def gershgoriny_dist_from_I_general(mat):
'''
Input: square matrix (Python 2D list)
Output: Gershgorin-approximated distance from identity matrix.
Thanks go to RWC for constructing+explaining this approach!
'''
# check for badness and fail
if not (mat):
print("** ERROR: matrix is null")
sys.exit(5)
if not (UTIL.is_matrix_square(mat, full_check=True)):
print("** ERROR: Matrix is not square")
sys.exit(5)
N = len(mat)
# Go through these steps to get D:
# Minp -> square form M -> D = M-I
D = copy.deepcopy(mat)
for i in range(N):
D[i][i] -= 1
Dtr = UTIL.transpose(D) # Make Dtranspose
DtrD = UTIL.matrix_multiply_2D(Dtr, D) # Calculated D'D
# Calc sum of abs vals of ele in rows (SAVER); then get the max of
# those, and sqrt it
SAVER = UTIL.matrix_sum_abs_val_ele_row(DtrD)
max_SAVER = max(SAVER)
max_SAVER_sqrt = max_SAVER**0.5
return max_SAVER_sqrt
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try: verb = int(opt.parlist[0])
except:
print "** error: verb must be int, have '%s'" % opt.parlist[0]
return
else: verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-offset')
if opt:
try: offset = float(opt.parlist[0])
except:
print "** error: offset must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try: tr = float(opt.parlist[0])
except:
print "** error: TR must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-nt')
try: nt = int(opt.parlist[0])
except:
print "** error: -nt must be int, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print "-- nt = %d, nruns = %d, TR = %s, %d labels" % \
(nt, nruns, str(tr), nlab)
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print '-- using amplitudes to Marry with times...'
newfile_index = 1 # index over output files
for file in files:
tmat = TD.read_1D_file(file, verb=verb)
if not tmat:
print "read_1D_file failed for file: %s" % file
return
mat = afni_util.transpose(tmat)
del(tmat)
if len(mat[0]) < nt * nruns:
print '** error: file %s has only %d entries (%d required)' % \
(file, len(mat[0]), nt*nruns)
return
elif len(mat[0]) > nt * nruns:
print '** warning: file %s has %d entries (expected only %d)' % \
(file, len(mat[0]), nt*nruns)
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index-1]
elif nlab == 0: label = ""
else:
print "** %d labels given, but we are on column %d..." % \
(nlab, newfile_index)
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix,newfile_index,label)
newfile = afni_util.change_path_basename(file, newp, ".1D")
if newfile == None: return
fp = open(newfile, 'w')
for run in range(nruns):
rindex = run * nt # point to start of run
# if empty run, use placeholders
if not stim_in_run(row[rindex:rindex+nt], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
for lcol in range(nt):
if row[rindex+lcol]:
nstim += 1
# if -amplitudes write as time:amplitude
if use_amp:
fp.write('%s*%s ' % \
(str(time+offset),str(row[rindex+lcol])))
else:
fp.write('%s ' % str(time+offset))
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
fp.close()
newfile_index += 1
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try:
verb = int(opt.parlist[0])
except:
print("** error: verb must be int, have '%s'" % opt.parlist[0])
return
else:
verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
consec_ok = (uopts.find_opt('-no_consec') == None)
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print('** please use either -run_trs or -nt/-nruns')
return 1
else:
if not uopts.find_opt('-nruns') or not uopts.find_opt('-nt'):
print('** please use either -run_trs or both -nt and -nruns')
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try:
nt = int(opt.parlist[0])
except:
print("** error: -nt must be int, have '%s'" % opt.parlist[0])
return
run_trs = [nt] * nruns
# note the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try:
offset = float(opt.parlist[0])
except:
print("** error: offset must be float, have '%s'" % opt.parlist[0])
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try:
tr = float(opt.parlist[0])
except:
print("** error: TR must be float, have '%s'" % opt.parlist[0])
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print("-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab))
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print('-- using amplitudes to Marry with times...')
newfile_index = 1 # index over output files
for fname in files:
tmat = TD.read_1D_file(fname, verb=verb)
if not tmat:
print("read_1D_file failed for file: %s" % fname)
return
mat = afni_util.transpose(tmat)
del (tmat)
if len(mat[0]) < ntotal:
print('** error: file %s has only %d entries (%d required)' % \
(fname, len(mat[0]), ntotal))
return
elif len(mat[0]) > ntotal:
print('** warning: file %s has %d entries (expected only %d)' % \
(fname, len(mat[0]), ntotal))
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index - 1]
elif nlab == 0: label = ""
else:
print("** %d labels given, but we are on column %d..." % \
(nlab, newfile_index))
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix, newfile_index, label)
newfile = afni_util.change_path_basename(fname, newp + ".1D")
if newfile == None: return
if prefix == '-' or prefix == 'stdout': fp = sys.stdout
elif prefix == 'stderr': fp = sys.stderr
else: fp = open(newfile, 'w')
blocked_consec = 0 # note whether we block consecutive events
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend + 1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
first = 1 # first occurance if no consec
for lcol in range(run_trs[run]):
if row[rindex + lcol]:
# note whether anything has been blocked
if not first and not consec_ok:
if verb > 2:
print('-- blocked consec: file %s, run %d, ind %d'\
% (newp, run, lcol))
blocked_consec = 1
# if consec is bad, only write on first occurance
if first or consec_ok:
nstim += 1
tstr = '%s' % str(time + offset)
# if -amplitudes write as time*amplitude
if use_amp: astr = '*%s' % str(row[rindex + lcol])
else: astr = ''
fp.write('%s%s ' % (tstr, astr))
first = 0 # not first occurance
else:
first = 1
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
if fp != sys.stdout and fp != sys.stderr: fp.close()
newfile_index += 1
if verb and blocked_consec:
print('-- blocked consecutive events file %s, output %s' \
% (fname, newp))
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try:
verb = int(opt.parlist[0])
except:
print "** error: verb must be int, have '%s'" % opt.parlist[0]
return
else:
verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns'
return 1
else:
if not uopts.find_opt('-nruns') and not uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns (missing one)'
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try:
nt = int(opt.parlist[0])
except:
print "** error: -nt must be int, have '%s'" % opt.parlist[0]
return
run_trs = [nt] * nruns
# not the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try:
offset = float(opt.parlist[0])
except:
print "** error: offset must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try:
tr = float(opt.parlist[0])
except:
print "** error: TR must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print "-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab)
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print '-- using amplitudes to Marry with times...'
newfile_index = 1 # index over output files
for file in files:
tmat = TD.read_1D_file(file, verb=verb)
if not tmat:
print "read_1D_file failed for file: %s" % file
return
mat = afni_util.transpose(tmat)
del (tmat)
if len(mat[0]) < ntotal:
print '** error: file %s has only %d entries (%d required)' % \
(file, len(mat[0]), ntotal)
return
elif len(mat[0]) > ntotal:
print '** warning: file %s has %d entries (expected only %d)' % \
(file, len(mat[0]), ntotal)
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index - 1]
elif nlab == 0: label = ""
else:
print "** %d labels given, but we are on column %d..." % \
(nlab, newfile_index)
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix, newfile_index, label)
newfile = afni_util.change_path_basename(file, newp, ".1D")
if newfile == None: return
fp = open(newfile, 'w')
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend + 1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
for lcol in range(run_trs[run]):
if row[rindex + lcol]:
nstim += 1
# if -amplitudes write as time:amplitude
if use_amp:
fp.write('%s*%s ' % \
(str(time+offset),str(row[rindex+lcol])))
else:
fp.write('%s ' % str(time + offset))
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
fp.close()
newfile_index += 1
def proc_mats(uopts):
offset = 0.0 # offset for output times
if uopts == None: return
opt = uopts.find_opt('-verb')
if opt:
try: verb = int(opt.parlist[0])
except:
print "** error: verb must be int, have '%s'" % opt.parlist[0]
return
else: verb = 0
opt = uopts.find_opt('-files')
files = opt.parlist
consec_ok = (uopts.find_opt('-no_consec') == None)
# set run_trs nruns from either -run_trs or -nruns and -nt
opt = uopts.find_opt('-run_trs')
if opt:
val, err = uopts.get_type_list(int, '', opt=opt)
if err: return 1
run_trs = val
nruns = len(run_trs)
if uopts.find_opt('-nruns') or uopts.find_opt('-nt'):
print '** please use either -run_trs or -nt/-nruns'
return 1
else:
if not uopts.find_opt('-nruns') or not uopts.find_opt('-nt'):
print '** please use either -run_trs or both -nt and -nruns'
return 1
opt = uopts.find_opt('-nruns')
nruns = int(opt.parlist[0])
opt = uopts.find_opt('-nt')
try: nt = int(opt.parlist[0])
except:
print "** error: -nt must be int, have '%s'" % opt.parlist[0]
return
run_trs = [nt]*nruns
# note the total number of TRs, regardless
ntotal = afni_util.loc_sum(run_trs)
opt = uopts.find_opt('-offset')
if opt:
try: offset = float(opt.parlist[0])
except:
print "** error: offset must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-prefix')
prefix = opt.parlist[0]
opt = uopts.find_opt('-tr')
try: tr = float(opt.parlist[0])
except:
print "** error: TR must be float, have '%s'" % opt.parlist[0]
return
opt = uopts.find_opt('-labels')
if opt: labels = opt.parlist
else: labels = []
nlab = len(labels)
# print some info
if verb: print "-- run_trs = %s, TR = %s, %d labels" \
% (run_trs, str(tr), nlab)
# new option, -amplitudes (columns of amplitudes to Marry, not just 1s)
use_amp = 0
opt = uopts.find_opt('-amplitudes')
if opt:
use_amp = 1
if verb: print '-- using amplitudes to Marry with times...'
newfile_index = 1 # index over output files
for fname in files:
tmat = TD.read_1D_file(fname, verb=verb)
if not tmat:
print "read_1D_file failed for file: %s" % fname
return
mat = afni_util.transpose(tmat)
del(tmat)
if len(mat[0]) < ntotal:
print '** error: file %s has only %d entries (%d required)' % \
(fname, len(mat[0]), ntotal)
return
elif len(mat[0]) > ntotal:
print '** warning: file %s has %d entries (expected only %d)' % \
(fname, len(mat[0]), ntotal)
for row in mat:
# maybe add a label to the file name
if newfile_index <= nlab: label = ".%s" % labels[newfile_index-1]
elif nlab == 0: label = ""
else:
print "** %d labels given, but we are on column %d..." % \
(nlab, newfile_index)
label = ".label%d" % (newfile_index)
newp = "%s.%02d%s" % (prefix,newfile_index,label)
newfile = afni_util.change_path_basename(fname, newp, ".1D")
if newfile == None: return
if prefix == '-' or prefix == 'stdout': fp = sys.stdout
elif prefix == 'stderr': fp = sys.stderr
else: fp = open(newfile, 'w')
blocked_consec = 0 # note whether we block consecutive events
runend = -1
for run in range(nruns):
runstart = runend + 1
runend = runstart + run_trs[run] - 1
# old: rindex = run * nt # point to start of run
rindex = runstart
# if empty run, use placeholders
if not stim_in_run(row[runstart:runend+1], use_amp):
if run == 0: fp.write('* *\n') # first run gets 2
else: fp.write('*\n')
continue
# print '=== have stim in run, row = %s' % row[rindex:rindex+nt]
time = 0 # in this run
nstim = 0 # be sure we have more than 1 somewhere
first = 1 # first occurance if no consec
for lcol in range(run_trs[run]):
if row[rindex+lcol]:
# note whether anything has been blocked
if not first and not consec_ok:
if verb > 2:
print '-- blocked consec: file %s, run %d, ind %d'\
% (newp, run, lcol)
blocked_consec = 1
# if consec is bad, only write on first occurance
if first or consec_ok:
nstim += 1
tstr = '%s' % str(time+offset)
# if -amplitudes write as time*amplitude
if use_amp: astr = '*%s' % str(row[rindex+lcol])
else: astr = ''
fp.write('%s%s ' % (tstr, astr))
first = 0 # not first occurance
else: first = 1
time += tr
if run == 0 and nstim == 1:
fp.write('*') # if first time has 1 stim, add '*'
fp.write('\n')
if fp != sys.stdout and fp != sys.stderr: fp.close()
newfile_index += 1
if verb and blocked_consec:
print '-- blocked consecutive events file %s, output %s' \
% (fname, newp)