merging clickable image and 2d projection examples #4098
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| @@ -1031,7 +1031,7 @@ def __init__(self, imdata, **kwargs): # noqa: D102 | |||
| self.ax = self.fig.add_subplot(111) | |||
| self.ymax = self.imdata.shape[0] | |||
| self.xmax = self.imdata.shape[1] | |||
| self.im = self.ax.imshow(imdata, aspect='auto', | |||
| self.im = self.ax.imshow(imdata, | |||
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maybe it should be aspect='equal'? Or is that the default?
| create scatterplots on top of a brain, with each point representing an | ||
| electrode. | ||
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| In this example, we'll show two ways of doing this in MNE-python. First, |
| if we have the 3D locations of each electrode then we can use Mayavi to | ||
| take a snapshot of a view of the brain. If we do not have these 3D locations, | ||
| and only have a 2D image of the electrodes on the brain, we can use the | ||
| `mne.viz.ClickableImage` class to choose our own electrode positions |
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mmk added reference and made changes etc |
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| # # The click coordinates are stored as a list of tuples | ||
| # im = plt.imread('./brain.png') | ||
| # click = ClickableImage(im) | ||
| # click.plot_clicks() |
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I tried to comment out
im = plt.imread('./brain.png')
click = ClickableImage(im)
click.plot_clicks()
but I get
ValueError: not enough values to unpack (expected 2, got 0)
I need I demo I guess...
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did you not click anywhere on the image? sounds like that might have been the issue. Either way the latest commit adds a check to make sure self.coords has something in it
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| # # Generate a layout from our clicks and normalize by the image | ||
| # print('Generating and saving layout...') | ||
| # lt = generate_2d_layout(np.vstack(coords), bg_image=im) |
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why the vstack? why not make coord already of the right shape?
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+1 for MRG when CIs are happy |
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any idea why circle just failed? |
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No idea, just restarted it. |
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thx @choldgraf |
…mne-python into refactor_xdawn * 'refactor_xdawn' of https://github.com/jona-sassenhagen/mne-python: (366 commits) fix lin reg test Test fixes. (mne-tools#4114) fix test fix test fix test and pep add error checks improve coverage simplify and add test simplify pep8 revert to cholesky default init_t_y [MRG] Optimize read_source_estimate function (mne-tools#4107) merging clickable image and 2d projection examples (mne-tools#4098) [MRG+2] adding receptive field module (mne-tools#3728) FIX: Found another FIX: Fix another FIX: No fname [MRG] Picks argument to layout.plot. (mne-tools#4106) remove transparent background for plot_compare_evoked (mne-tools#4111) ...
* 'master' of git://github.com/mne-tools/mne-python: fix lin reg test Test fixes. (mne-tools#4114) fix test fix test fix test and pep add error checks improve coverage simplify and add test simplify pep8 revert to cholesky default init_t_y [MRG] Optimize read_source_estimate function (mne-tools#4107) merging clickable image and 2d projection examples (mne-tools#4098) [MRG+2] adding receptive field module (mne-tools#3728) FIX: Found another FIX: Fix another
this converts the clickableimage example into a more general example showing how to convert 3D representations of electrodes into 2D, either using the mayavi 2D projection, or manually clicking w/ clickableimage