def create_catch_dataset(request):
download_path.mkdir(parents=True, exist_ok=True)
# If this is a POST request then process the Form data
if request.method == 'POST':
# Create a form instance and populate it with data from the request (binding):
new_form = CATCH_DatasetForm(request.POST)
# Check if the form is valid:
if new_form.is_valid():
errors = []
team = get_object_or_404(Team, id=new_form.data['team'])
image_set_name = new_form.data["name"]
product_name = "Skin Tissue Types"
# create imageset, product and annotation type etc.
with transaction.atomic():
labels = {
'Bone': None,
'Cartilage': None,
'Dermis': None,
'Epidermis': None,
'Subcutis': None,
'Inflamm/Necrosis': None,
'Melanoma': None,
'Plasmacytoma': None,
'Mast Cell Tumor': None,
'PNST': None,
'SCC': None,
'Trichoblastoma': None,
'Histiocytoma': None
}
# create or load product
product = Product.objects.filter(name=product_name,
team=team).first()
if product is None:
product = Product.objects.create(name=product_name,
team=team,
creator=request.user)
# create or load AnnotationType
for label, code in zip(labels.keys(), [
"#808000", "#008000", "#0000FF", "#00FFFF", "#FF0000",
"#FF00FF", "#FF8800", "#FFFF00", "#00FF00", "#A52A2A",
"#ADD8E6", "#00008B", "#800080"
]):
anno_type = AnnotationType.objects.filter(
name=label, product=product).first()
if anno_type is None:
anno_type = AnnotationType.objects.create(
name=label,
vector_type=5,
product=product,
color_code=code)
labels[label] = anno_type
# create imageset
image_set = ImageSet.objects.filter(name=image_set_name,
team=team).first()
if image_set is None:
image_set = ImageSet.objects.create(
team=team,
creator=request.user,
name=image_set_name,
)
image_set.product_set.add(product)
image_set.create_folder()
image_set.save()
annotations_path = download_path / "annotations.json"
url = 'https://wiki.cancerimagingarchive.net/download/attachments/101941773/CATCH.json?version=1&modificationDate=1641393368399&api=v2'
gdown.download(url,
str(annotations_path),
quiet=True,
proxy=new_form.data["proxy"])
rows = []
with open(annotations_path) as f:
data = json.load(f)
categories = {
cat["id"]: cat["name"]
for cat in data["categories"]
}
for row in data["images"]:
file_name = row["file_name"]
image_id = row["id"]
width = row["width"]
height = row["height"]
for annotation in [
anno for anno in data['annotations']
if anno["image_id"] == image_id
]:
polygon = annotation["segmentation"]
cat = categories[annotation["category_id"]]
rows.append([
file_name, image_id, width, height, polygon,
cat
])
df = pd.DataFrame(rows,
columns=[
"file_name", "image_id", "width",
"height", "polygon", "cat"
])
for f in request.FILES.getlist('images'):
old_filename = Path(f.file.name)
new_filename = Path(image_set.root_path()) / f._name
copy(old_filename, new_filename)
image = Image.objects.filter(filename=f._name,
image_set=image_set).first()
if image is None:
try:
# creates a checksum for image
fchecksum = hashlib.sha512()
with open(new_filename, 'rb') as fil:
buf = fil.read(10000)
fchecksum.update(buf)
fchecksum = fchecksum.digest()
image = Image(name=f._name,
image_set=image_set,
checksum=fchecksum)
image.save_file(new_filename)
imageDf = df[df["file_name"] == f._name]
for label, vector in zip(imageDf['cat'],
imageDf['polygon']):
if label in labels:
result_dict = {}
index = 1
vector = np.array(vector).reshape((-1, 2))
for x, y in vector:
result_dict['x{}'.format(index)] = int(
x)
result_dict['y{}'.format(index)] = int(
y)
index += 1
annotation_type = labels[label]
anno = Annotation.objects.create(
annotation_type=annotation_type,
user=request.user,
image=image,
vector=result_dict)
except Exception as e:
errors.append(e.message)
if image_set is not None:
# view last created image set
return view_imageset(request, image_set.id)
# If this is a GET (or any other method) create the default form.
form = CATCH_DatasetForm(user=request.user)
context = {
'catch_form': form,
}
return TemplateResponse(request, 'catch.html', context)
def create_eiph_dataset(request):
# If this is a POST request then process the Form data
if request.method == 'POST':
# Create a form instance and populate it with data from the request (binding):
form = DatasetForm(request.POST)
# Check if the form is valid:
if form.is_valid():
team = get_object_or_404(Team, id=form.data['team'])
image_set_name = form.data["name"]
product_name = form.data["name"] + " Product"
url = 'https://drive.google.com/uc?id='
annotations_path = download_path / "05_EIPH_BerlinerBalu.txt"
gdown.download(url,
str(annotations_path),
quiet=True,
proxy=form.data["proxy"])
# create imageset, product and annotation type etc.
with transaction.atomic():
labels = {
'0': None,
"1": None,
"2": None,
"3": None,
"4": None
}
annotations = pd.read_csv(annotations_path,
delimiter="|",
names=["file", "class", "vector"])
# create or load product
product = Product.objects.filter(name=product_name,
team=team).first()
if product is None:
product = Product.objects.create(name=product_name,
team=team,
creator=request.user)
product.save()
# create or load AnnotationType
for label in labels.keys():
anno_type = AnnotationType.objects.filter(
name=label, product=product).first()
if anno_type is None:
anno_type = AnnotationType.objects.create(
name=label, vector_type=1, product=product)
labels[label] = anno_type
#create imageset
image_set = ImageSet.objects.filter(name=image_set_name,
team=team).first()
if image_set is None:
image_set = ImageSet.objects.create(team=team,
creator=request.user,
name=image_set_name,
product=[product])
image_set.create_folder()
#create images
url = 'https://drive.google.com/uc?id=1N0tOpj-tVnTHkQIp15lSxn7HZbGJQ_qQ'
file_path = Path(image_set.root_path()
) / "26_EIPH_566482 L Berliner Blau.svs"
gdown.download(url,
str(file_path),
quiet=True,
proxy=form.data["proxy"])
image = Image.objects.filter(filename=file_path.name,
image_set=image_set).first()
if image is None:
try:
# creates a checksum for image
fchecksum = hashlib.sha512()
with open(file_path, 'rb') as fil:
buf = fil.read(10000)
fchecksum.update(buf)
fchecksum = fchecksum.digest()
image = Image(name=file_path.name,
image_set=image_set,
checksum=fchecksum)
image.save_file(file_path)
# save annotations for image
for label, vector in zip(annotations["class"],
annotations["vector"]):
vector = json.loads(vector)
annotation_type = labels[str(label)]
anno = Annotation.objects.create(
annotation_type=annotation_type,
user=request.user,
image=image,
vector=vector)
except Exception as e:
errors.append(e.message)
# view image set
return view_imageset(request, image_set.id)
# If this is a GET (or any other method) create the default form.
form = DatasetForm(user=request.user)
context = {
'asthma_form': form,
}
return TemplateResponse(request, 'dataset_asthma.html', context)
def create_mitos_wsi_cmc_dataset(request):
download_path.mkdir(parents=True, exist_ok=True)
# If this is a POST request then process the Form data
if request.method == 'POST':
# Create a form instance and populate it with data from the request (binding):
new_form = MITOS_WSI_CMCDatasetForm(request.POST)
# Check if the form is valid:
if new_form.is_valid():
files = new_form.cleaned_data["files"]
errors = []
team = get_object_or_404(Team, id=new_form.data['team'])
image_set_name = new_form.data["name"]
product_name = new_form.data["name"] + " Product"
# create imageset, product and annotation type etc.
with transaction.atomic():
labels = {
'Mitotic cell look-alike': None,
"Mitotic figure": None
}
# create or load product
product = Product.objects.filter(name=product_name,
team=team).first()
if product is None:
product = Product.objects.create(name=product_name,
team=team,
creator=request.user)
# create or load AnnotationType
for label, code in zip(labels.keys(), ["#21ff22", "#0000ef"]):
anno_type = AnnotationType.objects.filter(
name=label, product=product).first()
if anno_type is None:
anno_type = AnnotationType.objects.create(
name=label,
vector_type=1,
product=product,
color_code=code)
labels[label] = anno_type
#create imageset
image_set = ImageSet.objects.filter(name=image_set_name,
team=team).first()
if image_set is None:
image_set = ImageSet.objects.create(
team=team,
creator=request.user,
name=image_set_name,
)
image_set.product_set.add(product)
image_set.create_folder()
image_set.save()
#create images
url = new_form.data["database"]
annotations_path = download_path / "MITOS_WSI_CMC_MEL.txt"
gdown.download(url,
str(annotations_path),
quiet=True,
proxy=new_form.data["proxy"])
annotations = pd.read_csv(annotations_path, delimiter="|")
for url in files:
file_name = [
url_name[1] for url_name in new_form.FILE_CHOICES
if url_name[0] == url
][0]
file_path = Path(
image_set.root_path()) / "{0}.svs".format(file_name)
urllib.request.urlretrieve(url, str(file_path))
image = Image.objects.filter(filename=file_path.name,
image_set=image_set).first()
if image is None:
try:
# creates a checksum for image
fchecksum = hashlib.sha512()
with open(file_path, 'rb') as fil:
buf = fil.read(10000)
fchecksum.update(buf)
fchecksum = fchecksum.digest()
image = Image(name=file_path.name,
image_set=image_set,
checksum=fchecksum)
image.save_file(file_path)
image_annotations = annotations[annotations["file"]
== file_path.name]
# save annotations for image
for label, vector in zip(
image_annotations["class"],
image_annotations["vector"]):
if label in labels:
vector = json.loads(
vector.replace("'", "\""))
vector["x1"], vector["x2"], vector[
"y1"], vector["y2"] = int(
vector["x1"]), int(
vector["x2"]), int(
vector["y1"]), int(
vector["y2"])
annotation_type = labels[label]
anno = Annotation.objects.create(
annotation_type=annotation_type,
user=request.user,
image=image,
vector=vector)
except Exception as e:
errors.append(e.message)
# view image set
return view_imageset(request, image_set.id)
# If this is a GET (or any other method) create the default form.
form = MITOS_WSI_CMCDatasetForm(user=request.user)
context = {
'mitos_wsi_cmc_form': form,
}
return TemplateResponse(request, 'mitos_wsi_cmc_form.html', context)
def create_asthma_dataset(request):
download_path.mkdir(parents=True, exist_ok=True)
# If this is a POST request then process the Form data
if request.method == 'POST':
# Create a form instance and populate it with data from the request (binding):
form = DatasetForm(request.POST)
# Check if the form is valid:
if form.is_valid():
team = get_object_or_404(Team, id=form.data['team'])
image_set_name = form.data["name"]
product_name = form.data["name"] + " Product"
url = 'https://drive.google.com/uc?id=1_w_AcWa54yj1Ye4H4loEfBtgl4hvQFSp'
annotations_path = download_path / "Asthma_Annotations.pkl"
gdown.download(url,
str(annotations_path),
quiet=True,
proxy=form.data["proxy"])
# create imageset, product and annotation type etc.
with transaction.atomic():
labels = {
'Mastzellen': None,
"Makrophagen": None,
"Neutrophile": None,
"Eosinophile": None,
"Lymohozyten": None
}
annotations = pd.read_pickle(annotations_path)
annotations = annotations[annotations["deleted"] == False]
annotations = annotations[annotations["class"].isin(
labels.keys())]
# create or load product
product = Product.objects.filter(name=product_name,
team=team).first()
if product is None:
product = Product.objects.create(name=product_name,
team=team,
creator=request.user)
product.save()
# create or load AnnotationType
for label in labels.keys():
anno_type = AnnotationType.objects.filter(
name=label, product=product).first()
if anno_type is None:
anno_type = AnnotationType.objects.create(
name=label, vector_type=1, product=product)
labels[label] = anno_type
#create imageset
image_set = ImageSet.objects.filter(name=image_set_name,
team=team).first()
if image_set is None:
image_set = ImageSet.objects.create(team=team,
creator=request.user,
name=image_set_name,
product=[product])
image_set.create_folder()
#create images
url = 'https://drive.google.com/uc?id='
file_path = Path(
image_set.root_path()) / "BAL AIA Blickfang Luft.svs"
gdown.download(url,
str(file_path),
quiet=True,
proxy=form.data["proxy"])
image = Image.objects.filter(filename=file_path.name,
image_set=image_set).first()
if image is None:
try:
# creates a checksum for image
fchecksum = hashlib.sha512()
with open(file_path, 'rb') as fil:
buf = fil.read(10000)
fchecksum.update(buf)
fchecksum = fchecksum.digest()
image = Image(name=file_path.name,
image_set=image_set,
checksum=fchecksum)
image.save_file(file_path)
annotations = annotations[annotations["image_name"] ==
file_path.name]
# save annotations for image
for label, vector, uuid in zip(
annotations["class"], annotations["vector"],
annotations["unique_identifier"]):
annotation_type = labels[label]
anno = Annotation.objects.filter(
unique_identifier=uuid, image=image).first()
if anno is None:
anno = Annotation.objects.create(
annotation_type=annotation_type,
unique_identifier=uuid,
user=request.user,
image=image,
vector=vector)
except Exception as e:
errors.append(e.message)
# view image set
return view_imageset(request, image_set.id)
# If this is a GET (or any other method) create the default form.
form = DatasetForm(user=request.user)
context = {
'asthma_form': form,
}
return TemplateResponse(request, 'dataset_asthma.html', context)
def create_miccai_eiph_dataset(request):
download_path.mkdir(parents=True, exist_ok=True)
# If this is a POST request then process the Form data
if request.method == 'POST':
# Create a form instance and populate it with data from the request (binding):
form = DatasetForm(request.POST)
# Check if the form is valid:
if form.is_valid():
errors = []
team = get_object_or_404(Team, id=form.data['team'])
image_set_name = form.data["name"]
product_name = form.data["name"] + " Product"
# create imageset, product and annotation type etc.
with transaction.atomic():
labels = {
'0': None,
"1": None,
"2": None,
"3": None,
"4": None
}
# create or load product
product = Product.objects.filter(name=product_name,
team=team).first()
if product is None:
product = Product.objects.create(name=product_name,
team=team,
creator=request.user)
# create or load AnnotationType
for label, code in zip(
labels.keys(),
["#0000FF", "#FF00FF", "#FF0000", "#808000", "#FFFF00"]):
anno_type = AnnotationType.objects.filter(
name=label, product=product).first()
if anno_type is None:
anno_type = AnnotationType.objects.create(
name=label,
vector_type=1,
product=product,
color_code=code)
labels[label] = anno_type
#create imageset
image_set = ImageSet.objects.filter(name=image_set_name,
team=team).first()
if image_set is None:
image_set = ImageSet.objects.create(
team=team,
creator=request.user,
name=image_set_name,
)
image_set.product_set.add(product)
image_set.create_folder()
image_set.save()
#create images
url = 'https://drive.google.com/uc?id=1yFjYkLbXxcsG2s8Mk8XGGmLUHPaj8jnJ'
zip_path = Path(image_set.root_path()) / "EIPH.zip"
gdown.download(url,
str(zip_path),
quiet=True,
proxy=form.data["proxy"])
# unpack zip-file
zip_ref = zipfile.ZipFile(str(zip_path), 'r')
zip_ref.extractall(image_set.root_path())
zip_ref.close()
# delete zip-file
os.remove(str(zip_path))
filenames = [
Path(image_set.root_path()) / f.filename
for f in zip_ref.filelist if ".txt" not in f.filename
]
annotations_path = Path(
image_set.root_path()) / "ground truth.txt"
annotations = pd.read_csv(annotations_path,
delimiter="|",
names=[
"file", "class", "vector", "1",
"2", "3", "4", "5", "6", "7", "8"
])
for file_path in filenames:
image = Image.objects.filter(filename=file_path.name,
image_set=image_set).first()
if image is None:
try:
# creates a checksum for image
fchecksum = hashlib.sha512()
with open(file_path, 'rb') as fil:
buf = fil.read(10000)
fchecksum.update(buf)
fchecksum = fchecksum.digest()
image = Image(name=file_path.name,
image_set=image_set,
checksum=fchecksum)
image.save_file(file_path)
image_annotations = annotations[annotations["file"]
== file_path.name]
# save annotations for image
for label, vector in zip(
image_annotations["class"],
image_annotations["vector"]):
label = str(label)
if label in labels:
vector = json.loads(vector)
vector["x1"], vector["x2"], vector[
"y1"], vector["y2"] = int(
vector["x1"]), int(
vector["x2"]), int(
vector["y1"]), int(
vector["y2"])
annotation_type = labels[label]
anno = Annotation.objects.create(
annotation_type=annotation_type,
user=request.user,
image=image,
vector=vector)
except Exception as e:
errors.append(e.message)
# view image set
return view_imageset(request, image_set.id)
# If this is a GET (or any other method) create the default form.
form = DatasetForm(user=request.user)
context = {
'eiph_miccai_form': form,
}
return TemplateResponse(request, 'eiph_miccai_form.html', context)
