Tidied up files with folder structure

scripts/install_randomiser.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+source ~/.bash_profile
+
+# zip randomiser, launch blender and install+enable
+zip ../randomiser.zip -FS -r ../randomiser/
+blender ../blend_files/sample.blend --python ../install_and_enable_addons.py -- ../randomiser.zip

scripts/randomisation_seed.sh

@@ -1,77 +1,6 @@
 #!/usr/bin/env bash
 source ~/.bash_profile
 
-#Setup blender path
-alias blender=/home/lbinding/software/blender-4.2.3-linux-x64/blender
-blender=/home/lbinding/software/blender-4.2.3-linux-x64/blender
-
-# Get script name
-script_name=`basename $0`
-#Get script location
-script_path="$(dirname "$(realpath "$BASH_SOURCE")")"
-
-# 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 ( [ ${args[i]} = "-json_out" ] ) ; then
-      # Set json output
-      let i=$i+1
-      json_output=${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=${args[i]}
-    fi
-    let i=$i+1
-done
-
-#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 ( [[ ${correct_input} -eq 0 ]] ) ; then
-  echo ""
-  echo "Incorrect input. Please see below for correct use"
-  echo ""
-  echo "Options:"
-  echo " -blend:              Absolute path to working directory  -- REQUIRED"
-  echo " -json_in:            Input dwi data (full path)  -- REQUIRED"
-  echo " -json_out:           Input bvec data (full path)  -- REQUIRED"
-  echo " -seed:               Input bval data (full path)  -- REQUIRED"
-  echo " -frame:              Input number (full path)  -- REQUIRED"
-  echo " -basename:           Input basename (full path)  -- REQUIRED"
-  echo ""
-  echo "${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"
-  echo ""
-  exit
-fi
-
-
-
 # zip randomiser, launch blender and install+enable, set seed and input bounds
-zip ${script_path}/randomiser.zip -FS -r ${script_path}/randomiser/
-#${blender} ${blend_file} --python ${script_path}/install_and_enable_addons.py -- ${script_path}/randomiser.zip --seed 32 --input ${json_input} --output ${json_output}
-
-${blender} -b ${blend_file} --python ${script_path}/install_and_enable_addons.py -- ${script_path}/randomiser.zip --seed 32 --input ${json_input} --frame 10 --basename ${base_output}
+zip ../randomiser.zip -FS -r ../randomiser/
+blender ../blend_files/sample.blend --python ../install_and_enable_addons.py -- ../randomiser.zip --seed 32 --input ../input_files/input_bounds.json --output ../output_files/output_randomisations_per_frame1697116725.310647.json