def test_scmos_scmos_cal():
"""
Test that scmos calibration data is initialized correctly.
"""
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
parameters = params.ParametersSCMOS().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Get sCMOS calibration value.
scmos_cal_value = mfitter.scmos_cal[0,0]
# Initialize with an image.
image = numpy.ones(mfitter.scmos_cal.shape)
fitter.newImage(image)
# Verify that the image has the sCMOS term added.
resp = mfitter.getResidual()
assert(numpy.max(resp - (1.0 + scmos_cal_value)) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSCMOS().initFromFile(settings_name)
# Check for possibly v1.0 parameters.
if not parameters.hasAttr("background_sigma"):
raise Exception("Parameter 'background_sigma' is missing. Version 1.0 parameters?")
# Create finding and fitting object.
finder = find_peaks.initFindAndFit(parameters)
# Create object for reading sCMOS camera frames.
frame_reader = analysisIO.FrameReaderSCMOS(movie_file = movie_name,
parameters = parameters)
# Create movie reader (uses frame reader).
movie_reader = analysisIO.MovieReader(frame_reader = frame_reader,
parameters = parameters)
# Create localization file writer.
data_writer = analysisIO.DataWriterHDF5(data_file = mlist_name,
parameters = parameters,
sa_type = 'sCMOS')
# Run the analysis.
std_analysis.standardAnalysis(finder,
movie_reader,
data_writer,
parameters)
def test_scmos_scmos_cal():
"""
Test that scmos calibration data is initialized correctly.
"""
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
parameters = params.ParametersSCMOS().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Get sCMOS calibration value.
scmos_cal_value = mfitter.scmos_cal[0, 0]
# Initialize with an image.
image = numpy.ones(mfitter.scmos_cal.shape)
fitter.newImage(image)
# Verify that the image has the sCMOS term added.
resp = mfitter.getResidual()
assert (numpy.max(resp - (1.0 + scmos_cal_value)) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersDAO().initFromFile(settings_name)
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder,
movie_name,
mlist_name,
parameters)
def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSCMOS().initFromFile(settings_name)
# Check for possibly v1.0 parameters.
if not parameters.hasAttr("background_sigma"):
raise Exception(
"Parameter 'background_sigma' is missing. Version 1.0 parameters?")
# Create finding and fitting object.
finder = find_peaks.initFindAndFit(parameters)
# Create object for reading sCMOS camera frames.
frame_reader = analysisIO.FrameReaderSCMOS(movie_file=movie_name,
parameters=parameters)
# Create movie reader (uses frame reader).
movie_reader = analysisIO.MovieReader(frame_reader=frame_reader,
parameters=parameters)
# Create localization file writer.
data_writer = analysisIO.DataWriterHDF5(data_file=mlist_name,
parameters=parameters,
sa_type='sCMOS')
# Run the analysis.
std_analysis.standardAnalysis(finder, movie_reader, data_writer,
parameters)
def test_3ddao_scmos_cal():
"""
Test that scmos calibration data is initialized to 0.0.
"""
settings = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
parameters = params.ParametersDAO().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Initialize with an image.
image = numpy.ones((100, 100))
fitter.newImage(image)
# Verify that the image is still all ones.
resp = mfitter.getResidual()
assert (numpy.max(resp - 1.0) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def test_3ddao_scmos_cal():
"""
Test that scmos calibration data is initialized to 0.0.
"""
settings = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
parameters = params.ParametersDAO().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Initialize with an image.
image = numpy.ones((100,100))
fitter.newImage(image)
# Verify that the image is still all ones.
resp = mfitter.getResidual()
assert(numpy.max(resp - 1.0) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersDAO().initFromFile(settings_name)
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder, movie_name, mlist_name, parameters)
import storm_analysis.daostorm_3d.find_peaks as find_peaks
import storm_analysis.sa_library.parameters as params
import storm_analysis.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