init_DiffExtractPlot.py

#!/usr/bin/env python
"""
Used to plot betti numbers out of directory of .cbetti files

"""

import numpy
import Image
import rbc_basic as R
import fft_image as FFT
import chomp_betti as CB
import os
import matplotlib.pyplot as plt
#import convert2vtk as cc
from pylab import *

#fname = '/data/jberwald/wyss/data/Cells_Jesse/New/cells/new_140125-concatenated-ASCII'
#file = '/data/jberwald/wyss/data/Cells_Jesse/New/frames/new_140125/new_140125-concatenated-ASCII_24.npy'
#path = '/data/jberwald/wyss/data/Cells_Jesse/frames/new_140125/fft_frames/'
#bnd_file = '/data/jberwald/wyss/data/Cells_Jesse/New/cells/boundary_Nov_new140125'
#file = '/home/kellys/Dropbox/Shared-MSU-Kel/Research/RBC/frames/new_140125-concatenated-ASCII_24.npy'
#t_file = '/home/kellys/Dropbox/Shared-MSU-Kel/Research/RBC/frames/fft_frames/normed_frames/r05_cub/new_140125-concatenated-ASCII_0_r05.cub'

#Extracting fft code
#files = '/data/jberwald/wyss/data/Cells_Jesse/New/frames/new_110125/fft_frames/r10/new_110125-concatenated-ASCII_99_r10.pkl'
#files = '/data/jberwald/wyss/data/Cells_Jesse/New/frames/new_110125/fft_frames/r01/'
#files = '/data/jberwald/wyss/data/Cells_Jesse/Old/frames/old_120125/fft_frames/r01/'
#savedir = '/home/kellys/Dropbox/Shared-MSU-Kel/Research/RBC/'
#files = '/home/kellys/RBC_Deriv_120125_r01/'
#files = '/home/kellys/RBC_Deriv_120125_r005/'

#grab files, skip directories
if os.path.isdir (files):
	fdir = files + '/'
	dlist = os.listdir(fdir)
	frames = []
	for f in dlist:
		if f.endswith('cbetti') and not os.path.isdir(fdir+f):
			frames.append(f)
else:
	frames = [ files ]
	fdir = files.rpartition('/')[0].rpartition('/')[0]+'/'
#savedir = '/home/kellys/RBC_Deriv_120125_r01/'
#savedir = '/home/kellys/RBC_Deriv_110125_r01/'

print 'extracting from chomp Bettie'
frames.sort(key=R.natural_key)
k = 0
for frame in frames:
	k = k+1
	name = frame.rstrip('.cbetti')
	CB.extract_betti(fdir+name, fdir+name)


barr = CB.read_betti_dir(fdir)
CB.plot_betti(barr, 120125, savedir, 1, None, 5000)