Python standardAnalysis Examples

Example #1

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"

Example #2

File: StormAnalysisAdditions.py Project: zocean/ChromatinImaging

def fitFrame(dax_file, bin_file, parms, over_write=True, write_parms=True):
    """
    Constructs a bin_file
    Use getParms function to generate parms for this function
    getParms(xml_file,max_frame_=<frame>+1,start_frame_=<frame>) 
    """
    import find_peaks
    import sa_utilities.std_analysis as std_analysis
    mlist_file = bin_file
    if not over_write:
        if os.path.exists(bin_file):
            return parms
    if os.path.exists(bin_file):
        os.remove(bin_file)
    alist_file = bin_file.replace('_mlist', '_alist')
    if os.path.exists(alist_file):
        os.remove(alist_file)
    if write_parms:
        xmlFile = bin_file.replace('_mlist.bin', '_parms.xml')
        writeParms(parms, xmlFile)
    finder = find_peaks.initFindAndFit(parms)
    std_analysis.standardAnalysis(finder, dax_file, mlist_file, parms)
    return parms

Example #3

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
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.

Example #4

File: mufit_analysis.py Project: ebsamson3/storm-analysis

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()

std_analysis.standardAnalysis(find_peaks,
                              sys.argv[1],
                              mlist_file,
                              parameters)

#
# The MIT License
#
# Copyright (c) 2013 Zhuang Lab, Harvard University
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in