update documentation

README.rst

@@ -107,18 +107,22 @@ Download & Installation
 
 BCDI is available from:
 
-* Python Package Index: ``pip install bcdi``
-* `Most updated version on GitHub <https://github.com/carnisj/bcdi>`_
+* the Python Package Index: ``python -m pip install bcdi``
+* or on `GitHub <https://github.com/carnisj/bcdi>`_, where you will find the latest
+  version:
 
-- Upgrade your version with the latest changes from GitHub (main branch):
-  ``pip install --upgrade git+https://github.com/carnisj/bcdi.git``
-- Test a specific branch from GitHub:
-  ``pip install --upgrade git+https://github.com/carnisj/bcdi.git@branch_name``
+|  - to install the main branch, type:
+|    ``python -m pip install git+https://github.com/carnisj/bcdi.git``
+|  - to install a specific branch, type:
+|    ``python -m pip install git+https://github.com/carnisj/bcdi.git@branch_name``
+
+Add the flag ``--upgrade`` to the commands above in order to update an existing
+installation.
 
 Note that there are issues with installing scikit-image within an Anaconda environment.
 In such situation, the workaround is to create instead a virtual environment using pip.
 
-Please send feedback in `GitHub <https://github.com/carnisj/bcdi/issues>`_.
+Please send feedback in `GitHub issues <https://github.com/carnisj/bcdi/issues>`_.
 
 Documentation
 =============

doc/EXAMPLE_POSTPROCESSING.rst

@@ -1,17 +1,17 @@
 Example: postprocessing
 -----------------------
 
-This example will guide you throught the post-processing of an experimental BCDI dataset
+This example will guide you through the post-processing of an experimental BCDI dataset
 measured at the European Synchrotron Radiation Facility, beamline ID01. Postprocessing
-occurs after phase retrieval, and typically include the following steps: phase ramp
-removal, refraction correction, interpolation of the object from the detector frame to
-an orthonormal frame etc...
+occurs after phase retrieval, and typically includes the following steps: interpolation
+of the object from the detector frame to an orthonormal frame, refraction correction,
+phase ramp and phase offset removal, displacement and strain calculation etc...
 
 It is assumed that the phase retrieval of this dataset has been realized
 (e.g. using PyNX), and that the data provided as input is in direct space. If it is
 still in the detector frame, the first axis is expected to correspond to the rocking
-dimension, the second axis corresponds to the detector vertical axis and the third axis
-to the detector horizontal axis.
+dimension, the second axis to the detector vertical axis and the third axis to the
+detector horizontal axis.
 
 The most usefull script is ``bcdi_strain.py``. It requires a YAML config
 file, which for this example is ``bcdi/examples/S11_config_postprocessing.yml``.
@@ -20,7 +20,7 @@ output of the decomposition into orthogonal modes after phase retrieval with PyN
 convenience, copy ``S11_modes.h5`` to the data folder "path_to/CXIDB-I182/CH4760/S11/".
 
 In order to have it running correctly on your machine, you will have to modify the paths
-corresponding to the following parameters::
+for the following parameters::
 
     root_folder: "path_to/CXIDB-I182/CH4760/"
     save_dir: "path_to_saving_directory"
@@ -33,21 +33,7 @@ practice), run:
 
 ``python path_to/bcdi_strain.py --conf path_to/S11_config_postprocessing.yml``
 
-If you installed the package, the scripts and configuration files will be located at the
-following location (example with the ``bcdi`` package installed in a Python3.8 conda
-virtual environment named ``myenv``):
-
-- on Windows:
-
-    - scripts in ``path_to\anaconda3\envs\myenv\Scripts``
-    - config files in ``path_to\anaconda3\envs\myenv\Lib\site-packages\bcdi\examples``
-
-- on Linux:
-
-    - scripts in ``/path_to/anaconda3/envs/myenv/bin``
-    - config files in ``/path_to/anaconda3/envs/myenv/lib/python3.8/site-packages/bcdi/examples``
-
-After launching the script, a pop-up window opens, so that you can select the files to
+After launching the script, a pop-up window opens, allowing you to select the files to
 load. By default this window opens at the location defined by ``data_dir``, but you can
 navigate to any location on your computer.
 

doc/EXAMPLE_PREPROCESSING.rst

@@ -8,7 +8,7 @@ The most usefull script is ``bcdi_preprocessing_BCDI.py``. It requires a YAML co
 file, which for this example is ``bcdi/examples/S11_config_preprocessing.yml``.
 
 In order to have it running correctly on your machine, you will have to modify the paths
-corresponding to the following parameters::
+for the following parameters::
 
     root_folder: "path_to/CXIDB-I182/CH4760/"
     save_dir: "path_to_saving_directory"
@@ -21,20 +21,6 @@ practice), run:
 
 ``python path_to/bcdi_preprocessing_BCDI.py --conf path_to/S11_config_preprocessing.yml``
 
-If you installed the package, the scripts and configuration files will be located at the
-following location (example with the ``bcdi`` package installed in a Python3.8 conda
-virtual environment named ``myenv``):
-
-- on Windows:
-
-    - scripts in ``path_to\anaconda3\envs\myenv\Scripts``
-    - config files in ``path_to\anaconda3\envs\myenv\Lib\site-packages\bcdi\examples``
-
-- on Linux:
-
-    - scripts in ``/path_to/anaconda3/envs/myenv/bin``
-    - config files in ``/path_to/anaconda3/envs/myenv/lib/python3.8/site-packages/bcdi/examples``
-
 The data will be loaded and a plot is opened. This allows you to check whether, e.g.,
 the region of interest provided is correct. Click on the plot to resume the execution
 of the script.

doc/index.rst

@@ -40,6 +40,24 @@ Extract the files, you should get the following::
 For the demonstration, we will use the scan ``S11`` from the experiment ``CH4760``.
 The spec file for this scan is ``l5.spec``.
 
+If you installed the package, the scripts and configuration files will be located at the
+following location (example with the ``bcdi`` package installed in a Python3.8 conda
+virtual environment named ``myenv``):
+
+- on Windows:
+
+|    - scripts in:
+|      ``path_to\anaconda3\envs\myenv\Scripts``
+|    - config files in:
+|      ``path_to\anaconda3\envs\myenv\Lib\site-packages\bcdi\examples``
+
+- on Linux:
+
+|    - scripts in:
+|      ``/path_to/anaconda3/envs/myenv/bin``
+|    - config files in:
+|      ``/path_to/anaconda3/envs/myenv/lib/python3.8/site-packages/bcdi/examples``
+
 .. include:: EXAMPLE_PREPROCESSING.rst
 
 .. include:: EXAMPLE_POSTPROCESSING.rst