Resampling IndexError: tuple index out of range

[mahsa106]

Hi,

while trying to run TubeMap or CellMap, I get the following error:

The stitching process seems to go smoothly and I get stuck in resampling. In the file ClearMap/Alignment/Resampling.py, variables such as "source_shapeO", "source_resolutionO" or "sink_resolution" are arrays of size 1x3, but ndim can reach values of 5. Hence the lines such as:

sink_shape = tuple([int(np.ceil(source_shapeO[i] * float(source_resolutionO[i])/float(sink_resolution[i]))) for i in range(ndim)]);

cause the error. What could be the root issue? Is ndim supposed to be higher than 3?

[crousseau]

"Is ndim supposed to be higher than 3?", well definitely not more than 4 (with color)
This can happen in different situations unfortunately and is a reason for us to envision to work on the IO library when we are less busy with the next release.
Make sure that your paths are correct. I have see this happen for example when the channels were swapped between "raw" and "autofluorescence"

[hhbw16]

Hi,
Is the problem solved yet?
I'm facing exactly the same error, while my paths and channels are confirmed to be correct.

[crousseau]

@hhbw16 this can happen with incorrectly read metadata from tiff.
I just pushed to master a bugfix that was up untill now only on dev.
I hope this fixes it. If not, could you provide more info re the organisation of your raw data (i.e. pattern)

[hhbw16]

@crousseau thanks for your advice,
I just reorganized my tiff datas to the same format as the test datas on OSF(each tiff file contains only one image) and the porblem is solved.