Over on napari/napari#3357 we noticed that canvas widgets have a default _border_width of 1, which can result in unexpected/undesired borders. The only easy way I found to remove that border is to modify the vispy source to make the default border_width parameter 0 instead.
Before I open any issues/PRs on vispy, I wanted to check a few of things.
- Is this an intended behavior of vispy? If not, would you be open to changing the default
_border_widthto be 0? - Can you think of any other ways to make all canvas widgets have a
_border_widthof 0?
There are some code snippets on the napari issue, but I'm happy to try to create a minimal reproducer - napari's Qt widgets/layout are non-trivial, so it's very possible that the default 1-pixel transparent borders only cause an issue for us (e.g. because of the effective background color of some Qt widget). Though, when calling grabFrameBuffer on the native Qt widget, we'll also getting that border, so I think that constrains where that color is coming from.
@andy-sweet Thanks for reaching out.
- Is this intended? VisPy has been off and on with maintainers for so long that it is likely the people who originally made that suggestion don't even remember making it or why. I'll see if I can track something down in the git history
- You should be able to "manually" create Widget-subclass (ViewBox, Widget, Grid) and add them to the SceneCanvas instead of relying on the default behavior. For example,
canvas.central_widget.add_view()(or whatever it is) create a Grid widget as a central_widget implicitly and thenadd_viewcreates aViewBoxwidget. But I think at least for the view you should be able to import the ViewBox class, instantiate it, then add it to the grid widget withcentral_widget.add_widget(view, ...). At least I think so. I might be mixing up multiple interfaces.
Am I OK with border width being set to 0? Sure, probably. It will probably cause a lot of tests to fail. @almarklein @rougier @larsoner any memory of the border width stuff? Looks like it came from a PR by @campagnola in vispy/vispy#1030
@djhoese : thanks for the quick reply! I think you effectively solved this issue by educating me on add_view.
We have already have a VispyCanvas that extends SceneCanvas so by overriding the SceneCanvas.central_widget property there and by passing border_width=0 through to add_view, I think I'm able to get the desired behavior in napari, so I think that's probably going to be enough.
So unless I'm get some pushback from other people on napari, or you are / someone else is really curious about how many and what tests fails, I'm probably going to avoid opening that PR for now.
SceneCanvas.central_widget's border_width 0, since the other border widths can be more easily controlled (e.g. in add_view): vispy/vispy#2255
Markers (for example), you can do that with Compound._subvisuals[3].size (3 is the index of the Markers subvisual`)
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.
@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)
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()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?
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?
@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
https://en.wikipedia.org/wiki/Homogeneous_coordinates
Don't ask me any questions about it though. I only ever know as much as I need to when I need to
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.)
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 viewLooking 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()
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'] = newPosI 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._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()@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.
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 !
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.
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.
