def tracking(mol_list_filename, parameters):
[min_z, max_z] = params.getZRange(parameters)
proc_params = [src_dir + "tracker",
mol_list_filename,
parameters.descriptor,
str(parameters.radius),
str(1000.0*min_z),
str(1000.0*max_z)]
subprocess.call(proc_params)
def tracking(mol_list_filename, parameters):
[min_z, max_z] = params.getZRange(parameters)
proc_params = [
src_dir + "tracker", mol_list_filename, parameters.descriptor,
str(parameters.radius),
str(1000.0 * min_z),
str(1000.0 * max_z),
str(1)
]
subprocess.call(proc_params)
def peakFinding(find_peaks, movie_file, mlist_file, parameters):
# open files for input & output
movie_data = datareader.inferReader(movie_file)
[movie_x,movie_y,movie_l] = movie_data.filmSize()
# if the i3 file already exists, read it in,
# write it out & start the analysis from the
# end.
total_peaks = 0
if(os.path.exists(mlist_file)):
print "Found", mlist_file
i3data_in = readinsight3.loadI3File(mlist_file)
try:
curf = int(numpy.max(i3data_in['fr']))
except ValueError:
curf = 0
print " Starting analysis at frame:", curf
i3data = writeinsight3.I3Writer(mlist_file)
if (curf > 0):
i3data.addMolecules(i3data_in)
total_peaks = i3data_in['x'].size
else:
curf = 0
i3data = writeinsight3.I3Writer(mlist_file)
# process parameters
if (parameters.model == "Z"):
wx_params = params.getWidthParams(parameters, "x", for_mu_Zfit = True)
wy_params = params.getWidthParams(parameters, "y", for_mu_Zfit = True)
[min_z, max_z] = params.getZRange(parameters)
if(parameters.orientation == "inverted"):
find_peaks.initZParams(wx_params, wy_params, min_z, max_z)
else:
find_peaks.initZParams(wy_params, wx_params, min_z, max_z)
if hasattr(parameters, "start_frame"):
if (parameters.start_frame>=curf) and (parameters.start_frame<movie_l):
curf = parameters.start_frame
if hasattr(parameters, "max_frame"):
if (parameters.max_frame>0) and (parameters.max_frame<movie_l):
movie_l = parameters.max_frame
# analyze the movie
# catch keyboard interrupts & "gracefully" exit.
try:
while(curf<movie_l):
#for j in range(l):
# setup analysis
image = movie_data.loadAFrame(curf) - parameters.baseline
mask = (image < 1.0)
if (numpy.sum(mask) > 0):
print " Removing negative values in frame", curf
image[mask] = 1.0
# Find the peaks.
finder = find_peaks.Finder(image, parameters)
[peaks, residual] = finder.analyzeImage()
# Save the peaks.
if (type(peaks) == type(numpy.array([]))):
# remove unconverged peaks
peaks = find_peaks.getConvergedPeaks(peaks)
# save results
if(parameters.orientation == "inverted"):
i3data.addMultiFitMolecules(peaks, movie_x, movie_y, curf+1, parameters.pixel_size, inverted = True)
else:
i3data.addMultiFitMolecules(peaks, movie_x, movie_y, curf+1, parameters.pixel_size, inverted = False)
total_peaks += peaks.shape[0]
print "Frame:", curf, peaks.shape[0], total_peaks
else:
print "Frame:", curf, 0, total_peaks
curf += 1
print ""
i3data.close()
return 0
except KeyboardInterrupt:
print "Analysis stopped."
i3data.close()
return 1
