cleanImages.py

#!/usr/bin/env python

"""
Run the matlab cleanImageScript.m script

Note: Python 3

Inputs:
   directory of images to clean
   

Outputs:
   cleaned images 

Ben Ober-Reynolds
"""

import os
import sys
import argparse
import re
import uuid
import subprocess
import time
import numpy as np
from collections import OrderedDict
from joblib import Parallel, delayed
from PIL import Image
from glob import glob


##### Gloval vars #####
offset_scale_x = -3.7
offset_scale_y = 3.7


def main():  
    # set up command line argument parser
    parser = argparse.ArgumentParser(description='script for cleaning blobs from images')
    group = parser.add_argument_group('required arguments:')
    group.add_argument('-id', '--image_directory', required=True,
        help='directory containing images to clean')
    group.add_argument('-cd', '--cleaned_image_directory', required=True,
        help='directory that will contain cleaned images')
    group.add_argument('-gv','--global_vars_path', required=True, 
        help='path to the directory in which the "GlobalVars.m" parameter file \
        for the run can be found')
    group = parser.add_argument_group('optional arguments')
    group.add_argument('-ma', '--max_val', type=int, default=4095,
        help='fluorescence intensity value that triggers cleaning')
    group.add_argument('-mn', '--min_val', type=int, default=1500,
        help='fluorescence value that triggers end of cleaning')
    group.add_argument('-smax', '--smart_max', action="store_true",
        help='Pick the max_val based on the image directory provided. Set min to min(mean + 10*sigma, 4095) of the last image.')
    group.add_argument('-smin', '--smart_min', action="store_true",
        help='Pick the min_val based on the image directory provided. Set min to mean + 3*sigma of the first image.')

    # print help if no arguments provided
    if len(sys.argv) <= 1:
        parser.print_help()
        sys.exit()

    # parse command line arguments
    args = parser.parse_args()

    # Pre-defined variables, constants, and settings
    image_extension = 'tif'

    # Check directories and output files
    image_dir = args.image_directory
    if not os.path.isdir(image_dir):
        print("Error: invalid image directory selection. Exiting...")
        sys.exit()

    cleaned_image_dir = args.cleaned_image_directory
    if not os.path.isdir(image_dir):
        print("Error: invalid cleaned image directory selection. Exiting...")
        sys.exit()

    # Determine cleaning cutoffs
    # max_val is the pixel intensity that triggers cleaning
    # min_val is the pixel intensity that indicates when to stop cleaning
    min_val = args.min_val
    max_val = args.max_val
    if args.smart_min or args.smart_max:
        # Read in last image and estimate min_val
        im_file = glob(image_dir + '/*.' + image_extension)[-1]
        im = Image.open(im_file)
        px = list(im.getdata())
        # Remove 'blown out' values 
        px = [x for x in px if x != 4095]
        if args.smart_min:
            min_val = np.mean(px) + 5*np.std(px)
        if args.smart_max:
            max_val = min(np.mean(px) + 10*np.std(px), 4095)
            # Don't clean on less than 2000
            max_val = max(max_val, 2000)

    if min_val >= max_val:
        print "Image too bright, cleaning cannot proceed. Setting max_val to 5000 and min val to 4095."
        max_val = 5000
        min_val = 4095
    else:
        print "Cleaning images with max_val = {} and min_val = {}".format(max_val, min_val)

    # Run Clean image script

    logstring = cleanImages(image_dir, cleaned_image_dir, max_val, min_val, args.global_vars_path)


def cleanImages(image_dir, cleaned_image_dir, max_val, min_val, global_vars_path):
    """
    Run the matlab script 'CleanImageScript.m'
    """
    matlabFunctionCallString = "CleanImageScript('{0}','{1}',{2},{3});".format(image_dir, cleaned_image_dir, max_val, min_val)
    logstring = spawnMatlabJob(matlabFunctionCallString, global_vars_path)
    return logstring



def spawnMatlabJob(matlabFunctionCallString,globalVarsPath):
    """
    Adapted from CPlibs.py 

    """
    try:
        #construct the command-line matlab call 
        functionCallString =                      "try,"
        functionCallString = functionCallString +     "addpath('{0}');".format(globalVarsPath) #placeholder TEMP DEBUG CHANGE
        functionCallString = functionCallString +     matlabFunctionCallString + ';'
        functionCallString = functionCallString + "catch e,"
        functionCallString = functionCallString +     "disp(getReport(e,'extended'));"
        functionCallString = functionCallString + "end,"
        functionCallString = functionCallString + "quit;"
    
        logFilename = 'matlabProcess_' + str(uuid.uuid4()) + str(time.time()) + '.tempLog' #timestamped logfile filename
    
        cmdString ='matlab -nodesktop -nosplash -singleCompThread -r "{0}"'.format(functionCallString)
        cmdString = cmdString + ' 1>> {0}'.format(logFilename)
        cmdString = cmdString + ' 2>> {0}'.format(logFilename)
       
        print('issuing subprocess shell command: ' + cmdString)
       
        returnCode = subprocess.call(cmdString,shell=True) #execute the command in the shell
        returnCode2 = subprocess.call('stty sane',shell=True) #matlab messes up the terminal in a weird way--this fixes it 
    
        #read log file into a string
        try:
            with open(logFilename) as logFilehandle:
                logString = logFilehandle.read()
            # delete logfile
            try:
                os.unlink(logFilename)
            except OSError:
                pass
        except IOError:
            logString = 'Log file not generated for command "' + functionCallString + '".'
    
        # return log
        return logString
    except Exception as e:
        return 'Python exception generated in spawnMatlabJob: ' + e



if __name__ == '__main__':
    main()