def save_all_pages(self, fname=None):
if fname is None:
msg = ("Save all pages. Index is inserted before extension. "
"If no extension is provided, pdf is used.")
fname = ui.ask_saveas("title", msg, None)
if not fname:
return
head, tail = os.path.split(fname)
if os.path.extsep in tail:
root, ext = os.path.splitext(tail)
else:
root = fname
ext = '.pdf'
fntemp = os.path.join(head, root) + '_%i' + ext
i = self.current_page_i
self.figure.savefig(fntemp % i)
pages = range(self.n)
pages.remove(i)
prog = ui.progress_monitor(self.n - 1, "Saving Figures", "Saving Figures")
for i in pages:
self.show_page(i)
self.figure.savefig(fntemp % i)
prog.advance()
prog.terminate()
def mri_annotation2label(subject='*', annot='aparc',
dest=os.path.join("{sdir}", "label", "{annot}"),
hemi='*', subjects_dir=None):
"""
Calls ``mri_annotation2label`` (`freesurfer wiki
<http://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label>`_)
mri_dir : str(path)
Path containing mri subject directories (freesurfer's ``SUBJECTS_DIR``).
subject : str
Name of the subject ('*' uses fnmatch to find folders in ``mri_dir``).
annot : str
Name of the annotation file (e.g., ``'aparc'``, ...).
dest : str(path)
Destination for the label files. {sdir}" and "{annot}" are filled in
appropriately.
hemi : 'lh' | 'rh' | '*'
Hemisphere to process; '*' proceses both.
"""
hemis = _fs_hemis(hemi)
subjects = _fs_subjects(subject)
subjects_dir = get_subjects_dir(subjects_dir)
# progress monitor
i_max = len(subjects) * len(hemis)
if len(subjects) > 1:
prog = ui.progress_monitor(i_max, "mri_annotation2label", "")
else:
prog = None
for subject in subjects:
sdir = os.path.join(subjects_dir, subject)
outdir = dest.format(sdir=sdir, annot=annot)
for hemi in hemis:
if prog:
prog.message("Processing: %s - %s" % (subject, hemi))
cmd = [get_bin("freesurfer", "mri_annotation2label"),
'--annotation', annot,
'--subject', subject,
'--hemi', hemi,
'--outdir', outdir,
]
_run(cmd, cwd=subjects_dir)
if prog:
prog.advance()
from eelbrain import ui
import time
p = ui.progress_monitor(i_max=10, title='Progress', message='msg 1!', cancel=True)
for i in xrange(10):
p.message("sleeping for %s" % i)
time.sleep(.3)
p.advance("%s done!" % i)
time.sleep(.2)
"""
To remove the progress_monitor prematurely, uncomment the following three
lines:
"""
## if i == 7:
## p.terminate()
## break
"""
To cause a crash while the progress_monitor is shown, uncomment the
following two lines. To clear up the progress_monitor after the crash,
call::
>>> ui.kill_progress_monitors()
"""
## if i == 6:
## print 6/0