def merge_slices(datadir, fileregex, outfname, outdir='', cleanup=True):
if not outdir:
outdir = datadir
au.log.info('Merging the ' + fileregex + ' files in ' + outdir)
fregex = datadir + os.path.sep + fileregex
imglob = ''
imglob = au.exec_comm(['imglob', fregex])
imglob = imglob.strip()
outdata = ''
if imglob:
if os.path.isabs(outfname): outdata = outfname
else: outdata = outdir + os.path.sep + outfname
os.system('fslmerge -z ' + outdata + ' ' + imglob)
if cleanup:
au.imrm(fregex)
else:
au.log.error('aizkolari_postproc: Error: could not find ' + fregex +
' in ' + datadir)
return outdata
def merge_slices (datadir, fileregex, outfname, outdir='', cleanup=True):
if not outdir:
outdir = datadir
au.log.info ('Merging the ' + fileregex + ' files in ' + outdir)
fregex = datadir + os.path.sep + fileregex
imglob = ''
imglob = au.exec_comm(['imglob', fregex])
imglob = imglob.strip()
outdata = ''
if imglob:
if os.path.isabs (outfname): outdata = outfname
else: outdata = outdir + os.path.sep + outfname
os.system('fslmerge -z ' + outdata + ' ' + imglob)
if cleanup:
au.imrm(fregex)
else:
au.log.error ('aizkolari_postproc: Error: could not find ' + fregex + ' in ' + datadir)
return outdata
def get_image_size(fname):
return au.exec_comm(
['convert', fname, '-format', '%G', '-identify',
'null:']).strip().split('x')
#reading input
bg_range = au.get_volume_intrange(bg_img)
bg_min = bg_range[0]
bg_max = bg_range[1]
s1_range = au.get_volume_intrange(s1_img)
if not s1_min:
s1_min = s1_range[0]
if not s1_max:
s1_max = s1_range[1]
#get a temporal place to write stuff
statsvol = au.exec_comm('tmpnam').strip()
statsbar = au.exec_comm('tmpnam').strip()
#if not os.path.exists(tmpd):
# exec_comm(['mkdir', tmpd])
#statsvol = tmpd + os.path.sep + 'outvol'
#statsbar = tmpd + os.path.sep + 'outbar'
#overlay command
overlay = 'overlay 1 0 ' + bg_img + ' ' + str(bg_min) + ' ' + str(
bg_max) + ' ' + s1_img + ' ' + str(s1_min) + ' ' + str(
s1_max) + ' ' + statsbar + ' y ' + statsvol
au.exec_comm(overlay.split())
#slices command
olddir = os.getcwd()
def get_image_size(fname):
return au.exec_comm(['convert', fname, '-format', '%G', '-identify', 'null:']).strip().split('x')
#reading input
bg_range = au.get_volume_intrange(bg_img)
bg_min = bg_range[0]
bg_max = bg_range[1]
s1_range = au.get_volume_intrange(s1_img)
if not s1_min:
s1_min = s1_range[0]
if not s1_max:
s1_max = s1_range[1]
#get a temporal place to write stuff
statsvol = au.exec_comm('tmpnam').strip()
statsbar = au.exec_comm('tmpnam').strip()
#if not os.path.exists(tmpd):
# exec_comm(['mkdir', tmpd])
#statsvol = tmpd + os.path.sep + 'outvol'
#statsbar = tmpd + os.path.sep + 'outbar'
#overlay command
overlay = 'overlay 1 0 ' + bg_img + ' ' + str(bg_min) + ' ' + str(bg_max) + ' ' + s1_img + ' ' + str(s1_min) + ' ' + str(s1_max) + ' ' + statsbar + ' y ' + statsvol
au.exec_comm (overlay.split())
#slices command
olddir = os.getcwd()
outdir = os.path.dirname(os.path.abspath(ot_img))
