Utilities

image_stack_to_array

Takes all the images in a directory and saves it as a NumPy (.npy) file.

Contents of image_stack_to_array:

cli_entry_points:
- image_stack_to_array

# (str) absolute path to images
image_dir: ~/recon3d/tests/data/cylinder_machined_grayscale

# (str) .tif | .tiff options are supported
image_type: .tif

# (str) absolute path for the processed files
out_dir: ~/recon3d/tests/data/output

grayscale_image_stack_to_segmentation

This utility takes

• a stack of images in a directory, encoded as 8-bit grayscale (integers 0...255), and
• a threshold value (defaults to Otsu if no threshold value is provided),

to create

• a NumPy (.npy) segmentation, ready for additional image processing.

Contents of grayscale_image_stack_to_segmentation:

cli_entry_points:
- grayscale_image_stack_to_segmentation

# (str) absolute path to images
image_dir: ~/recon3d/tests/data/cylinder_machined_grayscale

# (str) .tif | .tiff options are supported
image_type: .tif

# (int) threshold, between 0 and 255, optional
# if absent, then Otsu's method is used
# threshold: 128

# (str) absolute path for the processed files
out_dir: ~/recon3d/tests/data/output