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