parallelism#

compare(img_0: str | ndarray, df_0: str | DataFrame, img_1: str | ndarray, df_1: str | DataFrame, scale, coord_names: list[str] | tuple[str], blob_diameter: int, size_min: int, size_max: int, processes: int | None, verbose: bool = True, are_already_clean: tuple[bool, bool] = (False, False))[source]#

Make a report on colocalization between two channels

Parameters:

  • img_0 (str | np.ndarray) – binary image or path to binary image for channel 0, as generated by cell_map

  • df_0 (str | pd.DataFrame) – dataframe or path to feather file for channel 0, as generated by cell_map

  • img_1 (str | np.ndarray) – binary image or path to binary image for channel 1, as generated by cell_map

  • df_1 (str) – dataframe or path to feather file for channel 1, as generated by cell_map

  • scale (array like) – list of values specifying voxel dimensions. Caution: this scale must be shared by both channels.

  • coord_names (list[str]) – list of string specifying the representative points coords columns in the dataframes

  • blob_diameter (int) – an upper bound for the sought blobs diameters, in PHYSICAL units

  • size_min (int) – minimum size of blobs to consider

  • size_max (int) – maximum size of blobs to consider

  • processes (int | None) – positive integer or None, the number of processes to use for block processing. Defaults to None, if None the number of processes will equal the computer’s number of processors.

  • verbose (bool) – print processing information if True. Defaults To true.

local_report(block_0: Block, block_1: Block, /, df_0: DataFrame, df_1: DataFrame, scale, coord_names, verbose: bool = True, are_already_clean: tuple[bool, bool] = (False, False))[source]#

Return a report dataframe for the locally computable information.

Parameters:

  • block_0 (Block) – block object for channel 0

  • block_1 (Block) – block object for channel 1

  • df_0 (pd.DataFrame) – dataframe for channel 0

  • df_1 (pd.DataFrame) – dataframe for channel 1

  • scale (array like) – list of values specifying voxel dimensions. Caution: this scale must be shared by both channels.

  • coord_names (list[str]) – list of string specifying the representative points coords columns in the dataframes

local_report_body(df_0, df_1, block_0, block_1, coord_names, scale, verbose, are_already_clean)[source]#