Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Refactor CTC dataset #215

Merged
merged 2 commits into from
Feb 9, 2024
Merged

Refactor CTC dataset #215

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
49ad7bd
Refactor ctc
anwai98 Feb 9, 2024
de8540b
Merge branch 'main' into rf-ctc
anwai98 Feb 9, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 2 additions & 4 deletions scripts/datasets/check_ctc.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
from torch_em.util.debug import check_loader
from torch_em.data.sampler import MinInstanceSampler

ROOT = "/home/pape/Work/data/ctc/ctc-training-data"
ROOT = "/scratch/projects/nim00007/sam/data/ctc/"


# Some of the datasets have partial sparse labels:
Expand All @@ -11,14 +11,12 @@
# Maybe depends on the split?!
def check_ctc_segmentation():
for name in CTC_URLS.keys():
if not name.startswith("DIC"):
continue
print("Checking dataset", name)
loader = get_ctc_segmentation_loader(
ROOT, name, (1, 512, 512), 1, download=True,
sampler=MinInstanceSampler()
)
check_loader(loader, 8, instance_labels=True)
check_loader(loader, 8, plt=True, save_path="ctc.png")


if __name__ == "__main__":
Expand Down
15 changes: 10 additions & 5 deletions torch_em/data/datasets/ctc.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,14 @@ def _require_ctc_dataset(path, dataset_name, download):

data_path = os.path.join(path, dataset_name)

if not os.path.exists(data_path):
url, checksum = CTC_URLS[dataset_name], CTC_CHECKSUMS[dataset_name]
zip_path = os.path.join(path, f"{dataset_name}.zip")
util.download_source(zip_path, url, download, checksum=checksum)
util.unzip(zip_path, path, remove=True)
if os.path.exists(data_path):
return data_path

os.makedirs(data_path)
url, checksum = CTC_URLS[dataset_name], CTC_CHECKSUMS[dataset_name]
zip_path = os.path.join(path, f"{dataset_name}.zip")
util.download_source(zip_path, url, download, checksum=checksum)
util.unzip(zip_path, path, remove=True)

return data_path

Expand Down Expand Up @@ -101,6 +104,8 @@ def get_ctc_segmentation_dataset(
splits = glob(os.path.join(data_path, "*_GT"))
splits = [os.path.basename(split) for split in splits]
splits = [split.rstrip("_GT") for split in splits]
else:
splits = split

image_path, label_path = _require_gt_images(data_path, splits)

Expand Down