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Merged
bhashemian merged 33 commits into from
Dec 8, 2022
Merged

ROI Inference pipeline for HoVerNet #1055

bhashemian merged 33 commits into from
Dec 8, 2022

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@bhashemian bhashemian commented Nov 17, 2022

Fixes Project-MONAI/MONAI#5539

Description

A few sentences describing the changes proposed in this pull request.

Checks

  • Notebook runs automatically ./runner [-p <regex_pattern>]

@bhashemian
Add a draft of inference
979e05a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Uncomment load weights
d3b77de 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add infer_roi
fc271ef 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Major updates
6582442 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian mentioned this pull request Nov 18, 2022
Merged
2 tasks
@bhashemian
Update the pipeline
d9d19b5 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' into wsi-inference-hovernet
4d6bd79
@bhashemian bhashemian mentioned this pull request Nov 21, 2022
Merged
6 tasks
@bhashemian
keep rio inference only
0cdac25 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian marked this pull request as ready for review November 21, 2022 18:18
@bhashemian
Remove test-oly lines
e58050c 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add sw batch size
123b721 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Change settings:
04c1f45 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Nic-Ma
Nic-Ma reviewed Nov 22, 2022
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Nic-Ma
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Same as @KumoLiu 's PR, I think we should put a README doc for these python code.

Thanks.

KumoLiu
KumoLiu reviewed Nov 22, 2022
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@bhashemian
Address comments
6b61c77 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' into wsi-inference-hovernet
a534937
@bhashemian
clean up
ea99823 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
fix a typo
e79f5f8 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
change logic of few args
0f0884f 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add multi-gpu
b1dac05 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add/remove prints
ccc62ed 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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bhashemian commented Nov 22, 2022 •
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Same as @KumoLiu 's PR, I think we should put a README doc for these python code.

Thanks.

I will update the same README in #999 is (after it merged) as they are going to be in the same folder.

@bhashemian
Rename to inference
a10f7a8 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add output class
ec9d8f1 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update to FalttenSubKeysd
73400f2 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' of https://github.com/Project-MONAI/tutorials int…
eb23e7d 
…o wsi-inference-hovernet
@bhashemian
Update with the new hovernet postprocessing
aa4a770 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' into wsi-inference-hovernet
5eb776f
@bhashemian
change to nuclear type
a4aa476 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
to png
4deb7c5 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
remove test transform
16ad09e 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' into wsi-inference-hovernet
f24b2c2
@bhashemian bhashemian requested a review from KumoLiu December 8, 2022 02:17
@bhashemian
Merge branch 'main' into wsi-inference-hovernet
7b06bb5
@bhashemian
Some updates
9c4a2bf 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian requested review from Nic-Ma and wyli December 8, 2022 15:21
@bhashemian
Remove device
d03067a 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
few improvements
0450963 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
improvments and bug fix
56d2e98 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update default run
8df9008 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian enabled auto-merge (squash) December 8, 2022 20:07
@bhashemian bhashemian merged commit 430cc81 into Project-MONAI:main Dec 8, 2022
@bhashemian bhashemian deleted the wsi-inference-hovernet branch December 8, 2022 20:36
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
@bhashemian
ROI Inference pipeline for HoVerNet (Project-MONAI#1055)
8de3193 
Fixes Project-MONAI/MONAI#5539

### Description
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>]`

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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@KumoLiu KumoLiu KumoLiu approved these changes

@SachidanandAlle SachidanandAlle Awaiting requested review from SachidanandAlle

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

@wyli wyli Awaiting requested review from wyli

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Pathology HoVerNet: Inference pipeline (large ROI)

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@bhashemian @Nic-Ma @KumoLiu