Intensity Correction¶
- cloudreg.scripts.correct_raw_data.correct_raw_data(raw_data_path, channel, subsample_factor=2, log_s3_path=None, background_correction=True)[source]¶
Correct vignetting artifact in raw data
- Parameters:
raw_data_path (str) – Path to raw data
channel (int) – Channel number to prcess
subsample_factor (int, optional) – Factor to subsample the raw data by to compute vignetting correction. Defaults to 2.
log_s3_path (str, optional) – S3 path to store intermediates at. Defaults to None.
background_correction (bool, optional) – If True, subtract estimated background value from all tiles. Defaults to True.
- cloudreg.scripts.correct_raw_data.correct_tile(raw_tile_path, bias, background_value=None)[source]¶
Apply vignetting corrrection to single tile
- Parameters:
raw_tile_path (str) – Path to raw data image
bias (np.ndarray) – Vignetting correction that is multiplied by image
background_value (float, optional) – Background value. Defaults to None.
- cloudreg.scripts.correct_raw_data.correct_tiles(tiles, bias, background_value=None)[source]¶
Correct a list of tiles
- Parameters:
tiles (list of str) – Paths to raw data images to correct
bias (np.ndarray) – Vignetting correction to multiply by raw data
background_value (float, optional) – Background value to subtract from raw data. Defaults to None.
- cloudreg.scripts.correct_raw_data.get_background_value(raw_data_path)[source]¶
Estimate background value for COLM data
- Parameters:
raw_data_path (str) – Path to raw data
- Returns:
Estimated value of background in image
- Return type:
float
- cloudreg.scripts.correct_raw_data.sum_tiles(files)[source]¶
Sum the images in files together
- Parameters:
files (list of str) – Local Paths to images to sum
- Returns:
Sum of the images in files
- Return type:
np.ndarray
- cloudreg.scripts.correct_stitched_data.correct_stitched_data(data_s3_path, out_s3_path, resolution=15, num_procs=12)[source]¶
Correct illumination inhomogeneity in stitched precomputed data on S3 and upload result back to S3 as precomputed
- Parameters:
data_s3_path (str) – S3 path to precomputed volume that needs to be illumination corrected
out_s3_path (str) – S3 path to store corrected precomputed volume
resolution (int, optional) – Resolution in microns at which illumination correction is computed. Defaults to 15.
num_procs (int, optional) – Number of proceses to use when uploading data to S3. Defaults to 12.
- cloudreg.scripts.correct_stitched_data.process_slice(bias_slice, z, data_orig_path, data_bc_path)[source]¶
Correct and upload a single slice of data
- Parameters:
bias_slice (sitk.Image) – Slice of illumination correction
z (int) – Z slice of data to apply correction to
data_orig_path (str) – S3 path to source data that needs to be corrected
data_bc_path (str) – S3 path where corrected data will be stored