Fixing Tests, renaming in Memory inference

pathopatch/patch_extraction/dataset.py

@@ -171,7 +171,7 @@ def __post_init_post_parse__(self) -> None:
                 raise ValueError("Only JSON annotations are supported")
 
 
-class PatchWSIDataset(Dataset):
+class LivePatchWSIDataset(Dataset):
     def __init__(
         self,
         slide_processor_config: PreProcessingDatasetConfig,

setup.py

@@ -1,6 +1,6 @@
 from setuptools import find_packages, setup
 
-VERSION = "0.9.2b"
+VERSION = "0.9.3a"
 DESCRIPTION = "PathoPatch - Accelerating Artificial Intelligence Based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline"
 with open("docs/README_pypi.md", "r") as fh:
     LONG_DESCRIPTION = fh.read()

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_0_0.yaml

@@ -1,6 +1,6 @@
 row: 0
 col: 0
-background_ratio: 1.0
+background_ratio: 0.96795654296875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_0_0.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_0_3.yaml

@@ -1,6 +1,6 @@
 row: 0
 col: 3
-background_ratio: 1.0
+background_ratio: 0.7503662109375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_0_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_0_4.yaml

@@ -1,6 +1,6 @@
 row: 0
 col: 4
-background_ratio: 1.0
+background_ratio: 0.597503662109375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_0_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_0_5.yaml

@@ -1,6 +1,6 @@
 row: 0
 col: 5
-background_ratio: 1.0
+background_ratio: 0.95184326171875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_0_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_10_2.yaml

@@ -1,6 +1,6 @@
 row: 10
 col: 2
-background_ratio: 1.0
+background_ratio: 0.12200927734375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_10_2.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_10_3.yaml

@@ -1,6 +1,6 @@
 row: 10
 col: 3
-background_ratio: 1.0
+background_ratio: 0.036285400390625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_10_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_10_4.yaml

@@ -1,6 +1,6 @@
 row: 10
 col: 4
-background_ratio: 1.0
+background_ratio: 0.0860748291015625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_10_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_10_5.yaml

@@ -1,6 +1,6 @@
 row: 10
 col: 5
-background_ratio: 1.0
+background_ratio: 0.08233642578125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_10_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_10_6.yaml

@@ -1,6 +1,6 @@
 row: 10
 col: 6
-background_ratio: 1.0
+background_ratio: 0.3464508056640625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_10_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_11_2.yaml

@@ -1,6 +1,6 @@
 row: 11
 col: 2
-background_ratio: 1.0
+background_ratio: 0.447601318359375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_11_2.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_11_3.yaml

@@ -1,6 +1,6 @@
 row: 11
 col: 3
-background_ratio: 1.0
+background_ratio: 0.4241180419921875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_11_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_11_4.yaml

@@ -1,6 +1,6 @@
 row: 11
 col: 4
-background_ratio: 1.0
+background_ratio: 0.4788818359375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_11_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_11_5.yaml

@@ -1,6 +1,6 @@
 row: 11
 col: 5
-background_ratio: 1.0
+background_ratio: 0.4787139892578125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_11_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_11_6.yaml

@@ -1,6 +1,6 @@
 row: 11
 col: 6
-background_ratio: 1.0
+background_ratio: 0.676055908203125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_11_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_1_3.yaml

@@ -1,6 +1,6 @@
 row: 1
 col: 3
-background_ratio: 1.0
+background_ratio: 0.59283447265625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_1_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_1_4.yaml

@@ -1,6 +1,6 @@
 row: 1
 col: 4
-background_ratio: 1.0
+background_ratio: 0.317657470703125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_1_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_1_5.yaml

@@ -1,6 +1,6 @@
 row: 1
 col: 5
-background_ratio: 1.0
+background_ratio: 0.6071319580078125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_1_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_2_3.yaml

@@ -1,6 +1,6 @@
 row: 2
 col: 3
-background_ratio: 1.0
+background_ratio: 0.7684478759765625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_2_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_2_4.yaml

@@ -1,6 +1,6 @@
 row: 2
 col: 4
-background_ratio: 1.0
+background_ratio: 0.272430419921875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_2_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_2_5.yaml

@@ -1,6 +1,6 @@
 row: 2
 col: 5
-background_ratio: 1.0
+background_ratio: 0.4964752197265625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_2_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_2_6.yaml

@@ -1,6 +1,6 @@
 row: 2
 col: 6
-background_ratio: 1.0
+background_ratio: 0.8046112060546875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_2_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_2_8.yaml

@@ -1,6 +1,6 @@
 row: 2
 col: 8
-background_ratio: 1.0
+background_ratio: 0.9529571533203125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_2_8.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_3_2.yaml

@@ -1,6 +1,6 @@
 row: 3
 col: 2
-background_ratio: 1.0
+background_ratio: 0.9785308837890625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_3_2.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_3_3.yaml

@@ -1,6 +1,6 @@
 row: 3
 col: 3
-background_ratio: 1.0
+background_ratio: 0.5664825439453125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_3_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_3_4.yaml

@@ -1,6 +1,6 @@
 row: 3
 col: 4
-background_ratio: 1.0
+background_ratio: 0.1289520263671875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_3_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_3_5.yaml

@@ -1,6 +1,6 @@
 row: 3
 col: 5
-background_ratio: 1.0
+background_ratio: 0.247100830078125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_3_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_3_6.yaml

@@ -1,6 +1,6 @@
 row: 3
 col: 6
-background_ratio: 1.0
+background_ratio: 0.7201995849609375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_3_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_0.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 0
-background_ratio: 1.0
+background_ratio: 0.8911895751953125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_0.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_1.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 1
-background_ratio: 1.0
+background_ratio: 0.75140380859375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_1.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_2.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 2
-background_ratio: 1.0
+background_ratio: 0.8090057373046875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_2.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_3.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 3
-background_ratio: 1.0
+background_ratio: 0.4293975830078125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_4.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 4
-background_ratio: 1.0
+background_ratio: 0.1377105712890625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_5.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 5
-background_ratio: 1.0
+background_ratio: 0.395355224609375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_6.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 6
-background_ratio: 1.0
+background_ratio: 0.4090728759765625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_4_7.yaml

@@ -1,6 +1,6 @@
 row: 4
 col: 7
-background_ratio: 1.0
+background_ratio: 0.8641510009765625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_4_7.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_5_3.yaml

@@ -1,6 +1,6 @@
 row: 5
 col: 3
-background_ratio: 1.0
+background_ratio: 0.363433837890625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_5_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_5_4.yaml

@@ -1,6 +1,6 @@
 row: 5
 col: 4
-background_ratio: 1.0
+background_ratio: 0.18402099609375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_5_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_5_5.yaml

@@ -1,6 +1,6 @@
 row: 5
 col: 5
-background_ratio: 1.0
+background_ratio: 0.3876800537109375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_5_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_5_6.yaml

@@ -1,6 +1,6 @@
 row: 5
 col: 6
-background_ratio: 1.0
+background_ratio: 0.6517791748046875
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_5_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_5_7.yaml

@@ -1,6 +1,6 @@
 row: 5
 col: 7
-background_ratio: 1.0
+background_ratio: 0.7496337890625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_5_7.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_6_3.yaml

@@ -1,6 +1,6 @@
 row: 6
 col: 3
-background_ratio: 1.0
+background_ratio: 0.3404541015625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_6_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_6_4.yaml

@@ -1,6 +1,6 @@
 row: 6
 col: 4
-background_ratio: 1.0
+background_ratio: 0.2693634033203125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_6_4.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_6_5.yaml

@@ -1,6 +1,6 @@
 row: 6
 col: 5
-background_ratio: 1.0
+background_ratio: 0.4165191650390625
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_6_5.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_6_6.yaml

@@ -1,6 +1,6 @@
 row: 6
 col: 6
-background_ratio: 1.0
+background_ratio: 0.7758636474609375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_6_6.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_7_2.yaml

@@ -1,6 +1,6 @@
 row: 7
 col: 2
-background_ratio: 1.0
+background_ratio: 0.9761810302734375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_7_2.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_7_3.yaml

@@ -1,6 +1,6 @@
 row: 7
 col: 3
-background_ratio: 1.0
+background_ratio: 0.149658203125
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_7_3.yaml

tests/static_test_files/preprocessing/baseline/results/CMU-1-Small-Region/metadata/CMU-1-Small-Region_7_4.yaml

@@ -1,6 +1,6 @@
 row: 7
 col: 4
-background_ratio: 1.0
+background_ratio: 0.099212646484375
 intersected_labels: []
 label_ratio: {}
 metadata_path: ./metadata/CMU-1-Small-Region_7_4.yaml