tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

tomwer/core/process/utils.py

@@ -1,36 +1,8 @@
 # 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__ = "04/03/2019"
-
+from __future__ import annotations
 
 import datetime
 import logging
-import typing
 from collections import OrderedDict
 
 import h5py
@@ -71,12 +43,11 @@ class IgnoreProcess:
     __call__ = process
 
 
-def get_scores(node: h5py.Group) -> typing.Union[None, dict]:
+def get_scores(node: h5py.Group) -> dict | None:
     """read all the score from the 'results' sub group. Read the url
     and computed scores
 
     :return: a dictionary with (url, ComputedScore) for each node
-    :rtype: dict or None
     """
     if "results" not in node:
         _logger.warning(f"no results found in {node}")

tomwer/core/process/visualization/dataviewer.py

@@ -1,30 +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__ = "23/08/2021"
+from __future__ import annotations
 
 
 from ewokscore.task import Task as EwoksTask

tomwer/core/process/visualization/diffviewer.py

@@ -1,30 +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__ = "23/08/2021"
+from __future__ import annotations
 
 
 from ewokscore.task import Task as EwoksTask

tomwer/core/process/visualization/imagestackviewer.py

@@ -1,30 +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__ = "23/08/2021"
 
 
 from ewokscore.task import Task as EwoksTask

tomwer/core/process/visualization/radiostack.py

@@ -1,30 +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__ = "23/08/2021"
 
 
 from ewokscore.task import Task as EwoksTask

tomwer/core/process/visualization/samplemoved.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__ = "23/08/2021"
-
 
 from ewokscore.task import Task as EwoksTask
 

tomwer/core/process/visualization/sinogramviewer.py

@@ -1,31 +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__ = "23/08/2021"
-
 
 from ewokscore.task import Task as EwoksTask
 

tomwer/core/process/visualization/slicestack.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__ = "23/08/2021"
-
 
 from ewokscore.task import Task as EwoksTask
 

tomwer/core/process/visualization/tests/test_data_viewer.py

@@ -0,0 +1,12 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.dataviewer import _DataViewerPlaceHolder
+
+
+def test_data_viewer():
+    process = _DataViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_diff_viewer.py

@@ -0,0 +1,12 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.diffviewer import _DiffViewerPlaceHolder
+
+
+def test_diff_viewer():
+    process = _DiffViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_image_stack_viewer.py

@@ -0,0 +1,14 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.imagestackviewer import (
+    _ImageStackViewerPlaceHolder,
+)
+
+
+def test_image_stack_viewer():
+    process = _ImageStackViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_radio_stack.py

@@ -0,0 +1,12 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.radiostack import _RadioStackPlaceHolder
+
+
+def test_radio_stack():
+    process = _RadioStackPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_sample_moved.py

@@ -0,0 +1,14 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.imagestackviewer import (
+    _ImageStackViewerPlaceHolder,
+)
+
+
+def test_sample_moved():
+    process = _ImageStackViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_sinogram_viewer.py

@@ -0,0 +1,13 @@
+# coding: utf-8
+
+
+from tomwer.core.process.visualization.sinogramviewer import _SinogramViewerPlaceHolder
+
+
+def test_sinogram_viewer():
+    process = _SinogramViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_slice_stack.py

@@ -0,0 +1,13 @@
+# coding: utf-8
+
+
+from tomwer.core.process.visualization.slicestack import _SliceStackPlaceHolder
+
+
+def test_slice_stack():
+    process = _SliceStackPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/tests/test_volume_viewer.py

@@ -0,0 +1,12 @@
+# coding: utf-8
+
+from tomwer.core.process.visualization.volumeviewer import _VolumeViewerPlaceHolder
+
+
+def test_volume_viewer():
+    process = _VolumeViewerPlaceHolder(
+        inputs={
+            "data": None,
+        }
+    )
+    process.run()

tomwer/core/process/visualization/volumeviewer.py

@@ -1,33 +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__ = "23/08/2021"
-
-
 from ewokscore.task import Task as EwoksTask
 
 

tomwer/core/scan/__init__.py

@@ -1,30 +1,6 @@
 # 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__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "09/08/2018"
+"""contains scan classes and function. Abstraction layer for scans, based on tomoscan classes.
+See https://gitlab.esrf.fr/tomotools/tomoscan
+"""
 
 TYPES = ["EDF", "HDF5"]

tomwer/core/scan/blissscan.py

@@ -1,32 +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__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "09/08/2018"
-
+from __future__ import annotations
 
 import os
 
@@ -51,7 +23,6 @@ except ImportError:
     from nxtomomill.settings import H5_PCOTOMO_INIT_TITLES
 
 import logging
-from typing import Optional
 
 from silx.io.utils import h5py_read_dataset
 from silx.io.utils import open as open_hdf5
@@ -63,7 +34,7 @@ class BlissScan:
     """Simple class to define a Bliss sequence aka as Bliss scan inside tomwer.
 
     :warning: BlissScan is not compatible with tomwer treatment. This is
-    why it does not inherit from TomwerScanBase. This is a utility class.
+        why it does not inherit from TomwerScanBase. This is a utility class.
     """
 
     _TYPE = "bliss_hdf5"
@@ -160,21 +131,21 @@ class BlissScan:
         # for now there is not real way to know if a scan is abort or not
         return False
 
-    def scan_dir_name(self) -> Optional[str]:
+    def scan_dir_name(self) -> str | None:
         """for 'this/is/my/acquisition' returns 'acquisition'"""
         if self.path is not None:
             return self.path.split(os.sep)[-1]
         else:
             return None
 
-    def scan_basename(self) -> Optional[str]:
+    def scan_basename(self) -> str | None:
         """for 'this/is/my/acquisition' returns 'acquisition'"""
         if self.path is not None:
             return self.path
         else:
             return None
 
-    def scan_parent_dir_basename(self) -> Optional[str]:
+    def scan_parent_dir_basename(self) -> str | None:
         if self.path is not None:
             try:
                 return os.path.dirname(self.path)