get_apr_interactive_demo.py

import os
import pyapr
from skimage import io as skio


"""
Interactive APR conversion. Reads in a selected TIFF image for interactive setting of the parameters:
    Ip_th       (intensity threshold)
    sigma_th    (local intensity scale threshold)
    grad_th     (gradient threshold)

Use the sliders to control the adaptation. The red overlay shows (approximately) the regions that will be fully
resolved (at pixel resolution).

Once the parameters are set, the final steps of the conversion pipeline are applied to produce the APR and sample
the particle intensities.

Note: The effect of grad_th may hide the effect of the other thresholds. It is thus recommended to keep grad_th
low while setting Ip_th and sigma_th, and then increasing grad_th.
"""

# Read in an image
io_int = pyapr.utils.InteractiveIO()
fpath = io_int.get_tiff_file_name()  # get image file path from gui (data type must be float32 or uint16)
img = skio.imread(fpath)

# Set some parameters (only Ip_th, grad_th and sigma_th are set interactively)
par = pyapr.APRParameters()
par.rel_error = 0.1              # relative error threshold
par.gradient_smoothing = 3       # b-spline smoothing parameter for gradient estimation
#                                  0 = no smoothing, higher = more smoothing
par.dx = 1
par.dy = 1                       # voxel size
par.dz = 1

# Compute APR and sample particle values
apr, parts = pyapr.converter.get_apr_interactive(img, params=par, verbose=True, slider_decimals=1)

# Display the APR
pyapr.viewer.parts_viewer(apr, parts)

# Write the resulting APR to file
print("Writing APR to file ... \n")
fpath_apr = io_int.save_apr_file_name()  # get path through gui
pyapr.io.write(fpath_apr, apr, parts)

if fpath_apr:
    # Display the size of the file
    file_sz = os.path.getsize(fpath_apr)
    print("APR File Size: {:7.2f} MB \n".format(file_sz * 1e-6))

    # Compute compression ratio
    mcr = os.path.getsize(fpath) / file_sz
    print("Memory Compression Ratio: {:7.2f}".format(mcr))