def _write_cremi_data(self, cremi_data, path, mode="a", **kwargs):
raw_vol = Volume(cremi_data.raw_data, resolution=cremi_data.res_list)
clefts_vol = Volume(
np.zeros(cremi_data.raw_data.shape, dtype=np.uint64),
resolution=cremi_data.res_list,
)
annotations = Annotations()
for annotation_tuple in cremi_data.annotation_tuples:
annotations.add_annotation(*annotation_tuple)
annotations.set_pre_post_partners(*cremi_data.annotation_partners)
def key(id_, **kwargs):
return (kwargs["type"], -id_)
annotations.sort(key_fn=key, reverse=True)
with closing(CremiFile(path, mode)) as f:
f.write_raw(raw_vol)
f.write_clefts(clefts_vol)
f.write_annotations(annotations)
f.h5file.attrs["project_offset"] = cremi_data.offset_nm.to_list()
f.h5file.attrs["stack_offset"] = cremi_data.offset_px.to_list()
for key, value in kwargs.items():
f.h5file.attrs[key] = value
def cremi_score(gt, seg, return_all_scores=False, border_threshold=None):
if cremi is None:
raise ImportError("The cremi package is necessary to run cremi_score()")
# # the zeros must be kept in the gt since they are the ignore label
gt = vigra.analysis.labelVolumeWithBackground(gt.astype(np.uint32))
# seg = vigra.analysis.labelVolume(seg.astype(np.uint32))
seg = np.array(seg)
seg = np.require(seg, requirements=['C'])
# Make sure that all labels are strictly positive:
seg = seg.astype('uint32')
# FIXME: it seems to have some trouble with label 0 in the segmentation:
seg += 1
gt = np.array(gt)
gt = np.require(gt, requirements=['C'])
gt = (gt - 1).astype('uint32')
# assert gt.min() >= -1
gt_ = Volume(gt)
seg_ = Volume(seg)
metrics = NeuronIds(gt_, border_threshold=border_threshold)
arand = metrics.adapted_rand(seg_)
vi_s, vi_m = metrics.voi(seg_)
cs = np.sqrt(arand * (vi_s + vi_m))
# cs = (vi_s + vi_m + arand) / 3.
if return_all_scores:
return {'cremi-score': cs.item(), 'vi-merge': vi_m.item(), 'vi-split': vi_s.item(), 'adapted-rand': arand.item()}
else:
return cs
def check_ccs():
binary = z5py.File('./binary_volume.n5')['data'][:]
ccs_vi = vigra.analysis.labelVolumeWithBackground(binary)
ccs = z5py.File('./ccs.n5')['data'][:]
print("Start comparison")
metric = NeuronIds(Volume(ccs_vi))
print("Arand", metric.adapted_rand(Volume(ccs)))
def eval_block(block_id, res_prefix):
gt = Volume(vigra.readHDF5('/home/papec/Work/neurodata_hdd/fib25/gt/gt_block%i.h5' % block_id,
'data'))
res = Volume(vigra.readHDF5('%s_%i.h5' % (res_prefix, block_id), 'data'))
metrics = NeuronIds(gt)
are = metrics.adapted_rand(res)
vi_s, vi_m = metrics.voi(res)
return are, vi_s, vi_m
def evaluate(gt, segmentation):
gt, _, _ = vigra.analysis.relabelConsecutive(gt, start_label=1)
evaluate = NeuronIds(Volume(gt))
segmentation = Volume(segmentation)
vi_split, vi_merge = evaluate.voi(segmentation)
ri = evaluate.adapted_rand(segmentation)
return vi_split, vi_merge, ri
def cremi_scores(seg, gt):
gt[gt == 0] = -1
seg = Volume(seg)
metric = NeuronIds(Volume(gt))
vis, vim = metric.voi(seg)
are = metric.adapted_rand(seg)
cs = (are + vis + vim) / 3
return {
'cremi-score': cs,
'vi-merge': vim,
'vi-split': vis,
'adapted-rand': are
}
def cremi_scores(seg, gt):
gt[gt == 0] = -1
seg = Volume(seg)
metric = NeuronIds(Volume(gt))
vis, vim = metric.voi(seg)
are = metric.adapted_rand(seg)
# cremi uses the geometric mean of rand and vi !
cs = sqrt(are * (vis + vim))
return {
'cremi-score': cs,
'vi-merge': vim,
'vi-split': vis,
'adapted-rand': are
}
def make_groundtruth(correct_resolution = True):
# fill gt with ignore labels (for whatever reason this is not 0...)
gt = 0xffffffffffffffff * np.ones(shape, dtype = 'uint64')
# make one gt synapse
rr, cc = circle(20, 20, syn_radius)
gt[0, rr, cc] = 1
if correct_resolution:
vol = Volume(gt, resolution = (40.,4.,4.) )
gt_name = 'gt_correct_res.h5'
else:
vol = Volume(gt)
gt_name = 'gt_incorrect_res.h5'
cremi_f = io.CremiFile('../data/%s' % gt_name, 'w')
cremi_f.write_clefts(vol)
return cremi_f
def _populate_clefts(self, unpadded_shape_px, padding_low_px,
skip_if_exists):
"""
Parameters
----------
unpadded_shape_px : CoordZYX
padding_low_px : CoordZYX
skip_if_exists
Returns
-------
"""
if self.has_clefts():
if skip_if_exists:
logger.info("Cleft data already exists, skipping")
return
else:
raise RuntimeError("Cleft data already exists")
logger.debug("generating cleft volume")
cleft_volume = Volume(
np.zeros(unpadded_shape_px.to_list(), dtype=np.uint64),
resolution=self.resolution,
offset=(padding_low_px * CoordZYX(self.resolution)).to_list(),
)
logger.debug("writing clefts")
with self:
self._cremi_file.write_clefts(cleft_volume)
self._cremi_file.h5file["volumes/labels/clefts"].attrs[
"refreshed_on"] = self.timestamp
def make_seg_submission(seg_valume_dict):
submission_folder = 'submission'
if not os.path.exists(submission_folder):
os.makedirs(submission_folder)
for name, seg_v in seg_valume_dict.iteritems():
seg_v = seg_v.astype(np.uint64)
neuron_ids = Volume(seg_v,
resolution=(40.0, 4.0, 4.0),
comment="Second submission in 2018")
file = CremiFile(submission_folder + '/' + name + '.hdf', "w")
file.write_neuron_ids(neuron_ids)
def make_predictions(fp_pos, correct_resolution = True):
prediction = 0xffffffffffffffff * np.ones(shape, dtype = 'uint64')
# make tp synapse prediction
rr, cc = circle(22, 18, syn_radius)
prediction[0, rr, cc] = 1
# make fp synapse prediction
rr, cc = circle(fp_pos[1], fp_pos[2], syn_radius)
prediction[fp_pos[0], rr, cc] = 2
if correct_resolution:
vol = Volume(prediction, resolution = (40.,4.,4.) )
prediction_name = 'prediction_correct_res_%s.h5' % '_'.join(map(str, fp_pos))
else:
vol = Volume(prediction)
prediction_name = 'prediction_incorrect_res_%s.h5' % '_'.join(map(str, fp_pos))
cremi_f = io.CremiFile('../data/%s' % prediction_name, 'w')
cremi_f.write_clefts(vol)
return cremi_f
def prepare_submission(sample,
path_segm,
inner_path_segm,
path_bbox_slice,
ds_factor=None):
"""
:param path_segm:
:param inner_path_segm:
:param path_bbox_slice: path to the csv file
:param ds_factor: for example (1, 2, 2)
"""
segm = segm_utils.readHDF5(path_segm, inner_path_segm)
bbox_data = np.genfromtxt(path_bbox_slice, delimiter=';', dtype='int')
assert bbox_data.shape[0] == segm.ndim and bbox_data.shape[1] == 2
# bbox_slice = tuple(slice(b_data[0], b_data[1]) for b_data in bbox_data)
if ds_factor is not None:
assert len(ds_factor) == segm.ndim
segm = zoom(segm, ds_factor, order=0)
padding = tuple(
(slc[0], shp - slc[1])
for slc, shp in zip(bbox_data, shape_padded_aligned_datasets[sample]))
padded_segm = np.pad(segm, pad_width=padding, mode="constant")
# Apply Constantin crop and then backalign:
cropped_segm = padded_segm[magic_bboxes[sample]]
tmp_file = path_segm.replace(".h5", "_submission_temp.hdf")
backalign_segmentation(sample,
cropped_segm,
tmp_file,
key="temp_data",
postprocess=False)
# Create a CREMI-style file ready to submit:
final_submission_path = path_segm.replace(".h5", "_submission.hdf")
file = CremiFile(final_submission_path, "w")
# Write volumes representing the neuron and synaptic cleft segmentation.
backaligned_segm = segm_utils.readHDF5(tmp_file, "temp_data")
neuron_ids = Volume(backaligned_segm.astype('uint64'),
resolution=(40.0, 4.0, 4.0),
comment="Emb-submission")
file.write_neuron_ids(neuron_ids)
file.close()
os.remove(tmp_file)
def agglomerate_sp_eval(ws_path, gt_path, prob_path):
probs = vigra.readHDF5(prob_path, 'data')
ws = vigra.readHDF5(ws_path, 'data')
n_nodes = int(ws.max()) + 1
rag = nrag.gridRag(ws, numberOfLabels=n_nodes)
# _, node_sizes = np.unique(ws, return_counts=True)
# edge_sizes = nrag.accumulateEdgeMeanAndLength(rag, np.zeros(rag.shape, dtype='float32'))[:, 1]
graph = nifty.graph.undirectedGraph(n_nodes)
graph.insertEdges(rag.uvIds())
gt = Volume(vigra.readHDF5(gt_path, 'data'))
# node_factor = [0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1][::-1]
node_factor = [.025, .05, .075, .1, .15, .2, .25, .4, .5]
for nf in node_factor:
# FIXME agglomerative clustering segfaults
# n_target_nodes = int(nf * n_nodes)
# agglomerator = cseg.AgglomerativeClustering(n_target_nodes)
# node_labeling = agglomerator(graph, probs, edge_sizes=edge_sizes, node_sizes=node_sizes)
agglomerator = cseg.MalaClustering(nf)
node_labeling = agglomerator(graph, probs)
vigra.analysis.relabelConsecutive(node_labeling, out=node_labeling)
seg = nrag.projectScalarNodeDataToPixels(rag, node_labeling)
seg = Volume(seg)
metrics = NeuronIds(gt)
vi_s, vi_m = metrics.voi(seg)
are = metrics.adapted_rand(seg)
print("Evaluation for reduction", nf)
print("Voi - Split ", vi_s)
print("Voi - Merge ", vi_m)
print("Adapted Rand", are)
print("N-Nodes:", int(node_labeling.max() + 1), '/', n_nodes)
def gt_projection(block_id):
ws_path = '/home/papec/Work/neurodata_hdd/fib25/watersheds/watershed_block%i.h5' % block_id
ws = vigra.readHDF5(ws_path, 'data')
ws = vigra.analysis.labelVolume(ws.astype('uint32'))
gt = vigra.readHDF5('/home/papec/Work/neurodata_hdd/fib25/gt/gt_block%i.h5' % block_id,
'data')
rag = nrag.gridRag(ws, numberOfLabels=int(ws.max()) + 1)
labeling = nrag.gridRagAccumulateLabels(rag, gt)
projected = Volume(nrag.projectScalarNodeDataToPixels(rag, labeling))
metrics = NeuronIds(Volume(gt))
vi_s, vi_m = metrics.voi(projected)
are = metrics.adapted_rand(projected)
print(vi_s)
print(vi_m)
print(are)
print()
os.remove(ws_path)
vigra.writeHDF5(ws, ws_path, 'data', compression='gzip')
def cremi_score(gt,
seg,
return_all_scores=True,
b_thresh=2,
data_resolution=(1.0, 1.0, 1.0)):
"""compute cremi scores from np.array"""
if len(gt.shape) == 2:
gt = gt[None, :, :]
seg = seg[None, :, :]
gt_ = Volume(gt, resolution=data_resolution)
seg_ = Volume(seg, resolution=data_resolution)
metrics = NeuronIds(gt_, b_thresh)
arand = metrics.adapted_rand(seg_)
vi_s, vi_m = metrics.voi(seg_)
# official cremi score
cs = np.sqrt(vi_s * (vi_m + arand))
if return_all_scores:
return cs, vi_s, vi_m, arand
else:
return cs
def _populate_raw(self, padded_offset_from_stack_px, padded_shape_px,
skip_if_exists):
"""
Parameters
----------
padded_offset_from_stack_px : CoordZYX
padded_shape_px : CoordZYX
skip_if_exists
Returns
-------
"""
if self.has_raw():
if skip_if_exists:
logger.info("Raw data already exists, skipping")
return
else:
raise RuntimeError("Raw data already exists")
logger.debug("reading raw volume")
raw_data = self.get_raw(padded_offset_from_stack_px, padded_shape_px)
raw_volume = Volume(raw_data, resolution=self.resolution)
logger.debug("writing raw volume")
with self:
self._cremi_file.write_raw(raw_volume)
self._cremi_file.h5file["volumes/raw"].attrs[
"data_source"] = self.data_source
self._cremi_file.h5file["volumes/raw"].attrs[
"populated_on"] = self.timestamp
self._cremi_file.h5file.attrs["roi_offset_from_stack"] = (
padded_offset_from_stack_px *
CoordZYX(self.resolution)).to_list()
random.randint(0, 100))
annotations.add_annotation(id, "presynaptic_site", location)
for id in [4, 5, 6, 7]:
location = (random.randint(0, 100), random.randint(0, 100),
random.randint(0, 100))
annotations.add_annotation(id, "postsynaptic_site", location)
for (pre, post) in [(0, 4), (1, 5), (2, 6), (3, 7)]:
annotations.set_pre_post_partners(pre, post)
annotations.add_comment(6, "unsure")
# Open a file for writing (deletes previous file, if exists)
file = CremiFile("example.hdf", "w")
# Write the raw volume. This is given here just for illustration. For your
# submission, you don't need to store the raw data. We have it already.
raw = Volume(np.zeros((10, 100, 100), dtype=np.uint8),
resolution=(40.0, 4.0, 4.0))
file.write_raw(raw)
# Write volumes representing the neuron and synaptic cleft segmentation.
neuron_ids = Volume(np.ones((10, 100, 100), dtype=np.uint64),
resolution=(40.0, 4.0, 4.0),
comment="just ones")
clefts = Volume(np.zeros((10, 100, 100), dtype=np.uint64),
resolution=(40.0, 4.0, 4.0),
comment="just zeros")
file.write_neuron_ids(neuron_ids)
file.write_clefts(clefts)
# Write synaptic partner annotations.
file.write_annotations(annotations)
def roi_and_rand_general(
sample, half, defect_correct, project_folder,
source_folder,
result_file, caching=False, debug=False
):
print '\nEvaluating spl{}_z{}'.format(sample, half)
print 'Result file: {}'.format(result_file)
experiment_folder = os.path.join(project_folder, 'spl{}_z{}/'.format(sample, half))
if caching:
cache_filepath = os.path.join(
experiment_folder,
re.sub('.h5$', '', result_file) + '_roi_and_rand_cache.pkl'
)
else:
cache_filepath = None
if caching and os.path.isfile(cache_filepath):
with open(cache_filepath, mode='r') as f:
voi_split, voi_merge, adapted_rand = pickle.load(f)
else:
if defect_correct:
defect_correct_str = '_defect_correct'
else:
defect_correct_str = ''
mc_result_key = 'z/{}/data'.format(half)
# # Load stuff
# source_folder = '/mnt/localdata02/jhennies/neuraldata/cremi_2016/170321_resolve_false_merges/'
# # TODO: Change here when switching sample
# ref_result_filepath = os.path.join(source_folder, 'cremi.spl{}.train.mcseg_betas.crop.axes_xyz.split_z.h5'.format(sample))
# # TODO: Change here when switching half
# ref_result_key = 'z/{}/beta_0.5'.format(half)
gt_filepath = os.path.join(source_folder, 'cremi.spl{}.train.raw_neurons{}.crop.axes_xyz.split_z.h5'.format(sample, defect_correct_str))
gt_key = 'z/{}/neuron_ids'.format(half)
# ref_result, _, _ = vigra.analysis.relabelConsecutive(vigra.readHDF5(ref_result_filepath, ref_result_key), start_label=1, keep_zeros=True)
if not debug:
gt = vigra.readHDF5(gt_filepath, gt_key)
vol_gt = Volume(gt)
neuron_ids_evaluation = NeuronIds(vol_gt)
mc_result_filepath = os.path.join(experiment_folder, result_file)
if not debug:
# Evaluate baseline
mc_result = vigra.readHDF5(mc_result_filepath, mc_result_key)
vol_mc_result = Volume(mc_result)
(voi_split, voi_merge) = neuron_ids_evaluation.voi(vol_mc_result)
adapted_rand = neuron_ids_evaluation.adapted_rand(vol_mc_result)
else:
voi_split = 1.09
voi_merge = 0.70
adapted_rand = 0.23
if caching:
with open(cache_filepath, mode='w') as f:
pickle.dump((voi_split, voi_merge, adapted_rand), f)
print "\tvoi split : " + str(voi_split)
print "\tvoi merge : " + str(voi_merge)
print "\tadapted RAND: " + str(adapted_rand)
return (voi_split, voi_merge, adapted_rand)
def write_multicremi(self, rows, path, mode="w-"):
offset_shapes = []
for _, row in rows.iterrows():
offset_px, shape_px = self.row_to_offset_shape_px(row)
offset_shapes.append(
(np.array(offset_px.to_list()), np.array(shape_px.to_list())))
super_offset_px, super_shape_px = get_superroi(*offset_shapes)
super_offset_nm = super_offset_px * RESOLUTION.to_list(
) + TRANSLATION.to_list()
raw_data = np.zeros(super_shape_px, dtype=np.uint8)
cleft_data = np.zeros(super_shape_px, dtype=np.uint64)
res_list = RESOLUTION.to_list()
id_gen = IdGenerator()
for col in [
"conn_id", "pre_tnid", "post_tnid", "pre_skid", "post_skid"
]:
id_gen.exclude.update(int(item) for item in rows[col])
annotations = Annotations()
zipped = list(zip(rows.iterrows(), offset_shapes))
pre_to_conn = dict()
for (_, row), (offset_px, shape_px) in tqdm(zipped,
desc="fetching data"):
raw_slicing = tuple(
slice(o - sup_o, o - sup_o + s)
for sup_o, o, s in zip(super_offset_px, offset_px, shape_px))
raw_data[raw_slicing] = self.get_raw(CoordZYX(offset_px),
CoordZYX(shape_px))
conn_zyx = -super_offset_nm + [row["conn_" + dim] for dim in "zyx"]
post_zyx = -super_offset_nm + [
row["post_tn_" + dim] for dim in "zyx"
]
post_id = int(row["post_tnid"])
pre_zyx = make_presynaptic_loc(conn_zyx, post_zyx,
EXTRUSION_FACTOR)
pre_id = id_gen.next()
pre_to_conn[pre_id] = int(row["conn_id"])
annotations.add_annotation(pre_id, "presynaptic_site",
list(pre_zyx))
annotations.add_annotation(post_id, "postsynaptic_site",
list(post_zyx))
annotations.set_pre_post_partners(pre_id, post_id)
pre_to_conn_arr = np.array(sorted(pre_to_conn.items()),
dtype=np.uint64)
logger.info("writing data")
with closing(CremiFile(path, mode)) as f:
f.write_raw(Volume(raw_data, resolution=res_list))
f.write_clefts(Volume(cleft_data, resolution=res_list))
f.write_annotations(annotations)
f.h5file.attrs["project_offset"] = list(super_offset_nm)
f.h5file.attrs["stack_offset"] = list(super_offset_px)
f.h5file.attrs["annotation_version"] = ANNOTATION_VERSION
f.h5file.attrs["next_id"] = id_gen.next()
ds = f.h5file.create_dataset(Dataset.PRE_TO_CONN,
data=pre_to_conn_arr)
ds.attrs["explanation"] = PRE_TO_CONN_EXPL
rows.to_hdf(path, "tables/connectors")
def write_monolithic_cremi(self, df, path, mode="a"):
# todo: unfinished
df = df.copy()
xmax, ymax = -1, -1
z_total = 0
offsets = dict()
logger.info("calculating ROIs")
for idx, row in tqdm(df.iterrows(), total=len(df)):
if z_total:
z_total += 3
offset_px, shape_px = self.row_to_offset_shape_px(row)
offset_nm = offset_px * RESOLUTION + TRANSLATION
ymax = max(shape_px["y"], ymax)
xmax = max(shape_px["x"], xmax)
z_total += shape_px["z"]
offsets[idx] = {
"offset_px": offset_px,
"shape_px": shape_px,
"offset_nm": offset_nm,
}
raw = np.zeros((z_total, ymax, xmax), dtype=np.uint8)
divider = np.ones((3, ymax, xmax), dtype=np.uint8) * 255
divider[1, :, :] = 0
annotations = Annotations()
z_offsets = []
stack_offsets_rows = []
px_shapes_rows = []
project_offsets_rows = []
last_z = 0
logger.info("fetching and writing data")
for idx, row in tqdm(df.iterrows(), total=len(df)):
this_offsets = offsets[idx]
stack_offsets_rows.append(this_offsets["offset_px"].to_list())
project_offsets_rows.append(this_offsets["offset_nm"].to_list())
px_shapes_rows.append(this_offsets["shape_px"].to_list())
z_offsets.append(last_z)
for side in ["pre", "post"]:
local_coords = (
CoordZYX({dim: row[side + "_tn_" + dim]
for dim in "zyx"}) -
this_offsets["offset_nm"]).to_list()
local_coords[0] += last_z * RESOLUTION["z"]
annotations.add_annotation(int(row[side + "_tnid"]),
side + "synaptic_site",
local_coords)
annotations.set_pre_post_partners(int(row["pre_tnid"]),
int(row["post_tnid"]))
raw[last_z:last_z + this_offsets["shape_px"]["z"],
0:this_offsets["shape_px"]["y"],
0:this_offsets["shape_px"]["x"], ] = self.get_raw(
this_offsets["offset_px"], this_offsets["shape_px"])
last_z += this_offsets["shape_px"]["z"]
raw[last_z:last_z + 3, :, :] = divider
last_z += 3
clefts = np.zeros(raw.shape, dtype=np.uint64)
res_list = RESOLUTION.to_list()
with closing(CremiFile(path, mode)) as f:
f.write_raw(Volume(raw, resolution=res_list))
f.write_clefts(Volume(clefts, resolution=res_list))
f.write_annotations(annotations)
f.h5file.attrs["project_offset"] = offset_nm.to_list()
f.h5file.attrs["stack_offset"] = offset_px.to_list()
for key, value in row.items():
f.h5file.attrs[key] = value
df.to_hdf(path, "tables/connectors")
for name, this_table in zip(
["stack_offset", "shape_px", "project_offset"],
[stack_offsets_rows, px_shapes_rows, project_offsets_rows],
):
this_df = pd.DataFrame(this_table,
columns=["z", "y", "x"],
index=df.index)
this_df.to_hdf(path, "tables/" + name)
z_df = pd.DataFrame(z_offsets, index=df.index, columns=["z"])
z_df.to_hdf(path, "tables/z_offset")