def plot(target_label,pred_label):
plt.figure(figsize=(16,10))
plt.subplot(211)
plt.imshow(target_label.squeeze(),cmap=random_label_cmap())
plt.axis('off')
plt.title('Ground truth')
plt.subplot(212)
plt.axis('off')
plt.imshow(pred_label,cmap=random_label_cmap())
plt.title('Predicted Label.')
plt.show()
def plot(volume, title=None, save=None, show=False):
if volume.ndim == 4:
for i in [1]:
plt.figure()
plt.imshow(volume[i, 1], vmin=0, vmax=a_max)
plt.title(title)
plt.colorbar()
if save:
plt.savefig(f'pics/{save}_dir_{title}')
elif volume.ndim == 3:
plt.figure()
plt.imshow(volume[1])
plt.title(title)
plt.colorbar()
if save:
plt.savefig(f'pics/{save}_dir_{title}')
else:
plt.figure()
plt.imshow(volume, cmap=random_label_cmap(n=1))
plt.title(title)
plt.colorbar()
if save:
plt.savefig(f'pics/{save}_dir_{title}')
if show:
plt.show()
def __init__(self,
from_pretrained='2D_versatile_fluo',
normalize_func=None):
if from_pretrained is None: # Train your own model
raise NotImplementedError
self.model = StarDist2D.from_pretrained(from_pretrained)
self.lbl_cmap = random_label_cmap()
if normalize_func is None:
self.normalize_func = self.default_normalize
def show_test_images(X, Y_truth, Y_pred, file_names, show_num=None):
num_images = min(show_num, len(X)) if show_num is not None else len(X)
lbl_cmap = random_label_cmap()
for i in range(num_images):
fig, axes = plt.subplots(1, 3, figsize=(20, 10))
axes[0].imshow(X[i], clim=(0, 1), cmap='gray')
axes[0].set_title(f'{file_names[i]}: raw image')
axes[0].axis('off')
axes[1].imshow(Y_truth[i], clim=(0, 1), cmap='gray')
axes[1].set_title(f'{file_names[i]}: ground truth')
axes[1].axis('off')
axes[2].imshow(X[i], clim=(0, 1), cmap='gray')
axes[2].imshow(Y_pred[i][0],
cmap=lbl_cmap,
interpolation="nearest",
alpha=0.5)
num_objects = len(Y_pred[i][1]['coord'])
axes[2].set_title(f'{file_names[i]}: predicted, {num_objects} objects')
axes[2].axis('off')
def main(argv):
base_path = "{}".format(os.getenv("HOME"))
problem_cls = CLASS_OBJSEG
with BiaflowsJob.from_cli(argv) as bj:
bj.job.update(status=Job.RUNNING,
progress=0,
statusComment="Initialization...")
# 1. Prepare data for workflow
in_imgs, gt_imgs, in_path, gt_path, out_path, tmp_path = prepare_data(
problem_cls, bj, is_2d=True, **bj.flags)
list_imgs = [image.filepath for image in in_imgs]
# 2. Run Stardist model on input images
bj.job.update(progress=25, statusComment="Launching workflow...")
#Loading pre-trained Stardist model
np.random.seed(17)
lbl_cmap = random_label_cmap()
model_fluo = StarDist2D(None,
name='2D_versatile_fluo',
basedir='/models/')
model_he = StarDist2D(None, name='2D_versatile_he', basedir='/models/')
#Go over images
for img_path in list_imgs:
fluo = True
img = imageio.imread(img_path)
n_channel = 3 if img.ndim == 3 else 1
if n_channel == 3:
# Check if 3-channel grayscale image or actually an RGB image
if np.array_equal(img[:, :, 0],
img[:, :, 1]) and np.array_equal(
img[:, :, 0], img[:, :, 2]):
img = skimage.color.rgb2gray(img)
else:
fluo = False
# normalize channels independently (0,1,2) normalize channels jointly (0,1)
axis_norm = (0, 1)
img = normalize(img,
bj.parameters.stardist_norm_perc_low,
bj.parameters.stardist_norm_perc_high,
axis=axis_norm)
#Stardist model prediction with thresholds
if fluo:
labels, details = model_fluo.predict_instances(
img,
prob_thresh=bj.parameters.stardist_prob_t,
nms_thresh=bj.parameters.stardist_nms_t)
else:
labels, details = model_he.predict_instances(
img,
prob_thresh=bj.parameters.stardist_prob_t,
nms_thresh=bj.parameters.stardist_nms_t)
# Convert labels to uint16 for BIAFLOWS
labels = labels.astype(np.uint16)
imageio.imwrite(os.path.join(out_path, os.path.basename(img_path)),
labels)
# 3. Upload data to BIAFLOWS
upload_data(problem_cls,
bj,
in_imgs,
out_path,
**bj.flags,
monitor_params={
"start": 60,
"end": 90,
"period": 0.1,
"prefix":
"Extracting and uploading polygons from masks"
})
# 4. Compute and upload metrics
bj.job.update(progress=90,
statusComment="Computing and uploading metrics...")
upload_metrics(problem_cls, bj, in_imgs, gt_path, out_path, tmp_path,
**bj.flags)
# 5. Pipeline finished
bj.job.update(progress=100,
status=Job.TERMINATED,
status_comment="Finished.")
def main(argv):
with CytomineJob.from_cli(argv) as conn:
conn.job.update(status=Job.RUNNING,
progress=0,
statusComment="Initialization...")
# base_path = "{}".format(os.getenv("HOME")) # Mandatory for Singularity
base_path = "/home/mmu/Desktop"
working_path = os.path.join(base_path, str(conn.job.id))
#Loading pre-trained Stardist model
np.random.seed(17)
lbl_cmap = random_label_cmap()
#Stardist H&E model downloaded from https://github.com/mpicbg-csbd/stardist/issues/46
#Stardist H&E model downloaded from https://drive.switch.ch/index.php/s/LTYaIud7w6lCyuI
model = StarDist2D(
None, name='2D_versatile_HE', basedir='/models/'
) #use local model file in ~/models/2D_versatile_HE/
#Select images to process
images = ImageInstanceCollection().fetch_with_filter(
"project", conn.parameters.cytomine_id_project)
list_imgs = []
if conn.parameters.cytomine_id_images == 'all':
for image in images:
list_imgs.append(int(image.id))
else:
list_imgs = [
int(id_img)
for id_img in conn.parameters.cytomine_id_images.split(',')
]
#Go over images
for id_image in conn.monitor(list_imgs,
prefix="Running detection on image",
period=0.1):
#Dump ROI annotations in img from Cytomine server to local images
#conn.job.update(status=Job.RUNNING, progress=0, statusComment="Fetching ROI annotations...")
roi_annotations = AnnotationCollection()
roi_annotations.project = conn.parameters.cytomine_id_project
roi_annotations.term = conn.parameters.cytomine_id_roi_term
roi_annotations.image = id_image #conn.parameters.cytomine_id_image
roi_annotations.showWKT = True
roi_annotations.fetch()
print(roi_annotations)
#Go over ROI in this image
#for roi in conn.monitor(roi_annotations, prefix="Running detection on ROI", period=0.1):
for roi in roi_annotations:
#Get Cytomine ROI coordinates for remapping to whole-slide
#Cytomine cartesian coordinate system, (0,0) is bottom left corner
print(
"----------------------------ROI------------------------------"
)
roi_geometry = wkt.loads(roi.location)
print("ROI Geometry from Shapely: {}".format(roi_geometry))
print("ROI Bounds")
print(roi_geometry.bounds)
minx = roi_geometry.bounds[0]
miny = roi_geometry.bounds[3]
#Dump ROI image into local PNG file
roi_path = os.path.join(
working_path,
str(roi_annotations.project) + '/' +
str(roi_annotations.image) + '/' + str(roi.id))
roi_png_filename = os.path.join(roi_path + '/' + str(roi.id) +
'.png')
print("roi_png_filename: %s" % roi_png_filename)
roi.dump(dest_pattern=roi_png_filename, mask=True, alpha=True)
#roi.dump(dest_pattern=os.path.join(roi_path,"{id}.png"), mask=True, alpha=True)
#Stardist works with TIFF images without alpha channel, flattening PNG alpha mask to TIFF RGB
im = Image.open(roi_png_filename)
bg = Image.new("RGB", im.size, (255, 255, 255))
bg.paste(im, mask=im.split()[3])
roi_tif_filename = os.path.join(roi_path + '/' + str(roi.id) +
'.tif')
bg.save(roi_tif_filename, quality=100)
X_files = sorted(glob(roi_path + '/' + str(roi.id) + '*.tif'))
X = list(map(imread, X_files))
n_channel = 3 if X[0].ndim == 3 else X[0].shape[-1]
axis_norm = (
0, 1
) # normalize channels independently (0,1,2) normalize channels jointly
if n_channel > 1:
print("Normalizing image channels %s." %
('jointly' if axis_norm is None or 2 in axis_norm
else 'independently'))
#Going over ROI images in ROI directory (in our case: one ROI per directory)
for x in range(0, len(X)):
print("------------------- Processing ROI file %d: %s" %
(x, roi_tif_filename))
img = normalize(X[x],
conn.parameters.stardist_norm_perc_low,
conn.parameters.stardist_norm_perc_high,
axis=axis_norm)
#Stardist model prediction with thresholds
labels, details = model.predict_instances(
img,
prob_thresh=conn.parameters.stardist_prob_t,
nms_thresh=conn.parameters.stardist_nms_t)
print("Number of detected polygons: %d" %
len(details['coord']))
cytomine_annotations = AnnotationCollection()
#Go over detections in this ROI, convert and upload to Cytomine
for pos, polygroup in enumerate(details['coord'], start=1):
#Converting to Shapely annotation
points = list()
for i in range(len(polygroup[0])):
#Cytomine cartesian coordinate system, (0,0) is bottom left corner
#Mapping Stardist polygon detection coordinates to Cytomine ROI in whole slide image
p = Point(minx + polygroup[1][i],
miny - polygroup[0][i])
points.append(p)
annotation = Polygon(points)
#Append to Annotation collection
cytomine_annotations.append(
Annotation(
location=annotation.wkt,
id_image=
id_image, #conn.parameters.cytomine_id_image,
id_project=conn.parameters.cytomine_id_project,
id_terms=[
conn.parameters.cytomine_id_cell_term
]))
print(".", end='', flush=True)
#Send Annotation Collection (for this ROI) to Cytomine server in one http request
ca = cytomine_annotations.save()
conn.job.update(status=Job.TERMINATED,
progress=100,
statusComment="Finished.")
return 'x=%1.4f, y=%1.4f' % (x, y)
return format_coord
#for i in range(labels_new.shape[0]):
# fig, ax = plt.subplots(1, 1)
# ax.imshow(labels_new[i], cmap='tab20b')
# ax.format_coord = format_maker(labels_new[i])
#plt.show()
fig, axes = plt.subplots(1, 3, figsize=(20, 8))
axes[0].imshow(labels_new[plot_slice], cmap=random_label_cmap())
axes[0].set_title('reconstruction')
axes[0].format_coord = format_maker(labels_new[plot_slice])
axes[1].imshow(labels[plot_slice], cmap=random_label_cmap())
axes[1].set_title('input')
x = [offset[2] for offset in offsets_new]
y = [offset[1] for offset in offsets_new]
#c = ['b']*number_of_attractive_channels + ['r']*(len(offsets_new)-number_of_attractive_channels)
axes[2].scatter(x[:number_of_attractive_channels], y[:number_of_attractive_channels], c='blue', label='attractive')
axes[2].scatter(x[number_of_attractive_channels:], y[number_of_attractive_channels:], c='red', label='repulsive')
axes[2].legend()
axes[2].set_title('attractive and repulsive edges')
my_parser.add_argument('--use_gpu',type=bool,default=True,help='Use GPU or not')
my_parser.add_argument('--grid',type=list,default=(2,2),help='Subsampled grid for increased efficiency and larger field of view')
my_parser.add_argument('--limit_gpu_mem',type=float,default=0.8,help='Limit for the GPU memory usage')
my_parser.add_argument('--model_dir',type=str,default='models',help='Models directory')
my_parser.add_argument('--model_name',type=str,default='stardist',help='Name of the model')
my_parser.add_argument('--quick_demo',type=bool,default='False',help='Run quick training demo (True) or full training (False)')
my_parser.add_argument('--epochs',type=int,default=400,help='Number of training epochs')
my_parser.add_argument('--steps_per_epoch',type=int,default=100,help='Steps per training epoch')
args = my_parser.parse_args()
trainpath=args.path
np.random.seed(42)
lbl_cmap = random_label_cmap()
X = sorted(glob(trainpath+'/images/*.tif'))
Y = sorted(glob(trainpath+'/masks/*.tif'))
assert all(Path(x).name==Path(y).name for x,y in zip(X,Y))
X = list(map(imread,X))
Y = list(map(imread,Y))
n_channel = 1 if X[0].ndim == 2 else X[0].shape[-1]
axis_norm = (0,1) # normalize channels independently
# axis_norm = (0,1,2) # normalize channels jointly
if n_channel > 1:
import sys
import numpy as np
import matplotlib.pyplot as plt
import skimage
import csbdeep.utils
import stardist
sys.path.append('../')
import utils.evaluation
import utils.predictions
lbl_cmap = stardist.random_label_cmap()
def _visualize_intersection(y_true, y_pred):
'''
'''
y_true = y_true > 0
y_pred = y_pred > 0
img = np.zeros([y_true.shape[0], y_true.shape[1], 3])
# Red – false negatives
img[:, :, 0] = np.where(y_true == y_pred, 0, 1)
# Green – true positives
img[:, :, 1] = np.where(y_true == y_pred, y_pred, 0)
# Blue – false positives
img[:, :, 2] = np.where(y_true == y_pred, y_true != y_pred, 0)
return img