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

tomwer/core/utils/locker.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__ = "20/04/2020"
-
+from __future__ import annotations
 
 import os
 from flufl.lock import Lock

tomwer/core/utils/logconfig.py

@@ -1,31 +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__ = "17/05/2017"
 
 DOC_TITLE = "doc_title"
 SCAN_ID = "scan_ID"

tomwer/core/utils/normalization.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__ = "30/05/2018"
-
+from __future__ import annotations
 
 import logging
 
@@ -41,10 +14,10 @@ def flatFieldCorrection(imgs, dark, flat):
     Normalization is made for X-Ray imaging:
     (img - dark) / (flat - dark)
 
-    :param dict imgs: list of imgs to correct. key: index of the image,
+    :param imgs: list of imgs to correct. key: index of the image,
                       value: the image path or numpy.ndarray
-    :param numpy.ndarray dark: dark image
-    :param numpy.ndarray flat: flat image
+    :param dark: dark image
+    :param flat: flat image
     :return: list of corrected images
     """
     res = {}

tomwer/core/utils/nxtomoutils.py

@@ -1,50 +1,20 @@
-# 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__ = "02/12/2021"
-
-
-from typing import Union
+from __future__ import annotations
 
 import numpy
 from nxtomo.nxobject.nxdetector import ImageKey
 
 
-def get_n_series(image_key_values: Union[tuple, list], image_key_type: ImageKey) -> int:
+def get_n_series(image_key_values: tuple | list, image_key_type: ImageKey) -> int:
     """
-    Return the number of series of an inage_key. Image key can be dark, flat, or projection.
-    A serie is defined as a contiguous elements in image_key_values
+    Return the number of series of an image_key. Image key can be dark, flat, or projection.
+    A series is defined as a contiguous elements in image_key_values
 
     :param image_key_values: list or tuple of image_keys to consider. Can be integers or tomoscan.esrf.scan.hdf5scan.ImageKey
     """
     image_key_type = ImageKey.from_value(image_key_type)
     if image_key_type is ImageKey.INVALID:
         raise ValueError(
-            "we can't count Invalid image keys serie because those are ignored from tomoscan"
+            "we can't count Invalid image keys series because those are ignored from tomoscan"
         )
     image_key_values = [ImageKey.from_value(img_key) for img_key in image_key_values]
 
@@ -54,12 +24,12 @@ def get_n_series(image_key_values: Union[tuple, list], image_key_type: ImageKey)
     )  # for filtering invalid value a numpy aray is requested
     image_key_values = image_key_values[image_key_values != ImageKey.INVALID]
 
-    n_serie = 0
+    n_series = 0
     is_in_a_serie = False
     for frame in image_key_values:
         if frame == image_key_type and not is_in_a_serie:
             is_in_a_serie = True
-            n_serie += 1
+            n_series += 1
         elif frame != image_key_type:
             is_in_a_serie = False
-    return n_serie
+    return n_series

tomwer/core/utils/resource.py

@@ -1,30 +1,4 @@
 # 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.
-#
-#############################################################################*/
-
-__authors__ = ["T. Vincent", "H.Payno"]
-__license__ = "MIT"
-__date__ = "25/11/2021"
 
 import logging
 import resource

tomwer/core/utils/scanutils.py

@@ -1,33 +1,8 @@
 # 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.
-#
-#############################################################################*/
 """
 Utils to mock scans
 """
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "11/08/2022"
+from __future__ import annotations
 
 import logging
 import os
@@ -40,11 +15,7 @@ from silx.io.utils import h5py_read_dataset
 from tomoscan.esrf.scan.mock import MockEDF as _MockEDF
 from tomoscan.esrf.scan.mock import MockNXtomo as _MockNXtomo
 from tomoscan.io import HDF5File
-
-try:
-    from tomoscan.test.utils import MockContext
-except ImportError:
-    from tomoscan.tests.utils import MockContext
+from tomoscan.tests.utils import MockContext
 
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.nxtomoscan import NXtomoScan
@@ -81,19 +52,19 @@ class MockEDF(_MockEDF):
         """
         Create some random radios and reconstruction in the folder
 
-        :param str scanID: the folder where to save the radios and scans
-        :param int nRadio: The number of radios to create
-        :param int nRecons: the number of reconstruction to mock
-        :param int nRecons: the number of paganin reconstruction to mock
-        :param int dim: dimension of the files (nb row/columns)
-        :param int scan_range: scan range, usually 180 or 360
-        :param int n_extra_radio: number of radio run after the full range is made
+        :param scanID: the folder where to save the radios and scans
+        :param nRadio: The number of radios to create
+        :param nRecons: the number of reconstruction to mock
+        :param nRecons: the number of paganin reconstruction to mock
+        :param dim: dimension of the files (nb row/columns)
+        :param scan_range: scan range, usually 180 or 360
+        :param n_extra_radio: number of radio run after the full range is made
                                   usually used to observe any sample movement
                                   during acquisition
-        :param bool start_dark: do we want to create dark serie at start
-        :param bool end_dark: do we want to create dark serie at end
-        :param bool start_flat: do we want to create flat serie at start
-        :param bool end_flat: do we want to create flat serie at end
+        :param start_dark: do we want to create dark serie at start
+        :param end_dark: do we want to create dark serie at end
+        :param start_flat: do we want to create flat serie at start
+        :param end_flat: do we want to create flat serie at end
         :param start_dark_data: if start_dark set to True Optional value for the dark serie. Else will generate some random values
         :param end_dark_data: if end_dark set to True Optional value for the dark serie. Else will generate some random values
         :param start_flat_data: if start_flat set to True Optional value for the flat serie. Else will generate some random values
@@ -115,15 +86,15 @@ class MockEDF(_MockEDF):
         )
 
         if start_dark:
-            _MockEDF.add_dark_serie(
+            _MockEDF.add_dark_series(
                 scan_path=scanID, n_elmt=4, index=0, dim=dim, data=start_dark_data
             )
         if start_flat:
-            _MockEDF.add_flat_serie(
+            _MockEDF.add_flat_series(
                 scan_path=scanID, n_elmt=4, index=0, dim=dim, data=start_flat_data
             )
         if end_dark:
-            _MockEDF.add_dark_serie(
+            _MockEDF.add_dark_series(
                 scan_path=scanID,
                 n_elmt=4,
                 index=nRadio - 1,
@@ -131,7 +102,7 @@ class MockEDF(_MockEDF):
                 data=end_dark_data,
             )
         if end_flat:
-            _MockEDF.add_flat_serie(
+            _MockEDF.add_flat_series(
                 scan_path=scanID,
                 n_elmt=4,
                 index=nRadio - 1,
@@ -143,7 +114,7 @@ class MockEDF(_MockEDF):
 
 class _BlissSample:
     """
-    Simple mock of a bliss sample. For now we wonyl create the hierarchy of
+    Simple mock of a bliss sample. For now we onyl create the hierarchy of
     files.
     """
 
@@ -322,13 +293,13 @@ class MockBlissAcquisition:
     """
 
     :param n_sequence: number of sequence to create
-    :param n_scan_per_sequence: number of scans (projection serie) per sequence
+    :param n_scan_per_sequence: number of scans (projection series) per sequence
     :param n_projections_per_scan: number of projection frame in a scan
-    :param n_darks: number of dark frame in the serie. Only one serie at the
+    :param n_darks: number of dark frame in the serie. Only one series at the
                     beginning
-    :param int n_flats: number of flats to create. In this case will only
-                        create one serie of n flats after dark if any
-    :param str output_dir: will contain the proposal file and one folder per
+    :param n_flats: number of flats to create. In this case will only
+                        create one series of n flats after dark if any
+    :param output_dir: will contain the proposal file and one folder per
                            sequence.
     """
 

tomwer/core/utils/slurm.py

@@ -1,34 +1,9 @@
 # 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.
-#
-#############################################################################*/
 """
 Utils for slurm
 """
 
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "11/10/2021"
-
+from __future__ import annotations
 
 import uuid
 from datetime import datetime
@@ -43,9 +18,11 @@ def is_slurm_available() -> bool:
     return has_sbatch_available()
 
 
-def get_slurm_script_name(prefix="") -> str:
-    now_str = str(datetime.now()).replace(" ", "_")
+def get_slurm_script_name(prefix: str | None = None) -> str:
+    now_str = datetime.now().strftime("%y-%m-%d_%H:%M:%S")
+    random_str = str(uuid.uuid4()).split("-")[0]
+    suffix = f"{now_str}_{random_str}_.sh"
     if prefix in ("", None):
-        return str(uuid.uuid4()).split("-")[0] + f"_{now_str}.sh"
+        return suffix
     else:
-        return f"{prefix}_" + str(uuid.uuid4()).split("-")[0] + f"_{now_str}.sh"
+        return f"{prefix}_{suffix}"

tomwer/core/utils/spec.py

@@ -1,10 +1,12 @@
+from __future__ import annotations
+
 import fileinput
 import logging
 import os
 
 import fabio.edfimage
 from lxml import etree
-from pyunitsystem import metricsystem
+from pyunitsystem.metricsystem import MetricSystem
 
 
 _logger = logging.getLogger(__name__)
@@ -163,12 +165,11 @@ def rebaseParFile(_file, oldfolder, newfolder):
             print(line)
 
 
-def getDim1Dim2(scan):
+def getDim1Dim2(scan: str) -> tuple[int]:
     """
 
     :param scan: path to the acquisition
     :return: detector definition
-    :rtype: tuple of int
     """
     d1 = _getInformation(
         scan=scan,
@@ -234,12 +235,11 @@ def getFirstProjFile(scan):
         return None
 
 
-def getPixelSize(scan):
+def getPixelSize(scan) -> float | None:
     """
     Try to retrieve the pixel size from the set of files.
 
     :return: the pixel size in meter or None
-    :rtype: None or float
     """
     if os.path.isdir(scan) is False:
         return None
@@ -258,6 +258,6 @@ def getPixelSize(scan):
                 value = float(ddict["IMAGE_PIXEL_SIZE_1".lower()])
     # for now pixel size are stored in microns. We want to return them in meter
     if value is not None:
-        return value * metricsystem.micrometer.value
+        return value * MetricSystem.MICROMETER.value
     else:
         return None

tomwer/core/utils/tests/test_image.py

@@ -0,0 +1,30 @@
+import numpy
+import pytest
+
+from tomwer.core.utils.image import ImageScaleMethod, scale_img2_to_img1, shift_img
+
+
+@pytest.mark.parametrize(
+    "use_scipy, dx, dy, cval", ((True, 1.0, -2.3, 0), (False, 0.0, 3.6, 2))
+)
+def test_shift_image(use_scipy, dx, dy, cval):
+    data = numpy.linspace(0, 12, 100 * 100).reshape(100, 100)
+    assert isinstance(
+        shift_img(data=data, dx=dx, dy=dy, cval=cval, use_scipy=use_scipy),
+        numpy.ndarray,
+    )
+
+
+def test_scale_img2_to_img1():
+    """
+    test scale_img2_to_img1 function
+    """
+    img_1 = numpy.linspace(0, 10, 100 * 100, dtype=numpy.float16).reshape(100, 100)
+    img_2 = numpy.linspace(20, 100, 100 * 100, dtype=numpy.float16).reshape(100, 100)
+
+    rescale_img = scale_img2_to_img1(img_2, img_1, method=ImageScaleMethod.MEAN)
+    numpy.testing.assert_array_almost_equal(
+        img_2,
+        rescale_img,
+        decimal=1,
+    )

tomwer/core/utils/tests/test_nxtomo.py

@@ -0,0 +1,38 @@
+# coding: utf-8
+
+import pytest
+from nxtomo.nxobject.nxdetector import ImageKey
+
+from tomwer.core.utils.nxtomoutils import get_n_series
+
+
+def test_get_n_series():
+    """test tomwer.core.utils.nxtomoutils.get_n_series function"""
+    array_1 = (
+        [ImageKey.DARK_FIELD] * 2
+        + [ImageKey.FLAT_FIELD]
+        + [ImageKey.PROJECTION] * 4
+        + [ImageKey.FLAT_FIELD]
+    )
+
+    with pytest.raises(ValueError):
+        get_n_series(array_1, ImageKey.INVALID)
+    with pytest.raises(ValueError):
+        get_n_series(array_1, 3)
+
+    assert len(array_1) == 8
+    assert get_n_series(array_1, ImageKey.DARK_FIELD) == 1
+    assert get_n_series(array_1, ImageKey.FLAT_FIELD) == 2
+    assert get_n_series(array_1, ImageKey.PROJECTION) == 1
+    assert get_n_series(array_1, 0) == 1
+
+    array_2 = (
+        [ImageKey.FLAT_FIELD.value]
+        + [ImageKey.PROJECTION.value] * 4
+        + [ImageKey.INVALID.value] * 2
+        + [ImageKey.PROJECTION.value] * 3
+        + [ImageKey.FLAT_FIELD.value]
+    )
+    assert get_n_series(array_2, ImageKey.DARK_FIELD) == 0
+    assert get_n_series(array_2, ImageKey.PROJECTION) == 1
+    assert get_n_series(array_2, ImageKey.FLAT_FIELD) == 2

tomwer/core/utils/tests/test_scan_utils.py

@@ -0,0 +1,46 @@
+import os
+
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import format_output_location
+
+
+def test_format_output_location(tmp_path):
+    """
+    test different use cases of 'format_output_location'
+    """
+    bliss_raw_dir = tmp_path / "raw"
+    bliss_raw_dir.mkdir()
+    bliss_sample_dir = bliss_raw_dir / "sample"
+    bliss_sample_dir.mkdir()
+    bliss_master_file = bliss_sample_dir / "dataset.h5"
+
+    bliss_proposal_file = bliss_raw_dir / "ihsample.h5"
+    bliss_proposal_file = os.path.abspath(bliss_proposal_file)
+
+    bliss_scan = BlissScan(
+        master_file=bliss_master_file, entry="1.1", proposal_file=bliss_proposal_file
+    )
+    expected_path = os.path.join(tmp_path, "reduced", "sample")
+    assert (
+        format_output_location(
+            location="{scan_parent_dir_basename}/../reduced/{scan_dir_name}",
+            scan=bliss_scan,
+        )
+        == expected_path
+    )
+
+    edf_scan = EDFTomoScan("/test/my/folder/")
+    assert (
+        format_output_location(
+            location="{scan_parent_dir_basename}/output", scan=edf_scan
+        )
+        == "/test/my/output"
+    )
+
+    hdf5_scan = NXtomoScan("/ddsad/my/file.hdf5", entry="entry0000")
+    assert (
+        format_output_location(location="{scan_basename}/output.nx", scan=hdf5_scan)
+        == "/ddsad/my/output.nx"
+    )

tomwer/core/utils/tests/test_time.py

@@ -0,0 +1,6 @@
+from tomwer.core.utils.time import Timer
+
+
+def test_timer():
+    with Timer("timer name"):
+        pass

tomwer/core/utils/threads.py

@@ -1,26 +1,4 @@
 # 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.
-#
-#############################################################################*/
 
 """
 This module is used to manage observations. Initially on files.
@@ -28,10 +6,6 @@ Observations are runned on a thread and run each n seconds.
 They are manage by thread and signals
 """
 
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "09/01/2019"
-
 
 import threading
 import time

tomwer/core/utils/time.py

@@ -1,26 +1,4 @@
 # 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.
-#
-#############################################################################*/
 
 """
 This module is used to manage observations. Initially on files.
@@ -28,11 +6,6 @@ Observations are runned on a thread and run each n seconds.
 They are manage by thread and signals
 """
 
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "20/10/2020"
-
-
 from time import time
 
 

tomwer/core/volume/__init__.py

@@ -1,3 +1,7 @@
+"""contains volumes classes and function. Abstraction layer for scans, based on tomoscan volumes.
+See https://gitlab.esrf.fr/tomotools/tomoscan
+"""
+
 from .edfvolume import EDFVolume  # noqa F401
 from .hdf5volume import HDF5Volume  # noqa F401
 from .jp2kvolume import JP2KVolume  # noqa F401