Clean the DTW code #311
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Clean the DTW code #311
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closes #286 |
* log the negative * add tests for the triplet anchor and positive * add also the euclidean
* simualte different embeddings * update the msd calculation to re-use cdist functions in the repo * adding a test for the msd * removing unused msd functions * renaming msd to compute_track_displacement * default to cosine distance * adding the gradient attribution video. * extend to training ratios * demo beta_vae 2.5D * improving the logging for readability and drop pythae baseclasses * condense the logging to have less tabs. * fix disentagle metrics * fixing beta warmup bug * renaming to loss * updating architecture to flatten vs spatial VAE with convs * chaning to use mse with mean reduction and normalizing the kl loss by batch size. * optunea proof of concept * add normalized sampled into the transforms so we can use it with MONAIs vae * update loss debugging code * adding sync for disentaglement metrics * adding the dataloader for rpe1 dataset and plotting utils * cleanup the vae and add the monai to lightning. adding configs * add saving hyperparameters * fix hyperparameter logging * add embedding logging to the CLIP version * test and plot of monaivae * handle monai_vae 2d * redifining rotation agumentsations * adding optional scaling to phate * adding alias and output 2d * normalizing by also the latent dim and swapping to FP32 for forward pass to avoid overflow with log and exp * update test for magnitudes * expose the normalization for vae * add sam 2 test * refactor smoothness metrics * rever to normalalize kl wrt to batch size and removing the the beta min value * commit dtwembeddings w sam * added a clamp to logvar, switch to mse loss sum reduction like the original formulation. * remove unecessary vae logging losses. * add a way to handle when using 'mean' reduction for proper scaling * adding optional config for middle slice index for computing sam2 embeddings and dinov3 * converting latent stats active_dimensions parameter to float to remove warning * ruff * removing the optuna config * numpy docstring * fix compute smoothness script * archiving old scripts * re org the pc features scripts * embeddings for phase * add smoothness (mean rand vs adj frame) to the csv * archiving old beta vae code * ruff * fix format * fix typo * remove the archived unecessary files * remove the test run archived file * adding normalizeintensity * fixing the vae_logging typing and removing PC plotting from here * fixing the compute_embedding_smoothness docstring * simplify the distance metrics and removing deprecated functions and scripts * remove deprecated functions from clustering.py * add timelpase to grad_attr.py script * refactoring the betavaemodule. removing the hyperparamter logging, adding the nn.Module as input for typing purposes and removing the fp32 custom fwd * remove the optuna dependency * deleting old msd test * ruff format * fix to explicitly stratify on fov level * adding reference to dataset for rpe1 * fix pyproject.toml dev * format and lint * restore no-augmentation flag effect * format tests * rename the sam2 file * removing unused arguments for logging embeddings. * removing duplication in the lca * remove disentaglement metrics * vectorized the anchor filtering for celldivisiontriplet dataset * map the channels to the rpe dataset convention * fix logistic regresion standardization * update rpe classifier to include mitosis * ruff * remove unused logging * datamodule agnostic * cleaning up duplicated code in the benchmarking * cleanup vae * keeping it consistent and using residual units * fix typings betavaemonai * update smoothness to handle adata * update clustering method and add test * pre-commit * Update viscy/data/cell_division_triplet.py Co-authored-by: Copilot <[email protected]> * Update applications/benchmarking/DynaCLR/SAM2/sam2_visualizations.py Co-authored-by: Copilot <[email protected]> * Update applications/pseudotime_analysis/evaluation/compare_dtw_embeddings_sam2.py Co-authored-by: Copilot <[email protected]> * Update applications/pseudotime_analysis/evaluation/compare_dtw_embeddings_sam2.py Co-authored-by: Copilot <[email protected]> * Update applications/contrastive_phenotyping/evaluation/smoothness/compute_smoothness.py Co-authored-by: Copilot <[email protected]> * Update applications/pseudotime_analysis/evaluation/compare_dtw_embeddings_sam2.py Co-authored-by: Copilot <[email protected]> * Update applications/contrastive_phenotyping/evaluation/smoothness/compute_smoothness.py Co-authored-by: Copilot <[email protected]> * Update applications/contrastive_phenotyping/evaluation/archive/ALFI_MSD_v2.py Co-authored-by: Copilot <[email protected]> * valuerror on the fidn peaks function * add literal to the betavae25d normalization * clipping similarity that was breaking the tests --------- Co-authored-by: Ziwen Liu <[email protected]> Co-authored-by: Copilot <[email protected]>
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PR add the refactored dtw code