def gershgoriny_dist_from_I_aff12_file(fname):
'''Input a file of an aff12 matrix (either MATRIX or ONELINE format).
Must have exactly 12 numbers.
See help of 'gershgoriny_dist_from_I_aff12()' for what happens
next.
Output is one scalar number.
'''
# read in, and get into proper shape with a transposition
x = LAD.Afni1D(fname)
x.transpose()
if len(x.mat) == 3 and len(x.mat[0]) == 4:
# then we have a MATRIX-format aff12.1D param already, and we
# are all set to go
out = gershgoriny_dist_from_I_aff12(x.mat)
elif len(x.mat) == 1 and len(x.mat[0]) == 12:
# then we have a ONELINE-format aff12.1D param, and we have to
# reshape it
M = [[0.0] * 4 for row in range(3)]
for i in range(3):
M[i][:] = x.mat[0][4 * i:4 * (i + 1)]
dist_gershgorin = gershgoriny_dist_from_I_aff12(M)
else:
print("** ERROR: Input matrix in {} has some problems! Doesn't look\n"
" like an aff12.1D format (ONELINE, 1x12; MATRIX, 3x4)\n"
"".format(fname))
sys.exit(3)
return dist_gershgorin
def process_matlab_file(self, fname, index=0):
"""process matlab files
"""
try:
import scipy.io
import numpy
except:
print('** missing library: scipy.io')
print(' (please install scipy)')
return 1
if not os.path.isfile(fname):
print("** missing file '%s'" % fname)
return 1
mfile = scipy.io.loadmat(fname)
if mfile == None: return 1
# prepare output prefix
prefix = self.prefix
if prefix != '' and len(self.infiles) > 1:
prefix = '%s.%02d' % (self.prefix, index+1)
klist = [key for key in list(mfile.keys()) if key[0:2] != '__']
maxlen = max([len(key) for key in klist])
if self.verb:
if self.verb > 1: print()
print('-- file %s has %d key(s)' % (fname, len(klist)))
for key in klist:
obj = mfile[key]
if self.verb > 1:
if type(obj) is numpy.ndarray:
shstr = ' shape %s' % str(obj.shape)
else:
shstr = ''
print(' %-*s %s%s' % (maxlen, key, type(obj), shstr))
# maybe write any numpy data
if prefix != '' and type(obj) is numpy.ndarray:
# convert object to Afni1D and transpose
olist = obj.tolist()
adata = LD.Afni1D(from_mat=1, matrix=olist, verb=self.verb)
adata.transpose()
# if model, break apart, else just write
if key == 'model' and adata.nvec >= 2:
self.write_model_files(adata, prefix)
else:
ofile = '%s.%s.1D'%(prefix,key)
print('++ writing ndarry to %s' % ofile)
adata.write(ofile, overwrite=self.overwrite)
return 0
def write_model_files(self, adata, prefix):
"""break model matrix into many 1D files
"""
if adata.nvec < 1: return 0
for ind in range(adata.nvec):
avec = LD.Afni1D(from_mat=1, matrix=[adata.mat[ind]], verb=self.verb)
ofile = '%s.model.%02d.1D' % (prefix, ind+1)
print('++ writing model file %s' % ofile)
avec.write(ofile, overwrite=self.overwrite)
return 0
print(help_str)
sys.exit(0)
an = 1
niter = 0
if sys.argv[an] == '-niter':
if an + 2 >= narg:
print(usage_str)
sys.exit(1)
niter = int(sys.argv[an + 1])
print('-- using niter = %d' % niter)
an += 2
infile = sys.argv[an]
mdata = LAD.Afni1D(infile, verb=0)
if not mdata.ready:
print('** failed to read maxdata file %s' % infile)
sys.exit(1)
try:
mdata = [int(round(m)) for m in mdata.mat[0]]
except:
print('** failed to process integers from maxdata file %s' % infile)
sys.exit(1)
mdata.sort()
cmax = mdata[-1]
mlen = len(mdata)
if niter > 0 and niter > mlen:
print('** have input niter (%d) > mlen(%d)' % (niter, mlen))