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

Jump to bottom

Update the SaveImage transform to support saving input-output mapping. #7557

Open
binliunls opened this issue Mar 18, 2024 · 1 comment · May be fixed by #7769
Open

Update the SaveImage transform to support saving input-output mapping. #7557

binliunls opened this issue Mar 18, 2024 · 1 comment · May be fixed by #7769

Comments

@binliunls
Copy link
Contributor

Is your feature request related to a problem? Please describe.
When I run a segmentation bundle like spleen segmentation, I would like to have a new json/yaml/csv file to explicitly show the input-output mapping between images and labels. For example if the input and output folders are like:

--input
   --input_0.nii.gz
   --input_1.nii.gz
   -- ...
   --input_n.nii.gz

--output
   --input_0/input_0_seg.nii.gz
   --input_1/input_1_seg.nii.gz
   --...
   --input_n/input_n_seg.nii.gz

Describe the solution you'd like
A json file with content shown below should be generated if the parameter is specified:

[
    {image: ["/path/to/image/input/input_0.nii.gz"], label: ["/path/to/seg/output/input_0/input_0_seg.nii.gz"]},
    {image: ["/path/to/image/input/input_1.nii.gz"], label: ["/path/to/seg/output/input_1/input_1_seg.nii.gz"]},
    ...,
    {image: ["/path/to/image/input/input_n.nii.gz"], label: ["/path/to/seg/output/input_n/input_n_seg.nii.gz"]},
]

The image and label parameters are set to lists in case there are multiple inputs/outputs.
@staydelight

This comment was marked as off-topic.

Sign in to view
staydelight pushed a commit to staydelight/MONAI that referenced this issue May 14, 2024
Fixes Project-MONAI#7557
9bc4cd6 
Add a function to create a JSON file that maps input and output paths.

Signed-off-by: staydelight <[email protected]>
@staydelight staydelight linked a pull request May 14, 2024 that will close this issue
Open
7 tasks
staydelight pushed a commit to staydelight/MONAI that referenced this issue May 14, 2024
Fixes Project-MONAI#7557
93ccbdb 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue May 14, 2024
Fixes Project-MONAI#7557
7d1c3f3 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue May 14, 2024
Fixes Project-MONAI#7557
103ecdd 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 1, 2024
Fixes Project-MONAI#7557
9420317 
Add code for generating a mapping json file.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 1, 2024
Fixes Project-MONAI#7557
25668ac 
Change mapping_json_path init way.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 3, 2024
Fixes Project-MONAI#7557
f70de5b 
Fixing unsuccessful checks.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 3, 2024
Fixes Project-MONAI#7557
3086cf9 
Fixes unseccessful ckecks. (if mapping_json_path is not None)

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 3, 2024
Fixes Project-MONAI#7557
266f87c 
Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
afae503 
Add a function to create a JSON file that maps input and output paths.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
542a77d 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
7969d21 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
3ce5f30 
Remove changes unrelated to this issue.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
bfb6d58 
Add code for generating a mapping json file.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
894854d 
Change mapping_json_path init way.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
682379b 
Fixing unsuccessful checks.

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
56d8df5 
Fixes unseccessful ckecks. (if mapping_json_path is not None)

Signed-off-by: staydelight <[email protected]>
staydelight pushed a commit to staydelight/MONAI that referenced this issue Jun 13, 2024
Fixes Project-MONAI#7557
8bab11b 
Signed-off-by: staydelight <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Add a mapping function in image_reader.py and image_writer.py staydelight/MONAI
2 participants
@staydelight @binliunls