def sub(master, tracks, outputFile=None, verbose=False, threadName="Global"):
"""
Subtract tracks from master. Both parameters are nibabel.trackvis.streamlines objects.
Calculation cost: O(M*N)
Returns the result as a nibabel.trackvis.streamlines object or writes it to the file system if an outputFile is specified.
"""
masterSizeBefore = len(master)
subtractedCount = 0
# O(M*N)
for t in xrange(masterSizeBefore):
if subtractedCount == len(tracks):
# no way we can subtract more.. stop the loop
return master
c.debug(
threadName
+ ": Looking for more tracks to subtract.. [Check #"
+ str(t)
+ "/"
+ str(masterSizeBefore)
+ "]",
verbose,
)
if master[t] == -1:
# this fiber was already removed, skip to next one
continue
for u in xrange(len(tracks)):
if tracks[u] == -1:
# this fiber was already removed, skip to next one
continue
# compare fiber
if [p for points in master[t][0] for p in points] == [p for points in tracks[u][0] for p in points]:
# fibers are equal, set them as dirty
master[t] = -1
tracks[u] = -1
subtractedCount += 1
# ... and jump out
break
master = filter(lambda t: t != -1, master)
if not outputFile:
return master
else:
# write it out to disk
io.saveTrk(outputFile, master, None, None, True)
def sub(master,
tracks,
outputFile=None,
verbose=False,
threadName='Global'):
'''
Subtract tracks from master. Both parameters are nibabel.trackvis.streamlines objects.
Calculation cost: O(M*N)
Returns the result as a nibabel.trackvis.streamlines object or writes it to the file system if an outputFile is specified.
'''
masterSizeBefore = len(master)
subtractedCount = 0
# O(M*N)
for t in xrange(masterSizeBefore):
if subtractedCount == len(tracks):
# no way we can subtract more.. stop the loop
return master
c.debug(
threadName +
': Looking for more tracks to subtract.. [Check #' + str(t) +
'/' + str(masterSizeBefore) + ']', verbose)
if master[t] == -1:
# this fiber was already removed, skip to next one
continue
for u in xrange(len(tracks)):
if tracks[u] == -1:
# this fiber was already removed, skip to next one
continue
# compare fiber
if [p for points in master[t][0] for p in points
] == [p for points in tracks[u][0] for p in points]:
# fibers are equal, set them as dirty
master[t] = -1
tracks[u] = -1
subtractedCount += 1
# ... and jump out
break
master = filter(lambda t: t != -1, master)
if not outputFile:
return master
else:
# write it out to disk
io.saveTrk(outputFile, master, None, None, True)
def run(self, input, output, mode, verbose, jobs):
if len(input) < 2:
c.error("Please specify at least two *.trk files as input!")
sys.exit(2)
if os.path.exists(output):
# abort if file already exists
c.error("File " + str(output) + " already exists..")
c.error("Aborting..")
sys.exit(2)
jobs = int(jobs)
if jobs < 1 or jobs > 32:
jobs = 1
# load 'master'
mTracks = io.loadTrk(input[0])
# copy the tracks and the header from the 'master'
c.info("Master is " + input[0])
outputTracks = mTracks[0]
c.info("Number of tracks: " + str(len(outputTracks)))
header = mTracks[1]
# remove the first input
input.pop(0)
if mode == "add":
#
# ADD
#
for i in input:
iTracks = io.loadTrk(i)
# add the tracks
c.debug("Adding " + str(len(iTracks[0])) + " tracks from " + i + " to master..", verbose)
outputTracks = TrackvisCalcLogic.add(outputTracks, iTracks[0])
c.debug("Number of output tracks after final addition: " + str(len(outputTracks)), verbose)
elif mode == "sub":
#
# SUB
#
c.debug("Using " + str(jobs) + " threads..", verbose)
mergedOutputTracks = outputTracks[:]
for i in input:
iTracks = io.loadTrk(i)
# subtract the tracks
c.info("Subtracting " + i + " (" + str(len(iTracks[0])) + " tracks) from master..")
#
# THREADED COMPONENT
#
numberOfThreads = jobs
c.info("Splitting master into " + str(jobs) + " pieces..")
splittedOutputTracks = u.split_list(mergedOutputTracks, 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):
# mark thread as alive
a[n] = True
# fire the thread and give it a filename based on the number
tmpFile = tempfile.mkstemp(".trk", "t_calc")[1]
f[n] = tmpFile
t[n] = Process(
target=TrackvisCalcLogic.sub,
args=(splittedOutputTracks[n][:], iTracks[0][:], tmpFile, verbose, "Thread-" + str(n + 1)),
)
c.info("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
#
c.info("All Threads done!")
c.info("Merging output..")
# now read all the created tempFiles and merge'em to one
# first thread output is the master here
tmpMaster = f[0]
tMasterTracks = io.loadTrk(tmpMaster)
for tmpFileNo in xrange(1, len(f)):
tTracks = io.loadTrk(f[tmpFileNo])
# add them
mergedOutputTracks = TrackvisCalcLogic.add(tMasterTracks[0], tTracks[0])
c.info("Merging done!")
# some stats
c.info("Number of output tracks after final removal: " + str(len(mergedOutputTracks)))
outputTracks = mergedOutputTracks
# now save the outputTracks
io.saveTrk(output, outputTracks, header)
c.info("All done!")
def run(self, input, output, mode, verbose, jobs):
if len(input) < 2:
c.error('Please specify at least two *.trk files as input!')
sys.exit(2)
if os.path.exists(output):
# abort if file already exists
c.error('File ' + str(output) + ' already exists..')
c.error('Aborting..')
sys.exit(2)
jobs = int(jobs)
if jobs < 1 or jobs > 32:
jobs = 1
# load 'master'
mTracks = io.loadTrk(input[0])
# copy the tracks and the header from the 'master'
c.info('Master is ' + input[0])
outputTracks = mTracks[0]
c.info('Number of tracks: ' + str(len(outputTracks)))
header = mTracks[1]
# remove the first input
input.pop(0)
if mode == 'add':
#
# ADD
#
for i in input:
iTracks = io.loadTrk(i)
# add the tracks
c.debug(
'Adding ' + str(len(iTracks[0])) + ' tracks from ' + i +
' to master..', verbose)
outputTracks = TrackvisCalcLogic.add(outputTracks, iTracks[0])
c.debug(
'Number of output tracks after final addition: ' +
str(len(outputTracks)), verbose)
elif mode == 'sub':
#
# SUB
#
c.debug('Using ' + str(jobs) + ' threads..', verbose)
mergedOutputTracks = outputTracks[:]
for i in input:
iTracks = io.loadTrk(i)
# subtract the tracks
c.info('Subtracting ' + i + ' (' + str(len(iTracks[0])) +
' tracks) from master..')
#
# THREADED COMPONENT
#
numberOfThreads = jobs
c.info('Splitting master into ' + str(jobs) + ' pieces..')
splittedOutputTracks = u.split_list(mergedOutputTracks,
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):
# mark thread as alive
a[n] = True
# fire the thread and give it a filename based on the number
tmpFile = tempfile.mkstemp('.trk', 't_calc')[1]
f[n] = tmpFile
t[n] = Process(target=TrackvisCalcLogic.sub,
args=(splittedOutputTracks[n][:],
iTracks[0][:], tmpFile, verbose,
'Thread-' + str(n + 1)))
c.info("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
#
c.info("All Threads done!")
c.info("Merging output..")
# now read all the created tempFiles and merge'em to one
# first thread output is the master here
tmpMaster = f[0]
tMasterTracks = io.loadTrk(tmpMaster)
for tmpFileNo in xrange(1, len(f)):
tTracks = io.loadTrk(f[tmpFileNo])
# add them
mergedOutputTracks = TrackvisCalcLogic.add(
tMasterTracks[0], tTracks[0])
c.info("Merging done!")
# some stats
c.info('Number of output tracks after final removal: ' +
str(len(mergedOutputTracks)))
outputTracks = mergedOutputTracks
# now save the outputTracks
io.saveTrk(output, outputTracks, header)
c.info('All done!')
def fyborg( trkFile, outputTrkFile, actions, *args ):
if not actions:
c.error( "We gotta do something.." )
return
showDebug = 'debug' in args
singleThread = 'singlethread' in args
c.debug( "trkFile:" + str( trkFile ), showDebug )
c.debug( "outputTrkFile:" + str( outputTrkFile ), showDebug )
c.debug( "args:" + str( args ), showDebug )
# load trk file
s = io.loadTrk( trkFile )
tracks = s[0]
origHeader = s[1]
tracksHeader = numpy.copy( s[1] )
numberOfScalars = origHeader['n_scalars']
scalars = origHeader['scalar_name'].tolist()
numberOfTracks = origHeader['n_count']
# show some file informations
printTrkInfo( tracksHeader, trkFile )
# grab the scalarNames
scalarNames = []
for a in actions:
if a.scalarName() != 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()
c.info( 'Splitting master into ' + str( numberOfThreads ) + ' pieces..' )
splittedOutputTracks = u.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=fyborgLooper_, args=( splittedOutputTracks[n][:], tracksHeader, tmpFile, __actions, showDebug, n + 1 ) )
c.info( "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
#
c.info( "All Threads done!" )
#
# Merging stage
#
c.info( "Merging tracks.." )
outputTracks = []
# now read all the created tempFiles and merge'em to one
for tmpFileNo in xrange( 0, len( f ) ):
tTracks = io.loadTrk( f[tmpFileNo] )
# add them
outputTracks.extend( tTracks[0] )
c.info( "Merging done!" )
io.saveTrk( outputTrkFile, outputTracks, tracksHeader, None, True )
c.info( "All done!" )
def fyborgLooper_( tracks, tracksHeader, outputTrkFile, actions, showDebug, threadNumber ):
import numpy
numberOfTracks = len( tracks )
# the buffer for the new tracks
newTracks = []
# now loop through the tracks
for tCounter, t in enumerate( tracks ):
# some debug stats
c.debug( 'Thread-' + str( threadNumber ) + ': Processing ' + str( tCounter + 1 ) + '/' + str( numberOfTracks ), showDebug )
# generate a unique ID for this track
uniqueId = str( threadNumber ) + str( tCounter )
tCoordinates = t[0]
tScalars = t[1]
# buffer for fiberScalars
_fiberScalars = {}
# first round: mapping per fiber
# .. execute each action and buffer return value (scalar)
for a in actions:
value = a.scalarPerFiber( uniqueId, tCoordinates, tScalars )
_fiberScalars[a.scalarName()] = value
#
# Coordinate Loop
#
# buffer for coordinate scalars)
scalars = []
# second round: mapping per coordinate
for cCounter, coords in enumerate( tCoordinates ):
_coordScalars = {}
_mergedScalars = [] # this is the actual buffer for ordered fiber and coord scalars merged together
# .. execute each action and buffer return value (scalar)
for a in actions:
value = a.scalarPerCoordinate( uniqueId, coords[0], coords[1], coords[2] ) # pass x,y,z
_coordScalars[a.scalarName()] = value
# now merge the old scalars and the fiber and coord scalars
# this preserves the ordering of the configured actions
if tScalars != None:
_mergedScalars.extend( tScalars[cCounter] )
for a in actions:
value = _fiberScalars[a.scalarName()]
if value != FyAction.NoScalar:
_mergedScalars.append( value )
else:
# no fiber scalar, check if there is a coord scalar
value = _coordScalars[a.scalarName()]
if value != FyAction.NoScalar:
_mergedScalars.append( value )
# attach scalars
scalars.append( _mergedScalars )
# validate the fibers using the action's validate methods
validator = []
for a in actions:
validator.append( a.validate( uniqueId ) )
if all( validator ):
# this is a valid fiber
# .. add the new track with the coordinates, the new scalar array and the properties
newScalars = numpy.asarray( scalars )
newTracks.append( ( t[0], newScalars, t[2] ) )
# save everything
io.saveTrk( outputTrkFile, newTracks, tracksHeader, None, True )
