TypeError: key must be an int, slice, or sequence

[Xiaoyan3333]

Hello! I am trying to p3d.plot to read ".tif" files, but it encountered a TypeError.

p3d.plot('test.tif') the test.file was downloaded from https://osf.io/b6kxw/ 【Traceback (most recent call last):

File "", line 1, in runfile('/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/spyder_test1.py', wdir='/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master')

File "/home/zhuhongyan/anaconda3/envs/ClearMap/lib/python3.6/site-packages/spyder_kernels/customize/spydercustomize.py", line 827, in runfile execfile(filename, namespace)

File "/home/zhuhongyan/anaconda3/envs/ClearMap/lib/python3.6/site-packages/spyder_kernels/customize/spydercustomize.py", line 110, in execfile exec(compile(f.read(), filename, 'exec'), namespace)

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/spyder_test1.py", line 24, in p3d.plot(ws.filename('raw'))

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/Visualization/Qt/Plot3d.py", line 60, in plot return multi_plot(source, axis=axis, scale=scale, title=title, invert_y=invert_y, min_max=min_max, screen=screen);

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/Visualization/Qt/Plot3d.py", line 96, in multi_plot invertY=invert_y, minMax=min_max) for s,t in zip(sources, title)];

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/Visualization/Qt/Plot3d.py", line 96, in invertY=invert_y, minMax=min_max) for s,t in zip(sources, title)];

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/Visualization/Qt/DataViewer.py", line 220, in init self.image_items = [pg.ImageItem(s[self.source_slice[:s.ndim]], **image_options) for s in self.sources];

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/Visualization/Qt/DataViewer.py", line 220, in self.image_items = [pg.ImageItem(s[self.source_slice[:s.ndim]], **image_options) for s in self.sources];

File "/home/zhuhongyan/zhy_tool/zhy_clearmap/ClearMap2master/ClearMap/IO/TIF.py", line 103, in getitem array = self._tif.asarray(key = slicing_z, maxworkers=processes);

File "/home/zhuhongyan/anaconda3/envs/ClearMap/lib/python3.6/site-packages/tifffile/tifffile.py", line 1882, in asarray raise TypeError('key must be an int, slice, or sequence')

TypeError: key must be an int, slice, or sequence】

I am new in scripe, so i really don't know how to deal with it. Thank you very much if you can help me on this matter!!!

[andrewsilberfeld]

I have this too. Did you ever solve it? I think its specific to installing ClearMap2 from the ClearMap_stable.yml file. Is this what you did? I originally installed from the ClearMap.yml file and didn't have this error but recently I messed up the environment and could only re-install from the ClearMap_stable.yml file. When I did this, I encountered this problem with viewing tif files.

[Xiaoyan3333]

I found that convert the file's format can help. Using 'io.convert_files()' to change format(.tiff to .npy), then you can view it directly using p3d.plot('x.npy').

[andrewsilberfeld]

Thanks. The viewer should work with tifs though but it may be a bug with one of the versions of the python packages. Just curious, did you install the python environment from the ClearMap_stable.yml file?

[andrewsilberfeld]

Okay I figured this out! The problem is that the tifffile version (0.1.5) in the clearmap2_stable.yml is not compatible with the p3d.plot viewer when running tif files... the tifffile version 2020.5.30 is. I solvevd by making a new python environment using a modified ClearMap2_stable.yml file in which I deleted the whole tifffile library from the file. Then install the clearmap2 environment without tifffile and activate the environment. Then run: pip install tifffile==2020.5.30 in the new environment. Resume with normal install and try viewing your tif files in the p3d viewer.

That rescued my p3d viewer for showing tifs when it previously wasn't!

[crousseau]

The exact specification is tifffile<2020.9.22

This is now included in the 2 environments ClearMapUi.yml and ClearMapUi39.yml