cyto_dl.datamodules.multidim_image module

class cyto_dl.datamodules.multidim_image.MultiDimImageDataset(csv_path: Path | str | None = None, img_path_column: str = 'path', channel_column: str = 'channel', spatial_dims: int = 3, scene_column: str = 'scene', resolution_column: str = 'resolution', time_start_column: str = 'start', time_stop_column: str = 'stop', time_step_column: str = 'step', dict_meta: Dict | None = None, transform: Callable | Sequence[Callable] | None = [], **cache_kwargs)

Bases: CacheDataset

Dataset converting a .csv file or dictionary listing multi dimensional (timelapse or multi-scene) files and some metadata into batches of metadata intended for the BioIOImageLoaderd class.

Parameterss

csv_path: Union[Path, str]

path to csv

img_path_column: str

column in csv_path that contains path to multi dimensional (timelapse or multi-scene) file

channel_column:str

Column in csv_path that contains which channel to extract from multi dimensional (timelapse or multi-scene) file. Should be an integer.

spatial_dims:int=3

Spatial dimension of output image. Must be 2 for YX or 3 for ZYX. Spatial dimensions are used to specify the dimension order of the output image, which will be in the format CZYX or CYX to ensure compatibility with dictionary-based MONAI-style transforms.

scene_column:str=”scene”,

Column in csv_path that contains scenes to extract from multi-scene file. If not specified, all scenes will be extracted. If multiple scenes are specified, they should be separated by a comma (e.g. scene1,scene2)

resolution_column:str=”resolution”

Column in csv_path that contains resolution to extract from multi-resolution file. If not specified, resolution is assumed to be 0.

time_start_column:str=”start”

Column in csv_path specifying which timepoint in timelapse image to start extracting. If any of start_column, stop_column, or step_column are not specified, all timepoints are extracted.

time_stop_column:str=”stop”

Column in csv_path specifying which timepoint in timelapse image to stop extracting. If any of start_column, stop_column, or step_column are not specified, all timepoints are extracted.

time_step_column:str=”step”

Column in csv_path specifying step between timepoints. For example, values in this column should be 2 if every other timepoint should be run. If any of start_column, stop_column, or step_column are not specified, all timepoints are extracted.

dict_meta: Optional[Dict]

Dictionary version of CSV file. If not provided, CSV file is read from csv_path.

transform: Optional[Callable] = []

List (or Compose Object) or Monai dictionary-style transforms to apply to the image metadata. Typically, the first transform should be BioIOImageLoaderd.

cache_kwargs:

Additional keyword arguments to pass to CacheDataset. To skip the caching mechanism, set cache_num to 0.

get_per_file_args(df)