def create_diff_image ( files , savedir ):
""" grab files, skip directories, unabashedly stolen from Jesse's code
e.g. new cell name on simplex:
'/data/jberwald/wyss/data/Cells_Jesse/New/frames/new_110125/new_110125-concatenated-ASCII_324.npy'
"""
if os.path.isdir (files):
fdir = files + '/'
dlist = os.listdir(fdir)
frames = []
for f in dlist:
if f.endswith('pkl') 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/'
#print 'attempting array creation..'
k= 0;
n=5000; #grab a selection of frames
derivArr = [];
parArr = [];
frames.sort(key=natural_key)
for frame in frames:
k = k+1
savename = frame.rstrip('.pkl')
D = FFT.extract_ifft(fdir+frame)
arr = D['ifft_nonzero']
masked_ifft = numpy.ma.masked_less_equal(arr,D['mean'])
if(k != 1 and k < n):
savename = frame.rstrip('.pkl')
newFile = numpy.abs(masked_ifft - prevFrame)
m = newFile.mean()
newFile = numpy.ma.masked_less_equal(newFile, m).mask
numpy.save(savedir+savename + '.npy', newFile)
#print k
prevFrame = masked_ifft
def save_masks ( files , savedir ):
#grab files, skip directories
if os.path.isdir (files):
fdir = files + '/'
dlist = os.listdir(fdir)
frames = []
for f in dlist:
if f.endswith('pkl') and not os.path.isdir(fdir+f):
frames.append(f)
else:
frames = [ files ]
fdir = files.rpartition('/')[0].rpartition('/')[0]+'/'
#savedir = '/home/kellys/RBC_120125_old_r005/'
frames.sort(key=natural_key)
for frame in frames:
savename = frame.rstrip('.pkl')
#print 'preparing to extract..'
D = FFT.extract_ifft( fdir+frame )
arr = D['ifft_nonzero']
masked_ifft = numpy.ma.masked_less_equal(arr, D['mean'] )
plt.imshow(masked_ifft.mask)
plt.savefig(savedir+savename+'.png')
else:
frames = [ files ]
fdir = files.rpartition('/')[0].rpartition('/')[0]+'/'
#savedir = '/home/kellys/RBC_Deriv_120125_r01/'
#savedir = '/home/kellys/RBC_Deriv_110125_r01/'
savedir = '/home/kellys/RBC_Deriv_120125_r005/'
print 'attempting array creation..'
k= 0;
derivArr = [];
parArr = [];
frames.sort(key=R.natural_key)
for frame in frames:
k = k+1
savename = frame.rstrip('.pkl')
D = FFT.extract_ifft(fdir+frame)
arr = D['ifft_nonzero']
masked_ifft = numpy.ma.masked_less_equal(arr,D['mean'])
if(k != 1):
savename = frame.rstrip('.pkl')
newFile = numpy.abs(masked_ifft - prevFrame)
m = newFile.mean()
newFile = numpy.ma.masked_less_equal(newFile, m).mask
numpy.save(savedir+savename + '.npy', newFile)
#plt.imshow(newFile)
#plt.savefig(savedir+savename+'.png')
print k
#derivArr.append(math.fabs(prevFrame[50][100] - masked_ifft[50][100]))
#parArr . append(k)
prevFrame = masked_ifft
prevMean = D['mean'] #not currently used
