Subplot x-axis shared with other subplots y-axis

Community matplotlib-users
1

Hello,

I?m trying to build an orthogonal-views volume viewer in Matplotlib like this one:
https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png

For this to work, I need to share the y-axis of the YZ (right) view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this possible?

Juan.

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2

There are callbacks that fire when the limits are changed. See

https://matplotlib.org/examples/event_handling/viewlims.html

for an example.

This is probably the best route to go down as you can do other interesting
things as the event goes by (like triggering computation, updating a openGL
view window, etc) as well as updating the Matplotlib limits.

Tom

···

On Mon, May 15, 2017 at 3:29 AM Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

Hello,

I?m trying to build an orthogonal-views volume viewer in Matplotlib like
this one:
https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png

For this to work, I need to share the y-axis of the YZ (right)
view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this
possible?

Juan.

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
Matplotlib-users Info Page

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3

Hey Tom,

Thanks for that response, it was just what I needed! I had a fun infinite loop where the x-axis was updating the y-axis which was updating the x-axis which... =P But it was easy enough to sort out. =)

I have a working orthogonal slice viewer here:

The problem I have now is that, if I set a mouse-click callback (this line and this line), and then I select any other tool from the toolbar, I get this super-obnoxious flickering, recorded here (macOS 10.12, Tk backend):

To reproduce:

- Download slice_view.py and put it in your PYTHONPATH or current working directory
- Download this example dataset:

- Run this code:

import matplotlib
matplotlib.use('TkAgg')

from skimage import io
import slice_view as sv

filename = '/path/to/E_z2_512_1um_CONTROL.tif'
image = io.imread(filename) / 4096

v = sv.SliceViewer(image, spacing=[5, 1, 1])
matplotlib.pyplot.show(block=True)

Questions:
1) Any ideas about how to fix the flickering?
2) Is there a cross-backend way to add buttons to the toolbar? All the examples I've found online were backend-specific. (This way I could at least disable the callback at will.)

Thanks!

Juan.

···

On 16 May 2017, 1:43 AM +1000, Thomas Caswell <tcaswell at gmail.com>, wrote:

There are callbacks that fire when the limits are changed.? See

https://matplotlib.org/examples/event_handling/viewlims.html

for an example.

This is probably the best route to go down as you can do other interesting things as the event goes by (like triggering computation, updating a openGL view window, etc) as well as updating the Matplotlib limits.

Tom

> On Mon, May 15, 2017 at 3:29 AM Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> > Hello,
> >
> > I?m trying to build an orthogonal-views volume viewer in Matplotlib like this one:
> > https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png
> >
> > For this to work, I need to share the y-axis of the YZ (right) view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this possible?
> >
> > Juan.
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Matplotlib-users at python.org
> > Matplotlib-users Info Page

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4

re: cross-backend way to add buttons: There is experimental feature called
"ToolManager", but I think it is only implemented for a couple of backends
currently. You can see an example here:

http://matplotlib.org/examples/user_interfaces/toolmanager.html

···

On Fri, Jun 23, 2017 at 12:17 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:

Hey Tom,

Thanks for that response, it was just what I needed! I had a fun infinite
loop where the x-axis was updating the y-axis which was updating the x-axis
which... =P But it was easy enough to sort out. =)

I have a working orthogonal slice viewer here:
GitHub - jni/mpl-volume-viewer: Simple matplotlib-based volume (3D image) viewer

The problem I have now is that, if I set a mouse-click callback (this line
<https://github.com/jni/mpl-volume-viewer/blob/6d863d2a28ced54576c6f4f8905d58e229f02042/slice_view.py#L71&gt;
and this line
<https://github.com/jni/mpl-volume-viewer/blob/6d863d2a28ced54576c6f4f8905d58e229f02042/slice_view.py#L101&gt;\),
and then I select any other tool from the toolbar, I get this
super-obnoxious flickering, recorded here (macOS 10.12, Tk backend):
Dropbox - mpl-click-bug.mov - Simplify your life

To reproduce:

- Download slice_view.py and put it in your PYTHONPATH or current working
directory
- Download this example dataset:
https://www.dropbox.com/s/dj3oarx7bqx4us2/E_z2_512_1um_CONTROL.tif?dl=1
- Run this code:

*import matplotlib*
*matplotlib.use('TkAgg')*

*from skimage import io*
*import slice_view as sv*

*filename = '/path/to/E_z2_512_1um_CONTROL.tif'*
*image = io.imread(filename) / 4096*

*v = sv.SliceViewer(image, spacing=[5, 1, 1])*
*matplotlib.pyplot.show(block=True)*

Questions:
1) Any ideas about how to fix the flickering?
2) Is there a cross-backend way to add buttons to the toolbar? All the
examples I've found online were backend-specific. (This way I could at
least disable the callback at will.)

Thanks!

Juan.

On 16 May 2017, 1:43 AM +1000, Thomas Caswell <tcaswell at gmail.com>, wrote:

There are callbacks that fire when the limits are changed. See

https://matplotlib.org/examples/event_handling/viewlims.html

for an example.

This is probably the best route to go down as you can do other interesting
things as the event goes by (like triggering computation, updating a openGL
view window, etc) as well as updating the Matplotlib limits.

Tom

On Mon, May 15, 2017 at 3:29 AM Juan Nunez-Iglesias <jni.soma at gmail.com> > wrote:

Hello,

I?m trying to build an orthogonal-views volume viewer in Matplotlib like
this one:
https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png

For this to work, I need to share the y-axis of the YZ (right)
view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this
possible?

Juan.

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
Matplotlib-users Info Page

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
Matplotlib-users Info Page

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5

Oops, revisiting this thread now, it looks like I only replied to Ben, instead of the list. Full thread below, but TL;DR: my 3D orthogonal views project:

is working (thanks to all on this list who helped so far!), but has the following problems:
- Experiences flickering when panning in the Tk backend
- Has no flickering with the MacOS backend, but then the keyboard bindings don?t work at all
- Is dog-slow in the nbagg backend.

Any suggestions to help with this would be much appreciated! To recap, here are the steps to reproduce:

- Download slice_view.py and put it in your PYTHONPATH or current working directory
- Download this example dataset:

- Run this code:

import matplotlib
matplotlib.use('TkAgg?) ?# change this to whatever you want to test

from skimage import io
import slice_view as sv

filename = '/path/to/E_z2_512_1um_CONTROL.tif'
image = io.imread(filename) / 4096

v = sv.SliceViewer(image, spacing=[5, 1, 1])
matplotlib.pyplot.show(block=True)

Thanks!

Juan.

···

---------- Forwarded message ----------
From: Juan Nunez-Iglesias <jni.soma@gmail.com>
Date: 11 Jul 2017, 12:06 PM +1000
To: Benjamin Root <ben.v.root at gmail.com>
Subject: Re: [Matplotlib-users] Subplot x-axis shared with other subplots y-axis

Hi Ben, thanks for the tip! The point of using the ToolManager would be to get cross-backend support, so it might be easier for me to implement the backends I want with if-else statements, or some other kludgey way?

I just thought I?d update the list with the status of my orthogonal views mini-project, which is backend-dependent:

- working on Tk except for the flickering
- working on macOS except the keyboard bindings don?t work ? they go straight to the Terminal.
- working on Notebook (Nbagg?), except it?s dog-slow.

If anyone has suggestions for any of these problems, I would be very grateful!

Juan.

On 28 Jun 2017, 1:08 AM +1000, Benjamin Root <ben.v.root at gmail.com>, wrote:
> re: cross-backend way to add buttons: There is experimental feature called "ToolManager", but I think it is only implemented for a couple of backends currently. You can see an example here:
>
> http://matplotlib.org/examples/user_interfaces/toolmanager.html
>
> > On Fri, Jun 23, 2017 at 12:17 AM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> > > Hey Tom,
> > >
> > > Thanks for that response, it was just what I needed! I had a fun infinite loop where the x-axis was updating the y-axis which was updating the x-axis which... =P But it was easy enough to sort out. =)
> > >
> > > I have a working orthogonal slice viewer here:
> > > GitHub - jni/mpl-volume-viewer: Simple matplotlib-based volume (3D image) viewer
> > >
> > > The problem I have now is that, if I set a mouse-click callback (this line and this line), and then I select any other tool from the toolbar, I get this super-obnoxious flickering, recorded here (macOS 10.12, Tk backend):
> > > Dropbox - mpl-click-bug.mov - Simplify your life
> > >
> > > To reproduce:
> > >
> > > - Download slice_view.py and put it in your PYTHONPATH or current working directory
> > > - Download this example dataset:
> > > https://www.dropbox.com/s/dj3oarx7bqx4us2/E_z2_512_1um_CONTROL.tif?dl=1
> > > - Run this code:
> > >
> > > import matplotlib
> > > matplotlib.use('TkAgg')
> > >
> > > from skimage import io
> > > import slice_view as sv
> > >
> > > filename = '/path/to/E_z2_512_1um_CONTROL.tif'
> > > image = io.imread(filename) / 4096
> > >
> > > v = sv.SliceViewer(image, spacing=[5, 1, 1])
> > > matplotlib.pyplot.show(block=True)
> > >
> > > Questions:
> > > 1) Any ideas about how to fix the flickering?
> > > 2) Is there a cross-backend way to add buttons to the toolbar? All the examples I've found online were backend-specific. (This way I could at least disable the callback at will.)
> > >
> > > Thanks!
> > >
> > > Juan.
> > >
> > > On 16 May 2017, 1:43 AM +1000, Thomas Caswell <tcaswell at gmail.com>, wrote:
> > > > There are callbacks that fire when the limits are changed.? See
> > > >
> > > > https://matplotlib.org/examples/event_handling/viewlims.html
> > > >
> > > > for an example.
> > > >
> > > > This is probably the best route to go down as you can do other interesting things as the event goes by (like triggering computation, updating a openGL view window, etc) as well as updating the Matplotlib limits.
> > > >
> > > > Tom
> > > >
> > > > > On Mon, May 15, 2017 at 3:29 AM Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> > > > > > Hello,
> > > > > >
> > > > > > I?m trying to build an orthogonal-views volume viewer in Matplotlib like this one:
> > > > > > https://imagej.nih.gov/ij/docs/guide/images/OrthogonalViews.png
> > > > > >
> > > > > > For this to work, I need to share the y-axis of the YZ (right) view/subplot with the x-axis of the XZ (bottom) view/subplot. Is this possible?
> > > > > >
> > > > > > Juan.
> > > > > >
> > > > > > _______________________________________________
> > > > > > Matplotlib-users mailing list
> > > > > > Matplotlib-users at python.org
> > > > > > Matplotlib-users Info Page
> > >
> > > _______________________________________________
> > > Matplotlib-users mailing list
> > > Matplotlib-users at python.org
> > > Matplotlib-users Info Page
> > >
>

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