tomwer 1.3.27__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/core/scan/tests/test_nxtomoscan.py

@@ -0,0 +1,143 @@
+import os
+import shutil
+import numpy
+
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import MockNXtomo
+from tomwer.tests.datasets import TomwerCIDatasets
+from tomwer.core.volume.hdf5volume import HDF5Volume
+from tomwer.core.volume.edfvolume import EDFVolume
+from tomwer.core.process.reconstruction.output import (
+    PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+)
+from nxtomomill.converter.hdf5.utils import PROCESSED_DATA_DIR_NAME, RAW_DATA_DIR_NAME
+
+
+def test_scan_dir(tmp_path):
+    """test result of NxtomoScan.scan_dir_name is correct"""
+    tmp_dir = tmp_path / "frm_edftomomill_twoentries_dataset"
+    tmp_dir.mkdir()
+    tmp_dir = str(tmp_dir)
+    dataset_file = os.path.join(tmp_dir, "frm_edftomomill_twoentries.nx")
+    shutil.copyfile(
+        TomwerCIDatasets.get_dataset(
+            "h5_datasets/frm_edftomomill_twoentries.nx",
+        ),
+        dataset_file,
+    )
+    assert os.path.isfile(dataset_file)
+    scan = NXtomoScan(scan=dataset_file, entry="entry0000")
+    assert scan.scan_dir_name() == tmp_dir.split(os.sep)[-1]
+
+
+def test_flat_field_interval(tmp_path):
+    """test the call to ff_interval"""
+    tmp_dir = tmp_path / "test_flat_field_interval"
+    scan_path = os.path.join(tmp_dir, "my_scan_1")
+    scan_1 = MockNXtomo(
+        scan_path=scan_path,
+        n_ini_proj=20,
+        n_proj=20,
+        n_alignement_proj=2,
+        create_final_flat=True,
+        create_ini_dark=True,
+        create_ini_flat=True,
+        n_refs=5,
+    ).scan
+    numpy.testing.assert_equal(scan_1.ff_interval, 20)
+
+    scan_path2 = os.path.join(tmp_dir, "my_scan_2")
+    scan_2 = MockNXtomo(
+        scan_path=scan_path2,
+        n_ini_proj=10,
+        n_proj=10,
+        n_alignement_proj=2,
+        create_final_flat=False,
+        create_ini_dark=True,
+        create_ini_flat=True,
+        n_refs=1,
+    ).scan
+    numpy.testing.assert_equal(scan_2.ff_interval, 0)
+
+
+def test_working_directory():
+    """test behavior of the working directory function"""
+    scan = NXtomoScan(scan=None, entry="my_entry")
+    assert scan.working_directory is None
+    scan = NXtomoScan(scan="/full/path/my_file.sh", entry="my_entry")
+    assert scan.working_directory == os.path.abspath("/full/path")
+    scan = NXtomoScan(scan="my_file.sh", entry="my_entry")
+    assert scan.working_directory == os.path.abspath(".")
+
+
+def test_get_reconstructions_slices(tmp_path):
+    """test NXtomoscan.get_reconstruction_urls and make sure all related scan can be found from a scan
+    (as long as they are stored at a 'searched' location)
+    """
+    test_dir = tmp_path / "test_get_reconstructions_urls"
+    test_dir.mkdir()
+    raw_data_dir = test_dir / RAW_DATA_DIR_NAME / "frm_edftomomill_twoentries"
+    raw_data_dir.mkdir(parents=True)
+    processed_data_dir = (
+        test_dir / PROCESSED_DATA_DIR_NAME / "frm_edftomomill_twoentries"
+    )
+    processed_data_dir.mkdir(parents=True)
+    third_path_dir = test_dir / "third_part"
+    third_path_dir.mkdir(parents=True)
+
+    output_file_path = os.path.join(raw_data_dir, "frm_edftomomill_twoentries.nx")
+    shutil.copyfile(
+        TomwerCIDatasets.get_dataset(
+            "h5_datasets/frm_edftomomill_twoentries.nx",
+        ),
+        output_file_path,
+    )
+    scan = NXtomoScan(
+        scan=output_file_path,
+        entry="entry0000",
+    )
+    assert scan.working_directory == str(raw_data_dir)
+    assert os.path.exists(output_file_path)
+
+    # create a edf volume in PROCESSED_DATA
+    data = numpy.linspace(start=0, stop=100, num=100).reshape(  # pylint: disable=E1121
+        1, 10, 10
+    )
+    edf_volume = EDFVolume(
+        folder=os.path.join(
+            raw_data_dir,
+            PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+        ),
+        volume_basename="frm_edftomomill_twoentries_slice",
+        data=data,
+    )
+    edf_volume.save()
+
+    # create an hdf5 volume in RAW_DATA
+    hdf5_volume = HDF5Volume(
+        file_path=os.path.join(
+            processed_data_dir,
+            PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+            "frm_edftomomill_twoentries_slice.h5",
+        ),
+        data_path="/entry0000",
+        data=data,
+    )
+    hdf5_volume.save()
+
+    # create a third hdf5 volume in 'third_part_dir'
+    third_part_volume = HDF5Volume(
+        file_path=os.path.join(
+            third_path_dir,
+            PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+            "frm_edftomomill_twoentries_slice.h5",
+        ),
+        data_path="entry0000",
+        data=data,
+    )
+    third_part_volume.save()
+
+    reconstructions_urls = scan.get_reconstructed_slices()
+    assert len(reconstructions_urls) == 2
+    assert edf_volume.get_identifier().to_str() in reconstructions_urls
+    assert hdf5_volume.get_identifier().to_str() in reconstructions_urls

tomwer/core/scan/tests/test_process_registration.py

@@ -0,0 +1,64 @@
+# coding: utf-8
+from __future__ import annotations
+
+import shutil
+import tempfile
+import unittest
+
+from tomoscan.io import HDF5File, get_swmr_mode
+
+from tomwer.core.process.task import Task
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+class TestProcessRegistration(unittest.TestCase):
+    """
+    Make sure utils link to the process registration are
+    correctly working
+    """
+
+    class DummyProcess(Task):
+        @staticmethod
+        def program_name():
+            """Name of the program used for this processing"""
+            return "dummy program"
+
+        @staticmethod
+        def program_version():
+            """version of the program used for this processing"""
+            return "0.0.0"
+
+        @staticmethod
+        def definition():
+            """definition of the process"""
+            return "no definition"
+
+    def setUp(self):
+        self.tmp_dir = tempfile.mkdtemp()
+        self.scan = MockNXtomo(scan_path=self.tmp_dir, n_proj=2).scan
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_dir)
+
+    def testGetProcessNodes(self):
+        """insure it return the last dark process based on the processing index"""
+
+        for i in range(20):
+            Task._register_process(
+                self.scan.process_file,
+                process=self.DummyProcess,
+                entry=self.scan.entry,
+                configuration=None,
+                results={"output": i},
+                process_index=i,
+            )
+
+        with HDF5File(self.scan.process_file, "r", swmr=get_swmr_mode()) as h5f:
+            nodes = Task._get_process_nodes(
+                root_node=h5f[self.scan.entry], process=self.DummyProcess
+            )
+            self.assertEqual(len(nodes), 20)
+            self.assertTrue("/entry/tomwer_process_16" in nodes)
+            self.assertEqual(nodes["/entry/tomwer_process_16"], 16)
+            self.assertTrue("/entry/tomwer_process_1" in nodes)
+            self.assertEqual(nodes["/entry/tomwer_process_1"], 1)

tomwer/core/settings.py

@@ -1,47 +1,17 @@
-# 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__ = "02/06/2017"
-
-
 import os
 from silx.utils.enum import Enum as _Enum
 
 
-__LBSRAM_PATH = '/lbsram'
+__LBSRAM_PATH = "/lbsram"
 
-__DEST_PATH = ''
+__DEST_PATH = ""
 
 MOCK_LBSRAM = False
 
 MAX_MEM_USED = 80
 "Maximal percentage of used memory from which we should skip some processing"
 
-MAKE_OAR_PYST2_PATH = '/data/id19/inhouse/OAR_UTILITIES/pyhst/make_oar_pyhst2'
+MAKE_OAR_PYST2_PATH = "/data/id19/inhouse/OAR_UTILITIES/pyhst/make_oar_pyhst2"
 """path to the make_oar_pyhst2 path"""
 
 JSON_RPC_HOST = None
@@ -49,6 +19,10 @@ JSON_RPC_HOST = None
 
 JSON_RPC_PORT = 4000
 
+TOMO_BEAMLINES = sorted(
+    ("bm05", "bm18", "id11", "id15a", "id16a", "id16b", "id17", "id19")
+)
+
 
 def mock_lsbram(b):
     assert type(b) is bool
@@ -128,7 +102,7 @@ class SlurmSettings:
     MEMORY_PER_WORKER = 128  # memory in GB
     """Amount of memory per worker"""
 
-    PARTITION = "p9gpu"
+    PARTITION = "gpu"
     """Queue / partition to use"""
 
     DEFAULT_WALLTIME = "01:00:00"  # None if the default wall time
@@ -144,7 +118,7 @@ class SlurmSettings:
     """Slurm cluster project name. `scan`, `process` and `info` will be format.
     """
 
-    MODULES_TO_LOAD = ("tomotools/stable", )
+    MODULES_TO_LOAD = ("tomotools/stable",)
 
     SBATCH_EXTRA_PARAMS = {
         "export": "NONE",  # value to provide to sbatch --export={}
@@ -153,21 +127,23 @@ class SlurmSettings:
 
 class DefaultSlurmSettingsCastVolume(SlurmSettings):
     """
-    default proposed configuration for casting a volume remotly
+    default proposed configuration for casting a volume remotely
     """
+
     N_GPUS_PER_WORKER = 0
 
     N_CORES_PER_TASK = 8
 
     MEMORY_PER_WORKER = 128  # memory in GB
 
-    PARTITION = "nice*"
+    PARTITION = "nice-long"
 
 
 class DefaultSlurmSettingsSliceReconstruction(SlurmSettings):
     """
-    default proposed configuration for reconstructing a single slice remotly
+    default proposed configuration for reconstructing a single slice remotely
     """
+
     MEMORY_PER_WORKER = 256  # memory in GB
 
     PARTITION = None
@@ -175,17 +151,19 @@ class DefaultSlurmSettingsSliceReconstruction(SlurmSettings):
 
 class DefaultSlurmSettingsVolumeReconstruction(SlurmSettings):
     """
-    default proposed configuration for reconstructing a full volume remotly
+    default proposed configuration for reconstructing a full volume remotely
     """
+
     MEMORY_PER_WORKER = 256  # memory in GB
 
     PARTITION = None
 
 
 class DefaultSlurmSettingsStitching(SlurmSettings):
-    """*
+    """
     default proposed configuration for stitching
     """
+
     N_JOBS = 15
 
     PARTITION = "nice-long"

tomwer/core/tests/test_scanutils.py

@@ -0,0 +1,26 @@
+# coding: utf-8
+
+import os
+import tempfile
+import unittest
+
+from nxtomo.application.nxtomo import NXtomo
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+class TestMockNXtomo(unittest.TestCase):
+    """Test the MockNXtomo file"""
+
+    def test_creation(self):
+        folder = tempfile.mkdtemp()
+        mock = MockNXtomo(scan_path=folder, n_proj=10, n_ini_proj=10)
+        self.assertEqual(
+            mock.scan_master_file,
+            os.path.join(folder, os.path.basename(folder) + ".h5"),
+        )
+        tomoScan = NXtomoScan(mock.scan_path, entry=mock.scan_entry)
+        self.assertEqual(len(NXtomo.get_valid_entries(mock.scan_master_file)), 1)
+        tomoScan.update()
+        self.assertEqual(tomoScan.scan_range, 360)
+        self.assertEqual(len(tomoScan.projections), 10)

tomwer/core/{test → tests}/test_utils.py

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 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__ = "02/08/2017"
-
+from __future__ import annotations
 
 import os
 import shutil

tomwer/core/tomwer_object.py

@@ -1,3 +1,7 @@
+"""contains TomwerObject class. Mother object of all the object used as input / output through the tomwer project.
+At the moment those objects are either a scan (ready to be processed), a volume or a bliss scan (raw scan that needs to be converted to scan to be processed)
+"""
+
 from processview.core.dataset import Dataset
 
 

tomwer/core/utils/__init__.py

@@ -0,0 +1,2 @@
+"""Several core utils
+"""

tomwer/core/utils/char.py

@@ -1,32 +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__ = "26/06/2018"
-
 
 ALPHA_CHAR = (b"\xce\xb1").decode("utf-8")
 

tomwer/core/utils/deprecation.py

@@ -1,32 +1,6 @@
 # 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.
-#
-# ###########################################################################*/
-"""Bunch of useful decorators"""
 
-__authors__ = ["Jerome Kieffer", "H. Payno", "P. Knobel"]
-__license__ = "MIT"
-__date__ = "26/02/2018"
+"""Bunch of useful decorators"""
 
 import functools
 import logging
@@ -49,15 +23,15 @@ def deprecated(
     """
     Decorator that deprecates the use of a function
 
-    :param str reason: Reason for deprecating this function
+    :param reason: Reason for deprecating this function
         (e.g. "feature no longer provided",
-    :param str replacement: Name of replacement function (if the reason for
+    :param replacement: Name of replacement function (if the reason for
         deprecating was to rename the function)
-    :param str since_version: First *silx* version for which the function was
+    :param since_version: First *silx* version for which the function was
         deprecated (e.g. "0.5.0").
-    :param bool only_once: If true, the deprecation warning will only be
+    :param only_once: If true, the deprecation warning will only be
         generated one time. Default is true.
-    :param int skip_backtrace_count: Amount of last backtrace to ignore when
+    :param skip_backtrace_count: Amount of last backtrace to ignore when
         logging the backtrace
     """
 
@@ -96,18 +70,18 @@ def deprecated_warning(
     """
     Function to log a deprecation warning
 
-    :param str type_: Nature of the object to be deprecated:
+    :param type_: Nature of the object to be deprecated:
         "Module", "Function", "Class" ...
     :param name: Object name.
-    :param str reason: Reason for deprecating this function
+    :param reason: Reason for deprecating this function
         (e.g. "feature no longer provided",
-    :param str replacement: Name of replacement function (if the reason for
+    :param replacement: Name of replacement function (if the reason for
         deprecating was to rename the function)
-    :param str since_version: First *silx* version for which the function was
+    :param since_version: First *silx* version for which the function was
         deprecated (e.g. "0.5.0").
-    :param bool only_once: If true, the deprecation warning will only be
+    :param only_once: If true, the deprecation warning will only be
         generated one time for each different call locations. Default is true.
-    :param int skip_backtrace_count: Amount of last backtrace to ignore when
+    :param skip_backtrace_count: Amount of last backtrace to ignore when
         logging the backtrace
     """
     if not depreclog.isEnabledFor(logging.WARNING):

tomwer/core/utils/dictutils.py

@@ -3,9 +3,7 @@ def concatenate_dict(dict_1, dict_2) -> dict:
     res = dict_1.copy()
     for key in dict_2:
         if key in dict_1:
-            if key in [f"axis_{axis}_params" for axis in (0, 1, 2)]:
-                res[key] = ";".join((dict_1[key], dict_2[key]))
-            elif isinstance(dict_1[key], dict):
+            if isinstance(dict_1[key], dict):
                 res[key] = concatenate_dict(dict_1=dict_1[key], dict_2=dict_2[key])
             else:
                 res.update({key: dict_2[key]})

tomwer/core/utils/ftseriesutils.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 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__ = "20/01/2017"
+from __future__ import annotations
 
 import logging
 import operator

tomwer/core/utils/gpu.py

@@ -1,32 +1,4 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 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__ = "09/11/2018"
-
 
 import logging
 

tomwer/core/utils/image.py

@@ -1,32 +1,4 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 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__ = "25/02/2019"
-
+from __future__ import annotations
 
 import enum
 import logging
@@ -55,15 +27,11 @@ def shift_img(
     Apply simple 2d image shift in 'constant mode'.
 
     :param data:
-    :type data: numpy.ndarray
     :param dx: x translation to be applied
-    :type dx: float
     :param dy: y translation to be applied
-    :type dy: float
-    :param float cval: value to replace the shifted values
+    :param cval: value to replace the shifted values
 
     :return: shifted image
-    :rtype: numpy.ndarray
     """
     assert data.ndim == 2
     assert dx is not None
@@ -112,17 +80,18 @@ class ImageScaleMethod(enum.Enum):
     MEDIAN = "median"
 
 
-def scale_img2_to_img1(img_1, img_2, method=ImageScaleMethod.MEAN):
+def scale_img2_to_img1(
+    img_1: numpy.array,
+    img_2: numpy.array,
+    method: ImageScaleMethod = ImageScaleMethod.MEAN,
+):
     """
     scale image2 relative to image 1 in such a way they have same min and
     max. Scale will be apply from and to 'data' / raw data
 
     :param img_1: reference image
-    :type: numpy.array
-    :param numpy.array img_2: image to scale
-    :type: numpy.array
+    :param img_2: image to scale
     :param method: method to apply scaling
-    :type: ImageScaleMethod
     :return:
     """
     assert method in ImageScaleMethod