Errors in importing Holoviews: No module named 'holoviews.ipython ;

[Hanbing1999]

ALL software version info

(this library, plus any other relevant software, e.g. bokeh, python, notebook, OS, browser, etc) bokeh 2.1.1 python 3.7.7 panel 0.9.7 jupyter 1.0.0 jupyterlab 2.1.5 jupyterlab-server 1.1.5 browser: Chrome windows 10

Description of expected behavior and the observed behavior

When importing the holoviews, it is reported that No module named 'holoviews.ipython ;

# Import our plotting toolbox, and enable options for embedded notebook figures import holoviews as hv; %reload_ext holoviews.ipython ; %output widgets='embed';

[philippjfr]

Could you also post the HoloViews version you are trying?

[Hanbing1999]

Could you also post the HoloViews version you are trying?

The version of holoviews is 1.13.3.

[Hanbing1999]

Could you also post the HoloViews version you are trying?

Actually, I now resolved this problem. But another problem occurs, I am unable to see the output figure in Jupyter notebook (in terms of Suite2p). It seems the data can be processed, but just cannot be plotted.

[jlstevens]

Could you post a screenshot of what is displayed (if anything) below the cell when you run it? From your screenshot above, it does look like the extension has loaded.

[Hanbing1999]

%%opts Curve {+axiswise}

def plot_cell_regions(roi_polys, plot_neuropil=False): ''' Plot a single cell region, using holoviews. ''' out = hv.Overlay()

if plot_neuropil:
    # Plot the neuropil as well as the ROI
    n_region = len(roi_polys)
else:
    # Just plot the ROI, not the neuropil
    n_region = 1

for i_region in range(n_region):
    for part in roi_polys[i_region]:
        x = part[:, 1]
        y = part[:, 0]
        out *= hv.Curve(zip(x, y)).opts(color='w')

return out

i_trial = 0

Generate plots for all detected regions

region_plots = { i_cell: plot_cell_regions(exp.roi_polys[i_cell][i_trial]) for i_cell in range(exp.nCell) }

Generate plots for raw extracts and neuropil removed

traces_plots = { i_cell: hv.Curve(exp.raw[i_cell][i_trial][0, :], label='suite2p') * hv.Curve(exp.result[i_cell][i_trial][0, :], label='FISSA') for i_cell in range(exp.nCell) }

Generate average image

avg_img = hv.Raster(exp.means[i_trial])

Generate overlay plot showing each cell location

cell_locs = hv.Overlay() for c in range(exp.nCell): roi_poly = exp.roi_polys[c][i_trial][0][0] x = roi_poly[:, 1] y = roi_poly[:, 0] cell_locs *= hv.Curve(zip(x, y))

Render holoviews

avg_img cell_locs hv.HoloMap(region_plots, kdims=['Cell']) + hv.HoloMap(traces_plots, kdims=['Cell'])

[Hanbing1999]

Could you post a screenshot of what is displayed (if anything) below the cell when you run it? From your screenshot above, it does look like the extension has loaded. Hi, I now can load the holoviews .

But it seems that the extraction process is a little bit strange, since it lacks some lines like 'NMF converged after 1158 iterations.' I only got the following lines:

Besides, when plotting, it turns out a IndexError: list index out of range in the line of average image.

Could you please help me deal with it? Thanks for your help!

[jbednar]

Those don't sound like HoloViews-related errors; seems like something in your own code, to me.

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