Render static images for ASE

[jan-janssen]

I try to render static images of an ASE structure:

from ase import Atoms
import nglview

d = 2.9
L = 10.0
wire = Atoms('Au', positions=[[0, L / 2, L / 2]], cell=[d, L, L], pbc=[1, 0, 0])
view = nglview.show_ase(wire)
view.add_spacefill(radius_type='vdw', scale=0.5)
view.add_unitcell()
view.render_image()
view._display_image()

I get the following error message:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/anaconda/lib/python3.5/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
    968 
    969             if method is not None:
--> 970                 return method(include=include, exclude=exclude)
    971             return None
    972         else:

~/anaconda/lib/python3.5/site-packages/IPython/core/display.py in _repr_mimebundle_(self, include, exclude)
   1190         if self.embed:
   1191             mimetype = self._mimetype
-> 1192             data, metadata = self._data_and_metadata(always_both=True)
   1193             if metadata:
   1194                 metadata = {mimetype: metadata}

~/anaconda/lib/python3.5/site-packages/IPython/core/display.py in _data_and_metadata(self, always_both)
   1199     def _data_and_metadata(self, always_both=False):
   1200         """shortcut for returning metadata with shape information, if defined"""
-> 1201         b64_data = b2a_base64(self.data).decode('ascii')
   1202         md = {}
   1203         if self.metadata:

TypeError: a bytes-like object is required, not 'str'
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-1-3319cfd15b05> in <module>()
      9 view.add_unitcell()
     10 view.render_image()
---> 11 view._display_image()

~/anaconda/lib/python3.5/site-packages/IPython/core/displayhook.py in __call__(self, result)
    255             self.start_displayhook()
    256             self.write_output_prompt()
--> 257             format_dict, md_dict = self.compute_format_data(result)
    258             self.update_user_ns(result)
    259             self.fill_exec_result(result)

~/anaconda/lib/python3.5/site-packages/IPython/core/displayhook.py in compute_format_data(self, result)
    149 
    150         """
--> 151         return self.shell.display_formatter.format(result)
    152 
    153     # This can be set to True by the write_output_prompt method in a subclass

~/anaconda/lib/python3.5/site-packages/IPython/core/formatters.py in format(self, obj, include, exclude)
    148             return {}, {}
    149 
--> 150         format_dict, md_dict = self.mimebundle_formatter(obj, include=include, exclude=exclude)
    151 
    152         if format_dict or md_dict:

TypeError: 'NoneType' object is not iterable

I tired Nglview versions 1.1.2 and 0.6.2.3, but was not able to get it to work.

[hainm]

hi, it's a known bug in nglview if you're using ipython 6.

ipython/ipython#10982

The current workaround is to use ipython 5.3. We will try to fix and make a new release.

[jan-janssen]

I tried to compile the example on mybinder: https://mybinder.org/v2/gh/jan-janssen/lammps-notebooks.git/ase-notebooks

The environment includes:

name: ase-notebooks
dependencies:
- python=3.6
- nomkl
- nglview=1.0
- ipywidgets==7.0.0
- widgetsnbextension==3.0.0
- ipykernel=4.6
- ipython=5.3
- ase

channels:
  - anaconda
  - bioconda
  - conda-forge

Basically inspired by yours https://github.com/hainm/notebook-nglview/blob/master/environment.yml as well as the requirements:

jupyter
git+https://github.com/arose/nglview.git

But I only get an image not found error!

[hainm]

I will have a look tonight. cheers.

[hainm]

Please try the master branch again. I have a fix here (turns out it's much simpler than I though). f6b665d

[hainm]

uhm, one more point. In your example, you need to run the code in three Cells.

# 1st cell
from ase import Atoms
import nglview

d = 2.9
L = 10.0
wire = Atoms('Au', positions=[[0, L / 2, L / 2]], cell=[d, L, L], pbc=[1, 0, 0])
view = nglview.show_ase(wire)
view.add_spacefill(radius_type='vdw', scale=0.5)
view.add_unitcell()
view # display it

# 2nd cell
view.render_image()

# 3rd cell
view._display_image()

[hainm]

If you just want to get the image (e.g: for presentation), you can use

# 1st cell
view # display

# 2nd cell
view.download_image() # see its options.

[hainm]

[jan-janssen]

Thanks a lot, locally everything is working fine now, I just realised that http://mybinder.org has issues loading nglview in general. I tried your notebook and that is not working either: https://hub.mybinder.org/user/hainm-nglview-notebooks-fhq6if62/notebooks/pytraj.ipynb so it seems to be binder related.

[hainm]

cool.