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

tomwer/io/utils/test/test_utils.py

@@ -0,0 +1,67 @@
+# coding: utf-8
+"""
+contains utils for inputs and outputs
+"""
+
+from __future__ import annotations
+
+import os
+
+import h5py
+import numpy
+from silx.io.url import DataUrl
+from tomoscan.io import HDF5File
+
+from tomwer.core.utils import scanutils
+from tomwer.io.utils import (
+    get_default_directory,
+    get_linked_files_with_entry,
+    get_slice_data,
+)
+
+
+def test_get_linked_files_with_entry(tmp_path):
+    """test get_linked_files_with_entry function"""
+    dir_test = tmp_path / "sub"
+    dir_test.mkdir()
+
+    layout = h5py.VirtualLayout(shape=(4, 10, 10), dtype="i4")
+    for i_file in range(4):
+        file_name = os.path.join(dir_test, f"file_{i_file}.hdf5")
+        with HDF5File(file_name, "w") as h5s:
+            h5s.create_dataset("data", (10, 10), "i4", numpy.ones((10, 10)))
+            vsource = h5py.VirtualSource(file_name, "data", shape=(10, 10))
+            layout[i_file] = vsource
+
+    test_with_vds = os.path.join(dir_test, "file_with_vds")
+    with HDF5File(test_with_vds, "w") as h5s:
+        h5s.create_virtual_dataset("vdata", layout, fillvalue=-1)
+
+    assert len(get_linked_files_with_entry(test_with_vds, "vdata")) == 4
+
+
+def test_get_default_directory():
+    get_default_directory()
+
+
+def test_get_slice_data_vol(tmp_path):
+    """test load of a .vol file"""
+    dir_test = tmp_path / "test_vol"
+    dir_test.mkdir()
+    vol_file_path = os.path.join(dir_test, "volume.vol")
+    vol_info_file_path = os.path.join(dir_test, "volume.vol.info")
+
+    shape = (4, 50, 20)
+    data = numpy.ones(shape)
+    data.astype(numpy.float32).tofile(vol_file_path)
+    scanutils.MockEDF._createVolInfoFile(
+        filePath=vol_info_file_path,
+        shape=shape,
+    )
+
+    vol = get_slice_data(DataUrl(file_path=vol_file_path))
+    assert vol is not None
+    assert vol.shape == shape
+    vol = get_slice_data(DataUrl(file_path=vol_info_file_path))
+    assert vol is not None
+    assert vol.shape == shape

tomwer/io/utils/utils.py

@@ -1,35 +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.
-#
-# ###########################################################################*/
 """
 contains utils for inputs and outputs
 """
 
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "07/09/2020"
-
+from __future__ import annotations
 
 import logging
 import os
@@ -40,7 +13,6 @@ from PIL import Image
 from silx.io.utils import open as open_hdf5
 from tomoscan.esrf import has_glymur
 from tomoscan.esrf.scan.utils import get_data as tomoscan_get_data
-from typing import Union
 
 from tomwer.core.utils import ftseriesutils
 
@@ -155,7 +127,6 @@ def get_default_directory() -> str:
     """
 
     :return: default directory where to open a QFolder dialdg for example
-    :rtype: str
     """
     if "TOMWER_DEFAULT_INPUT_DIR" in os.environ and os.path.exists(
         os.environ["TOMWER_DEFAULT_INPUT_DIR"]
@@ -273,7 +244,7 @@ def get_linked_files_with_vds(hdf5_file: str, dataset_path: str) -> set:
     return final_datasets
 
 
-def str_to_dict(my_str: Union[str, dict]):
+def str_to_dict(my_str: str | dict):
     """convert a string as key_1=value_2;key_2=value_2 to a dict"""
     if isinstance(my_str, dict):
         return my_str

tomwer/resources/__init__.py

@@ -1,35 +1,14 @@
-# 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.
-#
-# ###########################################################################*/
-
+"""
+project resources (icons... )
+"""
 
 from __future__ import annotations
+
 import os
 import sys
 import contextlib
 import atexit
-from typing import NamedTuple, Optional
+from typing import NamedTuple
 import importlib
 import functools
 
@@ -65,7 +44,7 @@ class _ResourceDirectory(NamedTuple):
     """Store a source of resources"""
 
     package_name: str
-    forced_path: Optional[str] = None
+    forced_path: str | None = None
 
 
 _TOMWER_DIRECTORY = _ResourceDirectory(
@@ -77,17 +56,18 @@ _RESOURCE_DIRECTORIES = {}
 _RESOURCE_DIRECTORIES["tomwer"] = _TOMWER_DIRECTORY
 
 
-def _get_package_and_resource(resource, default_directory=None):
+def _get_package_and_resource(
+    resource, default_directory=None
+) -> tuple[_ResourceDirectory, str]:
     """
     Return the resource directory class and a cleaned resource name without
     prefix.
 
-    :param str: resource: Name of the resource with resource prefix.
-    :param str default_directory: If the resource is not prefixed, the resource
+    :param resource: Name of the resource with resource prefix.
+    :param default_directory: If the resource is not prefixed, the resource
         will be searched on this default directory of the silx resource
         directory.
-    :rtype: tuple(_ResourceDirectory, str)
-    :raises ValueError: If the resource name uses an unregistred resource
+    :raises ValueError: If the resource name uses an unregistered resource
         directory name
     """
     if ":" in resource:
@@ -126,7 +106,7 @@ def _get_resource_filename(package: str, resource: str) -> str:
     return str(path.absolute())
 
 
-def _resource_filename(resource: str, default_directory: Optional[str] = None) -> str:
+def _resource_filename(resource: str, default_directory: str | None = None) -> str:
     """Return filename corresponding to resource.
 
     The existence of the resource is not checked.

tomwer/resources/gui/icons/edit_downstream.svg

@@ -0,0 +1,114 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   id="svg901"
+   width="40"
+   height="40"
+   version="1.1"
+   viewBox="0 0 10.583333 10.583333"
+   sodipodi:docname="edit_downstream.svg"
+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/">
+  <defs
+     id="defs18" />
+  <sodipodi:namedview
+     id="namedview16"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
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+     id="metadata898">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
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+  </g>
+</svg>

tomwer/resources/gui/icons/edit_upstream.svg

@@ -0,0 +1,112 @@
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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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+   id="svg901"
+   width="40"
+   height="40"
+   version="1.1"
+   viewBox="0 0 10.583333 10.583333"
+   sodipodi:docname="edit_upstream.svg"
+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
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+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:dc="http://purl.org/dc/elements/1.1/">
+  <defs
+     id="defs17" />
+  <sodipodi:namedview
+     id="namedview15"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
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+        <dc:type
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tomwer/resources/gui/icons/free_edition.svg

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
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+ <metadata id="metadata898">
+  <rdf:RDF>
+   <cc:Work rdf:about="">
+    <dc:format>image/svg+xml</dc:format>
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+  </g>
+ </g>
+</svg>

tomwer/resources/gui/icons/icat_gallery_opts.svg

@@ -0,0 +1,80 @@
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+
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+   height="48"
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tomwer/resources/gui/icons/search.svg

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+<?xml version="1.0" encoding="UTF-8"?>
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+ </defs>
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tomwer/synctools/__init__.py

@@ -1,4 +1,6 @@
 """
 Contains tools used by the orange add-on and used to keep the orange-add-on and
 gui 'alive', avoid gui freeze during processing.
+
+With time it should be replace by the ewoksorange mechanism (inheritance to ewoksorange widgets)
 """