ENH: button to save movie #9190

GuillaumeFavelier · 2021-03-24T15:52:38Z

This PR adds a button to save_movie for the notebook 3d backend.

import mne
mne.viz.set_3d_backend('notebook')
import os
from mne.datasets import sample
data_path = sample.data_path()
sample_dir = os.path.join(data_path, 'MEG', 'sample')
subjects_dir = os.path.join(data_path, 'subjects')
fname_stc = os.path.join(sample_dir, 'sample_audvis-meg')
stc = mne.read_source_estimate(fname_stc, subject='sample')
initial_time = 0.13
brain = stc.plot(subjects_dir=subjects_dir, initial_time=initial_time,
                 clim=dict(kind='value', lims=[3, 6, 9]),
                 size=600,
                 background="white",
                 hemi='split',
                 views=['lat', 'med']
)

ToDo:

Rework save_movie and remove PyQt5 dependency (ENH: button to save movie #9190 (comment))
Fix azure Notebook
Double-check the status bar layout

It's an item of #8704

GuillaumeFavelier · 2021-03-25T12:35:19Z

Now i get it! The Notebook job actually skips the notebook test 😅

...
mne/viz/_brain/tests/test_notebook.py::test_notebook_3d_backend[notebook] SKIPPED
...

https://dev.azure.com/mne-tools/mne-python/_build/results?buildId=12805&view=logs&j=f8b184f0-8536-5d07-cb2e-df31a09e5d0f&t=7eff19d8-9485-515c-ad38-577dd2e13f81&l=54

GuillaumeFavelier · 2021-03-25T12:43:06Z

The notebook test should fail until the following (naked PyQt5 everywhere) is reworked:

mne-python/mne/viz/_brain/_brain.py

Lines 3045 to 3109 in 874e8e1

    
           if self.time_viewer: 
        
               if filename is None: 
        
                   try: 
        
                       from pyvista.plotting.qt_plotting import FileDialog 
        
                   except ImportError: 
        
                       from pyvistaqt.plotting import FileDialog 
        
                   self.status_msg.set_value("Choose movie path ...") 
        
                   self.status_msg.show() 
        
                   self.status_progress.set_value(0) 
        
                   def _post_setup(unused): 
        
                       del unused 
        
                       self.status_msg.hide() 
        
                       self.status_progress.hide() 
        
                   dialog = FileDialog( 
        
                       self.plotter.app_window, 
        
                       callback=partial(self._save_movie, **kwargs) 
        
                   ) 
        
                   dialog.setDirectory(os.getcwd()) 
        
                   dialog.finished.connect(_post_setup) 
        
                   return dialog 
        
               else: 
        
                   from PyQt5.QtCore import Qt 
        
                   from PyQt5.QtGui import QCursor 
        
                   def frame_callback(frame, n_frames): 
        
                       if frame == n_frames: 
        
                           # On the ImageIO step 
        
                           self.status_msg.set_value( 
        
                               "Saving with ImageIO: %s" 
        
                               % filename 
        
                           ) 
        
                           self.status_msg.show() 
        
                           self.status_progress.hide() 
        
                           self._renderer._status_bar_update() 
        
                       else: 
        
                           self.status_msg.set_value( 
        
                               "Rendering images (frame %d / %d) ..." 
        
                               % (frame + 1, n_frames) 
        
                           ) 
        
                           self.status_msg.show() 
        
                           self.status_progress.show() 
        
                           self.status_progress.forward( 
        
                               "setRange", 0, n_frames - 1) 
        
                           self.status_progress.set_value(frame) 
        
                           self.status_progress.update() 
        
                       self.status_msg.update() 
        
                       self._renderer._status_bar_update() 
        
                   # set cursor to busy 
        
                   default_cursor = self._renderer._window_get_cursor() 
        
                   self._renderer._window_set_cursor(QCursor(Qt.WaitCursor)) 
        
                   try: 
        
                       self._save_movie( 
        
                           filename=filename, 
        
                           time_dilation=(1. / self.playback_speed), 
        
                           callback=frame_callback, 
        
                           **kwargs 
        
                       ) 
        
                   except (Exception, KeyboardInterrupt): 
        
                       warn('Movie saving aborted:\n' + traceback.format_exc()) 
        
                   finally: 
        
                       self._renderer._window_set_cursor(default_cursor)

GuillaumeFavelier · 2021-03-25T13:39:20Z

I removed the strange and untested use case where no filename is given considering that there are so many ways to input a filename (including generating one automatically). This simplifies save_movie a great deal.

Also this is how it looks for me with the notebook 3d backend after d711b14:

output.mp4

I'll try to fix the notebook CI and double-check the status bar layout.

GuillaumeFavelier · 2021-03-26T12:16:41Z

When I create server_environment.yml locally and test it manually, it says that it requires PyQt5 🤔

mne/viz/_brain/tests/test_notebook.py::test_notebook_3d_backend[notebook] SKIPPED (Test skipped, requires PyQt5.)

GuillaumeFavelier · 2021-03-26T12:23:56Z

Found it, it probably comes from _check_skip_backend:

mne-python/mne/conftest.py

Lines 341 to 342 in d711b14

    
           if not has_pyqt5(): 
        
               pytest.skip("Test skipped, requires PyQt5.")

GuillaumeFavelier · 2021-03-26T12:44:29Z

This time it passed:

...
mne/viz/_brain/tests/test_brain.py::test_brain_save_movie[pyvista] SKIPPED [ 16%]
mne/viz/_brain/tests/test_brain.py::test_calculate_lut PASSED            [ 16%]
mne/viz/_brain/tests/test_notebook.py::test_notebook_3d_backend[notebook] Coverage.py warning: --include is ignored because --source is set (include-ignored) 
PASSED [ 17%] 👈
mne/viz/backends/tests/test_renderer.py::test_backend_environment_setup[mayavi] SKIPPED [ 17%]
mne/viz/backends/tests/test_renderer.py::test_backend_environment_setup[pyvista] PASSED [ 18%]
mne/viz/backends/tests/test_renderer.py::test_backend_environment_setup[foo] XFAIL [ 18%]
...

GuillaumeFavelier · 2021-03-26T13:04:15Z

The layout is fixed after 6b6f5d6. I also set the attributes of the status bar and dock to private. It's now ready for reviews @agramfort, @larsoner

larsoner · 2021-03-26T13:59:30Z

Pushed a hotfix related to mne-bids branch renaming to our main and restarted the build here

larsoner

No need to update the test.ipynb? A quick look suggests there is no save_movie called in there, so we must be relying on the button press to get us there.

It's probably worthwhile to make a _TempDir, and monkey-patch _get_default_file_name to write to some known file like that op.join(tempdir, 'test.png') then assert op.isfile(fname) after clicking all the buttons. Or maybe simpler, figure out how to modify the "screenshot path" widget with this path before clicking all buttons. This text is about screenshots but the same could apply to movies (somehow). WDYT? To me the updated testing infrastructure is important...

larsoner · 2021-03-26T14:04:54Z

mne/viz/_brain/_brain.py

-        self._renderer.screenshot(mode=mode, filename=filename)
+        default_name = _generate_default_filename(".png")
+        filename = default_name if filename is None else filename
+        from ..utils import _save_ndarray_img


does not need to be nested

larsoner · 2021-03-26T14:05:22Z

mne/viz/_brain/_brain.py

+        default_name = _generate_default_filename(".png")
+        filename = default_name if filename is None else filename


Suggested change

default_name = _generate_default_filename(".png")

filename = default_name if filename is None else filename

if filename is None:

filename = _generate_default_filename(".png")

larsoner · 2021-03-26T14:06:09Z

mne/viz/_brain/_brain.py

+        filename = default_name if filename is None else filename
+        from ..utils import _save_ndarray_img
+        _save_ndarray_img(
+            filename, self.screenshot(mode=mode, time_viewer=True))


Do we even need a time_viewer op.tion in screenshot anymore? Nothing changes with the 3D rendering with this anymore because all controls are in Qt or ipywidgets, right?

But we probably should add a show_traces argument. But both of these could be in a quick follow-up PR I think.

You're right, I don't think this parameter is necessary anymore in here

GuillaumeFavelier · 2021-04-06T11:59:57Z

we must be relying on the button press to get us there.

Indeed, it is done in :

...
    "    for action in brain._renderer.actions.values():\n",
    "        if isinstance(action, Button):\n",
    "            action.click()\n",
    "            number_of_buttons += 1\n",
...

From:

mne-python/mne/viz/_brain/tests/test.ipynb

Lines 68 to 71 in e273cac

    
           "    for action in brain._renderer.actions.values():\n", 
        
           "        if isinstance(action, Button):\n", 
        
           "            action.click()\n", 
        
           "            number_of_buttons += 1\n",

It's probably worthwhile to make a _TempDir

I'm on it.

GuillaumeFavelier · 2021-04-06T14:03:54Z

I updated test.ipynb in 84296cd to use tempfile. I chose the second approach:

Or maybe simpler, figure out how to modify the "screenshot path" widget with this path before clicking all buttons

GuillaumeFavelier · 2021-04-06T14:07:36Z

I think it's ready now

GuillaumeFavelier · 2021-04-06T14:18:16Z

Actually, I can wait for #9034 and update accordingly.

GuillaumeFavelier · 2021-04-07T09:23:32Z

The GitHub Actions jobs fail with:

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Error: Process completed with exit code 2.

during the Installation dependencies step:

https://github.com/mne-tools/mne-python/runs/2285850191?check_suite_focus=true#step:5:308

It seems related to:

mne-python/tools/get_minimal_commands.sh

Line 24 in d0f71e5

curl -L https://osf.io/g7dzs/download | tar xz

Or:

mne-python/tools/get_minimal_commands.sh

Line 46 in d0f71e5

curl -L https://osf.io/rjcz4/download | tar xz

But I still have to confirm it.

GuillaumeFavelier · 2021-04-07T09:28:33Z

Locally I was able to reproduce:

❯ curl -L https://osf.io/rjcz4/download | tar xz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   290  100   290    0     0      2      0  0:02:25  0:02:01  0:00:24    71

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

There seem to be something wrong with this link. My web browser cannot process it either:

GuillaumeFavelier · 2021-04-07T09:38:52Z

It was only a temporary issue, probably server overload or something 🤔 I restarted the failing jobs.

GuillaumeFavelier · 2021-04-08T09:24:43Z

I updated testing in d0f71e5 after #9034 got merged, it's ready on my end.

larsoner · 2021-04-08T20:38:52Z

Thanks @GuillaumeFavelier

GuillaumeFavelier added 3 commits March 24, 2021 16:49

First commit

f2ebe9e

Merge branch 'main' into enh/save_movie

f19a1e0

Fix icon

ddc36f9

GuillaumeFavelier changed the title ~~ENHsave movie~~ ENH: button to save movie Mar 24, 2021

GuillaumeFavelier self-assigned this Mar 24, 2021

GuillaumeFavelier changed the title ~~ENH: button to save movie~~ WIP,ENH: button to save movie Mar 24, 2021

GuillaumeFavelier added the ENH label Mar 24, 2021

GuillaumeFavelier added 3 commits March 24, 2021 16:55

Remove cruft

4702a0e

Refactor

a46de62

Refactor

874e8e1

GuillaumeFavelier added 2 commits March 25, 2021 14:03

Refactor

bdcece5

Refactor

d711b14

Update conftest

fac7f93

GuillaumeFavelier added 2 commits March 26, 2021 13:46

Refactor

b77af73

Fix layout

6b6f5d6

GuillaumeFavelier changed the title ~~WIP,ENH: button to save movie~~ ENH: button to save movie Mar 26, 2021

GuillaumeFavelier mentioned this pull request Mar 26, 2021

ENH: Notebook 3d backend improvements (ipyvtklink) #8704

Closed

11 tasks

GuillaumeFavelier added 2 commits March 26, 2021 14:43

Nitpick

3fe5b88

Merge branch 'main' into enh/save_movie

e273cac

larsoner reviewed Mar 26, 2021

View reviewed changes

GuillaumeFavelier changed the title ~~ENH: button to save movie~~ WIP,ENH: button to save movie Apr 6, 2021

Merge branch 'main' into enh/save_movie

a33916d

GuillaumeFavelier added 2 commits April 6, 2021 14:02

Update based on reviews

c7658fa

Use tempfile

84296cd

GuillaumeFavelier changed the title ~~WIP,ENH: button to save movie~~ ENH: button to save movie Apr 6, 2021

Fix

4344e3c

GuillaumeFavelier mentioned this pull request Apr 6, 2021

MRG, MAINT: Better notebook tests #9034

Merged

3 tasks

GuillaumeFavelier added 2 commits April 7, 2021 10:42

Merge branch 'main' into enh/save_movie

adf37f6

Update testing

d0f71e5

larsoner merged commit 176680a into mne-tools:main Apr 8, 2021

GuillaumeFavelier deleted the enh/save_movie branch April 9, 2021 13:16

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ENH: button to save movie #9190

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larsoner commented Apr 8, 2021

		default_name = _generate_default_filename(".png")
		filename = default_name if filename is None else filename

ENH: button to save movie #9190

ENH: button to save movie #9190

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