def run(self):
ifile = self.options.input
ofile = self.options.output
reader = NrrdReader()
iparams, bindata = reader.getFileContent(ifile)
#iparams = iparams._data
b0n = iparams['b0num']
print "%d b0 to be averaged" % b0n
b0n -= 1
difcropstr = getOrderStr(options.aorder, b0n)
orderstr = getOrderStr(options.aorder, b0n)
print '###########',orderstr
if options.is_average:
cmd = "unu crop -i %s -min %s -max M M M M -o tmp.nhdr; " % ( ifile, difcropstr)
cmd += "unu crop -i %s -min 0 0 0 0 -max %d M M M | unu project -a %s -m mean | unu splice -i grad.nhdr -s - -a 0 -p 0 -o %s; rm tmp.*" % (ifile, b0n, options.aorder, ofile)
else:
cmd = "unu crop -i %s -min %s -max M M M M -o %s " % ( ifile, orderstr, ofile)
print cmd
os.system(cmd)
ofilein = open(ofile,'r')
content = []
while ofilein:
line = ofilein.readline()
if len(line) == 0:
break;
if line.startswith(NrrdReader.grdkey):
continue
content.append(line)
ofilein.close()
count = 0
for n,i in enumerate(iparams[NrrdReader.grdkey]):
if count > 0 and n <= b0n:
continue
oline = '%s_%04d:=' % (NrrdReader.grdkey,count)
for j in i:
oline += '%1.6f ' % j
content.append(oline+'\n')
count+=1
ofileout = open(ofile, 'w')
for l in content:
if options.verbose:
print l
ofileout.write(l)
ofileout.close()
def run():
global options,args
nrrdr = NrrdReader()
params, bindata = nrrdr.getFileContent(options.input)
for k in params.keys():
print k,' : ',params[k]
dim = params['sizes']
dimX = dim[0]
dimY = dim[1]
dimZ = dim[2]
numSeeds = 9
seedThresh = numSeeds * 30
radius = 0.5
spacing = options.spacing
if params['type'][0] == 'float':
datatype = numpy.float32
elif params['type'][0] == 'double':
datatype = numpy.double
elif params['type'][0] == 'short':
datatype = numpy.short
size = dimX*dimY*dimZ
shape = (dimX, dimY, dimZ)
if 'data file' in params:
filename = params['data file'][0]
f = gzip.open(filename, 'r')
FILE = f.read()
f.close()
else:
FILE=gzip.GzipFile(fileobj=StringIO(bindata)).read()
data = numpy.fromstring(FILE, dtype=datatype)
print data.shape
print shape
print shape[0]*shape[1]*shape[2]
data = data.reshape(shape, order='F') #matlab uses fortran order; numpy uses c order
if not os.path.isdir("seeds"):
print 'make seeds dirs'
os.mkdir("seeds")
os.chdir("seeds")
print os.getcwd()
filemap = {}
seedPoints = 0;
fileCount = 1;
for z in range(0, dimZ):
for y in range(0, dimY):
for x in range(0, dimX):
val = data[x][y][z]
if val > 0:
if not filemap.has_key(val):
filename = 'IC%d.txt' % val
filemap[val] = open(filename, 'w')
print '(%d,%d,%d) \t %d' % (x,y,z,data[x][y][z])
vx = x
vy = y
vz = z
if options.isRand:
points = numpy.random.uniform(size=[options.num_points, 3]) + [vx-0.5, vy-0.5, vz-0.5]
for p in points:
str = '%f %f %f\n' % (p[0],p[1],p[2])
filemap[val].write(str)
else:
for zz in numpy.arange(vz-radius,vz+radius,spacing):
for yy in numpy.arange(vy-radius,vy+radius,spacing):
for xx in numpy.arange(vx-radius,vx+radius,spacing):
str = '%f %f %f\n' % (xx,yy,zz)
filemap[val].write(str)
seedPoints = seedPoints + numSeeds;
# if seedPoints % seedThresh == 0:
# OUT.close()
# fileCount += 1
# newfile = 'IC%d.txt' % fileCount
# OUT = open(newfile, 'w')
for i in filemap.values():
i.close()
def run():
global options, args
nrrdr = NrrdReader()
params, bindata = nrrdr.getFileContent(options.input)
for k in params.keys():
print k, ' : ', params[k]
dim = params['sizes']
dimX = dim[0]
dimY = dim[1]
dimZ = dim[2]
numSeeds = 9
seedThresh = numSeeds * 30
radius = 0.5
spacing = options.spacing
if params['type'][0] == 'float':
datatype = numpy.float32
elif params['type'][0] == 'double':
datatype = numpy.double
elif params['type'][0] == 'short':
datatype = numpy.short
size = dimX * dimY * dimZ
shape = (dimX, dimY, dimZ)
if 'data file' in params:
filename = params['data file'][0]
f = gzip.open(filename, 'r')
FILE = f.read()
f.close()
else:
FILE = gzip.GzipFile(fileobj=StringIO(bindata)).read()
data = numpy.fromstring(FILE, dtype=datatype)
print data.shape
print shape
print shape[0] * shape[1] * shape[2]
data = data.reshape(
shape, order='F') #matlab uses fortran order; numpy uses c order
if not os.path.isdir("seeds"):
print 'make seeds dirs'
os.mkdir("seeds")
os.chdir("seeds")
print os.getcwd()
filemap = {}
seedPoints = 0
fileCount = 1
for z in range(0, dimZ):
for y in range(0, dimY):
for x in range(0, dimX):
val = data[x][y][z]
if val > 0:
if not filemap.has_key(val):
filename = 'IC%d.txt' % val
filemap[val] = open(filename, 'w')
print '(%d,%d,%d) \t %d' % (x, y, z, data[x][y][z])
vx = x
vy = y
vz = z
if options.isRand:
points = numpy.random.uniform(
size=[options.num_points, 3]) + [
vx - 0.5, vy - 0.5, vz - 0.5
]
for p in points:
str = '%f %f %f\n' % (p[0], p[1], p[2])
filemap[val].write(str)
else:
for zz in numpy.arange(vz - radius, vz + radius,
spacing):
for yy in numpy.arange(vy - radius, vy + radius,
spacing):
for xx in numpy.arange(vx - radius,
vx + radius, spacing):
str = '%f %f %f\n' % (xx, yy, zz)
filemap[val].write(str)
seedPoints = seedPoints + numSeeds
# if seedPoints % seedThresh == 0:
# OUT.close()
# fileCount += 1
# newfile = 'IC%d.txt' % fileCount
# OUT = open(newfile, 'w')
for i in filemap.values():
i.close()