tomwer 1.2.0a1__tar.gz → 1.2.0a3__tar.gz

tomwer-1.2.0a3/PKG-INFO

@@ -0,0 +1,139 @@
+Metadata-Version: 2.1
+Name: tomwer
+Version: 1.2.0a3
+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
+Provides-Extra: doc
+Provides-Extra: _full_base
+Provides-Extra: full_no_cuda
+Provides-Extra: full
+Provides-Extra: _dev_spec
+Provides-Extra: dev
+Provides-Extra: dev_no_cuda
+Provides-Extra: setup_requires
+License-File: LICENSE
+
+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-1.2.0a3/README.rst

@@ -0,0 +1,107 @@
+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-1.2.0a3/orangecontrib/__init__.py

@@ -0,0 +1,8 @@
+try:
+    __import__("pkg_resources").declare_namespace(__name__)
+except ImportError:
+    from pkgutil import extend_path
+
+    __path__ = extend_path(__path__, __name__)
+# orangecontrib is a namespace modules shared by multiple Orange add-on so it
+# needs to declare namespace.

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/append_raw_darks_and_flats_frames_to_NXtomos.ows

@@ -0,0 +1,44 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="Append dark and flat frames to an NXtomo" description="">
+	<nodes>
+		<node id="0" name="image-key-upgrader" qualified_name="orangecontrib.tomwer.widgets.edit.ImageKeyUpgraderOW.ImageKeyUpgraderOW" project_name="tomwer" version="" title="image-key-upgrader" position="(336.0, 221.0)" />
+		<node id="1" name="dark-flat-patch" qualified_name="orangecontrib.tomwer.widgets.edit.DarkFlatPatchOW.DarkFlatPatchOW" project_name="tomwer" version="" title="dark-flat-patch" position="(579.0, 221.0)" />
+		<node id="2" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(781.0, 221.0)" />
+		<node id="3" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(133.0, 222.0)" />
+		<node id="4" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector (1)" position="(981.0, 222.0)" />
+	</nodes>
+	<links>
+		<link id="0" source_node_id="3" sink_node_id="0" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="1" 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="2" 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="3" source_node_id="2" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<text id="0" type="text/plain" rect="(68.0, 8.0, 740.0, 86.0)" font-family="Sans" font-size="16">Context: we want to modify an NXtomo in order to append some (raw) darks / flats to it.
+Then those raw darks and flats will be used for reduced darks / flats calculation.
+
+warning: reduced darks and flats are usually mean / median of a serie of darks / flats. when raw darks and flats are raw frame before mean / median 'reduction'</text>
+		<text id="1" type="text/plain" rect="(65.0, 360.0, 150.0, 88.0)" font-family="Sans" font-size="16">NXtomo to be patched
+Step 3 : process NXtomo</text>
+		<text id="2" type="text/plain" rect="(249.0, 355.0, 220.0, 135.0)" font-family="Sans" font-size="16">step1: define frame series to be ignored (here darks and flats series to avoid conflict with the one added by the dark / flat patch)</text>
+		<arrow id="3" start="(130.0, 345.0)" end="(131.0, 286.0)" fill="#C1272D" />
+		<arrow id="4" start="(337.0, 345.0)" end="(336.99999999999994, 283.0)" fill="#C1272D" />
+		<text id="5" type="text/plain" rect="(912.0, 350.0, 233.0, 158.0)" font-family="Sans" font-size="16">result: NXtomo with patched frame (step 2) and reduced darks and flats to be used for reconstruction</text>
+		<arrow id="6" start="(981.9999999999999, 332.0)" end="(982.9999999999999, 278.0)" fill="#C1272D" />
+		<text id="7" type="text/plain" rect="(700.0, 349.0, 183.0, 126.0)" font-family="Sans" font-size="16">standard darks / flats reduction (but taking into account patched darks / flats frames)</text>
+		<arrow id="8" start="(780.0000000000001, 342.0)" end="(782.0000000000001, 296.0)" fill="#C1272D" />
+		<text id="9" type="text/plain" rect="(506.0, 347.0, 150.0, 145.0)" font-family="Sans" font-size="16">step2: provide series of darks / flats from other(s) NXtomo to be added to the `NXtomo to be patched`</text>
+		<arrow id="10" start="(574.0, 338.0)" end="(573.0, 281.0)" fill="#C1272D" />
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'operations': {}}, '_ewoks_execinfo': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x07\xe6\x00\x00\x01\x18\x00\x00\n/\x00\x00\x03-\x00\x00\x07\xeb\x00\x00\x015\x00\x00\n*\x00\x00\x03(\x00\x00\x00\x01\x00\x00\x00\x00\x07\x7f\x00\x00\x07\xeb\x00\x00\x015\x00\x00\n*\x00\x00\x03(', '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_urlsSetting': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': {'DOWHEN': 'before', 'DARKCAL': 'mean', 'DARKOVE': 0, 'DARKRMV': 0, 'DKFILE': 'darkend[0-9]{3,4}', 'REFSCAL': 'median', 'REFSOVE': 0, 'REFSRMV': 0, 'RFFILE': 'ref*.*[0-9]{3,4}_[0-9]{3,4}'}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x06\x9b\x00\x00\x02K\x00\x00\n\x95\x00\x00\x04\x8f\x00\x00\x06\xa0\x00\x00\x02h\x00\x00\n\x90\x00\x00\x04\x8a\x00\x00\x00\x01\x00\x00\x00\x00\x07\x7f\x00\x00\x06\xa0\x00\x00\x02h\x00\x00\n\x90\x00\x00\x04\x8a', '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="4" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth1.ows

@@ -0,0 +1,55 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="darks and flats copy - method 1" description="">
+	<nodes>
+		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(-519.0, -209.0)" />
+		<node id="1" name="image-key-upgrader" qualified_name="orangecontrib.tomwer.widgets.edit.ImageKeyUpgraderOW.ImageKeyUpgraderOW" project_name="tomwer" version="" title="image-key-upgrader" position="(-293.0, -209.0)" />
+		<node id="2" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(65.0, -226.0)" />
+		<node id="3" name="single tomo obj" qualified_name="orangecontrib.tomwer.widgets.control.SingleTomoObjOW.SingleTomoObjOW" project_name="tomwer" version="" title="scan with darks to be used" position="(-79.0, -439.0)" />
+		<node id="4" name="single tomo obj" qualified_name="orangecontrib.tomwer.widgets.control.SingleTomoObjOW.SingleTomoObjOW" project_name="tomwer" version="" title="scan with reduced flats to be used" position="(-191.0, -335.0)" />
+		<node id="5" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector (1)" position="(286.0, -227.0)" />
+	</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="3" sink_node_id="2" source_channel="reduced dark(s)" sink_channel="reduced dark(s)" enabled="true" source_channel_id="reduced_darks" sink_channel_id="reduced_darks" />
+		<link id="3" source_node_id="4" sink_node_id="2" source_channel="reduced flat(s)" sink_channel="reduced flat(s)" enabled="true" source_channel_id="reduced_flats" sink_channel_id="reduced_flats" />
+		<link id="4" source_node_id="2" sink_node_id="5" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<text id="0" type="text/plain" rect="(-597.0, -79.0, 150.0, 126.0)" font-family="Sans" font-size="16">step2: provide scans for which we need to copy reduced darks and flats</text>
+		<arrow id="1" start="(-522.0, -87.0)" end="(-523.0, -151.0)" fill="#C1272D" />
+		<text id="2" type="text/plain" rect="(-379.0, -87.0, 236.0, 111.0)" font-family="Sans" font-size="16">invalid any existing darks or flats frames (else reduced darks and flats will use them instead of making the copy)</text>
+		<arrow id="3" start="(-293.0, -97.0)" end="(-290.0, -158.0)" fill="#C1272D" />
+		<text id="4" type="text/plain" rect="(-71.0, -96.0, 270.0, 80.0)" font-family="Sans" font-size="16">will copy reduced darks / flats to `dataset_{darks|flats}.hdf5` to be used for reconstruction</text>
+		<arrow id="5" start="(69.99999999999997, -105.0)" end="(69.99999999999997, -156.0)" fill="#C1272D" />
+		<text id="6" type="text/plain" rect="(-390.0, -471.0, 150.0, 107.0)" font-family="Sans" font-size="16">step1: provide scan with already computed darks and flats</text>
+		<arrow id="7" start="(-236.0, -419.0)" end="(-130.0, -428.0)" fill="#C1272D" />
+		<arrow id="8" start="(-277.0, -357.00000000000006)" end="(-228.00000000000003, -333.00000000000006)" fill="#C1272D" />
+		<text id="9" type="text/plain" rect="(241.0, -96.0, 150.0, 88.0)" font-family="Sans" font-size="16">result: scans with copied reduced darks / flats</text>
+		<text id="10" type="text/plain" rect="(-623.0, -603.0, 932.0, 145.0)" font-family="Sans" font-size="16">Context: on this workflow we want to copy reduced flats / darks from a dataset to others.
+This one of the various way to do this.
+</text>
+		<text id="11" type="text/plain" rect="(-593.0, 94.0, 919.0, 84.0)" font-family="Sans" font-size="16">Note: You can also replace the two upper widgets (providing reduced darks and flats) by a python script providing a python dictionnary.
+* Key should be position of the flat / dark in the sequence (so 0 if at the beginning for example)
+* Value is the 2D numpy array with mean / median /xxx of the darks and flats serie</text>
+		<arrow id="12" start="(288.0, -105.0)" end="(286.0, -165.0)" 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="pickle">gASVLwEAAAAAAAB9lCiMFV9ld29rc19kZWZhdWx0X2lucHV0c5R9lIwKb3BlcmF0aW9uc5R9lCiM
+G3RvbW9zY2FuLmVzcmYuc2Nhbi5oZGY1c2NhbpSMCEltYWdlS2V5lJOUSwKFlFKUaAdLA4WUUpRo
+B0sBhZRSlGgLdXOMD19ld29rc19leGVjaW5mb5R9lIwOX2V3b2tzX3ZhcmluZm+UfZSMEmNvbnRy
+b2xBcmVhVmlzaWJsZZSIjA5kZWZhdWx0X2lucHV0c5R9lIwTc2F2ZWRXaWRnZXRHZW9tZXRyeZRD
+QgHZ0MsAAwAAAAAH5gAAARgAAAovAAADLQAAB+sAAAE1AAAKKgAAAygAAAABAAAAAAd/AAAH6wAA
+ATUAAAoqAAADKJSMC19fdmVyc2lvbl9flEsBdS4=
+</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x07\x0e\x00\x00\x015\x00\x00\x0b\x08\x00\x00\x03\x10\x00\x00\x07\x13\x00\x00\x01R\x00\x00\x0b\x03\x00\x00\x03\x0b\x00\x00\x00\x01\x00\x00\x00\x00\x07\x7f\x00\x00\x07\x13\x00\x00\x01R\x00\x00\x0b\x03\x00\x00\x03\x0b', '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_tomo_obj_setting': '', 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="4" format="literal">{'_tomo_obj_setting': '', 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="5" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/copy_reduced_darks_and_flats_meth2.ows

@@ -0,0 +1,48 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="darks and flats copy - method 2" description="">
+	<nodes>
+		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(-519.0, -209.0)" />
+		<node id="1" name="image-key-upgrader" qualified_name="orangecontrib.tomwer.widgets.edit.ImageKeyUpgraderOW.ImageKeyUpgraderOW" project_name="tomwer" version="" title="image-key-upgrader" position="(-293.0, -209.0)" />
+		<node id="2" name="reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.DarkRefAndCopyOW.DarkRefAndCopyOW" project_name="tomwer" version="" title="reduced darks and flats" position="(62.0, -212.0)" />
+		<node id="3" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector (1)" position="(291.0, -211.0)" />
+	</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" />
+	</links>
+	<annotations>
+		<text id="0" type="text/plain" rect="(-597.0, -79.0, 150.0, 126.0)" font-family="Sans" font-size="16">step2: provide scans for which we need to copy reduced darks and flats</text>
+		<arrow id="1" start="(-522.0, -87.0)" end="(-523.0, -151.0)" fill="#C1272D" />
+		<text id="2" type="text/plain" rect="(-379.0, -87.0, 236.0, 111.0)" font-family="Sans" font-size="16">invalid any existing darks or flats frames (else reduced darks and flats will use them instead of making the copy)</text>
+		<arrow id="3" start="(-293.0, -97.0)" end="(-290.0, -158.0)" fill="#C1272D" />
+		<text id="4" type="text/plain" rect="(-70.0, -81.0, 270.0, 80.0)" font-family="Sans" font-size="16">will copy reduced darks / flats to `dataset_{darks|flats}.hdf5` to be used for reconstruction</text>
+		<arrow id="5" start="(61.99999999999998, -91.0)" end="(61.99999999999998, -142.0)" fill="#C1272D" />
+		<text id="6" type="text/plain" rect="(-141.0, -427.0, 464.0, 85.0)" font-family="Sans" font-size="16">step1: provide reduced darks and flats from the 'copy' tab,
+unselecting auto and setting them through `select darks url` and `select flats url`</text>
+		<arrow id="7" start="(57.0, -334.0)" end="(58.99999999999997, -259.00000000000006)" fill="#C1272D" />
+		<text id="8" type="text/plain" rect="(241.0, -94.0, 150.0, 88.0)" font-family="Sans" font-size="16">result: scans with copied reduced darks / flats</text>
+		<text id="9" type="text/plain" rect="(-601.0, -590.0, 932.0, 68.0)" font-family="Sans" font-size="16">Context: on this workflow we want to copy reduced flats / darks from a dataset to others.
+This one of the various way to do this.
+</text>
+		<text id="10" type="text/plain" rect="(-593.0, 94.0, 919.0, 84.0)" font-family="Sans" font-size="16">Note: reduced darks / flats can be saved to disk from another python script using the `silx.io.dictdump` dicttoh5 function.
+Reduced darks and flats are dictionary with index in the sequence as key (so index==0 if the dark / flat serie is done at the beginning) and the reduced darks / flats as value (2D numpy array) </text>
+		<arrow id="11" start="(291.0, -109.0)" end="(290.0, -158.0)" 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="pickle">gASVLwEAAAAAAAB9lCiMFV9ld29rc19kZWZhdWx0X2lucHV0c5R9lIwKb3BlcmF0aW9uc5R9lCiM
+G3RvbW9zY2FuLmVzcmYuc2Nhbi5oZGY1c2NhbpSMCEltYWdlS2V5lJOUSwKFlFKUaAdLA4WUUpRo
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+ATUAAAoqAAADKJSMC19fdmVyc2lvbl9flEsBdS4=
+</properties>
+		<properties node_id="2" format="literal">{'_ewoks_default_inputs': {'data': None, 'dark_ref_params': {'DOWHEN': 'before', 'DARKCAL': 'mean', 'DARKOVE': 0, 'DARKRMV': 0, 'DKFILE': 'darkend[0-9]{3,4}', 'REFSCAL': 'median', 'REFSOVE': 0, 'REFSRMV': 0, 'RFFILE': 'ref*.*[0-9]{3,4}_[0-9]{3,4}'}}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x06\x9b\x00\x00\x02K\x00\x00\n\x95\x00\x00\x04\x8f\x00\x00\x06\xa0\x00\x00\x02h\x00\x00\n\x90\x00\x00\x04\x8a\x00\x00\x00\x01\x00\x00\x00\x00\x07\x7f\x00\x00\x06\xa0\x00\x00\x02h\x00\x00\n\x90\x00\x00\x04\x8a', '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/default_cor_search.ows

@@ -0,0 +1,40 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="default cor search" 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="(319.0, 189.0)" />
+		<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="(469.0, 237.0)" />
+		<node id="3" name="nabu slice reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuOW.NabuOW" project_name="tomwer" version="" title="nabu slice reconstruction" position="(659.0, 325.0)" />
+		<node id="4" name="data viewer" qualified_name="orangecontrib.tomwer.widgets.visualization.DataViewerOW.DataViewerOW" project_name="tomwer" version="" title="data viewer" position="(818.0, 362.0)" />
+	</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="3" sink_node_id="4" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="3" source_node_id="2" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<text id="0" type="text/plain" rect="(223.0, 32.0, 150.0, 26.0)" font-family="Ubuntu" font-size="16">provide dataset</text>
+		<arrow id="1" start="(210.0, 73.0)" end="(159.0, 116.0)" fill="#C1272D" />
+		<text id="2" type="text/plain" rect="(157.0, 304.0, 150.0, 49.0)" font-family="Ubuntu" font-size="16">compute reduced darks and flats</text>
+		<arrow id="3" start="(232.0, 299.0)" end="(290.0, 249.0)" fill="#C1272D" />
+		<arrow id="4" start="(550.0, 149.0)" end="(484.0, 201.0)" fill="#C1272D" />
+		<text id="5" type="text/plain" rect="(552.0, 76.0, 281.0, 72.0)" font-family="Ubuntu" font-size="16">compute center of rotation
+manually or using one of the numerous existing algorithms</text>
+		<arrow id="6" start="(754.0, 224.00000000000003)" end="(695.0, 277.0)" fill="#C1272D" />
+		<text id="7" type="text/plain" rect="(783.0, 183.0, 150.0, 50.0)" font-family="Ubuntu" font-size="16">reconstruct one or several slices</text>
+		<arrow id="8" start="(739.0, 486.0)" end="(782.0, 429.0)" fill="#C1272D" />
+		<text id="9" type="text/plain" rect="(709.2222222222222, 488.55555555555554, 150.0, 88.0)" font-family="Ubuntu" font-size="16">browse reconstructed slices and browse dataset</text>
+	</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>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/hello_world_python_script.ows

@@ -0,0 +1,50 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="Python script hello world" description="">
+	<nodes>
+		<node id="0" name="single tomo obj" qualified_name="orangecontrib.tomwer.widgets.control.SingleTomoObjOW.SingleTomoObjOW" project_name="tomwer" version="" title="single tomo obj" position="(215.0, 171.0)" />
+		<node id="1" name="Python Script" qualified_name="orangecontrib.tomwer.widgets.other.PythonScriptOW.OWPythonScript" project_name="tomwer" version="" title="Python Script" position="(395.0, 238.0)" />
+	</nodes>
+	<links>
+		<link id="0" source_node_id="0" sink_node_id="1" source_channel="tomo_obj" sink_channel="data" enabled="true" source_channel_id="tomo_obj" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<arrow id="0" start="(155.0, 343.0)" end="(199.0, 238.0)" fill="#C1272D" />
+		<text id="1" type="text/plain" rect="(22.0, 370.0, 211.0, 103.0)" font-family="Cantarell" font-size="16">1: provide a scan either by:
+* using the 'select button'
+* copy-paste a file containing a NXtomo to the interface</text>
+		<arrow id="2" start="(369.0, 406.0)" end="(374.0, 308.0)" fill="#C1272D" />
+		<text id="3" type="text/plain" rect="(329.0, 414.0, 150.0, 70.0)" font-family="Cantarell" font-size="16">2: print some information about this scan</text>
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_tomo_obj_setting': '', 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x08C\x00\x00\x02=\x00\x00\r\xb3\x00\x00\x02\xd8\x00\x00\x08C\x00\x00\x02b\x00\x00\r\xb3\x00\x00\x02\xd8\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\x08C\x00\x00\x02b\x00\x00\r\xb3\x00\x00\x02\xd8', '__version__': 1}</properties>
+		<properties node_id="1" format="pickle">gASVKQUAAAAAAAB9lCiMEmNvbnRyb2xBcmVhVmlzaWJsZZSIjBJjdXJyZW50U2NyaXB0SW5kZXiU
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+ZZROjAtfX3ZlcnNpb25fX5RLAXUu
+</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-1.2.0a3/orangecontrib/tomwer/tutorials/simple_slice_reconstruction_on_slurm.ows

@@ -0,0 +1,50 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="simple slice reconstruction on slurm" 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="(945.0, 368.0)" />
+		<node id="5" name="slurm cluster" qualified_name="orangecontrib.tomwer.widgets.cluster.SlurmClusterOW.SlurmClusterOW" project_name="tomwer" version="" title="slurm cluster" position="(412.0, 387.0)" />
+		<node id="6" name="future supervisor" qualified_name="orangecontrib.tomwer.widgets.cluster.FutureSupervisorOW.FutureSupervisorOW" project_name="tomwer" version="" title="future supervisor" position="(803.5, 315.5)" />
+	</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="5" sink_node_id="3" source_channel="cluster_config" sink_channel="cluster_config" enabled="true" source_channel_id="data_out" sink_channel_id="cluster_in" />
+		<link id="4" source_node_id="3" sink_node_id="6" source_channel="future_tomo_obj" sink_channel="future_tomo_obj" enabled="true" source_channel_id="future_out" sink_channel_id="future_in" />
+		<link id="5" source_node_id="6" sink_node_id="4" 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" />
+		<arrow id="1" start="(248.0, 298.0)" end="(292.0, 239.0)" fill="#C1272D" />
+		<arrow id="2" start="(576.0, 108.0)" end="(521.0, 168.0)" fill="#C1272D" />
+		<arrow id="3" start="(647.0, 420.0)" end="(649.0, 328.0)" fill="#C1272D" />
+		<arrow id="4" start="(1013.0, 272.0)" end="(951.0, 322.0)" fill="#C1272D" />
+		<text id="5" type="text/plain" rect="(275.0, 19.0, 150.0, 26.0)" font-family="Ubuntu" font-size="16">provide dataset</text>
+		<text id="6" type="text/plain" rect="(187.0, 309.0, 150.0, 26.0)" font-family="Ubuntu" font-size="16">compute reduced darks and flats</text>
+		<text id="7" type="text/plain" rect="(596.0, 53.0, 150.0, 26.0)" font-family="Ubuntu" font-size="16">compute center of rotation</text>
+		<text id="8" type="text/plain" rect="(557.0, 428.0, 214.0, 94.0)" font-family="Ubuntu" font-size="16">slice reconstruction will be done on slurm as it has a 'slurm cluster' input</text>
+		<text id="9" type="text/plain" rect="(979.4444444444443, 459.11111111111114, 150.0, 88.0)" font-family="Ubuntu" font-size="16">display reconstructed slices and browse dataset</text>
+		<arrow id="10" start="(256.0, 528.0)" end="(341.0, 433.0)" fill="#C1272D" />
+		<text id="11" type="text/plain" rect="(126.0, 534.0, 267.0, 77.0)" font-family="Cantarell" font-size="16">Define the slurm partition to be used for the reconstruction.
+Warning: you must ask for one GPU</text>
+		<arrow id="12" start="(854.0, 176.0)" end="(817.0, 273.0)" fill="#C1272D" />
+		<text id="13" type="text/plain" rect="(859.0, 112.0, 219.0, 50.0)" font-family="Cantarell" font-size="16">wait for reconstruction to be done over slurm</text>
+	</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': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\nH\x00\x00\x01l\x00\x00\x0c#\x00\x00\x02\xce\x00\x00\nH\x00\x00\x01\x91\x00\x00\x0c#\x00\x00\x02\xce\x00\x00\x00\x01\x00\x00\x00\x00\x07\x80\x00\x00\nH\x00\x00\x01\x91\x00\x00\x0c#\x00\x00\x02\xce', '__version__': 1}</properties>
+		<properties node_id="6" format="literal">{'_ewoks_default_inputs': {}, 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>