def norm_minmse(gt, x, normalize_gt=True):
"""
normalizes and affinely scales an image pair such that the MSE is minimized
Parameters
----------
gt: ndarray
the ground truth image
x: ndarray
the image that will be affinely scaled
normalize_gt: bool
set to True of gt image should be normalized (default)
Returns
-------
gt_scaled, x_scaled
"""
if normalize_gt:
gt = normalize(gt, 0.1, 99.9, clip=False).astype(np.float32,
copy=False)
x = x.astype(np.float32, copy=False) - np.mean(x)
gt = gt.astype(np.float32, copy=False) - np.mean(gt)
scale = np.cov(x.flatten(), gt.flatten())[0, 1] / np.var(x.flatten())
return gt, scale * x
def render_label_pred_example():
model_path = path_model2d()
model = StarDist2D(None,
name=model_path.name,
basedir=str(model_path.parent))
img, y_gt = real_image2d()
x = normalize(img, 1, 99.8)
y, _ = model.predict_instances(x)
im = render_label_pred(y_gt, y, img=x)
import matplotlib.pyplot as plt
plt.figure(1, figsize=(12, 4))
plt.subplot(1, 4, 1)
plt.imshow(x)
plt.title("img")
plt.subplot(1, 4, 2)
plt.imshow(render_label(y_gt, img=x))
plt.title("gt")
plt.subplot(1, 4, 3)
plt.imshow(render_label(y, img=x))
plt.title("pred")
plt.subplot(1, 4, 4)
plt.imshow(im)
plt.title("tp (green) fp (red) fn(blue)")
plt.tight_layout()
plt.show()
return im
def test_speed(model2d):
from time import time
model = model2d
img, mask = real_image2d()
x = normalize(img, 1, 99.8)
x = np.tile(x, (6, 6))
print(x.shape)
stats = []
for mode, n_tiles, sparse in product(("normal", "big"), (None, (2, 2)),
(True, False)):
t = time()
if mode == "normal":
labels, res = model.predict_instances(x,
n_tiles=n_tiles,
sparse=sparse)
else:
labels, res = model.predict_instances_big(x,
axes="YX",
block_size=1024 + 256,
context=64,
min_overlap=64,
n_tiles=n_tiles,
sparse=sparse)
t = time() - t
s = f"mode={mode}\ttiles={n_tiles}\tsparse={sparse}\t{t:.2f}s"
print(s)
stats.append(s)
for s in stats:
print(s)
def test_predict3D(model3d):
model = model3d
img = real_image3d()[0]
img = normalize(img, 1, 99.8)
img = repeat(img, 2)
ref_labels, ref_polys = model.predict_instances(img)
res_labels, res_polys = model.predict_instances_big(img,
axes='ZYX',
block_size=(55, 105,
105),
min_overlap=(13, 25,
25),
context=(17, 30, 30))
m = matching(ref_labels, res_labels)
assert (1.0, 1.0) == (m.accuracy, m.mean_true_score)
# sort them first lexicographic
ref_inds = np.lexsort(ref_polys["points"].T)
res_inds = np.lexsort(res_polys["points"].T)
assert np.allclose(ref_polys["dist"][ref_inds],
res_polys["dist"][res_inds],
atol=1e-2)
assert np.allclose(ref_polys["points"][ref_inds],
res_polys["points"][res_inds],
atol=1e-2)
assert np.allclose(ref_polys["prob"][ref_inds],
res_polys["prob"][res_inds],
atol=1e-2)
return ref_polys, res_polys
def test_predict2D(model2d, use_channel):
model = model2d
img = real_image2d()[0]
img = normalize(img, 1, 99.8)
img = repeat(img, 2)
axes = 'YX'
if use_channel:
img = img[...,np.newaxis]
axes += 'C'
ref_labels, ref_polys = model.predict_instances(img, axes=axes)
res_labels, res_polys = model.predict_instances_big(img, axes=axes, block_size=288, min_overlap=32, context=96)
m = matching(ref_labels, res_labels)
assert (1.0, 1.0) == (m.accuracy, m.mean_true_score)
m = matching(render_polygons(ref_polys, shape=img.shape),
render_polygons(res_polys, shape=img.shape))
assert (1.0, 1.0) == (m.accuracy, m.mean_true_score)
# sort them first lexicographic
ref_inds = np.lexsort(ref_polys["points"].T)
res_inds = np.lexsort(res_polys["points"].T)
assert np.allclose(ref_polys["coord"][ref_inds],
res_polys["coord"][res_inds],atol=1e-2)
assert np.allclose(ref_polys["points"][ref_inds],
res_polys["points"][res_inds],atol=1e-2)
assert np.allclose(ref_polys["prob"][ref_inds],
res_polys["prob"][res_inds],atol=1e-2)
return ref_polys, res_polys
def Optimize(self):
self.Y = [label(y) for y in tqdm(self.Y)]
self.X = [normalize(x,1,99.8,axis= (0,1)) for x in tqdm(self.X)]
print('Images to apply prediction on',len(self.X))
Yhat_val = [self.Starmodel.predict(x) for x in self.X]
opt_prob_thresh, opt_measure, opt_nms_thresh = None, -np.inf, None
for _opt_nms_thresh in self.nms_threshs:
_opt_prob_thresh, _opt_measure = self.optimize_threshold(self.Y, Yhat_val, model=self.Starmodel, nms_thresh=_opt_nms_thresh)
if _opt_measure > opt_measure:
opt_prob_thresh, opt_measure, opt_nms_thresh = _opt_prob_thresh, _opt_measure, _opt_nms_thresh
opt_threshs = dict(prob=opt_prob_thresh, nms=opt_nms_thresh)
self.thresholds = opt_threshs
print("Using optimized values: prob_thresh={prob:g}, nms_thresh={nms:g}.", opt_threshs)
if self.basedir is not None:
print("Saving to 'thresholds.json'.")
save_json(opt_threshs, str(self.basedir + '/' + 'thresholds.json'))
return opt_threshs
def norm_minmse(y, x):
y = normalize(y, 0.1, 99.9)
x = x - x.mean()
y = y - y.mean()
scale = np.cov(x.flatten(), y.flatten())[0, 1] / np.var(x.flatten())
x = scale * x
return y, x
def Run_StarDist2D(img, mdls, which_model):
# runs a Stardist 2D model
axis_norm = (0, 1) # normalize channels independently
im = normalize(img, 1, 99.8, axis=axis_norm)
model = mdls[which_model]
labels, details = model.predict_instances(im)
return labels
def load_training_data(root, image_folder, labels_folder, ext):
# get the image and label mask paths and validate them
image_pattern = os.path.join(root, image_folder, f'*{ext}')
print("Looking for images with the pattern", image_pattern)
train_images = glob(image_pattern)
assert len(train_images) > 0, "Did not find any images"
train_images.sort()
label_pattern = os.path.join(root, labels_folder, f'*{ext}')
print("Looking for labels with the pattern", image_pattern)
train_labels = glob(label_pattern)
assert len(train_labels) > 0, "Did not find any labels"
train_labels.sort()
check_training_data(train_images, train_labels)
# normalization parameters: lower and upper percentile used for image normalization
# maybe these should be exposed
lower_percentile = 1
upper_percentile = 99.8
ax_norm = (0, 1, 2)
train_images = [imageio.volread(im) for im in train_images]
train_labels = [imageio.volread(im) for im in train_labels]
check_training_images(train_images, train_labels)
train_images = [
normalize(im, lower_percentile, upper_percentile, axis=ax_norm)
for im in train_images
]
train_labels = [fill_label_holes(im) for im in train_labels]
return train_images, train_labels
def calculation_run(
self, report_fun: Callable[[str, int],
None]) -> SegmentationResult:
self.check_limitations()
denoised = noise_filtering_dict[
self.parameters["noise_filtering"]["name"]].noise_filter(
self.image.get_channel(self.parameters["channel"]),
self.image.spacing,
self.parameters["noise_filtering"]["values"],
)
model = self.get_model()
normalized = normalize(
denoised,
1,
99.8,
)
segmentation, details = model.predict_instances(
normalized, axes=self.image.return_order.replace("C", ""))
return SegmentationResult(
segmentation,
self.get_segmentation_profile(),
additional_layers={
"description":
AdditionalLayerDescription(details, layer_type="image"),
"segmentation":
AdditionalLayerDescription(segmentation, layer_type="labels")
})
def test_mesh_export(model3d):
model = model3d
img, mask = real_image3d()
x = normalize(img, 1, 99.8)
labels, polys = model.predict_instances(x, nms_thresh=.5, overlap_label=-3)
s = export_to_obj_file3D(polys, "mesh.obj", scale=(.2, .1, .1))
return s
def predictions(model_dist,i):
img = normalize(X[i],1,99.8,axis=axis_norm)
input = torch.tensor(img)
input = input.unsqueeze(0).unsqueeze(0)#unsqueeze 2 times
dist,prob = model_dist(input)
dist_numpy= dist.detach().cpu().numpy().squeeze()
prob_numpy= prob.detach().cpu().numpy().squeeze()
return dist_numpy,prob_numpy
def load_images(img_dir, img_ext):
# Read images, normalize images
print('Loading input images...')
img_names = sorted(glob(f'{img_dir}/*.{img_ext}'))
if len(img_names) == 0:
print(f'No images were able to be loaded from: {img_dir}.')
return
imgs = [normalize(img, 1, 99.8, axis=(0, 1)) for img in tqdm(list(map(io.imread, img_names)))]
return img_names, imgs
def make_target_image(tiff_image_metadata, labels): """ Loads the tiff images with the pahts in files_to_load. Then, it puts them in a list in the same order as labels and converts it to a [X, Y, C] numpy array. Then images are normalized by scaling from 0 to 1 """ filenames = [tiff_image_metadata[label] for label in labels] image = numpy.dstack(list(map(tifffile.imread, filenames))) #YXC image = normalize(image, 0, 100, axis = (0, 1)) return numpy.moveaxis(image, 0, 1) #XYC
def get_Yest_list(Y_est,
tag='instance_0',
ix_fg_list=[0],
pnorm=True,
tipo=0,
pmin=0.01,
pmax=99.9):
Y_est_list = []
if tipo == 0:
for i in np.arange(len(Y_est)):
start = True
for ix_fg in ix_fg_list:
if start:
Y_est_i = Y_est[i][tag][:, :, :, ix_fg]
else:
Y_est_i += Y_est[i][tag][:, :, :, ix_fg]
start = False
if (Y_est[i][tag].shape[0] == 1):
Y_est_i = Y_est[i][tag][0, ...]
if pnorm:
Y_est_i = normalize(Y_est_i, pmin=pmin, pmax=pmax, clip=True)
Y_est_list.append(Y_est_i)
else:
Y_est_aux = Y_est[tag]
for i in range(Y_est_aux.shape[0]):
start = True
for ix_fg in ix_fg_list:
if start:
Y_est_i = Y_est_aux[i, :, :, ix_fg]
else:
Y_est_i += Y_est_aux[i, :, :, ix_fg]
start = False
if pnorm:
Y_est_i = normalize(Y_est_i, pmin=pmin, pmax=pmax, clip=True)
Y_est_list.append(Y_est_i)
return Y_est_list
def display_img(filename, norm_min_percent, norm_max_percent):
img = tiff.imread(filename)
img = img.astype(np.float32)
t, x, y = img.shape[0:3]
img = img[int(t / 2), :, :]
img = normalize(img, norm_min_percent, norm_max_percent)
img = img * 255
return img
def test_load_and_predict_big():
model_path = path_model2d()
model = StarDist2D(None,
name=model_path.name,
basedir=str(model_path.parent))
img, _ = real_image2d()
x = normalize(img, 1, 99.8)
x = np.tile(x, (8, 8))
labels, polygons = model.predict_instances(x)
return labels
def test_load_and_predict_with_overlap(model3d):
model = model3d
img, mask = real_image3d()
x = normalize(img, 1, 99.8)
prob, dist = model.predict(x, n_tiles=(1, 2, 2))
assert prob.shape == dist.shape[:3]
assert model.config.n_rays == dist.shape[-1]
labels, _ = model.predict_instances(x, nms_thresh=.5, overlap_label=-3)
assert np.min(labels) == -3
return model, labels
def segment_nuclei_stardist(image2d,
sdmodel,
prob_thresh=0.5,
overlap_thresh=0.3,
norm=True,
norm_pmin=1.0,
norm_pmax=99.8,
norm_clip=False):
"""[summary]
:param image2d: 2d image to be segmented
:type image2d: NumPy.Array
:param sdmodel: stardit 2d model
:type sdmodel: StarDist Model
:param prob_thresh: probability threshold, defaults to 0.5
:type prob_thresh: float, optional
:param overlap_thresh: overlap threshold, defaults to 0.3
:type overlap_thresh: float, optional
:param norm: switch on image normalization, defaults to True
:type norm: bool, optional
:param norm_pmin: minimum percentile for normalization, defaults to 1.0
:type norm_pmin: float, optional
:param norm_pmax: maximum percentile for normalization, defaults to 99.8
:type norm_pmax: float, optional
:param norm_clip: clipping normalization, defaults to False
:type norm_clip: bool, optional
:return: mask - binary mask
:rtype: NumPy.Array
"""
# workaround explained here to avoid errors
# https://github.com/openai/spinningup/issues/16
# os.environ['KMP_DUPLICATE_LIB_OK'] = 'True'
# normalize image
image2d_norm = normalize(image2d,
pmin=norm_pmin,
pmax=norm_pmax,
axis=None,
clip=norm_clip,
eps=1e-20,
dtype=np.float32)
# predict the instances of th single nuclei
mask2d, details = sdmodel.predict_instances(image2d_norm,
axes=None,
normalizer=None,
prob_thresh=0.4,
nms_thresh=0.3,
n_tiles=None,
show_tile_progress=True,
overlap_label=None,
verbose=False)
return mask2d
def show_surface():
model = _model3d()
img, mask = test_image_nuclei_3d(return_mask=True)
x = normalize(img, 1, 99.8)
labels, polys = model.predict_instances(x)
surface = surface_from_polys(polys)
# add the surface
viewer = napari.view_image(img)
viewer.add_surface(surface)
return viewer
def test_load_and_predict_with_overlap():
model_path = path_model3d()
model = StarDist3D(None, name=model_path.name, basedir=str(model_path.parent))
img, mask = real_image3d()
x = normalize(img,1,99.8)
prob, dist = model.predict(x, n_tiles=(1,2,2))
assert prob.shape == dist.shape[:3]
assert model.config.n_rays == dist.shape[-1]
labels, _ = model.predict_instances(x, nms_thresh = .5,
overlap_label = -3)
assert np.min(labels) == -3
return model, labels
def render_label_example(model2d):
model = model2d
img, y_gt = real_image2d()
x = normalize(img, 1, 99.8)
y, _ = model.predict_instances(x)
# im = render_label(y,img = x, alpha = 0.3, alpha_boundary=1, cmap = (.3,.4,0))
im = render_label(y,img = x, alpha = 0.3, alpha_boundary=1)
import matplotlib.pyplot as plt
plt.figure(1)
plt.imshow(im)
plt.show()
return im
def _predict_stardist(self, model, file, T, channel, prob_thresh,
nms_thresh, out_dir):
axes = 'TCYX'
# if T.ndim==3:
# timelapse = T
if T.ndim == 4:
timelapse = T[:, channel]
else:
raise ValueError(
'Data has unexpected number of dimensions. Weird.')
# normalise
print(f'Normalizing each frame to run Stardist', flush=True)
timelapse = np.stack(
[normalize(frame, 1, 99.8) for frame in timelapse])
print(
f"Timelapse has axes {axes.replace('C','')} with shape {timelapse.shape}"
)
polygons = [
model.predict_instances(frame,
nms_thresh=nms_thresh,
prob_thresh=prob_thresh)[1]
for frame in tqdm(timelapse)
]
if prob_thresh is None:
prob_string = 'default'
else:
prob_string = f'{prob_thresh:.2f}'
if nms_thresh is None:
nms_string = 'default'
else:
nms_string = f'{nms_thresh:.2f}'
roi_path = out_dir / f"{file.stem}_prob={prob_string}_nms={nms_string}"
roi_path.parent.mkdir(parents=True, exist_ok=True)
rois_python = Path(str(roi_path) + '.npz')
rois_imagej = Path(str(roi_path) + '.zip')
print(f'Saving ImageJ ROIs to {rois_imagej}')
export_imagej_rois(str(rois_imagej),
[poly['coord'] for poly in polygons])
print(f'Saving Python rois to {rois_python}')
np.savez(
str(rois_python),
coord=[p['coord'] for p in polygons],
points=[p['points'] for p in polygons],
prob=[p['prob'] for p in polygons],
)
def test_polygon_order_2D(model2d):
model = model2d
img = real_image2d()[0]
img = normalize(img, 1, 99.8)
labels, polys = model.predict_instances(img, nms_thresh=0)
for i, coord in enumerate(polys['coord'], start=1):
# polygon representing object with id i
p = Polygon(coord, shape_max=labels.shape)
# mask of object with id i in label image (not occluded since nms_thresh=0)
mask_i = labels[p.slice] == i
assert np.all(p.mask == mask_i)
def STARPrediction3D(image,
model,
n_tiles,
MaskImage=None,
smartcorrection=None,
UseProbability=True):
copymodel = model
image = normalize(image, 1, 99.8, axis=(0, 1, 2))
shape = [image.shape[1], image.shape[2]]
image = zero_pad_time(image, 64, 64)
grid = copymodel.config.grid
MidImage, details = model.predict_instances(image, n_tiles=n_tiles)
SmallProbability, SmallDistance = model.predict(image, n_tiles=n_tiles)
StarImage = MidImage[:image.shape[0], :shape[0], :shape[1]]
SmallDistance = MaxProjectDist(SmallDistance, axis=-1)
Probability = np.zeros([
SmallProbability.shape[0] * grid[0],
SmallProbability.shape[1] * grid[1],
SmallProbability.shape[2] * grid[2]
])
Distance = np.zeros([
SmallDistance.shape[0] * grid[0], SmallDistance.shape[1] * grid[1],
SmallDistance.shape[2] * grid[2]
])
#We only allow for the grid parameter to be 1 along the Z axis
for i in range(0, SmallProbability.shape[0]):
Probability[i, :] = cv2.resize(
SmallProbability[i, :],
dsize=(SmallProbability.shape[2] * grid[2],
SmallProbability.shape[1] * grid[1]))
Distance[i, :] = cv2.resize(SmallDistance[i, :],
dsize=(SmallDistance.shape[2] * grid[2],
SmallDistance.shape[1] * grid[1]))
if UseProbability:
Probability[Probability < globalthreshold] = 0
MaxProjectDistance = Probability[:image.shape[0], :shape[0], :shape[1]]
else:
MaxProjectDistance = Distance[:image.shape[0], :shape[0], :shape[1]]
Watershed, Markers = WatershedwithMask3D(
MaxProjectDistance.astype('uint16'), StarImage.astype('uint16'),
MaskImage.astype('uint16'), grid)
Watershed = fill_label_holes(Watershed.astype('uint16'))
return Watershed, MaxProjectDistance, StarImage
def test_predict_dense_sparse(model2d):
model = model2d
img, mask = real_image2d()
x = normalize(img, 1, 99.8)
labels1, res1 = model.predict_instances(x, n_tiles=(2, 2), sparse=False)
labels2, res2 = model.predict_instances(x, n_tiles=(2, 2), sparse=True)
assert np.allclose(labels1, labels2)
assert all(
np.allclose(res1[k], res2[k])
for k in set(res1.keys()).union(set(res2.keys()))
if isinstance(res1[k], np.ndarray))
return labels2, res1, labels2, res2
def __getitem__(self, i):
#Read Raw images
if self.Normalize == True:
x = ReadFloat(self.files[i])
x = normalize(x, 1, 99.8, axis=self.axis_norm)
x = x
if self.labelMe == True:
#Read Label images
x = ReadInt(self.files[i])
x = x
return x
def test_load_and_predict(model3d):
model = model3d
img, mask = real_image3d()
x = normalize(img, 1, 99.8)
prob, dist = model.predict(x, n_tiles=(1, 2, 2))
assert prob.shape == dist.shape[:3]
assert model.config.n_rays == dist.shape[-1]
labels, _ = model.predict_instances(x)
assert labels.shape == img.shape[:3]
stats = matching(mask, labels, thresh=0.5)
assert (stats.fp, stats.tp, stats.fn) == (0, 30, 21)
return model, labels
def test_pretrained_integration():
from stardist.models import StarDist2D
img = normalize(real_image2d()[0])
model = StarDist2D.from_pretrained("2D_versatile_fluo")
prob, dist = model.predict(img)
y1, res1 = model._instances_from_prediction(img.shape,
prob,
dist,
nms_thresh=.3)
return y1, res1
def test_optimize_thresholds(model2d):
model = model2d
img, mask = real_image2d()
x = normalize(img, 1, 99.8)
res = model.optimize_thresholds([x], [mask],
nms_threshs=[.3, .5],
iou_threshs=[.3, .5],
optimize_kwargs=dict(tol=1e-1),
save_to_json=False)
np.testing.assert_almost_equal(res["prob"], 0.454617141955, decimal=3)
np.testing.assert_almost_equal(res["nms"] , 0.3, decimal=3)
