caticoa3

## ilastik_run.sh
LAZYFLOW_THREADS=2 LAZYFLOW_TOTAL_RAM_MB=2000 ~/Applications/ilastik-1.3.0-Linux/run_ilastik.sh --headless --project segmentation_0_corrected.ilp --raw_data IllumCorr/*.??.??/*/*CY3*IC.tiff --output_format tiff --output_filename_format {dataset_dir}/{nickname}_{result_type}.tiff --export_source="Simple Segmentation"

## ignore_CP_save_erros.sh
#!/bin/bash
n=1 #Image Set number to start processing batch
final_image=826 #Last Image Set number in your batch
cellprofiler -p ML/Batch_data.h5 -c -r -f $n -l $final_image |& tee log.txt #Here the output from terminal is save to log.txt.

while [ $? -ne 1 ]; do
  #Parse log.txt file, extracting the image set # at which the error occurs
  no_save_error_image=$(sed -n '/^.*ValueError:/{n;p}' log.txt | sed -n -e 's/^.Image # //p' | sed -n -e 's/, module SaveImages.$//p')
  n_=$(($no_save_error_image + 1))
  #Restart CellProfiler at the next image set

## ga_in_dash.py
app.index_string = '''<!DOCTYPE html>
<html>
<head>
  <!-- Global site tag (gtag.js) - Google Analytics -->
    <script>(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
    (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
    m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
    })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');

    ga('create', 'UA-XXXXXX', 'auto');

## .block
license: mit

## contour_crop.py
# coding: utf-8
import os
import numpy as np
import cv2
from pathlib2 import Path
#import re

'''Run on Python2.7'''

image_dir = '../IllumCorr/'
	#!/bin/bash
	n=1 #Image Set number to start processing batch
	final_image=826 #Last Image Set number in your batch
	cellprofiler -p ML/Batch_data.h5 -c -r -f $n -l $final_image \|& tee log.txt #Here the output from terminal is save to log.txt.

	while [ $? -ne 1 ]; do
	#Parse log.txt file, extracting the image set # at which the error occurs
	no_save_error_image=$(sed -n '/^.*ValueError:/{n;p}' log.txt \| sed -n -e 's/^.Image # //p' \| sed -n -e 's/, module SaveImages.$//p')
	n_=$(($no_save_error_image + 1))
	#Restart CellProfiler at the next image set
	app.index_string = '''<!DOCTYPE html>
	<html>
	<head>
	<!-- Global site tag (gtag.js) - Google Analytics -->
	<script>(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]\|\|function(){
	(i[r].q=i[r].q\|\|[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
	m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
	})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');

	ga('create', 'UA-XXXXXX', 'auto');
	# coding: utf-8
	import os
	import numpy as np
	import cv2
	from pathlib2 import Path
	#import re

	'''Run on Python2.7'''

	image_dir = '../IllumCorr/'