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 test_construction(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = one(coords) assert allclose(r.coordinates, coords) coords = [1, 1] r = one(coords) assert allclose(r.coordinates, [coords])
def test_inbounds(): coords = [[1, 1], [1, 2], [2, 1], [2, 2]] v = one(coords).inbounds([0, 0], [3, 3]) assert v == True v = one(coords).inbounds([0, 0], [2, 2]) assert v == False v = one(coords).inbounds([1, 1], [3, 3]) assert v == True
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_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(): 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 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 test_mask_no_fill(): coords = [[1, 1]] r = one(coords) im = r.mask(fill=None, stroke='black', dims=(2,2)) assert allclose(im[:,:,0], [[0, 0], [0, 1]]) assert allclose(im[:,:,1], [[0, 0], [0, 1]]) assert allclose(im[:,:,2], [[0, 0], [0, 1]])
def make_region(geometry):
assert geometry['geometry']['type'] == "Polygon"
return regional.one([
(coordinates[0], coordinates[1])
for coordinates in geometry['geometry']['coordinates']
])
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
def test_overlap(): coords = [[1, 1], [1, 2], [2, 1], [2, 2]] v = one(coords).overlap(one([1, 1]), 'fraction') assert v == 0.25 v = one(coords).overlap(one([[1, 1],[1, 2]]), 'fraction') assert v == 0.5 v = one(coords).overlap(one([1, 1]), 'rates') assert v == (0.25, 1.0) v = one(coords).overlap(one([[1, 1], [1, 2], [3, 3], [4, 4]]), 'rates') assert v == (0.5, 0.5)
def test_mask(): coords = [[1, 1]] r = one(coords) im = r.mask(fill='red') assert im.shape == (1, 1, 3) assert allclose(im, [[[1, 0, 0]]]) im = r.mask(fill=[1, 0, 0]) assert im.shape == (1, 1, 3) assert allclose(im, [[[1, 0, 0]]])
def _get(self, index, block, shape):
offset = (asarray(index[1]) * asarray(shape))[1:]
dims = block.shape[1:]
max_size = prod(dims) / 2 if self.max_size == 'full' else self.max_size
# reshape to t x spatial dimensions
data = block.reshape(block.shape[0], -1)
# build and apply NMF model to block
model = SKNMF(self.k, max_iter=self.max_iter)
model.fit(clip(data, 0, inf))
# reconstruct sources as spatial objects in one array
components = model.components_.reshape((self.k,) + dims)
# convert from basis functions into shape
# by median filtering (optional), applying a percentile threshold,
# finding connected components and removing small objects
combined = []
for component in components:
tmp = component > percentile(component, self.percentile)
regions = remove_small_objects(label(tmp), min_size=self.min_size)
ids = unique(regions)
ids = ids[ids > 0]
for ii in ids:
r = regions == ii
r = median_filter(r, 2)
coords = asarray(where(r)).T + offset
if (size(coords) > 0) and (size(coords) < max_size):
combined.append(one(coords))
# merge overlapping sources
if self.overlap is not None:
# iterate over source pairs and find a pair to merge
def merge(sources):
for i1, s1 in enumerate(sources):
for i2, s2 in enumerate(sources[i1+1:]):
if s1.overlap(s2) > self.overlap:
return i1, i1 + 1 + i2
return None
# merge pairs until none left to merge
pair = merge(combined)
testing = True
while testing:
if pair is None:
testing = False
else:
combined[pair[0]] = combined[pair[0]].merge(combined[pair[1]])
del combined[pair[1]]
pair = merge(combined)
return combined
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 mask_outlines(img, mask_arrs=[], colors=[]):
"""Apply each of the given masks (numpy arrays) to the base img with the given colors.
# Arguments
img: base image as a (height x width) numpy array.
mask_arrs: list of masks as (height x width) numpy arrays that should be outlined.
colors: one color (e.g. 'red' or hex code) for each mask.
# Returns
img: The base image with outlines applied.
"""
assert len(mask_arrs) == len(colors), 'One color per mask.'
img = img.astype(np.float32)
# Clip outliners, scale the img to [0,1].
img = np.clip(img, 0, np.percentile(img, 99))
img = (img - np.min(img)) / (np.max(img) - np.min(img))
# Convert the img to RGB.
if len(img.shape) == 2:
img_rgb = gray2rgb(img)
# Build up an image of combined outlines.
oln_rgb = np.zeros_like(img_rgb)
for m, c in zip(mask_arrs, colors):
if np.sum(m) == 0:
continue
r = one(list(zip(*np.where(m == 1))))
o = r.mask(dims=img_rgb.shape[:2],
fill=None,
stroke=c,
background='black')
yy, xx, cc = np.where(o != 0)
oln_rgb[yy, xx, cc] = o[yy, xx, cc]
# Merge the two images.
# Helpful stackoverflow post: https://stackoverflow.com/questions/40895785
oln_rgb = np.clip(oln_rgb, 0, 1)
oln_msk = np.max(oln_rgb, axis=-1)
img_msk = 1 - oln_msk
oln_msk = gray2rgb(oln_msk)
img_msk = gray2rgb(img_msk)
mrg = (((oln_rgb * oln_msk) + (img_rgb * img_msk)) * 255).astype(np.uint8)
return mrg
def test_mask_colors(): coords = [[1, 1]] r = one(coords) im = r.mask(fill='blue', stroke=None, dims=(2, 2)) assert im.shape == (2, 2, 3) assert allclose(im[:, :, 0], [[1, 1], [1, 0]]) assert allclose(im[:, :, 1], [[1, 1], [1, 0]]) assert allclose(im[:, :, 2], [[1, 1], [1, 1]]) im = r.mask(fill='red', stroke='black', dims=(2, 2)) assert im.shape == (2, 2, 3) assert allclose(im[:, :, 0], [[0, 0], [0, 1]]) assert allclose(im[:, :, 1], [[0, 0], [0, 0]]) assert allclose(im[:, :, 2], [[0, 0], [0, 0]]) im = r.mask(fill='red', stroke=None, background='blue', dims=(2, 2)) assert im.shape == (2, 2, 3) assert allclose(im[:, :, 0], [[0, 0], [0, 1]]) assert allclose(im[:, :, 1], [[0, 0], [0, 0]]) assert allclose(im[:, :, 2], [[1, 1], [1, 0]])
def dataset_to_mp4(s, m, mp4_path):
"""Converts the given series to an mp4 video. If the mask is given, adds an outline around each neuron.
# Arguments
s: imaging series as a (time x height x width) numpy array.
m: neuron masks as a (no. neurons x height x width) numpy array.
mp4_path: path where the mp4 file should be saved.
# Returns
Nothing
"""
from skvideo.io import vwrite
logger = logging.getLogger(funcname())
logger.info('Preparing video %s.' % mp4_path)
s = s.astype(np.float32)
s = (s - np.min(s)) / (np.max(s) - np.min(s)) * 255
# If mask is given make a color video with neurons outlined.
if m is not None:
video = np.zeros(s.shape + (3, ), dtype=np.uint8)
video[:, :, :, 0] = s
video[:, :, :, 1] = s
video[:, :, :, 2] = s
outlines = np.zeros(s.shape[1:] + (3, ), )
for i in range(m.shape[0]):
reg = one(list(zip(*np.where(m[i] == 1))))
outlines += reg.mask(dims=m.shape[1:],
fill=None,
stroke='white',
background='black')
yy, xx, _ = np.where(outlines != 0)
video[:, yy, xx, :] = [102, 255, 255]
else:
video = s.astype(np.uint8)
vwrite(mp4_path, video)
logger.info('Saved video %s.' % mp4_path)
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_exclude(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = one(coords).exclude(one([[0, 0], [0, 1]])) assert allclose(r.coordinates, [[1, 0], [1, 1]]) r = one(coords).exclude([[0, 0], [0, 1]]) assert allclose(r.coordinates, [[0, 0], [0, 1], [1, 0]])
def test_outline(): coords = [[1, 1]] r = one(coords).outline(0, 1) assert allclose(r.coordinates, [[0, 0], [0, 1], [0, 2], [1, 0], [1, 2], [2, 0], [2, 1], [2, 2]])
def test_center(): coords = [[0, 0], [0, 1], [1, 0], [1, 1]] r = one(coords) assert allclose(r.center, [0.5, 0.5])
def convert(array):
r, c = np.where(array > 0.0)
return one(zip(r, c))
def test_dilate(): v = one([1, 1]).dilate(1) assert allclose(v.coordinates, [[0, 0], [0, 1], [0, 2], [1, 0], [1, 1], [1, 2], [2, 0], [2, 1], [2, 2]]) v = one([1, 1]).dilate(0) assert allclose(v.coordinates, [[1, 1]])
def test_hull(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] r = one(coords) assert allclose(r.hull, [[0, 0], [2, 0], [2, 2], [0, 2]])
def test_bbox(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] r = one(coords) assert allclose(r.bbox, [0, 0, 2, 2])
def _construct_region_for_location(self, location, images, template,
mean_image):
"""
Given a location, build a mask around it. Just do some simple segmenting
to construct the mask.
"""
image_dims = images[0].shape
template_dims = template.shape
template_area = template_dims[0] * template_dims[1]
template_half_height = template_dims[0] / 2
template_half_width = template_dims[1] / 2
y, x = location
min_x = max(0, x - template_half_width)
max_x = min(image_dims[1], x + template_half_width)
min_y = max(0, y - template_half_height)
max_y = min(image_dims[0], y + template_half_height)
neuron = mean_image[min_y:max_y, min_x:max_x]
neuron_area = neuron.shape[0] * neuron.shape[1]
f = interpolate.interp1d([np.min(neuron), np.max(neuron)], [-1, 1])
scaled_neuron = f(neuron)
seg = segmentation.felzenszwalb(scaled_neuron,
scale=1000,
sigma=1,
min_size=int(.4 * template_area))
# Is this mask good to go?
seg_g2g = True
# if the mask is more than 75% percent of the window, its probably bad
if np.sum(seg) >= 0.75 * neuron_area:
seg_g2g = False
# did we even find a region?
if np.count_nonzero(seg) == 0:
seg_g2g = False
# did we find too many regions?
if np.unique(seg).shape[0] != 2: # we only want 0s and 1s
seg_g2g = False
# we didn't find a good segmentation
if not seg_g2g:
# Just make an ellipse?
# Rather than an ellipse, we should just use the template
cx = neuron.shape[1] / 2
cy = neuron.shape[0] / 2
rx = cx * 3 / 4
ry = cy * 3 / 4
seg = np.zeros(neuron.shape)
rr, cc = ellipse(cy, cx, ry, rx)
seg[rr, cc] = 1
mask = np.zeros(image_dims)
mask[min_y:max_y, min_x:max_x] = seg
coordinates = np.transpose(np.nonzero(mask)).tolist()
return regional.one(coordinates)
def convert(array):
r,c = np.where(array > 0.0)
return one(zip(r,c))
def _get(self, block): """ Performs Sparse PCA on a block to identify spatial regions Arguments --------- block : thunder block Block of images Returns ------- combined : list List of regions """ dims = block.shape[1:] max_size = prod(dims) / 2 if self.max_size == 'full' else self.max_size data = block.reshape(block.shape[0], -1) model = SparsePCA(self.k, normalize_components=True) model.fit(clip(data, 0, inf)) components = model.components_.reshape((self.k, ) + dims) combined = [] for component in components: tmp = component > percentile(component, self.percentile) labels, num = label(tmp, return_num=True) if num == 1: counts = bincount(labels.ravel()) if counts[1] < self.min_size: continue else: regions = labels else: regions = remove_small_objects(labels, min_size=self.min_size) ids = unique(regions) ids = ids[ids > 0] for ii in ids: r = regions == ii r = median_filter(r, 2) coords = asarray(where(r)).T if (size(coords) > 0) and (size(coords) < max_size): combined.append(one(coords)) # merge overlapping sources if self.overlap is not None: # iterate over source pairs and find a pair to merge def merge(sources): for i1, s1 in enumerate(sources): for i2, s2 in enumerate(sources[i1+1:]): if s1.overlap(s2) > self.overlap: return i1, i1 + 1 + i2 return None # merge pairs until none left to merge pair = merge(combined) testing = True while testing: if pair is None: testing = False else: combined[pair[0]] = combined[pair[0]].merge(combined[pair[1]]) del combined[pair[1]] pair = merge(combined) return combined
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_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_extent(): coords = [[0, 0], [0, 2], [2, 0], [1, 1], [2, 2]] r = one(coords) assert allclose(r.extent, [3, 3])
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_area(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = one(coords) assert r.area == 4
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_distance(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = one(coords) assert r.distance([1, 1]) == 0
def _get(self, block):
"""
Perform NMF on a block to identify spatial regions.
"""
dims = block.shape[1:]
max_size = prod(dims) / 2 if self.max_size == 'full' else self.max_size
# reshape to t x spatial dimensions
data = block.reshape(block.shape[0], -1)
# build and apply NMF model to block
model = SKNMF(self.k, max_iter=self.max_iter)
model.fit(clip(data, 0, inf))
# reconstruct sources as spatial objects in one array
components = model.components_.reshape((self.k, ) + dims)
# convert from basis functions into shape
# by median filtering (optional), applying a percentile threshold,
# finding connected components and removing small objects
combined = []
for component in components:
tmp = component > percentile(component, self.percentile)
labels, num = label(tmp, return_num=True)
if num == 1:
counts = bincount(labels.ravel())
if counts[1] < self.min_size:
continue
else:
regions = labels
else:
regions = remove_small_objects(labels, min_size=self.min_size)
ids = unique(regions)
ids = ids[ids > 0]
for ii in ids:
r = regions == ii
r = median_filter(r, 2)
coords = asarray(where(r)).T
if (size(coords) > 0) and (size(coords) < max_size):
combined.append(one(coords))
# merge overlapping sources
if self.overlap is not None:
# iterate over source pairs and find a pair to merge
def merge(sources):
for i1, s1 in enumerate(sources):
for i2, s2 in enumerate(sources[i1 + 1:]):
if s1.overlap(s2) > self.overlap:
return i1, i1 + 1 + i2
return None
# merge pairs until none left to merge
pair = merge(combined)
testing = True
while testing:
if pair is None:
testing = False
else:
combined[pair[0]] = combined[pair[0]].merge(
combined[pair[1]])
del combined[pair[1]]
pair = merge(combined)
return combined
def test_merge_nonunique(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = one(coords).merge([[1, 1], [0, 0]]) assert equal_sets(r.coordinates.tolist(), coords + [[1,1]]) r = one(coords).merge(one([[1, 1], [0, 0]])) assert equal_sets(r.coordinates.tolist(), coords + [[1,1]])
def test_crop(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = one(coords).crop([0, 0], [1, 1]) assert allclose(r.coordinates, [[0, 0]])
def test_merge(): coords = [[0, 0], [0, 2], [2, 0], [2, 2]] r = one(coords).merge([1, 1]) assert allclose(r.coordinates, coords + [[1,1]]) r = one(coords).merge(one([1, 1])) assert allclose(r.coordinates, coords + [[1,1]])