run_classification

#!/bin/bash

# Version 0.1
# license http://creativecommons.org/licenses/by-nc-sa/4.0/

home="$(cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"/
miniconda=~/miniconda3/etc/profile.d/conda.sh
keras="keras"
keras_version_expected="2.4.3"

# Check the miniconda3 installation
if [[ -f $miniconda ]]; then
  echo "$miniconda exists."
  source $miniconda
else
  echo -e "[error]\tCould not find miniconda installation."
  exit 1
fi

# Check the Leaf-disc-install folder
if [[ -d "$home" ]]; then
    echo -e "[info]\tRunning from $home."
  else
    echo -e "CNN home not found. Make sure to adjust line 4 in the run_classification script."
    exit 1
fi

plot_coords=$home"plot_coords.R"
plot_pheno=$home"plot_pheno.R"
classify_leaf_disc=$home"classify_leaf_disc.py"

helpFunction()
{
  echo ""
  echo "Usage: $( basename -- "$0" ) -f path/to/leaf/disc/dir/ -e Inoculation1 -l model_l_vs_b.h5 -s model_s_vs_no-s.h5 -e keras"
  echo -e "\t-f Path to leaf disc containing folder. Don't forget the / at the end"
  echo -e "\t-e Give your experiment a name"
  echo -e "\t-l Path to custom Keras model: leaf vs background (if not supplied standard model will be used)"
  echo -e "\t-s Path to custom Keras model: sporangia vs no-sporangia (if notsupplied standard model will be used)"
  echo -e "\t-k name of the conda environment with Leaf-disc-scoring dependencies installed (default: keras)"
  echo -e ""
  exit 1
}

while getopts "e:f:l:s:k:" opt
do
  case "$opt" in
    e ) parameterE="$OPTARG" ;;
    f ) parameterF="$OPTARG" ;;
    l ) parameterL="$OPTARG" ;;
    s ) parameterS="$OPTARG" ;;
    k ) parameterK="$OPTARG" ;;
    ? ) helpFunction ;;
  esac
done

if [ -z "$parameterK" ]
then
  echo -e "[warning] No conda environment name given. Defaulting to: keras"
  parameterK="keras"
fi

conda activate $parameterK

# Get the version number of the installed Keras
keras_version=$(python -c 'import keras; print(keras.__version__)' 2> /dev/null)

# Check if it is installed
if [ -z $keras_version ]
then
  echo $keras_version
  echo -e "\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  echo -e "\t!!No Keras installation found in conda environment       !!"
  echo -e "\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  exit 1
else
  # Check if the right version is installed
  if [ "$keras_version" != "$keras_version_expected" ]
  then
    echo -e "[error]\tWrong Keras version found. Make sure to install Keras v2.4.3"
    exit 1
  else
    echo -e "[info]\tRunning Keras in version: "$keras_version
  fi
fi

# Check if the specified folder with leaf disc images exists
if [[ -d "$parameterF" ]]; then
    echo -e "[info]\tLeaf disc folder exists."
  else
    helpFunction
fi

# Check if there was a name given for the experiment
if [ -z "$parameterE" ]
then
    echo -e "[info]\tNo experiment name supplied. Using: Inoculation1"
    parameterE=Inoculation1
else
    echo -e "[info]\tExperiment name : "$parameterE
fi

# Check if an alternative CNN1 model was supplied
if [ -z "$parameterL" ]
then
   echo -e "[info]\tNo -l option. Using standard model: CNN1_model.h5";
   parameterL=$home"CNN1_model.h5"
fi

#Check if an alternative CNN2 model was supplied
if [ -z "$parameterS" ]
then
   echo -e "[info]\tNo -S option. Using standard model: CNN2_model.h5";
   parameterS=$home"CNN2_model.h5"
fi

# Create directories and output files
mkdir $parameterF"results"
mkdir $parameterF"spo"
touch $parameterF"classify_results.txt"
touch $parameterF"error.log"

# Start the python script for clasification
echo -e "[info]\tRunning classify_leaf_disc.py. This might take some time."
python $classify_leaf_disc $parameterF $parameterL $parameterS $parameterE 2> $parameterF"error.log"

# Plotting the data on the RGB images
echo -e "[info]\tRunning plot_coords.R"
coords=$parameterF*.jpg
for f in $coords
do
  echo -e "[info]\t\tPlotting "$(basename -- $f )
  Rscript $plot_coords -c $f"spo_coord.txt" 2>> $parameterF"error.log"
done

# Plotting the results overview
Rscript $plot_pheno -r $parameterF"classify_results.txt" 2>> $parameterF"error.log"

# Moving everything to a folder
mkdir $parameterF$parameterE

mv $parameterF"results" $parameterF$parameterE
mv $parameterF"spo" $parameterF$parameterE
mv $parameterF"classify_results.txt" $parameterF$parameterE
mv $parameterF"error.log" $parameterF$parameterE

for f in $parameterF*_coord.txt
do
  mv $f $parameterF$parameterE
done