Adding new shell script to process tobii records.

1 files changed, 172 insertions, 0 deletions

diff --git a/utils/processTobiiRecords.sh b/utils/processTobiiRecords.sh
new file mode 100644
index 0000000..8ee5773
--- /dev/null
+++ b/utils/processTobiiRecords.sh
@@ -0,0 +1,172 @@
+#! /bin/bash
+#
+# Load json ArGaze context file ($1) then, look for all Tobii record segments into input folder ($2).
+#
+# For each Tobii record segment found: 
+# - context "segment" field is modified to bind on it,
+# - context "pipeline" field is modified to bind on a temporary patched pipeline \ 
+#	resulting from the merging of the given pipeline and an optionnal "patch.json" file in Tobii record segment,
+# - then, ArGaze executes the modified context from output folder ($3) to export all records into it,
+# - finally, context is resetted and temporary patched pipeline is removed.
+#
+# Arguments:
+# $1: ArGaze context file
+# $2: folder from where to look for Tobii records
+# $3: folder where to export ArGaze processing outputs
+#######################################
+
+# Check required arguments
+if [ "$#" -ne 3 ]; then
+  echo "!!! Incorrect number of arguments"
+  exit 1
+fi
+
+context_file=$1
+input_folder=$2
+output_folder=$3
+
+# Check requirements:
+if brew ls --versions jq > /dev/null; then
+ 	: # jq installed
+else
+	echo "*** Installing jq package"
+ 	brew install jq
+fi
+
+# Check context
+ctx_folder="$(dirname "$context_file")"
+ctx_class=$(jq "keys[0]" $context_file)
+ctx_name=$(jq .$ctx_class.name $context_file)
+ctx_segment=$(jq .$ctx_class.segment $context_file)
+pipeline_file=$(jq -r .$ctx_class.pipeline $context_file)
+
+echo "*** Loading $ctx_class context:"
+echo "- Name: $ctx_name"
+
+# Move to context folder
+cd $ctx_folder
+
+# Check pipeline
+if [ -f "$pipeline_file" ]; then
+	
+	ppl_class=$(jq "keys[0]" $pipeline_file)
+	ppl_name=$(jq .$ppl_class.name $pipeline_file)
+	echo "- Pipeline: $ppl_name"
+
+else 
+
+	echo "!!! Missing $pipeline_file pipeline file"
+	exit 1
+
+fi
+
+#######################################
+# Process Tobii segment folder
+# Arguments:
+#   $1: Path to Tobii segment
+#######################################
+function process_segment() {
+
+	local rec_id=$1
+	local seg_folder=$2
+	local seg_id=$(basename $seg_folder)
+	local seg_length=$(jq .seg_length $seg_folder/segment.json)
+
+	local ca_state=$(jq -r .ca_state $seg_folder/calibration.json)
+
+	echo "- Segment $seg_id:"
+	echo "	- Lenght: $seg_length"
+	echo "	- Calibration: $ca_state"
+
+	# Check patch
+	patch_file="$seg_folder/patch.json"
+	if [ -f "$patch_file" ]; then
+		
+		echo "+ Patch:"
+		echo "$(jq . $patch_file)"
+
+		# Edit temporary patched pipeline
+		temp_file=".$rec_id-$seg_id.patch.json"
+		echo "$(jq --tab -s ".[0] * .[1]" $pipeline_file $patch_file)" > "$ctx_folder/$temp_file"
+
+		# Modify context pipeline
+		echo "$(jq --tab ".$ctx_class.pipeline = \"$temp_file\"" $context_file)" > $context_file
+
+		echo "*** $ctx_folder/$temp_file file created"
+	fi
+
+	# Modify context segment
+	echo "$(jq --tab ".$ctx_class.segment = \"$seg_folder\"" $context_file)" > $context_file
+
+	# Create segment output folder then, move into
+	seg_output=$output_folder/$rec_id/segments/$seg_id
+	mkdir -p $seg_output
+	cd $seg_output
+
+	# Launch argaze with modified context
+	echo "*** ArGaze processing starts"
+
+	python -m argaze $context_file
+
+	echo "*** ArGaze processing ends"
+
+	# Move back to context folder
+	cd $ctx_folder
+
+	# Reset context segment
+	echo "$(jq --tab ".$ctx_class.segment = $ctx_segment" $context_file)" > $context_file
+
+	# Check temporary pipeline
+	if [ -f "$temp_file" ]; then
+
+		# Delete temporary patched pipeline
+		rm "$ctx_folder/$temp_file"
+
+		# Reset context pipeline
+		echo "$(jq --tab ".$ctx_class.pipeline = \"$pipeline_file\"" $context_file)" > $context_file
+	
+		echo "*** $ctx_folder/$temp_file file removed"
+	fi
+}
+
+#######################################
+# Process Tobii record folder
+# Arguments:
+#   $1: Path to Tobii record
+#######################################
+function process_record() {
+
+	local rec_folder=$1
+	local rec_id=$(basename $rec_folder)
+	local rec_name=$(jq .rec_info.Name $rec_folder/recording.json)
+
+	local pa_id=$(jq .pa_id $rec_folder/participant.json)
+	local pa_name=$(jq .pa_info.Name $rec_folder/participant.json)
+
+	echo "*** Loading record $rec_id:"
+	echo "- Name: $rec_name"
+	echo "- Participant:"
+	echo "	- Id: $pa_id"
+	echo "	- Name: $pa_name"
+
+	for segment in $rec_folder/segments/*; do
+		process_segment $rec_id "$rec_folder/segments/$(basename $segment)"
+	done
+}
+
+echo "*** Looking for Tobii records into $2 folder"
+
+# Check if the path is directly a path to a record segment
+if [ -f "$input_folder/livedata.json.gz" ]; then
+
+	process_record "$(dirname "$(dirname "$input_folder")")"
+
+# Otherwise, look for all Tobii record segment
+else
+
+	for tobii_data in $input_folder/**/segments/*/livedata.json.gz; do
+	    process_record "$(dirname "$(dirname "$(dirname "$tobii_data")")")"
+	done
+
+fi
+