Pyramidal Image Stitching

[veyselolgun]

Hi, thanks for this big library.

I am trying to stitch below images to create as a pyramidal .ome.tif file.

When I am trying to stitch these images with below code, I am facing with some issue on the overlap areas, I tried with different overlap percent but result is not good. I think I am doing wrong somewhere but I could not find it.

Where I am wrong, is my overlap area to small or different problem or my parameters is incorrect ?

Also elapsed time is too long, maybe I need to change the some parameters, but I am not sure which parameters affect the speed (quantifying alignment error takes much time) ?

I also tried with %15 overlap, but result is distorted like when I choose %20 overlap

from ashlar import fileseries, thumbnail, reg
from ashlar.scripts.ashlar import process_axis_flip
import numpy as np

import time

s= time.perf_counter()
readers = []

for i in range(3):
    readers.append(fileseries.FileSeriesReader(
        r"C:\Users\Veysel\Desktop\stitch",
        pattern='image_{series:1}.jpg',
        overlap=0.20,
        width=4000,
        height=3000,
        layout="snake",
        direction='vertical',)
        )



aligner0 = reg.EdgeAligner(readers[0], channel=0, filter_sigma=1, verbose=True)
aligner0.run()

mosaic_args = {}
mosaic_args['verbose'] = True
aligners = []
aligners.append(aligner0)

mosaics = []
for j in range(1,3):
    aligners.append(
        reg.LayerAligner(readers[j], aligners[0], channel=j, filter_sigma=1, verbose=True)
    )
    aligners[j].run()
    print("aligners[0].mosaic_shape", aligners[0].mosaic_shape, aligners[0])
    mosaic = reg.Mosaic(
        aligners[j], aligners[0].mosaic_shape, None, **mosaic_args
    )
    mosaics.append(mosaic)

writer = reg.PyramidWriter(mosaics, r"C:\Users\Veysel\Desktop\stitch\out.ome.tif")
writer.run()

print("elapsed time: ",time.perf_counter()-s)

Output:

    assembling thumbnail 8/8
    quantifying alignment error 1000/1000
    aligning edge 7/7
    assembling thumbnail 8/8
    estimated cycle offset [y x] = [0. 0.]
    aligning tile 8/8
aligners[0].mosaic_shape (19590, 4000) <ashlar.reg.EdgeAligner object at 0x0000027E238C7340>
        merging tile 8/8
        merging tile 8/8
        merging tile 8/8
elapsed time:  553.6804612000001

Below image has distorted pixels (screenshot from overlap area of out.ome.tif)

Below image has distorted pixels (screenshot from overlap area of out.ome.tif)

Below image has distorted pixels (screenshot from overlap area of out.ome.tif)

Below image has distorted pixels (screenshot from overlap area of out.ome.tif)