def set_censor_arr(self):
self.censor_width = self.all_x[1] - self.all_x[0]
# add to this in different forms, where True values mean
# censoring is flagged to have occured
cen_arr = [False] * self.npts
# combine all strings of censor lists:
# ... from user-entered strings
if self.censor_in_trs:
maxind = self.npts - 1
for ttt in self.censor_in_trs:
ll = au.decode_1D_ints(ttt, imax=maxind)
for ii in ll:
cen_arr[ii] = True
# ... from user-entered files
if self.censor_in_files:
for fff in self.censor_in_files:
x = LAD.Afni1D(fff)
if x.nt != self.npts :
sys.exit("** ERROR: len of censor file {} ({}) does not "
"match Npts={}".format(fff, x.nt, self.npts))
for i in range(self.npts):
val = x.mat[0][i]
if not(val):
cen_arr[i] = True
# And finally store the list of xvals to censor
self.ncensor = cen_arr.count(True)
if self.ncensor :
for i in range(self.npts):
if cen_arr[i]:
self.censor_arr.append(self.all_x[i])
def set_cols_from_string(self, cstr):
"""decode the string into a 1D column selection and apply it to col_list
return an error message string, or None on success"""
if not self.matX: return "please load an X matrix, first"
ncols = self.matX.ncols
clist = UTIL.decode_1D_ints(cstr, imax=ncols-1)
if not clist:
return "invalid column list\n\n--> please use AFNI sub-brick notation"
elif not self.AM.list2_is_in_list1(range(ncols), clist):
return "column list outside xmat cols 0..%d" % (ncols-1)
self.col_list = clist
return None # be explicit
def set_cols_from_string(self, cstr):
"""decode the string into a 1D column selection and apply it to col_list
return an error message string, or None on success"""
if not self.matX: return "please load an X matrix, first"
ncols = self.matX.ncols
clist = UTIL.decode_1D_ints(cstr, imax=ncols - 1)
if not clist:
return "invalid column list\n\n--> please use AFNI sub-brick notation"
elif not self.AM.list2_is_in_list1(range(ncols), clist):
return "column list outside xmat cols 0..%d" % (ncols - 1)
self.col_list = clist
return None # be explicit
def init_from_1D(self, fname):
"""initialize AfniXmat from a 1D file"""
mat, clines = TD.read_data_file(fname)
if not mat: return
if not TD.data_is_rect(mat):
print '** matrix is not rectangular in %s' % fname
return
self.mat = N.array(mat)
self.nrows = len(mat)
self.ncols = len(mat[0])
self.ready = 1
for line in clines:
label, data = c1D_line2labelNdata(line)
if not label: continue
verb_level = 3 # cutoff for verbose level
try: # to process some of the data
if label == 'ni_type':
ncols, type = data.split('*')
ncols = int(ncols)
if self.verb > verb_level:
print "-- label %s: cols = %d, type = %s" % \
(label, ncols, type)
if ncols != self.ncols:
print "** matrix cols %d != %s cols %d" % \
(self.ncols, label, ncols)
elif label == 'ni_dimen':
nrows = int(data)
if self.verb > verb_level:
print "-- label %s: rows = %d" % (label, nrows)
if nrows != self.nrows:
print "** matrix rows %d != %s rows %d" % \
(self.nrows, label, nrows)
elif label == 'ColumnLabels':
self.labels = [str.strip() for str in data.split(';')]
if self.verb > verb_level:
print "-- label %s: labels = %s" % (label, self.labels)
if self.ncols != len(self.labels):
print "** %d ColumnLabels but %d columns" % \
(len(self.labels), self.ncols)
self.labels = None
elif label == 'ColumnGroups':
self.groups = UTIL.decode_1D_ints(data)
if self.groups:
if len(self.groups) != self.ncols:
print "** ColumnGroups len %d != ncols %d" % \
(len(self.groups), self.ncols)
if self.verb > verb_level:
print "-- label %s: groups %s" % (label,self.groups)
elif label == 'RowTR':
self.tr = float(data)
if self.verb > verb_level:
print "-- label %s: TR %s" % (label,self.tr)
elif label == 'GoodList':
self.goodlist = UTIL.decode_1D_ints(data)
if self.goodlist:
if len(self.goodlist) != self.nrows:
print "** GoodList missing %d rows" % \
self.nrows-len(self.goodlist)
if self.verb > verb_level:
print "-- label %s: goodlist %s" % (label,self.goodlist)
elif label == 'NRowFull':
self.nrowfull = int(data)
if self.verb > verb_level:
print "-- label %s: nrowfull %s" % (label,self.nrowfull)
elif self.verb > 2:
print "** unknown comment label '%s'" % label
except:
print "** failed to process comment label '%s'" % label
def init_from_1D(self, fname):
"""initialize AfniXmat from a 1D file"""
mat, clines = TD.read_data_file(fname)
if not mat: return
if not TD.data_is_rect(mat):
print '** matrix is not rectangular in %s' % fname
return
self.mat = N.array(mat)
self.nrows = len(mat)
self.ncols = len(mat[0])
self.ready = 1
for line in clines:
label, data = c1D_line2labelNdata(line)
if not label: continue
verb_level = 3 # cutoff for verbose level
try: # to process some of the data
if label == 'ni_type':
ncols, type = data.split('*')
ncols = int(ncols)
if self.verb > verb_level:
print "-- label %s: cols = %d, type = %s" % \
(label, ncols, type)
if ncols != self.ncols:
print "** matrix cols %d != %s cols %d" % \
(self.ncols, label, ncols)
elif label == 'ni_dimen':
nrows = int(data)
if self.verb > verb_level:
print "-- label %s: rows = %d" % (label, nrows)
if nrows != self.nrows:
print "** matrix rows %d != %s rows %d" % \
(self.nrows, label, nrows)
elif label == 'ColumnLabels':
self.labels = [str.strip() for str in data.split(';')]
if self.verb > verb_level:
print "-- label %s: labels = %s" % (label, self.labels)
if self.ncols != len(self.labels):
print "** %d ColumnLabels but %d columns" % \
(len(self.labels), self.ncols)
self.labels = None
elif label == 'ColumnGroups':
self.groups = UTIL.decode_1D_ints(data)
if self.groups:
if len(self.groups) != self.ncols:
print "** ColumnGroups len %d != ncols %d" % \
(len(self.groups), self.ncols)
if self.verb > verb_level:
print "-- label %s: groups %s" % (label, self.groups)
elif label == 'RowTR':
self.tr = float(data)
if self.verb > verb_level:
print "-- label %s: TR %s" % (label, self.tr)
elif label == 'GoodList':
self.goodlist = UTIL.decode_1D_ints(data)
if self.goodlist:
if len(self.goodlist) != self.nrows:
print "** GoodList missing %d rows" % \
self.nrows-len(self.goodlist)
if self.verb > verb_level:
print "-- label %s: goodlist %s" % (label,
self.goodlist)
elif label == 'NRowFull':
self.nrowfull = int(data)
if self.verb > verb_level:
print "-- label %s: nrowfull %s" % (label,
self.nrowfull)
elif self.verb > 2:
print "** unknown comment label '%s'" % label
except:
print "** failed to process comment label '%s'" % label
return ofile, maxind, lstr
# =================================================================
if __name__ == "__main__":
# --------------------- get input ------------------------
print "++ Command line:\n ", ' '.join(sys.argv)
(ofile, maxind, lstr) = get_arg(sys.argv[1:])
# put all selectors together
sss = set()
for ll in lstr:
sss = set.union(sss, set(au.decode_1D_ints(ll, imax=maxind)))
# listify and sort
list_final = list(sss)
list_final.sort()
good_encoded = au.encode_1D_ints(list_final)
# ------------------- write out -------------------------
print "++ OK, the list of good indices in AFNI selector format is:"
print "\n %s\n" % good_encoded
f = open(ofile, 'w')
f.write(good_encoded)
f.close()
# =================================================================
if __name__=="__main__":
# --------------------- get input ------------------------
print("++ Command line:\n ", ' '.join(sys.argv))
(ofile, maxind, lstr) = get_arg(sys.argv[1:])
# [PT: May 22, 2018] want INTERSECTION, not union...
Nlstr = len(lstr)
if Nlstr < 1:
sys.exit("Couldn't find any number strings??")
# put all selectors together
sss = set(au.decode_1D_ints(lstr[0], imax=maxind))
for i in range(1,Nlstr):
ll = lstr[i]
sss = set.intersection(sss, set(au.decode_1D_ints(ll, imax=maxind)))
# listify and sort
list_final = list(sss)
list_final.sort()
good_encoded = au.encode_1D_ints( list_final )
# ------------------- write out -------------------------
print("++ OK, the list of good indices in AFNI selector format is:")
print("\n %s\n" % good_encoded)
