def getMolecule(self, molecule):
if(molecule<self.molecules):
if (type(self.localizations) == type(numpy.array([]))):
return self.localizations[molecule:molecule+1]
else:
cur = self.fp.tell()
self.fp.seek(16 + molecule*self.record_size)
data = numpy.fromfile(self.fp,
dtype=i3dtype.i3DataType(),
count=1)
self.fp.seek(cur)
return data
def getMolecule(self, molecule):
if(molecule<self.molecules):
if (type(self.localizations) == type(numpy.array([]))):
return self.localizations[molecule:molecule+1]
else:
cur = self.fp.tell()
self.fp.seek(16 + molecule*self.record_size)
data = numpy.fromfile(self.fp,
dtype=i3dtype.i3DataType(),
count=1)
self.fp.seek(cur)
return data
def getMoleculesInFrameRange(self, start, stop, good_only = True):
start_mol_num = self.findFrame(start)
stop_mol_num = self.findFrame(stop)
if (type(self.localizations) == type(numpy.array([]))):
data = self.localizations[start_mol_num:stop_mol_num]
else:
cur = self.fp.tell()
self.fp.seek(16 + start_mol_num*self.record_size)
size = stop_mol_num - start_mol_num
data = numpy.fromfile(self.fp,
dtype=i3dtype.i3DataType(),
count=size)
self.fp.seek(cur)
if good_only:
return i3dtype.maskData(data, (data['c'] != 9))
else:
return data
def getMoleculesInFrameRange(self, start, stop, good_only = True):
start_mol_num = self.findFrame(start)
stop_mol_num = self.findFrame(stop)
if (type(self.localizations) == type(numpy.array([]))):
data = self.localizations[start_mol_num:stop_mol_num]
else:
cur = self.fp.tell()
self.fp.seek(16 + start_mol_num*self.record_size)
size = stop_mol_num - start_mol_num
data = numpy.fromfile(self.fp,
dtype=i3dtype.i3DataType(),
count=size)
self.fp.seek(cur)
if good_only:
return i3dtype.maskData(data, (data['c'] != 9))
else:
return data
def loadI3FileNumpy(filename, verbose = 1):
fp = open(filename, "rb")
# Read header
[frames, molecules, version, status] = readHeader(fp, verbose)
data = numpy.fromfile(fp, dtype=i3dtype.i3DataType())
# If the analysis crashed, the molecule list may still
# be valid, but the molecule number will be incorrect.
if(molecules==0):
print("File appears empty, trying to load anyway.")
try:
molecules = numpy.max(data['fr'])
except:
molecules = 0
data = data[:][0:molecules]
fp.close()
return data
def loadI3FileNumpy(filename, verbose = 1):
fp = open(filename, "rb")
# Read header
[frames, molecules, version, status] = readHeader(fp, verbose)
data = numpy.fromfile(fp, dtype=i3dtype.i3DataType())
# If the analysis crashed, the molecule list may still
# be valid, but the molecule number will be incorrect.
if(molecules==0):
print "File appears empty, trying to load anyway."
try:
molecules = numpy.max(data['fr'])
except:
molecules = 0
data = data[:][0:molecules]
fp.close()
return data
def nextBlock(self, block_size=400000, good_only=True):
# check if we have read all the molecules.
if (self.cur_molecule >= self.molecules):
return False
size = block_size
# adjust size if we'll read past the end of the file.
if ((self.cur_molecule + size) > self.molecules):
size = self.molecules - self.cur_molecule
self.cur_molecule += size
# read the data
data = numpy.fromfile(self.fp, dtype=i3dtype.i3DataType(), count=size)
if good_only:
return i3dtype.maskData(data, (data['c'] != 9))
else:
return data
def nextBlock(self, block_size = 400000, good_only = True):
# check if we have read all the molecules.
if(self.cur_molecule>=self.molecules):
return False
size = block_size
# adjust size if we'll read past the end of the file.
if((self.cur_molecule+size)>self.molecules):
size = self.molecules - self.cur_molecule
self.cur_molecule += size
# read the data
data = numpy.fromfile(self.fp,
dtype=i3dtype.i3DataType(),
count=size)
if good_only:
return i3dtype.maskData(data, (data['c'] != 9))
else:
return data