to_tif#

Convert *.nd2 or *.raw file to image sequence of raw and 8-bit grayscale images. For *.nd2, output image sequences are saved in a subfolder under the same folder as the *.nd2 file with corresponding name as the *.nd2 file name. For raw, output image sequences are saved in subfolders in the same folder as the .raw files.

Note

Autocontrast is applied to 8-bit folder, but not to raw folder.

Syntax

python to_tif.py nd2Dir remove

Test

python to_tif.py test_images est.nd2
python to_tif.py test_images

awRawImage.raw

Edit

  • Jun 16, 2020 – No longer export 16-bit images.

  • Aug 16, 2020 – (i) write input arguments in log.txt (ii) (important) add illumination correction. All frames will be corrected according to the whole video.

  • Aug 18, 2020 – Add argument ‘remove’, determining if background subtraction is applied or not. Default to False.

  • Oct 28, 2021 – Remove “8-bit” folder, export original images instead of converting to 8-bit

  • Nov 04, 2021 – (i) Set check_contrast to False to avoid CLI spamming, (ii) Add ‘exp1’ before the image number, in accordance to Cristian’s image naming convention

  • Nov 26, 2021 – (i) Remove the ‘exp1’ flag at the beginning of each image file, (ii) Add saturated 8-bit image output for visualization (this means we need a big overhead of disk space!)

  • Nov 30, 2021 – Add disk_capacity_check function to avoid running out disk space

  • Jan 22, 2022 – disk_capacity_check, use os.split(file)[1] to check, because windows does not recognize file directory as a valid directory for disk size check

  • Feb 02, 2022 – Print dir info, so in batch_to_tif I can follow the progress.

  • Mar 15, 2022 – (i) Rewrite using the rawImage class defined in myImageLib.

    1. Temporarily discontinue the “remove background functionality”.

    2. Include .raw functionality – with memory check.

    3. Update the doc string.

  • Jan 05, 2023 – Adapt myimagelib import style.

  • Feb 08, 2023 – Rewrite in function wrapper form, to make autodoc work properly. (autodoc import the script and execute it, so anything outside if __name__=="__main__" will be executed, causing problems)