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

tomwer/core/volume/edfvolume.py

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "05/07/2022"
-
+from __future__ import annotations
 
 import pathlib
 from datetime import datetime

tomwer/core/volume/hdf5volume.py

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "05/07/2022"
-
+from __future__ import annotations
 
 import pathlib
 from datetime import datetime

tomwer/core/volume/jp2kvolume.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "05/07/2022"
+from __future__ import annotations
 
 
 import pathlib

tomwer/core/volume/rawvolume.py

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2023 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__ = "11/01/2023"
-
+from __future__ import annotations
 
 import pathlib
 from datetime import datetime

tomwer/core/volume/tests/test_volumes.py

@@ -0,0 +1,21 @@
+from tomwer.core.volume import EDFVolume, HDF5Volume, RawVolume
+from tomwer.core.volume.rawvolume import RawVolumeIdentifier
+
+
+def test_volume_data_parent_folder():
+    edf_volume = EDFVolume(folder="/my/folder/path")
+    assert edf_volume.volume_data_parent_folder() == "/my/folder"
+
+    hdf5_volume = HDF5Volume(file_path="/path/to/hdf5/file.hdf5", data_path="entry")
+    assert hdf5_volume.volume_data_parent_folder() == "/path/to/hdf5"
+
+    raw_volume = RawVolume(file_path="/path/to/raw.vol")
+    assert raw_volume.volume_data_parent_folder() == "/path/to"
+
+
+def test_raw_identifier():
+    raw_volume = RawVolume(file_path="/path/to/raw.vol")
+    assert (
+        RawVolumeIdentifier.from_str(raw_volume.get_identifier().to_str())
+        == raw_volume.get_identifier()
+    )

tomwer/core/volume/tiffvolume.py

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "05/07/2022"
-
+from __future__ import annotations
 
 import os
 import pathlib

tomwer/core/volume/volumebase.py

@@ -9,6 +9,11 @@ class TomwerVolumeBase(TomwerObject):
         self.data = None
         self.metadata = None
 
+    @property
+    def icat_data_dir(self) -> str:
+        """Return the data directory to be used by icat for the volume"""
+        return os.path.dirname(self.data_url.file_path())  # pylint: disable=E1101
+
     @staticmethod
     def format_output_location(location: str, volume):
         if not isinstance(volume, TomwerVolumeBase):

tomwer/core/volume/volumefactory.py

@@ -1,35 +1,7 @@
-# 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__ = "13/07/2022"
+from __future__ import annotations
 
 
 import logging
-from typing import Optional, Union
 from urllib.parse import urlparse
 
 from tomoscan import identifier as _identifier_mod
@@ -39,6 +11,7 @@ from tomoscan.identifier import BaseIdentifier, ScanIdentifier, VolumeIdentifier
 
 from tomwer.core.scan.edfscan import EDFTomoScan, EDFTomoScanIdentifier
 from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 from tomwer.core.volume import (
     EDFVolume,
     HDF5Volume,
@@ -62,7 +35,7 @@ _logger = logging.getLogger(__name__)
 
 class VolumeFactory(_oVolumeFactory):
     @staticmethod
-    def from_identifier_to_vol_urls(identifier) -> Optional[tuple]:
+    def from_identifier_to_vol_urls(identifier) -> tuple | None:
         """
         convert an identifier to a volume
         and return all the existing url of this volume
@@ -79,16 +52,17 @@ class VolumeFactory(_oVolumeFactory):
 
     @docstring(_oVolumeFactory.create_tomo_object_from_identifier)
     @staticmethod
-    def create_tomo_object_from_identifier(identifier: Union[str, BaseIdentifier]):
+    def create_tomo_object_from_identifier(
+        identifier: str | BaseIdentifier,
+    ) -> TomwerVolumeBase:
         """
 
-        :param TextIOWrapper scan_path: path to the scan directory or file
+        :param scan_path: path to the scan directory or file
         :param entry: entry on the file. Requested for hdf5 files
         :param accept_bliss_scan: if True the factory can return some BlissScan
                                   But this is only compatible with the
                                   Tomomill processing.
         :return: TomwerScanBase instance fitting the scan folder or scan path
-        :rtype: tomwer.core.scan.scanbase.TomwerScanBase
         :raises: ValueError if scan_path is not containing a scan
         """
         if isinstance(identifier, BaseIdentifier):

tomwer/gui/__init__.py

@@ -1,31 +1,3 @@
-# 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.
-#
-# ###########################################################################*/
 """This package contains all the widget which are not inheriting from
 WidgetOW (orange widgets)
 """
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "02/06/2017"

tomwer/gui/cluster/__init__.py

@@ -0,0 +1,2 @@
+"""Widgets for remote processing
+"""