content: '''
  Code for error analysis
  
  Copyright (c) 2014, Helen Ramsden
  All rights reserved.
  
  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
  following conditions are met:
  
  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
  disclaimer.
  
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
  disclaimer in the documentation and/or other materials provided with the distribution.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
  USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  '''
  
  import Image, ImageChops
  import numpy as np
  from scipy import ndimage
  from GenericFunctions import checkOSpath, adjust_spines,st
  import matplotlib.pyplot as plt
  plt.rc('ytick', labelsize=12)
  plt.rc('xtick', labelsize=12)
  plt.rc('axes', labelsize=12)
  plt.rc('axes', titlesize=20)
  
  
  def checksegmented(segmaskfilepath,filedict,resultsfilepath):
  	'''
  	FUNCTION runs through all segmented masks and checks location of centre of mass and size of mask
  	input SegmentedMask/
  	output is a list containing name of file, size of mask,
  	'''
  	newfile = open(resultsfilepath + 'maskstatssize.txt','w')
  	for f in filedict:
  		# print f
  		newfile.write(f )
  		for filepath in [segmaskfilepath]:#, segmask2filepath]:
  			maskim =  Image.open(filepath+ f).convert('L') # need to convert to 8 bit (not rgb)
  			maskim = ImageChops.invert(maskim)
  			maskarray = np.array(maskim)
  			# print maskarray.shape
  			com = ndimage.measurements.center_of_mass(maskarray)
  			blackpixels = np.nonzero(maskarray==0)
  			whitepixels = np.nonzero(maskarray>0)
  			# print len(blackpixels[0]),len(whitepixels[0])
  			masksize = len(blackpixels[0])
  			newfile.write('\t' + '\t'.join([str(com[0]),str(com[1]),str(masksize)]))
  		newfile.write('\n')
  
  def plotmi():
  	'''
  	Plot the distribution of MI scores from the registration output
  	'''
  	milog = np.loadtxt('alllogdata.txt',delimiter = '\t',dtype = float,usecols=[2,3])
  	diffs = milog[:,0] - milog[:,1]
  	milognew = np.ma.masked_array(milog, np.isnan(milog))
  	diffsnew = np.ma.masked_array(diffs, np.isnan(diffs))
  
  	# Get rid of nans
  	milogmaskpre = np.ma.masked_array(milog[:,0],np.isnan(milog[:,0]))
  	milogmaskpost = np.ma.masked_array(milog[:,1],np.isnan(milog[:,1]))
  	milogmaskpre = milogmaskpre[milogmaskpre>-1000]
  	milogmaskpost = milogmaskpost[milogmaskpost>-1000]
  
  
  	fig = plt.figure(figsize = (8,8))
  	fig.subplots_adjust(bottom=0.2)
  	fig.subplots_adjust(left=0.2)
  	ax = fig.add_subplot(1,1,1)
  	adjust_spines(ax, ['left','bottom'])
  	cols = ['r','b','k','g','m','y']
  #	histpre, binspre = np.histogram(milogmaskpre, bins=20)
  #	histpost, binspre = np.histogram(milogmaskpre, bins=20)
  	ax.hist(milogmaskpre, bins=20,histtype='step',color='b', range = [-600,0])
  	ax.hist(milogmaskpost,bins=20,histtype='step',color='g', range = [-600,0]) # normed=True,
  	[xmin, xmax, ymin, ymax] = ax.axis()
  	ax.set_yticks([ymin,ymax])
  	ax.set_yticklabels([int(ymin),int(ymax)], fontsize = 25)
  	ax.xaxis.set_label_coords(0.5, -0.15)
  	ax.set_xticks([xmin,xmax])
  	ax.set_xticklabels([xmin,xmax], fontsize = 25)
  	ax.set_xlabel('Joint Entropy', fontsize = 25)
  	ax.set_ylabel('Frequency', fontsize = 25)
  	ax.yaxis.set_label_coords( -0.15, 0.5)
  
  	fig.savefig('MIlogdata.png', transparent = True)
  
  