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  • Jan 31 2019 16:26
    kmuehlbauer commented #1568
  • Jan 31 2019 16:15
    kmuehlbauer commented #1568
  • Jan 31 2019 15:53
    djhoese commented #1568
  • Jan 31 2019 15:46
    kmuehlbauer edited #1568
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    kmuehlbauer opened #1568
  • Jan 31 2019 15:32
    djhoese commented #1566
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    djhoese commented #1567
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  • Jan 31 2019 09:54
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  • Jan 31 2019 09:17
    kmuehlbauer opened #1567
Lorenzo Gaifas
@brisvag
If you're trying to access the size of the Markers (for example), you can do that with Compound._subvisuals[3].size (3 is the index of the Markers subvisual`)
Jordão Bragantini
@JoOkuma
I'm trying to add a radius to the napari tracks layer. Here you can find the visuals and the filter.
I'm using a filter because that's how the tracks control their tail length.
Jordão Bragantini
@JoOkuma
I want to change the size of markers as the user navigates over the z-slices of the 3d-volume.
Lorenzo Gaifas
@brisvag
ah, I see! On the fork you linked I don't see anything that quickly screams wrong at me, except that you refer to self._current_time in the current_z property, which is probably not what you wanted
is there an issue/pr open in napari so we can discuss there with some context?
loctran15
@loctran15
Hi Guys, is there a way to identify x, y position of a point of an image inside a scenecanvas. The camera I am using is PanZoomCamera. Thank you
Jordão Bragantini
@JoOkuma
I haven't created the issue/pr yet. I forgot to commit the latest change, this line causes the issue
your suggestion of setting the subvisuals size might be better, but requires more change in the napari layer. I might continue the discussion in the napari board
dvsphanindra
@dvsphanindra
Hi all,
I am using the PanZoom camera for displaying a 2D grayscale image. I would like to determine the pixel under the mouse cursor when the button is clicked. What I am able to access are the coordinates in the scene coordinate framework. Also, how do I determine the pixel where the mouse is clicked even when the image is panned or zoomed. Can someone help me with a small code snippet. Thank you.
David Hoese
@djhoese
@dvsphanindra did you ask this question somewhere else? I could have sworn I just answered this question. I'll have to go searching...

@dvsphanindra Here it is: https://stackoverflow.com/questions/70193398/vispy-2d-coordinate-x-y-of-a-point-of-an-image-inside-a-scenecanvas

See my comment there, but please respond here (unless that was your question)

dvsphanindra
@dvsphanindra
@djhoese Thanks for the reply. I have the same requirement as given in the question although I am not the one who asked the question. Also, let me tell you I have already tried the transform with map and imap. I could not figure out what I was missing because I get wrong outputs with both map and imap. Can you please point out the steps to configure the transform to work properly.
David Hoese
@djhoese
@dvsphanindra it would be easiest if you could provide me a minimal example that I could run (with no extra data files) and I could see how the map/imap calls could be updated to work properly
dvsphanindra
@dvsphanindra
@djhoese Here is an example code of what I am trying to do:
I would like to recover the positions of the bright pixels that are generated randomly after clicking on the image visual which I am printing in ImageOnClickRelease() function
import numpy as np
import sys
from vispy import scene

def ImageOnClickRelease(event):
    if event.button == 1:
        print("Position: ", event.pos)
        print(view.camera.center, view.camera.get_state(), "map= ", transform.map(event.pos))

canvas = scene.SceneCanvas(keys='interactive', bgcolor='white', size=(800, 600), show=True)

view = canvas.central_widget.add_view()
Set 2D camera (the camera will scale to the contents in the scene)

view.camera = scene.PanZoomCamera()
view.camera.flip = (0, 1, 0) # Y-Axis should be flipped for displaying images
canvas.events.mouse_release.connect(ImageOnClickRelease)

img_data = np.zeros((100,100))
points=np.random.randint(100,size=(30,2))
print(points)
for p in points:
    img_data[p[0],p[1]] = 0.5

image_visual = scene.visuals.Image(img_data, cmap='grays', clim=(0,1), parent=view.scene)
view.camera.set_range(margin=0)
transform = image_visual.transforms.get_transform()

if name == 'main' and sys.flags.interactive == 0:
     canvas.app.run()
David Hoese
@djhoese
@dvsphanindra Thanks for the example. It made it much easier to test. In your call to get_transform() pass map_to="canvas" and then .imap(event.pos) will give you the correct X/Y coordinate on the image. So that solves the mouse click -> image location problem, but you say you want to know where the bright pixels are. Are you the user supposed to click on the bright pixels? What is your end goal? I'm confused because couldn't you check the image data without the clicking to find the bright spots?
dvsphanindra
@dvsphanindra
@djhoese Thanks for the suggestion. The code is working now. I am working on pattern recognition wherein after the identification of various pixel groups in an image, the user can get info regarding the object pointed by mouse. I just created a small example to demonstrate my requirement.
Also can you please explain the output of map() and imap(). I have noticed that the pixel info is in the first two coordinates returned by imap(). What are the remaining two coordinates?
David Hoese
@djhoese

@dvsphanindra The transforms are going between coordinate systems. On your screen you have a 2D set of pixels, but in a Visual you could have a 3D coordinate system (ex. Volumes, Meshes, etc), but your ImageVisual is just 2D so the third z coordinate doesn't mean anything regarding that. The pan/zoom camera is kind of 3D because you are zooming in and out, but it is still a 2D view. I don't remember off the top of my head how the pan/zoom camera internally implements that, but same kind of point.

Typically the 4th dimension is a normalization value. Let me see if I can find the documentation on that, but for your application don't worry too much about it

David Hoese
@djhoese
dvsphanindra
@dvsphanindra
@djhoese Thank you I got some idea ;)
cgharib
@cgharib

Hi everyone !

So I'm trying to change two vertices coordinates over time in python and then send this information to OpenGL. I was able to do it in glumpy using :

x = .5*np.cos(totalTime)
program['position'] = np.array([(x, 0.), (-x, 0.)])

In vispy however it has been more complicated. I looked a bit in the code and finally managed to do it using :

x = .5*np.cos(totalTime)
newPos = np.array([(x, 0.), (-x, 0.)])
self.program['position'].base.set_subdata(newPos.astype(np.float32))

So this works but I was wondering about why this is so different and wether it's really the simplest way to do that. Does anyone have an idea ? Thank you !

(I think my variables are quite clear but if not I would be happy to send a more complete source.)

David Hoese
@djhoese
@cgharib It is hard to tell based on what you've provided so far. Something like what you have in glumpy should have worked in vispy. If not then I would have expected self.program['position'][:] = np.array(...) to work. What kind of error, if any, are you getting?
cgharib
@cgharib

Hey. Thanks for your answer.

With :

self.program['position'][:] = np.array([(x, 0.), (-x, 0.)]) #even with .astype(np.float32)

I get the following error :

File "/home/.../vispy/gloo/buffer.py", line 400, in __setitem__
    raise RuntimeError("Cannot set data on Buffer view")
RuntimeError: Cannot set data on Buffer view

Looking in buffer.py I concluded that I had to access to the DataBuffer that is associated with this DataBufferView. Therefore I added .base. Then I found the method set_subdata in DataBuffer. Finally I had to convert my np.float64 x to a np.float32 (because of line 426 in buffer.py).

The relevant variables are instantiated that way (in the __init__ method):

self.program = gloo.Program(vertex, fragment, count=2)
self.program['position'] = [(.5, 0), (-.5, 0)]

And I'm updating the position this way :

class MyCanvas(app.Canvas):
    def __init__....
        ...
        self.timer = app.Timer('auto', self.on_timer)
        self.timer.start()
    def on_timer(self, event):
        totalTime = self.timer.elapsed
        x =...
        newPos =...
        self.program['position'].base.set_subdata(newPos.astype(np.float32))
        self.update()
Kai Mühlbauer
@kmuehlbauer
@cgharib I would have a look into this too. Would you mind creating a minimal reproducible example we could run?
David Hoese
@djhoese
Ok so that error makes sense now that I think about it with [:]. But what do you get with self.program['position'] = np.array(...)?
cgharib
@cgharib
Thanks. So here's the code that works :
from vispy import app, gloo
import numpy as np

vertex = """
attribute vec2 position;

void main() {
    gl_Position = vec4(position, 0., 1.);
}
"""

fragment = """
void main() {
    gl_FragColor = vec4(1., 0., 0., 1.);
}
"""

class MyCanvas(app.Canvas):
    def __init__(self):
        app.Canvas.__init__(self)

        self.program = gloo.Program(vertex, fragment, count=2)
        self.program['position']= [(.5, 0), (-.5, 0)]

        self.timer = app.Timer("auto", self.on_timer)
        self.timer.start()

        self.show()

    def on_timer(self, event):
        totalTime = self.timer.elapsed
        x = .5*np.cos(totalTime)
        newPos = np.array([(x, 0), (-x, 0)])
        self.program['position'].base.set_subdata(newPos.astype(np.float32))
        self.update()

    def on_draw(self, event):
        gloo.clear()
        self.program.draw("lines")

c = MyCanvas()
app.run()

And with

self.program['position'] = newPos

I get the following error :

File "testVispy.py", line 34, in on_timer
    self.program['position'] = newPos
  File "/home/chams/.local/lib/python3.6/site-packages/vispy/gloo/program.py", line 409, in __setitem__
    vbo.set_data(data)
  File "/home/chams/.local/lib/python3.6/site-packages/vispy/gloo/buffer.py", line 381, in set_data
    raise RuntimeError("Cannot set data on buffer view.")
RuntimeError: Cannot set data on buffer view.
David Hoese
@djhoese
@cgharib This is definitely a surprise to me, but I don't have the historic context for why it is this way. A workaround is to reuse a VertexBuffer (or other buffer type) yourself, update the data, then reset that buffer. Like this with _pos:
class MyCanvas(app.Canvas):
    def __init__(self):
        app.Canvas.__init__(self)

        self.program = gloo.Program(vertex, fragment, count=2)
        self._pos = gloo.VertexBuffer()
        self.program['position'] = np.array([[.5, 0], [-.5, 0]], dtype=np.float32)

        self.timer = app.Timer("auto", self.on_timer)
        self.timer.start()

        self.show()

    def on_timer(self, event):
        totalTime = self.timer.elapsed
        x = .5*np.cos(totalTime)
        newPos = np.array([(x, 0), (-x, 0)])
        self._pos.set_data(newPos.astype(np.float32))
        self.program['position'] = self._pos
        self.update()
David Hoese
@djhoese

@almarklein @rougier Any memory why gloo.Program creates a View for each of the buffers? Meaning self.program['position'] is a DataBufferView when the program is created?

@cgharib Actually if you set the VertexBuffer in the __init__ and then do self.program['position'] = newPos.astype(np.float32) then it seems to work. The main problem seems to be that the gloo.Program creation defaults to creating a View. I'm not exactly sure why the original self.program['position'] = works as that should be a View too.

Nicolas P. Rougier
@rougier
Not sure, but maybe this is for handling the case where buffers are only one structured buffer (for example mixing position and color) and the view offers a consistent view...
Almar Klein
@almarklein
No idea ...
cgharib
@cgharib

Hey. Thanks for all your answers. So here's how I would write it based on @djhoese 's code.

import numpy as np
from vispy import app, gloo

vertex = """
attribute vec2 position;

void main() {
    gl_Position = vec4(position, 0., 1.);
}
"""

fragment = """
void main() {
    gl_FragColor = vec4(1.,0.,0.,1.);
}
"""

class MyCanvas(app.Canvas):
    def __init__(self):
        app.Canvas.__init__(self)
        self.program = gloo.Program(vertex, fragment, count=2)

        self.vertexBuffer = gloo.VertexBuffer(np.array([(.5, 0), (-.5, 0)], dtype=np.float32))
        self.program['position'] = self.vertexBuffer

        self.timer = app.Timer('auto', self.on_timer)
        self.timer.start()

        self.show()

    def on_draw(self, event):
        gloo.clear()
        self.program.draw('lines')

    def on_timer(self, event):
        totalTime = self.timer.elapsed
        x = .5*np.cos(totalTime)
        newPos = np.array([(x, 0), (-x, 0)], dtype=np.float32)
        self.vertexBuffer.set_data(newPos)
        self.update()

c = MyCanvas()
app.run()

Does it seem idiomatic to you ? Thanks a lot !

David Hoese
@djhoese
@cgharib I personally would change your timer handler to do self.program['position'] = newPos. It feels more future-proof and avoids the possibility of the VertexBuffer being copied inside the Program and your set_data not having an effect. Hopefully that makes sense. Either way should work so do what feels good to you.
cgharib
@cgharib
I understand. Thanks !
Thomas Doman
@tjjdoman_gitlab
Hello all, I am trying to specify a z position of an EllipseVisual's center so that I can layer it on image visuals, but it seems as if that is not allowed as only the first 2 elements of the passed center are used to create the vertices of the ellipse. Is there something I am missing or does this require an edit?
David Hoese
@djhoese
@tjjdoman_gitlab It looks like you are right that the center point is only 2D. You could try using an STTransform to force the Z position by doing ellipse.transform = STTransform(translate=(0, 0, some_z_shift)). You may also run into issues with drawing order between the Image and Ellipse where you may need to do something like ellipse.order = -5, but see if the Z position works well enough first.
IsolatedSushi2
@IsolatedSushi2
Hey, quick question. Im working with a 3d point cloud. I can't find how to make the camera rotate around a specific point (not the center perse). How can this be done?
David Hoese
@djhoese
@IsolatedSushi2 What camera are you using? And if the point isn't the center, then what is it as far as the camera thinks of it? Or how is it related to the center of the view?
IsolatedSushi2
@IsolatedSushi2
image.png
@djhoese I'm using the turntable camera with the vispy.scene. I have a bunch of points in 3d space, and would like to have the camera rotate around its center of mass instead of the origin point
David Hoese
@djhoese
@IsolatedSushi2 Does doing something like camera.center = (x, y, z) work? If not, why not? You will need to calculate the center of mass to become this origin point but otherwise looking at the code this should "just work"
Thomas Doman
@tjjdoman_gitlab
@djhoese Thanks, your advice helped! Have not needed to specify the order yet, but will keep that in mind.
Omicron91
@Omicron91

Hello guys. I'm developing a software to visualize thickness maps by using PyQt as Desktop Framework, however, I'm experiencing some problems. The central widget is a grid layout with multiple scatter plots, in a sub grid each, When i minimize and maximize the window multiple times the layout tends to collapse, then i get the following error

WARNING: Traceback (most recent call last):         
  File ".\src\CrushingApp.py", line 324, in <module>
    sys.exit(app.exec_())
  File "C:\Users\site-packages\vispy\app\backends\_qt.py", line 508, in event
    out = super(QtBaseCanvasBackend, self).event(ev)
  File "C:\Users\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
  File "C:\Users\\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
  File "C:\Users\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
  << caught exception here: >>
  File "C:\Users\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
  File "C:\Users\site-packages\vispy\scene\canvas.py", line 217, in on_draw
    self._draw_scene()
  File "C:\Users\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
  File "C:\Users\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    self.add_with_artificial_variable(expr)
  File "C:\Users\site-packages\vispy\ext\_bundled\cassowary\simplex_solver.py", line 381, in 
add_with_artificial_variable
    raise RequiredFailure()
vispy.ext._bundled.cassowary.error.RequiredFailure
ERROR: Invoking <bound method SceneCanvas.on_draw of <CanvasMapaEspesores (PyQt5) at 0x149ed69fe08>> for DrawEvent

is there a way to avoi

avoid/fix* this
Omicron91
@Omicron91
test_err1.PNG
test_err2.PNG
sometimes collapse the entire layout
David Hoese
@djhoese
@Omicron91 What version of vispy are you using? We no longer use cassowary as our grid solver. Could you try this with the most recent release of vispy?
Omicron91
@Omicron91
I'm using 0.6.4, i'll try. The team had been working for a while with this version, so i don't know if it could cause problems
David Hoese
@djhoese
It might. Depending on what you/they were using, but it will be hard for us to help with cassowary issues as it has been deprecated for quite a few releases now