vima-spatial 0.2.0__tar.gz → 0.2.1__tar.gz

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Files changed (38) hide show
  1. {vima_spatial-0.2.0/src/vima_spatial.egg-info → vima_spatial-0.2.1}/PKG-INFO +1 -1
  2. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/setup.cfg +1 -1
  3. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/ingest.py +1 -1
  4. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/__init__.py +1 -1
  5. {vima_spatial-0.2.0 → vima_spatial-0.2.1/src/vima_spatial.egg-info}/PKG-INFO +1 -1
  6. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/MANIFEST.in +0 -0
  7. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/README.md +0 -0
  8. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/pyproject.toml +0 -0
  9. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/__init__.py +0 -0
  10. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/cc.py +0 -0
  11. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/data/__init__.py +0 -0
  12. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/data/patchcollection.py +0 -0
  13. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/data/samples.py +0 -0
  14. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/fingerprints.py +0 -0
  15. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/__init__.py +0 -0
  16. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/dimreduce.py +0 -0
  17. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/nonst.py +0 -0
  18. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/st.py +0 -0
  19. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/util.py +0 -0
  20. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/__init__.py +0 -0
  21. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/resnet_vae.py +0 -0
  22. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/resnetlight_decoder.py +0 -0
  23. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/resnetlight_encoder.py +0 -0
  24. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/simple_vae.py +0 -0
  25. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/models/vae.py +0 -0
  26. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/patchfeatures.py +0 -0
  27. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/train/__init__.py +0 -0
  28. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/train/logging.py +0 -0
  29. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/train/training.py +0 -0
  30. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/features.py +0 -0
  31. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/patches.py +0 -0
  32. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/patchexamples.py +0 -0
  33. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/spatial.py +0 -0
  34. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/umaps.py +0 -0
  35. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima_spatial.egg-info/SOURCES.txt +0 -0
  36. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima_spatial.egg-info/dependency_links.txt +0 -0
  37. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima_spatial.egg-info/requires.txt +0 -0
  38. {vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima_spatial.egg-info/top_level.txt +0 -0
{vima_spatial-0.2.0/src/vima_spatial.egg-info → vima_spatial-0.2.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: vima-spatial
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- Version: 0.2.0
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+ Version: 0.2.1
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  Summary: variational inference-based microniche analysis
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  Home-page: https://github.com/yakirr/vima
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  Author: Yakir Reshef
{vima_spatial-0.2.0 → vima_spatial-0.2.1}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
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  [metadata]
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  name = vima-spatial
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- version = 0.2.0
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+ version = 0.2.1
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  author = Yakir Reshef
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  author_email = yreshef@broadinstitute.org
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  description = variational inference-based microniche analysis
{vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/ingest/ingest.py RENAMED
@@ -129,12 +129,12 @@ def write_harmonized(outdir, repname, harmpixels):
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  pl = harmpixels[harmpixels.sid == sid]
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  s_ = np.zeros((*mask.shape, len(hpcs)))
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  s_[mask.data] = pl[pcs].values
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- mask.close(); del mask
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  s = xr.DataArray(s_,
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  dims=['y', 'x', 'marker'],
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  coords={'x': mask.x, 'y': mask.y, 'marker': hpcs})
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  s.name = sid
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  s.to_netcdf(f'{processeddir}/{sid}.nc', encoding={s.name: util.compression}, engine="netcdf4")
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+ mask.close(); del mask
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  gc.collect()
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  def sanity_checks(outdir, repname, npcs=1, nskip=3):
{vima_spatial-0.2.0 → vima_spatial-0.2.1}/src/vima/vis/__init__.py RENAMED
@@ -5,4 +5,4 @@ from .patchexamples import (scaler, apply_colormap, plot_with_reconstruction,
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  plot_patches_separatechannels, plot_patches_overlaychannels,
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  plot_patches_overlaychannels_linsum,
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  plot_patches_overlaychannels_sorted, plot_patches_fourcolors)
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- from .spatial import spatialplot, annotate_spatialplot
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+ from .spatial import spatialplot, annotate_spatialplot, plot_npatches_per_sample, plot_samples_with_patches, plot_sample_with_patches
{vima_spatial-0.2.0 → vima_spatial-0.2.1/src/vima_spatial.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: vima-spatial
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- Version: 0.2.0
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+ Version: 0.2.1
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  Summary: variational inference-based microniche analysis
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  Home-page: https://github.com/yakirr/vima
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  Author: Yakir Reshef
{vima_spatial-0.2.0 → vima_spatial-0.2.1}/MANIFEST.in RENAMED
File without changes
{vima_spatial-0.2.0 → vima_spatial-0.2.1}/README.md RENAMED
File without changes