tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

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

@@ -1,40 +1,10 @@
-# coding: utf-8
-###########################################################################
-# Copyright (C) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#############################################################################
-
 """contain the SAAxisProcess. Half automatic center of rotation calculation
 """
 
-__authors__ = [
-    "H.Payno",
-]
-__license__ = "MIT"
-__date__ = "10/02/2021"
-
+from __future__ import annotations
 
 import logging
 import os
-from typing import Optional
 
 import h5py
 import numpy
@@ -61,6 +31,7 @@ from tomwer.core.process.reconstruction.scores import (
     get_disk_mask_radius,
 )
 from tomwer.core.process.reconstruction.scores.params import ScoreMethod
+from tomwer.core.process.reconstruction.utils.cor import relative_pos_to_absolute
 from tomwer.core.process.task import Task
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -83,9 +54,7 @@ from tomwer.core.process.reconstruction.nabu.utils import (
     get_multi_cor_recons_volume_identifiers,
     get_nabu_multicor_file_prefix,
 )
-from tomwer.core.process.reconstruction.nabu.nabuscores import _ReconstructorMultiCor
 
-from ..nabu import utils
 from .params import SAAxisParams
 
 _logger = logging.getLogger(__name__)
@@ -97,7 +66,7 @@ DEFAULT_RECONS_FOLDER = "multi_cor_results"
 def one_slice_several_cor(
     scan,
     configuration: dict,
-    process_id: Optional[int] = None,
+    process_id: int | None = None,
 ) -> tuple:
     """
     Run a slice reconstruction using nabu per Center Of Rotation (cor) provided
@@ -106,13 +75,12 @@ def one_slice_several_cor(
     .. warning:: if target if the slurm cluster this will wait for the processing to be done to return the result.
                  as this function is returning the result of the score process on reconstructed slices
 
-    :param TomwerScanBase scan:
-    :param dict configuration: nabu reconstruction parameters (can include 'slurm-cluster' key defining the slurm configuration)
-    :param int process_id: process id
+    :param scan:
+    :param configuration: nabu reconstruction parameters (can include 'slurm-cluster' key defining the slurm configuration)
+    :param process_id: process id
     :return: cor_reconstructions, outs, errs
              cor_reconstructions is a dictionary of cor as key and a tuple
              (url, score) as value
-    :rtype: tuple
     """
     task = SAAxisTask(
         process_id=process_id,
@@ -197,7 +165,7 @@ class SAAxisTask(
         self._dump_roi = dump
 
     @staticmethod
-    def autofocus(scan) -> Optional[float]:
+    def autofocus(scan) -> float | None:
         scores = scan.saaxis_params.scores
         if scores is None:
             return
@@ -258,9 +226,9 @@ class SAAxisTask(
         nabu_configuration["output"]["location"] = output_dir
         nabu_configuration["output"]["file_format"] = file_format
         # handle resources section
-        nabu_configuration["resources"] = utils.get_nabu_resources_desc(
-            scan=scan, workers=1, method="local"
-        )
+        nabu_configuration["resources"] = nabu_configuration.get("resources", {})
+        nabu_configuration["resources"]["method"] = "local"
+
         return nabu_configuration
 
     def _run_nabu_multicor(
@@ -270,7 +238,7 @@ class SAAxisTask(
         cors,
         slice_index,
         file_format,
-        cluster_config: Optional[dict],
+        cluster_config: dict | None,
         dry_run=False,
     ):
         if not (cluster_config is None or isinstance(cluster_config, dict)):
@@ -286,7 +254,7 @@ class SAAxisTask(
             file_format=file_format,
             cluster_config=cluster_config if cluster_config is not None else None,
             process_id=self.process_id,
-            instanciate_classes_only=True,
+            instantiate_classes_only=True,
             output_file_prefix_pattern="cor_{file_name}_{value}",  # as the cor is evolving, create different files to make sure the name will be unique
         )
 
@@ -348,9 +316,9 @@ class SAAxisTask(
                 continue
 
             for cor in cors:
-                cor_nabu_ref = _ReconstructorMultiCor.convert_cor_from_rel_to_abs(
-                    scan=scan,
-                    cor=cor,
+                cor_nabu_ref = relative_pos_to_absolute(
+                    relative_pos=cor,
+                    det_width=scan.dim_1,
                 )
                 volume_identifiers = get_multi_cor_recons_volume_identifiers(
                     scan=scan,
@@ -371,7 +339,7 @@ class SAAxisTask(
         """
         compute score along the different slices
 
-        :param dict cor_reconstructions: key is expected to be a float with the cor value and the value is expected to be a volume identifier (volume with a single frame)
+        :param cor_reconstructions: key is expected to be a float with the cor value and the value is expected to be a volume identifier (volume with a single frame)
         """
         post_processing = _PostProcessing(
             slice_index=slice_index,
@@ -447,9 +415,12 @@ class SAAxisTask(
                 _logger.info(
                     f"{scan}: set estimated cor from previously computed cor ({params.estimated_cor})"
                 )
-        #  from scan.estimated_cor_position
-        if params.estimated_cor is None and scan.estimated_cor_frm_motor is not None:
-            params.estimated_cor = scan.estimated_cor_frm_motor
+        #  from scan.x_rotation_axis_pixel_position
+        if (
+            params.estimated_cor is None
+            and scan.x_rotation_axis_pixel_position is not None
+        ):
+            params.estimated_cor = scan.x_rotation_axis_pixel_position
             _logger.info(
                 f"{scan}: set estimated cor from motor position ({params.estimated_cor})"
             )

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

@@ -1,34 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "04/05/2021"
-
-
-import typing
+from __future__ import annotations
 
 from tomwer.core.process.reconstruction.nabu.utils import retrieve_lst_of_value_from_str
 from tomwer.core.process.reconstruction.scores.params import SABaseParams
@@ -59,7 +30,7 @@ class SADeltaBetaParams(SABaseParams):
         self._selected_db = value
 
     @property
-    def selected_delta_beta_value(self) -> typing.Union[None, float]:
+    def selected_delta_beta_value(self) -> float | None:
         return self._selected_db
 
     def to_dict(self) -> dict:

tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py

@@ -1,45 +1,17 @@
-# coding: utf-8
-###########################################################################
-# Copyright (C) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#############################################################################
-
 """contain the SADeltaBetaProcess. Half automatic best delta / beta finder
 """
 
-__authors__ = [
-    "H.Payno",
-]
-__license__ = "MIT"
-__date__ = "28/10/2021"
-
+from __future__ import annotations
 
 import logging
 import os
 from copy import copy, deepcopy
-from typing import Optional, Union
 
 import h5py
 import numpy
 from multiprocessing import Pool
+from tqdm import tqdm
+
 from nabu.pipeline.config import get_default_nabu_config
 from nabu.pipeline.fullfield.nabu_config import (
     nabu_config as nabu_fullfield_default_config,
@@ -56,6 +28,7 @@ from tomwer.core.process.reconstruction.nabu.nabucommon import (
     ResultsWithStd,
 )
 from tomwer.core.process.reconstruction.nabu.nabuslices import SingleSliceRunner
+from tomwer.core.process.reconstruction.utils.cor import relative_pos_to_absolute
 from tomwer.core.process.reconstruction.scores import (
     ComputedScore,
     ScoreMethod,
@@ -65,7 +38,6 @@ from tomwer.core.process.reconstruction.scores import (
 )
 from tomwer.core.utils.locker import FileLockerManager
 from tomwer.core.process.task import Task
-from tomwer.core.progress import Progress
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
@@ -92,19 +64,18 @@ DEFAULT_RECONS_FOLDER = "multi_delta_beta_results"
 
 def one_slice_several_db(
     scan: TomwerScanBase,
-    configuration: Union[dict, SADeltaBetaParams],
-    process_id: Optional[int] = None,
+    configuration: dict | SADeltaBetaParams,
+    process_id: int | None = None,
 ) -> tuple:
     """
     Run a slice reconstruction using nabu per Center Of Rotation (cor) provided
     Then for each compute a score (quality) of the center of rotation
 
-    :param TomwerScanBase scan:
-    :param Union[dict,SADeltaBetaParams] configuration:
+    :param scan:
+    :param configuration:
     :return: cor_reconstructions, outs, errs
              cor_reconstructions is a dictionary of cor as key and a tuple
              (url, score) as value
-    :rtype: tuple
     """
     if isinstance(configuration, SADeltaBetaParams):
         configuration = configuration.to_dict()
@@ -208,7 +179,7 @@ class SADeltaBetaTask(
             )
 
     @staticmethod
-    def autofocus(scan) -> Optional[float]:
+    def autofocus(scan) -> float | None:
         scores = scan.sa_delta_beta_params.scores
         if scores is None:
             return
@@ -283,8 +254,8 @@ class SADeltaBetaTask(
             output_dir=params.output_dir,
         )
         # step 2: run reconstructions
-        advancement = Progress(
-            f"sa-delta-beta - slice {slice_index} of {scan.get_identifier().short_description()}"
+        advancement = tqdm(
+            desc=f"sa-delta-beta - slice {slice_index} of {scan.get_identifier().short_description()}"
         )
 
         dbs_res = {}
@@ -390,14 +361,15 @@ class SADeltaBetaTask(
 
     def _config_preprocessing(self, scan, config, delta_beta_s, output_dir) -> dict:
         config.get("phase", {}).pop("beam_shape", None)
-        # if scan contains some center of position copy it to nabu
         if (
             scan.axis_params is not None
             and scan.axis_params.relative_cor_value is not None
         ):
             if "reconstruction" in config:
-                # move the cor value to the nabu reference
-                cor_nabu_ref = scan.axis_params.relative_cor_value + scan.dim_1 / 2.0
+                cor_nabu_ref = relative_pos_to_absolute(
+                    relative_pos=scan.axis_params.relative_cor_value,
+                    det_width=scan.dim_1,
+                )
                 config["reconstruction"]["rotation_axis_position"] = str(cor_nabu_ref)
 
         _logger.info(f"set nabu reconstruction parameters to {scan}")
@@ -430,7 +402,7 @@ class SADeltaBetaTask(
         advancement,
         dry_run,
         axis,
-        cluster_config: Optional[dict],
+        cluster_config: dict | None,
     ):
         future_tomo_objs = {}
         success = True
@@ -452,7 +424,7 @@ class SADeltaBetaTask(
             advancement=advancement,
             cluster_config=cluster_config,
             process_id=self.process_id,
-            instanciate_classes_only=True,
+            instantiate_classes_only=True,
             output_file_prefix_pattern=None,
             axis=axis,
         )
@@ -493,7 +465,7 @@ class SADeltaBetaTask(
                         future_tomo_objs[db] = future_tomo_obj
 
             if advancement is not None:
-                advancement.increaseAdvancement(1)
+                advancement.update()
 
         return success, recons_urls, future_tomo_objs, std_outs, std_errs
 

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

@@ -1,34 +1,4 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "04/05/2021"
-
-
-from typing import Optional, Union
+from __future__ import annotations
 
 from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.process.reconstruction.scores.scores import ScoreMethod
@@ -71,11 +41,11 @@ class SABaseParams:
         self._n_reconstruction = n
 
     @property
-    def slice_indexes(self) -> Union[None, dict, str]:
+    def slice_indexes(self) -> dict | str | None:
         return self._slice_indexes
 
     @slice_indexes.setter
-    def slice_indexes(self, indexes: Union[None, dict, str]):
+    def slice_indexes(self, indexes: dict | str | None):
         if isinstance(indexes, str):
             if not indexes == "middle":
                 raise ValueError("the only valid indexes values is 'middle'")
@@ -116,12 +86,12 @@ class SABaseParams:
         self._dry_run = dry_run
 
     @property
-    def output_dir(self) -> Union[str, None]:
+    def output_dir(self) -> str | None:
         """nabu cfg_files output dir. If not provided will use nabu slice output with saaxis/cfg_files as postfix"""
         return self._output_dir
 
     @output_dir.setter
-    def output_dir(self, output_dir: Union[str, None]) -> None:
+    def output_dir(self, output_dir: str | None) -> None:
         if not isinstance(output_dir, (str, type(None))):
             raise TypeError("output_dir should be None or a str")
         self._output_dir = output_dir
@@ -135,11 +105,11 @@ class SABaseParams:
         self._score_method = ScoreMethod.from_value(method)
 
     @property
-    def scores(self) -> Union[dict, None]:
+    def scores(self) -> dict | None:
         return self._scores
 
     @scores.setter
-    def scores(self, scores: Union[None, dict]):
+    def scores(self, scores: dict | None):
         if not isinstance(scores, (type(None), dict)):
             raise TypeError("scores should be None or a dictionary")
         self._scores = scores
@@ -159,11 +129,11 @@ class SABaseParams:
         self._file_format = format_
 
     @property
-    def cluster_config(self) -> Optional[dict]:
+    def cluster_config(self) -> dict | None:
         return self._cluster_config
 
     @cluster_config.setter
-    def cluster_config(self, config: Optional[dict]):
+    def cluster_config(self, config: dict | None):
         if isinstance(config, SlurmClusterConfiguration):
             config = config.to_dict()
         if not isinstance(config, (dict, type(None))):

tomwer/core/process/reconstruction/scores/scores.py

@@ -1,36 +1,7 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "18/02/2021"
-
+from __future__ import annotations
 
 import logging
 import sys
-from typing import Union
 
 import numpy
 from silx.utils.enum import Enum as _Enum
@@ -120,9 +91,8 @@ def compute_score_contrast_std(data: numpy.ndarray):
     """
     Compute a contrast score by simply computing the standard deviation of
     the frame
-    :param numpy.ndarray data: frame for which we should compute the score
+    :param data: frame for which we should compute the score
     :return: score of the frame
-    :rtype: float
     """
     if data is None:
         return None
@@ -134,9 +104,8 @@ def compute_tv_score(data: numpy.ndarray):
     """
     Compute the data score as image total variation
 
-    :param numpy.ndarray data: frame for which we should compute the score
+    :param data: frame for which we should compute the score
     :return: score of the frame
-    :rtype: float
     """
     tv = numpy.sum(
         numpy.sqrt(
@@ -155,17 +124,16 @@ _METHOD_TO_FCT = {
 def compute_score(
     data: numpy.ndarray,
     method: ScoreMethod,
-    angles: Union[None, list] = None,
-    original_sinogram: Union[None, numpy.array] = None,
-    original_axis_position: Union[float, None] = None,
-    detector_width: Union[float, None] = None,
-) -> Union[float, None]:
+    angles: list | None = None,
+    original_sinogram: numpy.array | None = None,
+    original_axis_position: float | None = None,
+    detector_width: float | None = None,
+) -> float | None:
     """
 
-    :param numpy.ndarray data: frame for which we should compute the score
-    :param str method:
+    :param data: frame for which we should compute the score
+    :param method:
     :return: score of the frame
-    :rtype: float
     """
     method = ScoreMethod.from_value(method)
     if data.ndim == 3:

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

@@ -0,0 +1,46 @@
+import h5py
+from nxtomo.paths.nxtomo import get_paths as get_nexus_paths
+from tomwer.core.process.reconstruction.axis import AxisTask
+from tomwer.tests.conftest import nxtomo_scan_360  # noqa F811
+from tomwer.core.process.reconstruction.axis import AxisRP
+
+
+def test_read_x_rotation_axis_pixel_position(nxtomo_scan_360):  # noqa F811
+    """
+    test reading of the estimated cor from the motor using scan metadata
+    """
+    nexus_paths = get_nexus_paths(None)
+
+    x_rotation_axis_pixel_position_path = "/".join(
+        [
+            nxtomo_scan_360.entry,
+            nexus_paths.INSTRUMENT_PATH,
+            nexus_paths.nx_instrument_paths.DETECTOR_PATH,
+            nexus_paths.nx_detector_paths.X_ROTATION_AXIS_PIXEL_POSITION
+            or nexus_paths.nx_detector_paths.ESTIMATED_COR_FRM_MOTOR_PATH,
+        ]
+    )
+    with h5py.File(nxtomo_scan_360.master_file, mode="r") as h5f:
+        assert x_rotation_axis_pixel_position_path not in h5f
+
+    axis_params = AxisRP()
+    axis_params.mode = "read"
+    task = AxisTask(
+        inputs={
+            "data": nxtomo_scan_360,
+            "axis_params": axis_params,
+        }
+    )
+    # test the task when there is no metadata
+    task.run()
+    assert nxtomo_scan_360.axis_params.absolute_cor_value is None
+    assert nxtomo_scan_360.axis_params.relative_cor_value is None
+
+    # test the task when there is metadata
+    with h5py.File(nxtomo_scan_360.master_file, mode="a") as h5f:
+        h5f[x_rotation_axis_pixel_position_path] = 12.5
+
+    nxtomo_scan_360.clear_caches()
+    task.run()
+    assert nxtomo_scan_360.axis_params.absolute_cor_value == 22.5
+    assert nxtomo_scan_360.axis_params.relative_cor_value == 12.5

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

@@ -0,0 +1,33 @@
+# coding: utf-8
+from __future__ import annotations
+
+from tomwer.core.process.reconstruction.darkref.darkrefs import (
+    requires_reduced_dark_and_flat,
+)
+from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
+
+
+def test_quick_run_necessary_edf(tmpdir):
+    """test the `quick_run_necessary` function for EDFTomoScan"""
+    scan = MockEDF.mockScan(scanID=str(tmpdir), start_dark=True, start_flat=True)
+    assert scan.reduced_darks in (None, {})
+    assert scan.reduced_flats in (None, {})
+    requires_reduced_dark_and_flat(scan=scan)
+    assert len(scan.reduced_darks) == 1
+    assert len(scan.reduced_flats) == 1
+
+
+def test_quick_run_necessary_hdf5(tmpdir):
+    """test the `quick_run_necessary` function for NXtomoScan"""
+    scan = MockNXtomo(
+        scan_path=tmpdir,
+        n_proj=20,
+        n_ini_proj=20,
+        dim=10,
+    ).scan
+    assert scan.reduced_darks in (None, {})
+    assert scan.reduced_flats in (None, {})
+    computed = requires_reduced_dark_and_flat(scan=scan)
+    assert len(computed) == 2
+    assert len(scan.reduced_darks) == 1
+    assert len(scan.reduced_flats) == 1

tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "27/02/2021"
+from __future__ import annotations
 
 
 import os