File location manager module

This module takes care of all the file locations of all the czi, tiff and log files.

class library.image_manipulation.filelocation_manager.FileLocationManager(stack, data_path='/net/birdstore/Active_Atlas_Data/data_root')

Bases: object

Master class to house all file paths for preprocessing-pipeline

All file locations are defined in this class for reference by other methods/functions. Default root is UCSD-specific (birdstore fileshare) but may be modified in data_path Subfolders to each brain are defined based on usage (some examples below): -czi folder [stores raw scanner images from which tiff images are extracted] -tif [stores full resolution images extracted from czi files] -neuroglancer_data [stores ‘precomputed’ format of entire image stack for loading into Neuroglancer visualization tool]

get_alignment_directories(channel, downsample, iteration=0)

get_alignments(iteration=0)

get_cell_labels()

Returns path to store cell labels

Note: This path is also web-accessbile [@ UCSD]

get_czi()

get_directory(channel: int, downsample: bool, inpath: str) → str

get_full(channel=1)

get_full_aligned(channel=1): This is used in cell labeling

get_full_colored(channel=1)

get_full_masked(channel=1)

get_histogram(channel=1)

get_logdir(): This method is only called on first instance then stored as environment variable [See: FileLogger class for more information]

get_neuroglancer(downsample=True, channel=1, iteration=0)

Returns path to store neuroglancer files (‘precomputed’ format)

Note: This path is also web-accessbile [@ UCSD]

get_neuroglancer_progress(downsample=True, channel=1, iteration=0)

get_neuroglancer_rechunkme(downsample: bool = True, channel: int = 1, iteration: int = 0, use_scratch_dir: bool = False) → str

Generates the file path for the Neuroglancer rechunkme file based on the given parameters. DK37 uses 552G for 478 images or 1.15G per image

Args:: downsample (bool): If True, includes a ‘T’ in the output directory name to indicate downsampling. Default is True. channel (int): The channel number to include in the output directory name. Default is 1. iteration (int): The iteration number to include in the alignment path. Default is 0.
Returns:: str: The generated file path for the Neuroglancer rechunkme file.

get_normalized(channel=1)

get_thumbnail(channel=1)

get_thumbnail_colored(channel=1)

get_thumbnail_masked(channel=1)