Reorganize EASY module

workflow/apps/matlab/easy/EASYconsole.m

@@ -273,7 +273,7 @@ function NewExpDat_Callback(~, ~, ~)
     questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
     [inputFile,inputPath]=uiputfile('.mat');
     inputFileName=strrep(inputFile,'.mat','');
-    easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);
+    % easyResultsDirName=strcat('Results_',todayStr,'_',userName,'_',inputFileName);
 
     % Set paths
     scansDir=fullfile(inputPath);

workflow/qhtcp-workflow

@@ -588,43 +588,42 @@ easy() {
 	EOF
 
   declare -gx EASY_DIR="$APPS_DIR/matlab/easy"
+  declare -gx EASY_RESULTS_DIR="$EASY_OUT_DIR/$PROJECT_PREFIX"
   script="$EASY_DIR/EASYconsole.m"
 
-  # Copy templates
+  # Prompt user for suffix
+  echo "Default EASY results directory: $EASY_RESULTS_DIR"
+  read -r -p "Enter a custom suffix and/or hit enter to use the default (no suffix): " EASY_SUFFIX
+  [[ -n $EASY_SUFFIX ]] && EASY_RESULTS_DIR+="_$EASY_SUFFIX"
 
-  # Add EASY directory to the Matlab path
+  # Backup and create EASY results dirs
-  # If this does not work we can try changing the -sd argument and if that fails then pushing/popping
+  [[ -d $EASY_RESULTS_DIR ]] && backup "$EASY_RESULTS_DIR"
-  debug "Adding EASY directory to the Matlab path"
+  [[ -d $EASY_RESULTS_DIR ]] || mkdir -p "$EASY_RESULTS_DIR"
-  hash matlab &>/dev/null && 
+
-    matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
+  # Make EASY dirs
+  dirs=('PrintResults' 'CFfigs' 'Fotos')
+  for d in "${dirs[@]}"; do
+    if [[ ! -d $EASY_RESULTS_DIR/$d ]]; then
+      debug "mkdir $EASY_RESULTS_DIR/$d" 
+      mkdir "$EASY_RESULTS_DIR/$d"
+    fi
+  done
+
+  # Copy Templates
+  declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
+  declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
+  rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
 
   # Ask the user to launch EASYconsole.m in MATLAB
   # MATLAB doesn't support passing args to scripts se we have to use ENV VARS instead
-  # These are proably already set in our scope but be explicit just in case so we don't have to export?
   # TODO will need to play with the -sd startup option to see what works (well)
   # Skip this step altogether in auto mode since it requires graphical interaction
   if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
-    # export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER PROJECT
+    # Add EASY directory to the Matlab path
-    # export EASY_DIR EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR 
+    # If this does not work we can try changing the -sd argument and if that fails then pushing/popping
-    # export MASTER_PLATE_FILE DRUG_MEDIA_FILE
+    debug "Adding EASY directory to the Matlab path"
-
+    hash matlab &>/dev/null && 
-    declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
+    matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
-    declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
-
-    # Make EASY dirs
-    debug "mkdir -p $EASY_RESULTS_DIR"
-    mkdir -p "$EASY_RESULTS_DIR"
-    dirs=('PrintResults' 'CFfigs' 'Fotos')
-    for d in "${dirs[@]}"; do
-      if [[ ! -d $EASY_RESULTS_DIR/$d ]]; then
-        debug "mkdir $EASY_RESULTS_DIR/$d" 
-        mkdir "$EASY_RESULTS_DIR/$d"
-      fi
-    done
-
-    # Copy templates
-    rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
-
     # Launch matlab
     # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
     matlab -nosplash -r "run $script"
@@ -1577,7 +1576,7 @@ main() {
     declare -gx QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
     declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
     declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
-    declare -gx EASY_RESULTS_DIR="$QHTCP_PROJECT_DIR/easy"
+    declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy"
     if ((DEBUG)); then
       declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
       PROJECTS PROJECT \