Updated docs -Linux install instructions

README.rst

@@ -7,6 +7,8 @@ provides higher-level interface, with abstractions such as 'trial' and
 'gait cycle'. Data can be read from Vicon Nexus or directly from c3d
 files.
 
+gaitutils is primarily developed for Windows, but there is also some support for Linux.
+
 Example: to read the current trial from Vicon Nexus and plot the Plug-in Gait
 lower body kinematics:
 

docs/index.rst

@@ -2,7 +2,9 @@
 
 .. include:: readme.rst
 
-.. include:: install.rst
+.. include:: install_win.rst
+
+.. include:: install_lin.rst
 
 .. include:: gui.rst
 

docs/install_lin.rst

@@ -0,0 +1,109 @@
+Installation (Linux)
+====================
+Linux support is somewhat experimental, however you should be able to get it
+running on Linux (sans Vicon Nexus integration, naturally).
+
+The installation instructions are in general similar to those for Windows
+(see :doc:`install_win`) with a few differences.
+
+Conda environment file
+----------------------
+
+You should use ``environment_linux.yml`` file (instead of ``environment.yml``)
+for creating the conda environment for Linux:
+
+::
+
+    curl -O https://raw.githubusercontent.com/NCH-Motion-Laboratory/gaitutils/master/environment_linux.yml
+    conda env create -f environment_linux.yml
+
+No viconnexusapi
+----------------
+
+There is no viconnexusapi for Linux, so you just skip the viconnexusapi installation step.
+
+Setting up BTK
+--------------
+
+If you want support for reading C3D files (and gaitutils on Linux is pretty
+useless without it), you'll have to build BTK yourself. Here are the main
+steps:
+
+Building and installing BTK
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+#. Activate the gaitutils environment
+
+#. Clone BTKCore (unless it has already been cloned as a submodule)
+
+    ::
+
+        git clone [email protected]:Biomechanical-ToolKit/BTKCore.git
+    
+#. Run cmake
+
+    ::
+
+        cd BTKCore
+        cmake . -DBTK_WRAP_PYTHON=True -DNUMPY_INCLUDE_DIR=/home/andrey/opt/anaconda3/envs/gaitutils/lib/python3.11/site-packages/numpy/core/include/ -DNUMPY_VERSION=1.23.4 -DCMAKE_CXX_STANDARD=11 -DCMAKE_POSITION_INDEPENDENT_CODE=True -DCMAKE_INSTALL_PREFIX=/home/andrey/opt/anaconda3/envs/gaitutils/
+
+    You will likely need to change the values of ``-DNUMPY_INCLUDE_DIR``, 
+    ``-DNUMPY_VERSION``, and ``-DCMAKE_INSTALL_PREFIX`` to correctly
+    reflect your installation.
+
+#. Build:
+
+    ::
+
+        make
+
+    **NOTE!** This uses the system's gcc compiler (and probably other tools).
+    It doesn't work with the gcc installed through conda, co there should
+    be no gcc in your conda environment.
+
+#. Install:
+
+    ::
+
+        make install
+
+#. In the site-packages folder of the anaconda environment create a new subfolder
+   called ``btk``. Assuming that you installed anaconda in
+   ``/home/andrey/opt/anaconda3`` and you are using Python 3.11:
+
+    ::
+
+        mkdir /home/andrey/opt/anaconda3/envs/gaitutils/lib/python3.11/site-packages/btk
+
+#. Copy the package files there:  
+
+    ::
+
+        cp bin/btk.py bin/_btk.so /home/andrey/opt/anaconda3/envs/gaitutils/lib/python3.11/site-packages/btk
+
+#. Rename ``btk.py`` to ``__init__.py``:
+
+    ::
+
+        cd /home/andrey/opt/anaconda3/envs/gaitutils/lib/python3.11/site-packages/btk
+        mv btk.py __init__.py
+
+
+Testing BTK installation
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+#.  Open a new terminal and activate the environment  
+
+#.  Run python  
+
+#.  In Python run:  
+
+    ::
+
+        import btk
+        reader = btk.btkAcquisitionFileReader()
+        reader.SetFilename("dynamic.c3d")    # replace dynamic.c3d with your own file
+        reader.Update()
+        acq = reader.GetOutput()
+        acq.GetPointFrequency()
+        

docs/install.rst → docs/install_win.rst

@@ -1,5 +1,5 @@
-Installation
-============
+Installation (Windows)
+======================
 
 Python
 ------

docs/readme.rst

@@ -6,3 +6,5 @@ plotting of 3D gait analysis data. Compared to packages such as btk, it
 provides higher-level interface, with abstractions such as 'trial' and
 'gait cycle'. Data can be read from Vicon Nexus or directly from c3d
 files.
+
+gaitutils is primarily developed for Windows, but there is also some support for Linux.