tomwer 1.2.8__tar.gz → 1.3.10__tar.gz

tomwer-1.3.10/PKG-INFO

@@ -0,0 +1,306 @@
+Metadata-Version: 2.1
+Name: tomwer
+Version: 1.3.10
+Summary: "tomography workflow tools"
+Home-page: https://gitlab.esrf.fr/tomotools/tomwer
+Author: data analysis unit
+Author-email: henri.payno@esrf.fr
+License: MIT
+Project-URL: Bug Tracker, https://gitlab.esrf.fr/tomotools/tomwer/-/issues
+Keywords: orange3 add-on,ewoks
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Environment :: Console
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Operating System :: POSIX
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: psutil
+Requires-Dist: silx[full]>=2.0
+Requires-Dist: tomoscan>=2.0.0a11
+Requires-Dist: nxtomo>=1.2.3rc1
+Requires-Dist: nxtomomill>=1.0dev
+Requires-Dist: processview>=1.3
+Requires-Dist: ewoks>=0.1.1
+Requires-Dist: ewoksorange==0.6
+Requires-Dist: sluurp>=0.3.3
+Requires-Dist: packaging
+Requires-Dist: flufl-lock
+Requires-Dist: pyunitsystem>=1.1.0
+Provides-Extra: full-base
+Requires-Dist: orange-canvas-core; extra == "full-base"
+Requires-Dist: orange-widget-base; extra == "full-base"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-base"
+Requires-Dist: rsyncmanager; extra == "full-base"
+Requires-Dist: graypy; extra == "full-base"
+Requires-Dist: fabio; extra == "full-base"
+Requires-Dist: h5py>=3; extra == "full-base"
+Requires-Dist: lxml; extra == "full-base"
+Requires-Dist: werkzeug; extra == "full-base"
+Requires-Dist: json-rpc; extra == "full-base"
+Requires-Dist: scipy; extra == "full-base"
+Requires-Dist: Pillow; extra == "full-base"
+Requires-Dist: glymur; extra == "full-base"
+Requires-Dist: resource; extra == "full-base"
+Requires-Dist: tifffile; extra == "full-base"
+Requires-Dist: hdf5plugin; extra == "full-base"
+Requires-Dist: pyicat_plus; extra == "full-base"
+Provides-Extra: full-no-nabu
+Requires-Dist: orange-canvas-core; extra == "full-no-nabu"
+Requires-Dist: orange-widget-base; extra == "full-no-nabu"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-nabu"
+Requires-Dist: rsyncmanager; extra == "full-no-nabu"
+Requires-Dist: graypy; extra == "full-no-nabu"
+Requires-Dist: fabio; extra == "full-no-nabu"
+Requires-Dist: h5py>=3; extra == "full-no-nabu"
+Requires-Dist: lxml; extra == "full-no-nabu"
+Requires-Dist: werkzeug; extra == "full-no-nabu"
+Requires-Dist: json-rpc; extra == "full-no-nabu"
+Requires-Dist: scipy; extra == "full-no-nabu"
+Requires-Dist: Pillow; extra == "full-no-nabu"
+Requires-Dist: glymur; extra == "full-no-nabu"
+Requires-Dist: resource; extra == "full-no-nabu"
+Requires-Dist: tifffile; extra == "full-no-nabu"
+Requires-Dist: hdf5plugin; extra == "full-no-nabu"
+Requires-Dist: pyicat_plus; extra == "full-no-nabu"
+Provides-Extra: full-no-cuda
+Requires-Dist: orange-canvas-core; extra == "full-no-cuda"
+Requires-Dist: orange-widget-base; extra == "full-no-cuda"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "full-no-cuda"
+Requires-Dist: rsyncmanager; extra == "full-no-cuda"
+Requires-Dist: graypy; extra == "full-no-cuda"
+Requires-Dist: fabio; extra == "full-no-cuda"
+Requires-Dist: h5py>=3; extra == "full-no-cuda"
+Requires-Dist: lxml; extra == "full-no-cuda"
+Requires-Dist: werkzeug; extra == "full-no-cuda"
+Requires-Dist: json-rpc; extra == "full-no-cuda"
+Requires-Dist: scipy; extra == "full-no-cuda"
+Requires-Dist: Pillow; extra == "full-no-cuda"
+Requires-Dist: glymur; extra == "full-no-cuda"
+Requires-Dist: resource; extra == "full-no-cuda"
+Requires-Dist: tifffile; extra == "full-no-cuda"
+Requires-Dist: hdf5plugin; extra == "full-no-cuda"
+Requires-Dist: pyicat_plus; extra == "full-no-cuda"
+Requires-Dist: nabu>=2023.3.1dev; extra == "full-no-cuda"
+Provides-Extra: full
+Requires-Dist: orange-canvas-core; extra == "full"
+Requires-Dist: orange-widget-base; extra == "full"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "full"
+Requires-Dist: rsyncmanager; extra == "full"
+Requires-Dist: graypy; extra == "full"
+Requires-Dist: fabio; extra == "full"
+Requires-Dist: h5py>=3; extra == "full"
+Requires-Dist: lxml; extra == "full"
+Requires-Dist: werkzeug; extra == "full"
+Requires-Dist: json-rpc; extra == "full"
+Requires-Dist: scipy; extra == "full"
+Requires-Dist: Pillow; extra == "full"
+Requires-Dist: glymur; extra == "full"
+Requires-Dist: resource; extra == "full"
+Requires-Dist: tifffile; extra == "full"
+Requires-Dist: hdf5plugin; extra == "full"
+Requires-Dist: pyicat_plus; extra == "full"
+Requires-Dist: nabu[full]>=2023.3.1dev; extra == "full"
+Requires-Dist: pycuda; extra == "full"
+Requires-Dist: scikit-cuda; extra == "full"
+Provides-Extra: doc
+Requires-Dist: orange-canvas-core; extra == "doc"
+Requires-Dist: orange-widget-base; extra == "doc"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "doc"
+Requires-Dist: rsyncmanager; extra == "doc"
+Requires-Dist: graypy; extra == "doc"
+Requires-Dist: fabio; extra == "doc"
+Requires-Dist: h5py>=3; extra == "doc"
+Requires-Dist: lxml; extra == "doc"
+Requires-Dist: werkzeug; extra == "doc"
+Requires-Dist: json-rpc; extra == "doc"
+Requires-Dist: scipy; extra == "doc"
+Requires-Dist: Pillow; extra == "doc"
+Requires-Dist: glymur; extra == "doc"
+Requires-Dist: resource; extra == "doc"
+Requires-Dist: tifffile; extra == "doc"
+Requires-Dist: hdf5plugin; extra == "doc"
+Requires-Dist: pyicat_plus; extra == "doc"
+Requires-Dist: nabu>=2023.3.1dev; extra == "doc"
+Requires-Dist: Sphinx>=4.0.0; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: pandoc; extra == "doc"
+Requires-Dist: jupyterlab; extra == "doc"
+Requires-Dist: pydata_sphinx_theme; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints; extra == "doc"
+Provides-Extra: dev-spec
+Requires-Dist: black; extra == "dev-spec"
+Requires-Dist: flake8; extra == "dev-spec"
+Requires-Dist: timeout-decorator; extra == "dev-spec"
+Requires-Dist: pyopencl; extra == "dev-spec"
+Provides-Extra: dev
+Requires-Dist: orange-canvas-core; extra == "dev"
+Requires-Dist: orange-widget-base; extra == "dev"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev"
+Requires-Dist: rsyncmanager; extra == "dev"
+Requires-Dist: graypy; extra == "dev"
+Requires-Dist: fabio; extra == "dev"
+Requires-Dist: h5py>=3; extra == "dev"
+Requires-Dist: lxml; extra == "dev"
+Requires-Dist: werkzeug; extra == "dev"
+Requires-Dist: json-rpc; extra == "dev"
+Requires-Dist: scipy; extra == "dev"
+Requires-Dist: Pillow; extra == "dev"
+Requires-Dist: glymur; extra == "dev"
+Requires-Dist: resource; extra == "dev"
+Requires-Dist: tifffile; extra == "dev"
+Requires-Dist: hdf5plugin; extra == "dev"
+Requires-Dist: pyicat_plus; extra == "dev"
+Requires-Dist: nabu[full]>=2023.3.1dev; extra == "dev"
+Requires-Dist: pycuda; extra == "dev"
+Requires-Dist: scikit-cuda; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: timeout-decorator; extra == "dev"
+Requires-Dist: pyopencl; extra == "dev"
+Provides-Extra: dev-no-cuda
+Requires-Dist: orange-canvas-core; extra == "dev-no-cuda"
+Requires-Dist: orange-widget-base; extra == "dev-no-cuda"
+Requires-Dist: ewoks[orange]>=0.1.1; extra == "dev-no-cuda"
+Requires-Dist: rsyncmanager; extra == "dev-no-cuda"
+Requires-Dist: graypy; extra == "dev-no-cuda"
+Requires-Dist: fabio; extra == "dev-no-cuda"
+Requires-Dist: h5py>=3; extra == "dev-no-cuda"
+Requires-Dist: lxml; extra == "dev-no-cuda"
+Requires-Dist: werkzeug; extra == "dev-no-cuda"
+Requires-Dist: json-rpc; extra == "dev-no-cuda"
+Requires-Dist: scipy; extra == "dev-no-cuda"
+Requires-Dist: Pillow; extra == "dev-no-cuda"
+Requires-Dist: glymur; extra == "dev-no-cuda"
+Requires-Dist: resource; extra == "dev-no-cuda"
+Requires-Dist: tifffile; extra == "dev-no-cuda"
+Requires-Dist: hdf5plugin; extra == "dev-no-cuda"
+Requires-Dist: pyicat_plus; extra == "dev-no-cuda"
+Requires-Dist: nabu>=2023.3.1dev; extra == "dev-no-cuda"
+Requires-Dist: black; extra == "dev-no-cuda"
+Requires-Dist: flake8; extra == "dev-no-cuda"
+Requires-Dist: timeout-decorator; extra == "dev-no-cuda"
+Requires-Dist: pyopencl; extra == "dev-no-cuda"
+Provides-Extra: test
+Requires-Dist: pytest-asyncio; extra == "test"
+Requires-Dist: tomoscan[test]>=2.0.2rc17; extra == "test"
+Provides-Extra: setup-requires
+Requires-Dist: setuptools; extra == "setup-requires"
+Requires-Dist: numpy>=1.12; extra == "setup-requires"
+
+tomwer
+======
+
+tomwer is offering tools to automate acquisition and reconstruction processes for Tomography.
+It contains:
+
+- a library to access each acquisition process individually
+- gui and applications to control main processes (reconstruction, data transfert...) and execute them as a stand alone application.
+- an orange add-on to help users defining their own workflow (http://orange.biolab.si)
+
+
+
+.. image:: http://www.edna-site.org/pub/doc/tomwer/extra/tomwer_start_short.gif
+
+
+.. |Gitlab Status| image:: https://gitlab.esrf.fr/tomotools/tomwer/badges/master/pipeline.svg
+    :target: https://gitlab.esrf.fr/tomotools/tomwer/pipelines
+
+
+Documentation
+-------------
+
+`Latest documentation <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_
+
+
+Installation
+------------
+
+Step 1 - tomwer
+'''''''''''''''
+
+To install it with all 'features':
+
+.. code-block:: bash
+
+    pip install tomwer[full]
+
+alternatively you can install the master branch from
+
+.. code-block:: bash
+
+    pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
+
+
+Step 2 - update orange-canvas-core and orange-widget-base (Optional)
+''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
+To access 'processing' wheels and 'reprocess action' you might want to install forks of update orange-canvas-core and orange-widget-base. This is optional and projects works with native orange projects
+
+.. code-block:: bash
+
+    pip install git+https://github.com/payno/orange-canvas-core --no-deps --upgrade
+    pip install git+https://github.com/payno/orange-widget-base --no-deps --upgrade
+
+
+Launching applications
+::::::::::::::::::::::
+
+After the installation tomwer is embedding several applications.
+
+Those applications can be launched by calling:
+
+.. code-block:: bash
+
+   tomwer appName {options}
+
+.. note:: if you only call `tomwer` then the man page will be displayed.
+
+.. note:: You can access each application help using ``
+
+    .. code-block:: bash
+
+       tomwer appName --help
+
+
+tomwer canvas - orange canvas
+'''''''''''''''''''''''''''''
+
+You can launch the canvas to create workflows from the different 'bricks'
+
+.. code-block:: bash
+
+   tomwer canvas
+
+.. note:: you can also use `orange-canvas`
+
+.. note:: if your installed a virtual environment do not forget to active it :
+
+    .. code-block:: bash
+
+       source myvirtualenv/bin/activate
+
+
+Documentation
+:::::::::::::
+
+.. code-block:: bash
+
+   sphinx-build doc build/html
+
+The documentation is build in doc/build/html and the entry point is index.html
+
+.. code-block:: bash
+
+   firefox build/html/index.html
+
+.. note:: the build of the documentation need sphinx to be installed. This is not an hard dependacy. So you might need to install it.

tomwer-1.3.10/orangecontrib/tomwer/tutorials/icat_publication.ows

@@ -0,0 +1,58 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="Reconstruction of a volume and publication to icat" description="">
+	<nodes>
+		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(150, 150)" />
+		<node id="1" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(324.0, 183.0)" />
+		<node id="2" name="default center of rotation" qualified_name="orangecontrib.tomwer.widgets.reconstruction.AxisOW.AxisOW" project_name="tomwer" version="" title="default center of rotation" position="(490.0, 218.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(649.0, 261.0)" />
+		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(818.0, 248.0)" />
+		<node id="5" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(812.0, 391.0)" />
+		<node id="6" name="volume viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.VolumeViewerOW.VolumeViewerOW" project_name="tomwer" version="" title="volume viewer" position="(986.75, 383.25)" />
+		<node id="7" name="create raw data screenshots" qualified_name="orangecontrib.tomwer.widgets.icat.RawDataScreenshotCreatorOW.RawDataScreenshotCreatorOW" project_name="tomwer" version="" title="create raw data screenshots" position="(321.0, 509.0)" />
+		<node id="8" name="save to gallery and publish" qualified_name="orangecontrib.tomwer.widgets.icat.SaveToGalleryAndPublishOW.SaveToGalleryAndPublishOW" project_name="tomwer" version="" title="save to gallery and publish" position="(506.0, 510.0)" />
+		<node id="9" name="save to gallery and publish" qualified_name="orangecontrib.tomwer.widgets.icat.SaveToGalleryAndPublishOW.SaveToGalleryAndPublishOW" project_name="tomwer" version="" title="save to gallery and publish (1)" position="(731.0, 514.0)" />
+		<node id="10" name="Publish processed data to icat" qualified_name="orangecontrib.tomwer.widgets.icat.PublishProcessedDataOW.PublishProcessedDataOW" project_name="tomwer" version="" title="Publish processed data to icat" position="(990.0, 514.0)" />
+	</nodes>
+	<links>
+		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="1" source_node_id="1" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="2" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="3" source_node_id="3" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="4" source_node_id="3" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="5" source_node_id="5" sink_node_id="6" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="6" source_node_id="0" sink_node_id="7" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="7" source_node_id="7" sink_node_id="8" source_channel="screenshots" sink_channel="screenshots" enabled="true" source_channel_id="screenshots" sink_channel_id="screenshots" />
+		<link id="8" source_node_id="3" sink_node_id="9" source_channel="screenshots" sink_channel="screenshots" enabled="true" source_channel_id="screenshots" sink_channel_id="screenshots" />
+		<link id="9" source_node_id="5" sink_node_id="10" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<arrow id="0" start="(267.0, 56.0)" end="(194.0, 105.0)" fill="#C1272D" />
+		<text id="1" type="text/plain" rect="(276.25, 17.75, 150.0, 31.0)" font-family="Ubuntu" font-size="16">provide dataset</text>
+		<text id="2" type="text/plain" rect="(146.0, 597.0, 168.0, 89.0)" font-family="Cantarell" font-size="16">create screenshot for raw projection, raw falt and raw dark</text>
+		<text id="3" type="text/plain" rect="(413.0, 612.0, 215.0, 62.0)" font-family="Cantarell" font-size="16">save screenshot to the gallry and publish to icat</text>
+		<arrow id="4" start="(630.0, 605.0)" end="(674.0, 573.0)" fill="#C1272D" />
+		<arrow id="5" start="(475.99999999999994, 612.0)" end="(477.99999999999994, 568.0)" fill="#C1272D" />
+		<arrow id="6" start="(607.0, 387.0)" end="(671.0, 395.0)" fill="#C1272D" />
+		<text id="7" type="text/plain" rect="(449.0, 350.0, 150.0, 51.0)" font-family="Cantarell" font-size="16">screenshot of the reconstructed slice</text>
+		<arrow id="8" start="(235.0, 592.0)" end="(281.0, 521.0)" fill="#C1272D" />
+		<text id="9" type="text/plain" rect="(901.0, 618.0, 179.0, 70.0)" font-family="Cantarell" font-size="16">publish reconstructed volume to icat</text>
+		<arrow id="10" start="(980.0, 621.0)" end="(981.0, 579.0)" fill="#C1272D" />
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'axis_params': {'MODE': 'manual', 'POSITION_VALUE': None, 'CALC_INPUT_TYPE': 'transmission_nopag', 'ANGLE_MODE': '0-180', 'USE_SINOGRAM': False, 'SINOGRAM_LINE': '', 'SINOGRAM_SUBSAMPLING': 10, 'AXIS_URL_1': '', 'AXIS_URL_2': '', 'LOOK_AT_STDMAX': False, 'NEAR_WX': 5, 'FINE_STEP_X': 0.1, 'SCALE_IMG2_TO_IMG1': False, 'NEAR_POSITION': 0.0, 'PADDING_MODE': 'edge', 'FLIP_LR': True, 'COMPOSITE_OPTS': {'theta': 10, 'n_subsampling_y': 10, 'oversampling': 4, 'take_log': True, 'near_pos': 0, 'near_width': 20}, 'SIDE': 'all', 'COR_OPTIONS': ''}, 'gui': {'mode_is_lock': False, 'value_is_lock': False, 'auto_update_estimated_cor': True}}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="4" format="literal">{'_viewer_config': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="5" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_volume_params': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="6" format="literal">{'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="7" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="8" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="9" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="10" format="literal">{'_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.3.10/orangecontrib/tomwer/widgets/__init__.py

@@ -0,0 +1,63 @@
+# 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.
+#
+#############################################################################
+
+try:
+    from orangecanvas.utils.pkgmeta import get_distribution
+except ImportError:
+    from pkg_resources import get_distribution
+
+ICON = "../widgets/icons/tomwer.png"
+
+BACKGROUND = "#C0CCFF"
+
+
+# Entry point for main Orange categories/widgets discovery
+def widget_discovery(discovery):
+    dist = get_distribution("tomwer")
+    pkgs = [
+        "orangecontrib.tomwer.widgets.cluster",
+        "orangecontrib.tomwer.widgets.control",
+        "orangecontrib.tomwer.widgets.debugtools",
+        "orangecontrib.tomwer.widgets.edit",
+        # "orangecontrib.tomwer.widgets.icat",
+        "orangecontrib.tomwer.widgets.reconstruction",
+        # "orangecontrib.tomwer.widgets.stitching",
+        "orangecontrib.tomwer.widgets.visualization",
+        "orangecontrib.tomwer.widgets.other",
+    ]
+    for pkg in pkgs:
+        discovery.process_category_package(pkg, distribution=dist)
+
+
+WIDGET_HELP_PATH = (
+    # Used for development.
+    # You still need to build help pages using
+    # make htmlhelp
+    # inside doc folder
+    # (
+    #     "/home/payno/Documents/dev/tomography/tomwer/build/html/canvas/widgets/widgets.html",
+    #     None,
+    # ),
+    ("https://tomwer.readthedocs.io/en/latest/canvas/widgets/widgets.html", None),
+)

tomwer-1.3.10/orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py

@@ -0,0 +1,230 @@
+import fnmatch
+import logging
+import os
+from typing import Optional
+
+import h5py
+from orangewidget import gui, widget
+from orangewidget.widget import Output
+from silx.gui import qt
+from orangewidget.settings import Setting
+
+import tomwer.core.process.control.datadiscovery
+from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.scan.scantype import ScanType
+from tomwer.gui.control.datadiscovery import DataDiscoveryWidget
+
+logger = logging.getLogger(__name__)
+
+
+class DataDiscoveryOW(widget.OWBaseWidget, WidgetLongProcessing, openclass=True):
+    """
+    This widget will browse a folder and sub folder to find valid tomo scan project.
+    Contrary to the scan watcher it will parse all folder / sub folders then stop.
+    """
+
+    name = "scan discovery"
+    id = "orangecontrib.widgets.tomwer.control.DataDiscoveryOW.DataDiscoveryOW"
+    description = (
+        "This widget will browse a folder and sub folder to find valid tomo scan project. \n"
+        "Contrary to the scan watcher it will parse all folder / sub folders then stop."
+    )
+    icon = "icons/datadiscover.svg"
+    priority = 11
+    keywords = [
+        "tomography",
+        "tomwer",
+        "datadiscovery",
+        "data",
+        "discovery",
+        "search",
+        "research",
+        "hdf5",
+        "NXtomo",
+    ]
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    ewokstaskclass = tomwer.core.process.control.datadiscovery._DataDiscoveryPlaceHolder
+
+    class Outputs:
+        data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
+
+    settings = Setting(dict())
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._widget = DataDiscoveryWidget(parent=self)
+
+        self._box = gui.vBox(self.mainArea, self.name)
+        layout = self._box.layout()
+        layout.addWidget(self._widget)
+
+        self._widget.setConfiguration(self.settings)
+
+        # getting ready for processing
+        self._processingThread = _DiscoverThread()
+
+        # connect signal / slot
+        self._processingThread.sigDataFound.connect(self._sendData)
+        self._processingThread.finished.connect(self._endProcessing)
+        self._widget.widget.controlWidget._qpbstartstop.released.connect(
+            self._switchObservation
+        )
+        # dedicated one for settings
+        self._widget.widget.controlWidget._filterQLE.editingFinished.connect(
+            self._updatesettings
+        )
+        self._widget.widget.controlWidget._qteFolderSelected.editingFinished.connect(
+            self._updatesettings
+        )
+        self._widget.widget.configWidget.sigScanTypeChanged.connect(
+            self._updatesettings
+        )
+
+    def _updatesettings(self):
+        self.settings = self.getConfiguration()
+
+    # expose some API
+    def getConfiguration(self) -> dict:
+        return self._widget.getConfiguration()
+
+    def setConfiguration(self, config: dict):
+        self._widget.setConfiguration(config)
+
+    def getProcessingThread(self) -> qt.QThread:
+        return self._processingThread
+
+    def setFolderObserved(self, dir_: str):
+        self._widget.widget.setFolderObserved(dir_)
+
+    def setSearchScanType(self, scan_type):
+        self._widget.widget.setSearchScanType(scan_type)
+
+    def setFilePattern(self, pattern: Optional[str]):
+        self._widget.widget.setLinuxFilePattern(pattern)
+
+    def _switchObservation(self, *args, **kwargs):
+        """stop or start the disceovery according to the thread state"""
+        thread = self.getProcessingThread()
+        if thread.isRunning():
+            thread.quit()
+            self._endProcessing()
+        else:
+            self.start_discovery()
+
+    def start_discovery(self, wait: Optional[int] = None):
+        """start the discovery of scans
+        :param int wait: optional waiting time in second
+        """
+        thread = self.getProcessingThread()
+        if thread.isRunning():
+            logger.warning("Discovery is already running")
+            return
+        self._startProcessing()
+        thread.setConfiguration(self.getConfiguration())
+        thread.start()
+        if wait is not None:
+            thread.wait(wait)
+
+    def _sendData(self, data):
+        if data is not None:
+            self.Outputs.data.send(data)
+
+    def _startProcessing(self, *args, **kwargs):
+        self._widget.widget.controlWidget._qpbstartstop.setText("stop discovery")
+        return super()._startProcessing(*args, **kwargs)
+
+    def _endProcessing(self, *args, **kwargs):
+        self._widget.widget.controlWidget._qpbstartstop.setText("start discovery")
+        return super()._endProcessing(*args, **kwargs)
+
+
+class _DiscoverThread(qt.QThread):
+    """
+    Thread to browse folder and sub folder and looking for some scan
+    """
+
+    sigDataFound = qt.Signal(object)
+    """emit each time a new dataset is found"""
+
+    def __init__(self, **kwargs) -> None:
+        super().__init__(**kwargs)
+        self._root_dir = None
+        self._research_type = None
+        self._file_filter = None
+        self._look_for_hdf5 = False
+
+    def setConfiguration(self, config: dict):
+        self._root_dir = config.get("start_folder", None)
+        self._research_type = ScanType.from_value(config["scan_type_searched"])
+        self._file_filter = config.get("file_filter", None)
+        self._look_for_hdf5 = self._research_type in (
+            ScanType.BLISS,
+            ScanType.NX_TOMO,
+        )
+
+    def run(self):
+        if self._research_type is None:
+            logger.error("No reserach type defined. Cannot research scan")
+        elif not os.path.isdir(self._root_dir):
+            logger.error(f"{self._root_dir} is not a directory")
+        else:
+            self.discover_scan(file_path=self._root_dir)
+
+    def discover_scan(self, file_path):
+        if (
+            os.path.isfile(file_path)
+            and self._look_for_hdf5
+            and h5py.is_hdf5(file_path)
+        ) or (os.path.isdir(file_path) and not self._look_for_hdf5):
+            try:
+                name_match = self._file_filter is None or fnmatch.fnmatch(
+                    os.path.basename(file_path), self._file_filter
+                )
+            except Exception as e:
+                logger.error(f"fnmatch fail. Error is {e}")
+                name_match = True
+            if name_match:
+                self._treat_path(file_path)
+        if os.path.isdir(file_path):
+            [
+                self.discover_scan(file_path=os.path.join(file_path, file_))
+                for file_ in os.listdir(file_path)
+            ]
+
+    def _treat_path(self, folder_path: str):
+        """treat file / folder at a specific location"""
+        try:
+            scan_objs = ScanFactory.create_scan_objects(
+                scan_path=folder_path,
+                accept_bliss_scan=(self._research_type == ScanType.BLISS),
+            )
+        except Exception as e:
+            logger.info(f"Fail to treat {folder_path}. Error is {e}")
+        else:
+            for scan in scan_objs:
+                if (
+                    isinstance(scan, BlissScan)
+                    and self._research_type is ScanType.BLISS
+                ):
+                    self.sigDataFound.emit(scan)
+                elif (
+                    isinstance(scan, NXtomoScan)
+                    and self._research_type is ScanType.NX_TOMO
+                ):
+                    self.sigDataFound.emit(scan)
+                elif (
+                    isinstance(scan, EDFTomoScan)
+                    and self._research_type is ScanType.SPEC
+                ):
+                    self.sigDataFound.emit(scan)
+                else:
+                    raise NotImplementedError("case not handled", self._research_type)