# PALM installation

Use these instructions to install PALM and enable its use with either MATLAB or Octave. These instructions were written for PALM version alpha-1.1.2.

## 1. Download PALM

To install PALM for use with QuNex, we recommend to generate a folder `PALM` within `$TOOLS` directory, and either download or clone the current version of PALM from <https://github.com/andersonwinkler/PALM> in this directory. If you are planning to support the use of PALM with both MATLAB and Octave, we recommend creating two copies of the PALM distribution with different names, e.g.:

``` bash
$TOOLS/PALM/palm-alpha112m      # to use with MATLAB
$TOOLS/PALM/palm-alpha112o      # to use with Octave
```

## 2. Set up PALM

Open `$TOOLS/PALM/palm-alpha112m/palm` and/or `$TOOLS/PALM/palm-alpha112o` in a text editor and set up the following variables:

``` bash
# To use with MATLAB
WHICH_TO_RUN=2
MATLABPATH=<path to your MATLAB installation>

# To use with Octave
WHICH_TO_RUN=1
OCTAVEPATH=<path to your Octave installation>
```

## 3. Compile mex files

We have found that for use with MATLAB, no compilation of `mex` files was required; however, to work with Octave additional steps had to be taken. In all the following steps, `$PALMPATH` refers to the location of the PALM distribution, e.g. `$TOOLS/PALM/palm-alpha112o`.

**Compile `@file_array` `mex` files**:

``` bash
cd $PALMPATH/fileio/@file_array/private
./compile.sh

mv file2mat.m x_file2mat.m
mv init.m x_init.m
mv mat2file.m x_mat2file.m
```

In our experience the last three lines were necessary, as Octave was loading the `.m` files instead of the compiled `.mex` files even when the latter were present. The same strategy of masking the `.m` files is employed in the following steps.

**Compile `@gifti` `mex` files**:

``` bash
cd $PALMPATH/fileio/@gifti/private
./compile.sh

mv zstream.m x_zstream.m
```

**Compile `@nifti` `mex` files**:

``` bash
cd $PALMPATH/fileio/@nifti/private
octave
mkoctfile --mex nifti_stats.c nifti_stats_mex.c -O
exit

mv nifti_stats.m x_nifti_stats.m
```

**Compile `@xmltree` `mex` files**:

``` bash
cd $PALMPATH/fileio/@xmltree/private
cp $PALMPATH/fileio/@file_array/private/Makefile.var .
cp $PALMPATH/fileio/@file_array/private/compile.sh .
sed -i -e 's|include ../../src/Makefile.var|include Makefile.var|g' Makefile
./compile.sh

mv xml_findstr.m x_xml_findstr.m
```

## 4. Edit qunex_environment.sh

To make sure that QuNex 'sees' the correct PALM installation, edit the following segment of the `$TOOLS/qunex/env/qunex_environment.sh` file so that `PALMDIR` variable in `qunex_environment.sh` references the PALM installation that matches with the PALM `WHICH_TO_RUN` variable set in step 2.:

``` bash
# ------------------------------------------------------------------------------
# -- Running matlab vs. octave
# ------------------------------------------------------------------------------

if [ "$USEOCTAVE" == "TRUE" ]; then
    if [[ ${OctaveTest} == "fail" ]]; then 
        reho " ===> ERROR: Cannot setup Octave because module test failed."
    else
         ln -s `which octave` ${OCTAVEDIR}/octave > /dev/null 2>&1
         export OCTAVEPKGDIR
         export OCTAVEDIR
         export OCTAVEBINDIR
         cyaneho " ---> Setting up Octave "; echo ""
         QUNEXMCOMMAND='octave -q --no-init-file --eval'
         if [ ! -e ~/.octaverc ]; then
             cp ${QUNEXPATH}/qx_library/.octaverc ~/.octaverc
         fi
         export LD_LIBRARY_PATH=/usr/lib64/hdf5/:${LD_LIBRARY_PATH} > /dev/null 2>&1
         if [[ -z ${PALMDIR} ]]; then PALMDIR="${TOOLS}/palm/palm-latest-o"; fi
    fi
else
    # if [[ ${MatlabTest} == "fail" ]]; then
    #     reho " ===> ERROR: Cannot setup Matlab because module test failed."
    # else

         cyaneho " ---> Setting up Matlab "; echo ""
         QUNEXMCOMMAND='matlab -nodisplay -nosplash -r'
         if [[ -z ${PALMDIR} ]]; then PALMDIR="${TOOLS}/palm/palm-latest-m"; fi
    # fi
fi
# -- Use the following command to run .m code in MATLAB
export QUNEXMCOMMAND
```