def loop( fibers_file, volume, lh_mesh_file, rh_mesh_file, neighbors, singleThread=False ):
# load trk file
s = nibabel.trackvis.read( fibers_file )
tracks = s[0]
# load meshes
lh_verts, lh_faces = nibabel.freesurfer.read_geometry( lh_mesh_file )
rh_verts, rh_faces = nibabel.freesurfer.read_geometry( rh_mesh_file )
# load volume and get qForm matrix
_image = nibabel.load( volume )
qForm = _image.get_header().get_qform()
qFormM = numpy.matrix( qForm )
#
# THREADED COMPONENT
#
if singleThread:
numberOfThreads = 1
else:
numberOfThreads = 1#3#multiprocessing.cpu_count()
print 'Splitting master into ' + str( numberOfThreads ) + ' pieces..'
splittedOutputTracks = Utility.split_list( tracks[:], numberOfThreads )
# list of threads
t = [None] * numberOfThreads
# list of alive flags
a = [None] * numberOfThreads
# list of matrix tempFiles
mf = [None] * numberOfThreads
for n in xrange( numberOfThreads ):
# mark thread as alive
a[n] = True
# also create a temp file for the hdf5 file
matrix_file = tempfile.mkstemp( '.h5', 'fyborg' )[1]
mf[n] = matrix_file
t[n] = Process( target=LooperWithMatrix._looper_, args=( splittedOutputTracks[n][:], lh_mesh_file, rh_mesh_file, int(neighbors), qFormM, matrix_file, n + 1 ) )
print "Starting Thread-" + str( n + 1 ) + "..."
t[n].start()
allDone = False
while not allDone:
time.sleep( 1 )
for n in xrange( numberOfThreads ):
a[n] = t[n].is_alive()
if not any( a ):
# if no thread is alive
allDone = True
#
# END OF THREADED COMPONENT
#
print "All Threads done!"
#print mf
return mf
def loop(fibers_file, fibers_output_file, actions, singleThread=False):
# load trk file
s = nibabel.trackvis.read( fibers_file )
tracks = s[0]
origHeader = s[1]
tracksHeader = numpy.copy( s[1] )
numberOfScalars = origHeader['n_scalars']
scalars = origHeader['scalar_name'].tolist()
numberOfTracks = origHeader['n_count']
# grab the scalarNames
scalarNames = []
for a in actions:
if a.scalarName() != _actions.FyAction.NoScalar:
scalarNames.append( a.scalarName() )
# increase the number of scalars
tracksHeader['n_scalars'] += len( scalarNames )
# .. attach the new scalar names
for i in range( len( scalarNames ) ):
tracksHeader['scalar_name'][numberOfScalars + i] = scalarNames[i]
#
# THREADED COMPONENT
#
if singleThread:
numberOfThreads = 1
else:
numberOfThreads = multiprocessing.cpu_count()
print 'Splitting master into ' + str( numberOfThreads ) + ' pieces..'
splittedOutputTracks = Utility.split_list( tracks[:], numberOfThreads )
# list of threads
t = [None] * numberOfThreads
# list of alive flags
a = [None] * numberOfThreads
# list of tempFiles
f = [None] * numberOfThreads
for n in xrange( numberOfThreads ):
# configure actions
__actions = []
for act in actions:
__actions.append( act )
# mark thread as alive
a[n] = True
# fire the thread and give it a filename based on the number
tmpFile = tempfile.mkstemp( '.trk', 'fyborg' )[1]
f[n] = tmpFile
t[n] = Process( target=Looper._looper_, args=( splittedOutputTracks[n][:], tracksHeader, tmpFile, __actions, n + 1 ) )
print "Starting Thread-" + str( n + 1 ) + "..."
t[n].start()
allDone = False
while not allDone:
time.sleep( 1 )
for n in xrange( numberOfThreads ):
a[n] = t[n].is_alive()
if not any( a ):
# if no thread is alive
allDone = True
#
# END OF THREADED COMPONENT
#
print "All Threads done!"
#
# Merging stage
#
print "Merging tracks..", f
outputTracks = []
# now read all the created tempFiles and merge'em to one
for tmpFileNo in xrange( 0, len( f ) ):
tTracks = nibabel.trackvis.read( f[tmpFileNo] )
# add them
outputTracks.extend( tTracks[0] )
print "Merging done!"
nibabel.trackvis.write( fibers_output_file, outputTracks, tracksHeader )
print "All done!"
