Code

Integration tests#30

Code

Merged

christinab12 merged 50 commits intomainHelmholtzAI-Consultants-Munich/data-centric-platform:mainfrom integration-testsHelmholtzAI-Consultants-Munich/data-centric-platform:integration-testsCopy head branch name to clipboardNov 15, 2023

+1,015-156

Commits

Commits on Jul 12, 2023

• integration of patch model

  

  Mariia Koren

  committed
  e918071

Commits on Jul 13, 2023

• add comments with to dos

  

  Christina Bukas

  committed
  effbe6a

Commits on Jul 15, 2023

• added train and eval parts in models

  

  Mariia Koren

  committed
  325b849

Commits on Jul 17, 2023

• add comments and small changes

  

  Mariia Koren

  committed
  5ca7b15

Commits on Jul 23, 2023

• finished create_patch_datasetand fixed errors

  

  Mariia Koren

  committed
  7b4d847

Commits on Jul 27, 2023

• rewrite the tests from unittest to pytest

  KorenMary

  committed
  38a8140

Commits on Sep 26, 2023

• add integration tests

  KorenMary

  committed
  c18a796

Commits on Sep 27, 2023

• add integration tests and adjusted models.py

  KorenMary

  committed
  8a03102

Commits on Oct 18, 2023

• added channel axis to rescale so mask retains channel dim

  

  Christina Bukas

  committed
  c0443b6

• adapted config for CellposePatchCNN model

  

  Christina Bukas

  committed
  76fde8b

• adapted to allow for 2 channel mask (class+intance) to be resized correctly

  

  Christina Bukas

  committed
  2755ad5

• major changes in CellClassifierFCNN and CellposePatchCNN to make compatible with DCP

  

  Christina Bukas

  committed
  1325572

Commits on Oct 19, 2023

• adapted integration tests for test and train of patch model

  

  Christina Bukas

  committed
  42c3e77

• added tests to seperate folder

  

  Christina Bukas

  committed
  df065a4

Commits on Oct 27, 2023

• Added and tested synthetic data generation on-the-fly for integration tests.

  KorenMary

  committed
  d972364

Commits on Oct 29, 2023

• Update requirements.txt

  KorenMary

  authored
  5ce4845

• requirements modified

  KorenMary

  committed
  9de2a22

• fixed test paths

  KorenMary

  committed
  c5de9ba

• Updates according to code review

  KorenMary

  committed
  eb5c1f4

Commits on Oct 30, 2023

• updated eval config to include channel and z axis

  

  Christina Bukas

  committed
  1c97344

• updated get_image_size_properties to return z and channel axis

  

  Christina Bukas

  committed
  a3f9ab5

• updated the way conifgs are passed to models

  

  Christina Bukas

  committed
  7d128a2

• updated with z and channel axis args and removed eval_config from eval since it is in init

  

  Christina Bukas

  committed
  d05c84f

• removed eval config from eval since it is in model init

  

  Christina Bukas

  committed
  a06f057

Commits on Oct 31, 2023

• search seg bug fix

  hpelin

  committed
  ffe5adf

• passed 'segmentor' into initi of CustomCellP.

  hpelin

  committed
  eb0d9c2

Commits on Nov 3, 2023

• Merge branch 'integration-tests' of https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform into integration-tests

  

  Christina Bukas

  committed
  49a3d96

• moved image processing and dataset creation functions to utils

  

  Christina Bukas

  committed
  6f6d2fc

• commenting lines which print model weights

  

  Christina Bukas

  committed
  460cdaf

• added comment on expected formats

  

  Christina Bukas

  committed
  266bb72

• added new mask_channel_axis arg in config which stores channel axis of mask

  

  Christina Bukas

  committed
  a36ec9e

• Merge branch 'integration-tests' of https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform into integration-tests

  

  Christina Bukas

  committed
  9615f57

Commits on Nov 5, 2023

• tested on 3 channel images

  KorenMary

  committed
  3c86217

• 3 channel input tested

  KorenMary

  committed
  b1dcda1

• mask paths fixed

  KorenMary

  committed
  389dab0

Commits on Nov 6, 2023

• changed the synthetic mask format to (2,512,512) in the pytest and tested

  KorenMary

  committed
  b189b40

• tested train function

  KorenMary

  committed
  11d02ed

• changed the paths to the files due to test error

  KorenMary

  committed
  fe52557

• fixed the bug

  KorenMary

  committed
  c607154

• changed the paths for shapes

  KorenMary

  committed
  58bebd3

Commits on Nov 8, 2023

• added pytest to requirements

  

  Christina Bukas

  committed
  a74daf6

• changed convention to always convert image to grayscale on read, input channels to net adapted accordingly

  

  Christina Bukas

  committed
  a070912

• changed documentation for channel_axis

  

  Christina Bukas

  committed
  6e270dc

• since grayscale convention changed arguments of channel_axis

  

  Christina Bukas

  committed
  bf62ccf

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

  

  Christina Bukas

  committed
  5b60b1f

• removed merging of image, adapted class mask to ensure label corresponds to right object

  

  Christina Bukas

  committed
  f7c795d

• added min_train_masks arg

  

  Christina Bukas

  committed
  f4f75f0

• included height and width computations for elif statements

  

  Christina Bukas

  committed
  e5f9afc

Commits on Nov 12, 2023

• Add tests for multiple models including CustomCellposeModel

  KorenMary

  committed
  10d4ed4

Commits on Nov 13, 2023

• fix the test in train part

  KorenMary

  committed
  90e7b25