2D FCMAE (#71)

* refactor data loading into its own module

* update type annotations

* move the logging module out

* move old logging into utils

* rename tests to match module name

* bump torch

* draft fcmae encoder

* add stem to the encoder

* wip: masked stem layernorm

* wip: patchify masked features for linear

* use mlp from timm

* hack: POC training script for FCMAE

* fix mask for fitting

* remove training script

* default architecture

* fine-tuning options

* fix cli for finetuning

* draft combined data module

* fix import

* manual validation loss reduction

* update linting
new black version has different rules

* update development guide

* update type hints

* bump iohub

* draft ctmc v1 dataset

* update tests

* move test_data

* remove path conversion

* configurable normalizations (#68)

* inital commit adding the normalization.

* adding dataset_statistics to each fov to facilitate the configurable augmentations

* fix indentation

* ruff

* test preprocessing

* remove redundant field

* cleanup

---------

Co-authored-by: Ziwen Liu <ziwen.liu@czbiohub.org>

* fix ctmc dataloading

* add example ctmc v1 loading script

* changing the normalization and augmentations default from None to empty list.

* invert intensity transform

* concatenated data module

* subsample videos

* livecell dataset

* all sample fields are optional

* fix multi-dataloader validation

* lint

* fixing preprocessing for varying array shapes (i.e aics dataset)

* update loading scripts

* fix CombineMode

* always use untrainable head for FCMAE

* move log values to GPU before syncing
Lightning-AI/pytorch-lightning#18803

* custom head

* ddp caching fixes

* fix caching when using combined loader

* compose normalizations for predict and test stages

* black

* fix normalization in example config

* fix normalization in example config

* prefetch more in validation

* fix collate when multi-sample transform is not used

* ddp caching fixes

* fix caching when using combined loader

* typing fixes

* fix test dataset

* fix invert transform

* add ddp prepare flag for combined data module

* remove redundant operations

* filter empty detections

* pass trainer to underlying data modules in concatenated

* hack: add test dataloader for LiveCell dataset

* test datasets for livecell and ctmc

* fix merge error

* fix merge error

* fix mAP default for over 100 detections

* bump torchmetric

* fix combined loader training for virtual staining task

* fix non-combined data loader training

* add fcmae to graph script

* fix type hint

* format

* add back convolutiuon option for fcmae head

---------

Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com>

Author: ziw-liu

pyproject.toml

@@ -26,7 +26,7 @@ dynamic = ["version"]
 metrics = [
     "cellpose==2.1.0",
     "scikit-learn>=1.1.3",
-    "torchmetrics[detection]>=1.0.0",
+    "torchmetrics[detection]>=1.3.1",
     "ptflops>=0.7",
 ]
 visual = ["ipykernel", "graphviz", "torchview"]

tests/unet/test_fcmae.py

@@ -6,6 +6,7 @@
     MaskedConvNeXtV2Block,
     MaskedConvNeXtV2Stage,
     MaskedMultiscaleEncoder,
+    PixelToVoxelShuffleHead,
     generate_mask,
     masked_patchify,
     masked_unpatchify,
@@ -104,6 +105,13 @@ def test_masked_multiscale_encoder():
         assert afeat.shape[2] == afeat.shape[3] == xy_size // stride
 
 
+def test_pixel_to_voxel_shuffle_head():
+    head = PixelToVoxelShuffleHead(240, 3, out_stack_depth=5, xy_scaling=4)
+    x = torch.rand(2, 240, 16, 16)
+    y = head(x)
+    assert y.shape == (2, 3, 5, 64, 64)
+
+
 def test_fcmae():
     x = torch.rand(2, 3, 5, 128, 128)
     model = FullyConvolutionalMAE(3, 3)
@@ -113,3 +121,16 @@ def test_fcmae():
     y, m = model(x, mask_ratio=0.6)
     assert y.shape == x.shape
     assert m.shape == (2, 1, 128, 128)
+
+
+def test_fcmae_head_conv():
+    x = torch.rand(2, 3, 5, 128, 128)
+    model = FullyConvolutionalMAE(
+        3, 3, head_conv=True, head_conv_expansion_ratio=4, head_conv_pool=True
+    )
+    y, m = model(x)
+    assert y.shape == x.shape
+    assert m is None
+    y, m = model(x, mask_ratio=0.6)
+    assert y.shape == x.shape
+    assert m.shape == (2, 1, 128, 128)

viscy/data/combined.py

@@ -79,7 +79,6 @@ class ConcatDataModule(LightningDataModule):
     The concatenated data module will have the same
     batch size and number of workers as the first data module.
     Each element will be sampled uniformly regardless of their original data module.
-
     :param Sequence[LightningDataModule] data_modules: data modules to concatenate
     """
 
@@ -93,9 +92,11 @@ def __init__(self, data_modules: Sequence[LightningDataModule]):
                 raise ValueError("Inconsistent number of workers")
             if dm.batch_size != self.batch_size:
                 raise ValueError("Inconsistent batch size")
+        self.prepare_data_per_node = True
 
     def prepare_data(self):
         for dm in self.data_modules:
+            dm.trainer = self.trainer
             dm.prepare_data()
 
     def setup(self, stage: Literal["fit", "validate", "test", "predict"]):

viscy/data/ctmc_v1.py

@@ -10,9 +10,8 @@
 
 
 class CTMCv1ValidationDataset(SlidingWindowDataset):
-    subsample_rate: int = 30
 
-    def __len__(self) -> int:
+    def __len__(self, subsample_rate: int = 30) -> int:
         # sample every 30th frame in the videos
         return super().__len__() // self.subsample_rate
 

viscy/data/hcs.py

@@ -191,8 +191,6 @@ def __getitem__(self, index: int) -> Sample:
             sample_images["norm_meta"] = norm_meta
         if self.transform:
             sample_images = self.transform(sample_images)
-        # if isinstance(sample_images, list):
-        #     sample_images = sample_images[0]
         if "weight" in sample_images:
             del sample_images["weight"]
         sample = {

viscy/data/livecell.py

@@ -3,9 +3,11 @@
 
 import torch
 from lightning.pytorch import LightningDataModule
-from monai.transforms import Compose, Transform
+from monai.transforms import Compose, MapTransform
+from pycocotools.coco import COCO
 from tifffile import imread
 from torch.utils.data import DataLoader, Dataset
+from torchvision.ops import box_convert
 
 from viscy.data.typing import Sample
 
@@ -15,10 +17,10 @@ class LiveCellDataset(Dataset):
     LiveCell dataset.
 
     :param list[Path] images: List of paths to single-page, single-channel TIFF files.
-    :param Transform | Compose transform: Transform to apply to the dataset
+    :param MapTransform | Compose transform: Transform to apply to the dataset
     """
 
-    def __init__(self, images: list[Path], transform: Transform | Compose) -> None:
+    def __init__(self, images: list[Path], transform: MapTransform | Compose) -> None:
         self.images = images
         self.transform = transform
 
@@ -32,36 +34,100 @@ def __getitem__(self, idx: int) -> Sample:
         return {"source": image, "target": image}
 
 
+class LiveCellTestDataset(Dataset):
+    """
+    LiveCell dataset.
+
+    :param list[Path] images: List of paths to single-page, single-channel TIFF files.
+    :param MapTransform | Compose transform: Transform to apply to the dataset
+    """
+
+    def __init__(
+        self,
+        image_dir: Path,
+        transform: MapTransform | Compose,
+        annotations: Path,
+        load_target: bool = False,
+        load_labels: bool = False,
+    ) -> None:
+        self.image_dir = image_dir
+        self.transform = transform
+        self.coco = COCO(str(annotations))
+        self.image_ids = list(self.coco.imgs.keys())
+        self.load_target = load_target
+        self.load_labels = load_labels
+
+    def __len__(self) -> int:
+        return len(self.image_ids)
+
+    def __getitem__(self, idx: int) -> Sample:
+        image_id = self.image_ids[idx]
+        file_name = self.coco.imgs[image_id]["file_name"]
+        image_path = self.image_dir / file_name
+        image = imread(image_path)[None, None]
+        image = torch.from_numpy(image).to(torch.float32)
+        sample = Sample(source=image)
+        if self.load_target:
+            sample["target"] = image
+        if self.load_labels:
+            anns = self.coco.loadAnns(self.coco.getAnnIds(image_id)) or []
+            boxes = [torch.tensor(ann["bbox"]).to(torch.float32) for ann in anns]
+            masks = [
+                torch.from_numpy(self.coco.annToMask(ann)).to(torch.bool)
+                for ann in anns
+            ]
+            dets = {
+                "boxes": box_convert(torch.stack(boxes), in_fmt="xywh", out_fmt="xyxy"),
+                "labels": torch.zeros(len(anns)).to(torch.uint8),
+                "masks": torch.stack(masks),
+            }
+            sample["detections"] = dets
+            sample["file_name"] = file_name
+        self.transform(sample)
+        return sample
+
+
 class LiveCellDataModule(LightningDataModule):
     def __init__(
         self,
-        train_val_images: Path,
-        train_annotations: Path,
-        val_annotations: Path,
-        train_transforms: list[Transform],
-        val_transforms: list[Transform],
+        train_val_images: Path | None = None,
+        test_images: Path | None = None,
+        train_annotations: Path | None = None,
+        val_annotations: Path | None = None,
+        test_annotations: Path | None = None,
+        train_transforms: list[MapTransform] = [],
+        val_transforms: list[MapTransform] = [],
+        test_transforms: list[MapTransform] = [],
         batch_size: int = 16,
         num_workers: int = 8,
     ) -> None:
         super().__init__()
         self.train_val_images = Path(train_val_images)
         if not self.train_val_images.is_dir():
             raise NotADirectoryError(str(train_val_images))
+        self.test_images = Path(test_images)
+        if not self.test_images.is_dir():
+            raise NotADirectoryError(str(test_images))
         self.train_annotations = Path(train_annotations)
         if not self.train_annotations.is_file():
             raise FileNotFoundError(str(train_annotations))
         self.val_annotations = Path(val_annotations)
         if not self.val_annotations.is_file():
             raise FileNotFoundError(str(val_annotations))
+        self.test_annotations = Path(test_annotations)
+        if not self.test_annotations.is_file():
+            raise FileNotFoundError(str(test_annotations))
         self.train_transforms = Compose(train_transforms)
         self.val_transforms = Compose(val_transforms)
+        self.test_transforms = Compose(test_transforms)
         self.batch_size = batch_size
         self.num_workers = num_workers
 
     def setup(self, stage: str) -> None:
-        if stage != "fit":
-            raise NotImplementedError("Only fit stage is supported")
-        self._setup_fit()
+        if stage == "fit":
+            self._setup_fit()
+        elif stage == "test":
+            self._setup_test()
 
     def _parse_image_names(self, annotations: Path) -> list[Path]:
         with open(annotations) as f:
@@ -80,6 +146,14 @@ def _setup_fit(self) -> None:
             transform=self.val_transforms,
         )
 
+    def _setup_test(self) -> None:
+        self.test_dataset = LiveCellTestDataset(
+            self.test_images,
+            transform=self.test_transforms,
+            annotations=self.test_annotations,
+            load_labels=True,
+        )
+
     def train_dataloader(self) -> DataLoader:
         return DataLoader(
             self.train_dataset,
@@ -96,3 +170,8 @@ def val_dataloader(self) -> DataLoader:
             num_workers=self.num_workers,
             persistent_workers=bool(self.num_workers),
         )
+
+    def test_dataloader(self) -> DataLoader:
+        return DataLoader(
+            self.test_dataset, batch_size=self.batch_size, num_workers=self.num_workers
+        )

viscy/evaluation/evaluation_metrics.py

@@ -9,7 +9,7 @@
 from monai.metrics.regression import compute_ssim_and_cs
 from scipy.optimize import linear_sum_assignment
 from skimage.measure import label, regionprops
-from torchmetrics.detection import MeanAveragePrecision
+from torchmetrics.detection.mean_ap import MeanAveragePrecision
 from torchvision.ops import masks_to_boxes
 
 
@@ -172,7 +172,12 @@ def mean_average_precision(
         :py:class:`torchmetrics.detection.MeanAveragePrecision`
     :return dict[str, torch.Tensor]: COCO-style metrics
     """
-    map_metric = MeanAveragePrecision(box_format="xyxy", iou_type="segm", **kwargs)
+    defaults = dict(
+        iou_type="segm", box_format="xyxy", max_detection_thresholds=[1, 100, 10000]
+    )
+    if not kwargs:
+        kwargs = {}
+    map_metric = MeanAveragePrecision(**(defaults | kwargs))
     map_metric.update(
         [labels_to_detection(pred_labels)], [labels_to_detection(target_labels)]
     )

viscy/light/engine.py

@@ -153,6 +153,7 @@ def __init__(
         self.log_batches_per_epoch = log_batches_per_epoch
         self.log_samples_per_batch = log_samples_per_batch
         self.training_step_outputs = []
+        self.validation_losses = []
         self.validation_step_outputs = []
         # required to log the graph
         if architecture == "2D":
@@ -179,32 +180,49 @@ def __init__(
     def forward(self, x: Tensor) -> Tensor:
         return self.model(x)
 
-    def training_step(self, batch: Sample, batch_idx: int):
-        source = batch["source"]
-        target = batch["target"]
-        pred = self.forward(source)
-        loss = self.loss_function(pred, target)
+    def training_step(self, batch: Sample | Sequence[Sample], batch_idx: int):
+        losses = []
+        batch_size = 0
+        if not isinstance(batch, Sequence):
+            batch = [batch]
+        for b in batch:
+            source = b["source"]
+            target = b["target"]
+            pred = self.forward(source)
+            loss = self.loss_function(pred, target)
+            losses.append(loss)
+            batch_size += source.shape[0]
+            if batch_idx < self.log_batches_per_epoch:
+                self.training_step_outputs.extend(
+                    self._detach_sample((source, target, pred))
+                )
+        loss_step = torch.stack(losses).mean()
         self.log(
             "loss/train",
-            loss,
+            loss_step.to(self.device),
             on_step=True,
             on_epoch=True,
             prog_bar=True,
             logger=True,
             sync_dist=True,
+            batch_size=batch_size,
         )
-        if batch_idx < self.log_batches_per_epoch:
-            self.training_step_outputs.extend(
-                self._detach_sample((source, target, pred))
-            )
-        return loss
+        return loss_step
 
     def validation_step(self, batch: Sample, batch_idx: int, dataloader_idx: int = 0):
-        source = batch["source"]
-        target = batch["target"]
+        source: Tensor = batch["source"]
+        target: Tensor = batch["target"]
         pred = self.forward(source)
         loss = self.loss_function(pred, target)
-        self.log("loss/validate", loss, sync_dist=True, add_dataloader_idx=False)
+        if dataloader_idx + 1 > len(self.validation_losses):
+            self.validation_losses.append([])
+        self.validation_losses[dataloader_idx].append(loss.detach())
+        self.log(
+            f"loss/val/{dataloader_idx}",
+            loss.to(self.device),
+            sync_dist=True,
+            batch_size=source.shape[0],
+        )
         if batch_idx < self.log_batches_per_epoch:
             self.validation_step_outputs.extend(
                 self._detach_sample((source, target, pred))
@@ -364,8 +382,16 @@ def on_train_epoch_end(self):
         self.training_step_outputs = []
 
     def on_validation_epoch_end(self):
+        super().on_validation_epoch_end()
         self._log_samples("val_samples", self.validation_step_outputs)
         self.validation_step_outputs = []
+        # average within each dataloader
+        loss_means = [torch.tensor(losses).mean() for losses in self.validation_losses]
+        self.log(
+            "loss/validate",
+            torch.tensor(loss_means).mean().to(self.device),
+            sync_dist=True,
+        )
 
     def on_test_start(self):
         """Load CellPose model for segmentation."""
@@ -477,7 +503,6 @@ class FcmaeUNet(VSUNet):
     def __init__(self, fit_mask_ratio: float = 0.0, **kwargs):
         super().__init__(architecture="fcmae", **kwargs)
         self.fit_mask_ratio = fit_mask_ratio
-        self.validation_losses = []
 
     def forward(self, x: Tensor, mask_ratio: float = 0.0):
         return self.model(x, mask_ratio)
@@ -529,13 +554,3 @@ def validation_step(self, batch: Sample, batch_idx: int, dataloader_idx: int = 0
             self.validation_step_outputs.extend(
                 self._detach_sample((source, target * mask.unsqueeze(2), pred))
             )
-
-    def on_validation_epoch_end(self):
-        super().on_validation_epoch_end()
-        # average within each dataloader
-        loss_means = [torch.tensor(losses).mean() for losses in self.validation_losses]
-        self.log(
-            "loss/validate",
-            torch.tensor(loss_means).mean().to(self.device),
-            sync_dist=True,
-        )