tomwer 1.5.0rc0__tar.gz → 1.5.1__tar.gz

{tomwer-1.5.0rc0/src/tomwer.egg-info → tomwer-1.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 1.5.0rc0
+Version: 1.5.1
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/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>
 		<properties node_id="2" format="pickle">gASVPgEAAAAAAAB9lCiMDl92aWV3ZXJfY29uZmlnlH2UKIwEbW9kZZSMI3RvbXdlci5ndWkudmlz
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{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/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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{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/app/axis.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/control/datalistener/rpcserver.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/drac/binning.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/drac/output.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/axis/mode.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/axis/params.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/axis/projectiontype.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/axis/side.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/darkref/params.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 
 import enum
 
-from silx.utils.enum import Enum as _Enum
 from tomoscan.framereducer.method import ReduceMethod
 
 from tomwer.core.process.reconstruction.darkref.settings import (
@@ -17,7 +16,7 @@ from tomwer.core.utils.deprecation import deprecated
 # TODO: those classes (when, method) should be linked / embedded in the DarkRef
 # method
 @enum.unique
-class When(_Enum):
+class When(enum.Enum):
     never = (0,)
     before = (1,)
     after = (2,)

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -205,7 +205,7 @@ class _NabuBaseReconstructor:
         axis: NabuPlane = NabuPlane.XY,
     ) -> None:
         self._scan = scan
-        self._target = Target.from_value(target)
+        self._target = Target(target)
         self._dry_run = dry_run
         self._process_name = process_name
         self._process = None
@@ -564,7 +564,7 @@ class _NabuBaseReconstructor:
         )
 
         source = extra_infos.get("source", INormSource.NONE)
-        source = INormSource.from_value(source)
+        source = INormSource(source)
 
         if source is INormSource.NONE:
             pass

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/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-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/nabu/target.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py

@@ -275,3 +275,12 @@ def test_nabu_std_err_has_error():
         )
         is False
     )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""Performing MLEM-WL2 iterations: 0%|     | 0/200[00:00<?, ?its/s]
+            Performing MLEM-WL2 iterations: 82%|     | 163/200[00:00<?, 828.12its/s]
+            """
+        )
+        is False
+    )

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/nabu/utils.py

@@ -409,6 +409,9 @@ def nabu_std_err_has_error(errs: bytes | None):
             or " unable to import 'siphash24.siphash13" in line
             or "_create_built_program_from_source_cached" in line
             or "prg.build(options_bytes," in line
+            or (
+                "Performing MLEM" in line and "iterations" in line
+            )  # corrct usage of tqdm (goes to stderr)
         )
 
     if errs is None:

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/normalization/normalization.py

@@ -140,7 +140,7 @@ class SinoNormalizationTask(
         if calc_fct is None:
             raise ValueError("calc_fct should be provided")
         else:
-            calc_fct = _ValueCalculationFct.from_value(calc_fct)
+            calc_fct = _ValueCalculationFct(calc_fct)
 
         try:
             value = self._cache_compute_from_manual_roi(

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/normalization/params.py

@@ -4,7 +4,7 @@ material for radio and sinogram normalization
 """
 from __future__ import annotations
 
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 from tomoscan.normalization import Method
 
 
@@ -39,7 +39,7 @@ class _DatasetInfos:
 
     @scope.setter
     def scope(self, scope: str | _DatasetScope):
-        self._scope = _DatasetScope.from_value(scope)
+        self._scope = _DatasetScope(scope)
 
     @property
     def file_path(self):
@@ -96,7 +96,7 @@ class SinoNormalizationParams:
     def source(self, source):
         if source is None:
             source = _ValueSource.NONE
-        self._source = _ValueSource.from_value(source)
+        self._source = _ValueSource(source)
 
     @property
     def extra_infos(self):

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/saaxis/params.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 from typing import Iterable
 
 import numpy
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 from tomwer.core.process.reconstruction.scores.params import SABaseParams
 
@@ -56,7 +56,7 @@ class SAAxisParams(SABaseParams):
 
     @mode.setter
     def mode(self, mode):
-        mode = ReconstructionMode.from_value(mode)
+        mode = ReconstructionMode(mode)
         self._mode = mode
 
     @property
@@ -91,7 +91,7 @@ class SAAxisParams(SABaseParams):
         if "n_reconstruction" in dict_:
             self.n_reconstruction = dict_["n_reconstruction"]
         if "mode" in dict_:
-            self.mode = ReconstructionMode.from_value(dict_["mode"])
+            self.mode = ReconstructionMode(dict_["mode"])
 
     @staticmethod
     def from_dict(dict_):

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/saaxis/saaxis.py

@@ -430,7 +430,7 @@ class SAAxisTask(
             params.image_width = scan.dim_1
         scan.saaxis_params = params
 
-        mode = ReconstructionMode.from_value(params.mode)
+        mode = ReconstructionMode(params.mode)
         if mode is not ReconstructionMode.VERTICAL:
             raise ValueError(f"{mode} is not handled for now")
 
@@ -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-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/scores/params.py

@@ -102,7 +102,7 @@ class SABaseParams:
 
     @score_method.setter
     def score_method(self, method):
-        self._score_method = ScoreMethod.from_value(method)
+        self._score_method = ScoreMethod(method)
 
     @property
     def scores(self) -> dict | None:
@@ -170,7 +170,7 @@ class SABaseParams:
                 output_dir = None
             self.output_dir = output_dir
         if "score_method" in dict_:
-            self.score_method = ScoreMethod.from_value(dict_["score_method"])
+            self.score_method = ScoreMethod(dict_["score_method"])
         if "cluster_config" in dict_:
             if dict_["cluster_config"] in (None, ""):
                 self.cluster_config = None

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/reconstruction/scores/scores.py

@@ -4,7 +4,7 @@ import logging
 import sys
 
 import numpy
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 _logger = logging.getLogger(__name__)
 
@@ -36,7 +36,7 @@ class ComputedScore:
         return self._tomo_consistency
 
     def get(self, method: ScoreMethod):
-        method = ScoreMethod.from_value(method)
+        method = ScoreMethod(method)
         if method is ScoreMethod.TV:
             return self.total_variation / float(10e5)
         elif method is ScoreMethod.TV_INVERSE:
@@ -135,7 +135,7 @@ def compute_score(
     :param method:
     :return: score of the frame
     """
-    method = ScoreMethod.from_value(method)
+    method = ScoreMethod(method)
     if data.ndim == 3:
         if data.shape[0] == 1:
             data = data.reshape(data.shape[1], data.shape[2])

tomwer-1.5.1/src/tomwer/core/process/reconstruction/tests/test_saaxis.py

@@ -0,0 +1,81 @@
+# coding: utf-8
+from __future__ import annotations
+
+
+import os
+import pytest
+
+import numpy
+
+from tomwer.core.process.reconstruction.saaxis.params import SAAxisParams
+from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisTask
+from tomwer.core.process.reconstruction.scores.scores import (
+    _METHOD_TO_FCT,
+    compute_score_contrast_std,
+)
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+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)
+
+
+@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)
+
+
+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
+
+    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"
+
+    # test processing
+    process = SAAxisTask(
+        inputs={
+            "data": scan,
+            "sa_axis_params": default_saaxis_params.to_dict(),
+            "serialize_output_data": False,
+        }
+    )
+
+    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-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/process/tests/test_normalization.py

@@ -54,7 +54,8 @@ class TestNormalization(unittest.TestCase):
             "median": numpy.array([800.5, 10800.5]),
         }
 
-        for calc_fct in params._ValueCalculationFct.values():
+        for item in params._ValueCalculationFct:
+            calc_fct = item.value
             with self.subTest(calc_fct=calc_fct):
                 process_params.extra_infos = {
                     "start_x": 0,

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/scan/scanbase.py

@@ -10,7 +10,7 @@ from typing import Iterable
 
 import numpy
 from silx.io.url import DataUrl
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 from tomoscan.identifier import VolumeIdentifier
 from tomoscan.normalization import IntensityNormalization

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/scan/scantype.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/core/settings.py

@@ -1,5 +1,5 @@
 import os
-from silx.utils.enum import Enum as _Enum
+from enum import Enum as _Enum
 
 
 __LBSRAM_PATH = "/lbsram"

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/gui/cluster/slurm.py

@@ -94,7 +94,7 @@ class SlurmSettingsWindow(qt.QMainWindow):
 
         self._modeCombox = qt.QComboBox(self)
         self._mainWidget.layout().addRow("configuration: ", self._modeCombox)
-        self._modeCombox.addItems(SlurmSettingsMode.values())
+        self._modeCombox.addItems([item.value for item in SlurmSettingsMode])
         self._modeCombox.setCurrentText(SlurmSettingsMode.GENERIC.value)
 
         self._settingsWidget = SlurmSettingsWidget(self, jobLimitation=None)
@@ -155,10 +155,10 @@ class SlurmSettingsWindow(qt.QMainWindow):
         self._modeCombox.setCurrentText(SlurmSettingsMode.MANUAL.value)
 
     def getCurrentSettingsMode(self) -> SlurmSettingsMode:
-        return SlurmSettingsMode.from_value(self._modeCombox.currentText())
+        return SlurmSettingsMode(self._modeCombox.currentText())
 
     def setCurrentSettingsMode(self, mode: SlurmSettingsMode) -> SlurmSettingsMode:
-        mode = SlurmSettingsMode.from_value(mode)
+        mode = SlurmSettingsMode(mode)
         self._modeCombox.setCurrentText(mode.value)
 
     def setMode(self, mode: SlurmSettingsMode) -> None:

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/gui/configuration/level.py

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

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/gui/control/actions.py

@@ -86,7 +86,7 @@ class TomoObjDisplayModeToolButton(qt.QToolButton):
         urlDescAction.triggered.connect(partial(self.setDisplayMode, DisplayMode.URL))
 
     def setDisplayMode(self, mode: DisplayMode):
-        mode = DisplayMode.from_value(mode)
+        mode = DisplayMode(mode)
         if mode is DisplayMode.SHORT:
             self.setIcon(self._shortDescIcon)
             self.setToolTip(self._SHORT_DESC_TOOLTIP)

{tomwer-1.5.0rc0 → tomwer-1.5.1}/src/tomwer/gui/control/datalist.py

@@ -616,7 +616,7 @@ class _TomwerObjectList(qt.QTableWidget):
         self.setDisplayMode(DisplayMode.SHORT)
 
     def setDisplayMode(self, mode: DisplayMode) -> None:
-        self._displayMode = DisplayMode.from_value(mode)
+        self._displayMode = DisplayMode(mode)
         self._update()
 
     def n_data(self):