class BRAINSClassPlugsInputSpec(CommandLineInputSpec):
t1Volume = File(exists="True", argstr="--t1Volume %s")
t2Volume = File(exists="True", argstr="--t2Volume %s")
pdVolume = File(exists="True", argstr="--pdVolume %s")
searchVolume = File(exists="True", argstr="--searchVolume %s")
gmPlugs = traits.Either(traits.Bool, File, argstr="--gmPlugs %s")
wmPlugs = traits.Either(traits.Bool, File, argstr="--wmPlugs %s")
csfPlugs = traits.Either(traits.Bool, File, argstr="--csfPlugs %s")
plugClassNames = traits.List("traits.Str",
sep=",",
argstr="--plugClassNames %s")
t1ClassMeans = traits.List("traits.Float",
sep=",",
argstr="--t1ClassMeans %f")
t2ClassMeans = traits.List("traits.Float",
sep=",",
argstr="--t2ClassMeans %f")
pdClassMeans = traits.List("traits.Float",
sep=",",
argstr="--pdClassMeans %f")
randomSeed = traits.Int(argstr="--randomSeed %d")
numberOfPlugs = traits.Int(argstr="--numberOfPlugs %d")
coverage = traits.Float(argstr="--coverage %f")
permissiveness = traits.Float(argstr="--permissiveness %f")
meanOutlier = traits.Float(argstr="--meanOutlier %f")
varOutlier = traits.Float(argstr="--varOutlier %f")
plugSize = traits.Float(argstr="--plugSize %f")
partitions = traits.List("traits.Int", sep=",", argstr="--partitions %d")
numberOfClassPlugs = traits.List("traits.Int",
sep=",",
argstr="--numberOfClassPlugs %d")
bloodMode = traits.Enum("Manual", "Top", "Bottom", argstr="--bloodMode %s")
bloodImage = traits.Enum("T1", "T2", "PD", argstr="--bloodImage %s")
vbPlugs = File(exists="True", argstr="--vbPlugs %s")
class N4ITKInputSpec(CommandLineInputSpec):
inputImageName = File(exists="True", argstr="--inputimage %s")
maskImageName = File(exists="True", argstr="--maskimage %s")
outputImageName = traits.Either(traits.Bool,
File,
argstr="--outputimage %s")
outputBiasFieldName = traits.Either(traits.Bool,
File,
argstr="--outputbiasfield %s")
Force2D = traits.Bool(argstr="--force2D ")
numberOfIterations = traits.List("traits.Int",
sep=",",
argstr="--iterations %d")
convergenceThreshold = traits.Float(argstr="--convergencethreshold %f")
initialMeshResolution = traits.List("traits.Float",
sep=",",
argstr="--meshresolution %f")
splineDistance = traits.Float(argstr="--splinedistance %f")
shrinkFactor = traits.Int(argstr="--shrinkfactor %d")
bsplineOrder = traits.Int(argstr="--bsplineorder %d")
weightImageName = File(exists="True", argstr="--weightimage %s")
alpha = traits.Float(argstr="--bsplinealpha %f")
beta = traits.Float(argstr="--bsplinebeta %f")
histogramSharpening = traits.List("traits.Float",
sep=",",
argstr="--histogramsharpening %f")
biasFieldFullWidthAtHalfMaximum = traits.Float(
argstr="--biasFieldFullWidthAtHalfMaximum %f")
weinerFilterNoise = traits.Float(argstr="--weinerFilterNoise %f")
numberOfHistogramBins = traits.Int(argstr="--numberOfHistogramBins %d")
class BRAINSTalairachInputSpec(CommandLineInputSpec):
AC = traits.List("traits.Float", sep=",", argstr="--AC %f")
ACisIndex = traits.Bool(argstr="--ACisIndex ")
PC = traits.List("traits.Float", sep=",", argstr="--PC %f")
PCisIndex = traits.Bool(argstr="--PCisIndex ")
SLA = traits.List("traits.Float", sep=",", argstr="--SLA %f")
SLAisIndex = traits.Bool(argstr="--SLAisIndex ")
IRP = traits.List("traits.Float", sep=",", argstr="--IRP %f")
IRPisIndex = traits.Bool(argstr="--IRPisIndex ")
inputVolume = File(exists="True", argstr="--inputVolume %s")
outputBox = traits.Either(traits.Bool, File, argstr="--outputBox %s")
outputGrid = traits.Either(traits.Bool, File, argstr="--outputGrid %s")
class BRAINSDiscreteClassInputSpec(CommandLineInputSpec):
inputVolume = File(exists="True", argstr="--inputVolume %s")
subcorticalMask = File(exists="True", argstr="--subcorticalMask %s")
outputVolume = traits.Either(traits.Bool, File, argstr="--outputVolume %s")
subcorticalThreshold = traits.Float(argstr="--subcorticalThreshold %f")
corticalThreshold = traits.Float(argstr="--corticalThreshold %f")
csfThreshold = traits.Float(argstr="--csfThreshold %f")
class BRAINSApplySurfaceLabelsInputSpec(CommandLineInputSpec):
inputLabelMap = File(exists="True", argstr="--inputLabelMap %s")
inputSurface = File(exists="True", argstr="--inputSurface %s")
cellDataName = traits.Str(exists="True", argstr="--cellDataName %s")
outputSurface = traits.Either(traits.Bool,
File,
argstr="--outputSurface %s")
class DicomToNrrdConverterInputSpec(CommandLineInputSpec):
inputDicomDirectory = Directory( exists = "True",argstr = "--inputDicomDirectory %s")
outputDirectory = traits.Either(traits.Bool, Directory, argstr = "--outputDirectory %s")
outputVolume = traits.Str( argstr = "--outputVolume %s")
smallGradientThreshold = traits.Float( argstr = "--smallGradientThreshold %f")
writeProtocolGradientsFile = traits.Bool( argstr = "--writeProtocolGradientsFile ")
useIdentityMeaseurementFrame = traits.Bool( argstr = "--useIdentityMeaseurementFrame ")
useBMatrixGradientDirections = traits.Bool( argstr = "--useBMatrixGradientDirections ")
class BRAINSTalairachMaskInputSpec(CommandLineInputSpec):
inputVolume = File(exists="True", argstr="--inputVolume %s")
talairachParameters = File(exists="True",
argstr="--talairachParameters %s")
talairachBox = File(exists="True", argstr="--talairachBox %s")
hemisphereMode = traits.Enum("left",
"right",
"both",
argstr="--hemisphereMode %s")
expand = traits.Bool(argstr="--expand ")
outputVolume = traits.Either(traits.Bool, File, argstr="--outputVolume %s")
class BRAINSMeasureSurfaceInputSpec(CommandLineInputSpec):
inputSurface = File( exists = "True",argstr = "--inputSurface %s")
arrayName = traits.Str( argstr = "--arrayName %s")
labels = traits.List("traits.Str", sep = ",",argstr = "--labelNames %s")
subjectId = traits.Str( argstr = "--subjectId %s")
scanId = traits.Str( argstr = "--scanId %s")
writeCsvFile = traits.Bool( argstr = "--writeCsvFile ")
writeXmlFile = traits.Bool( argstr = "--writeXmlFile ")
csvFile = traits.Either(traits.Bool, File, argstr = "--csvFile %s")
xmlFile = traits.Either(traits.Bool, File, argstr = "--xmlFile %s")
testDepth = traits.Bool( argstr = "--testDepth ")
totalDepthResults = traits.List("traits.Float", sep = ",",argstr = "--totalDepthResults %f")
gyralDepthResults = traits.List("traits.Float", sep = ",",argstr = "--gyralDepthResults %f")
sulcalDepthResults = traits.List("traits.Float", sep = ",",argstr = "--sulcalDepthResults %f")
testArea = traits.Bool( argstr = "--testArea ")
totalAreaResults = traits.List("traits.Float", sep = ",",argstr = "--totalAreaResults %f")
gyralAreaResults = traits.List("traits.Float", sep = ",",argstr = "--gyralAreaResults %f")
sulcalAreaResults = traits.List("traits.Float", sep = ",",argstr = "--sulcalAreaResults %f")
testCurvature = traits.Bool( argstr = "--testCurvature ")
totalCurvatureResults = traits.List("traits.Float", sep = ",",argstr = "--totalCurvatureResults %f")
gyralCurvatureResults = traits.List("traits.Float", sep = ",",argstr = "--gyralCurvatureResults %f")
sulcalCurvatureResults = traits.List("traits.Float", sep = ",",argstr = "--sulcalCurvatureResults %f")
class BRAINSClassifyInputSpec(CommandLineInputSpec):
t1Volume = File(exists="True", argstr="--t1Volume %s")
t2Volume = File(exists="True", argstr="--t2Volume %s")
pdVolume = File(exists="True", argstr="--pdVolume %s")
gmPlugs = File(exists="True", argstr="--gmPlugs %s")
wmPlugs = traits.Either(traits.Bool, File, argstr="--wmPlugs %s")
csfPlugs = File(exists="True", argstr="--csfPlugs %s")
bloodPlugs = File(exists="True", argstr="--bloodPlugs %s")
BrainVolume = File(exists="True", argstr="--BrainVolume %s")
classVolume = traits.Either(traits.Bool, File, argstr="--classVolume %s")
grossTrim = traits.Float(argstr="--grossTrim %f")
spatialTrim = traits.Float(argstr="--spatialTrim %f")
x = traits.Bool(argstr="--x ")
y = traits.Bool(argstr="--y ")
z = traits.Bool(argstr="--z ")
xx = traits.Bool(argstr="--xx ")
yy = traits.Bool(argstr="--yy ")
zz = traits.Bool(argstr="--zz ")
xy = traits.Bool(argstr="--xy ")
xz = traits.Bool(argstr="--xz ")
yz = traits.Bool(argstr="--yz ")
histogramEqualize = traits.Bool(argstr="--histogramEqualize ")
generateSeperateImages = traits.Bool(argstr="--generateSeperateImages ")
excludeVolume = File(exists="True", argstr="--excludeVolume %s")
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec
import enthought.traits.api as traits
import os
from nipype.interfaces.traits import File
from nipype.interfaces.traits import Directory
from nipype.utils.misc import isdefined
class test.xmlInputSpec(CommandLineInputSpec):
houghEyeDetectorMode = traits.Int( argstr = "--houghEyeDetectorMode %d")
inputTemplateModel = File( exists = "True",argstr = "--inputTemplateModel %s")
inputLLSModel = File( exists = "True",argstr = "--inputLLSModel %s")
inputEPCAModelMat = File( exists = "True",argstr = "--inputEPCAModelMat %s")
inputEPCAModelTxt = File( exists = "True",argstr = "--inputEPCAModelTxt %s")
inputVolume = File( exists = "True",argstr = "--inputVolume %s")
outputVolume = traits.Either(traits.Bool, File, argstr = "--outputVolume %s")
outputResampledVolume = traits.Either(traits.Bool, File, argstr = "--outputResampledVolume %s")
outputTransform = traits.Either(traits.Bool, File, argstr = "--outputTransform %s")
outputLandmarksInInputSpace = traits.Either(traits.Bool, File, argstr = "--outputLandmarksInInputSpace %s")
outputLandmarksInACPCAlignedSpace = traits.Either(traits.Bool, File, argstr = "--outputLandmarksInACPCAlignedSpace %s")
inputLandmarksPaired = File( exists = "True",argstr = "--inputLandmarksPaired %s")
outputLandmarksPaired = traits.Either(traits.Bool, File, argstr = "--outputLandmarksPaired %s")
outputMRML = traits.Either(traits.Bool, File, argstr = "--outputMRML %s")
outputVerificationScript = traits.Either(traits.Bool, File, argstr = "--outputVerificationScript %s")
mspQualityLevel = traits.Int( argstr = "--mspQualityLevel %d")
otsuPercentileThreshold = traits.Float( argstr = "--otsuPercentileThreshold %f")
acLowerBound = traits.Float( argstr = "--acLowerBound %f")
cutOutHeadInOutputVolume = traits.Bool( argstr = "--cutOutHeadInOutputVolume ")
outputUntransformedClippedVolume = traits.Either(traits.Bool, File, argstr = "--outputUntransformedClippedVolume %s")
rescaleIntensities = traits.Bool( argstr = "--rescaleIntensities ")
trimRescaledIntensities = traits.Float( argstr = "--trimRescaledIntensities %f")
rescaleIntensitiesOutputRange = traits.List("traits.Int", sep = ",",argstr = "--rescaleIntensitiesOutputRange %d")
class Passenger(PrtEvent):
"""A passenger."""
mass = traits.Int()
_loc = traits.Either(traits.Instance('pyprt.sim.station.Station'),
traits.Instance('pyprt.sim.vehicle.BaseVehicle'),
None)
traits_view = ui.View(
ui.Item(name='label'),
ui.Item(name='ID'),
ui.Item(name='loc'),
ui.Item(name='mass'), # in kg
ui.Item(name='trip_success'),
ui.Item(name='wait_time', format_func=sec_to_hms),
ui.Item(name='walk_time', format_func=sec_to_hms),
ui.Item(name='ride_time', format_func=sec_to_hms),
ui.Item(name='will_share'),
ui.Item(name='src_station'),
ui.Item(name='dest_station'),
ui.Item(name='load_delay', format_func=sec_to_hms),
ui.Item(name='unload_delay', format_func=sec_to_hms),
style='readonly',
handler=NoWritebackOnCloseHandler())
## # Subset of passenger data in table format.
## table_editor = ui.TableEditor(
## columns = [ui_tc.ObjectColumn(name='ID', label='ID'),
## ui_tc.ObjectColumn(name='src_station', label='Origin'),
## ui_tc.ObjectColumn(name='dest_station', label='Destination'),
## ui_tc.ExpressionColumn(label='Waiting',
## expression='sec_to_hms(object.wait_time)',
## globals={'sec_to_hms':sec_to_hms},
## tooltip='Time spent waiting'),
## ui_tc.ExpressionColumn(label='Riding',
## expression='sec_to_hms(object.ride_time)',
## globals={'sec_to_hms':sec_to_hms},
## tooltip='Time spent riding'),
## ui_tc.ExpressionColumn(label='Walking',
## expression='sec_to_hms(object.walk_time)',
## globals={'sec_to_hms':sec_to_hms},
## tooltip='Time spent walking'),
## ui_tc.ExpressionColumn(label='Total',
## expression='sec_to_hms(object.total_time)',
## globals={'sec_to_hms':sec_to_hms},
## tooltip='Total time spent on trip'),
## ui_tc.ObjectColumn(name='trip_success', label='Success',
## tooltip='Sucessfully reached destination'),
## ui_tc.ObjectColumn(name='loc', label='Current Location')
## ],
## other_columns = [ui_tc.ObjectColumn(name='label', label='Label'),
## ui_tc.ObjectColumn(name='will_share', label='Will Share',
## tooltip='Willing to share vehicle when destinations match'),
## ui_tc.ObjectColumn(name='load_delay', label='Load Delay',
## tooltip='Time that passenger takes to embark'),
## ui_tc.ObjectColumn(name='unload_delay', label='Unload Delay',
## tooltip='Time that passenger takes to disembark'),
## ui_tc.ObjectColumn(name='mass', label='Mass',
## tooltip='Includes luggage (kg)')
## ],
## # more...
## deletable = False,
## editable=False,
## sortable = True,
## sort_model = False,
## auto_size = True,
## orientation = 'vertical',
## show_toolbar = True,
## reorderable = False,
## rows = 15,
## row_factory = traits.This)
def __init__(self, time, ID, src_station, dest_station, load_delay,
unload_delay, will_share, mass):
super(Passenger, self).__init__(time, ID)
self.src_station = src_station
self.dest_station = dest_station
self.load_delay = load_delay
self.unload_delay = unload_delay
self.will_share = will_share # Willing to share pod (if same dest)
self.mass = mass
self.trip_success = False
self._loc = src_station
# For the following, where start and end are times in seconds, with 0 being the start of the sim.
self._wait_times = [[time, None, self._loc]
] # contains triples: [[start, end, loc], ...]
self._walk_times = [
] # containing pairs: [[start, end], [start, end], ...]
self._ride_times = [
] # contains triples: [[start, end, vehicle], [start, end, vehicle], ...]
self._start_time = time
self._end_time = None
@property
def wait_time(self): # in seconds
total = 0
for start, end, loc in self._wait_times:
if end is None:
total += Sim.now() - start
else:
total += end - start
return total
@property
def ride_time(self): # in seconds
total = 0
for start, end, vehicle in self._ride_times:
if end is None:
total += Sim.now() - start
else:
total += end - start
return total
@property
def walk_time(self): # in seconds
total = 0
for start, end in self._walk_times:
if end is None:
total += Sim.now() - start
else:
total += end - start
return total
@property
def total_time(self):
if self._end_time is None:
return Sim.now() - self._start_time
else:
return self._end_time - self._start_time
def get_loc(self):
return self._loc
def set_loc(self, loc):
"""Changes the loc, and keeps track of how much time is spent in each
mode of transit: waiting, riding, or walking."""
### Track time spent in each mode of transit ###
if self._loc is None: # Was walking
self._walk_times[-1][1] = Sim.now()
elif hasattr(self._loc, 'vehicle_mass'): # was in vehicle
self._ride_times[-1][1] = Sim.now()
elif hasattr(self._loc, 'platforms'): # was at station
self._wait_times[-1][1] = Sim.now()
else:
raise Exception("Unknown loc type")
### Note if trip is completed. ###
if loc is self.dest_station:
self._end_time = Sim.now()
self.trip_success = True
### More time tracking ###
if not self.trip_success:
if loc is None: self._walk_times.append([Sim.now(), None])
elif hasattr(loc, 'vehicle_mass'):
self._ride_times.append([Sim.now(), None,
loc]) # isinstance(loc, BaseVehicle)
elif hasattr(loc, 'platforms'):
self._wait_times.append([Sim.now(), None,
loc]) # isinstance(loc, TrackSegment)
else:
raise Exception("Unknown loc type")
self._loc = loc
loc = property(
get_loc,
set_loc,
doc="loc is expected to be a Station, a "
"Vehicle, or None (which indicates walking from one station "
"to another). Setting the loc has side-effects, see set_loc.")
def walk(self, origin_station, dest_station, travel_time, cmd_msg, cmd_id):
assert self._loc is origin_station
assert travel_time >= 0
assert isinstance(cmd_msg, api.CtrlCmdPassengerWalk)
assert isinstance(cmd_id, int)
self.loc = None
common.AlarmClock(Sim.now() + travel_time, self._post_walk,
dest_station, cmd_msg, cmd_id)
def _post_walk(self, dest_station, cmd_msg, cmd_id):
"""Updates stats, changes location, and sends a SimCompletePassengerWalk
message. To be called once the walk is complete."""
assert self._loc is None
self.loc = dest_station
msg = api.SimCompletePassengerWalk()
msg.msgID = cmd_id
msg.cmd.CopyFrom(cmd_msg)
msg.time = Sim.now()
common.interface.send(api.SIM_COMPLETE_PASSENGER_WALK, msg)
def fill_PassengerStatus(self, ps):
ps.pID = self.ID
# I'd much rather use isinstance checks, but circular imports are killing me
if self._loc is None:
ps.loc_type = api.WALKING
ps.locID = api.NONE_ID
elif hasattr(self._loc, 'vehicle_mass'): # a vehicle
ps.loc_type = api.VEHICLE
ps.locID = self._loc.ID
elif hasattr(self._loc, 'platforms'): # a station
ps.loc_type = api.STATION
ps.locID = self._loc.ID
else:
raise Exception, "Unknown passenger location type: %s" % self._loc
ps.src_stationID = self.src_station.ID
ps.dest_stationID = self.dest_station.ID
ps.creation_time = self._start_time
ps.mass = self.mass
ps.trip_success = self.trip_success