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))