def _generate_setup(self):
r"""
Perform applicable preliminary checks and calculations required for generation
"""
self._Nx = 5
self._Ny = 5
self._Nz = 5
self._Lc = 1
self._Lx = sp.float16(self._Nx * self._Lc)
self._Ly = sp.float16(self._Ny * self._Lc)
self._Lz = sp.float16(self._Nz * self._Lc)
def _generate_setup(self):
r"""
Perform applicable preliminary checks and calculations required for generation
"""
self._Nx = 5
self._Ny = 5
self._Nz = 5
self._Lc = 1
self._Lx = sp.float16(self._Nx*self._Lc)
self._Ly = sp.float16(self._Ny*self._Lc)
self._Lz = sp.float16(self._Nz*self._Lc)
def find_clusters_from_3D(fnifti, thr):
"""
Function to use afni command line to find clusters from a 3D nifti.
TODO(dhjelm): change this to use nipy functions.
Parameters
----------
fnifti: nifti file
Nifti file to process.
thr: float
Threshold used for clusters.
Returns
-------
cluster: a list of floats
"""
cmd = ("3dclust "
"-1Dformat -quiet -nosum -2thresh -2 %.2f "
"-dxyz=1 2 80 2>/dev/null" % thr)
awk = "awk '{ print $1\"\t\"$2\"\t\"$3\"\t\"$4\"\t\"$5\"\t\"$6\"\t\"$11\"\t\"$14\"\t\"$15\"\t\"$16}'"
cmdline = cmd + " '%s'| " % fnifti + awk
proc = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate()
if "#**" in out.split(): return []
cluster = float16(out.split())
return cluster
def find_clusters_from_3D(fnifti, thr):
"""
Function to use afni command line to find clusters from a 3D nifti.
TODO(dhjelm): change this to use nipy functions.
Parameters
----------
fnifti: nifti file
Nifti file to process.
thr: float
Threshold used for clusters.
Returns
-------
cluster: a list of floats
"""
cmd = ("3dclust "
"-1Dformat -quiet -nosum -2thresh -2 %.2f "
"-dxyz=1 2 80 2>/dev/null" % thr)
awk = "awk '{ print $1\"\t\"$2\"\t\"$3\"\t\"$4\"\t\"$5\"\t\"$6\"\t\"$11\"\t\"$14\"\t\"$15\"\t\"$16}'"
cmdline = cmd + " '%s'| " % fnifti + awk
proc = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate()
if "#**" in out.split(): return []
cluster = float16(out.split())
return cluster
def find_clusters_from_4D(fnifti, i, thr):
"""
Function to use afni command line to find clusters from a 4D nifti.
TODO(dhjelm): change this to use nipy functions.
Parameters
----------
fnifti: nifti file
Nifti file to process.
i: integer
Index of the feature in the nifti file.
thr: float
Threshold used for clusters.
Returns
-------
clusters: list of tuples of floats
List of 3d clusters.
"""
assert isinstance(i, int)
assert isinstance(thr, (int, float))
cmd = ("3dclust "
"-1Dformat -quiet -nosum -1dindex %d -1tindex %d -2thresh -2 %.2f "
"-dxyz=1 2 80 2>/dev/null" % (i, i, thr))
awk = "awk '{ print $1\"\t\"$2\"\t\"$3\"\t\"$4\"\t\"$5\"\t\"$6\"\t\"$11\"\t\"$14\"\t\"$15\"\t\"$16}'"
cmdline = cmd + " '%s'| " % fnifti + awk
proc = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate()
if "#**" in out.split(): return []
clusters = float16(out.split())
return clusters
def find_clusters_from_4D(fnifti, i, thr):
"""
Function to use afni command line to find clusters from a 4D nifti.
TODO(dhjelm): change this to use nipy functions.
Parameters
----------
fnifti: nifti file
Nifti file to process.
i: integer
Index of the feature in the nifti file.
thr: float
Threshold used for clusters.
Returns
-------
clusters: list of tuples of floats
List of 3d clusters.
"""
assert isinstance(i, int)
assert isinstance(thr, (int, float))
cmd = ("3dclust "
"-1Dformat -quiet -nosum -1dindex %d -1tindex %d -2thresh -2 %.2f "
"-dxyz=1 2 80 2>/dev/null" %
(i, i, thr))
awk = "awk '{ print $1\"\t\"$2\"\t\"$3\"\t\"$4\"\t\"$5\"\t\"$6\"\t\"$11\"\t\"$14\"\t\"$15\"\t\"$16}'"
cmdline = cmd + " '%s'| " % fnifti + awk
proc = subprocess.Popen(cmdline, stdout=subprocess.PIPE, shell=True)
(out, err) = proc.communicate()
if "#**" in out.split(): return []
clusters = float16(out.split())
return clusters