299 add inference script (#338)

* add inference script

Signed-off-by: Yiheng Wang <[email protected]>

* add inference in train.py

Signed-off-by: Yiheng Wang <[email protected]>

* remove useless code

Signed-off-by: Yiheng Wang <[email protected]>

* update readme

Signed-off-by: Yiheng Wang <[email protected]>

* fix typos

Signed-off-by: Yiheng Wang <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* chmod -x for https://results.pre-commit.ci/run/github/288774122/1630661608.M-BPKNA4RVK82RHlCwxs9A

Signed-off-by: Wenqi Li <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fixes https://results.pre-commit.ci/run/github/288774122/1630661992.jBhcFROLTdee4TA3rmB0jQ

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: yiheng-wang-nv

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,7 +8,7 @@ assignees: ''
 ---
 
 **Describe the bug**
-A clear and concise description of what the bug is. 
+A clear and concise description of what the bug is.
 
 Please only create issues here relating to the functioning of the tutorials. For all other questions/problems/bugs, please refer to MONAI's [main repository](https://github.com/Project-MONAI/MONAI). For MONAI bugs (not just a problem in the notebook), please create an [issue](https://github.com/Project-MONAI/MONAI/issues). For questions, please use the [Discussions tab](https://github.com/Project-MONAI/MONAI/discussions).
 

.github/ISSUE_TEMPLATE/question.md

@@ -9,4 +9,4 @@ assignees: ''
 **Please use MONAI's Discussions tab**
 For questions relating to MONAI usage, please do not create an issue.
 
-Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found on the MONAI repository's main page (not the tutorials) next to Issues and Pull Requests along the top.
+Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found on the MONAI repository's main page (not the tutorials) next to Issues and Pull Requests along the top.

.github/pull_request_template.md

@@ -8,4 +8,4 @@ A few sentences describing the changes proposed in this pull request.
 
 ### Checks
 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
-- [ ] Notebook runs automatically `./runner [-p <regex_pattern>]`
+- [ ] Notebook runs automatically `./runner [-p <regex_pattern>]`

2d_classification/mednist_tutorial.ipynb

@@ -1347,4 +1347,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

3d_segmentation/brats_segmentation_3d.ipynb

@@ -58,7 +58,7 @@ def get_xforms(mode="train", keys=("image", "label")):
                     keys,
                     prob=0.15,
                     rotate_range=(0.05, 0.05, None),  # 3 parameters control the transform on 3 dimensions
-                    scale_range=(0.1, 0.1, None), 
+                    scale_range=(0.1, 0.1, None),
                     mode=("bilinear", "nearest"),
                     as_tensor_output=False,
                 ),

3d_segmentation/challenge_baseline/run_net.py

@@ -65,7 +65,7 @@ def main(tempdir):
     dataloader = DataLoader(dataset, batch_size=2, num_workers=4)
     # define post transforms
     post_transforms = Compose([
-        EnsureTyped(keys="pred"), 
+        EnsureTyped(keys="pred"),
         Activationsd(keys="pred", sigmoid=True),
         Invertd(
             keys="pred",  # invert the `pred` data field, also support multiple fields