Error in blending images tile is missing

[ViriatoII]

Hey,

I'm calling Ashlar with a Python wrapper for a set of tiff files in a folder. It fails if one tile is missing.

Traceback (most recent call last):
File "C:\Users\ricardo.guerreiro\Experiments\24_stitching\run_ashlar.py", line 110, in
aligner0.run()
File "C:\Users\ricardo.guerreiro\Experiments\pipelines\ashlar\ashlar\reg.py", line 550, in run
self.make_thumbnail()
File "C:\Users\ricardo.guerreiro\Experiments\pipelines\ashlar\ashlar\reg.py", line 562, in make_thumbnail
self.reader.thumbnail = thumbnail.make_thumbnail(
File "C:\Users\ricardo.guerreiro\Experiments\pipelines\ashlar\ashlar\thumbnail.py", line 41, in make_thumbnail
utils.paste(mosaic, img_s, pos_s, utils.pastefunc_blend)
File "C:\Users\ricardo.guerreiro\Experiments\pipelines\ashlar\ashlar\utils.py", line 181, in paste
target_slice[:] = func(target_slice, img)
File "C:\Users\ricardo.guerreiro\Experiments\pipelines\ashlar\ashlar\utils.py", line 207, in pastefunc_blend
alpha[skimage.morphology.binary_dilation(img == 0)] = 1
IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed

So my tiles now are in this disposition:
1_2_3_4
5___7_8

My tile 6 is missing, it could not be created. Ashlar should have a mechanism of ignoring a missing tile and jumping to the next one.

This is the code I'm using:

    for i in range(3):
        readers.append(fileseries.FileSeriesReader(
            my_data_folder,                            
            pattern='my_images_*{series:1}.ome.tiff',
            overlap=0.01, #.1,
            width= len(rows),
            height=len(cols),
            layout='raster',
            direction='horizontal', )
        )

    aligner0 = reg.EdgeAligner(readers[0], channel=0, 
                            filter_sigma=15, verbose=True)
    aligner0.run()

    mosaic_args = {}
    mosaic_args['verbose'] = True
    mosaic_args['flip_mosaic_y'] = False 
    mosaic_args['channels'] = [20] #,22]
    aligners = []
    aligners.append(aligner0)


    mosaics = []
    for j in range(1, 2):
        aligners.append(
            reg.LayerAligner(readers[j], aligners[0], channel=j, filter_sigma=15, verbose=True)
        )
        aligners[j].run()

        mosaic = reg.Mosaic(
            aligners[j], aligners[0].mosaic_shape, **mosaic_args
        )
        mosaics.append(mosaic)
    ```

[jmuhlich]

Yes, the fileseries reader is not fully ready for general use yet. Handling of missing tiles is one thing it could do better.