New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Integration tests #30

Merged

christinab12 merged 50 commits into main from integration-tests

Nov 15, 2023

Collaborator

KorenMary commented Oct 9, 2023

Added PatchNet with the integration tests

Mariia Koren and others added 8 commits

July 12, 2023 15:36


          integration of patch model

e918071


          add comments with to dos

effbe6a


          added train and eval parts in models

325b849


          add comments and small changes

5ca7b15


          finished create_patch_datasetand fixed errors

7b4d847


          rewrite the tests from unittest to pytest

38a8140


          add integration tests

c18a796


          add integration tests and adjusted models.py

8a03102

KorenMary requested review from hpelin and christinab12

October 9, 2023 13:45

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/models.py Outdated Show resolved Hide resolved

Christina Bukas added 4 commits

October 18, 2023 18:51


          added channel axis to rescale so mask retains channel dim

c0443b6


          adapted config for CellposePatchCNN model

76fde8b


          adapted to allow for 2 channel mask (class+intance) to be resized cor…

2755ad5

…rectly


          major changes in CellClassifierFCNN and CellposePatchCNN to make comp…

…atible with DCP

christinab12 reviewed

View reviewed changes

src/server/dcp_server/test_integration.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/test_integration.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/test_integration.py Outdated Show resolved Hide resolved

christinab12 reviewed

View reviewed changes

src/server/dcp_server/test_integration.py Outdated Show resolved Hide resolved


          adapted integration tests for test and train of patch model

42c3e77

christinab12 reviewed

View reviewed changes

src/server/dcp_server/test.py Outdated Show resolved Hide resolved


          added tests to seperate folder

df065a4

Christina Bukas and others added 26 commits

October 30, 2023 11:47


          removed eval config from eval since it is in model init

a06f057


          search seg bug fix

ffe5adf


          passed 'segmentor' into initi of CustomCellP.

eb0d9c2


          Merge branch 'integration-tests' of https://github.com/HelmholtzAI-Co…

49a3d96

…nsultants-Munich/data-centric-platform into integration-tests


          moved image processing and dataset creation functions to utils

6f6d2fc


          commenting lines which print model weights

460cdaf


          added comment on expected formats

266bb72


          added new mask_channel_axis arg in config which stores channel axis o…

a36ec9e

…f mask


          Merge branch 'integration-tests' of https://github.com/HelmholtzAI-Co…

9615f57

…nsultants-Munich/data-centric-platform into integration-tests


          tested on 3 channel images

3c86217


          3 channel input tested

b1dcda1


          mask paths fixed

389dab0


          changed the synthetic mask format to (2,512,512) in the pytest and te…

b189b40

…sted


          tested train function

11d02ed


          changed the paths to the files due to test error

fe52557


          fixed the bug

c607154


          changed the paths for shapes

58bebd3


          added pytest to requirements

a74daf6


          changed convention to always convert image to grayscale on read, inpu…

a070912

…t channels to net adapted accordingly


          changed documentation for channel_axis

6e270dc


          since grayscale convention changed arguments of channel_axis

bf62ccf


          changed method to compute center of mass and return instance label as…

5b60b1f

… well


          removed merging of image, adapted class mask to ensure label correspo…

f7c795d

…nds to right object


          added min_train_masks arg

f4f75f0


          included height and width computations for elif statements

e5f9afc


          Add tests for multiple models including CustomCellposeModel

10d4ed4

christinab12 approved these changes

View reviewed changes


          fix the test in train part

90e7b25

christinab12 merged commit 6ccb734 into main

18 checks passed

christinab12 deleted the integration-tests branch

November 15, 2023 10:59

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet