#!/usr/bin/python
from numpy import array, matrix, shape, reshape, zeros, diag
from scipy.io import read_array, write_array
from scipy.linalg import svd
from glob import glob
from os import chdir

fllist = ['tmp'] # List of folders in which the TiffToTxtImages ImageJ macro has saved the text images
for fl in fllist:
	chdir(fl)
	flist = glob('Slice*')

	n = len(flist)
	fi = read_array(flist[0])
	x, y = shape(fi)
	m = len(fi.ravel())

	data = zeros((m,n), 'l')

	for i, f in enumerate(flist):
		fi = read_array(f, atype='l').ravel()
		data[:,i] = fi

	## All data assembled into one matrix of pixel vs. time
	write_array('data.txt', data)

	## SVD
	u, s, v = svd(data)
	del data

	## Filtering
	rank = 30 ## Controls the level of filtering (lower = less noise)
	ur = matrix(u[:,:rank])
	sr = diag(s[:rank])
	vr = matrix(v[:rank,:])

	write_array('v.txt', v)
	
	del u, s, v
	modelr = array(ur*sr*vr, 'l')
	del ur, sr, vr

	## Output
	write_array('model.txt', modelr)

	for i in range(n):
		fname = "Slice_%.5i.txt" % (i+1)
		fo = modelr[:,i].reshape(x,y)
		write_array(fname, fo)
	chdir('..')
	del modelr, fname, fo