Skip to content

Commit 5c9a0ac

Browse files
Update pathology tumor detection readme (#584)
Fixes # . ### Description This bundle takes large system RAM, thus It would be helpful to add a warning. ### Status **Ready** ### Please ensure all the checkboxes: <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Codeformat tests passed locally by running `./runtests.sh --codeformat`. - [ ] In-line docstrings updated. - [ ] Update `version` and `changelog` in `metadata.json` if changing an existing bundle. - [ ] Please ensure the naming rules in config files meet our requirements (please refer to: `CONTRIBUTING.md`). - [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy` are correct in `metadata.json`. - [ ] Descriptions should be consistent with the content, such as `eval_metrics` of the provided weights and TorchScript modules. - [ ] Files larger than 25MB are excluded and replaced by providing download links in `large_file.yml`. - [ ] Avoid using path that contains personal information within config files (such as use `/home/your_name/` for `"bundle_root"`). --------- Signed-off-by: Yiheng Wang <[email protected]>
1 parent de5a004 commit 5c9a0ac

File tree

2 files changed

+6
-1
lines changed

2 files changed

+6
-1
lines changed

models/pathology_tumor_detection/configs/metadata.json

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,8 @@
11
{
22
"schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
3-
"version": "0.5.7",
3+
"version": "0.5.8",
44
"changelog": {
5+
"0.5.8": "update readme to add memory warning",
56
"0.5.7": "update channel_def in metadata",
67
"0.5.6": "fix the wrong GPU index issue of multi-node",
78
"0.5.5": "modify mgpu logging level",

models/pathology_tumor_detection/docs/README.md

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -62,6 +62,10 @@ The training pipeline is a json file (dataset.json) which includes path to each
6262

6363
A probability number of the input patch being tumor or normal.
6464

65+
### Memory Consumption Warning
66+
67+
If you face memory issues in traning, you can lower the `batch_size` in the configurations to reduce the System RAM requirements.
68+
6569
### Inference on a WSI
6670

6771
Inference is performed on WSI in a sliding window manner with specified stride. A foreground mask is needed to specify the region where the inference will be performed on, given that background region which contains no tissue at all can occupy a significant portion of a WSI. Output of the inference pipeline is a probability map of size 1/stride of original WSI size.

0 commit comments

Comments
 (0)