🆕 Add GrandQC Tissue Segmentation Model

tests/models/test_arch_grandqc.py

@@ -0,0 +1,122 @@
+"""Unit test package for GrandQC Tissue Model."""
+
+import numpy as np
+import torch
+from torch import nn
+
+from tiatoolbox.models.architecture import (
+    fetch_pretrained_weights,
+    get_pretrained_model,
+)
+from tiatoolbox.models.architecture.grandqc import (
+    CenterBlock,
+    GrandQCModel,
+    SegmentationHead,
+    UnetPlusPlusDecoder,
+)
+from tiatoolbox.models.engine.io_config import IOSegmentorConfig
+from tiatoolbox.utils.misc import select_device
+from tiatoolbox.wsicore.wsireader import VirtualWSIReader
+
+ON_GPU = False
+
+
+def test_functional_grandqc() -> None:
+    """Test for GrandQC model."""
+    # test fetch pretrained weights
+    pretrained_weights = fetch_pretrained_weights("grandqc_tissue_detection_mpp10")
+    assert pretrained_weights is not None
+
+    # test creation
+    model = GrandQCModel(num_output_channels=2)
+    assert model is not None
+
+    # load pretrained weights
+    pretrained = torch.load(pretrained_weights, map_location="cpu")
+    model.load_state_dict(pretrained)
+
+    # test get pretrained model
+    model, ioconfig = get_pretrained_model("grandqc_tissue_detection_mpp10")
+    assert isinstance(model, GrandQCModel)
+    assert isinstance(ioconfig, IOSegmentorConfig)
+    assert model.num_output_channels == 2
+    assert model.decoder_channels == (256, 128, 64, 32, 16)
+
+    # test inference
+    generator = np.random.default_rng(1337)
+    test_image = generator.integers(0, 256, size=(2048, 2048, 3), dtype=np.uint8)
+    reader = VirtualWSIReader.open(test_image)
+    read_kwargs = {"resolution": 0, "units": "level", "coord_space": "resolution"}
+    batch = np.array(
+        [
+            reader.read_bounds((0, 0, 512, 512), **read_kwargs),
+            reader.read_bounds((512, 512, 1024, 1024), **read_kwargs),
+        ],
+    )
+    batch = torch.from_numpy(batch)
+    output = model.infer_batch(model, batch, device=select_device(on_gpu=ON_GPU))
+    assert output.shape == (2, 512, 512, 2)
+
+
+def test_grandqc_preproc_postproc() -> None:
+    """Test GrandQC preproc and postproc functions."""
+    model = GrandQCModel(num_output_channels=2)
+
+    generator = np.random.default_rng(1337)
+    # test preproc
+    dummy_image = generator.integers(0, 256, size=(512, 512, 3), dtype=np.uint8)
+    preproc_image = model.preproc(dummy_image)
+    assert preproc_image.shape == dummy_image.shape
+    assert preproc_image.dtype == np.float64
+
+    # test postproc
+    dummy_output = generator.random(size=(512, 512, 2), dtype=np.float32)
+    postproc_image = model.postproc(dummy_output)
+    assert postproc_image.shape == (512, 512)
+    assert postproc_image.dtype == np.int64
+
+
+def test_segmentation_head_behaviour() -> None:
+    """Verify SegmentationHead defaults and upsampling."""
+    head = SegmentationHead(3, 5, activation=None, upsampling=1)
+    assert isinstance(head[1], nn.Identity)
+    assert isinstance(head[2], nn.Identity)
+
+    x = torch.randn(1, 3, 6, 8)
+    out = head(x)
+    assert out.shape == (1, 5, 6, 8)
+
+    head = SegmentationHead(3, 2, activation=nn.Sigmoid(), upsampling=2)
+    x = torch.ones(1, 3, 4, 4)
+    out = head(x)
+    assert out.shape == (1, 2, 8, 8)
+    assert torch.all(out >= 0)
+    assert torch.all(out <= 1)
+
+
+def test_unetplusplus_decoder_forward_shapes() -> None:
+    """Ensure UnetPlusPlusDecoder handles dense connections."""
+    decoder = UnetPlusPlusDecoder(
+        encoder_channels=[1, 2, 4, 8],
+        decoder_channels=[8, 4, 2],
+        n_blocks=3,
+    )
+
+    features = [
+        torch.randn(1, 1, 32, 32),
+        torch.randn(1, 2, 16, 16),
+        torch.randn(1, 4, 8, 8),
+        torch.randn(1, 8, 4, 4),
+    ]
+
+    output = decoder(features)
+    assert output.shape == (1, 2, 32, 32)
+
+
+def test_center_block_behavior() -> None:
+    """Test CenterBlock behavior in UnetPlusPlusDecoder."""
+    center_block = CenterBlock(in_channels=8, out_channels=8)
+
+    x = torch.randn(1, 8, 4, 4)
+    out = center_block(x)
+    assert out.shape == (1, 8, 4, 4)

tests/models/test_arch_timm_efficientnet.py

@@ -0,0 +1,177 @@
+"""Unit tests for timm EfficientNet encoder helpers."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
+import pytest
+import torch
+from torch import nn
+
+from tiatoolbox.models.architecture import timm_efficientnet as effnet_mod
+from tiatoolbox.models.architecture.timm_efficientnet import (
+    DEFAULT_IN_CHANNELS,
+    EfficientNetEncoder,
+    EncoderMixin,
+    replace_strides_with_dilation,
+)
+
+
+class DummyEncoder(nn.Module, EncoderMixin):
+    """Lightweight encoder for testing mixin behavior."""
+
+    def __init__(self) -> None:
+        """Initialize EncoderMixin for testing."""
+        nn.Module.__init__(self)
+        EncoderMixin.__init__(self)
+        self.conv = nn.Conv2d(3, 4, kernel_size=3, padding=1)
+        self.conv32 = nn.Conv2d(4, 4, 3)
+        self._out_channels = [DEFAULT_IN_CHANNELS, 4, 8]
+        self._depth = 2
+
+    def get_stages(self) -> dict[int, Sequence[torch.nn.Module]]:
+        """Get stages for dilation modification.
+
+        Returns:
+            Dictionary with keys as output stride and values as list of modules.
+        """
+        return {16: [self.conv], 32: [self.conv32]}
+
+
+def test_patch_first_conv() -> None:
+    """patch_first_conv should reduce or expand correctly."""
+    # create simple conv
+    model = nn.Sequential(nn.Conv2d(3, 2, kernel_size=1, bias=False))
+    conv = model[0]
+
+    # collapsing 3 channels into 1
+    effnet_mod.patch_first_conv(model, new_in_channels=1, pretrained=True)
+    assert conv.in_channels == 1
+
+    # expanding to 5 channels
+    model = nn.Sequential(nn.Conv2d(3, 2, kernel_size=1, bias=False))
+    conv = model[0]
+
+    effnet_mod.patch_first_conv(model, new_in_channels=5, pretrained=True)
+    assert conv.in_channels == 5
+
+
+def test_patch_first_conv_reset_weights_when_not_pretrained() -> None:
+    """Ensure random reinit happens when pretrained flag is False."""
+    # start from known weights
+    model = nn.Sequential(nn.Conv2d(3, 1, kernel_size=1, bias=False))
+    original = model[0].weight.clone()
+    # changing channel count without pretrained should reinit parameters
+    effnet_mod.patch_first_conv(model, new_in_channels=4, pretrained=False)
+    assert model[0].in_channels == 4
+    assert model[0].weight.shape[1] == 4
+    # Almost surely changed due to reset_parameters
+    assert not torch.equal(original, model[0].weight[:1, :3])
+
+
+def test_patch_first_conv_no_matching_layer_is_safe() -> None:
+    """The function should silently exit when no suitable conv exists."""
+    model = nn.Sequential(nn.Conv2d(5, 1, kernel_size=1))
+    original = model[0].weight.clone()
+    # no conv with default channel count, so weights stay unchanged
+    effnet_mod.patch_first_conv(model, new_in_channels=3, pretrained=True)
+    assert torch.equal(original, model[0].weight)
+
+
+def test_replace_strides_with_dilation_applies_to_nested_convs() -> None:
+    """Strides become dilation and static padding gets removed."""
+    module = nn.Sequential(
+        nn.Conv2d(1, 1, kernel_size=3, stride=2, padding=1),
+    )
+    # attach static_padding to mirror EfficientNet convs
+    module[0].static_padding = nn.Conv2d(1, 1, 1)
+
+    # applying dilation should also strip static padding
+    replace_strides_with_dilation(module, dilation_rate=3)
+    conv = module[0]
+    assert conv.stride == (1, 1)
+    assert conv.dilation == (3, 3)
+    assert conv.padding == (3, 3)
+    assert isinstance(conv.static_padding, nn.Identity)
+
+
+def test_encoder_mixin_properties_and_set_in_channels() -> None:
+    """EncoderMixin should expose out_channels/output_stride and patch convs."""
+    # use dummy encoder to check property logic
+    encoder = DummyEncoder()
+    assert encoder.out_channels == [3, 4, 8]
+    # adjust internals to check min logic in output_stride
+    encoder._output_stride = 4
+    encoder._depth = 3
+    assert encoder.output_stride == 4  # min(output_stride, 2**depth)
+
+    # calling set_in_channels should patch first conv and update bookkeeping
+    encoder.set_in_channels(5, pretrained=False)
+    assert encoder._in_channels == 5
+    assert encoder.out_channels[0] == 5
+    assert encoder.conv.in_channels == 5
+
+
+def test_encoder_mixin_make_dilated_and_validation() -> None:
+    """make_dilated should error on invalid stride and patch convs otherwise."""
+    encoder = DummyEncoder()
+
+    # invalid stride raises
+    with pytest.raises(ValueError, match="Output stride should be 16 or 8"):
+        encoder.make_dilated(output_stride=4)
+
+    # valid stride should touch both stage groups
+    encoder.make_dilated(output_stride=8)
+    conv16, conv32 = encoder.get_stages()[16][0], encoder.get_stages()[32][0]
+    assert conv16.stride == (1, 1)
+    assert conv16.dilation == (2, 2)
+    assert conv32.stride == (1, 1)
+    assert conv32.dilation == (4, 4)
+
+
+def test_get_efficientnet_kwargs_shapes_and_values() -> None:
+    """get_efficientnet_kwargs should produce expected keys and scaling."""
+    # confirm output contains decoded blocks and scaled channels
+    kwargs = effnet_mod.get_efficientnet_kwargs(
+        channel_multiplier=1.2, depth_multiplier=1.4, drop_rate=0.3
+    )
+    assert kwargs.get("block_args")
+    assert kwargs["num_features"] == effnet_mod.round_channels(1280, 1.2, 8, None)
+    assert kwargs["drop_rate"] == 0.3
+
+
+def test_efficientnet_encoder_depth_validation_and_forward() -> None:
+    """EfficientNetEncoder should validate depth and run forward returning features."""
+    # invalid depth should fail fast
+    with pytest.raises(
+        ValueError, match=r"EfficientNetEncoder depth should be in range\s+\[1, 5\]"
+    ):
+        EfficientNetEncoder(
+            stage_idxs=[2, 3, 5],
+            out_channels=[3, 32, 24, 40, 112, 320],
+            depth=6,
+        )
+
+    # build shallow encoder and run a forward pass
+    encoder = EfficientNetEncoder(
+        stage_idxs=[2, 3, 5],
+        out_channels=[3, 32, 24, 40, 112, 320],
+        depth=3,
+        channel_multiplier=0.5,
+        depth_multiplier=0.5,
+    )
+    x = torch.randn(1, 3, 32, 32)
+    features = encoder(x)
+    assert len(features) == encoder._depth + 1
+    assert torch.equal(features[0], x)
+
+    # ensure classifier keys are dropped before loading into the model
+    extended_state = dict(encoder.state_dict())
+    extended_state["classifier.bias"] = torch.tensor([1.0])
+    extended_state["classifier.weight"] = torch.tensor([[1.0]])
+    load_result = encoder.load_state_dict(extended_state, strict=True)
+    assert not load_result.missing_keys
+    assert not load_result.unexpected_keys

tiatoolbox/data/pretrained_model.yaml

@@ -815,7 +815,7 @@ mapde-crchisto:
             threshold_abs: 250
             num_classes: 1
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - { "units": "mpp", "resolution": 0.5 }
@@ -837,7 +837,7 @@ mapde-conic:
             threshold_abs: 205
             num_classes: 1
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - { "units": "mpp", "resolution": 0.5 }
@@ -860,7 +860,7 @@ sccnn-crchisto:
             threshold_abs: 0.20
             patch_output_shape: [ 13, 13 ]
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - { "units": "mpp", "resolution": 0.25 }
@@ -883,7 +883,7 @@ sccnn-conic:
             threshold_abs: 0.05
             patch_output_shape: [ 13, 13 ]
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - { "units": "mpp", "resolution": 0.25 }
@@ -903,7 +903,7 @@ nuclick_original-pannuke:
             num_input_channels: 5
             num_output_channels: 1
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - {'units': 'baseline', 'resolution': 0.25}
@@ -925,7 +925,7 @@ nuclick_light-pannuke:
             decoder_block: [3,3]
             skip_type: "add"
     ioconfig:
-        class: semantic_segmentor.IOSegmentorConfig
+        class: io_config.IOSegmentorConfig
         kwargs:
             input_resolutions:
                 - {'units': 'baseline', 'resolution': 0.25}
@@ -934,3 +934,21 @@ nuclick_light-pannuke:
             patch_input_shape: [128, 128]
             patch_output_shape: [128, 128]
             save_resolution: {'units': 'baseline', 'resolution': 1.0}
+
+grandqc_tissue_detection_mpp10:
+    hf_repo_id: TIACentre/GrandQC_Tissue_Detection
+    architecture:
+        class: grandqc.GrandQCModel
+        kwargs:
+            num_output_channels: 2
+    ioconfig:
+        class: io_config.IOSegmentorConfig
+        kwargs:
+            input_resolutions:
+                - {'units': 'mpp', 'resolution': 10.0}
+            output_resolutions:
+                - {'units': 'mpp', 'resolution': 10.0}
+            patch_input_shape: [512, 512]
+            patch_output_shape: [512, 512]
+            stride_shape: [256, 256]
+            save_resolution: {'units': 'mpp', 'resolution': 10.0}