Deep learning scripts

batch_cluster.sh

REM This is the batch file script for autogenerating yaml files for windows
SET sigma=60
SET exptName=PA_Bifurcation_sigma_%sigma%
echo sigma
SET template=%CD%\\settings\\data_pipeline_settings.yaml
SET pipeline_yaml=%CD%\\settings\\%ExptName%.yaml
SET ai_yaml=%CD%\\settings\\ai_settings.yaml
SET data_output=%ExptName%

REM Generate the new data_pipeline yaml file with defined parameters
python write_data_pipeline_yaml.py -s %sigma% -t %template% -o %pipeline_yaml%

REM run process_data
python process_data.py -s %pipeline_yaml% -o %data_output%

REM run train_cv
python train_cv.py -s %ai_yaml% -d %data_output%

batchScript4DL.sh

# i iterable are values of sigma to probe
template=$PWD"/settings/data_pipeline_settings_ns.yaml"
outputHeader=$PWD"/settings/sigma_"
outputEnder=".yaml"
aiSettings=$PWD"/settings/ai_settings.yaml"
for i in 10 20 30 40 50 60 70 80 90
do
  sigma=$i
  output=$outputHeader$sigma$outputEnder
  echo $output
  python3 write_data_pipeline_yaml.py -s $sigma -t $template -o $output
  exptName="sigma_"$sigma
  python3 process_data_ns.py -s $output -o $exptName
  python3 train_cv.py -s $aiSettings -d $PWD"/output_data/"$exptName -n $exptName
  killall python3
done

#

windows_python_script.py

#!/usr/bin/env python

# import libraries
import os

# define parts of program call
interpreter_call = "python"
base_call = 'process_data.py'
anatomies_call = '-a etc\primary_anatomies.yaml'

# make into a list
cmd_lst = [
    interpreter_call,
    base_call,
    anatomies_call,
]

# source and run file
os.system(" ".join(cmd_lst))