ccf_struct

#!/bin/bash

SCRIPT_NAME=$(basename "${0}")
SCRIPT_DIRECTORY=$(dirname "${0}")
DEFAULT_GRADIENT_COEFFS_DIR="${HOME}/projects/HCPpipelinesPrereqs/gradient_coefficients_files"
DEFAULT_FREESURFER_LICENSE_DIR="${HOME}/projects/HCPpipelinesPrereqs/FreeSurferLicense"
DEFAULT_APP="PROCESS"
DEFAULT_ENV="CONTAINER"

source ${SCRIPT_DIRECTORY}/user_utils.shlib
source ${SCRIPT_DIRECTORY}/struct_utils.shlib

usage()
{
	cat <<EOF

${SCRIPT_NAME}: 

  This script demonstrates how to run Structural Preprocessing related applications 
  available within the HCPprocessPipelines.simg Singularity container or within the
  corresponding HCPprocessPipelinesSandbox on CCF subjects.

Usage: ${SCRIPT_NAME} PARAMETER ...

PARAMETERs are: [ ] = optional; < > = user supplied value

  [--help] : show this usage information and exit

  Path to gradient coefficients files
  -----------------------------------

  [--gradient-coeffs-dir=<path-to-gradient-coefficients-directory>]

    The specified path will be bound (i.e. mounted) from your system
    to a known location (/export/HCP/gradient_coefficient_files) in the
    container or sandbox. This is where the gradient coefficients
    files must be found within the container or sandbox.

    This gradient coefficients files directory must contain the
    proprietary gradient coefficients files for any scanners used in 
    collecting your image data files.

    If you do not specify a gradient coefficients files directory, it will
    default to: ${DEFAULT_GRADIENT_COEFFS_DIR}.  

    NOTE: The path to the gradient coefficients files is only necessary
    for actual processing of data. If you are running a completion
    check, you can allow this to take its default value even if that
    value is incorrect.  

  Path to FreeSurfer license file
  -------------------------------

  [--freesurfer-license-dir=<path-to-freesurfer-license-directory>]

    The specified path will be bound (i.e. mounted) from your system
    to a known location (/export/freesurfer_license) in the container
    or sandbox. This is where the FreeSurfer license file must be
    found within the container or sandbox.

    If you do not specify a FreeSurfer license directory, it will 
    default to: ${DEFAULT_FREESURFER_LICENSE_DIR}.

    NOTE: The path to the FreeSurfer license file is only necessary
    for actual processing of data. If you are running a completion
    check, you can allow this to take its default value even if that
    value is incorrect.  

  Specification of environment
  ----------------------------

    You may specify whether to perform the requested processing
    in the Singularity Container (HCPprocessPipelines.simg) or 
    in the Singularity Sandbox (HCPprocessPipelinesSandbox/).

    One of the following options may be specified:

      --env=[CONTAINER|SANDBOX]
      --container
      --sandbox

    The value specified for the --env= parameter is not case
    sensitive, but must be either CONTAINER or SANDBOX. For example, 
    --env=ConTAiner, --env=SandBox, and --env=sandbox
    are all valid, but --env=CONTAIN is not valid.

      --container is equivalent to --env=CONTAINER
      --sandbox is equivalent to --env=SANDBOX

    If no --env= option is specified, this script defaults to --env=${DEFAULT_ENV}.

    NOTE: To run some apps, you will need sudo privileges
    on the machine on which you are running. When commands are run
    with sudo, you may be prompted for your password to validate 
    your sudo privileges. 

  Subject List File
  -----------------

    You must specify a file containing a list of subject information lines.

    The --subject-list= option is used to specify the path to the subject file.

    Each line in the subject file must contain the following information:

      <study-dir>:<subject-id>:<positive-spin-echo-fieldmap-name>:<negative-spin-echo-fieldmap-name>

    Anything after a # on a line is considered a comment. To comment out a subject
    information line, simply insert a # as the very first character on the line

    Each subject information line will be parsed and the container or sandbox will 
    be used to run the specified processing for the specified subject.

  Processing
  ----------

    This script can:

      1. run the actual Structural Preprocessing for the specified subjects 
      2. run the completion check for Structural Preprocessing for the specified subjects.
      3. show the help provided by the container for Structural Preprocessing
      4. remove the results of Structural Preprocessing for the specified subjects
         (either prompting you for confirmation of files to delete first, or
         with no prompting at all)

    You specify which type of processing to perform using one of the following options:

      --app=[PROCESS|CHECK|REMOVE_RESULTS|FORCE_REMOVE_RESULTS|PROCESSHELP]
      --process
      --check
      --process-help
      --remove-results        (prompts for confirmation)
      --force-remove-results  (no prompting - dangerous)

    The value specified for the --app= parameter is not case sensitive, but must be
    one of the listed apps. For example, --app=Process, --app=PROCess, and 
    --app=ChecK are all valid, but --app=PRO is not valid.

      --process is equivalent to --app=PROCESS
      --check is equivalent to --app=CHECK
      --remove-results is equivalent to --app=REMOVE_RESULTS
      --force-remove-results is equivalent to --app=FORCE_REMOVE_RESULTS
      --process-help is equivalent to --app=PROCESSHELP

    If no --app= option is specified, this script defaults to --app=${DEFAULT_APP}.

EOF
}

get_options()
{
	local arguments=($@)
	
	# initialize global output variables
	unset g_subject_list_file
	g_gradient_coeffs_dir="${DEFAULT_GRADIENT_COEFFS_DIR}"
	g_freesurfer_license_dir="${DEFAULT_FREESURFER_LICENSE_DIR}"
	g_env="${DEFAULT_ENV}"
	g_app="${DEFAULT_APP}"
	
	# parse arguments
	local num_args=${#arguments[@]}
	local argument
	local index=0

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

		case ${argument} in
			--help)
				usage
				exit 1
				;;
			--gradient-coeffs_dir=*)
				g_gradient_coeffs_dir=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--freesurfer-license-dir=*)
				g_freesurfer_license_dir=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--env=*)
				g_env=${argument/*=/""}
				g_env=$(echo ${g_env} | tr '[:lower:]' '[:upper:]')
				index=$(( index + 1 ))
				;;
			--container)
				g_env="CONTAINER"
				index=$(( index + 1 ))
				;;
			--sandbox)
				g_env="SANDBOX"
				index=$(( index + 1 ))
				;;
			--subject-list=*)
				g_subject_list_file=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--app=*)
				g_app=${argument/*=/""}
				g_app=$(echo ${g_app} | tr '[:lower:]' '[:upper:]')
				index=$(( index + 1 ))
				;;
			--process)
				g_app="PROCESS"
				index=$(( index + 1 ))
				;;
			--check)
				g_app="CHECK"
				index=$(( index + 1 ))
				;;
			--process-help)
				g_app="PROCESSHELP"
				index=$(( index + 1 ))
				;;
			--remove-results)
				g_app="REMOVE_RESULTS"
				index=$(( index + 1 ))
				;;
			--force-remove-results)
				g_app="FORCE_REMOVE_RESULTS"
				index=$(( index + 1 ))
				;;
			*)
				abort "Unrecognized option: ${argument}"
				;;
		esac

	done

	# check parameters

	if [ -n "${g_gradient_coeffs_dir}" ]; then
		echo "INFO: gradient coefficients directory: ${g_gradient_coeffs_dir}"
	else
		abort "--gradient-coeffs-dir=<gradient-coeffs-directory> must be specified"
	fi

	if [ -n "${g_freesurfer_license_dir}" ]; then
		echo "INFO: FreeSurfer license directory: ${g_freesurfer_license_dir}"
	else
		abort "--freesurfer-license-dir=<freesurfer-license-directory> must be specified"
	fi
	
	if [ -z "${g_env}" ]; then
		abort "environment (--env=[CONTAINER|SANDBOX], --container, or --sandbox) required"
	fi

	if [ "${g_env}" != "CONTAINER" -a "${g_env}" != "SANDBOX" ]; then 
		abort "environment must be CONTAINER or SANDBOX"
	else
		echo "INFO: Environment: ${g_env}"
	fi

	if [ -z "${g_app}" ]; then
		abort "app to run (--app=<value>, --process, --check, --process-help, --remove-results, --force-remove-results) required"
	fi

	if [ "${g_app}" != "PROCESS" \
		 -a "${g_app}" != "CHECK" \
		 -a "${g_app}" != "PROCESSHELP" \
	     -a "${g_app}" != "REMOVE_RESULTS" \
	     -a "${g_app}" != "FORCE_REMOVE_RESULTS" ]; then 
		abort "Unrecognized app: ${g_app}"
	fi

	if [ -n "${g_subject_list_file}" ]; then
		echo "INFO: running requested app, ${g_app}, for subjects listed in file: ${g_subject_list_file}"
	else
		if [ "${g_app}" != "PROCESSHELP" ]; then
			abort "--subject-list=<subject-list-filename> must be specified"
		fi
	fi
}

main()
{
	local line
	local study_dir
	local subject_id
	local pos_fieldmap
	local neg_fieldmap
	local run_cmd
	local where_study_is_on_my_system
	local where_study_must_be_in_container
	local where_gc_files_are_on_my_system
	local where_gc_files_must_be_in_container
	local where_license_file_is_on_my_system
	local where_license_file_must_be_in_container
		
	get_options "$@"

	if [ "${g_app}" = "PROCESSHELP" ]; then

		run_cmd=""
		
		if [ "${g_env}" = "CONTAINER" ]; then
			# Note: If all applications are run from the CONTAINER, the sudo at the beginning
			#       of this command is unnecessary. However, if you run some processing first
			#       within the SANDBOX, in which the sudo is needed, then try to run some
			#       subsequent processing from the CONTAINER, the processing run from the
			#       SANDBOX will have left around files and directories owned by root and
			#       the CONTAINER run (if run without the sudo) will not be able to delete
			#       or update these files or directories.
			run_cmd+="sudo singularity run --app StructuralPreprocessing HCPprocessPipelines.simg"
		elif [ "${g_env}" = "SANDBOX" ]; then
			run_cmd+="sudo singularity exec HCPprocessPipelinesSandbox/ /pipeline_tools/HCPpipelinesRunUtils/StructuralPreprocessing/StructuralPreprocessing.SINGULARITY_PROCESS"
		else
			abort "Unrecognized environment: ${g_env}"
		fi

		run_cmd+=" --help"

		echo "run_cmd: ${run_cmd}"

		time ${run_cmd}

		exit
	fi

	
	while read -r -u9 line; do

		# remove comments - anything after a #
		line=${line%%\#*}
		
		# trim leading and trailing whitespace
		line=$(echo ${line} | xargs)
		
		if [ -z "${line}" ]; then
			continue
		fi
			
		# break into study_dir, subject_id, pos_fieldmap, and neg_fieldmap
		study_dir=${line%%:*}			# study_dir is everything before the first ":"
		line=${line#${study_dir}:}		# strip study_dir and : from the front of the line
		
		subject_id=${line%%:*}			# subject_id is everything before the first :
		line=${line#${subject_id}:} 	# strip subject_id and : from the front of line
		
		pos_fieldmap=${line%%:*}		# pos_fieldmap is everything before the first :
		line=${line#${pos_fieldmap}:}	# strip pos_fieldmap and : from the front of line
		
		neg_fieldmap=${line}			# neg_fieldmap is everything that is left

		if [ "${g_app}" = "PROCESS" ]; then

			echo ""
			echo "-- Running processing for subject: "
			echo "--     study directory: ${study_dir}"
			echo "--          subject id: ${subject_id}"
			echo "--   positive fieldmap: ${pos_fieldmap}"
			echo "--   negative fieldmap: ${neg_fieldmap}"
			echo ""
			
			run_cmd=""
			
			# Base Singularity command
			if [ "${g_env}" = "CONTAINER" ]; then
				# Note: If all applications are run from the CONTAINER, the sudo at the beginning
				#       of this command is unnecessary. However, if you run some processing first
				#       within the SANDBOX, in which the sudo is needed, then try to run some
				#       subsequent processing from the CONTAINER, the processing run from the
				#       SANDBOX will have left around files and directories owned by root and
				#       the CONTAINER run (if run without the sudo) will not be able to delete
				#       or update these files or directories.
				run_cmd+="sudo singularity run"
			elif [ "${g_env}" = "SANDBOX" ]; then
				run_cmd+="sudo singularity exec"
			else
				abort "Unrecognized environment: ${g_env}"
			fi
			
			# Bind your study directory
			# Needs to show up as the /study directory in the Container/Sandbox
			where_study_is_on_my_system="${study_dir}"
			where_study_must_be_in_container="/study"
			
			run_cmd+=" -B ${where_study_is_on_my_system}:${where_study_must_be_in_container}"
			
			# Bind gradient coefficients files directory
			# Needs to show up as the /export/HCP/gradient_coefficient_files directory in the Container/Sandbox
			where_gc_files_are_on_my_system="${g_gradient_coeffs_dir}"
			where_gc_files_must_be_in_container="/export/HCP/gradient_coefficient_files"
			
			run_cmd+=" -B ${where_gc_files_are_on_my_system}:${where_gc_files_must_be_in_container}"
			
			# Bind folder with FreeSurfer License
			# Needs to show up as the /export/freesurfer_license directory in the Container/Sandbox
			# Must contain a file named 'license.txt'
			where_license_file_is_on_my_system="${g_freesurfer_license_dir}"
			where_license_file_must_be_in_container="/export/freesurfer_license"
			
			run_cmd+=" -B ${where_license_file_is_on_my_system}:${where_license_file_must_be_in_container}"
			
			# Specify command or script to run
			if [ "${g_env}" = "CONTAINER" ]; then
				# application in the container to run
				run_cmd+=" --app StructuralPreprocessing"
				# container image file
				run_cmd+=" HCPprocessPipelines.simg"
			elif [ "${g_env}" = "SANDBOX" ]; then
				# sandbox directory 
				run_cmd+=" HCPprocessPipelinesSandbox/"
				# full path to script within sandbox to execute
				run_cmd+=" /pipeline_tools/HCPpipelinesRunUtils/StructuralPreprocessing/StructuralPreprocessing.SINGULARITY_PROCESS"
			else
				abort "Unrecognized environment: ${g_env}"
			fi
			
			# Add command line parameters for command/script to run
			run_cmd+=" --working-dir=/study" # Note: this path is from within the container
			run_cmd+=" --subject=${subject_id}"
			run_cmd+=" --classifier=V1_MR"
			run_cmd+=" --brainsize=150"
			
			run_cmd+=" --first-t1w-directory-name=T1w_MPR_vNav_4e_RMS"
			run_cmd+=" --first-t1w-file-name=${subject_id}_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz"
			
			run_cmd+=" --first-t2w-directory-name=T2w_SPC_vNav"
			run_cmd+=" --first-t2w-file-name=${subject_id}_V1_MR_T2w_SPC_vNav.nii.gz"
			
			run_cmd+=" --t1template=MNI152_T1_0.8mm.nii.gz"
			run_cmd+=" --t1templatebrain=MNI152_T1_0.8mm_brain.nii.gz"
			run_cmd+=" --t1template2mm=MNI152_T1_2mm.nii.gz"
			
			run_cmd+=" --t2template=MNI152_T2_0.8mm.nii.gz"
			run_cmd+=" --t2templatebrain=MNI152_T2_0.8mm_brain.nii.gz"
			run_cmd+=" --t2template2mm=MNI152_T2_2mm.nii.gz"
			
			run_cmd+=" --templatemask=MNI152_T1_0.8mm_brain_mask.nii.gz"
			run_cmd+=" --template2mmmask=MNI152_T1_2mm_brain_mask_dil.nii.gz"
			
			run_cmd+=" --fnirtconfig=T1_2_MNI152_2mm.cnf"
			run_cmd+=" --gdcoeffs=Prisma_3T_coeff_AS82.grad"
			run_cmd+=" --topupconfig=b02b0.cnf"
			
			run_cmd+=" --fieldmap-type=SpinEcho"
			run_cmd+=" --se-phase-pos=${pos_fieldmap}"
			run_cmd+=" --se-phase-neg=${neg_fieldmap}"
			
			echo "run_cmd: ${run_cmd}"
			
			time ${run_cmd}

		elif [ "${g_app}" = "CHECK" ]; then

			echo ""
			echo "-- Checking completeness for subject: "
			echo "--     study directory: ${study_dir}"
			echo "--          subject id: ${subject_id}"
			echo "--   positive fieldmap: ${pos_fieldmap}"
			echo "--   negative fieldmap: ${neg_fieldmap}"
			echo ""
			
			run_cmd=""
			
			# Base Singularity command
			if [ "${g_env}" = "CONTAINER" ]; then
				# Note: If all applications are run from the CONTAINER, the sudo at the beginning
				#       of this command is unnecessary. However, if you run some processing first
				#       within the SANDBOX, in which the sudo is needed, then try to run some
				#       subsequent processing from the CONTAINER, the processing run from the
				#       SANDBOX will have left around files and directories owned by root and
				#       the CONTAINER run (if run without the sudo) will not be able to delete
				#       or update these files or directories.
				run_cmd+="sudo singularity run"
			elif [ "${g_env}" = "SANDBOX" ]; then
				run_cmd+="sudo singularity exec"
			else
				abort "Unrecognized environment: ${g_env}"
			fi
			
			# Bind your data directory
			# Needs to show up as the /data directory in the Container/Sandbox
			where_study_is_on_my_system="${study_dir}"
			where_study_must_be_in_container="/study"
			
			run_cmd+=" -B ${where_study_is_on_my_system}:${where_study_must_be_in_container}"
			
			# Specify command or script to run
			if [ "${g_env}" = "CONTAINER" ]; then
				# application in the container to run
				run_cmd+=" --app StructuralPreprocessingCheckData"
				# container image file
				run_cmd+=" HCPprocessPipelines.simg"
			elif [ "${g_env}" = "SANDBOX" ]; then
				# sandbox directory 
				run_cmd+=" HCPprocessPipelinesSandbox/"
				# full path to script within sandbox to execute
				run_cmd+=" /pipeline_tools/HCPpipelinesRunUtils/StructuralPreprocessing/StructuralPreprocessing.CHECK"
			else
				abort "Unrecognized environment: ${g_env}"
			fi
			
			# Add command line parameters for command/script to run
			run_cmd+=" --working-dir=/study"
			run_cmd+=" --subject=${subject_id}"
			run_cmd+=" --classifier=V1_MR"
			
			echo "run_cmd: ${run_cmd}"
			
			time ${run_cmd}

		elif [ "${g_app}" = "REMOVE_RESULTS" ]; then

			echo ""
			echo "WARNING: Working on subject: ${subject_id}."
			echo ""
            echo "         Cleaning all files in the subject's data directory that are"
			echo "         newer than the Structural Preprocessing start time marker  "
			echo "         file. This means that Structural Preprocessing results and "
			echo "         any results of processing subsequent to Structural         "
			echo "         Preprocessing will be removed."
			echo ""

			if should_proceed; then
				remove_ccf_struct_results "${study_dir}" "${subject_id}"
			else
				echo ""
				echo "FILES NOT DELETED - RESULTS NOT REMOVED FOR SUBJECT: ${subject_id}"
				echo ""
			fi

		elif [ "${g_app}" == "FORCE_REMOVE_RESULTS" ]; then

			remove_ccf_struct_results "${study_dir}" "${subject_id}"
			
		else

			abort "Unrecognized app: ${g_app}"
			
		fi
			
	done 9< "${g_subject_list_file}"
}

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