def test_match():
a = many([[[0, 0], [0, 1], [1, 0], [1, 1]],
[[10, 10], [10, 11], [11, 10], [11, 11]]])
b = many([[[0, 0], [0, 1], [1, 0], [1, 1]], [[30, 30], [31, 30], [31,
31]]])
assert match(a, b) == [0, 1]
assert match(a, b, threshold=5) == [0, nan]
def test_construction(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = many([one(coords), one(coords)]) assert r.count == 2 assert allclose(r.coordinates, [coords, coords]) r = many([coords, coords]) assert r.count == 2 assert allclose(r.coordinates, [coords, coords]) r = many([coords, coords, coords]) assert r.count == 3 assert allclose(r.coordinates, [coords, coords, coords])
def bifurcated_regions(n):
"""
generate an intensity table with diagonal coordinates ((1, 1), (2, 2), ... (n, n)) over 3
channels and four rounds, where intensities are randomly generated.
Split the region into two block-diagonal cells which should encompass 1/2 of the total area but
all of the points in the domain, since intensities is a diagonal table.
"""
np.random.seed(777)
data = np.random.random_sample((n, 3, 4))
diagonal_intensities = intensity_table_factory(data)
x = diagonal_intensities[Indices.X.value].max() + 1
y = diagonal_intensities[Indices.Y.value].max() + 1
box_one_coords = [[0, 0], [0, np.floor(x / 2)], [np.ceil(y / 2), 0],
[np.floor(y / 2), np.floor(x / 2)]]
box_two_coords = [[np.floor(y / 2), np.floor(x / 2)], [np.floor(y / 2), x],
[y, np.floor(x / 2)], [y, x]]
regions = regional.many(
[regional.one(box_one_coords),
regional.one(box_two_coords)])
# assign intensity_table some target values that are just sequential numbers
diagonal_intensities[Features.TARGET] = (Features.AXIS,
np.arange(n).astype(str))
return diagonal_intensities, regions
def __init__(self, regions):
if isinstance(regions, list):
self.regions = many(regions)
elif isinstance(regions, many):
self.regions = regions
else:
raise Exception("Input type not recognized, must be many regions")
def __init__(self, regions):
if isinstance(regions, list):
self.regions = many(regions)
elif isinstance(regions, many):
self.regions = regions
else:
raise Exception("Input type not recognized, must be many regions")
def fit(self, images, block_size=None):
images = check_images(images)
block_size = block_size if block_size is not None else images.shape[1:]
blocks = images.toblocks(size=block_size)
shape = blocks.blockshape
sources = blocks.tordd().map(lambda kv: self._get(kv[0], kv[1], shape))
collected = sources.collect()
return ExtractionModel(many(list(itertools.chain.from_iterable(collected))))
def _mask_to_regional(m):
"""Convert a 2D numpy mask to a regional many object so it can be measured
using the neurofinder library."""
mlbl = measure.label(m)
coords = []
for lbl in range(1, np.max(mlbl) + 1):
yy, xx = np.where(mlbl == lbl)
coords.append([[y, x] for y, x in zip(yy, xx)])
return many(coords)
def test_model_transform_single(eng):
regions = many([[[0, 0], [0, 1]]])
model = ExtractionModel(regions=regions)
im0 = [[0, 1], [1, 2]]
im1 = [[3, 4], [5, 6]]
im2 = [[7, 8], [9, 10]]
data = fromarray([im0, im1, im2], engine=eng)
transformed = model.transform(data)
assert allclose(transformed.toarray(), [[0.5, 3.5, 7.5]])
def test_mask_colors(): r = many([one([0, 0]), one([1, 1])]) im = r.mask(fill=['red','blue'], background='black') assert allclose(im[:,:,0], [[1, 0], [0, 0]]) assert allclose(im[:,:,1], [[0, 0], [0, 0]]) assert allclose(im[:,:,2], [[0, 0], [0, 1]]) im = r.mask(fill=[[1, 0, 0], [0, 0, 1]], background='black') assert allclose(im[:,:,0], [[1, 0], [0, 0]]) assert allclose(im[:,:,1], [[0, 0], [0, 0]]) assert allclose(im[:,:,2], [[0, 0], [0, 1]])
def test_mask_background(): r = many([one([0, 0]), one([1, 1])]) im = r.mask(fill='red', stroke=None, background='black') assert allclose(im[:,:,0], [[1, 0], [0, 1]]) assert allclose(im[:,:,1], [[0, 0], [0, 0]]) assert allclose(im[:,:,2], [[0, 0], [0, 0]]) im = r.mask(fill=[1, 0, 0], stroke=None, background='black') assert allclose(im[:,:,0], [[1, 0], [0, 1]]) assert allclose(im[:,:,1], [[0, 0], [0, 0]]) assert allclose(im[:,:,2], [[0, 0], [0, 0]])
def test_mask(): r = many([one([0, 0]), one([1, 1])]) im = r.mask(fill='red') assert allclose(im[:,:,0], [[1, 1], [1, 1]]) assert allclose(im[:,:,1], [[0, 1], [1, 0]]) assert allclose(im[:,:,2], [[0, 1], [1, 0]]) im = r.mask(fill=[1, 0, 0]) assert allclose(im[:,:,0], [[1, 1], [1, 1]]) assert allclose(im[:,:,1], [[0, 1], [1, 0]]) assert allclose(im[:,:,2], [[0, 1], [1, 0]])
def load(file):
"""
Load neuronal regions from a file or string.
"""
if os.path.isfile(file):
with open(file, 'r') as f:
values = json.load(f)
else:
values = json.loads(file)
return many([v['coordinates'] for v in values])
def load(file):
"""
Load neuronal regions from a file or string.
"""
if os.path.isfile(file):
with open(file, 'r') as f:
values = json.load(f)
else:
values = json.loads(file)
return many([v['coordinates'] for v in values])
def geojson_to_region(geojson: Dict[Any, Any]) -> regional.many:
"""
Convert geojson data to region geometrical data.
"""
def make_region(geometry):
assert geometry['geometry']['type'] == "Polygon"
region = [(coordinates[0], coordinates[1])
for coordinates in geometry['geometry']['coordinates']]
return regional.one(region)
return regional.many([make_region(geometry) for geometry in geojson])
def load_regions(dataset_path):
"""
Load in the ROIs for a dataset.
Returns a regional.many object
"""
with open(os.path.join(dataset_path, 'regions/regions.json')) as f:
data = json.load(f)
regions = []
for i in range(len(data)):
regions.append(regional.one(data[i]['coordinates']))
return regional.many(regions)
def load_regions(dataset_path):
"""
Load in the ROIs for a dataset.
Returns a regional.many object
"""
with open(os.path.join(dataset_path, 'regions/regions.json')) as f:
data = json.load(f)
regions = []
for i in range(len(data)):
regions.append(regional.one(data[i]['coordinates']))
return regional.many(regions)
def label_to_regions(labels) -> regional.many:
label_mat_coo = coo_matrix(labels)
def region_for(label_mat_coo, label):
ind = label_mat_coo.data == label
# TODO does this work in 3D?
x = label_mat_coo.row[ind]
y = label_mat_coo.col[ind]
re = regional.one(list(zip(x, y)))
return re
unique_labels = sorted(set(label_mat_coo.data))
regions = [region_for(label_mat_coo, label) for label in unique_labels]
return regional.many(regions)
def fit(self, images, chunk_size=None, padding=None):
images = check_images(images)
chunk_size = chunk_size if chunk_size is not None else images.shape[1:]
blocks = images.toblocks(chunk_size=chunk_size, padding=padding)
sources = asarray(blocks.map_generic(self._get))
# add offsets based on block coordinates
for inds in itertools.product(*[range(d) for d in sources.shape]):
offset = (asarray(inds) * asarray(blocks.blockshape)[1:])
for source in sources[inds]:
source.coordinates += offset
if padding:
leftpad = [blocks.padding[i + 1] if inds[i] != 0 else 0 for i in range(len(inds))]
source.coordinates -= asarray(leftpad)
# flatten list and create model
flattened = list(itertools.chain.from_iterable(sources.flatten().tolist()))
return ExtractionModel(many(flattened))
def predict_conv_net(network, data, truth=None):
'''
Applies the ConvNet to data to predictions
'''
from regional import many
predictions = []
cropped = []
for i in range(len(data)):
predictions.append(network.predict_proba(data[i][newaxis, ...])[0,...,0])
if truth is not None:
mask = many(truth[i]).mask(data[i].shape[:2], fill='black')[...,0]
clip = data[i].shape[0] - predictions[i].shape[0]
left = clip/2
right = left + clip%2
cropped.append(mask[left:-right, left:-right])
if truth:
return predictions, cropped
else:
return predictions
def predict_conv_net(network, data, truth=None):
'''
Applies the ConvNet to data to predictions
'''
from regional import many
predictions = []
cropped = []
for i in range(len(data)):
predictions.append(
network.predict_proba(data[i][newaxis, ...])[0, ..., 0])
if truth is not None:
mask = many(truth[i]).mask(data[i].shape[:2], fill='black')[..., 0]
clip = data[i].shape[0] - predictions[i].shape[0]
left = clip / 2
right = left + clip % 2
cropped.append(mask[left:-right, left:-right])
if truth:
return predictions, cropped
else:
return predictions
def merge_once(initial):
centers = asarray(initial.center)
nearest = [top_k(centers, source.center, k_nearest) for source in initial]
regions = []
skip = []
keep = []
for ia, source in enumerate(initial):
for ib in nearest[ia]:
other = initial[ib]
if not ia == ib and source.overlap(other) > overlap:
source = source.merge(other)
if ib not in keep:
skip.append(ib)
regions.append(source)
keep.append(ia)
return many([region for ir, region in enumerate(regions) if ir not in skip])
def region_to_mask(self, regions_json):
"""
Converts region JSON file into mask
Arguments
---------
regions_json : json file
JSON file which needs to be converted into corresponding mask
Returns
-------
output : 2D numpy array
Mask image
"""
regions = many([region['coordinates'] for region in regions_json])
_mask = regions.mask(dims=(512, 512),
stroke='white',
fill='white',
background='black')
return color.rgb2gray(_mask)
def fit(self, images, chunk_size=None, padding=None):
images = check_images(images)
chunk_size = chunk_size if chunk_size is not None else images.shape[1:]
blocks = images.toblocks(chunk_size=chunk_size, padding=padding)
sources = asarray(blocks.map_generic(self._get))
# add offsets based on block coordinates
for inds in itertools.product(*[range(d) for d in sources.shape]):
offset = (asarray(inds) * asarray(blocks.blockshape)[1:])
for source in sources[inds]:
source.coordinates += offset
if padding:
leftpad = [
blocks.padding[i + 1] if inds[i] != 0 else 0
for i in range(len(inds))
]
source.coordinates -= asarray(leftpad)
# flatten list and create model
flattened = list(
itertools.chain.from_iterable(sources.flatten().tolist()))
return ExtractionModel(many(flattened))
def merge_once(initial):
centers = asarray(initial.center)
nearest = [
top_k(centers, source.center, k_nearest) for source in initial
]
regions = []
skip = []
keep = []
for ia, source in enumerate(initial):
for ib in nearest[ia]:
other = initial[ib]
if not ia == ib and source.overlap(other) > overlap:
source = source.merge(other)
if ib not in keep:
skip.append(ib)
regions.append(source)
keep.append(ia)
return many([
region for ir, region in enumerate(regions) if ir not in skip
])
def test_dilate(): v = many([one([1, 1]), one([1, 1])]).dilate(1) truth = [[0, 0], [0, 1], [0, 2], [1, 0], [1, 1], [1, 2], [2, 0], [2, 1], [2, 2]] assert allclose(v.coordinates, [truth, truth])
def test_overlap(): coords = [[1, 1], [1, 2], [2, 1], [2, 2]] v = many([coords, coords]).overlap(one([1, 1])) assert v == [0.25, 0.25]
def test_model_construction():
regions = many([[[0, 1], [0, 2]], [[0, 2], [0, 3]]])
model = ExtractionModel(regions=regions)
assert isinstance(model.regions, many)
assert model.regions.count == 2
def test_similarity_perfect_flipped():
a = many([[[0, 0], [0, 1], [1, 0], [1, 1]],
[[10, 10], [10, 11], [11, 10], [11, 11]]])
b = many([[[10, 10], [10, 11], [11, 10], [11, 11]],
[[0, 0], [0, 1], [1, 0], [1, 1]]])
assert centers(a, b) == (1.0, 1.0)
def overlay(model, image=None, compare=None, threshold=inf, correct=False):
"""
Overlay regions onto reference image, with optional comparison regions.
Parameters
----------
model : ExtractionModel
image : array-like, optional, default = None
Base image, can provide a 2d array,
if unspecified will be black.
modelCompare : ExtractionModel, default = None
Regions to be compared to if provided.
threshold : float, default = inf
Distance threshold for matching sources.
correct : bool, default = False
If True and a comparision given will only show correct regions
"""
if image is not None:
if image.max() > 1:
im = norm(image)
else:
im = image
size = im.shape
else:
size = (max([r.bbox[2] for r in model.regions]) + 1,
max([r.bbox[3] for r in model.regions]) + 1)
if compare is not None:
sizeCompare = (max([r.bbox[2] for r in compare.regions]) + 1,
max([r.bbox[3] for r in compare.regions]) + 1)
size = (maximum(size[0],
sizeCompare[0]), maximum(size[1], sizeCompare[1]))
im = full(size, 0.0)
if compare is not None:
matches = match(model.regions, compare.regions, threshold)
matchesCompare = full(compare.regions.count, nan)
for ii in where(~isnan(matches))[0]:
matchesCompare[matches[ii]] = ii
if any(~isnan(matches)):
hits = many([model.regions[i] for i in where(~isnan(matches))[0]])
h = hits.mask(size,
background='black',
fill=None,
stroke=[0, 0.7, 0])
else:
h = full((size[0], size[1], 3), 0.0)
if any(isnan(matches)):
falseAlarms = many(
[model.regions[i] for i in where(isnan(matches))[0]])
fA = falseAlarms.mask(size,
background='black',
fill=None,
stroke=[0.7, 0, 0])
else:
fA = full((size[0], size[1], 3), 0.0)
if any(~isnan(matchesCompare)):
truePositives = many(
[compare.regions[i] for i in where(~isnan(matchesCompare))[0]])
tP = truePositives.mask(size,
background='black',
fill=None,
stroke=[0, 0, 0.7])
else:
tP = full((size[0], size[1], 3), 0.0)
if any(isnan(matchesCompare)):
misses = many(
[compare.regions[i] for i in where(isnan(matchesCompare))[0]])
m = misses.mask(size,
background='black',
fill=None,
stroke=[0.7, 0.7, 0])
else:
m = full((size[0], size[1], 3), 0.0)
if correct:
mask = maximum(tP, h)
else:
mask = maximum(maximum(maximum(tP, fA), h), m)
else:
mask = model.regions.mask(size,
background='black',
fill=None,
stroke=[0, 0.7, 0])
base = tile(im, (3, 1, 1)).transpose(1, 2, 0)
return maximum(base, mask)
##produce fake calcium imaging data from showit import image import matplotlib.pyplot as plot from regional import many from fakearray import calcium_imaging data, series, truth = calcium_imaging(shape=(100,300), n=5, t=50, seed=42, noise=0.5, withparams=True) base = data.mean().toarray() image(base); plot.show() image(many(truth).mask(dims=data.shape[1:], cmap='rainbow', stroke='black', base=base)); plot.show()
def test_bbox(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] truth = [0, 0, 2, 2] r = many([coords, coords]) assert allclose(r.bbox, [truth, truth])
def test_extent(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] r = many([coords, coords]) assert allclose(r.extent, [[3, 3], [3, 3]])
def test_hull(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] truth = [[0, 0], [2, 0], [2, 2], [0, 2]] r = many([coords, coords]) assert allclose(r.hull, [truth, truth])
def test_overlap_too_many():
a = many([[[0, 0], [0, 1]], [[10, 10], [10, 11]]])
b = many([[[0, 0], [0, 1]], [[10, 10], [10, 11], [11, 10], [11, 12]]])
assert shapes(a, b) == (1.0, 0.75)
def test_center(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = many([coords, coords]) assert allclose(r.center, [[0.5, 0.5], [0.5, 0.5]])
def test_index(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = many([one(coords), one(coords)]) assert allclose(r[0].coordinates, coords) assert allclose(r[int64(0)].coordinates, coords)
def test_similarity_no_threshold():
a = many([[[0, 0], [0, 1], [1, 0], [1, 1]],
[[10, 10], [10, 11], [11, 10], [11, 11]]])
b = many([[[0, 0], [0, 1], [1, 0], [1, 1]], [[30, 30], [31, 30], [31,
31]]])
assert centers(a, b) == (1.0, 1.0)
def test_exclude(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] truth = [[1, 0], [1, 1]] r = many([coords, coords]).exclude(one([[0, 0], [0, 1]])) assert allclose(r.coordinates, [truth, truth])
def test_area(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = many([coords, coords]) assert r.area == [4, 4]
def test_overlap_perfect_flipped():
a = many([[[0, 0], [0, 1]], [[10, 10], [10, 11]]])
b = many([[[10, 10], [10, 11]], [[0, 0], [0, 1]]])
assert shapes(a, b) == (1.0, 1.0)
def test_distance(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = many([coords, coords]) assert r.distance([1, 1]) == [0, 0]
withparams=True)
base = data.mean(0)
image(base, size=10)
plot.show()
algorithm = CNMF(k=5, gSig=[4, 4], merge_thresh=0.8)
model, temporaldata = algorithm.fit(data)
def convert(array):
r, c = np.where(array > 0.0)
return one(zip(r, c))
regions = many([convert(model[:, :, i]) for i in range(model.shape[2])])
#show true solution
image(
many(truth).mask(dims=data.shape[1:],
cmap='rainbow',
stroke='black',
base=base))
plot.show()
#show algorithm solution
masks = regions.mask(cmap_stroke='rainbow',
fill=None,
base=base.clip(0, 4000) / 4000)
image(masks, size=14)
plot.show()
def test_merge(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] truth = coords + [[1,1]] r = many([coords, coords]).merge([1, 1]) assert allclose(r.coordinates, [truth, truth])
from showit import image
from fakearray import calcium_imaging
from cnmf import CNMF
data, series, truth = calcium_imaging(n=5, t=10, seed=42, noise=0.5, withparams=True)
base = data.mean(0)
image(base, size=10);
plot.show()
algorithm = CNMF( k=5, gSig=[4,4], merge_thresh=0.8)
model,temporaldata = algorithm.fit(data)
def convert(array):
r,c = np.where(array > 0.0)
return one(zip(r,c))
regions = many([convert(model[:,:,i]) for i in range(model.shape[2])])
#show true solution
image(many(truth).mask(dims=data.shape[1:], cmap='rainbow', stroke='black', base=base));
plot.show()
#show algorithm solution
masks = regions.mask(cmap_stroke='rainbow', fill=None, base=base.clip(0,4000) / 4000)
image(masks, size=14);
plot.show()
def test_crop(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] truth = [[0, 0]] r = many([coords, coords]).crop([0, 0], [1, 1]) assert allclose(r.coordinates, [truth, truth])
def load(path):
with open(path, 'r') as f:
raw = load(f)
regions = many([x['coordinates'] for x in raw['regions']])
return ExtractionModel(regions)
def test_inbounds(): coords = [[1, 1], [1, 2], [2, 1], [2, 2]] v = many([coords, coords]).inbounds([0, 0], [3, 3]) assert v == [True, True]
def test_overlap_too_few():
a = many([[[0, 0], [0, 1], [1, 0], [1, 1]],
[[10, 10], [10, 11], [11, 10], [11, 11]]])
b = many([[[0, 0], [0, 1], [1, 0], [1, 1]], [[10, 10], [11, 11]]])
assert shapes(a, b) == (0.75, 1.0)
def test_outline(): coords = [[1, 1]] truth = [[0, 0], [0, 1], [0, 2], [1, 0], [1, 2], [2, 0], [2, 1], [2, 2]] r = many([coords, coords]).outline(0, 1) assert allclose(r.coordinates, [truth, truth])
def test_mask_colormap(): r = many([one([0, 0]), one([1, 1])]) im = r.mask(cmap='gray', value=[0, 1], background='red') assert allclose(im[:,:,0], [[0, 1], [1, 1]]) assert allclose(im[:,:,1], [[0, 0], [0, 1]]) assert allclose(im[:,:,2], [[0, 0], [0, 1]])
def test_similarity():
a = many([[[0, 0], [0, 1], [1, 0], [1, 1]],
[[10, 10], [10, 11], [11, 10], [11, 11]]])
b = many([[[0, 0], [0, 1], [1, 0], [1, 1]], [[30, 30], [31, 30], [31,
31]]])
assert centers(a, b, threshold=5) == (0.5, 0.5)