Add extended .sh and rendering

Co-authored-by: Lawrence Binding <[email protected]>

scripts/run_RandomiserBlender.sh

@@ -0,0 +1,102 @@
+#!/usr/bin/env bash
+#
+# run_RandomiserBlender.sh
+#   Takes user inputs and randomises these on a blend file and saves a frame
+#
+# Created by ruaridhg & lbinding
+#   08/11/2024
+#
+
+source ~/.bash_profile
+
+#Setup blender path
+alias blender=/Applications/Blender.app/Contents/MacOS/Blender
+blender=/Applications/Blender.app/Contents/MacOS/Blender
+
+# Get script name
+script_name=`basename $0`
+#Get script location
+main_dir="$(dirname "$(realpath "$BASH_SOURCE")")/.."
+script_path="$(dirname "$(realpath "$BASH_SOURCE")")"
+
+#Check if files are in the script directory
+if [ ! -f ../install_and_enable_addons.py ]; then
+  echo "ERROR: 'install_and_enable_addons.py' is not located in the main directory"
+  echo "exiting..."
+fi
+if [ ! -f ../randomiser.zip ]; then
+  echo "ERROR: 'randomiser.zip' is not located in the main directory"
+  echo "exiting..."
+fi
+
+# Setup user paths
+# Loop over arguments looking for -i and -o
+args=("$@")
+i=0
+while [ $i -lt $# ]; do
+    # Set blender data
+    if [ "${args[i]}" = "-blend" ]; then
+      let i=i+1
+      blend_file="${args[i]}"
+    elif [ "${args[i]}" = "-seed" ]; then
+      # Set seed value
+      let i=i+1
+      seed_num="${args[i]}"
+    elif [ "${args[i]}" = "-json_in" ]; then
+      # Set json input
+      let i=i+1
+      json_input="${args[i]}"
+    elif [ "${args[i]}" = "-frame" ]; then
+      # Set frame number
+      let i=i+1
+      frame="${args[i]}"
+    elif [ "${args[i]}" = "-basename" ]; then
+      # Set base output
+      let i=i+1
+      base_output="${args[i]}"
+    elif [ "${args[i]}" = "-render_main" ]; then
+      # Set Render main as true or false
+      let i=i+1
+      render_main=True
+    fi
+    let i=i+1
+done
+
+# Debugging: Print each variable to check values
+echo "Blend file: ${blend_file}"
+echo "Seed: ${seed_num}"
+echo "JSON input: ${json_input}"
+echo "Frame: ${frame}"
+echo "Base output: ${base_output}"
+
+# Check to make sure all required inputs are assigned
+if [ -z "${blend_file}" ] || [ -z "${seed_num}" ] || [ -z "${json_input}" ]; then
+    correct_input=0
+else
+    correct_input=1
+fi
+
+#Check the user has provided the correct inputs
+if ( [[ ${correct_input} -eq 0 ]] ) ; then
+  echo ""
+  echo "Incorrect input. Please see below for correct use"
+  echo ""
+  echo "Options:"
+  echo " -blend:              Absolute path to working directory  -- REQUIRED"
+  echo " -json_in:            Input dwi data (full path)  -- REQUIRED"
+  echo " -json_out:           Input bvec data (full path)  -- REQUIRED"
+  echo " -seed:               Input bval data (full path)  -- REQUIRED"
+  echo " -frame:              Input number (full path)  -- REQUIRED"
+  echo " -basename:           Input basename (full path)  -- REQUIRED"
+  echo " -render_main:        Sets variable to true to run main image generation (full path)  -- OPTIONAL"
+  echo ""
+  echo "${script_name} -blend /home/username/colon.blend -json_in /home/username/input.json -json_out  /home/username/output.json -json /home/username/synb0/dwi.json -seed 32 -frame 10 -basename /home/username/output_frame -render_main"
+  echo ""
+  exit
+fi
+
+# zip randomiser
+zip ../randomiser.zip -FS -r ../randomiser/
+
+# Run blender in the background (-b) and run the python script inputting the seed,
+${blender} -b ${blend_file} --python ../install_and_enable_addons.py -- ../randomiser.zip --seed ${seed_num} --input ${json_input} --frame ${frame} --basename ${base_output} --render_main ${render_main}