def alignRec(record, template=template, bgfile='image_Ch1.nrrd', alignSet='', threshold=0.6):
record = checkDir(record)
record['last_host'] = host
print 'Finalising alignment for: ' + record['name']
# bgfile = record['original_nrrd'][('Ch' + str(record['background_channel']) + '_file')]
record['aligned_bg'], r = cmtk.align(bgfile, template=template, settings=alignSet)
record['aligned_avgslice_score'] = str(
ci.rateOne(record['aligned_bg'], results=None, methord=slicescore.avgOverlapCoeff, template=template))
record['aligned_slice_score'] = str(
ci.rateOne(record['aligned_bg'], results=None, methord=slicescore.OverlapCoeff, template=template))
record['aligned_score'] = str(
np.mean([np.float128(record['aligned_avgslice_score']), np.float128(record['aligned_slice_score'])]))
# Note: np.float128 array score converted to string as mongoDB only supports float(64/32 dependant on machine).
record['aligned_bg'] = str(record['aligned_bg']).replace(tempfolder, '')
print 'Result: ' + record['aligned_score']
if record['aligned_score'] > threshold:
record['alignment_stage'] = 6
print 'Passed!'
else:
record['alignment_stage'] = 0
print 'Failed!'
if r > 0:
print 'Error Code:' + str(r)
record['alignment_stage'] = 0
record['max_stage'] = 6
return record
def initialRec(record, template=template, init_threshold=0.3, bgfile='image_Ch1.nrrd', alignSet='',
initialSet='--principal-axes'):
start = datetime.datetime.now()
record = checkDir(record)
record['last_host'] = host
print 'Staring initial alignment for: ' + record['name']
# bgfile = record['original_nrrd'][('Ch' + str(record['background_channel']) + '_file')]
record['temp_initial_nrrd'], r = cmtk.align(bgfile, cmtk.initial(bgfile, template=template, mode=initialSet)[0],
imageOUT=tempfolder + record['name'] + '_initial.nrrd',
template=template, settings=alignSet)
record['temp_initial_score'] = str(ci.rateOne(record['temp_initial_nrrd'], results=None, template=template))
# Note: np.float128 array score converted to string as mongoDB only supports float(64/32 dependant on machine).
record['temp_initial_nrrd'] = str(record['temp_initial_nrrd']).replace(tempfolder, '')
print 'Result: ' + record['temp_initial_score']
totaltime = datetime.datetime.now() - start
if record['temp_initial_score'] > init_threshold:
record['alignment_stage'] = 3
else:
record['alignment_stage'] = 0
if r > 0:
record['alignment_stage'] = 1002
else:
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Initial alignment performed by ' + host + ' in ' + str(totaltime) + ' scoring ' + record[
'temp_initial_score'] + '/' + str(init_threshold)
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Initial alignment performed by ' + host + ' in ' + str(totaltime) + ' scoring ' + record[
'temp_initial_score'] + '/' + str(init_threshold)
record['max_stage'] = 3
return record
def alignRem(record, template=template, chfile='image_Ch1.nrrd', alignSet=''):
record = checkDir(record)
print 'Aligning signal, etc. for: ' + record['name']
record['last_host'] = host
# bgfile = record['original_nrrd'][('Ch' + str(record['background_channel']) + '_file')]
# sgfile = record['original_nrrd'][('Ch' + str(record['signal_channel']) + '_file')]
# a=0
# for i in range(1,6):
# if not i == record['background_channel']:
# if i == record['signal_channel']:
if record['ac1_channel'] < 1:
for i in range(1, 4):
print 'Checking for AC1 in channel ' + str(i)
if not (i == int(record['signal_channel']) or i == int(record['background_channel'])):
record['ac1_channel'] = i
print 'Set AC1 Channel to ' + str(i)
r = 0
sgchan = '_Ch' + str(record['signal_channel'])
bgchan = '_Ch' + str(record['background_channel'])
acchan = '_Ch' + str(record['ac1_channel'])
chfile = chfile.replace(bgchan, acchan).replace(acchan, sgchan)
if os.path.isfile(chfile):
record['aligned_sg'], r = cmtk.align(chfile, xform=chfile.replace(sgchan + '.nrrd', bgchan + '_warp.xform'),
template=template, settings=alignSet)
record['alignment_stage'] = 7
record['max_stage'] = 7
record['aligned_sg'] = str(record['aligned_sg']).replace(tempfolder, '')
else:
print chfile + ' not found'
r = 5
chfile = chfile.replace(sgchan, acchan)
if os.path.isfile(chfile):
record['aligned_ac1'], r = cmtk.align(chfile, xform=chfile.replace(acchan + '.nrrd', bgchan + '_warp.xform'),
template=template, settings=alignSet)
record['max_stage'] = 7
record['aligned_ac1'] = str(record['aligned_ac1']).replace(tempfolder, '')
else:
print chfile + ' not found'
if r > 0:
print 'Error code:' + str(r)
record['alignment_stage'] = 0
return record