def downsample_channel(image_in,
ch,
resolution_level=-1,
dsfacs=[1, 4, 4, 1, 1],
ismask=False,
output='',
report={}):
"""Downsample an image."""
ods = 'data' if not ismask else 'mask'
# return in case no mask provided
if not image_in:
return None, report, ''
if resolution_level != -1 and not ismask: # we should have an Imaris pyramid
image_in = '{}/DataSet/ResolutionLevel {}'.format(
image_in, resolution_level)
# load data
im = Image(image_in, permission='r')
im.load(load_data=False)
props = im.get_props()
if len(im.dims) > 4:
im.slices[im.axlab.index('t')] = slice(0, 1, 1)
props = im.squeeze_props(props, dim=4)
if len(im.dims) > 3:
im.slices[im.axlab.index('c')] = slice(ch, ch + 1, 1)
props = im.squeeze_props(props, dim=3)
data = im.slice_dataset()
im.close()
# downsample
dsfac = tuple(dsfacs[:len(data.shape)])
if not ismask:
data = downscale_local_mean(data, dsfac).astype('float32')
else:
data = block_reduce(data, dsfac, np.max)
# generate output
props['axlab'] = 'zyx' # FIXME: axlab returns as string-list
props['shape'] = data.shape
props['elsize'] = [es * ds for es, ds in zip(im.elsize[:3], dsfac)]
props['slices'] = None
mo = write_data(data, props, output, ods)
# report data
thr = 1000
meds_mask = data < thr
report['medians'][ods] = get_zyx_medians(data, meds_mask)
c_slcs = {dim: get_centreslice(mo, '', dim) for dim in 'zyx'}
report['centreslices'][ods] = c_slcs
return mo, report, meds_mask
def mergeblocks(
images_in,
dataslices=None,
blocksize=[],
blockmargin=[],
blockrange=[],
blockoffset=[0, 0, 0],
fullsize=[],
is_labelimage=False,
relabel=False,
neighbourmerge=False,
save_fwmap=False,
blockreduce=[],
func='np.amax',
datatype='',
usempi=False,
outputpath='',
save_steps=False,
protective=False,
):
"""Merge blocks of data into a single hdf5 file."""
if blockrange:
images_in = images_in[blockrange[0]:blockrange[1]]
mpi = wmeMPI(usempi)
im = Image(images_in[0], permission='r')
im.load(mpi.comm, load_data=False)
props = im.get_props(protective=protective, squeeze=True)
ndim = im.get_ndim()
props['dtype'] = datatype or props['dtype']
props['chunks'] = props['chunks'] or None
# get the size of the outputfile
# TODO: option to derive fullsize from dset_names?
if blockreduce:
datasize = np.subtract(fullsize, blockoffset)
outsize = [
int(np.ceil(d / np.float(b)))
for d, b in zip(datasize, blockreduce)
]
props['elsize'] = [e * b for e, b in zip(im.elsize, blockreduce)]
else: # FIXME: 'zyx(c)' stack assumed
outsize = np.subtract(fullsize, blockoffset)
if ndim == 4:
outsize = list(outsize) + [im.ds.shape[3]] # TODO: flexible insert
if outputpath.endswith('.ims'):
mo = LabelImage(outputpath)
mo.create(comm=mpi.comm)
else:
props['shape'] = outsize
mo = LabelImage(outputpath, **props)
mo.create(comm=mpi.comm)
mpi.blocks = [{'path': image_in} for image_in in images_in]
mpi.nblocks = len(images_in)
mpi.scatter_series()
# merge the datasets
maxlabel = 0
for i in mpi.series:
block = mpi.blocks[i]
# try:
maxlabel = process_block(block['path'], ndim, blockreduce, func,
blockoffset, blocksize, blockmargin, fullsize,
mo, is_labelimage, relabel, neighbourmerge,
save_fwmap, maxlabel, mpi)
print('processed block {:03d}: {}'.format(i, block['path']))
# except Exception as e:
# print('failed block {:03d}: {}'.format(i, block['path']))
# print(e)
im.close()
mo.close()
return mo
def apply_bias_field_full(image_in,
bias_in,
dsfacs=[1, 64, 64, 1],
in_place=False,
write_to_single_file=False,
blocksize_xy=1280,
outputpath='',
channel=None):
"""single-core in ~200 blocks"""
perm = 'r+' if in_place else 'r'
im = Image(image_in, permission=perm)
im.load(load_data=False)
bf = Image(bias_in, permission='r')
bf.load(load_data=False)
if channel is not None:
im.slices[3] = slice(channel, channel + 1)
if write_to_single_file: # assuming single-channel copied file here
mo = Image(outputpath)
mo.load()
mo.slices[3] = slice(0, 1, 1)
mpi = wmeMPI(usempi=False)
mpi_nm = wmeMPI(usempi=False)
if blocksize_xy:
blocksize = [im.dims[0], blocksize_xy, blocksize_xy, 1, 1]
blockmargin = [0, im.chunks[1], im.chunks[2], 0, 0]
else:
blocksize = im.dims[:3] + [1, 1]
blockmargin = [0] * len(im.dims)
mpi.set_blocks(im, blocksize, blockmargin)
mpi_nm.set_blocks(im, blocksize)
mpi.scatter_series()
for i in mpi.series:
print(i)
block = mpi.blocks[i]
data_shape = list(im.slices2shape(block['slices']))
block_nm = mpi_nm.blocks[i]
it = zip(block['slices'], block_nm['slices'], blocksize, data_shape)
data_shape = list(im.slices2shape(block_nm['slices']))
data_slices = []
for b_slc, n_slc, bs, ds in it:
m_start = n_slc.start - b_slc.start
m_stop = m_start + bs
m_stop = min(m_stop, ds)
data_slices.append(slice(m_start, m_stop, None))
data_slices[3] = block['slices'][3]
data_shape = list(im.slices2shape(data_slices))
# get the fullres image block
im.slices = block['slices']
data = im.slice_dataset().astype('float')
# get the upsampled bias field
bias = get_bias_field_block(bf, im.slices, data.shape)
data /= bias
data = np.nan_to_num(data, copy=False)
if in_place:
im.slices = block_nm['slices']
data = data[tuple(data_slices[:3])].astype(im.dtype)
im.write(data)
elif write_to_single_file:
mo.slices = block_nm['slices']
mo.slices[3] = slice(0, 1, 1)
data = data[tuple(data_slices[:3])].astype(mo.dtype)
mo.write(data)
else:
props = im.get_props()
if len(im.dims) > 4:
props = im.squeeze_props(props, dim=4)
if len(im.dims) > 3:
props = im.squeeze_props(props, dim=3)
props['axlab'] = 'zyx' # FIXME: axlab return as string-list
props['shape'] = bias.shape
props['slices'] = None
props['dtype'] = bias.dtype
mo = Image(block['path'], **props) # FIXME: needs channel
mo.create(comm=mpi.comm)
mo.slices = None
mo.set_slices()
mo.write(data=bias)
mo.close()
im.close()
bf.close()
def cell_segmentation(
plan_path,
memb_path,
dapi_path,
mean_path,
dapi_shift_planes=0,
nucl_opening_footprint=[3, 7, 7],
dapi_filter='median',
dapi_sigma=1,
dapi_dog_sigma1=2,
dapi_dog_sigma2=4,
dapi_thr=0,
sauvola_window_size=[19, 75, 75],
sauvola_k=0.2,
dapi_absmin=500,
dapi_erodisk=0,
dist_max=5,
peaks_size=[11, 19, 19],
peaks_thr=1.0,
peaks_dil_footprint=[3, 7, 7],
compactness=0.80,
memb_filter='median',
memb_sigma=3,
planarity_thr=0.0005,
dset_mask_filter='gaussian',
dset_mask_sigma=50,
dset_mask_thr=1000,
steps=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
outputstem='',
save_steps=False,
):
step = 'segment'
paths = get_paths(plan_path, -1, 0, outputstem, step, save_steps)
report = {
'parameters': locals(),
'paths': paths,
'medians': {},
'centreslices': {}
}
# load images
im_dapi = Image(dapi_path)
im_dapi.load()
nucl_props = im_dapi.get_props()
im_memb = MaskImage(memb_path)
im_memb.load()
memb_props = im_memb.get_props()
im_plan = MaskImage(plan_path)
im_plan.load()
# im_dset_mask = Image(dset_mask_path, permission='r')
# im_dset_mask.load(load_data=False)
im_mean = Image(mean_path)
im_mean.load()
# preprocess dapi channel
# .h5/nucl/dapi<_shifted><_opened><_preprocess>
stage = 'nucleus channel'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/nucl/dapi')
if 0 not in steps:
op = 'reading'
im_dapi_pp = get_image('{}{}'.format(outstem, '_preprocess'))
else:
op = 'processing'
im_dapi_pp = preprocess_nucl(
im_dapi,
dapi_shift_planes,
dapi_filter,
dapi_sigma,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# create a nuclear mask from the dapi channel
# .h5/nucl/dapi<_mask_thr><_sauvola><_mask><_mask_ero>
stage = 'nucleus mask'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/nucl/dapi')
if 1 not in steps:
op = 'reading'
im_dapi_mask = get_image('{}{}'.format(outstem, '_mask_ero'))
else:
op = 'processing'
im_dapi_mask = create_nuclear_mask(
im_dapi_pp,
dapi_thr,
sauvola_window_size,
sauvola_k,
dapi_absmin,
dapi_erodisk,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# create a membrane mask from the membrane mean
# .h5/memb/planarity<_mask>
stage = 'membrane mask'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/memb/planarity')
if 2 not in steps:
op = 'reading'
im_memb_mask = get_image('{}{}'.format(outstem, '_mask'))
else:
op = 'processing'
im_memb_mask = create_membrane_mask(
im_plan,
planarity_thr,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# combine nuclear and membrane mask
# .h5/segm/seeds<_mask>
stage = 'mask combination'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/segm/seeds')
if 3 not in steps:
op = 'reading'
im_nucl_mask = get_image('{}{}'.format(outstem, '_mask'))
else:
op = 'processing'
im_nucl_mask = combine_nucl_and_memb_masks(
im_memb_mask,
im_dapi_mask,
nucl_opening_footprint,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# find seeds for watershed
stage = 'nucleus detection'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/segm/seeds')
if 4 not in steps:
op = 'reading'
im_dt = get_image('{}{}'.format(outstem, '_edt'))
im_peaks = get_image('{}{}'.format(outstem, '_peaks'))
# .h5/segm/seeds<_edt><_mask_distmax><_peaks><_peaks_dil>
else:
op = 'processing'
im_dt, im_peaks = define_seeds(
im_nucl_mask,
im_memb_mask,
im_dapi_pp,
dapi_dog_sigma1,
dapi_dog_sigma2,
dist_max,
peaks_size,
peaks_thr,
peaks_dil_footprint,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# preprocess membrane mean channel
# .h5/memb/preprocess<_smooth>
stage = 'membrane channel'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/memb/mean')
if 5 not in steps:
op = 'reading'
im_memb_pp = get_image('{}{}'.format(outstem, '_smooth'))
else:
op = 'processing'
im_memb_pp = preprocess_memb(
im_memb,
memb_filter,
memb_sigma,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# perform watershed from the peaks to fill the nuclei
# .h5/segm/labels<_edt><_memb>
stage = 'watershed'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/segm/labels')
if 6 not in steps:
op = 'reading'
im_ws = get_image('{}{}'.format(outstem, '_memb'), imtype='Label')
else:
op = 'processing'
im_ws = perform_watershed(
im_peaks,
im_memb_pp,
im_dt,
peaks_thr,
memb_sigma,
memb_filter,
compactness,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# generate a dataset mask from the mean of all channels
# .h5/mean<_smooth><_mask>
stage = 'dataset mask'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/mean')
if 7 not in steps:
op = 'reading'
im_dset_mask = get_image('{}{}'.format(outstem, '_mask'),
imtype='Mask')
else:
op = 'processing'
im_dset_mask = create_dataset_mask(
im_mean,
filter=dset_mask_filter,
sigma=dset_mask_sigma,
threshold=dset_mask_thr,
outstem=outstem,
save_steps=save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# filter the segments with the dataset mask
# .h5/segm/labels<_memb_del>
# .h5/mask
stage = 'segment filter'
t = time.time()
outstem = '{}.h5{}'.format(outputstem, '/segm/labels')
if 8 not in steps:
im_ws_pp = get_image('{}{}'.format(outstem, '_memb_del'),
imtype='Label')
else:
op = 'processing'
im_ws_pp = segmentation_postprocessing(
im_dset_mask,
im_ws,
outstem,
save_steps,
)
elapsed = time.time() - t
print('{} ({}) took {:1f} s'.format(stage, op, elapsed))
# write report
generate_report('{}.h5/{}'.format(outputstem, 'mean_mask'))
return im_ws_pp