From 4bfc8e97661d44cc13553721e5025005757bad91 Mon Sep 17 00:00:00 2001
From: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Date: Tue, 2 May 2023 14:50:17 +0000
Subject: [PATCH] Auto3DSeg ensemble tests images depend on #GPUs + docstring
improvement (#6457)
Fixes #6456.
### Description
- Make the test images also depend on GPUs
- Improve docstring for infer
### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.
---------
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
---
docs/source/apps.rst | 1 +
monai/apps/auto3dseg/ensemble_builder.py | 20 ++++++++++++++------
tests/test_auto3dseg_ensemble.py | 2 +-
tests/test_integration_autorunner.py | 2 +-
4 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/docs/source/apps.rst b/docs/source/apps.rst
index 8c422b16c5..e543859b7c 100644
--- a/docs/source/apps.rst
+++ b/docs/source/apps.rst
@@ -252,6 +252,7 @@ FastMRIReader
-----------
.. automodule:: monai.apps.auto3dseg
:members:
+ :special-members: __call__
:imported-members:
`nnUNet`
diff --git a/monai/apps/auto3dseg/ensemble_builder.py b/monai/apps/auto3dseg/ensemble_builder.py
index db304a6860..d95222946c 100644
--- a/monai/apps/auto3dseg/ensemble_builder.py
+++ b/monai/apps/auto3dseg/ensemble_builder.py
@@ -136,14 +136,22 @@ def __call__(self, pred_param: dict | None = None) -> list:
in this function, and the second group will be passed to the `InferClass` to override the
parameters of the class functions.
The first group contains:
- 'files_slices': a value type of `slice`. The files_slices will slice the infer_files and only
- make prediction on the infer_files[file_slices].
- 'mode': ensemble mode. Currently "mean" and "vote" (majority voting) schemes are supported.
- 'sigmoid': use the sigmoid function (e.g. x>0.5) to convert the prediction probability map to
- the label class prediction, otherwise argmax(x) is used.
+
+ - ``"infer_files"``: file paths to the images to read in a list.
+ - ``"files_slices"``: a value type of `slice`. The files_slices will slice the ``"infer_files"`` and
+ only make prediction on the infer_files[file_slices].
+ - ``"mode"``: ensemble mode. Currently "mean" and "vote" (majority voting) schemes are supported.
+ - ``"image_save_func"``: a dictionary used to instantiate the ``SaveImage`` transform. When specified,
+ the ensemble prediction will save the prediciton files, instead of keeping the files in the memory.
+ Example: `{"_target_": "SaveImage", "output_dir": "./"}`
+ - ``"sigmoid"``: use the sigmoid function (e.g. x > 0.5) to convert the prediction probability map
+ to the label class prediction, otherwise argmax(x) is used.
+
+ The parameters in the second group is defined in the ``config`` of each Algo templates. Please check:
+ https://github.com/Project-MONAI/research-contributions/tree/main/auto3dseg/algorithm_templates
Returns:
- A list of tensors.
+ A list of tensors or file paths, depending on whether ``"image_save_func"`` is set.
"""
param = {} if pred_param is None else deepcopy(pred_param)
files = self.infer_files
diff --git a/tests/test_auto3dseg_ensemble.py b/tests/test_auto3dseg_ensemble.py
index a95f30cfb4..e5eb957b1c 100644
--- a/tests/test_auto3dseg_ensemble.py
+++ b/tests/test_auto3dseg_ensemble.py
@@ -46,7 +46,7 @@
num_images_per_batch = 2
fake_datalist: dict[str, list[dict]] = {
- "testing": [{"image": "val_001.fake.nii.gz"}, {"image": "val_002.fake.nii.gz"}],
+ "testing": [{"image": f"ts_image_{idx:03d}.nii.gz"} for idx in range(num_images_perfold)],
"training": [
{
"fold": f,
diff --git a/tests/test_integration_autorunner.py b/tests/test_integration_autorunner.py
index 62951ea5d6..7110db568d 100644
--- a/tests/test_integration_autorunner.py
+++ b/tests/test_integration_autorunner.py
@@ -38,7 +38,7 @@
num_images_per_batch = 2
sim_datalist: dict[str, list[dict]] = {
- "testing": [{"image": "val_001.fake.nii.gz"}, {"image": "val_002.fake.nii.gz"}],
+ "testing": [{"image": f"ts_image__{idx:03d}.nii.gz"} for idx in range(num_images_perfold)],
"training": [
{
"fold": f,