NEW: Add PCam Patch Classification Models (#225)

- Add patch classification models trained on the [Patch Camelyon dataset](https://github.com/basveeling/pcam). We include all models that were used for the Kather100K dataset. 

- As part of this PR, we : 
  - Add new model links
  - Add tests for model output
  - Add links to 2 new sample patches for testing


Co-authored-by: Simon Graham <[email protected]>
Co-authored-by: Dang Vu <[email protected]>
Co-authored-by: Shan E Ahmed Raza <[email protected]>

Author: 3 people

tests/conftest.py

@@ -299,7 +299,7 @@ def patch_extr_svs_npy_read(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch1(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 1.
-    Download sample patch 1 for pytest.
+    Download sample patch 1 (Kather100K) for pytest.
 
     """
     return remote_sample("sample-patch-1")
@@ -308,12 +308,30 @@ def sample_patch1(remote_sample) -> pathlib.Path:
 @pytest.fixture(scope="session")
 def sample_patch2(remote_sample) -> pathlib.Path:
     """Sample pytest fixture for sample patch 2.
-    Download sample patch 2 for pytest.
+    Download sample patch 2 (Kather100K) for pytest.
 
     """
     return remote_sample("sample-patch-2")
 
 
+@pytest.fixture(scope="session")
+def sample_patch3(remote_sample) -> pathlib.Path:
+    """Sample pytest fixture for sample patch 3.
+    Download sample patch 3 (PCam) for pytest.
+
+    """
+    return remote_sample("sample-patch-3")
+
+
+@pytest.fixture(scope="session")
+def sample_patch4(remote_sample) -> pathlib.Path:
+    """Sample pytest fixture for sample patch 4.
+    Download sample patch 4 (PCam) for pytest.
+
+    """
+    return remote_sample("sample-patch-4")
+
+
 @pytest.fixture(scope="session")
 def dir_sample_patches(sample_patch1, sample_patch2, tmpdir_factory):
     """Directory of sample image patches for testing."""

tests/models/test_patch_predictor.py

@@ -937,8 +937,8 @@ def _test_predictor_output(
         )
 
 
-def test_patch_predictor_output(sample_patch1, sample_patch2):
-    """Test the output of patch prediction models."""
+def test_patch_predictor_kather100k_output(sample_patch1, sample_patch2):
+    """Test the output of patch prediction models on Kather100K dataset."""
     inputs = [pathlib.Path(sample_patch1), pathlib.Path(sample_patch2)]
     pretrained_info = {
         "alexnet-kather100k": [1.0, 0.9999735355377197],
@@ -972,6 +972,41 @@ def test_patch_predictor_output(sample_patch1, sample_patch2):
             break
 
 
+def test_patch_predictor_pcam_output(sample_patch3, sample_patch4):
+    """Test the output of patch prediction models on PCam dataset."""
+    inputs = [pathlib.Path(sample_patch3), pathlib.Path(sample_patch4)]
+    pretrained_info = {
+        "alexnet-pcam": [0.999980092048645, 0.9769067168235779],
+        "resnet18-pcam": [0.999992847442627, 0.9466130137443542],
+        "resnet34-pcam": [1.0, 0.9976525902748108],
+        "resnet50-pcam": [0.9999270439147949, 0.9999996423721313],
+        "resnet101-pcam": [1.0, 0.9997289776802063],
+        "resnext50_32x4d-pcam": [0.9999996423721313, 0.9984435439109802],
+        "resnext101_32x8d-pcam": [0.9997072815895081, 0.9969086050987244],
+        "wide_resnet50_2-pcam": [0.9999837875366211, 0.9959040284156799],
+        "wide_resnet101_2-pcam": [1.0, 0.9945427179336548],
+        "densenet121-pcam": [0.9999251365661621, 0.9997479319572449],
+        "densenet161-pcam": [0.9999969005584717, 0.9662821292877197],
+        "densenet169-pcam": [0.9999998807907104, 0.9993504881858826],
+        "densenet201-pcam": [0.9999942779541016, 0.9950824975967407],
+        "mobilenet_v2-pcam": [0.9999876022338867, 0.9942564368247986],
+        "mobilenet_v3_large-pcam": [0.9999922513961792, 0.9719613790512085],
+        "mobilenet_v3_small-pcam": [0.9999963045120239, 0.9747149348258972],
+        "googlenet-pcam": [0.9999929666519165, 0.8701475858688354],
+    }
+    for pretrained_model, expected_prob in pretrained_info.items():
+        _test_predictor_output(
+            inputs,
+            pretrained_model,
+            probabilities_check=expected_prob,
+            predictions_check=[1, 0],
+            on_gpu=ON_GPU,
+        )
+        # only test 1 on travis to limit runtime
+        if ON_TRAVIS:
+            break
+
+
 # -------------------------------------------------------------------------------------
 # Command Line Interface
 # -------------------------------------------------------------------------------------

tiatoolbox/data/pretrained_model.yaml

@@ -237,6 +237,245 @@ googlenet-kather100k:
             input_resolutions: [{"resolution": 0.5, "units": "mpp"}]
     dataset: kather100k
 
+alexnet-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/alexnet-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: alexnet
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnet18-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnet18-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnet18
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnet34-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnet34-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnet34
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnet50-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnet50-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnet50
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnet101-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnet101-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnet101
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnext50_32x4d-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnext50_32x4d-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnext50_32x4d
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+resnext101_32x8d-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/resnext101_32x8d-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: resnext101_32x8d
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+wide_resnet50_2-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/wide_resnet50_2-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: wide_resnet50_2
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+wide_resnet101_2-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/wide_resnet101_2-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: wide_resnet101_2
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+densenet121-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/densenet121-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: densenet121
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+densenet161-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/densenet161-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: densenet161
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+densenet169-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/densenet169-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: densenet169
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+densenet201-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/densenet201-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: densenet201
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+mobilenet_v2-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/mobilenet_v2-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: mobilenet_v2
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+mobilenet_v3_large-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/mobilenet_v3_large-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: mobilenet_v3_large
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+mobilenet_v3_small-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/mobilenet_v3_small-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: mobilenet_v3_small
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+googlenet-pcam:
+    url: https://tiatoolbox.dcs.warwick.ac.uk/models/pc/googlenet-pcam.pth
+    architecture:
+        class: vanilla.CNNModel
+        kwargs:
+            backbone: googlenet
+            num_classes: 2
+    ioconfig:
+        class: patch_predictor.IOPatchPredictorConfig
+        kwargs:
+            patch_input_shape: [96, 96]
+            stride_shape: [96, 96]
+            input_resolutions: [{"resolution": 1.0, "units": "mpp"}]
+    dataset: pcam
+
 resnet18-idars-tumour:
     url: https://tiatoolbox.dcs.warwick.ac.uk/models/idars/resnet18-idars-tumour.pth
     architecture:

tiatoolbox/data/remote_samples.yaml

@@ -59,6 +59,10 @@ files:
     url: [*modelroot, "samples/kather_patch1.tif"]
   sample-patch-2:
     url: [*modelroot, "samples/kather_patch2.tif"]
+  sample-patch-3:
+    url: [*modelroot, "samples/pcam_patch1.png"]
+  sample-patch-4:
+    url: [*modelroot, "samples/pcam_patch2.png"]
   wsi1_2k_2k_svs:
     url: [*modelroot, "samples/wsi1_2k_2k.svs"]
   wsi1_8k_8k_svs: