}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\t\xb8\x00\x00\x00\xdb\x00\x00\x0c\xb4\x00\x00\x03!', '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py

@@ -206,6 +206,8 @@ class FutureTomwerObjectObserverWidget(
             return
         elif future_tomo_obj.status == "error":
             state = DatasetState.FAILED
+            if future_tomo_obj.job_id is None:
+                details = "Job submission to Slurm has failed. This is likely due to an invalid configuration request, such as requesting a GPU on a partition that does not support GPUs. Please review your configuration and try again."
         elif future_tomo_obj.status == "pending":
             details = "\n".join([details, "pending"])
             state = DatasetState.PENDING

tomwer/app/canvas_launcher/config.py

@@ -9,7 +9,11 @@ import logging
 import tomwer.version
 from tomwer.gui import icons
 
-from ewoksorange.pkg_meta import iter_entry_points
+try:
+    from ewoksorange.pkg_meta import entry_points
+except ImportError:
+    # ewoksorange < 2.0
+    from ewoksorange.pkg_meta import iter_entry_points as entry_points
 from . import environ
 from .splash import getIcon, splash_screen
 from .widgetsscheme import WidgetsScheme
@@ -82,7 +86,7 @@ class TomwerConfig(config.Config):
             return entry.name.lower() not in ("ewoks demo",)
 
         try:
-            all_eps = filter(accept_extension, iter_entry_points(group=WIDGETS_ENTRY))
+            all_eps = filter(accept_extension, entry_points(group=WIDGETS_ENTRY))
         except Exception as e:
             _logger.error(f"fail to find add-ons. Error is {e}")
         return iter(all_eps)

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

@@ -5,6 +5,7 @@ import functools
 import logging
 import os
 import gc
+from collections.abc import Callable
 from tomwer.io.utils import format_stderr_stdout
 from silx.utils.deprecation import deprecated, deprecated_warning
 from silx.io.utils import open as open_hdf5
@@ -85,6 +86,7 @@ def run_slices_reconstruction(
     advancement=None,
     process_id: int | None = None,
     instantiate_classes_only: bool = False,
+    invalid_slice_callback: Callable[[str], None] | None = None,
 ) -> tuple:
     """
     call nabu for a reconstruction on scan with the given configuration
@@ -142,7 +144,9 @@ def run_slices_reconstruction(
     scan.nabu_recons_params = sc_config
 
     # handle special cases like several db...
-    nabu_configurations = interpret_tomwer_configuration(config, scan=scan)
+    nabu_configurations = interpret_tomwer_configuration(
+        config, scan=scan, invalid_slice_callback=invalid_slice_callback
+    )
     output_urls = []
     stderrs = []
     stdouts = []
@@ -227,6 +231,7 @@ class NabuSlicesTask(
     optional_input_names=(
         "dry_run",
         "serialize_output_data",
+        "invalid_slice_callback",
     ),
     output_names=("data", "nabu_params", "future_tomo_obj"),
 ):
@@ -288,6 +293,9 @@ class NabuSlicesTask(
                 dry_run=self._dry_run,
                 process_id=self.process_id,
                 instantiate_classes_only=True,
+                invalid_slice_callback=self.get_input_value(
+                    "invalid_slice_callback", None
+                ),
             )
         except Exception as e:
             mess = f"Fail to instantiate slice reconstructor for {str(scan)}. Reason is {e}."
@@ -425,7 +433,11 @@ class NabuSlicesTask(
             self._current_processing.cancel()
 
 
-def interpret_tomwer_configuration(config: dict, scan: TomwerScanBase | None) -> tuple:
+def interpret_tomwer_configuration(
+    config: dict,
+    scan: TomwerScanBase | None,
+    invalid_slice_callback: Callable[[str], None] | None = None,
+) -> tuple:
     """
     tomwer can 'mock' the nabu reconstruction to request more feature.
     Typical use case is that we can ask for reconstruction of several
@@ -471,9 +483,10 @@ def interpret_tomwer_configuration(config: dict, scan: TomwerScanBase | None) ->
             index_max = index_max - 1
 
             if slice_index > index_max:
-                _logger.error(
-                    f"slice index {slice_index} requested. But slice index must be in 0-{index_max} - ignore this request"
-                )
+                error_message = f"{scan.get_identifier().short_description()}\n\nCannot reconstruct slice {slice_index} along plane {axis.value}. Must be in [0-{index_max}]"
+                _logger.error(error_message)
+                if invalid_slice_callback is not None:
+                    invalid_slice_callback(error_message)
                 return False
             return True
 

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

@@ -342,6 +342,7 @@ class _NabuPhaseMethod(Enum):
     PAGANIN = "Paganin"
     CTF = "CTF"
     NONE = "None"
+    CONE = "cone"
 
     @classmethod
     def from_value(cls, value):

tomwer/core/process/reconstruction/saaxis/saaxis.py

@@ -628,6 +628,10 @@ class SAAxisTask(
 
         saaxis_results_url = SAAxisTask.get_results_url(scan=scan)
 
+        if not os.path.exists(saaxis_results_url.file_path()):
+            _logger.error("no result saved")
+            return
+
         # save it to the file
         with HDF5File(saaxis_results_url.file_path(), mode="a") as h5f:
             nx_process = h5f.require_group(saaxis_results_url.data_path())

tomwer/core/process/reconstruction/tests/test_saaxis.py

@@ -3,9 +3,7 @@ from __future__ import annotations
 
 
 import os
-import shutil
-import tempfile
-import unittest
+import pytest
 
 import numpy
 
@@ -18,74 +16,66 @@ from tomwer.core.process.reconstruction.scores.scores import (
 from tomwer.core.utils.scanutils import MockNXtomo
 
 
-class TestScoreFunctions(unittest.TestCase):
-    """Test all the score functions"""
+def test_img_contrast_std_score():
+    """simple test of the API to call compute_score_contrast_std"""
+    data = numpy.random.random(100 * 100).reshape(100, 100)
+    compute_score_contrast_std(data)
 
-    def test_img_contrast_std_score(self):
-        """simple test of the API to call compute_score_contrast_std"""
-        data = numpy.random.random(100 * 100).reshape(100, 100)
-        compute_score_contrast_std(data)
 
-    def test_method_to_function(self):
-        """Test the dictionary used to for linking the score method to the
-        callback function"""
-        data = numpy.random.random(100 * 100).reshape(100, 100)
-        for method_name, fct in _METHOD_TO_FCT.items():
-            with self.subTest(method_name=method_name, fct=fct):
-                res = fct(data)
-                self.assertFalse(res is None)
-                self.assertTrue(isinstance(res, float))
+@pytest.mark.parametrize("fct", _METHOD_TO_FCT.values())
+def test_method_to_function(fct):
+    """Test the dictionary used to for linking the score method to the
+    callback function"""
+    data = numpy.random.random(100 * 100).reshape(100, 100)
+    res = fct(data)
+    assert res is not None
+    assert isinstance(res, float)
 
 
-class TestSAAxisProcess(unittest.TestCase):
+def testSAAxisProcess(tmp_path):
     """Test the SAAxisProcess class"""
+    scan_path = tmp_path / "mock_nxtomo"
+    scan_path.mkdir()
+    # set up
+    dim = 10
+    mock = MockNXtomo(
+        scan_path=scan_path, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
+    )
+    mock.add_alignment_radio(index=10, angle=90)
+    mock.add_alignment_radio(index=10, angle=0)
+    scan = mock.scan
 
-    def setUp(self) -> None:
-        self.tempdir = tempfile.mkdtemp()
-        dim = 10
-        mock = MockNXtomo(
-            scan_path=self.tempdir, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
-        )
-        mock.add_alignment_radio(index=10, angle=90)
-        mock.add_alignment_radio(index=10, angle=0)
-        self.scan = mock.scan
+    default_saaxis_params = SAAxisParams()
+    default_saaxis_params.output_dir = os.path.join(scan_path, "output_dir")
+    default_saaxis_params.slice_indexes = {"slice": 4}
+    default_saaxis_params.nabu_config = {}
+    default_saaxis_params.dry_run = True
+    default_saaxis_params.file_format = "hdf5"
 
-        self._default_saaxis_params = SAAxisParams()
-        self._default_saaxis_params.output_dir = os.path.join(
-            self.tempdir, "output_dir"
-        )
-        self._default_saaxis_params.slice_indexes = {"slice": 4}
-        self._default_saaxis_params.nabu_config = {}
-        self._default_saaxis_params.dry_run = True
-        self._default_saaxis_params.file_format = "hdf5"
+    # test processing
+    process = SAAxisTask(
+        inputs={
+            "data": scan,
+            "sa_axis_params": default_saaxis_params.to_dict(),
+            "serialize_output_data": False,
+        }
+    )
 
-    def tearDown(self) -> None:
-        shutil.rmtree(self.tempdir)
-
-    def test(self):
-        process = SAAxisTask(
-            inputs={
-                "data": self.scan,
-                "sa_axis_params": self._default_saaxis_params.to_dict(),
-                "serialize_output_data": False,
-            }
-        )
-
-        self._default_saaxis_params.estimated_cor = 11
-        self._default_saaxis_params.research_width = 2
-        process = SAAxisTask(
-            inputs={
-                "data": self.scan,
-                "sa_axis_params": self._default_saaxis_params.to_dict(),
-                "serialize_output_data": False,
-            },
-        )
-        process.run()
-        process = SAAxisTask(
-            inputs={
-                "data": self.scan,
-                "sa_axis_params": self._default_saaxis_params.to_dict(),
-                "serialize_output_data": False,
-            },
-        )
-        process.run()
+    default_saaxis_params.estimated_cor = 11
+    default_saaxis_params.research_width = 2
+    process = SAAxisTask(
+        inputs={
+            "data": scan,
+            "sa_axis_params": default_saaxis_params.to_dict(),
+            "serialize_output_data": False,
+        },
+    )
+    process.run()
+    process = SAAxisTask(
+        inputs={
+            "data": scan,
+            "sa_axis_params": default_saaxis_params.to_dict(),
+            "serialize_output_data": False,
+        },
+    )
+    process.run()

tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py

@@ -9,8 +9,6 @@ from tomwer.gui.reconstruction.nabu.nabuconfig import base
 from tomwer.gui.utils.illustrations import _IllustrationWidget
 from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel
 
-from .reconstruction import AnglesFileWidget as Filewidget
-
 
 def nabu_param_ligne_to_dict(str_ligne: str) -> dict:
     ddict = {}
@@ -324,10 +322,6 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
         self._geometryWidget = CTFGeometry(parent=self, title="geometry")
         self.layout().addRow(self._geometryWidget)
         self.registerWidget(self._geometryWidget, "optional")
-        # translation file
-        self._translationFile = Filewidget(self)
-        self.layout().addRow("translation file", self._translationFile)
-        self.registerWidget(self._translationFile, "optional")
         # advanced parameters
         self._advancedParamsWidget = CTFAdvancedParams(
             parent=self, title="advanced parameters"
@@ -338,7 +332,6 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
         # connect signal / slot
         self._geometryWidget.sigConfChanged.connect(self._confChanged)
         self._advancedParamsWidget.sigConfChanged.connect(self._confChanged)
-        self._translationFile._qle.textEdited.connect(self._confChanged)
 
     def _confChanged(self, *args, **kwargs):
         self.sigConfChanged.emit("phase")
@@ -346,11 +339,8 @@ class CTFConfig(qt.QGroupBox, base._NabuStageConfigBase):
     def getConfiguration(self) -> dict:
         ddict = self._geometryWidget.getConfiguration()
         ddict.update(self._advancedParamsWidget.getConfiguration())
-        ddict["ctf_translations_file"] = self._translationFile.getFile()
         return ddict
 
     def setConfiguration(self, ddict):
         self._geometryWidget.setConfiguration(ddict=ddict)
         self._advancedParamsWidget.setConfiguration(ddict=ddict)
-        if "ctf_translations_file" in ddict:
-            self._translationFile.setFile(ddict["ctf_translations_file"])

tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -221,7 +221,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self._signalConfChanged("flatfield")
 
     def _dffChanged(self, *args, **kwargs):
-        self._signalConfChanged("double_flatfield_enabled")
+        self._signalConfChanged("double_flatfield")
 
     def _dffSigmaChanged(self, *args, **kwargs):
         self._signalConfChanged("dff_sigma")
@@ -337,7 +337,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         tilt_correction, autotilt_opts = self._tiltCorrection.getTiltCorrection()
         return {
             "flatfield": int(self.isFlatFieldActivate()),
-            "double_flatfield_enabled": int(self.isDoubleFlatFieldActivate()),
+            "double_flatfield": int(self.isDoubleFlatFieldActivate()),
             "dff_sigma": self.getDFFSigma(),
             "ccd_filter_enabled": int(self.isCCDFilterActivate()),
             "ccd_filter_threshold": self.getCCDThreshold(),
@@ -365,7 +365,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         if ff is not None:
             self._flatFieldCB.setChecked(bool(ff))
 
-        dff = conf.get("double_flatfield_enabled", None)
+        dff = conf.get("double_flatfield", None)
         if dff is not None:
             self._dffCB.setChecked(bool(dff))
 

tomwer/gui/reconstruction/nabu/nabuconfig/tests/test_NabuConfiguration.py

@@ -0,0 +1,42 @@
+from __future__ import annotations
+
+from tomwer.tests.conftest import qtapp  # noqa F401
+from tomwer.gui.reconstruction.nabu.nabuconfig.nabuconfig import (
+    NabuConfiguration,
+)
+from nabu.pipeline.config import _extract_nabuconfig_keyvals
+from nabu.pipeline.fullfield.nabu_config import (
+    nabu_config as nabu_fullfield_default_config,
+)
+
+
+def test_NabuConfiguration(
+    qtapp,  # noqa F811
+):
+    """Test that the 'NabuConfiguration' produce only keys understandable by nabu"""
+    widget = NabuConfiguration(parent=None)
+
+    tomwer_config = widget.getConfiguration()
+    nabu_config = _extract_nabuconfig_keyvals(nabu_fullfield_default_config)
+
+    tomwer_section_keys = set(tomwer_config.keys())
+    nabu_section_keys = set(nabu_config.keys())
+    tomwer_section_keys.remove("tomwer_slices")
+    assert tomwer_section_keys.issubset(
+        nabu_section_keys
+    ), f"tomwer provide sections undefined by nabu: {tomwer_section_keys - nabu_section_keys}"
+
+    for section_key in nabu_config.keys():
+        if section_key in tomwer_config:
+            nabu_sub_section_keys = set(nabu_config[section_key].keys())
+            tomwer_sub_section_keys = set(tomwer_config[section_key].keys())
+            if section_key == "phase":
+                # this key is pop by tomwer before calling nabu. It is used internally only
+                tomwer_sub_section_keys.remove("beam_shape")
+            elif section_key == "reconstruction":
+                tomwer_sub_section_keys.remove("slice_plane")
+            elif section_key == "output":
+                tomwer_sub_section_keys.remove("output_dir_mode")
+            assert tomwer_sub_section_keys.issubset(
+                nabu_sub_section_keys
+            ), f"tomwer provides keys undefined by nabu: {tomwer_sub_section_keys - nabu_sub_section_keys}"

tomwer/gui/reconstruction/nabu/slices.py

@@ -323,7 +323,7 @@ class NabuWindow(qt.QMainWindow):
         self._mainWidget.nabuSettingsWidget._configuration._preProcessingWidget._sinoRingsOpts.resetConfiguration()
         default_config["tomwer_slices"] = "middle"
         default_config["preproc"]["ccd_filter_enabled"] = False
-        default_config["preproc"]["double_flatfield_enabled"] = False
+        default_config["preproc"]["double_flatfield"] = False
         default_config["preproc"]["flatfield"] = True
         default_config["preproc"]["take_logarithm"] = True
         self.setConfiguration(default_config)

tomwer/gui/reconstruction/nabu/test/test_ctf.py

@@ -29,12 +29,10 @@ class TestFutureSupervisorOW(TestCaseQt):
         assert config == {
             "ctf_geometry": " z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
-            "ctf_translations_file": "",
             "beam_shape": "parallel",
         }
 
         config["beam_shape"] = "cone"
-        config["ctf_translations_file"] = "my_file.txt"
         config["ctf_geometry"] = (
             " z1_v=10.2; z1_h=3.6; detec_pixel_size=1e-05; magnification=False"
         )

tomwer/gui/reconstruction/sacommon.py

@@ -87,7 +87,7 @@ class NabuWidgetWithToolbar(qt.QMainWindow):
         self._nabuSettings._configuration._preProcessingWidget._sinoRingsOpts.resetConfiguration()
         default_config["tomwer_slices"] = "middle"
         default_config["preproc"]["ccd_filter_enabled"] = False
-        default_config["preproc"]["double_flatfield_enabled"] = False
+        default_config["preproc"]["double_flatfield"] = False
         default_config["preproc"]["flatfield"] = True
         default_config["preproc"]["take_logarithm"] = True
         self._nabuSettings.setConfiguration(default_config)

tomwer/gui/reconstruction/tests/test_nabu.py

@@ -90,7 +90,7 @@ class TestNabuPreProcConfig(TestCaseQt):
         """Test that the get configuration is working"""
         ini_conf = {
             "flatfield": 1,
-            "double_flatfield_enabled": 0,
+            "double_flatfield": 0,
             "dff_sigma": 0.0,
             "ccd_filter_enabled": 0,
             "ccd_filter_threshold": 0.04,
@@ -110,7 +110,7 @@ class TestNabuPreProcConfig(TestCaseQt):
         """Test that the set configuration is working"""
         conf = {
             "flatfield": 0,
-            "double_flatfield_enabled": 1,
+            "double_flatfield": 1,
             "dff_sigma": 2.0,
             "ccd_filter_enabled": 1,
             "ccd_filter_threshold": 0.98,
@@ -150,7 +150,6 @@ class TestNabuPhaseConfig(TestCaseQt):
             "beam_shape": "parallel",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
             "ctf_geometry": " z1_v=None; z1_h=None; detec_pixel_size=None; magnification=True",
-            "ctf_translations_file": "",
         }
         self.assertEqual(self.nabuWidget.getConfiguration(), ini_conf)
 
@@ -165,7 +164,6 @@ class TestNabuPhaseConfig(TestCaseQt):
             "beam_shape": "cone",
             "ctf_advanced_params": " length_scale=1e-05; lim1=1e-05; lim2=0.2; normalize_by_mean=True",
             "ctf_geometry": " z1_v=0.0; z1_h=0.0; detec_pixel_size=None; magnification=True",
-            "ctf_translations_file": "",
         }
         self.nabuWidget.setConfiguration(conf)
         self.nabuWidget.show()

tomwer/gui/utils/buttons.py

@@ -111,7 +111,7 @@ class TapeMeasureToolButton(PlotToolButton):
             self._lastRoiCreated.setVisible(self.isChecked())
         if self.isChecked():
             self._roiManager.start(
-                self.TapeMeasureROI,
+                TapeMeasureROI,
                 self,
             )
             self.__interactiveModeStarted(self._roiManager)

tomwer/synctools/stacks/processingstack.py

@@ -17,6 +17,9 @@ class ProcessingThread(qt.QThread):
     sigComputationStarted = qt.Signal()
     """Signal emitted when a computation is started"""
 
+    sigError = qt.Signal(str)
+    """Error found during processing. Parameter is the error raised"""
+
 
 class FIFO(SuperviseProcess):
     """Processing Queue with a First In, First Out behavior"""
@@ -29,17 +32,22 @@ class FIFO(SuperviseProcess):
 
     def __init__(self, process_id=None):
         SuperviseProcess.__init__(self, process_id=process_id)
+        self._errors: list[qt.QErrorMessage] = []
         self._deque = deque()
         self._computationThread = self._create_processing_thread(process_id=process_id)
         assert isinstance(self._computationThread, ProcessingThread)
-        self._computationThread.sigComputationStarted.connect(
-            self._start_threaded_computation
-        )
+
         """scan process by the thread"""
         self._data_currently_computed = None
         """Scan computed currently"""
         self._processing = False
 
+        # connect signal / slot
+        self._computationThread.sigComputationStarted.connect(
+            self._start_threaded_computation
+        )
+        self._computationThread.sigError.connect(self._displayError)
+
     @property
     def data_currently_computed(self) -> TomwerObject | None:
         return self._data_currently_computed
@@ -146,6 +154,14 @@ class FIFO(SuperviseProcess):
         self._processing = False
         self._data_currently_computed = None
 
+    def _displayError(self, error_msg: str):
+        err = qt.QMessageBox()
+        err.setText(error_msg)
+        err.setIcon(qt.QMessageBox.Warning)
+        self._errors.append(err)
+        err.setModal(False)
+        err.show()
+
     # expose deque API
     def append(self, value):
         self._deque.append(value)

tomwer/synctools/stacks/reconstruction/nabu.py

@@ -6,6 +6,7 @@ import logging
 
 from processview.core.manager import DatasetState, ProcessManager
 from processview.core.superviseprocess import SuperviseProcess
+
 from silx.gui import qt
 from silx.gui.utils import blockSignals
 
@@ -138,6 +139,7 @@ class _SliceProcessingThread(ProcessingThread, SuperviseProcess):
                 "nabu_params": self._configuration,
                 "dry_run": self._dry_run,
                 "serialize_output_data": False,
+                "invalid_slice_callback": self.showErrorSliceInvalid,
             },
         )
         self._task.run()
@@ -148,6 +150,9 @@ class _SliceProcessingThread(ProcessingThread, SuperviseProcess):
             self._task.cancel()
         self.quit()
 
+    def showErrorSliceInvalid(self, error_message):
+        self.sigError.emit(error_message)
+
 
 class _VolumeProcessingThread(_SliceProcessingThread):
     """

tomwer/version.py

@@ -77,9 +77,9 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 5
-MICRO = 0
-RELEV = "rc"  # <16
-SERIAL = 3  # <16
+MICRO = 2
+RELEV = "final"  # <16
+SERIAL = 0  # <16
 
 date = __date__
 

{tomwer-1.5.0rc3.dist-info → tomwer-1.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.5.0rc3
+Version: 1.5.2
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -25,12 +25,11 @@ Requires-Dist: numpy
 Requires-Dist: setuptools
 Requires-Dist: psutil
 Requires-Dist: silx[full]>=2.1.1
-Requires-Dist: tomoscan>=2.2.0a6
+Requires-Dist: tomoscan[full_no_compression_plugins]>=2.2.0a6
 Requires-Dist: nxtomo>=2.0.0dev2
 Requires-Dist: nxtomomill>=1.2.0dev1
 Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
-Requires-Dist: ewokscore<1.1.0
 Requires-Dist: sluurp>=0.4.1
 Requires-Dist: packaging
 Requires-Dist: pint
@@ -39,83 +38,63 @@ Provides-Extra: full-base
 Requires-Dist: orange-canvas-core; extra == "full-base"
 Requires-Dist: orange-widget-base; extra == "full-base"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-base"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-base"
+Requires-Dist: ewoksorange==1.1; extra == "full-base"
 Requires-Dist: rsyncmanager; extra == "full-base"
 Requires-Dist: fabio; extra == "full-base"
-Requires-Dist: h5py>=3; extra == "full-base"
-Requires-Dist: lxml; extra == "full-base"
 Requires-Dist: werkzeug; extra == "full-base"
 Requires-Dist: json-rpc; extra == "full-base"
 Requires-Dist: scipy; extra == "full-base"
 Requires-Dist: Pillow; extra == "full-base"
-Requires-Dist: glymur<0.14; extra == "full-base"
 Requires-Dist: resource; extra == "full-base"
-Requires-Dist: tifffile; extra == "full-base"
 Requires-Dist: hdf5plugin; extra == "full-base"
 Requires-Dist: pyicat_plus; extra == "full-base"
 Requires-Dist: ewoksnotify[full]; extra == "full-base"
-Requires-Dist: pyicat_plus; extra == "full-base"
 Provides-Extra: full-no-nabu
 Requires-Dist: orange-canvas-core; extra == "full-no-nabu"
 Requires-Dist: orange-widget-base; extra == "full-no-nabu"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-nabu"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-nabu"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-nabu"
 Requires-Dist: rsyncmanager; extra == "full-no-nabu"
 Requires-Dist: fabio; extra == "full-no-nabu"
-Requires-Dist: h5py>=3; extra == "full-no-nabu"
-Requires-Dist: lxml; extra == "full-no-nabu"
 Requires-Dist: werkzeug; extra == "full-no-nabu"
 Requires-Dist: json-rpc; extra == "full-no-nabu"
 Requires-Dist: scipy; extra == "full-no-nabu"
 Requires-Dist: Pillow; extra == "full-no-nabu"
-Requires-Dist: glymur<0.14; extra == "full-no-nabu"
 Requires-Dist: resource; extra == "full-no-nabu"
-Requires-Dist: tifffile; extra == "full-no-nabu"
 Requires-Dist: hdf5plugin; extra == "full-no-nabu"
 Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-nabu"
-Requires-Dist: pyicat_plus; extra == "full-no-nabu"
 Provides-Extra: full-no-cuda
 Requires-Dist: orange-canvas-core; extra == "full-no-cuda"
 Requires-Dist: orange-widget-base; extra == "full-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "full-no-cuda"
 Requires-Dist: rsyncmanager; extra == "full-no-cuda"
 Requires-Dist: fabio; extra == "full-no-cuda"
-Requires-Dist: h5py>=3; extra == "full-no-cuda"
-Requires-Dist: lxml; extra == "full-no-cuda"
 Requires-Dist: werkzeug; extra == "full-no-cuda"
 Requires-Dist: json-rpc; extra == "full-no-cuda"
 Requires-Dist: scipy; extra == "full-no-cuda"
 Requires-Dist: Pillow; extra == "full-no-cuda"
-Requires-Dist: glymur<0.14; extra == "full-no-cuda"
 Requires-Dist: resource; extra == "full-no-cuda"
-Requires-Dist: tifffile; extra == "full-no-cuda"
 Requires-Dist: hdf5plugin; extra == "full-no-cuda"
 Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "full-no-cuda"
-Requires-Dist: pyicat_plus; extra == "full-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "full-no-cuda"
 Provides-Extra: full
 Requires-Dist: orange-canvas-core; extra == "full"
 Requires-Dist: orange-widget-base; extra == "full"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "full"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "full"
+Requires-Dist: ewoksorange==1.1; extra == "full"
 Requires-Dist: rsyncmanager; extra == "full"
 Requires-Dist: fabio; extra == "full"
-Requires-Dist: h5py>=3; extra == "full"
-Requires-Dist: lxml; extra == "full"
 Requires-Dist: werkzeug; extra == "full"
 Requires-Dist: json-rpc; extra == "full"
 Requires-Dist: scipy; extra == "full"
 Requires-Dist: Pillow; extra == "full"
-Requires-Dist: glymur<0.14; extra == "full"
 Requires-Dist: resource; extra == "full"
-Requires-Dist: tifffile; extra == "full"
 Requires-Dist: hdf5plugin; extra == "full"
 Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: ewoksnotify[full]; extra == "full"
-Requires-Dist: pyicat_plus; extra == "full"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "full"
 Requires-Dist: pycuda<2024.1.1; extra == "full"
 Requires-Dist: scikit-cuda; extra == "full"
@@ -123,22 +102,17 @@ Provides-Extra: doc
 Requires-Dist: orange-canvas-core; extra == "doc"
 Requires-Dist: orange-widget-base; extra == "doc"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "doc"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "doc"
+Requires-Dist: ewoksorange==1.1; extra == "doc"
 Requires-Dist: rsyncmanager; extra == "doc"
 Requires-Dist: fabio; extra == "doc"
-Requires-Dist: h5py>=3; extra == "doc"
-Requires-Dist: lxml; extra == "doc"
 Requires-Dist: werkzeug; extra == "doc"
 Requires-Dist: json-rpc; extra == "doc"
 Requires-Dist: scipy; extra == "doc"
 Requires-Dist: Pillow; extra == "doc"
-Requires-Dist: glymur<0.14; extra == "doc"
 Requires-Dist: resource; extra == "doc"
-Requires-Dist: tifffile; extra == "doc"
 Requires-Dist: hdf5plugin; extra == "doc"
 Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: ewoksnotify[full]; extra == "doc"
-Requires-Dist: pyicat_plus; extra == "doc"
 Requires-Dist: nabu>=2023.3.1dev; extra == "doc"
 Requires-Dist: Sphinx>=4.0.0; extra == "doc"
 Requires-Dist: nbsphinx; extra == "doc"
@@ -157,22 +131,17 @@ Provides-Extra: dev
 Requires-Dist: orange-canvas-core; extra == "dev"
 Requires-Dist: orange-widget-base; extra == "dev"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev"
+Requires-Dist: ewoksorange==1.1; extra == "dev"
 Requires-Dist: rsyncmanager; extra == "dev"
 Requires-Dist: fabio; extra == "dev"
-Requires-Dist: h5py>=3; extra == "dev"
-Requires-Dist: lxml; extra == "dev"
 Requires-Dist: werkzeug; extra == "dev"
 Requires-Dist: json-rpc; extra == "dev"
 Requires-Dist: scipy; extra == "dev"
 Requires-Dist: Pillow; extra == "dev"
-Requires-Dist: glymur<0.14; extra == "dev"
 Requires-Dist: resource; extra == "dev"
-Requires-Dist: tifffile; extra == "dev"
 Requires-Dist: hdf5plugin; extra == "dev"
 Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: ewoksnotify[full]; extra == "dev"
-Requires-Dist: pyicat_plus; extra == "dev"
 Requires-Dist: nabu[full]>=2023.3.1dev; extra == "dev"
 Requires-Dist: pycuda<2024.1.1; extra == "dev"
 Requires-Dist: scikit-cuda; extra == "dev"
@@ -184,22 +153,17 @@ Provides-Extra: dev-no-cuda
 Requires-Dist: orange-canvas-core; extra == "dev-no-cuda"
 Requires-Dist: orange-widget-base; extra == "dev-no-cuda"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev-no-cuda"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "dev-no-cuda"
+Requires-Dist: ewoksorange==1.1; extra == "dev-no-cuda"
 Requires-Dist: rsyncmanager; extra == "dev-no-cuda"
 Requires-Dist: fabio; extra == "dev-no-cuda"
-Requires-Dist: h5py>=3; extra == "dev-no-cuda"
-Requires-Dist: lxml; extra == "dev-no-cuda"
 Requires-Dist: werkzeug; extra == "dev-no-cuda"
 Requires-Dist: json-rpc; extra == "dev-no-cuda"
 Requires-Dist: scipy; extra == "dev-no-cuda"
 Requires-Dist: Pillow; extra == "dev-no-cuda"
-Requires-Dist: glymur<0.14; extra == "dev-no-cuda"
 Requires-Dist: resource; extra == "dev-no-cuda"
-Requires-Dist: tifffile; extra == "dev-no-cuda"
 Requires-Dist: hdf5plugin; extra == "dev-no-cuda"
 Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: ewoksnotify[full]; extra == "dev-no-cuda"
-Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
 Requires-Dist: nabu>=2023.3.1dev; extra == "dev-no-cuda"
 Requires-Dist: black; extra == "dev-no-cuda"
 Requires-Dist: flake8; extra == "dev-no-cuda"
@@ -209,22 +173,17 @@ Provides-Extra: test
 Requires-Dist: orange-canvas-core; extra == "test"
 Requires-Dist: orange-widget-base; extra == "test"
 Requires-Dist: ewoks[orange]>=0.1.1; extra == "test"
-Requires-Dist: ewoksorange>=0.7.0rc0; extra == "test"
+Requires-Dist: ewoksorange==1.1; extra == "test"
 Requires-Dist: rsyncmanager; extra == "test"
 Requires-Dist: fabio; extra == "test"
-Requires-Dist: h5py>=3; extra == "test"
-Requires-Dist: lxml; extra == "test"
 Requires-Dist: werkzeug; extra == "test"
 Requires-Dist: json-rpc; extra == "test"
 Requires-Dist: scipy; extra == "test"
 Requires-Dist: Pillow; extra == "test"
-Requires-Dist: glymur<0.14; extra == "test"
 Requires-Dist: resource; extra == "test"
-Requires-Dist: tifffile; extra == "test"
 Requires-Dist: hdf5plugin; extra == "test"
 Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: ewoksnotify[full]; extra == "test"
-Requires-Dist: pyicat_plus; extra == "test"
 Requires-Dist: nabu>=2023.3.1dev; extra == "test"
 Requires-Dist: pytest-asyncio; extra == "test"
 Requires-Dist: tomoscan[test]>=2.2.0a6; extra == "test"

{tomwer-1.5.0rc3.dist-info → tomwer-1.5.2.dist-info}/RECORD

@@ -18,15 +18,16 @@ orangecontrib/tomwer/tutorials/simple_slice_reconstruction.ows,sha256=O9Bnunjh0Q
 orangecontrib/tomwer/tutorials/simple_slice_reconstruction_on_slurm.ows,sha256=t-fwTMCvqQV17AIZWM0lSCmjC6loLEHNZSFmAADF9xY,6584
 orangecontrib/tomwer/tutorials/simple_volume_local_reconstruction.ows,sha256=mhvCyFqXnFznRPaTG6wgjpxkte8n_SOzg3W8yJkWy1s,7025
 orangecontrib/tomwer/tutorials/simple_volume_to_slurm_reconstruction.ows,sha256=jHOERmyBFo7NmmmOUO6KroAfvyAD8ds92lkl0g73C-8,9830
+orangecontrib/tomwer/tutorials/untitled.ows,sha256=dBokmKHOdqZqHTrZqrZgjBg7xzQacKWUXBjY7lTaYVU,2731
 orangecontrib/tomwer/tutorials/using_saaxis_to_find_cor.ows,sha256=TUZNkXEsQyj7Qra1GEb4IhGFDWv3uJzqXbp3P04jwbs,5192
 orangecontrib/tomwer/tutorials/volume_casting_on_slurm.ows,sha256=yKa6pvd4UB6XDDlj_o7T8Md6bI8aQJXMCUnxyecdXbc,7568
 orangecontrib/tomwer/tutorials/id16b/ID16b_full_volume.ows,sha256=eSxYxrZ-0WKsmDqXivsHxND7SR2dSwdgG6Wcjbr06Ew,1727
-orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows,sha256=lmn7C0LQIzJpxVJjHajyPKfJZZSHSNBG2x8uxnv6Zg8,29566
-orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows,sha256=kFGXGxc3eW7iG5TcAxaOwEwh1cvsKZEO3T_cA3mrd1k,22602
+orangecontrib/tomwer/tutorials/id16b/ID16b_insitu.ows,sha256=sdo7YmzVUSBf61hsMUg7zOiGtDa21eitCx08fYY93LI,29558
+orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows,sha256=eufyC3wPbnzpUIQyno4mTrGXGtRayRFQbo0OAyYCds8,22594
 orangecontrib/tomwer/tutorials/id16b/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 orangecontrib/tomwer/widgets/__init__.py,sha256=dX_TpkBh3mVsrj3EeGglEESsnZAEVq7V0Nb9bnBrb-8,1214
 orangecontrib/tomwer/widgets/utils.py,sha256=yq1wZfpfY3iVAhwMRBls57q02lhljO89WRKN7MxMMNg,983
-orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py,sha256=zXjddYmkhyBnoRCstZ6AYN1mG84xiOKaIntg5tqe4jw,9927
+orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py,sha256=JodqMVgu2krTWmrPEPze0E_SinOyX7UghDDbbsN8dSE,10210
 orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py,sha256=O44AZGt7cC1KaAl4U9f78OuzKKMXOSm22voUodyvqnk,3003
 orangecontrib/tomwer/widgets/cluster/__init__.py,sha256=vOOJnIIaLWAj8tnxD9MRzWDyYgk-cyuBsN7QQ5FrIoQ,385
 orangecontrib/tomwer/widgets/cluster/icons/slurm.png,sha256=C-YBLwXCnh0oo4nvEt80WxX_jKYGUAFpWMUSlzt6ke0,1995
@@ -219,7 +220,7 @@ orangecontrib/tomwer/widgets/visualization/tests/__init__.py,sha256=47DEQpj8HBSa
 tomwer/__init__.py,sha256=cMIyH-uRxpa9WVnAuWjiBD7k9TK57WO21RzP_S-Mb8I,460
 tomwer/__main__.py,sha256=7tCADiS4u7k1PCxFhlRAcYSIOpxQTGUTx8sCEQ-hi1E,8707
 tomwer/utils.py,sha256=7h7dEgKAEUmQ43jkULvC1B9Adl55nkCty-SEKUKCl4U,7008
-tomwer/version.py,sha256=IOZpFmn_ZYCZdQ7uWHxTD8i-UUzpUH1YscQBAfHyqpY,4383
+tomwer/version.py,sha256=DKeug4r2Q7g-Ny4eovdPe5bCCM6RkITFNm8wikj1IUE,4386
 tomwer/app/__init__.py,sha256=h1FKED7Tw5f99yikygt7ruXsdrxQhcJxO7kagLGxhJg,84
 tomwer/app/axis.py,sha256=1TZU27QPhq6Sa5-1kRMr4VDv2Qntg4ZHTQOjwucXf4I,5842
 tomwer/app/canvas.py,sha256=y8rYOiwmv6ug7JcjgkOzEiGQnNXjKWNNmKofT0n8TFg,1538
@@ -245,7 +246,7 @@ tomwer/app/stopdatalistener.py,sha256=WADEHM5LHHjWP2HM-ru-RinXWzvV3PQv72E5Y1Xeio
 tomwer/app/ystitching.py,sha256=QvXUHBnmr3R--lTvd_RkjpXMAedbnpiC01bSD99_BPE,562
 tomwer/app/zstitching.py,sha256=pTV_ESnARpabvo038pSCuUoV0DjrPxKubIKfhjyIZZ0,562
 tomwer/app/canvas_launcher/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer/app/canvas_launcher/config.py,sha256=sLlsp7iy1s2IyxqvSohGbaOpPUP6syuj5P-8bvyPNzI,3952
+tomwer/app/canvas_launcher/config.py,sha256=vzpYdoPI0zP3uogwU5TLggDGQrSpw2ew-Fvs0-wjinU,4066
 tomwer/app/canvas_launcher/environ.py,sha256=ljQyPL_u9ai1CWmmq8uGHbn437CZWyX4uJtrDIyabGk,2453
 tomwer/app/canvas_launcher/mainwindow.py,sha256=KZzbY3AuHITdaS8K4jG2QomD5DEgQqHRYcIe9hymC9g,22283
 tomwer/app/canvas_launcher/splash.py,sha256=cpUuZVKwlQbeAWfAqjpjP4q1v1MmkfxU6WWllLSVZo8,508
@@ -336,12 +337,12 @@ tomwer/core/process/reconstruction/nabu/castvolume.py,sha256=yTdVMGjG8gnByNi7D1X
 tomwer/core/process/reconstruction/nabu/helical.py,sha256=twqUNAatBAAK2K0cTmqcWb4py_nHif6Vsr3ms6Pqbag,2051
 tomwer/core/process/reconstruction/nabu/nabucommon.py,sha256=GGhM3jl2OVbI2mr4-bMlMOyON2Ss0dEOU_v9SmixhTo,24532
 tomwer/core/process/reconstruction/nabu/nabuscores.py,sha256=fjOtWxPOoVHq5E1mkbpfVglWNq5HfP1VAzhaLu1jd1M,25291
-tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=CybiZOf0qATMeLkYyC_UuYVfReJku_-2BS0BQbq7xxs,32084
+tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=9w_DPooYn8l9rSGZJhYFmWlPO0L-DkuEKvKmb-Q9Sao,32648
 tomwer/core/process/reconstruction/nabu/nabuvolume.py,sha256=Fn0tkPDTDJQaMEJA4LzpPp0ZtG4MIu9YN82-jesxRKo,20052
 tomwer/core/process/reconstruction/nabu/plane.py,sha256=1SFNJgl1_cDYVW6gq7zjw2jpvRjiEmzzEQEBCxUseGM,380
 tomwer/core/process/reconstruction/nabu/settings.py,sha256=3AJpxVQbJziw4v6F26Ppz8Q9vc9ZNepTWygqpCAbIEM,955
 tomwer/core/process/reconstruction/nabu/target.py,sha256=I_7X2Nfr5VC4doaodtCzTeg7JVG1Lnbv123uI8AKEeU,111
-tomwer/core/process/reconstruction/nabu/utils.py,sha256=VLyF3JUBSCDOfOB4gtKuQoFr0ZwpbgeuJ1wZL5NZ4wM,16253
+tomwer/core/process/reconstruction/nabu/utils.py,sha256=YtcEj3pLYKjArklZD7cREsuafeNMjQ203VIR8Oeo-i4,16271
 tomwer/core/process/reconstruction/nabu/test/test_castvolume.py,sha256=yEqVFrmp8vVpiIuhASMR9bWLF3Cgnag2u8S_SaI8BSo,3985
 tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py,sha256=vmB02KUGcP_AyUEWuDByGm0UAOCDIHEhePfRV1UGQQg,15608
 tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py,sha256=5rHDwUROEBlsEFsZoy8mmcdRpziEetF9g_oFyxlvS6k,6010
@@ -350,7 +351,7 @@ tomwer/core/process/reconstruction/normalization/normalization.py,sha256=8rW9D6e
 tomwer/core/process/reconstruction/normalization/params.py,sha256=BqZPnaAeCi0CVkNxVKcS188oCb2y6RUxY-c5pLdOIDk,3374
 tomwer/core/process/reconstruction/saaxis/__init__.py,sha256=ZEOu0nZWlMyBoX_A64yeEjVflE5x4iWSpYLTgs45g0o,137
 tomwer/core/process/reconstruction/saaxis/params.py,sha256=tCV5QLu7jqLwmoRnUGCNxXgdXZ_WRRuuIxbmXG18mH0,4171
-tomwer/core/process/reconstruction/saaxis/saaxis.py,sha256=FDzM-N_kHvCbTe7rvt6tMYuC6slCG45t5ptadLcpfd8,30154
+tomwer/core/process/reconstruction/saaxis/saaxis.py,sha256=g3p8_cI1KTasAc4183pXKa22jwml-CfAbhwF8dvZLlo,30282
 tomwer/core/process/reconstruction/sadeltabeta/__init__.py,sha256=WDYJxfqPnz5IeLPCX5W8UEO8-Z-NSH79gkqp2DZn1bM,162
 tomwer/core/process/reconstruction/sadeltabeta/params.py,sha256=ziAlTtQLy4EItIprFxDOm2Td1emHpSpnQb58niF1tI0,2691
 tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py,sha256=bAO0dYSnMdgbBHlcU-roRC7sGqLIpi_rlC7cMXFInLI,29075
@@ -364,7 +365,7 @@ tomwer/core/process/reconstruction/tests/test_darkref.py,sha256=KkdZ4epw9fYOPT3e
 tomwer/core/process/reconstruction/tests/test_darkref_copy.py,sha256=Cl8qLAMZxLHDJp2oMDusr6q2WfALIg6mpbvuGyJJY7M,6090
 tomwer/core/process/reconstruction/tests/test_params_cache.py,sha256=mNqWbOLr4mo06mwF3KhFpQPRvGgFxsCTPhLlK-fF2Ro,1238
 tomwer/core/process/reconstruction/tests/test_paramsbase.py,sha256=n9x9BZV4I9uF7DM5QjCelfxaAzWQ6vx9N9BsjysW6RU,1505
-tomwer/core/process/reconstruction/tests/test_saaxis.py,sha256=yaxm2Iob6jhSxMdiHP-B093HOoKb6rfBoqPVxOsGMgU,2972
+tomwer/core/process/reconstruction/tests/test_saaxis.py,sha256=iuDJW3Wr5vbS19UZO49a7ohcJBX5vhQytzvOEPUusIQ,2362
 tomwer/core/process/reconstruction/tests/test_sadeltabeta.py,sha256=24JRMIocNYLMdX_xFgOCUUo_VA61BPzz3HTaRTzDFhE,1232
 tomwer/core/process/reconstruction/tests/test_utils.py,sha256=o_w8Bkk3T0btLCAan2UPq9U45y9vfh8ihyaHnZ7fEb0,1006
 tomwer/core/process/reconstruction/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -539,7 +540,7 @@ tomwer/gui/edit/tests/test_dkrf_patch.py,sha256=L0fO2nqqK74EOIZTPQKjO03qsAiXbqjj
 tomwer/gui/edit/tests/test_image_key_editor.py,sha256=6sIGM_DjU_KjspnVKB2UDhWh_BLDhYP8rS6U1fAZXkk,4647
 tomwer/gui/edit/tests/test_nx_editor.py,sha256=y4_-g1-8rj0NkhAZ9HeebH-CIcUrvrH3q-s2RnBRQMo,17501
 tomwer/gui/reconstruction/__init__.py,sha256=Ozf9bYay5hVhe1clExeM_MLhcAuu624i5BP1xonWlB0,95
-tomwer/gui/reconstruction/sacommon.py,sha256=8-xaFjmtvxzJSWRLl985IcaCYVXQ_Kq-Rp91nYoW0Pc,5990
+tomwer/gui/reconstruction/sacommon.py,sha256=1ZT51WRkajkWsyaJmnH1Fi2QxHzyEa8Pqf7DAyF47lQ,5982
 tomwer/gui/reconstruction/axis/AxisMainWindow.py,sha256=7w2LhdQ1pa8vU9U-XTA3ohGQfYKk5ETZ79s_xl4Zxx8,9641
 tomwer/gui/reconstruction/axis/AxisOptionsWidget.py,sha256=M47xflZ68KkTDg8tksFt8n7ZFVIr8tJxstlPyG4Odq0,12168
 tomwer/gui/reconstruction/axis/AxisSettingsWidget.py,sha256=7GpHteE2j9RUo-jUQoJdXJ-GnIi9VnY13Lveq3mvd1M,28120
@@ -561,20 +562,22 @@ tomwer/gui/reconstruction/nabu/check.py,sha256=5DYLlVCyXm3ax5VgogX79n1Oyl3O_JUvZ
 tomwer/gui/reconstruction/nabu/helical.py,sha256=TAVPcuZdgtZSz37ESqi_yuLhYuNnGde_0drvjTntahs,3708
 tomwer/gui/reconstruction/nabu/nabuflow.py,sha256=mnFFd9z7IC9FFZ3xcOr-6g2hvY0R7PtnFI-AMgWqHhI,14977
 tomwer/gui/reconstruction/nabu/platform.py,sha256=eSPs2yUfBSHsqZ8bYY_BJ7zuRXc5sxXA4lRxlQaFBz0,3859
-tomwer/gui/reconstruction/nabu/slices.py,sha256=fnWfbF2O7f5D4WOVcx4L1pu9WVRN_4A_122b8R-R_48,24291
+tomwer/gui/reconstruction/nabu/slices.py,sha256=fDvYrDDvwYmXFmjEKU4zv3NdkUciPYM4rqteSb9pQD8,24283
 tomwer/gui/reconstruction/nabu/slurm.py,sha256=yfJD8KgX45Be5CUi6bn2CdocrQemJPxDYBBqoLoXqn0,1268
 tomwer/gui/reconstruction/nabu/volume.py,sha256=OGstMDOd7DHY0PVUJdPRxOtSH7SaJyy7VNWU1F6ci6g,17826
 tomwer/gui/reconstruction/nabu/nabuconfig/__init__.py,sha256=WgEFXIrUDhX0vpBNlKiymHEY9p1DMdk4QZkvnXIC8yk,77
 tomwer/gui/reconstruction/nabu/nabuconfig/base.py,sha256=7jB8VKVk5zt2QP4z1Vx2k7vLfPN5jjeGnCL_dLXr1J4,2133
-tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py,sha256=_2eDt-Y5LaJ5J0Q2wm0sIFQuSHXYjPqQGYC28Iqr4LE,13095
+tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py,sha256=6zFiWhaJcJAWsZS0-djZ3HUROxUGHKa0Zw_XTsDvN10,12559
 tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py,sha256=5tCkwvgCv_Rdt7yP4ZUrq9ZGKE7Yy9Ht-n7XvCGIoTw,9048
 tomwer/gui/reconstruction/nabu/nabuconfig/output.py,sha256=0SShYqvFj-motxTw20e3I1Z0WiierSqgOsN15qwe-TY,11907
 tomwer/gui/reconstruction/nabu/nabuconfig/phase.py,sha256=t4rVi6DCwRkrfGv_9hD1SWMwu9CMpzxjAwyH_YmC3Gw,16238
-tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py,sha256=3FME_SNO-cvek-hzuhh87cesuH3cdfqBI8w-fgwBO4U,32556
+tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py,sha256=utJgcburzX_WNdXItAKuENd97oLIs4QzFmLrNUF0n3c,32532
 tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py,sha256=W0EXvvEgtlOtxgg7CjsSj2aTjfpRwYfQ_I1fDX0cPxE,42571
+tomwer/gui/reconstruction/nabu/nabuconfig/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tomwer/gui/reconstruction/nabu/nabuconfig/tests/test_NabuConfiguration.py,sha256=xORtyJ9I4UDC_COEA2RMqvEAARLLorZFkwZoeuDa67c,1811
 tomwer/gui/reconstruction/nabu/test/test_cast_volume.py,sha256=Gtz_LduqKQNiVuVYrvtoPkE-DgG9QotS1mK-siSl8HU,3451
 tomwer/gui/reconstruction/nabu/test/test_check.py,sha256=KXg1Gg4FVjQ9GkBOgb0ZJh6_c3JMeJTtyX5UVY6vdms,2318
-tomwer/gui/reconstruction/nabu/test/test_ctf.py,sha256=uiJznrY6ScH51xaaSUFfplg9XJcFacczIV8_7k9tuRg,1554
+tomwer/gui/reconstruction/nabu/test/test_ctf.py,sha256=9LaonqdG7kp1Tst_kzTnVp9HCCGQjxo1vIKWj1zCFiY,1457
 tomwer/gui/reconstruction/nabu/test/test_helical.py,sha256=6vB_xXJOuNPHbXKLw8JWUtl-BB-Ntm8xkNEMV08ocEM,754
 tomwer/gui/reconstruction/nabu/test/test_nabu_preprocessing.py,sha256=OcTJ6-GQrIMETlezvJ7HlWE7_eWMKdfbfueohl_lZ-c,2258
 tomwer/gui/reconstruction/normalization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -592,7 +595,7 @@ tomwer/gui/reconstruction/scores/control.py,sha256=SVWMruB--sa_LSM1oZhjoFM5ci1oQ
 tomwer/gui/reconstruction/scores/scoreplot.py,sha256=_mHvuc8EoSgEFiQkDJM9p21CLkgLe3c3d-bvPfQ0mFc,31166
 tomwer/gui/reconstruction/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/gui/reconstruction/tests/test_axis.py,sha256=h0u_tTnQp57rg4oFtwjGSYNw5IujoxydOpnvNd98INA,7498
-tomwer/gui/reconstruction/tests/test_nabu.py,sha256=MRSxOYRbiZQ4P3jvSj_YMQofK5y_IgHNIb6TmuLFqAc,13644
+tomwer/gui/reconstruction/tests/test_nabu.py,sha256=MbyaQcRYGOs20fO3sUY-KPHhOoRzXpEPrx_jCjKwLiA,13546
 tomwer/gui/reconstruction/tests/test_saaxis.py,sha256=dQjhULF913WMevo0ePIy6JQbnrP6zGVnde9XLRLBtFM,6792
 tomwer/gui/reconstruction/tests/test_sadeltabeta.py,sha256=96tE_gxIcmp0qDXQmIwSEkYl3Js7dT2CyUH1doyjGc0,4491
 tomwer/gui/samplemoved/__init__.py,sha256=jNA03mYWfP3_S1MRet6ijYe5DNCTK3Br7-5yrW3oEG4,8240
@@ -635,7 +638,7 @@ tomwer/gui/tests/test_axis_gui.py,sha256=7Sz7LKTADuRCxaPYFGes22-0AItYwfrcd6kgk4X
 tomwer/gui/tests/test_qfolder_dialog.py,sha256=hwN7uEDUYoGsHeJgjTvgMLV21umt_LTIemDsUTU2UvA,352
 tomwer/gui/utils/RangeWidget.py,sha256=HERjGePh_LxkJEELt2ZVOL_D8G_0xmaP4OotZlASPEo,1327
 tomwer/gui/utils/__init__.py,sha256=zRGvzYC0R676iDAjHIERQJlV4YgTcsXc3G34f6cUCK8,66
-tomwer/gui/utils/buttons.py,sha256=SAkd82M7jLYeSnUZ1E5IyIqQKfSKc18UcEEFFXzodjA,7366
+tomwer/gui/utils/buttons.py,sha256=czf14thj6yC9oqrSga77pBDFUtizuAlsIG39GSfpIss,7361
 tomwer/gui/utils/completer.py,sha256=XQGVSiUdLa1MfgXPDY5qfcTxtjVerxmVKXmWDb-kQ-I,3606
 tomwer/gui/utils/flow.py,sha256=DO9QhS_0dOxMArowqDGU5yZ_a36CsvwQUoFPwuxjxkE,10646
 tomwer/gui/utils/gpu.py,sha256=R2sRA77zyxdy5bVYGNltQpKS_9wuaj9eIn6rglsWGWg,2223
@@ -689,7 +692,6 @@ tomwer/io/utils/tomoobj.py,sha256=PGcTc2nMDMzKGvL7u5LgIMc9MYhJwLN9yecA1gttmzE,28
 tomwer/io/utils/utils.py,sha256=BGXWRMl0l0VNHJDo5EA33gs9IHLiVCYbc4ThtU8-xPU,9292
 tomwer/io/utils/test/test_raw_and_processed_data.py,sha256=2TgR3GZZ1PJ2wlyCqRU4qxh6XrQF-thvSqLZFMSV5es,552
 tomwer/io/utils/test/test_utils.py,sha256=1EVY_N0vryUJYAe-l_CM0HbqQr-8tf7DAM6XyVy_4-U,1922
-tomwer/model/dataset.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/resources/__init__.py,sha256=yGvSUNzqb_1F2qvcXARl3m6yqZYagpeUWjOayUY4B8s,4613
 tomwer/resources/gui/icons/Imagej_icon.png,sha256=JFDzPw20pzRrf6wLBnScXEcmTVt6orXPzwPwniKeVss,1618960
 tomwer/resources/gui/icons/a.png,sha256=YrYFndLl3SUcsYNJDloU9YeJLBUkiMmgvDjDNJCMipI,3858
@@ -833,14 +835,14 @@ tomwer/synctools/rsyncmanager.py,sha256=4SvN0Bk_D_WavBWFvF64Vxmll5kXeOrhmgOI4k0g
 tomwer/synctools/saaxis.py,sha256=hvsJ3g189fA3FWZUdUFrqPLDRh5T-V7ptWY2YhJJ13I,669
 tomwer/synctools/sadeltabeta.py,sha256=WCrBx-2lBlQUuoZlbR_HQaBAH8owsghh2j1TQXiBMIw,694
 tomwer/synctools/stacks/__init__.py,sha256=wWN09X2qRXzBSekl5nkpEx1WDAcU2LQLxO9NpmW3bDU,165
-tomwer/synctools/stacks/processingstack.py,sha256=egB5kg5DesKkfzGhfcM9_ffozPFwBYupdPiebSQMQXU,5472
+tomwer/synctools/stacks/processingstack.py,sha256=3FE7Z_dHvPS6k3HoYr1WJSkdOk4mM_R8OgFylw2tTc4,5959
 tomwer/synctools/stacks/control/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/stacks/control/datalistener.py,sha256=XN40esWfSQPgsy9HHrjvd3imSg7gcTzZ2OJgAFEtbEs,3785
 tomwer/synctools/stacks/reconstruction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/stacks/reconstruction/axis.py,sha256=yq36BFGUGq0dtrDYE581nA2kMomMex6Nl7JSF2EVa_U,6088
 tomwer/synctools/stacks/reconstruction/castvolume.py,sha256=hyLW_M6uR81nUAk1ZvyyYMd3gvIcWfqKF7RSdUgVzmQ,6795
 tomwer/synctools/stacks/reconstruction/dkrefcopy.py,sha256=bemmlZajyoT7hAvGeEfhEXuxIN1IwhgEwnYSe1htXKA,6171
-tomwer/synctools/stacks/reconstruction/nabu.py,sha256=sSrxcUdn3B6u4gKtevlw5Vc5wI9Qf-mzCbOowT2W0zM,6495
+tomwer/synctools/stacks/reconstruction/nabu.py,sha256=fr86pc9XJahx3tel1lRoZU1GQZ64px3R11W4IMWhLAE,6661
 tomwer/synctools/stacks/reconstruction/normalization.py,sha256=WSlx-aad8OhKI-2wZDe2pKzu9ht-446Yrwo0Z0cUaE0,4044
 tomwer/synctools/stacks/reconstruction/saaxis.py,sha256=6HHfNfT4n6podzB_X88AjC7simiFAHpoi520nt3OexY,5808
 tomwer/synctools/stacks/reconstruction/sadeltabeta.py,sha256=Oo0mczxv3-DxedpOybyMSUZAlcf65W8ZiCeTvPMHEas,5796
@@ -849,7 +851,6 @@ tomwer/synctools/tests/test_darkRefs.py,sha256=1OgWaV-hgDmi4rkh0hxjCW_codBAnxNhp
 tomwer/synctools/tests/test_foldertransfer.py,sha256=ZFIJWSjgYAWw3ktzamid5DJZNnMkAV6Pj72dKG69cJc,12024
 tomwer/synctools/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/utils/scanstages.py,sha256=xd27Y1mIcL9YGTHER7MX7oS_ky12R_y2fjIznT6p2rg,7797
-tomwer/tasks/reconstruction/cleardarkflat.py,sha256=_V_x7W8vp1_AqqtQ9xk2VRgwlivn4IPTLEpWySjSZRE,1353
 tomwer/tests/__init__.py,sha256=dPPaIvpzHssjwxsMzYJM_gxQ2e0cnRyQHXxi9ux6ZOY,19
 tomwer/tests/conftest.py,sha256=0XlKfOrVtPg8VmyQn4BoK_mzcliFUtacDGLlZ5wD_PM,1912
 tomwer/tests/datasets.py,sha256=QXQ3jSwgWzfq4CaELOSrk9kHg5GmrP7kGHsdOlNSEIE,336
@@ -906,9 +907,9 @@ tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewer
 tomwer/tests/test_ewoks/test_conversion.py,sha256=a8cEWbErXiFCAkaapi0jeEoRKYxcFQCoa-Jr_u77_OM,3656
 tomwer/tests/test_ewoks/test_single_node_execution.py,sha256=YBUHfiAnkciv_kjj7biC5fOs7c7ofNImM_azGMn4LZM,2813
 tomwer/tests/test_ewoks/test_workflows.py,sha256=Eq80eexf5NVL7SzvwctLOaUeuQ8V3vDiFiHgbJA4Yb8,4871
-tomwer-1.5.0rc3.dist-info/licenses/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.5.0rc3.dist-info/METADATA,sha256=Kd1h0AEyK9dV1mG7iP5DfNXBkabmhYXMM9b6QJyHcik,13459
-tomwer-1.5.0rc3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tomwer-1.5.0rc3.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.5.0rc3.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.5.0rc3.dist-info/RECORD,,
+tomwer-1.5.2.dist-info/licenses/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
+tomwer-1.5.2.dist-info/METADATA,sha256=GIxAXiLuueEJjDNgHpJLxxSxCWI3nXYdkWvtn9wWo88,11636
+tomwer-1.5.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+tomwer-1.5.2.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
+tomwer-1.5.2.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.5.2.dist-info/RECORD,,

tomwer/tasks/reconstruction/cleardarkflat.py

@@ -1,42 +0,0 @@
-"""
-Contains task to clear reduced dark and flat frames
-"""
-
-from __future__ import annotations
-
-from tomoscan.scanbase import TomoScanBase as TomoscanScanBase
-
-from processview.core.manager import DatasetState, ProcessManager
-from processview.core.superviseprocess import SuperviseProcess
-
-from tomwer.tasks.task import Task
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.utils.scanutils import data_identifier_to_scan
-from tomwer.core.reconstruction.darkflat import params as dkrf_reconsparams
-from tomwer.utils import docstring
-
-
-class ClearReducedDarkAndFlat(
-    Task,
-    SuperviseProcess,
-    input_names=("data",),
-    output_names=("data",),
-):
-    """
-    Task to clear reduced darks and flats. Both on disk and on the object cache.
-    th goal of this task is to make sure the scan is cleared of any reduced frames to reprocess it later.
-    """
-
-    def run(self):
-        scan = self.inputs.data
-        if not isinstance(scan, TomoscanScanBase):
-            raise TypeError(
-                f"scan should be an instance of {TomoscanScanBase}. Got {type(scan)}"
-            )
-        scan.set_reduced_flats(None)
-        scan.reduced_flats_infos = None
-        scan.set_reduced_darks(None)
-        scan.reduced_darks_infos = None
-
-        self.outputs.data = scan