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 affineRec(record, template=template, bgfile="image_Ch1.nrrd", affineSet="--dofs 6,9 --auto-multi-levels 4"):
start = datetime.datetime.now()
record = checkDir(record)
print "Staring affine alignment for: " + record["name"]
# bgfile = record['original_nrrd'][('Ch' + str(record['background_channel']) + '_file')]
affine, r = cmtk.affine(bgfile, template=template, scale=affineSet)
print affine
totaltime = datetime.datetime.now() - start
record["alignment_stage"] = 4
if r > 0:
record["alignment_stage"] = 1003
else:
if record["notes"] is None:
record["notes"] = time.strftime("%c") + " Affine alignment performed by " + host + " in " + str(totaltime)
else:
record["notes"] = (
record["notes"]
+ "\n"
+ time.strftime("%c")
+ " Affine alignment performed by "
+ host
+ " in "
+ str(totaltime)
)
if r == 99:
record["alignment_stage"] = 2
record["max_stage"] = 4
record["last_host"] = host
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
def warpRec(record, template=template, bgfile='image_Ch1.nrrd',
warpSet='--grid-spacing 80 --exploration 30 --coarsest 4 --accuracy 0.2 --refine 4 --energy-weight 1e-1'):
start = datetime.datetime.now()
record = checkDir(record)
print 'Staring warping alignment for: ' + record['name']
# bgfile = record['original_nrrd'][('Ch' + str(record['background_channel']) + '_file')]
warp, r = cmtk.warp(bgfile, template=template, settings=warpSet)
totaltime = datetime.datetime.now() - start
record['alignment_stage'] = 5
if r > 0:
record['alignment_stage'] = 1004
else:
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Warp alignment performed by ' + host + ' in ' + str(totaltime)
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Warp alignment performed by ' + host + ' in ' + str(totaltime)
if r == 99: record['alignment_stage'] = 2
record['max_stage'] = 5
record['last_host'] = host
return record
def convRec(record):
try:
if not 'loading_host' in record:
record['loading_host'] = 'roberts-mbp'
if not record['loading_host'] == host:
print 'Warning: ' + host + ' is not the loading host (' + record['loading_host'] + ')'
if str(record['original_path']).endswith(os.path.sep):
file = record['original_path'] + record['name'] + record['original_ext']
else:
file = record['original_path'] + os.path.sep + record['name'] + record['original_ext']
print 'Converting ' + file
if (os.path.exists(file) or os.path.exists(file + '.gz')):
record['last_host'] = host
if (os.path.exists(file + '.gz') and (not os.path.exists(file))):
check_call(['gzip', '-d', file + '.gz'])
if '.gz' in file:
check_call(['gzip', '-df', file])
file = str(file).replace('.gz', '')
if str(record['original_ext']) == '.gz':
record['name'] = str(os.path.splitext(os.path.basename(file))[0])
record['original_ext'] = str(os.path.splitext(os.path.basename(file))[1])
print 'Opening file: ' + file + '...'
tif = TiffFile(file)
image = tif.asarray()
print 'Converting file: ' + file + '...'
record = checkDir(record)
if tif.is_lsm:
metadata = tif[0].cz_lsm_scan_information
voxelZ = metadata['plane_spacing']
voxelY = metadata['line_spacing']
voxelX = metadata['sample_spacing']
header = {}
header['encoding'] = 'gzip'
header['space directions'] = [[float(voxelX), 0.0, 0.0], [0.0, float(voxelY), 0.0],
[0.0, 0.0, float(voxelZ)]]
header['space units'] = ['"microns"', '"microns"', '"microns"']
# header['keyvaluepairs'] = dict(metadata)
# print header
else:
metadata = tif[0].image_description
# metadata = json.loads(metadata.decode('utf-8'))
# voxel = metadata['Voxel size']
# TBD: resolve zoxel size!
voxelZ = 0.5
voxelY = 0.5
voxelX = 0.5
#temp fix for zebrafish:
if (record['settings_id'] == 10):
voxelZ = 1
voxelY = 1
voxelX = 1
header = {}
header['encoding'] = 'gzip'
header['space directions'] = [[float(voxelX), 0.0, 0.0], [0.0, float(voxelY), 0.0],
[0.0, 0.0, float(voxelZ)]]
header['space units'] = ['"px"', '"px"', '"px"']
print(image.shape, image.dtype)
if image.ndim > 4:
sh = np.array(image.shape)
rmdim = np.argmin(sh)
if sh[rmdim] > 1:
sh[rmdim] = np.max(sh)
rmdim = np.argmin(sh)
image = np.max(image, axis=rmdim)
print 'slimmed down to:'
print(image.shape, image.dtype)
print metadata
# TBD: add voxel size data
# header['keyvaluepairs'] = dict(metadata)
tif.close()
check_call(['gzip', '-f', file])
image = np.squeeze(image)
sh = np.array(np.shape(image))
ch = np.argmin(sh)
iy = np.argmax(sh)
sh[iy] = 0
ix = np.argmax(sh)
sh[ix] = 0
iz = np.argmax(sh)
sh = np.shape(image)
# move channel to last axis:
image = np.swapaxes(image, ch, -1)
# move smalest (Z) axis to last axis before channel:
image = np.swapaxes(image, iz, -2)
# swap X & Y to match NRRD standard order for saving:
image = np.swapaxes(image, 0, 1)
print record['name'] + record['original_ext'] + ' - ' + str(np.shape(image))
rt = 0
mt = 0
sg = 0
bg = 0
cur.execute(
"SELECT system_template.orientation FROM system_template, system_setting, images_alignment WHERE images_alignment.id = %s AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id",
[record['id']])
tempOrien = cur.fetchone()[0]
cur.execute(
"SELECT system_setting.auto_balance_th FROM system_template, system_setting, images_alignment WHERE images_alignment.id = %s AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id",
[record['id']])
tempTresh = float(cur.fetchone()[0])
if 'orig_orientation' not in record.keys():
if sh[ch] == 2:
record['orig_orientation'] = comp_orien[tempOrien]
else:
record['orig_orientation'] = 'right-posterior-inferior' # needs to be set at load
if record['orig_orientation'] == '':
if sh[ch] == 2:
record['orig_orientation'] = comp_orien[tempOrien]
else:
record['orig_orientation'] = 'right-posterior-inferior' # needs to be set at load
header['space'] = comp_orien[tempOrien]
for c in xrange(0, sh[ch]):
upd = {}
chan, Nbound, hist = ab.AutoBalance(np.squeeze(image[:, :, :, c]), threshold=tempTresh, background=0)
print 'Ch' + str(c + 1) + ' - ' + str(np.shape(chan))
Sname = tempfolder + record['name'] + '_Ch' + str(c + 1) + '.nrrd'
if not record['orig_orientation'] == comp_orien[tempOrien]:
chan = ro.reorientate(np.uint8(chan), curOr=record['orig_orientation'],
targOr=comp_orien[tempOrien])
else:
chan = np.uint8(chan)
if not ((record['crop_xyz'] is None) or (record['crop_xyz'] is '')):
cut = map(int, str(record['crop_xyz']).replace('[', '').replace(']', '').split(','))
cut = np.array(cut)
if np.sum(cut) > 0:
print 'cropping: (' + str(cut) + ')...'
sh = np.shape(chan)
print sh
chan = chan[cut[0]:sh[0] - cut[1], cut[2]:sh[1] - cut[3], cut[4]:sh[2] - cut[5]]
print np.shape(chan)
print 'saving...'
nrrd.write(Sname, chan, options=header)
upd.update(
{'image_id': record['id'], 'channel': + int(c + 1), 'file': str(Sname).replace(tempfolder, ''),
'pre_histogram': list(hist), 'new_min': int(Nbound['min']), 'new_max': int(Nbound['max'])})
print str(upd)
cur.execute(
"SELECT count(*) FROM images_original_nrrd WHERE image_id = %(image_id)s AND channel = %(channel)s",
upd)
r = cur.fetchone()[0]
if r > 0:
cur.execute(
"UPDATE images_original_nrrd SET file = %(file)s, pre_hist = %(pre_histogram)s, new_min = %(new_min)s, new_max = %(new_max)s, is_index = False WHERE image_id = %(image_id)s AND channel = %(channel)s",
upd)
cur.connection.commit()
else:
cur.execute(
"INSERT INTO images_original_nrrd (image_id, channel, file, pre_hist, new_min, new_max, is_index) VALUES (%(image_id)s, %(channel)s, %(file)s, %(pre_histogram)s, %(new_min)s, %(new_max)s, False)",
upd)
cur.connection.commit()
try:
os.chmod(Sname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
except:
pass
ct = sum(chan[chan > 20])
if ct > rt:
rt = ct
bg = c + 1
if mt == 0:
mt = ct
sg = c + 1
if ct < mt:
mt = ct
sg = c + 1
print 'BG: ' + str(bg) + ', SG: ' + str(sg)
if record['background_channel'] == 0:
record['background_channel'] = bg
if record['signal_channel'] == 0:
record['signal_channel'] = sg
record['alignment_stage'] = 2
# record.update({'original_nrrd': upd})
record['max_stage'] = 2
# collection.save(record)
print 'conversion complete.'
del upd, hist, chan, Nbound, tif, image, sh, ch, iy, ix, iz, Sname, rt, bg, ct, mt, sg
else:
record['alignment_stage'] = 1001
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Error finding file ' + file + ' on ' + host
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Error finding file ' + file + ' on ' + host
except Exception, e:
print str(e)
record['alignment_stage'] = 0
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Error with handling uploaded file by ' + host
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Error with handling uploaded file by ' + host
