Update docstrings

torch_em/data/datasets/light_microscopy/cellseg_3d.py

@@ -1,4 +1,4 @@
-"""This dataset contains annotation for nucleus segmentation in 3d fluorescence microscopy.
+"""This dataset contains annotation for nucleus segmentation in 3d fluorescence microscopy from mesoSPIM microscopy.
 
 This dataset is from the publication https://doi.org/10.1101/2024.05.17.594691 .
 Please cite it if you use this dataset in your research.

torch_em/data/datasets/light_microscopy/embedseg_data.py

@@ -1,5 +1,4 @@
-# https://github.com/juglab/EmbedSeg/releases/tag/v0.1.0
-"""This dataset contains annotation for nucleus segmentation in 3d fluorescence microscopy
+"""This dataset contains annotation for 3d fluorescence microscopy segmentation
 that were introduced by the EmbedSeg publication.
 
 This dataset is from the publication https://proceedings.mlr.press/v143/lalit21a.html.
@@ -29,17 +28,19 @@
 
 
 def get_embedseg_data(path: Union[os.PathLike, str], name: str, download: bool) -> str:
- """Download the CellSeg3d training data.
+ """Download the EmbedSeg training data.
 
  Args:
  path: Filepath to a folder where the downloaded data will be saved.
- name:
- split:
+ name: Name of the dataset to download.
  download: Whether to download the data if it is not present.
 
  Returns:
  The filepath to the training data.
  """
+ if name not in URLS:
+ raise ValueError(f"The dataset name must be in {list(URLS.keys())}. You provided {name}.")
+
  url = URLS[name]
  checksum = CHECKSUMS[name]
 
@@ -63,11 +64,13 @@ def get_embedseg_dataset(
  download: bool = False,
  **kwargs
 ) -> Dataset:
- """Get the CellSeg3d dataset for segmenting nuclei in 3d fluorescence microscopy.
+ """Get an EmbedSeg dataset for 3d fluorescence microscopy segmentation.
 
  Args:
  path: Filepath to a folder where the downloaded data will be saved.
  patch_shape: The patch shape to use for training.
+ name: Name of the dataset to download.
+ split: The split to use for the dataset.
  download: Whether to download the data if it is not present.
  kwargs: Additional keyword arguments for `torch_em.default_segmentation_dataset`.
 
@@ -97,12 +100,14 @@ def get_embedseg_loader(
  download: bool = False,
  **kwargs
 ) -> DataLoader:
- """Get the CovidIF dataloder for segmenting nuclei or cells in immunofluorescence microscopy.
+ """Get an EmbedSeg dataloader for 3d fluorescence microscopy segmentation.
 
  Args:
  path: Filepath to a folder where the downloaded data will be saved.
  patch_shape: The patch shape to use for training.
  batch_size: The batch size for training.
+ name: Name of the dataset to download.
+ split: The split to use for the dataset.
  download: Whether to download the data if it is not present.
  kwargs: Additional keyword arguments for `torch_em.default_segmentation_dataset` or for the PyTorch DataLoader.