def mufit_run(mufit, dax, binfile, paramfile):
global src_dir
src_dir = mufit
print src_dir
parameters = params.Parameters(paramfile)
mlist_file = binfile
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder, dax, mlist_file, parameters)
print "Analysis complete"
if (__name__ == "__main__"):
import sys
import sa_library.datareader as datareader
import sa_library.parameters as parameters
import setup_A_matrix
if (len(sys.argv) != 3):
print("usage <dax> <xml>")
exit()
dax_file = datareader.DaxReader(sys.argv[1])
params = parameters.Parameters(sys.argv[2])
a_mat_file = params.a_matrix
print("Using A matrix file:", a_mat_file)
a_mat = setup_A_matrix.loadAMatrix(a_mat_file)
image = dax_file.loadAFrame(30)
htia = HomotopyIA(a_mat, params.epsilon, image.shape)
hres_image = htia.analyzeImage(image)
[cs_x, cs_y, cs_a, cs_i] = htia.getPeaks(hres_image)
print("Number peaks:", cs_x.size)
htia.printProfilingData()
#!/usr/bin/python
#
# Perform mufit analysis on a dax file given parameters.
#
# Hazen 10/13
#
import sys
import find_peaks
import sa_library.parameters as params
import sa_utilities.std_analysis as std_analysis
# setup
if (len(sys.argv) == 3):
parameters = params.Parameters(sys.argv[2])
mlist_file = sys.argv[1][:-4] + "_mlist.bin"
elif (len(sys.argv) == 4):
parameters = params.Parameters(sys.argv[3])
mlist_file = sys.argv[2]
else:
print "usage: <movie> <bin> <parameters.xml>"
exit()
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder, sys.argv[1], mlist_file, parameters)
#
# The MIT License
#
# Copyright (c) 2013 Zhuang Lab, Harvard University
def loadParms(xml_file):
parms = params.Parameters(xml_file)
return parms