ENH: add initial streamline widget #4

satra · 2017-09-24T04:19:38Z

added a streamline widget. usage example here: https://nbviewer.jupyter.org/urls/dl.dropbox.com/s/oukfh9agca5k9im/streamlines.ipynb

this requires a few changes to ipyvolume that i will be submitting as a PR shortly.

additional things to consider:

use header information for size and affine
allow different coloring schemes, although per vertex colors are quite slow
allow support for a streamline object in addition to a file
allow more control for figure options (view, zoom, etc.,.)

satra · 2017-09-24T04:25:10Z

needs: widgetti/ipyvolume#72

janfreyberg · 2017-09-27T10:29:29Z

any chance you could make a .trk file available to try this out?

satra · 2017-09-27T11:01:45Z

@janfreyberg - here you go:

https://www.dropbox.com/s/dbexuhk7fsawvox/streamlines.trk?dl=0

janfreyberg · 2017-09-27T12:20:57Z

Thanks.

For some reason I can't get it to work - it doesn't work with ipyvolume from pypi but even if I install from your repo with the fix it's throwing errors. I'll wait until your fix is merged and try it out then!

satra · 2017-09-27T14:57:19Z

$ wget https://github.com/satra/ipyvolume/archive/enh/line-visibility-control.zip

unzip and cd to the ipyvolume folder

$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix ipyvolume
$ jupyter nbextension enable --py --sys-prefix ipyvolume

note these last steps set up ipyvolume in dev mode and requires nodejs. and any jupyter instance needs to be restarted for this to take effect.

arokem · 2017-09-27T22:30:54Z

I tried following this and am getting:


D-173-250-183-82:~  $jupyter nbextension install --py --symlink --sys-prefix ipyvolume
Traceback (most recent call last):
  File "/Users/arokem/anaconda3/bin/jupyter-nbextension", line 11, in <module>
    load_entry_point('notebook', 'console_scripts', 'jupyter-nbextension')()
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/jupyter_core/application.py", line 267, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/notebook/nbextensions.py", line 900, in start
    super(NBExtensionApp, self).start()
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/jupyter_core/application.py", line 256, in start
    self.subapp.start()
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/notebook/nbextensions.py", line 678, in start
    self.install_extensions()
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/notebook/nbextensions.py", line 657, in install_extensions
    **kwargs
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/notebook/nbextensions.py", line 211, in install_nbextension_python
    m, nbexts = _get_nbextension_metadata(module)
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/notebook/nbextensions.py", line 1034, in _get_nbextension_metadata
    m = import_item(module)
  File "/Users/arokem/anaconda3/lib/python3.5/site-packages/traitlets/utils/importstring.py", line 42, in import_item
    return __import__(parts[0])
  File "/Users/arokem/source/ipyvolume/ipyvolume/__init__.py", line 10, in <module>
    from .pylab import *
  File "/Users/arokem/source/ipyvolume/ipyvolume/pylab.py", line 362, in <module>
    size_selected=1, size=1, connected=True, visible_markers=False,
  File "/Users/arokem/source/ipyvolume/ipyvolume/pylab.py", line 25, in _docsubst
    f.__doc__ = f.__doc__.format(**_doc_snippets)
KeyError: 'visible_lines'

Any ideas?

satra · 2017-09-27T22:37:52Z

@arokem - hold on based on a conversion on ipyvolume i sent some updates that i didn't test. perhaps those are inappropriate. give me a minute to check.

satra · 2017-09-27T22:43:29Z

@arokem - try now - you will have to wget the zip file again.

arokem · 2017-09-27T22:50:54Z

Yep - installing/enabling seems to work now! Thanks!

using Mesh for efficient streamline plotting

satra · 2017-10-28T14:51:41Z

@janfreyberg, @arokem - this does require ipyvolume master, but it works well now at scale.

once this branch is installed together with ipyvolume master, you can test with:

https://www.dropbox.com/s/oukfh9agca5k9im/streamlines.ipynb?dl=0

https://www.dropbox.com/s/dbexuhk7fsawvox/streamlines.trk?dl=0

satra · 2017-10-28T14:52:58Z

@arokem - with this new mechanism, it would not take much work to refactor to draw bundles.

janfreyberg · 2017-11-01T10:03:35Z

Thanks, will test this ASAP. Any idea yet when the required changes will be released by ipyvolume?

janfreyberg · 2017-11-01T15:37:53Z

Working great for me, awesome!

Two thoughts I have:

allowing people to pass in a nibabel.streamlines structure, rather than just a filename - in case people have them loaded in memory rather than saved to disk
so far there's no documentation on colors, would be nice to include this as well

arokem

A couple of small comments from my end.

arokem · 2017-11-01T21:28:17Z

niwidgets/streamlines.py

+def color(x):
+    """Returns an approximation for color of line based on its endpoints"""
+    dirvec = (x[0, :] - x[-1, :])
+    return (dirvec/(np.sqrt(np.sum(dirvec*dirvec, axis=-1)))).dot(np.eye(3))


Does this do the same thing as this?

https://github.com/nipy/dipy/blob/master/dipy/viz/colormap.py#L211-L240

I'm not sure it does.

given this line, https://github.com/nipy/dipy/blob/master/dipy/viz/colormap.py#L257, i think they are doing exactly the same thing. line 19 can be simplified because i'm not really using anything other than rgb extremes. but instead of eye, one could use three different colors in the colorspace, and a non-linearity on the normalized direction vector.

arokem · 2017-11-01T21:32:37Z

niwidgets/streamlines.py

+
+        Args
+        ----
+            skip : int


The explanation of this parameter could be understood as the number of streamlines to omit from the beginning of the collection, or something of that sort.

Might be easier if it is formulated as proportion_to_display, from which the skip is calculated.

BTW: the default here and in the _default_plotter method is different. Is that intentional?

Also, what would a None input do here?

None would use all streamlines. i will change this to proportion_to_display.

the defaults were not updated since the efficiency boost. initially we couldn't display more than 5k lines, but now it can handle much more.

satra · 2017-11-02T00:33:50Z

@janfreyberg - thanks for the review. those suggestions are great. whenever i get some time next, i'll add those in together with @arokem's suggestions.

* upstream/master: Update path to repos for direct pip install from git niwidget_volume- delete os import Added flipping to the left for sagittal view version number change Some formatting changes allow taking in nifti file Use the scaled rather than the unscaled data stored in nifti file change default for background masking Backwards compatibility to 3.5 Revert from using Path's `strict` kwarg to using explicit file check, since `strict` was only added in 3.6.

…eamline data

satra · 2018-02-14T19:27:11Z

@arokem and @janfreyberg - finally got to this. should have all the pieces in place now.

added small data file in example data
updated index.ipynb with streamline example
updated api of streamlinewidget to take file or streamline
updated plot api to use display_fraction

satra · 2018-02-23T01:09:35Z

@arokem and @janfreyberg - any chance this can be reviewed soon.

arokem · 2018-02-23T23:49:59Z

Did your changes make it upstream to current ipyvolume?

satra · 2018-02-24T02:22:08Z

Did your changes make it upstream to current ipyvolume?

yes

arokem

Looks good, and works well. I had a couple of small comments, and found one error that should be easy to work around. +1 from my end for the merge, once these small things are resolved.

arokem · 2018-02-24T03:48:33Z

niwidgets/exampledata.py

@@ -25,3 +25,5 @@
    surface_dir / f
    for f in ('lh.area', 'lh.curv', 'lh.thickness', 'lh.aparc.annot')
 ]
+
+streamlines = root_dir / 'streamlines.trk'


Because this returns a PosixPath object, the example in the index file raises an error, unless I pass sw = StreamlineWidget(filename=streamlines.as_posix())

arokem · 2018-02-24T03:49:41Z

niwidgets/streamlines.py

+    ----
+        filename : str
+                The path to your ``.trk`` file. Can be a string, or a
+                ``PosixPath`` from python3's pathlib.


PosixPath doesn't work for me. Raises:

--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-9-09a88a08f323> in <module>() ----> 1 sw = StreamlineWidget(filename=streamlines) 2 3 style = {'axes': {'color': 'red', 4 'label': {'color': 'white'}, 5 'ticklabel': {'color': 'white'}, ~/source/niwidgets/niwidgets/streamlines.py in __init__(self, filename, streamlines) 41 42 if filename: ---> 43 if not os.path.isfile(filename): 44 # for Python3 should have FileNotFoundError here 45 raise IOError('file {} not found'.format(filename)) ~/anaconda3/lib/python3.5/genericpath.py in isfile(path) 28 """Test whether a path is a regular file""" 29 try: ---> 30 st = os.stat(path) 31 except OSError: 32 return False TypeError: argument should be string, bytes or integer, not PosixPath

i'm curious as to your environment:

on my osx with py36 i get this:

In [1]: from niwidgets.exampledata import streamlines In [2]: streamlines Out[2]: PosixPath('/software/nipy-repo/niwidgets/niwidgets/data/streamlines.trk') In [3]: from niwidgets.streamlines import StreamlineWidget In [4]: sw = StreamlineWidget(filename=streamlines)

arokem · 2018-02-24T03:50:23Z

niwidgets/streamlines.py

+
+class StreamlineWidget:
+    """
+    Turns mrtrix track or trackvis files into interactive plots using ipyvolume.


The safest here would be to say that this can use any file type that nibabel knows how to read. This will be true even for future versions that implement reading of any other streamline file.

ENH: add initial streamline widget

7d7722f

satra and others added 7 commits October 6, 2017 08:42

resolved conflict

aca33f1

resolved conflicts

70dafa3

using Mesh for efficient streamline plotting

b017781

Merge pull request #1 from maartenbreddels/mesh_streamline

ef3811a

using Mesh for efficient streamline plotting

initial pass to disabling/enabling lines by setting to background color

79b0b71

updated to mesh regeneration on threshold change

4e893e8

fix: efficient streamline plotting with threshold interaction

fbe8bda

satra mentioned this pull request Oct 28, 2017

Add bundle drawing when streamlines are merged #15

Open

arokem reviewed Nov 1, 2017

View reviewed changes

satra added 2 commits December 18, 2017 21:41

fix: updated the streamlines widget and api, and added simplified str…

5ed9e86

…eamline data

arokem reviewed Feb 24, 2018

View reviewed changes

doc: improve docstring to reflect future nibabel track support

e487b1c

janfreyberg merged commit 3d59f58 into nipy:master Apr 22, 2018

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ENH: add initial streamline widget #4

ENH: add initial streamline widget #4

satra commented Sep 24, 2017

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ENH: add initial streamline widget #4

ENH: add initial streamline widget #4

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