#!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
# 
# # DiffPreprocPipeline_PostEddy.sh
# 
# ## Copyright Notice
# 
# Copyright (C) 2012-2014 The Human Connectome Project
# 
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
# 
# ## Author(s)
# 
# * Stamatios Sotiropoulos, FMRIB Analysis Group, Oxford University
# * Saad Jbabdi, FMRIB Analysis Group, Oxford University
# * Jesper Andersson, FMRIB Analysis Group, Oxford University
# * Matthew F. Glasser, Department of Anatomy and Neurobiology, Washington University in St. Louis
# * Timothy B. Brown, Neuroinformatics Research Group, Washington University in St. Louis
# 
# ## Product
# 
# [Human Connectome Project][HCP] (HCP) Pipelines
# 
# ## License
# 
# See the [LICENSE](https://github.com/Washington-University/Pipelines/blob/master/LICENCE.md) file
# 
# ## Description
# 
# This script, <code>DiffPreprocPipeline_PostEddy.sh</code>, implements the 
# third (and last) part of the Preprocessing Pipeline for diffusion MRI described
# in [Glasser et al. 2013][GlasserEtAl]. The entire Preprocessing Pipeline for 
# diffusion MRI is split into pre-eddy, eddy, and post-eddy scripts so that 
# the running of eddy processing can be submitted to a cluster scheduler to 
# take advantage of running on a set of GPUs without forcing the entire diffusion
# preprocessing to occur on a GPU enabled system.  This particular script 
# implements the post-eddy part of the diffusion preprocessing.
# 
# ## Prerequisite Installed Software for the Diffusion Preprocessing Pipeline
# 
# * [FSL][FSL] - FMRIB's Software Library (version 5.0.6)
#
#   FSL's environment setup script must also be sourced
# 
# * [FreeSurfer][FreeSurfer] (version 5.3.0-HCP)
# 
# * [HCP-gradunwarp][HCP-gradunwarp] (HCP version 1.0.2)
#
# ## Prerequisite Environment Variables
# 
# See output of usage function: e.g. <code>$ ./DiffPreprocPipeline_PostEddy.sh --help</code>
# 
# <!-- References -->
# 
# [HCP]: http://www.humanconnectome.org
# [GlasserEtAl]: http://www.ncbi.nlm.nih.gov/pubmed/23668970
# [FSL]: http://fsl.fmrib.ox.ac.uk
# [FreeSurfer]: http://freesurfer.net
# [HCP-gradunwarp]: https://github.com/Washington-University/gradunwarp/releases
# 
#~ND~END~

# Setup this script such that if any command exits with a non-zero value, the 
# script itself exits and does not attempt any further processing.
set -e

# Load Function Libraries
source ${HCPPIPEDIR}/global/scripts/log.shlib     # log_ functions
source ${HCPPIPEDIR}/global/scripts/version.shlib # version_ functions 

#
# Function Description
#  Show usage information for this script
#
usage() {
    local scriptName=$(basename ${0})
    echo ""
    echo "  Perform the Post-Eddy steps of the HCP Diffusion Preprocessing Pipeline"
    echo ""
    echo "  Usage: ${scriptName} <options>"
    echo ""
    echo "  Options: [ ] = optional; < > = user supplied value"
    echo ""
    echo "    [--help] : show usage information and exit with non-zero return code"
    echo ""
    echo "    [--version] : show version information and exit with 0 as return code"
    echo ""
    echo "    --path=<study-path>"
    echo "    : path to subject's data folder"
    echo ""
    echo "    --subject=<subject-id>"
    echo "    : Subject ID"
    echo ""
    echo "    --gdcoeffs=<path-to-gradients-coefficients-file>"
    echo "    : path to file containing coefficients that describe spatial variations"
    echo "      of the scanner gradients. Use --gdcoeffs=NONE if not available"
    echo ""
    echo "    [--printcom=<print-command>]"
    echo "    : Use the specified <print-command> to echo or otherwise output the commands"
    echo "      that would be executed instead of actually running them"
    echo "      --printcom=echo is intended for testing purposes"
    echo ""
    echo "  Return Code:"
    echo ""
    echo "    0 if help was not requested, all parameters were properly formed, and processing succeeded"
    echo "    Non-zero otherwise - malformed parameters, help requested, or processing failure was detected"
    echo ""
    echo "  Required Environment Variables:"
    echo ""
    echo "    HCPPIPEDIR"
    echo ""
    echo "      The home directory for the version of the HCP Pipeline Tools product"
    echo "      being used."
    echo ""
    echo "      Example value: /nrgpackages/tools.release/hcp-pipeline-tools-3.0"
    echo ""
    echo "    HCPPIPEDIR_dMRI"
    echo ""
    echo "      Location of Diffusion MRI sub-scripts that are used to carry out some of the"
    echo "      steps of the Diffusion Preprocessing Pipeline"
    echo ""
    echo "      Example value: ${HCPPIPEDIR}/DiffusionPreprocessing/scripts"
    echo ""
    echo "    FSLDIR"
    echo ""
    echo "      The home directory for FSL"
    echo ""
}

#
# Function Description
#  Get the command line options for this script
#
# Global Output Variables
#  ${StudyFolder} - Path to subject's data folder
#  ${Subject}     - Subject ID
#  ${GdCoeffs}    - Path to file containing coefficients that describe spatial variations
#                   of the scanner gradients. Use NONE if not available.
#  ${runcmd}      - Set to a user specifed command to use if user has requested
#                   that commands be echo'd (or printed) instead of actually executed.
#                   Otherwise, set to empty string.
#
get_options() {
    local scriptName=$(basename ${0})
    local arguments=($@)

    # initialize global output variables
    unset StudyFolder
    unset Subject
    unset GdCoeffs
    runcmd=""

    # parse arguments
    local index=0
    local numArgs=${#arguments[@]}
    local argument

    while [ ${index} -lt ${numArgs} ]; do
        argument=${arguments[index]}

        case ${argument} in
            --help)
                usage
                exit 1
                ;;
            --version)
                version_show $@
                exit 0
                ;;
            --path=*)
                StudyFolder=${argument/*=/""}
                index=$(( index + 1 ))
                ;;
            --subject=*)
                Subject=${argument/*=/""}
                index=$(( index + 1 ))
                ;;
            --gdcoeffs=*)
                GdCoeffs=${argument/*=/""}
                index=$(( index + 1 ))
                ;;
            --printcom=*)
                runcmd=${argument/*=/""}
                index=$(( index + 1 ))
                ;;
            *)
                usage
                echo "ERROR: Unrecognized Option: ${argument}"
                exit 1
                ;;
        esac
    done

    # check required parameters
    if [ -z ${StudyFolder} ]; then
        usage
        echo "ERROR: <study-path> not specified"
        exit 1
    fi

    if [ -z ${Subject} ]; then
        usage
        echo "ERROR: <subject-id> not specified"
        exit 1
    fi

    if [ -z ${GdCoeffs} ]; then
        usage
        echo "ERROR: <path-to-gradients-coefficients-file> not specified"
        exit 1
    fi

    # report options
    echo "-- ${scriptName}: Specified Command-Line Options - Start --"
    echo "   StudyFolder: ${StudyFolder}"
    echo "   Subject: ${Subject}"
    echo "   GdCoeffs: ${GdCoeffs}"
    echo "   runcmd: ${runcmd}"
    echo "-- ${scriptName}: Specified Command-Line Options - End --"
}

# 
# Function Description
#  Validate necessary environment variables
#
validate_environment_vars() {
    local scriptName=$(basename ${0})
    # validate
    if [ -z ${HCPPIPEDIR_dMRI} ]; then
        usage
        echo "ERROR: HCPPIPEDIR_dMRI environment variable not set"
        exit 1
    fi

    if [ ! -e ${HCPPIPEDIR_dMRI}/eddy_postproc.sh ]; then 
        usage
        echo "ERROR: HCPPIPEDIR_dMRI/eddy_postproc.sh not found"
        exit 1
    fi

    if [ ! -e ${HCPPIPEDIR_dMRI}/DiffusionToStructural.sh ]; then 
        usage
        echo "ERROR: HCPPIPEDIR_dMRI/DiffusionToStructural.sh not found"
        exit 1
    fi

    if [ -z ${FSLDIR} ]; then
        usage
        echo "ERROR: FSLDIR environment variable not set"
        exit 1
    fi

    # report
    echo "-- ${scriptName}: Environment Variables Used - Start --"
    echo "   HCPPIPEDIR_dMRI: ${HCPPIPEDIR_dMRI}"
    echo "   FSLDIR: ${FSLDIR}"
    echo "-- ${scriptName}: Environment Variables Used - End --"
}

#
# Function Description
#  Main processing of script
#
#  Gets user specified command line options, runs Post-Eddy steps of Diffusion Preprocessing
#
main() {
    # Hard-Coded variables for the pipeline
    CombineDataFlag=1  # If JAC resampling has been used in eddy, decide what to do with the output file
                       # 2 for including in the output all volumes uncombined (i.e. output file of eddy)
                       # 1 for including in the output and combine only volumes where both LR/RL 
                       #   (or AP/PA) pairs have been acquired
                       # 0 As 1, but also include uncombined single volumes

    # Get Command Line Options
    #
    # Global Variables Set
    #  ${StudyFolder} - Path to subject's data folder
    #  ${Subject}     - Subject ID
    #  ${GdCoeffs}    - Path to file containing coefficients that describe spatial variations
    #                   of the scanner gradients. Use NONE if not available.
    #  ${runcmd}      - Set to a user specifed command to use if user has requested
    #                   that commands be echo'd (or printed) instead of actually executed.
    #                   Otherwise, set to empty string.
    get_options $@

    # Validate environment variables
    validate_environment_vars $@

    # Establish tool name for logging
    log_SetToolName "DiffPreprocPipeline_PostEddy.sh"

    # Establish output directory paths
    outdir=${StudyFolder}/${Subject}/Diffusion
    outdirT1w=${StudyFolder}/${Subject}/T1w/Diffusion

    # Determine whether Gradient Nonlinearity Distortion coefficients are supplied
    GdFlag=0
    if [ ! ${GdCoeffs} = "NONE" ]; then
        log_Msg "Gradient nonlinearity distortion correction coefficients found!"
        GdFlag=1
    fi

    log_Msg "Running Eddy PostProcessing"
    ${runcmd} ${HCPPIPEDIR_dMRI}/eddy_postproc.sh ${outdir} ${GdCoeffs} ${CombineDataFlag}

    # Establish variables that follow naming conventions
    T1wFolder="${StudyFolder}/${Subject}/T1w" #Location of T1w images
    T1wImage="${T1wFolder}/T1w_acpc_dc"
    T1wRestoreImage="${T1wFolder}/T1w_acpc_dc_restore"
    T1wRestoreImageBrain="${T1wFolder}/T1w_acpc_dc_restore_brain"
    BiasField="${T1wFolder}/BiasField_acpc_dc"
    FreeSurferBrainMask="${T1wFolder}/brainmask_fs"
    RegOutput="${outdir}"/reg/"Scout2T1w"
    QAImage="${outdir}"/reg/"T1wMulEPI"
    DiffRes=`${FSLDIR}/bin/fslval ${outdir}/data/data pixdim1`
    DiffRes=`printf "%0.2f" ${DiffRes}`

    log_Msg "Running Diffusion to Structural Registration"
    ${runcmd} ${HCPPIPEDIR_dMRI}/DiffusionToStructural.sh \
        --t1folder="${T1wFolder}" \
        --subject="${Subject}" \
        --workingdir="${outdir}/reg" \
        --datadiffdir="${outdir}/data" \
        --t1="${T1wImage}" \
        --t1restore="${T1wRestoreImage}" \
        --t1restorebrain="${T1wRestoreImageBrain}" \
        --biasfield="${BiasField}" \
        --brainmask="${FreeSurferBrainMask}" \
        --datadiffT1wdir="${outdirT1w}" \
        --regoutput="${RegOutput}" \
        --QAimage="${QAImage}" \
        --gdflag=${GdFlag} --diffresol=${DiffRes}

    log_Msg "Completed"
    exit 0
}

#
# Invoke the main function to get things started
#
main $@