Error while making video using brainrender 1.0.1.1: AttributeError: 'NoneType' object has no attribute 'Elevation'

Hello,

I am using brainrender Version: 1.0.1.1 within jupyter notebook inside Chrome.

I am unable to recreate the video example mentioned in old Github “examples” repository [here].(https://github.com/brainglobe/brainrender/blob/4c087bc4cb8f94ba394dc0cf75baa646065ea44b/Examples/advanced/videomaker.py)

Following is my code:

import brainrender
brainrender.SHADER_STYLE = 'cartoon'
from brainrender.scene import Scene
from brainrender.animation.video import BasicVideoMaker as VideoMaker


scene = Scene()
scene.add_brain_regions(['RN'], color="violet")

scene.add_cells_from_file("C:\\Users\\7057mehrav\\Documents\\164-test\\cells_in_standard_space.h5", radius=15,alpha=0.5)

# Create an instance of VideoMaker with our scene
vm = VideoMaker(scene, niters=30)  # niters = number of frames

# Make a video!
vm.make_video(
    elevation=1, roll=5
)  # specify how the scene rotates at each frame

After promising messages, I get an error:

Bg_atlasapi: allen_mouse_25um version 1.1 is not the latest available (1.2). To update the 
atlas run in the terminal:
    brainglobe update -a allen_mouse_25um
allen mouse atlas (res. 25um)
From: http://www.brain-map.com (Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007 )
Setting 'display_inset' to False as this feature is not                             available in juputer notebooks
Setting window size to 'auto' as whole screen is not available in jupyter
Added 15473 cells to the scene
Saving video in C:\Users\7057mehrav\.brainrender\Output/Videos
('\x0bideo Video', 'brainrender_video__20201203_123641', 'is open...')
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-4-3ee3c505a465> in <module>
     15 # Make a video!
     16 vm.make_video(
---> 17     elevation=1, roll=5
     18 )  # specify how the scene rotates at each frame

c:\users\7057mehrav\appdata\local\continuum\anaconda3\envs\brainrender\lib\site-packages\brainrender\animation\video.py in make_video(self, azimuth, elevation, roll, **kwargs)
    144         for i in range(self.niters):
    145             self.scene.plotter.show()  # render(interactive=False, video=True)  # render the scene first
--> 146             self.scene.plotter.camera.Elevation(elevation)
    147             self.scene.plotter.camera.Azimuth(azimuth)
    148             self.scene.plotter.camera.Roll(roll)

AttributeError: 'NoneType' object has no attribute 'Elevation'

What could be causing this? I have already looked in the location where it tries to save the output but that folder is empty. Is it because I am running this functionality from within jupyter?

[FedeClaudi]

I see, okay. To use the .h5 files you just need a function that loads the file and gets the coordinates 😃

def load_cells(path):
    return pd.read_hdf(path).values

Anyway, I’ll close this for now then but let me know if you bump into other problems

[rdbcasillas]

Hey @FedeClaudi,

I haven’t tested it yet because I am still working with h5 files which new version doesn’t support. We created a lot of h5 files using cellfinder’s function “points_to_brainrender” which converts xml output from cellfinder to h5. So we will have to continue using older version of brainrender for a while.

Thanks!