Explicit target shape argument in the HCS data module (#212)

* explicit target shape argument in the HCS data module

* update docstring

* update test cases

tests/data/test_data.py

@@ -58,7 +58,7 @@ def test_datamodule_setup_fit(preprocessed_hcs_dataset, multi_sample_augmentatio
         batch_size=batch_size,
         num_workers=0,
         augmentations=transforms,
-        architecture="3D",
+        target_2d=False,
         split_ratio=split_ratio,
         yx_patch_size=yx_patch_size,
     )
@@ -78,9 +78,9 @@ def test_datamodule_setup_fit(preprocessed_hcs_dataset, multi_sample_augmentatio
         )
 
 
-def test_datamodule_setup_predict(preprocessed_hcs_dataset):
+@mark.parametrize("z_window_size", [1, 5])
+def test_datamodule_setup_predict(preprocessed_hcs_dataset, z_window_size):
     data_path = preprocessed_hcs_dataset
-    z_window_size = 5
     channel_split = 2
     with open_ome_zarr(data_path) as dataset:
         channel_names = dataset.channel_names
@@ -91,6 +91,7 @@ def test_datamodule_setup_predict(preprocessed_hcs_dataset):
         source_channel=channel_names[:channel_split],
         target_channel=channel_names[channel_split:],
         z_window_size=z_window_size,
+        target_2d=bool(z_window_size == 1),
         batch_size=2,
         num_workers=0,
     )

viscy/data/hcs.py

@@ -274,33 +274,52 @@ def __getitem__(self, index: int) -> Sample:
 
 
 class HCSDataModule(LightningDataModule):
-    """Lightning data module for a preprocessed HCS NGFF Store.
-
-    :param str data_path: path to the data store
-    :param str | Sequence[str] source_channel: name(s) of the source channel,
-        e.g. ``'Phase'``
-    :param str | Sequence[str] target_channel: name(s) of the target channel,
-        e.g. ``['Nuclei', 'Membrane']``
-    :param int z_window_size: Z window size of the 2.5D U-Net, 1 for 2D
-    :param float split_ratio: split ratio of the training subset in the fit stage,
-        e.g. 0.8 means a 80/20 split between training/validation,
-        by default 0.8
-    :param int batch_size: batch size, defaults to 16
-    :param int num_workers: number of data-loading workers, defaults to 8
-    :param Literal["2D", "UNeXt2", "2.5D", "3D"] architecture: U-Net architecture,
-        defaults to "2.5D"
-    :param tuple[int, int] yx_patch_size: patch size in (Y, X),
-        defaults to (256, 256)
-    :param list[MapTransform] normalizations: MONAI dictionary transforms
-        applied to selected channels, defaults to [] (no normalization)
-    :param list[MapTransform] augmentations: MONAI dictionary transforms
-        applied to the training set, defaults to [] (no augmentation)
-    :param bool caching: whether to decompress all the images and cache the result,
-        will store in ``/tmp/$SLURM_JOB_ID/`` if available,
-        defaults to False
-    :param Path | None ground_truth_masks: path to the ground truth masks,
+    """
+    Lightning data module for a preprocessed HCS NGFF Store.
+
+    Parameters
+    ----------
+    data_path : str
+        Path to the data store.
+    source_channel : str or Sequence[str]
+        Name(s) of the source channel, e.g. 'Phase'.
+    target_channel : str or Sequence[str]
+        Name(s) of the target channel, e.g. ['Nuclei', 'Membrane'].
+    z_window_size : int
+        Z window size of the 2.5D U-Net, 1 for 2D.
+    split_ratio : float, optional
+        Split ratio of the training subset in the fit stage,
+        e.g. 0.8 means an 80/20 split between training/validation,
+        by default 0.8.
+    batch_size : int, optional
+        Batch size, defaults to 16.
+    num_workers : int, optional
+        Number of data-loading workers, defaults to 8.
+    target_2d : bool, optional
+        Whether the target is 2D (e.g. in a 2.5D model),
+        defaults to False.
+    yx_patch_size : tuple[int, int], optional
+        Patch size in (Y, X), defaults to (256, 256).
+    normalizations : list of MapTransform, optional
+        MONAI dictionary transforms applied to selected channels,
+        defaults to ``[]`` (no normalization).
+    augmentations : list of MapTransform, optional
+        MONAI dictionary transforms applied to the training set,
+        defaults to ``[]`` (no augmentation).
+    caching : bool, optional
+        Whether to decompress all the images and cache the result,
+        will store in `/tmp/$SLURM_JOB_ID/` if available,
+        defaults to False.
+    ground_truth_masks : Path or None, optional
+        Path to the ground truth masks,
         used in the test stage to compute segmentation metrics,
-        defaults to None
+        defaults to None.
+    persistent_workers : bool, optional
+        Whether to keep the workers alive between fitting epochs,
+        defaults to False.
+    prefetch_factor : int or None, optional
+        Number of samples loaded in advance by each worker during fitting,
+        defaults to None (2 per PyTorch default).
     """
 
     def __init__(
@@ -312,7 +331,7 @@ def __init__(
         split_ratio: float = 0.8,
         batch_size: int = 16,
         num_workers: int = 8,
-        architecture: Literal["2D", "UNeXt2", "2.5D", "3D", "fcmae"] = "2.5D",
+        target_2d: bool = False,
         yx_patch_size: tuple[int, int] = (256, 256),
         normalizations: list[MapTransform] = [],
         augmentations: list[MapTransform] = [],
@@ -327,7 +346,7 @@ def __init__(
         self.target_channel = _ensure_channel_list(target_channel)
         self.batch_size = batch_size
         self.num_workers = num_workers
-        self.target_2d = False if architecture in ["UNeXt2", "3D", "fcmae"] else True
+        self.target_2d = target_2d
         self.z_window_size = z_window_size
         self.split_ratio = split_ratio
         self.yx_patch_size = yx_patch_size