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soma object has no attribute 'pad'

Open argunsah opened this issue 5 years ago • 7 comments

Hello, I am tracing a neuron with a clear soma but I get this :

python ./apps/rtrace -f testlila4.tif -t 25 -z 0.5 --soma --save-soma

The shape of the image is (926, 742, 212) -- Zooming image to 0.50 of original size (1) -- Detecting Soma...Reconstructing Soma with Simple Mask (2) --Boundary DT... (3) --Fast Marching with low quality... (4) --Compute Gradients... (5) --Start Backtracking with standard stopping criteria ... 36888.0it [15:03, 24.15it/s] Traceback (most recent call last): File "./apps/rtrace", line 147, in soma.pad(crop_region) AttributeError: 'Soma' object has no attribute 'pad' 36888.0it [15:08, 40.61it/s]

Also when I try to use --view option I get this:

The shape of the image is (926, 742, 212) -- Zooming image to 0.50 of original size (1) -- Detecting Soma...Reconstructing Soma with Simple Mask (2) --Boundary DT... (3) --Fast Marching with low quality... (4) --Compute Gradients... (5) --Start Backtracking with standard stopping criteria ... 26445.0it [09:24, 21.93it/s] -- Finshed: 687.66 sec. Traceback (most recent call last): File "./apps/rtrace", line 173, in s.view() File "c:\users\argunsah-adm\documents\github\rivuletpy\rivuletpy\swc.py", line 221, in view viewer.render(return_rgb_array=False) File "c:\users\argunsah-adm\documents\github\rivuletpy\rivuletpy\utils\rendering3.py", line 177, in render self.transform.enable() File "c:\users\argunsah-adm\documents\github\rivuletpy\rivuletpy\utils\rendering3.py", line 96, in enable glPushMatrix() File "C:\ProgramData\Anaconda3\lib\site-packages\pyglet-2.0.dev0-py3.7.egg\pyglet\gl\lib.py", line 105, in errcheck raise GLException(msg) pyglet.gl.lib.GLException: b'invalid operation'

Do you have any recommendation about how to solve these issues?

Thanks,

Ali

argunsah avatar Nov 25 '19 16:11 argunsah