kaiko-eva 0.0.1__py3-none-any.whl → 0.1.0__py3-none-any.whl

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Files changed (168) hide show
  1. eva/core/callbacks/__init__.py +3 -2
  2. eva/core/callbacks/config.py +143 -0
  3. eva/core/callbacks/writers/__init__.py +6 -3
  4. eva/core/callbacks/writers/embeddings/__init__.py +6 -0
  5. eva/core/callbacks/writers/embeddings/_manifest.py +71 -0
  6. eva/core/callbacks/writers/embeddings/base.py +192 -0
  7. eva/core/callbacks/writers/embeddings/classification.py +117 -0
  8. eva/core/callbacks/writers/embeddings/segmentation.py +78 -0
  9. eva/core/callbacks/writers/embeddings/typings.py +38 -0
  10. eva/core/data/datasets/__init__.py +10 -2
  11. eva/core/data/datasets/classification/__init__.py +5 -2
  12. eva/core/data/datasets/classification/embeddings.py +15 -135
  13. eva/core/data/datasets/classification/multi_embeddings.py +110 -0
  14. eva/core/data/datasets/embeddings.py +167 -0
  15. eva/core/data/splitting/__init__.py +6 -0
  16. eva/core/data/splitting/random.py +41 -0
  17. eva/core/data/splitting/stratified.py +56 -0
  18. eva/core/data/transforms/__init__.py +3 -1
  19. eva/core/data/transforms/padding/__init__.py +5 -0
  20. eva/core/data/transforms/padding/pad_2d_tensor.py +38 -0
  21. eva/core/data/transforms/sampling/__init__.py +5 -0
  22. eva/core/data/transforms/sampling/sample_from_axis.py +40 -0
  23. eva/core/loggers/__init__.py +7 -0
  24. eva/core/loggers/dummy.py +38 -0
  25. eva/core/loggers/experimental_loggers.py +8 -0
  26. eva/core/loggers/log/__init__.py +6 -0
  27. eva/core/loggers/log/image.py +71 -0
  28. eva/core/loggers/log/parameters.py +74 -0
  29. eva/core/loggers/log/utils.py +13 -0
  30. eva/core/loggers/loggers.py +6 -0
  31. eva/core/metrics/__init__.py +6 -2
  32. eva/core/metrics/defaults/__init__.py +10 -3
  33. eva/core/metrics/defaults/classification/__init__.py +1 -1
  34. eva/core/metrics/defaults/classification/binary.py +0 -9
  35. eva/core/metrics/defaults/classification/multiclass.py +0 -8
  36. eva/core/metrics/defaults/segmentation/__init__.py +5 -0
  37. eva/core/metrics/defaults/segmentation/multiclass.py +43 -0
  38. eva/core/metrics/generalized_dice.py +59 -0
  39. eva/core/metrics/mean_iou.py +120 -0
  40. eva/core/metrics/structs/schemas.py +3 -1
  41. eva/core/models/__init__.py +3 -1
  42. eva/core/models/modules/head.py +16 -15
  43. eva/core/models/modules/module.py +25 -1
  44. eva/core/models/modules/typings.py +14 -1
  45. eva/core/models/modules/utils/batch_postprocess.py +37 -5
  46. eva/core/models/networks/__init__.py +1 -2
  47. eva/core/models/networks/mlp.py +2 -2
  48. eva/core/models/transforms/__init__.py +6 -0
  49. eva/core/models/{networks/transforms → transforms}/extract_cls_features.py +10 -2
  50. eva/core/models/transforms/extract_patch_features.py +47 -0
  51. eva/core/models/wrappers/__init__.py +13 -0
  52. eva/core/models/{networks/wrappers → wrappers}/base.py +3 -2
  53. eva/core/models/{networks/wrappers → wrappers}/from_function.py +5 -12
  54. eva/core/models/{networks/wrappers → wrappers}/huggingface.py +15 -11
  55. eva/core/models/{networks/wrappers → wrappers}/onnx.py +6 -3
  56. eva/core/trainers/_recorder.py +69 -7
  57. eva/core/trainers/functional.py +23 -5
  58. eva/core/trainers/trainer.py +20 -6
  59. eva/core/utils/__init__.py +6 -0
  60. eva/core/utils/clone.py +27 -0
  61. eva/core/utils/memory.py +28 -0
  62. eva/core/utils/operations.py +26 -0
  63. eva/core/utils/parser.py +20 -0
  64. eva/vision/__init__.py +2 -2
  65. eva/vision/callbacks/__init__.py +5 -0
  66. eva/vision/callbacks/loggers/__init__.py +5 -0
  67. eva/vision/callbacks/loggers/batch/__init__.py +5 -0
  68. eva/vision/callbacks/loggers/batch/base.py +130 -0
  69. eva/vision/callbacks/loggers/batch/segmentation.py +188 -0
  70. eva/vision/data/datasets/__init__.py +24 -4
  71. eva/vision/data/datasets/_utils.py +3 -3
  72. eva/vision/data/datasets/_validators.py +15 -2
  73. eva/vision/data/datasets/classification/__init__.py +6 -2
  74. eva/vision/data/datasets/classification/bach.py +10 -15
  75. eva/vision/data/datasets/classification/base.py +17 -24
  76. eva/vision/data/datasets/classification/camelyon16.py +244 -0
  77. eva/vision/data/datasets/classification/crc.py +10 -15
  78. eva/vision/data/datasets/classification/mhist.py +10 -15
  79. eva/vision/data/datasets/classification/panda.py +184 -0
  80. eva/vision/data/datasets/classification/patch_camelyon.py +13 -16
  81. eva/vision/data/datasets/classification/wsi.py +105 -0
  82. eva/vision/data/datasets/segmentation/__init__.py +15 -2
  83. eva/vision/data/datasets/segmentation/_utils.py +38 -0
  84. eva/vision/data/datasets/segmentation/base.py +31 -47
  85. eva/vision/data/datasets/segmentation/bcss.py +236 -0
  86. eva/vision/data/datasets/segmentation/consep.py +156 -0
  87. eva/vision/data/datasets/segmentation/embeddings.py +34 -0
  88. eva/vision/data/datasets/segmentation/lits.py +178 -0
  89. eva/vision/data/datasets/segmentation/monusac.py +236 -0
  90. eva/vision/data/datasets/segmentation/total_segmentator_2d.py +325 -0
  91. eva/vision/data/datasets/wsi.py +187 -0
  92. eva/vision/data/transforms/__init__.py +3 -2
  93. eva/vision/data/transforms/common/__init__.py +2 -1
  94. eva/vision/data/transforms/common/resize_and_clamp.py +51 -0
  95. eva/vision/data/transforms/common/resize_and_crop.py +6 -7
  96. eva/vision/data/transforms/normalization/__init__.py +6 -0
  97. eva/vision/data/transforms/normalization/clamp.py +43 -0
  98. eva/vision/data/transforms/normalization/functional/__init__.py +5 -0
  99. eva/vision/data/transforms/normalization/functional/rescale_intensity.py +28 -0
  100. eva/vision/data/transforms/normalization/rescale_intensity.py +53 -0
  101. eva/vision/data/wsi/__init__.py +16 -0
  102. eva/vision/data/wsi/backends/__init__.py +69 -0
  103. eva/vision/data/wsi/backends/base.py +115 -0
  104. eva/vision/data/wsi/backends/openslide.py +73 -0
  105. eva/vision/data/wsi/backends/pil.py +52 -0
  106. eva/vision/data/wsi/backends/tiffslide.py +42 -0
  107. eva/vision/data/wsi/patching/__init__.py +6 -0
  108. eva/vision/data/wsi/patching/coordinates.py +98 -0
  109. eva/vision/data/wsi/patching/mask.py +123 -0
  110. eva/vision/data/wsi/patching/samplers/__init__.py +14 -0
  111. eva/vision/data/wsi/patching/samplers/_utils.py +50 -0
  112. eva/vision/data/wsi/patching/samplers/base.py +48 -0
  113. eva/vision/data/wsi/patching/samplers/foreground_grid.py +99 -0
  114. eva/vision/data/wsi/patching/samplers/grid.py +47 -0
  115. eva/vision/data/wsi/patching/samplers/random.py +41 -0
  116. eva/vision/losses/__init__.py +5 -0
  117. eva/vision/losses/dice.py +40 -0
  118. eva/vision/models/__init__.py +4 -2
  119. eva/vision/models/modules/__init__.py +5 -0
  120. eva/vision/models/modules/semantic_segmentation.py +161 -0
  121. eva/vision/models/networks/__init__.py +1 -2
  122. eva/vision/models/networks/backbones/__init__.py +6 -0
  123. eva/vision/models/networks/backbones/_utils.py +39 -0
  124. eva/vision/models/networks/backbones/pathology/__init__.py +31 -0
  125. eva/vision/models/networks/backbones/pathology/bioptimus.py +34 -0
  126. eva/vision/models/networks/backbones/pathology/gigapath.py +33 -0
  127. eva/vision/models/networks/backbones/pathology/histai.py +46 -0
  128. eva/vision/models/networks/backbones/pathology/kaiko.py +123 -0
  129. eva/vision/models/networks/backbones/pathology/lunit.py +68 -0
  130. eva/vision/models/networks/backbones/pathology/mahmood.py +62 -0
  131. eva/vision/models/networks/backbones/pathology/owkin.py +22 -0
  132. eva/vision/models/networks/backbones/registry.py +47 -0
  133. eva/vision/models/networks/backbones/timm/__init__.py +5 -0
  134. eva/vision/models/networks/backbones/timm/backbones.py +54 -0
  135. eva/vision/models/networks/backbones/universal/__init__.py +8 -0
  136. eva/vision/models/networks/backbones/universal/vit.py +54 -0
  137. eva/vision/models/networks/decoders/__init__.py +6 -0
  138. eva/vision/models/networks/decoders/decoder.py +7 -0
  139. eva/vision/models/networks/decoders/segmentation/__init__.py +11 -0
  140. eva/vision/models/networks/decoders/segmentation/common.py +74 -0
  141. eva/vision/models/networks/decoders/segmentation/conv2d.py +114 -0
  142. eva/vision/models/networks/decoders/segmentation/linear.py +125 -0
  143. eva/vision/models/wrappers/__init__.py +6 -0
  144. eva/vision/models/wrappers/from_registry.py +48 -0
  145. eva/vision/models/wrappers/from_timm.py +68 -0
  146. eva/vision/utils/colormap.py +77 -0
  147. eva/vision/utils/convert.py +67 -0
  148. eva/vision/utils/io/__init__.py +10 -4
  149. eva/vision/utils/io/image.py +21 -2
  150. eva/vision/utils/io/mat.py +36 -0
  151. eva/vision/utils/io/nifti.py +40 -15
  152. eva/vision/utils/io/text.py +10 -3
  153. kaiko_eva-0.1.0.dist-info/METADATA +553 -0
  154. kaiko_eva-0.1.0.dist-info/RECORD +205 -0
  155. {kaiko_eva-0.0.1.dist-info → kaiko_eva-0.1.0.dist-info}/WHEEL +1 -1
  156. {kaiko_eva-0.0.1.dist-info → kaiko_eva-0.1.0.dist-info}/entry_points.txt +2 -0
  157. eva/core/callbacks/writers/embeddings.py +0 -169
  158. eva/core/callbacks/writers/typings.py +0 -23
  159. eva/core/models/networks/transforms/__init__.py +0 -5
  160. eva/core/models/networks/wrappers/__init__.py +0 -8
  161. eva/vision/data/datasets/classification/total_segmentator.py +0 -213
  162. eva/vision/data/datasets/segmentation/total_segmentator.py +0 -212
  163. eva/vision/models/networks/postprocesses/__init__.py +0 -5
  164. eva/vision/models/networks/postprocesses/cls.py +0 -25
  165. kaiko_eva-0.0.1.dist-info/METADATA +0 -405
  166. kaiko_eva-0.0.1.dist-info/RECORD +0 -110
  167. /eva/core/models/{networks → wrappers}/_utils.py +0 -0
  168. {kaiko_eva-0.0.1.dist-info → kaiko_eva-0.1.0.dist-info}/licenses/LICENSE +0 -0
kaiko_eva-0.0.1.dist-info/RECORD DELETED
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/eva/core/models/{networks → wrappers}/_utils.py RENAMED
File without changes