plot_surface shading and clipping error

Community matplotlib-users
1

Hi,
i'm trying to make a simple 3d plot of a cylinder with plot_surface.
There are two problems in my output:
1) the shading, shading does not work on the cylindric shell and at the same
time produces weird
artifacts on the top cover.
http://old.nabble.com/file/p29254649/cyl-shade-error.png

2) Sometimes, not reproducible, the inner back of the cylindric shell is
plotted in front of the top cover. It seems, that it depends somehow on the
order of the plot commands, so that switching the two plot command helps...
but not all the time.
http://old.nabble.com/file/p29254649/cyl-clip-error.png

Am I doing something fundamentally wrong here?

···

##########################
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
fig = plt.figure()
ax = Axes3D(fig)

# Cylindrical shell
phi = np.linspace(0, 2 * np.pi, 100)
r = np.ones(100)
h = np.linspace(0, 1, 100)

x = 10 * np.outer(np.cos(phi), r)
y = 10 * np.outer(np.sin(phi), r)
z = 10 * np.outer(np.ones(np.size(r)), h)

# Top cover
phi_a = np.linspace(0, 2 * np.pi, 100)
h_2 = np.ones(100)
r_2 = np.linspace(0, 1, 100)

x_2 = 10 * np.outer(np.cos(phi), r_2)
y_2 = 10 * np.outer(np.sin(phi), r_2)
z_2 = 10 * np.ones([100,100])

ax.plot_surface(x, y, z, rstride=9, cstride=15, linewidth=1, alpha=1)
ax.plot_surface(x_2, y_2, z_2, rstride=5, cstride=20, linewidth=1, alpha=1)

ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')

plt.show()
##########################

I'm just a beginner and installed the Enthought Python Distribution 6.2-2,
which unfortunately
does not use the matplotlib version 1.0. Since I could not find the .egg
install file on the matplotlib site I guess I'll have to wait until they
update EPD.... self compiling is not a real option for me.

Thanks any suggestions!

--
View this message in context: http://old.nabble.com/plot_surface-shading-and-clipping-error-tp29254649p29254649.html
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2

arsbbr,

The second problem you mention is a known issue with 3D axes and it is largely due to issues with overlapping objects and trying to determine which one gets displayed on top of the other in a 3D → 2D environment (oh, how I wish holographic displays were a reality!). You will find that viewing an object from certain angles will cause this issue, and then slightly moving away from those angles will make everything right again. Unfortunately, I do not anticipate this issue being solved anytime soon, although it probably should become a higher priority to me.

I think I have seen the first issue before, but I never fully explored it. I think I just found my mini-project for the weekend! I will let you know what I find.

Ben Root

···

On Sat, Jul 24, 2010 at 7:18 AM, arsbbr <arsbbr@…361…> wrote:

Hi,

i’m trying to make a simple 3d plot of a cylinder with plot_surface.

There are two problems in my output:

  1. the shading, shading does not work on the cylindric shell and at the same

time produces weird

artifacts on the top cover.

http://old.nabble.com/file/p29254649/cyl-shade-error.png

  1. Sometimes, not reproducible, the inner back of the cylindric shell is

plotted in front of the top cover. It seems, that it depends somehow on the

order of the plot commands, so that switching the two plot command helps…

but not all the time.

http://old.nabble.com/file/p29254649/cyl-clip-error.png

Am I doing something fundamentally wrong here?

##########################

from mpl_toolkits.mplot3d import Axes3D

import matplotlib.pyplot as plt

import numpy as np

from matplotlib import cm

fig = plt.figure()

ax = Axes3D(fig)

Cylindrical shell

phi = np.linspace(0, 2 * np.pi, 100)

r = np.ones(100)

h = np.linspace(0, 1, 100)

x = 10 * np.outer(np.cos(phi), r)

y = 10 * np.outer(np.sin(phi), r)

z = 10 * np.outer(np.ones(np.size(r)), h)

Top cover

phi_a = np.linspace(0, 2 * np.pi, 100)

h_2 = np.ones(100)

r_2 = np.linspace(0, 1, 100)

x_2 = 10 * np.outer(np.cos(phi), r_2)

y_2 = 10 * np.outer(np.sin(phi), r_2)

z_2 = 10 * np.ones([100,100])

ax.plot_surface(x, y, z, rstride=9, cstride=15, linewidth=1, alpha=1)

ax.plot_surface(x_2, y_2, z_2, rstride=5, cstride=20, linewidth=1, alpha=1)

ax.set_xlabel(‘X’)

ax.set_ylabel(‘Y’)

ax.set_zlabel(‘Z’)

plt.show()

##########################

I’m just a beginner and installed the Enthought Python Distribution 6.2-2,

which unfortunately

does not use the matplotlib version 1.0. Since I could not find the .egg

install file on the matplotlib site I guess I’ll have to wait until they

update EPD… self compiling is not a real option for me.

Thanks any suggestions!

3

Thank you for looking into it!
It would be perfectly fine for me to merge the two objects, so that one
surface_plot command will do it.
Maybe someone can give me a hint how to accomplish that?

I appreciate any tips.

Benjamin Root-2 wrote:

···

On Sat, Jul 24, 2010 at 7:18 AM, arsbbr <arsbbr@...361...> wrote:

Hi,
i'm trying to make a simple 3d plot of a cylinder with plot_surface.
There are two problems in my output:
1) the shading, shading does not work on the cylindric shell and at the
same
time produces weird
artifacts on the top cover.
http://old.nabble.com/file/p29254649/cyl-shade-error.png

2) Sometimes, not reproducible, the inner back of the cylindric shell is
plotted in front of the top cover. It seems, that it depends somehow on
the
order of the plot commands, so that switching the two plot command
helps...
but not all the time.
http://old.nabble.com/file/p29254649/cyl-clip-error.png

Am I doing something fundamentally wrong here?

##########################
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
fig = plt.figure()
ax = Axes3D(fig)

# Cylindrical shell
phi = np.linspace(0, 2 * np.pi, 100)
r = np.ones(100)
h = np.linspace(0, 1, 100)

x = 10 * np.outer(np.cos(phi), r)
y = 10 * np.outer(np.sin(phi), r)
z = 10 * np.outer(np.ones(np.size(r)), h)

# Top cover
phi_a = np.linspace(0, 2 * np.pi, 100)
h_2 = np.ones(100)
r_2 = np.linspace(0, 1, 100)

x_2 = 10 * np.outer(np.cos(phi), r_2)
y_2 = 10 * np.outer(np.sin(phi), r_2)
z_2 = 10 * np.ones([100,100])

ax.plot_surface(x, y, z, rstride=9, cstride=15, linewidth=1, alpha=1)
ax.plot_surface(x_2, y_2, z_2, rstride=5, cstride=20, linewidth=1,
alpha=1)

ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')

plt.show()
##########################

I'm just a beginner and installed the Enthought Python Distribution
6.2-2,
which unfortunately
does not use the matplotlib version 1.0. Since I could not find the .egg
install file on the matplotlib site I guess I'll have to wait until they
update EPD.... self compiling is not a real option for me.

Thanks any suggestions!

arsbbr,

The second problem you mention is a known issue with 3D axes and it is
largely due to issues with overlapping objects and trying to determine
which
one gets displayed on top of the other in a 3D -> 2D environment (oh, how
I
wish holographic displays were a reality!). You will find that viewing an
object from certain angles will cause this issue, and then slightly moving
away from those angles will make everything right again. Unfortunately, I
do not anticipate this issue being solved anytime soon, although it
probably
should become a higher priority to me.

I think I have seen the first issue before, but I never fully explored it.
I think I just found my mini-project for the weekend! I will let you know
what I find.

Ben Root

------------------------------------------------------------------------------
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What will you do first with EVO, the first 4G phone?
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View this message in context: http://old.nabble.com/plot_surface-shading-and-clipping-error-tp29254649p29256632.html
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4

Actually, looks like your problem was relatively simple. The construction of the top surface wasn’t done quite right and the striding was causing blocks to be skipped. Try this:

phi_grid, r_grid = np.meshgrid(phi_a, r_2)
x_2 = 10 * np.cos(phi_grid) * r_grid
y_2 = 10 * np.sin(phi_grid) * r_grid
z_2 = 10 * np.ones([100,100])

The thing to keep in mind when creating a surface in 3d is that the data needs to be considered as parameterizable in 2D and constructed as such.

I hope that helps,

Ben Root

···

On Sat, Jul 24, 2010 at 2:46 PM, arsbbr <arsbbr@…361…> wrote:

Thank you for looking into it!

It would be perfectly fine for me to merge the two objects, so that one

surface_plot command will do it.

Maybe someone can give me a hint how to accomplish that?

I appreciate any tips.

Benjamin Root-2 wrote:

On Sat, Jul 24, 2010 at 7:18 AM, arsbbr <arsbbr@…361…> wrote:

Hi,

i’m trying to make a simple 3d plot of a cylinder with plot_surface.

There are two problems in my output:

  1. the shading, shading does not work on the cylindric shell and at the

same

time produces weird

artifacts on the top cover.

http://old.nabble.com/file/p29254649/cyl-shade-error.png

  1. Sometimes, not reproducible, the inner back of the cylindric shell is

plotted in front of the top cover. It seems, that it depends somehow on

the

order of the plot commands, so that switching the two plot command

helps…

but not all the time.

http://old.nabble.com/file/p29254649/cyl-clip-error.png

Am I doing something fundamentally wrong here?

##########################

from mpl_toolkits.mplot3d import Axes3D

import matplotlib.pyplot as plt

import numpy as np

from matplotlib import cm

fig = plt.figure()

ax = Axes3D(fig)

Cylindrical shell

phi = np.linspace(0, 2 * np.pi, 100)

r = np.ones(100)

h = np.linspace(0, 1, 100)

x = 10 * np.outer(np.cos(phi), r)

y = 10 * np.outer(np.sin(phi), r)

z = 10 * np.outer(np.ones(np.size(r)), h)

Top cover

phi_a = np.linspace(0, 2 * np.pi, 100)

h_2 = np.ones(100)

r_2 = np.linspace(0, 1, 100)

x_2 = 10 * np.outer(np.cos(phi), r_2)

y_2 = 10 * np.outer(np.sin(phi), r_2)

z_2 = 10 * np.ones([100,100])

ax.plot_surface(x, y, z, rstride=9, cstride=15, linewidth=1, alpha=1)

ax.plot_surface(x_2, y_2, z_2, rstride=5, cstride=20, linewidth=1,

alpha=1)

ax.set_xlabel(‘X’)

ax.set_ylabel(‘Y’)

ax.set_zlabel(‘Z’)

plt.show()

##########################

I’m just a beginner and installed the Enthought Python Distribution

6.2-2,

which unfortunately

does not use the matplotlib version 1.0. Since I could not find the .egg

install file on the matplotlib site I guess I’ll have to wait until they

update EPD… self compiling is not a real option for me.

Thanks any suggestions!

arsbbr,

The second problem you mention is a known issue with 3D axes and it is

largely due to issues with overlapping objects and trying to determine

which

one gets displayed on top of the other in a 3D → 2D environment (oh, how

I

wish holographic displays were a reality!). You will find that viewing an

object from certain angles will cause this issue, and then slightly moving

away from those angles will make everything right again. Unfortunately, I

do not anticipate this issue being solved anytime soon, although it

probably

should become a higher priority to me.

I think I have seen the first issue before, but I never fully explored it.

I think I just found my mini-project for the weekend! I will let you know

what I find.

5

Thanks, this was quite a tiny weekend project for you :slight_smile:
I'll keep you tip in mind.

Concerning the foreground/background issue: The problem here seems quite
random. It does not depend on the viewing angle. I rather just have to be
lucky everytime the plot command is executed.
If the plotting went right, I can rotate everything without any errors.

I'm by no means a coder, but I find it hard to understand that executing the
same script leads to a different outcome. My plan is to make a movie of the
cylinder while shrinking. If the problem would
just depend on the viewing angle, I would find a 'good angle', make it
constant and start the loop. But at the moment the outcome is just
arbitrary.

Regards,
arsbbr

Benjamin Root-2 wrote:

···

On Sat, Jul 24, 2010 at 2:46 PM, arsbbr <arsbbr@...361...> wrote:

The thing to keep in mind when creating a surface in 3d is that the data
needs to be considered as parameterizable in 2D and constructed as such.

I hope that helps,

Ben Root

------------------------------------------------------------------------------
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What will you do first with EVO, the first 4G phone?
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6

arsbor,

Actually, in your case, I think the issue was also caused by the bad array construction and plot_surface() was getting bad data depending on the strides. There is no random number generator in the code-path, so something must change. I noticed that it would happen as I changed the cstride/rstride values for the top cover (before I had fixed the top cover). If you still notice the issue now, let me know and I will look into it further, but it shouldn’t be happening for you.

Ben Root

···

On Sun, Jul 25, 2010 at 5:19 AM, arsbbr <arsbbr@…361…> wrote:

Thanks, this was quite a tiny weekend project for you :slight_smile:

I’ll keep you tip in mind.

Concerning the foreground/background issue: The problem here seems quite

random. It does not depend on the viewing angle. I rather just have to be

lucky everytime the plot command is executed.

If the plotting went right, I can rotate everything without any errors.

I’m by no means a coder, but I find it hard to understand that executing the

same script leads to a different outcome. My plan is to make a movie of the

cylinder while shrinking. If the problem would

just depend on the viewing angle, I would find a ‘good angle’, make it

constant and start the loop. But at the moment the outcome is just

arbitrary.

Regards,

arsbbr

7

Ben,

your code fixed the shading problem, but it did not change anything on the
clipping error.
I also found that changing the cstride/rstride helps 'sometimes'. But also
does changing the
linewidth. The problem is consistency with my loop...

I understand this is a bug that is not easy to fix. It would be totally
sufficient for me if I could only find some parameters that'll always work.
But this is not the case. Since there is no random procedure in the code
there must be some footprint so that the starting parameters are not the
same all the time. Maybe it is a memory thing and I have just to clear a
cache/display buffer or something?

Benjamin Root-2 wrote:

···

arsbor,

Actually, in your case, I think the issue was also caused by the bad array
construction and plot_surface() was getting bad data depending on the
strides. There is no random number generator in the code-path, so
*something* must change. I noticed that it would happen as I changed the
cstride/rstride values for the top cover (before I had fixed the top
cover). If you still notice the issue now, let me know and I will look
into
it further, but it shouldn't be happening for you.

Ben Root

--
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