idinteraction.nw

#!/usr/bin/env nextflow

/*
vim: syntax=groovy
-*- mode: groovy;-*-
*/

// Experimental processing pipeline for idinteraction using nextflow

params.indir = "./participants/*"
params.eventfile = "./particiants/transitionannotations.csv"

participant_dir = Channel.fromPath(params.indir, type: 'dir').map {
	path -> tuple(path.baseName, 
			path.toRealPath(),
			 path)
	}

keyframefile = Channel.fromPath(params.eventfile)

eventnames = Channel.from ("start1",
			"end1",
			"start2",
			"end2")

process enter_participant {
	// Separate each participant's data into its constituent 
	// streams
	input: 
	set participantcode, fullpath, path from participant_dir

	output:
	set participantcode, 'attention.txt' into attention_for_groundtruth, attention_for_events
	set participantcode, 'frontkinect.mp4', val("kinect"),
		val("front")  into frontkinectfile
	set participantcode, 'webcam.mp4', val("webcam"), val("front")  into webcamfile
	set participantcode, 'depthdata.tar' into depthfile

	"""
	# TODO - check each only matches a single file
	cat ${fullpath}/*_attention.txt > attention.txt
	cat ${fullpath}/*_kinect.mp4 > frontkinect.mp4
	cat ${fullpath}/*_webcam.mp4 > webcam.mp4
	tar czf depthdata.tar ${fullpath}/P??depth/*
	"""
}


process attention_to_groundtruth {
	// Convert an attention file to a groundtruth file
	input:
	set val(participantcode), file(attentionfile) from attention_for_groundtruth

	output:
	set file('groundtruth.csv'), val(participantcode) into csvfile

	"""
	echo "groundtruth" > groundtruth.csv
	cat  ${attentionfile} >> groundtruth.csv
	
	"""
}

process extract_eventframe {
	input:
	file attentionfile from attention_for_events
	file keyframefile from keyframefile
	val event from eventnames

	output:
	set val(event), val(eventframe) into eventframe
	
	exec:
	eventframe = "123"

}

// Split channel so we can use it in following two filters
eventframe.into {eventframe1; eventframe2}
startevents = eventframe1.filter {it[0] =~/^start./}
endevents = eventframe2.filter{it[0] =~/^end./}

/*
process map_frame_to_kinect {
	// Transform a frame from Webcam to Kinect time 
	input:
	set val(webcamframe), val(event), val(participantcode) from xxx
	val map from mappingfile // Not sure how we'll implement this

	output:
	val webcamframe from eventframe
	
	exec:
	// Stuff to do the mapping
}
*/

// Combine both video sources
videofiles = frontkinectfile.mix(webcamfile)

// Combine all combinations of startevents and video sources
cppmt_runs = videofiles.combine(startevents)

// Run them
process run_cppmt {
	echo true
	input:
	set val(event), val(eventframe) ,
val(participantcode), file(videofile), val(timebase),
		val(source) from cppmt_runs
	
	output:
	set participantcode, "cppmt_tracking.csv", timebase, source into cppmttrackingfile

	"""
	echo "Running cppmt tracking"
	echo "${videofile} ${event} ${eventframe}"
	echo "${participantcode}, ${timebase}"
	echo "${event}, ${eventframe}"
	echo "Cppmt tracking" > cppmt_tracking.csv
	echo ${participantcode} >> cppmt_tracking
	cat ${videofile} >> cppmt_tracking
	echo ${event} >> cppmt_tracking
	echo ${eventframe} >> cppmt_tracking
	"""
}

process report_cppmt {
	input: 
	set val(participantcode), file("cppmttrack.csv"),
	val(timebase), val(source) from cppmttrackingfile

	exec:
	println "in report_cppmt"
	println "pcode:" + participantcode
	println timebase
	println source
	println "end report_cppmt"

}