tomwer 1.5.1__py3-none-any.whl → 1.5.2__py3-none-any.whl

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/utils.py

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

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/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/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/tests/test_nabu.py

@@ -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/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 5
-MICRO = 1
+MICRO = 2
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.5.1.dist-info → tomwer-1.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.5.1
+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-1.5.1.dist-info → tomwer-1.5.2.dist-info}/RECORD

@@ -18,6 +18,7 @@ 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
@@ -26,7 +27,7 @@ orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows,sha256=eufyC3wPbnzp
 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=K5a0x_MIZk2c2KnjS9jTsWtptvB-LYnkQQEw0IH9mdc,4386
+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
@@ -341,7 +342,7 @@ tomwer/core/process/reconstruction/nabu/nabuvolume.py,sha256=Fn0tkPDTDJQaMEJA4Lz
 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
@@ -566,15 +567,17 @@ tomwer/gui/reconstruction/nabu/slurm.py,sha256=yfJD8KgX45Be5CUi6bn2CdocrQemJPxDY
 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=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=JI3GFzUXR_SsDMQfj2joVv6ToEqS-QdMyB12y14OvdI,13628
+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
@@ -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
@@ -704,7 +706,6 @@ tomwer/resources/gui/icons/background.png,sha256=o4479aVkI5oI6LyiHVbRnFtnfwXP-wS
 tomwer/resources/gui/icons/background.svg,sha256=ydyBCNZy_uQK7ro1L-e03qJyACmOb1GoB9OuFwlcIzg,10778
 tomwer/resources/gui/icons/basic_user.png,sha256=9bHI9dU-6SVbVGxokRZTq4XyK8lNDwTd1HU2tSseM4w,4694
 tomwer/resources/gui/icons/basic_user.svg,sha256=KOk8j33FLmie4cGpD4wJN9UYIKQfXOyK9_5_id6Iaa4,9246
-tomwer/resources/gui/icons/borders.png,sha256=E8rkw2TiZSgBzSiuLz6DdFw6cyKOI7K5bIAcIz85J5k,1541
 tomwer/resources/gui/icons/cfg_file_active.png,sha256=XA80Ltn7y9I5MlQHTrjKi-WO5RpI2_z-zrIgHUG0GO8,2150
 tomwer/resources/gui/icons/cfg_file_active.svg,sha256=ExCvTt8QZ99q3B9WqfsMTqfylv_hjvvZjSB615GWkro,7344
 tomwer/resources/gui/icons/cfg_file_inactive.png,sha256=9ezxJCR6jIQhFbJ8kOGSQ_klpwjp-rKiU135ddvtywo,1979
@@ -850,7 +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
@@ -907,9 +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-1.5.1.dist-info/licenses/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.5.1.dist-info/METADATA,sha256=hQC84pwhh-IbdRxuVIaVjU_GixxKgGbcVX4dywQxhwU,13456
-tomwer-1.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tomwer-1.5.1.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.5.1.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.5.1.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