def __init__(self, filename, frame_sx, frame_sy, type):
self.i3_bin = readinsight3.I3Reader(filename)
self.frame_sx = frame_sx
self.frame_sy = frame_sy
self.last_frame = -1
self.last_i = 0
self.mol_items = []
self.type = type
import matplotlib.pyplot as pyplot
import numpy
import sys
import sa_library.gaussfit as gaussfit
import sa_library.readinsight3 as readinsight3
import sa_library.ia_utilities_c as utilC
if (len(sys.argv) != 3):
print "usage: <true locations> <measured locations>"
exit()
# For converting XY units to nanometers.
pixel_size = 160.0
truth_i3 = readinsight3.I3Reader(sys.argv[1])
measured_i3 = readinsight3.I3Reader(sys.argv[2])
all_dx = None
all_dy = None
all_dz = None
for i in range(truth_i3.getNumberFrames()):
t_locs = truth_i3.getMoleculesInFrame(i+1)
m_locs = measured_i3.getMoleculesInFrame(i+1, good_only = False)
p_index = utilC.peakToPeakIndex(m_locs['xc'], m_locs['yc'], t_locs['xc'], t_locs['yc'])
dx = numpy.zeros(m_locs.size)
dy = numpy.zeros(m_locs.size)
dz = numpy.zeros(m_locs.size)
for i in range(m_locs.size):
dx[i] = pixel_size * (m_locs['xc'][i] - t_locs['xc'][p_index[i]])
#
# Convert a .bin format file to the Single Molecule
# Localization Challenge format.
#
# Hazen 03/14
#
import sys
import sa_library.readinsight3 as readinsight3
if (len(sys.argv)!=4):
print "usage: <bin_file> <smlc_file> <pix_to_nm>"
exit()
i3_reader = readinsight3.I3Reader(sys.argv[1])
i3_block = i3_reader.nextBlock(block_size = 1000, good_only = False)
smlc_file_fp = open(sys.argv[2], "w")
smlc_file_fp.write("frame,xnano,ynano,intensity\n")
pix_to_nm = float(sys.argv[3])
print "Saving Localizations"
localization_number = 0
while (type(i3_block) != type(False)):
print " saving localization", localization_number
for i in range(len(i3_block)):
fr = i3_block['fr'][i]