def process_logfile(self):
"""main function to process logfile
"""
# replace any known label groups
self.expand_labels()
# read logfile
inlines = UTIL.read_text_file(self.logfile, lines=1, verb=self.verb)
llist = self.make_label_list(inlines)
if self.show_vals & SHOW_RANK:
if self.verb: pref = 'rank : '
else: pref = ''
lshow = [ll[2] for ll in llist if ll[2] != None]
print '%s%s' % (pref, ','.join(lshow))
if self.show_vals & SHOW_ORIG:
if self.verb: pref = 'orig : '
else: pref = ''
if self.show_vals & SHOW_ALL_ORIG:
lshow = [ll[1] for ll in llist]
else:
lshow = [ll[1] for ll in llist if ll[2] != None]
print '%s%s' % (pref, ','.join(lshow))
return 0
def parse_3col_tsv(fname, verb=1):
"""Read one 3 column tsv (tab separated value) file, and return:
- status (0 if okay)
- header list (length 3?)
- list of onset, duration, label values
A 3 column tsv file should have an optional header line,
followed by rows of VAL VAL LABEL, separated by tabs.
"""
lines = UTIL.read_text_file(fname, lines=1)
if len(lines) < 1:
print("** failed parse_3col_tsv for '%s'" % fname)
return 1, [], []
# pare lines down to useful ones
newlines = []
for lind, line in enumerate(lines):
vv = line.split('\t')
if len(vv) == 3:
newlines.append(vv)
elif len(vv) > 0:
print('** skipping bad line %d of 3col tsv file %s' %
(lind, fname))
if verb > 2: print(' vals[%d] = %s' % (len(vv), vv))
elif verb > 2:
print('** skipping empty line %d of 3col tsv file %s' %
(lind, fname))
lines = newlines
if len(lines) < 1:
print("** parse_3col_tsv for '%s' is empty" % fname)
return 1, [], []
# set header list, if a header exists
header = []
l0 = lines[0]
try:
onset = float(l0[0])
dur = float(l0[1])
lab = l0[2].replace(' ', '_') # and convert spaces to underscores
except:
header = lines.pop(0)
# now lines should be all: onset, duration, label
slist = []
for line in lines:
try:
onset = float(line[0])
dur = float(line[1])
lab = line[2].replace(' ', '_') # convert spaces to underscores
except:
print('** bad line 3col tsv file %s: %s' % (fname, ' '.join(line)))
return 1, [], []
slist.append([onset, dur, lab])
return 0, header, slist
def check_dotfiles(self, show=0, pack=0):
global g_dotfiles
home = os.environ['HOME']
# get list of existing files
dfound = []
for dfile in g_dotfiles:
if os.path.isfile('%s/%s' % (home, dfile)):
dfound.append(dfile)
print('found under $HOME : %s' % dfile)
if show:
for dfile in dfound:
print(UTIL.section_divider(dfile, hchar='='))
print('%s\n' %
UTIL.read_text_file('%s/%s' % (home, dfile), lines=0))
if pack:
import shutil
package = self.dot_file_pack
pgz = '%s.tgz' % package
# maybe user included the extension
ext = package.find('.tgz')
if ext >= 0:
pgz = package
package = package[0:ext]
if os.path.exists(package) or os.path.exists('%s.tgz' % package):
print("** error: package dir '%s' or file '%s' already exists"\
% (package, pgz))
return 1
try:
os.mkdir(package)
except:
print("** failed to make dot file package dir '%s'" % package)
return 1
for dfile in dfound:
shutil.copy2('%s/%s' % (home, dfile), package)
os.system("tar cfz %s %s" % (pgz, package))
shutil.rmtree(package)
if os.path.exists(pgz): print('++ dot file package is in %s' % pgz)
else: print('** failed to make dot file packge %s' % pgz)
return 0
def check_dotfiles(self, show=0, pack=0):
global g_dotfiles
home = os.environ['HOME']
# get list of existing files
dfound = []
for dfile in g_dotfiles:
if os.path.isfile('%s/%s' % (home, dfile)):
dfound.append(dfile)
print 'found under $HOME : %s' % dfile
if show:
for dfile in dfound:
print UTIL.section_divider(dfile, hchar='=')
print '%s\n' % UTIL.read_text_file('%s/%s' % (home, dfile), lines=0)
if pack:
import shutil
package = self.dot_file_pack
pgz = '%s.tgz' % package
# maybe user included the extension
ext = package.find('.tgz')
if ext >= 0:
pgz = package
package = package[0:ext]
if os.path.exists(package) or os.path.exists('%s.tgz'%package):
print "** error: package dir '%s' or file '%s' already exists"\
% (package, pgz)
return 1
try: os.mkdir(package)
except:
print "** failed to make dot file package dir '%s'" % package
return 1
for dfile in dfound:
shutil.copy2('%s/%s' % (home, dfile), package)
os.system("tar cfz %s %s" % (pgz, package))
shutil.rmtree(package)
if os.path.exists(pgz): print '++ dot file package is in %s' % pgz
else: print '** failed to make dot file packge %s' % pgz
fff.write(text_title_desc)
grp = ""
for x in lll:
# make new table if grp
if x[0] != grp:
grp = x[0]
fff.write(table_head % (grp))
fff.write(" * - %s\n" % (x[3]))
fff.write(" - :ref:`%s <ahelp_%s>`\n" % (x[2], x[2]))
fff.write(" - %s\n" % (x[4]))
fff.close()
# =================================================================
if __name__ == "__main__":
# --------------------- get input ------------------------
print "++ Command line:\n ", ' '.join(sys.argv)
(ifile, ofile) = get_arg(sys.argv[1:])
all_lines = au.read_text_file(ifile)
lll = parse_field_lines(all_lines)
write_out_edu_rst(ofile, lll)
print("++ Done writing educational classification rst!")
return GG
# =================================================================
if __name__ == "__main__":
# --------------------- get input ------------------------
print("++ Command line:\n ", ' '.join(sys.argv))
(ifile, inumb, ofile) = get_arg(sys.argv[1:])
# --------------------- proc it ------------------------
bad_list_init = au.read_text_file(ifile)
bad_list_proc = Convert_StrList_to_NumArr(bad_list_init)
good_list = Invert_BadInd_List(bad_list_proc, inumb)
good_encoded = au.encode_1D_ints(good_list)
# ------------------- 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()
print(" ... which has been written to file: %s" % ofile)
def parse_Ncol_tsv(fname, verb=1):
"""Read one N column tsv (tab separated value) file, and return:
- ncol: -1 on error, else >= 0
- header list (length ncol)
- list of onset, duration, label values, amplitudes?
An N column tsv file should have an optional header line,
followed by rows of VAL VAL LABEL, separated by tabs.
"""
lines = UTIL.read_text_file(fname, lines=1)
if len(lines) < 1:
print("** failed parse_3col_tsv for '%s'" % fname)
return -1, [], []
# pare lines down to useful ones
newlines = []
norig = 0
for lind, line in enumerate(lines):
vv = line.split('\t')
vlen = len(vv)
if len == 0:
if verb > 2: print('** skipping empty line %d of 3col tsv file %s' \
% (lind, fname))
continue
# possibly initialize norig
if norig == 0: norig = vlen
# require consistency
if vlen != norig:
print('** line %d ncol=%d, mismatch with orig ncol %d' % \
(lind, vlen, norig))
print('** skipping bad line: %s' % line)
continue
newlines.append(vv)
lines = newlines
if len(lines) < 1:
print("** parse_Ncol_tsv for '%s' is empty" % fname)
return -1, [], []
if norig < 3:
print("** parse_Ncol_tsv: bad ncols = %d" % norig)
return -1, [], []
# set header list, if a header exists
header = []
l0 = lines[0]
try:
onset = float(l0[0])
dur = float(l0[1])
lab = l0[2].replace(' ', '_') # and convert spaces to underscores
except:
header = lines.pop(0)
# decide whether there are amplitudes
ainds = []
if len(lines) > 0 and norig > 3:
line = lines[0]
# find all columns that look like floats
for ind in range(3, len(line)):
try:
amp = float(line[ind])
ainds.append(ind)
except:
pass
# now lines should be all: onset, duration, label and possibly amplitudes
slist = []
for line in lines:
try:
onset = float(line[0])
dur = float(line[1])
lab = line[2].replace(' ', '_') # convert spaces to underscores
if len(ainds) > 0:
amps = [float(line[aind]) for aind in ainds]
except:
print('** bad line Ncol tsv file %s: %s' % (fname, ' '.join(line)))
return -1, [], []
if len(ainds) > 0: slist.append([onset, dur, lab, amps])
else: slist.append([onset, dur, lab])
if len(ainds) > 0: nuse = 4
else: nuse = 3
return nuse, header, slist
def parse_Ncol_tsv(fname, verb=1, hlabels=['onset', 'duration', 'trial_type']):
"""Read one N column tsv (tab separated value) file, and return:
- ncol: -1 on error, else >= 0
- header list (length ncol)
- list of onset, duration, label values, amplitudes?
If all hlabels exist in header labels, then extract those columns.
If all hlabels are integers, extract those 0-based columns.
The format for hlabels should indicate :
onset, duration, type and amplitudes, if any:
onset time, duration, trial type, amp1, amp2, ... ampA
An N column tsv file should have an optional header line,
followed by rows of VAL VAL LABEL, separated by tabs.
"""
lines = UTIL.read_text_file(fname, lines=1)
if len(lines) < 1:
print("** failed parse_3col_tsv for '%s'" % fname)
return -1, [], []
# pare lines down to useful ones
newlines = []
norig = 0
for lind, line in enumerate(lines):
vv = line.split('\t')
vlen = len(vv)
if len == 0:
if verb > 2: print('** skipping empty line %d of 3col tsv file %s' \
% (lind, fname))
continue
# possibly initialize norig
if norig == 0: norig = vlen
# require consistency
if vlen != norig:
print('** line %d ncol=%d, mismatch with orig ncol %d' % \
(lind, vlen, norig))
print('** skipping bad line: %s' % line)
continue
newlines.append(vv)
lines = newlines
if len(lines) < 1:
print("** parse_Ncol_tsv for '%s' is empty" % fname)
return -1, [], []
if norig < 3:
print("** parse_Ncol_tsv: bad ncols = %d in %s" % (norig, fname))
return -1, [], []
# decide on column extration indices, based on hlabels and lines[0:2]
col_inds = tsv_hlabels_to_col_list(hlabels, lines, verb=verb)
if len(col_inds) < 3:
print("** failed to make tsv column index list in %s" % fname)
return -1, [], []
# set header list, if a header exists
header = []
l0 = lines[0]
try:
onset = float(l0[col_inds[0]])
dur = float(l0[col_inds[1]])
lab = l0[col_inds[2]].replace(' ',
'_') # convert spaces to underscores
except:
l0 = lines.pop(0)
header = [l0[col_inds[i]] for i in range(len(col_inds))]
# decide whether there are amplitudes
ainds = col_inds[3:]
#if len(lines) > 0 and norig > 3:
# line = lines[0]
# # find all columns that look like floats
# for ind in range(3, len(line)):
# try:
# amp = float(line[ind])
# ainds.append(ind)
# except: pass
# now lines should be all: onset, duration, label and possibly amplitudes
slist = []
oind = col_inds[0]
dind = col_inds[1]
lind = col_inds[2]
for line in lines:
try:
onset = float(line[oind])
dur = float(line[dind])
lab = line[lind].replace(' ', '_') # convert spaces to underscores
if len(ainds) > 0:
amps = [float(line[aind]) for aind in ainds]
except:
print('** bad line Ncol tsv file %s: %s' % (fname, ' '.join(line)))
return -1, [], []
if len(ainds) > 0: slist.append([onset, dur, lab, amps])
else: slist.append([onset, dur, lab])
nuse = len(col_inds)
return nuse, header, slist
