def read(self, path):
"""
Read tubes from path;
A tube is a tupel of 4 numbers (xmin, ymin, xmax, ymax).
"""
if not os.path.exists(path):
raise Exception('Path does not exist: %s' % (path) )
pp = os.path.join(path, '*.txt')
#print pp
files = glob.glob( pp )
nrFiles = len(files) # nr Frames
print '\treading tubes:', path, '; Number of tubes read:', nrFiles
if nrFiles == 0:
raise Exception('No files found in: %s' % (pp) )
files.sort()
#files.reverse()
for i in xrange(nrFiles):
f = files[i]
tube = SingleTube()
tube.read(f)
self._tubes.append( tube )
def read(self, path):
"""
Read tubes from path;
A tube is a tupel of 4 numbers (xmin, ymin, xmax, ymax).
"""
if not os.path.exists(path):
raise Exception('Path does not exist: %s' % (path))
pp = os.path.join(path, '*.txt')
#print pp
files = glob.glob(pp)
nrFiles = len(files) # nr Frames
print '\treading tubes:', path, '; Number of tubes read:', nrFiles
if nrFiles == 0:
raise Exception('No files found in: %s' % (pp))
files.sort()
#files.reverse()
for i in xrange(nrFiles):
f = files[i]
tube = SingleTube()
tube.read(f)
self._tubes.append(tube)
def traj2tube(frameNumEnd, tubeFeatSpat, xmax=np.inf, ymax=np.inf, regionSize=15, framesPerTrack=15):
"""convert a trajectory to a SingleTube proposal"""
frameNumStart = int(frameNumEnd - framesPerTrack)
# make a tube as a tupel of 4 numbers (xmin, ymin, xmax, ymax).
tube = np.zeros( (framesPerTrack, 4), dtype='float32' )
# a trajectory has x,y in the center, with a size of 2*regionSize
i = np.arange(framesPerTrack)
tube[i,0] = np.maximum(0,tubeFeatSpat[i*2] - regionSize) # xmin
tube[i,1] = np.maximum(0,tubeFeatSpat[i*2+1] - regionSize) # ymin
tube[i,2] = np.minimum(xmax,tubeFeatSpat[i*2] + regionSize) # xmax
tube[i,3] = np.minimum(ymax,tubeFeatSpat[i*2+1] + regionSize) # ymax
return SingleTube(frameNumStart,tube)
def readHDF5(self, inHDF5fileName):
"""
Read tubes from hdf5 fileName;
A tube is a tupel of 4 numbers (xmin, ymin, xmax, ymax).
"""
if not os.path.exists(inHDF5fileName):
print 'Path does not exist: %s' % (inHDF5fileName)
raise Exception('Path does not exist: %s' % (inHDF5fileName) )
inHDF5file = h5py.File(inHDF5fileName, 'r')
nrTubes = len(inHDF5file)
print '\treading tubes:', inHDF5fileName, '; Number of tubes to read:', nrTubes
if nrTubes == 0:
raise Exception('No tubes found in: %s' % (pp) )
for i in xrange(nrTubes):
tube = SingleTube()
tube.readHDF5(inHDF5file, str(i) )
self._tubes.append( tube )
inHDF5file.close()
def readHDF5(self, inHDF5fileName):
"""
Read tubes from hdf5 fileName;
A tube is a tupel of 4 numbers (xmin, ymin, xmax, ymax).
"""
if not os.path.exists(inHDF5fileName):
print 'Path does not exist: %s' % (inHDF5fileName)
raise Exception('Path does not exist: %s' % (inHDF5fileName))
inHDF5file = h5py.File(inHDF5fileName, 'r')
nrTubes = len(inHDF5file)
print '\treading tubes:', inHDF5fileName, '; Number of tubes to read:', nrTubes
if nrTubes == 0:
raise Exception('No tubes found in: %s' % (pp))
for i in xrange(nrTubes):
tube = SingleTube()
tube.readHDF5(inHDF5file, str(i))
self._tubes.append(tube)
inHDF5file.close()
def readFrameFormat(self,
path,
readWHformat=False,
spatialSubSampleRate=1):
"""
Read tubes from path; dense format = a tube at each frame number
A tube is a tupel of 4 numbers (xmin, ymin, xmax, ymax).
if readWHformat == True:
A tube is converted from (xmin, ymin, w, h) format.
Every frame X should have a X.txt file with tubes.
Every .txt file has a fixed nr of lines, each line is a tube; All .txt files have the same nr of tubes.
If a tube is not visible in a frame XXX.txt, set the tube to (0,0,0,0)
"""
if not os.path.exists(path):
raise Exception('Path does not exist: %s' % (path))
pp = os.path.join(path, '*.txt')
#print pp
files = glob.glob(pp)
nrFiles = len(files) # nr Frames
print 'readFrameFormat:', path, 'nrFiles', nrFiles,
if nrFiles == 0:
raise Exception('No files found in: %s' % (pp))
files.sort()
#files.reverse()
for i in xrange(nrFiles):
f = files[i]
#print f
fileIn = open(f, 'r')
lines = fileIn.readlines()
nrLines = len(lines) # nr proposals
if i == 0:
# if first element, reserve space
data = np.zeros((nrFiles, nrLines, 4), dtype='float32')
print 'nrTubes', nrLines
else:
# nr tubes cannot differ per file
if nrLines != data.shape[1]:
raise Exception('NrLines in %s should be %d, but is %d' %
(f, nrLines, data.shape[0]))
for j in range(nrLines):
line = lines[j]
d = line.split(',')
if len(d) == 1:
d = line.split()
data[i, j, :] = np.array(
[float(s) / spatialSubSampleRate for s in d[:4]])
if readWHformat:
data[i, j, 2] = data[i, j, 2] + data[i, j, 0]
data[i, j, 3] = data[i, j, 3] + data[i, j, 1]
fileIn.close()
# convert data array to SingleTube objects
nrTubes = data.shape[1]
for t in range(nrTubes):
# find frames without BBs: sum the BBs, empty are <= 0
minFrameNr = 0
maxFrameNr = nrFiles - 1
summedBB = np.sum(data[:, t, :], axis=1)
emptyIdx = np.nonzero(summedBB <= 0)[0]
# if pre-BB empty
if summedBB[0] < 0:
minFrameNr = min(emptyIdx)
# if post-BB empty
if summedBB[-1] < 0:
maxFrameNr = max(emptyIdx)
bbList = []
for f in range(nrFiles):
if f >= minFrameNr and f <= maxFrameNr:
bb = data[f, t, :]
bbList.append(bb)
tube = SingleTube(minFrameNr, bbList)
# add tube to list
self._tubes.append(tube)