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Merged
Nic-Ma merged 34 commits into from
Jul 20, 2022
Merged

Update tumor detection pipline with new components #697

Nic-Ma merged 34 commits into from
Jul 20, 2022

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@bhashemian bhashemian commented May 11, 2022 •
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Fixes #636

Description

Updates the ignite-based tumor detection pipeline that uses numpy and pytorch tensors with the new components in MONAI.

Status

Ready

Checks

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

@bhashemian
Update tumor detection pipline with new components
6d49bba 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian mentioned this pull request May 11, 2022
Merged
5 tasks
bhashemian added 3 commits May 11, 2022 20:21
@bhashemian
formatting
3745cf9 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
formatting
414fea7 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add sub dataset
96c9b46 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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Nic-Ma commented May 12, 2022

Hi @drbeh ,

Do you also need to update the code under tumor_detection/torch/ folder?

Thanks.

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bhashemian commented May 12, 2022

Hi @drbeh ,

Do you also need to update the code under tumor_detection/torch/ folder?

Thanks.

Hey @Nic-Ma, yes of course. All the tumor detection tutorials need to be updated.

bhashemian added 4 commits May 12, 2022 13:06
@bhashemian
Merge branch 'master' into update-tumor-det
27717a1
@bhashemian
Convert xxxD transforms to xxxd
bbf2720 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'update-tumor-det' of github.com:drbeh/tutorials into up…
b6bfd46 
…date-tumor-det
@bhashemian
Update pipline with nvtx annotation
041ede0 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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bhashemian added 6 commits May 13, 2022 10:47
@bhashemian
Merge branch 'master' into update-tumor-det
cb830be
@bhashemian
Add transforms to validation
13acc50 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update tumor notebook
dd918f1 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update torch-based pipeline
358e809 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update perfomance profiling code
e8bcced 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update grid shape
6a2c468 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian marked this pull request as ready for review May 16, 2022 14:06
This was linked to issues May 16, 2022
[MONAI Pathology] Update pathology performance profiling #702
Closed
[MONAI Pathology] Update tumor detection tutorial #639
Closed
bhashemian added 8 commits May 16, 2022 14:15
@bhashemian
Update
1e94103 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update a comment
6a624f2 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'update-tumor-det' of github.com:drbeh/tutorials into up…
2514271 
…date-tumor-det
@bhashemian
Update training/validation dataset and their links
0e59498 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'master' into update-tumor-det
87cae7b
@bhashemian
Fix image path
936ecd7 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Change to validate by default
cdeef33 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' of github.com:Project-MONAI/tutorials into update…
6a0aa32 
…-tumor-det
bhashemian added 7 commits June 2, 2022 22:55
@bhashemian
Flip back the location dims
be9c6e4 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Add filtered datasets
0a64d80 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Update csv loading
819b45d 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'main' into update-tumor-det
35ad2f8
@bhashemian
Update validation defaults
f648faa 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian
Merge branch 'update-tumor-det' of github.com:drbeh/tutorials into up…
b71fa5e 
…date-tumor-det
@bhashemian
Merge branch 'main' into update-tumor-det
4cddebf
@bhashemian bhashemian enabled auto-merge (squash) July 7, 2022 17:37
@bhashemian bhashemian requested a review from Nic-Ma July 7, 2022 17:38
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bhashemian commented Jul 7, 2022

@Nic-Ma this pipeline is already tested by @ZiyueXu77 and FROC is maintained (~0.7).

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Nic-Ma commented Jul 8, 2022

Hi @drbeh ,

Could you please help remove the 2 CSV files from the PR? It makes the PR around 200000 lines change.

Thanks.

@bhashemian
Remove csv files
f8c04c3 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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bhashemian commented Jul 8, 2022

Hi @drbeh ,

Could you please help remove the 2 CSV files from the PR? It makes the PR around 200000 lines change.

Thanks.

Hi @Nic-Ma,
Absolutely! I left them there for Ziyue while we were changing things.

@Nic-Ma Nic-Ma disabled auto-merge July 18, 2022 07:30
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Thanks for the update, looks good to me.
@wyli Do you have any other comments?

Thanks.

@Nic-Ma Nic-Ma merged commit a08b8e0 into Project-MONAI:main Jul 20, 2022
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
@bhashemian @Nic-Ma
Update tumor detection pipline with new components (Project-MONAI#697)
a010c68 
* Update tumor detection pipline with new components

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

* formatting

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

* formatting

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

* Add sub dataset

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

* Convert xxxD transforms to xxxd

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

* Update pipline with nvtx annotation

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

* Add transforms to validation

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

* Update tumor notebook

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

* Update torch-based pipeline

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

* Update perfomance profiling code

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

* Update grid shape

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

* Update

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

* Update a comment

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

* Update training/validation dataset and their links

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

* Fix image path

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

* Change to validate by default

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

* Flip back the location dims

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

* Add filtered datasets

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

* Update csv loading

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

* Update validation defaults

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

* Remove csv files

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

Co-authored-by: Nic Ma <nma@nvidia.com>
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