Commit 3202b6f9 authored by payno's avatar payno

[refactoring] rename xas -> est

parent 1b5f6831
......@@ -14,7 +14,7 @@ variables:
- export PYTHONPATH="${PYTHONPATH}:/usr/lib/python3/dist-packages/"
- export LD_LIBRARY_PATH=/lib/i386-linux-gnu/:${LD_LIBRARY_PATH}
- export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
- export XAS_TEST_PROCESS=False
- export EST_TEST_PROCESS=False
- python --version
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
......@@ -30,8 +30,8 @@ variables:
- python -m pip install pymca --upgrade --pre
- git submodule update --init --recursive
- python -m pip install -e .
- python -m xas --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a xas test -v
- python -m est --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
.build_template: &test_linux_template_larch
......@@ -41,7 +41,7 @@ variables:
- export PYTHONPATH="${PYTHONPATH}:/usr/lib/python3/dist-packages/"
- export LD_LIBRARY_PATH=/lib/i386-linux-gnu/:${LD_LIBRARY_PATH}
- export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
- export XAS_TEST_PROCESS=False
- export EST_TEST_PROCESS=False
- python --version
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
......@@ -57,8 +57,8 @@ variables:
- install_larch
- git submodule update --init --recursive
- python -m pip install -e .
- python -m xas --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a xas test -v
- python -m est --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
.build_template: &test_linux_template_pymca_larch
......@@ -68,7 +68,7 @@ variables:
- export PYTHONPATH="${PYTHONPATH}:/usr/lib/python3/dist-packages/"
- export LD_LIBRARY_PATH=/lib/i386-linux-gnu/:${LD_LIBRARY_PATH}
- export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
- export XAS_TEST_PROCESS=False
- export EST_TEST_PROCESS=False
- python --version
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
......@@ -85,8 +85,8 @@ variables:
- install_larch
- git submodule update --init --recursive
- python -m pip install -e .
- python -m xas --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a xas test -v
- python -m est --help
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
test:python3.5-stretch-pyqt5_pymca:
......@@ -104,7 +104,7 @@ test:python3.5-stretch-pyqt5_pymca_larch:
<<: *test_linux_template_pymca_larch
test:test-xas-tutorials_pymca:
test:test-est-tutorials_pymca:
type: test
image: docker-registry.esrf.fr/dau/tomwer:python3.5_stretch_pyqt5
before_script:
......@@ -130,4 +130,4 @@ test:test-xas-tutorials_pymca:
- python -m pip install .
script:
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a jupyter nbconvert --to notebook --execute doc/tutorials/pymca_xas_process.ipynb
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a jupyter nbconvert --to notebook --execute doc/tutorials/pymca_est_process.ipynb
[submodule "xas/pushworkflow"]
path = xas/pushworkflow
[submodule "est/pushworkflow"]
path = est/pushworkflow
url = https://gitlab.esrf.fr/payno/pushworkflow.git
branch = master
......@@ -4,21 +4,21 @@ Change Log
0.2.0: 13/08/2019
-----------------
* xas
* est
* core
* add larch processes:
* autobk (xas.core.process.larch.autobk)
* mback (xas.core.process.larch.mback)
* mback_norm (xas.core.process.larch.mback_norm)
* pre_edge (xas.core.process.larch.pre_edge)
* xftf (xas.core.process.larch.xftf)
* autobk (est.core.process.larch.autobk)
* mback (est.core.process.larch.mback)
* mback_norm (est.core.process.larch.mback_norm)
* pre_edge (est.core.process.larch.pre_edge)
* xftf (est.core.process.larch.xftf)
* add roi process: data reduction
* move pymca processes to xas.core.process.pymca
* move pymca processes to est.core.process.pymca
* input / output
......@@ -26,7 +26,7 @@ Change Log
* app
* add reprocessing application: take one .h5 file generated by the xas library and reprocess the workflow
* add reprocessing application: take one .h5 file generated by the est library and reprocess the workflow
* orangecontrib
......@@ -43,16 +43,16 @@ Change Log
0.1.0
-----
* xas
* est
* core
* add core processes to access the PyMca XASClass main functionnalities
* spectra normalization (xas.core.process.normalization)
* exafs - Extended X-Ray Absorption Fine Structure (xas.core.process.exafs)
* fourier transform (xas.core.process.ft)
* weight (xas.core.process.weight)
* spectra normalization (est.core.process.normalization)
* exafs - Extended X-Ray Absorption Fine Structure (est.core.process.exafs)
* fourier transform (est.core.process.ft)
* weight (est.core.process.weight)
* input / output
......
The xas library goal is to provide some usefull process for acquisition/reconstruction automation.
The est library goal is to provide some usefull process for acquisition/reconstruction automation.
xas is distributed under the MIT license.
est is distributed under the MIT license.
xas is using the Qt library. A word of caution is to be provided. If users develop and distribute software using modules accessing Qt by means of Riverbank Computing Qt bindings PyQt4 or PyQt5, those users will be conditioned by the license of their PyQt4/5 software (GPL or commercial). If the end user does not own a commercial license of PyQt4 or PyQt5 and wishes to be free of any distribution condition, (s)he should be able to use PySide because it uses the LGPL license.
est is using the Qt library. A word of caution is to be provided. If users develop and distribute software using modules accessing Qt by means of Riverbank Computing Qt bindings PyQt4 or PyQt5, those users will be conditioned by the license of their PyQt4/5 software (GPL or commercial). If the end user does not own a commercial license of PyQt4 or PyQt5 and wishes to be free of any distribution condition, (s)he should be able to use PySide because it uses the LGPL license.
It can also be used as an Orange3 add-on. If you wan't to distribute Orange you must stick to there license (GNU [GPL-3.0]+ license)
......
# Description
XAS is a library providing tools to define a workflow of treatments for X-ray Absorption Structure analysis.
`est` is a library providing tools to define a workflow of treatments for X-ray Absorption Structure analysis.
Treatments are based on eather [PyMca](https://github.com/vasole/pymca)_ or [Larch](https://xraypy.github.io/xraylarch/)
The library offers a convenient object for connecting those two.
......@@ -12,4 +12,4 @@ An [Orange3](https://github.com/biolab/orange3) add-on is also provided by the l
from git repository
-------------------
see [install](http://www.edna-site.org/pub/doc/xas/latest/install.html) from documentation
see [install](http://www.edna-site.org/pub/doc/est/latest/install.html) from documentation
......@@ -8,5 +8,5 @@ For this you should execute the `process` application
.. code-block:: bash
xas process pymca_workflow.ows -i [input_spectrum_file] -o [output_file]
est process pymca_workflow.ows -i [input_spectrum_file] -o [output_file]
......@@ -2,13 +2,13 @@ reprocessing
------------
A file containing information about raw data and xas process flow (output file generated by the xas output orange widget for example) can
A file containing information about raw data and est process flow (output file generated by est output orange widget for example) can
be reprocess from the reprocessing application.
This will reprocess raw data (spectra, energy) through the processing flow.
.. code-block:: bash
xas reprocessing myfile.h5 [--spectra_path path1] [--energy_path path2] [--configuration_path path3] [--entry entry]
est reprocessing myfile.h5 [--spectra_path path1] [--energy_path path2] [--configuration_path path3] [--entry entry]
note: path is relative to the entry. By default entry is 'scan1' and path are also set to default values.
......@@ -53,7 +53,7 @@ source_suffix = ['.rst', '.md']
master_doc = 'index'
# General information about the project.
project = 'xas'
project = 'est'
copyright = '2016-2019, ESRF'
author = 'ESRF'
......@@ -134,7 +134,7 @@ html_theme = 'nature'
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = "img/xas.png"
html_logo = "img/est.png"
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
......@@ -207,7 +207,7 @@ html_logo = "img/xas.png"
#html_search_scorer = 'scorer.js'
# Output file base name for HTML help builder.
htmlhelp_basename = 'xas'
htmlhelp_basename = 'est'
# -- Options for LaTeX output ---------------------------------------------
......@@ -251,12 +251,12 @@ latex_elements = {
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'xas', 'xas Documentation',
(master_doc, 'est', 'est Documentation',
[author], 1)
]
htmlhelp_pages = [
(master_doc, 'xas', 'xas Add-on Documentation',
(master_doc, 'est', 'est Add-on Documentation',
[author], 1)
]
......@@ -270,8 +270,8 @@ htmlhelp_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'xas', 'xas Documentation',
author, 'xas', 'One line description of project.',
(master_doc, 'est', 'est Documentation',
author, 'est', 'One line description of project.',
'Miscellaneous'),
]
......
===
XAS
est
===
XAS is a library providing tools to define a workflow of treatments for X-ray Absorption Structure analysis.
`est` is a library providing tools to define a workflow of treatments for X-ray Absorption Structure analysis.
Treatments are based on eather `PyMca <https://github.com/vasole/pymca>`_ or `Larch <https://xraypy.github.io/xraylarch/>`_.
The library offers a convenient object for connecting those two.
......@@ -33,7 +33,7 @@ An `Orange3 <https://github.com/biolab/orange3>`_ add-on is also provided by the
API
:doc:`tutorials/index`
tutorials for using the xas library
tutorials for using the est library
:doc:`larch_pymca`
pymca and larch coexistence
......
installation
::::::::::::
xas is library made to link several xas libraries together and define treatment workflows.
est is library made to link several libraries together and define treatment workflows.
This is the recommended way to install xas.
This is the recommended way to install est.
Step 1 - Create a virtual env
'''''''''''''''''''''''''''''
......@@ -33,20 +33,20 @@ Step 2 installation
clone the git repository ( and the submodule - --recursive option)
git clone --recursive https://gitlab.esrf.fr/workflow/xas.git
git clone --recursive https://gitlab.esrf.fr/workflow/est.git
You can install from the code source (https://gitlab.esrf.fr/workflow/xas)
You can install from the code source (https://gitlab.esrf.fr/workflow/est)
.. code-block:: bash
pip install .[full]
.. note:: Has explained in the description the goal of xas is to link pymca and / or larch treatments to define a workflow. By default neither pymca or larch are installed. To use xas you should have at least one installed.
.. note:: Has explained in the description the goal of est is to link pymca and / or larch treatments to define a workflow. By default neither pymca or larch are installed. To use est you should have at least one installed.
Orange3 add-on
::::::::::::::
xas is offering an orange add-on for having a convenient and user friendly way to define a treatment workflow.
est is offering an orange add-on for having a convenient and user friendly way to define a treatment workflow.
To benefit from the orange add-on you will need to have orange3 canvas installed.
.. code-block:: bash
......@@ -54,7 +54,7 @@ To benefit from the orange add-on you will need to have orange3 canvas installed
pip install orange3
To launch orange and access the xas add-on you can simply launch Orange2 with the command:
To launch orange and access the est add-on you can simply launch Orange2 with the command:
.. code-block:: bash
......@@ -101,7 +101,7 @@ You also should generate documentation to be accessible from Orange GUI (pressin
Warning
:::::::
At the time being (August 2019) the xas GUI is using silx from the silx.gui.qt module which try to use PyQt5, then PySide2, then PyQt4
At the time being (August 2019) the est GUI is using silx from the silx.gui.qt module which try to use PyQt5, then PySide2, then PyQt4
Order is different for AnyQt, used by Orange3. So some incoherence might append (will bring errors) in the Signal/SLOT connection
during widget instantiation.
......
Larch and pymca compatibility
-----------------------------
xas library is using the :class:`XASObject` to associate larch and pymca treatments and create as much as possible a bridge between those two.
The library is using the :class:`XASObject` to associate larch and pymca treatments and create as much as possible a bridge between those two.
Here is a small summary about current (August 2019) larch processes and pymca processes :
Original functions goals:
+-----------------------------+----------------------+---------------------------------------------------------------+----------------------------------+
| larch functions | pymca functions | description | is currently accessible from xas |
| larch functions | pymca functions | description | is currently accessible from est |
+=============================+======================+===============================================================+==================================+
| | processSpectrum | compute all variables for the given spectrum | YES |
+-----------------------------+----------------------+---------------------------------------------------------------+----------------------------------+
......
xas.core package
est.core package
================
Subpackages
......@@ -9,26 +9,26 @@ Subpackages
utils/index.rst
process/index.rst
xas.core.io module
est.core.io module
------------------
.. automodule:: xas.core.io
.. automodule:: est.core.io
:members:
:undoc-members:
:show-inheritance:
xas.core.reprocessing module
est.core.reprocessing module
----------------------------
.. automodule:: xas.core.reprocessing
.. automodule:: est.core.reprocessing
:members:
:undoc-members:
:show-inheritance:
xas.core.types module
est.core.types module
---------------------
.. automodule:: xas.core.types
.. automodule:: est.core.types
:members:
:undoc-members:
:show-inheritance:
......@@ -37,7 +37,7 @@ xas.core.types module
Module contents
---------------
.. automodule:: xas.core
.. automodule:: est.core
:members:
:undoc-members:
:show-inheritance:
......
xas.core.process package
est.core.process package
========================
Subpackages
......@@ -6,37 +6,37 @@ Subpackages
.. toctree::
xas.core.process.larch
xas.core.process.pymca
est.core.process.larch
est.core.process.pymca
xas.core.process.process module
est.core.process.process module
-------------------------------
.. automodule:: xas.core.process.process
.. automodule:: est.core.process.process
:members:
:undoc-members:
:show-inheritance:
xas.core.process.progress module
est.core.process.progress module
--------------------------------
.. automodule:: xas.core.process.progress
.. automodule:: est.core.process.progress
:members:
:undoc-members:
:show-inheritance:
xas.core.process.roi module
est.core.process.roi module
---------------------------
.. automodule:: xas.core.process.roi
.. automodule:: est.core.process.roi
:members:
:undoc-members:
:show-inheritance:
xas.core.process.setup module
est.core.process.setup module
-----------------------------
.. automodule:: xas.core.process.setup
.. automodule:: est.core.process.setup
:members:
:undoc-members:
:show-inheritance:
......@@ -45,7 +45,7 @@ xas.core.process.setup module
Module contents
---------------
.. automodule:: xas.core.process
.. automodule:: est.core.process
:members:
:undoc-members:
:show-inheritance:
xas.core.process.larch package
est.core.process.larch package
==============================
xas.core.process.larch.autobk module
est.core.process.larch.autobk module
------------------------------------
.. automodule:: xas.core.process.larch.autobk
.. automodule:: est.core.process.larch.autobk
:members:
:undoc-members:
:show-inheritance:
xas.core.process.larch.mback module
est.core.process.larch.mback module
-----------------------------------
.. automodule:: xas.core.process.larch.mback
.. automodule:: est.core.process.larch.mback
:members:
:undoc-members:
:show-inheritance:
xas.core.process.larch.mback\_norm module
est.core.process.larch.mback\_norm module
-----------------------------------------
.. automodule:: xas.core.process.larch.mback_norm
.. automodule:: est.core.process.larch.mback_norm
:members:
:undoc-members:
:show-inheritance:
xas.core.process.larch.pre\_edge module
est.core.process.larch.pre\_edge module
---------------------------------------
.. automodule:: xas.core.process.larch.pre_edge
.. automodule:: est.core.process.larch.pre_edge
:members:
:undoc-members:
:show-inheritance:
xas.core.process.larch.xftf module
est.core.process.larch.xftf module
----------------------------------
.. automodule:: xas.core.process.larch.xftf
.. automodule:: est.core.process.larch.xftf
:members:
:undoc-members:
:show-inheritance:
......@@ -45,7 +45,7 @@ xas.core.process.larch.xftf module
Module contents
---------------
.. automodule:: xas.core.process.larch
.. automodule:: est.core.process.larch
:members:
:undoc-members:
:show-inheritance:
xas.core.process.pymca package
est.core.process.pymca package
==============================
xas.core.process.pymca.exafs module
est.core.process.pymca.exafs module
-----------------------------------
.. automodule:: xas.core.process.pymca.exafs
.. automodule:: est.core.process.pymca.exafs
:members:
:undoc-members:
:show-inheritance:
xas.core.process.pymca.ft module
est.core.process.pymca.ft module
--------------------------------
.. automodule:: xas.core.process.pymca.ft
.. automodule:: est.core.process.pymca.ft
:members:
:undoc-members:
:show-inheritance:
xas.core.process.pymca.k\_weight module
est.core.process.pymca.k\_weight module
---------------------------------------
.. automodule:: xas.core.process.pymca.k_weight
.. automodule:: est.core.process.pymca.k_weight
:members:
:undoc-members:
:show-inheritance:
xas.core.process.pymca.normalization module
est.core.process.pymca.normalization module
-------------------------------------------
.. automodule:: xas.core.process.pymca.normalization
.. automodule:: est.core.process.pymca.normalization
:members:
:undoc-members:
:show-inheritance:
xas.core.process.pymca.setup module
est.core.process.pymca.setup module
-----------------------------------
.. automodule:: xas.core.process.pymca.setup
.. automodule:: est.core.process.pymca.setup
:members:
:undoc-members:
:show-inheritance:
......@@ -45,7 +45,7 @@ xas.core.process.pymca.setup module
Module contents
---------------
.. automodule:: xas.core.process.pymca
.. automodule:: est.core.process.pymca
:members:
:undoc-members:
:show-inheritance:
xas.core.utils package
est.core.utils package
======================
xas.core.utils.designpattern module
est.core.utils.designpattern module
-----------------------------------
.. automodule:: xas.core.utils.designpattern
.. automodule:: est.core.utils.designpattern
:members:
:undoc-members:
:show-inheritance:
xas.core.utils.spectra module
est.core.utils.spectra module
-----------------------------
.. automodule:: xas.core.utils.spectra
.. automodule:: est.core.utils.spectra
:members:
:undoc-members:
:show-inheritance:
......@@ -21,7 +21,7 @@ xas.core.utils.spectra module
Module contents
---------------
.. automodule:: xas.core.utils
.. automodule:: est.core.utils
:members:
:undoc-members:
:show-inheritance:
xas.gui package
est.gui package
===============
Subpackages
-----------
xas.gui.XasObjectViewer module
est.gui.XasObjectViewer module
------------------------------
.. automodule:: xas.gui.XasObjectViewer
.. automodule:: est.gui.XasObjectViewer
:members:
:undoc-members: