def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersPSFFFT().initFromFile(settings_name, warnings = False)
# Create finding and fitting object.
finder = findPeaksStd.initFindAndFit(parameters)
# Create appropriate reader.
if parameters.hasAttr("camera_offset"):
frame_reader = analysisIO.FrameReaderStd(movie_file = movie_name,
parameters = parameters)
else:
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 = "PSF-FFT")
std_analysis.standardAnalysis(finder,
movie_reader,
data_writer,
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 analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSpliner().initFromFile(settings_name,
warnings=False)
# Check for v1.0 parameters.
if not (parameters.hasAttr("camera_gain")
or parameters.hasAttr("camera_calibration")):
raise Exception(
"Camera parameters are missing. Version 1.0 parameters?")
# Create appropriate finding and fitting object.
if (parameters.getAttr("use_fista", 0) != 0):
parameters = params.ParametersSplinerFISTA().initFromFile(
settings_name)
finder = find_peaks_fista.initFindAndFit(parameters)
else:
parameters = params.ParametersSplinerSTD().initFromFile(settings_name)
finder = find_peaks_std.initFindAndFit(parameters)
# Create appropriate reader.
if parameters.hasAttr("camera_offset"):
frame_reader = analysisIO.FrameReaderStd(movie_file=movie_name,
parameters=parameters)
else:
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="Spliner")
std_analysis.standardAnalysis(finder, movie_reader, data_writer,
parameters)