Add doc-strings.

src/faim_hcs/hcs/acquisition.py

@@ -61,10 +61,20 @@ def get_channel_metadata(self) -> dict[int, ChannelMetadata]:
         raise NotImplementedError()
 
     def get_well_names(self) -> Iterable[str]:
+        """
+        Get the names of all wells in the acquisition.
+        """
         for well in self.get_well_acquisitions():
             yield well.name
 
     def get_omero_channel_metadata(self) -> list[dict]:
+        """
+        Get the channel metadata in OMERO format.
+
+        Returns
+        -------
+            List of channel metadata.
+        """
         ome_channels = []
         ch_metadata = self.get_channel_metadata()
         max_channel = max(list(ch_metadata.keys()))
@@ -115,7 +125,6 @@ def get_common_well_shape(self) -> tuple[int, int, int, int, int]:
 
         Returns
         -------
-        tuple[int, int, int, int, int]
             (time, channel, z, y, x)
         """
         well_shapes = []
@@ -126,6 +135,10 @@ def get_common_well_shape(self) -> tuple[int, int, int, int, int]:
 
 
 class WellAcquisition(ABC):
+    """
+    A single well of a plate acquisition.
+    """
+
     name: str = None
     _files = None
     _alignment: TileAlignmentOptions = None
@@ -157,6 +170,13 @@ def _assemble_tiles(self) -> list[Tile]:
         raise NotImplementedError()
 
     def get_dtype(self) -> np.dtype:
+        """
+        Get the data type of the well acquisition.
+
+        Returns
+        -------
+            type
+        """
         return self._tiles[0].load_data().dtype
 
     def _align_tiles(self, tiles: list[Tile]) -> list[Tile]:
@@ -177,23 +197,52 @@ def get_tiles(self) -> list[Tile]:
         return self._tiles
 
     def get_row_col(self) -> tuple[str, str]:
+        """
+        Get the row and column of the well acquisition.
+
+        Returns
+        -------
+            row, column
+        """
         return self.name[0], self.name[1:]
 
     @abstractmethod
     def get_axes(self) -> list[str]:
+        """
+        Get the axes of the well acquisition.
+        """
         raise NotImplementedError()
 
     @abstractmethod
     def get_yx_spacing(self) -> tuple[float, float]:
+        """
+        Get the yx spacing of the well acquisition.
+        """
         raise NotImplementedError()
 
     @abstractmethod
     def get_z_spacing(self) -> Optional[float]:
+        """
+        Get the z spacing of the well acquisition.
+        """
         raise NotImplementedError()
 
     def get_coordinate_transformations(
         self, max_layer: int, yx_binning: int
     ) -> list[dict[str, Any]]:
+        """
+        Get the NGFF conform coordinate transformations for the well
+        acquisition.
+
+        Parameters
+        ----------
+        max_layer : Maximum layer of the resolution pyramid.
+        yx_binning : Bin factor of the yx resolution.
+
+        Returns
+        -------
+            List of coordinate transformations.
+        """
         transformations = []
         for s in range(max_layer + 1):
             if self.get_z_spacing() is not None:

src/faim_hcs/hcs/cellvoyager/CellVoyagerWellAcquisition.py

@@ -9,6 +9,10 @@
 
 
 class CellVoyagerWellAcquisition(WellAcquisition):
+    """
+    Data structure for a CellVoyager well acquisition.
+    """
+
     def __init__(
         self,
         files: pd.DataFrame,

src/faim_hcs/hcs/converter.py

@@ -27,6 +27,10 @@ class NGFFPlate(BaseModel):
 
 
 class ConvertToNGFFPlate:
+    """
+    Convert a plate acquisition to an NGFF plate.
+    """
+
     _ngff_plate: NGFFPlate
 
     def __init__(
@@ -37,6 +41,21 @@ def __init__(
         warp_func: Callable = stitching_utils.translate_tiles_2d,
         fuse_func: Callable = stitching_utils.fuse_mean,
     ):
+        """
+        Parameters
+        ----------
+        ngff_plate :
+            NGFF plate information.
+        yx_binning :
+            YX binning factor.
+        dask_chunk_size_factor :
+            Dask chunk size factor. Increasing this will increase the memory
+            usage.
+        warp_func :
+            Function used to warp tile images.
+        fuse_func :
+            Function used to fuse tile images.
+        """
         assert (
             isinstance(yx_binning, int) and yx_binning >= 1
         ), "yx_binning must be an integer >= 1."
@@ -84,6 +103,26 @@ def run(
         max_layer: int = 3,
         storage_options: dict = None,
     ) -> zarr.Group:
+        """
+        Convert a plate acquisition to an NGFF plate.
+
+        Parameters
+        ----------
+        plate_acquisition :
+            A single plate acquisition.
+        well_sub_group :
+            Name of the well sub-group.
+        chunks :
+            Chunk size in (Z)YX.
+        max_layer :
+            Maximum layer of the resolution pyramid layers.
+        storage_options :
+            Zarr storage options.
+
+        Returns
+        -------
+            zarr.Group of the plate.
+        """
         assert 2 <= len(chunks) <= 3, "Chunks must be 2D or 3D."
         plate = self._create_zarr_plate(plate_acquisition)
         for well_acquisition in tqdm(plate_acquisition.get_well_acquisitions()):

src/faim_hcs/hcs/imagexpress/ImageXpressPlateAcquisition.py

@@ -43,15 +43,15 @@ def _parse_files(self) -> pd.DataFrame:
             Table of all files in the acquisition.
         """
         return pd.DataFrame(
-            self._list_and_match_files(
+            ImageXpressPlateAcquisition._list_and_match_files(
                 root_dir=self._acquisition_dir,
                 root_re=self._get_root_re(),
                 filename_re=self._get_filename_re(),
             )
         )
 
+    @staticmethod
     def _list_and_match_files(
-        self,
         root_dir: Union[Path, str],
         root_re: re.Pattern,
         filename_re: re.Pattern,

src/faim_hcs/hcs/imagexpress/MixedAcquisition.py

@@ -9,6 +9,36 @@
 
 
 class MixedAcquisition(StackAcquisition):
+    """Image stack acquisition with Projectsion acquired with a Molecular
+    Devices ImageXpress Micro Confocal system.
+
+    MIP-2P-2sub-Stack --> {name} [Optional]
+    └── 2023-02-21 --> {date}
+        └── 1334 --> {acquisition id}
+            ├── Projection-Mix_E07_s1_w1E94C24BD-45E4-450A-9919-257C714278F7.tif
+            ├── Projection-Mix_E07_s1_w1_thumb4BFD4018-E675-475E-B5AB-2E959E6B6DA1.tif
+            ├── ...
+            ├── Projection-Mix_E08_s2_w3CCE83D85-0912-429E-9F18-716A085BB5BC.tif
+            ├── Projection-Mix_E08_s2_w3_thumb4D88636E-181E-4AF6-BC53-E7A435959C8F.tif
+            ├── ZStep_1
+            │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
+            │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif
+            │   ├── Projection-Mix_E07_s1_w2C0A49256-E289-4C0F-ADC9-F7728ABDB141.tif
+            │   ├── Projection-Mix_E07_s1_w2_thumb57D4B151-71BF-480E-8CC4-C23A2690B763.tif
+            │   ├── Projection-Mix_E07_s1_w427CCB2E4-1BF4-45E7-8BC7-264B48EF9C4A.tif
+            │   ├── Projection-Mix_E07_s1_w4_thumb555647D0-77F1-4A43-9472-AE509F95E236.tif
+            │   ├── ...
+            │   └── Projection-Mix_E08_s2_w4_thumbD2785594-4F49-464F-9F80-1B82E30A560A.tif
+            ├── ...
+            └── ZStep_9
+                ├── Projection-Mix_E07_s1_w1091EB8A5-272A-466D-B8A0-7547C6BA392B.tif
+                ├── ...
+                └── Projection-Mix_E08_s2_w2_thumb210C0D5D-C20E-484D-AFB2-EFE669A56B84.tif
+
+    Image data is stored in {name}_{well}_{field}_w{channel}{md_id}.tif.
+    The *_thumb*.tif files, used by Molecular Devices as preview, are ignored.
+    """
+
     def __init__(
         self,
         acquisition_dir: Union[Path, str],

src/faim_hcs/hcs/imagexpress/StackAcquisition.py

@@ -17,11 +17,6 @@ class StackAcquisition(ImageXpressPlateAcquisition):
     MIP-2P-2sub-Stack --> {name} [Optional]
     └── 2023-02-21 --> {date}
         └── 1334 --> {acquisition id}
-            ├── Projection-Mix_E07_s1_w1E94C24BD-45E4-450A-9919-257C714278F7.tif
-            ├── Projection-Mix_E07_s1_w1_thumb4BFD4018-E675-475E-B5AB-2E959E6B6DA1.tif
-            ├── ...
-            ├── Projection-Mix_E08_s2_w3CCE83D85-0912-429E-9F18-716A085BB5BC.tif
-            ├── Projection-Mix_E08_s2_w3_thumb4D88636E-181E-4AF6-BC53-E7A435959C8F.tif
             ├── ZStep_1
             │   ├── Projection-Mix_E07_s1_w1E78EB128-BD0D-4D94-A6AD-3FF28BB1B105.tif
             │   ├── Projection-Mix_E07_s1_w1_thumb187DE64B-038A-4671-BF6B-683721723769.tif

src/faim_hcs/stitching/DaskTileStitcher.py

@@ -21,6 +21,18 @@ def __init__(
         output_shape: Optional[tuple[int, int, int, int, int]] = None,
         dtype: np.dtype = np.uint16,
     ):
+        """
+        Parameters
+        ----------
+        tiles :
+            Tiles to stitch.
+        yx_chunk_shape :
+            Chunk shape in y and x.
+        output_shape :
+            Shape of the output image. If None, the shape is computed from the tiles.
+        dtype :
+            Data type of the output image.
+        """
         self.tiles: list[Tile] = stitching_utils.shift_to_origin(tiles)
         self.chunk_shape = (
             1,
@@ -96,7 +108,7 @@ def get_stitched_dask_array(
 
         Returns
         -------
-
+            Dask array of the stitched image.
         """
         func = partial(
             stitching_utils.assemble_chunk,

src/faim_hcs/stitching/stitching_utils.py

@@ -95,6 +95,24 @@ def fuse_sum(warped_tiles: NDArray, warped_masks: NDArray) -> NDArray:
 
 @threadpool_limits.wrap(limits=1, user_api="blas")
 def translate_tiles_2d(block_info, yx_chunk_shape, dtype, tiles):
+    """
+    Translate tiles to their relative position inside the given block.
+
+    Parameters
+    ----------
+    block_info :
+        da.map_blocks block_info.
+    yx_chunk_shape :
+        shape of the chunk in yx.
+    dtype :
+        dtype of the tiles.
+    tiles :
+        list of tiles.
+
+    Returns
+    -------
+        translated tiles, translated masks
+    """
     array_location = block_info[None]["array-location"]
     chunk_yx_origin = np.array([array_location[3][0], array_location[4][0]])
     warped_tiles = []
@@ -126,6 +144,26 @@ def translate_tiles_2d(block_info, yx_chunk_shape, dtype, tiles):
 def assemble_chunk(
     block_info=None, tile_map=None, warp_func=None, fuse_func=None, dtype=None
 ):
+    """
+    Assemble a chunk of the stitched image.
+
+    Parameters
+    ----------
+    block_info :
+        da.map_blocks block_info.
+    tile_map :
+        map of block positions to tiles.
+    warp_func :
+        function used to warp tiles.
+    fuse_func :
+        function used to fuse tiles.
+    dtype :
+        tile data type.
+
+    Returns
+    -------
+        fused tiles corresponding to this block/chunk
+    """
     chunk_location = block_info[None]["chunk-location"]
     chunk_shape = block_info[None]["chunk-shape"]
     tiles = tile_map[chunk_location]