There is a pull request for this here:

https://github.com/matplotlib/matplotlib/pull/695

If you're able to checkout and build that branch from git, I would appreciate hearing if it resolves your issue.

Mike

On 02/06/2012 12:58 PM, Chris wrote:
JJ,

Thanks for the clarification.  Now I understand why EPS outputs of
pixel plot from mpl is a few times bigger than those from SuperMongo.
I guess that mpl uses the square implementation for pixel so that it
would use the same method to handle all marker types.  I will file an
issue report on git.  Meanwhile, is there any easy workaround?

Jonathan,

Tom Robitaille's module does help reducing file size of postscript,
but by rasterize a scalable plot.  It doesn't really help my problem
since the markers are still drawn with the same method as other
plotting methods.

Bests,
Chris


On Mon, Feb 6, 2012 at 4:28 AM, Jae-Joon Lee<lee.j.j...@gmail.com>  wrote:
Thanks. Now I understand the situation.

As far as I can see, marker="," is implemented as a rectangle path
with width/height of 1 pixel, so this result in 2x2 pixel filled
square.
I tried to change the size of the rectangle, etc, to get a single
pixel filled square, but did not get a satisfactory result.
I think we need an Agg expert. I hope Mike or others take a look.

Chris,
if you do not get a response from others in this mailing list, I
recommend you to open a new issue in our github page.

Regards,

-JJ


On Mon, Feb 6, 2012 at 6:19 AM, Jonathan Slavin<jsla...@cfa.harvard.edu>  wrote:
Chris,

You might want to try a module written by Tom Robitaille (aka astrofrog)
called rasterized_scatter.  Look for it on github.

Jon

On Mon, 2012-02-06 at 21:28 +0900, Jae-Joon Lee wrote:
Thanks. Now I understand the situation.

As far as I can see, marker="," is implemented as a rectangle path
with width/height of 1 pixel, so this result in 2x2 pixel filled
square.
I tried to change the size of the rectangle, etc, to get a single
pixel filled square, but did not get a satisfactory result.
I think we need an Agg expert. I hope Mike or others take a look.

Chris,
if you do not get a response from others in this mailing list, I
recommend you to open a new issue in our github page.

Regards,

-JJ


On Mon, Feb 6, 2012 at 1:53 AM, Chris<plut...@gmail.com>  wrote:
Thanks JJ.

The problem seems not to be a size issue --  markersize has no effect
when use marker="," (pixel).  I have also tried to turn off aa, and it
doesn't help either.  I also tried different backends.  The PNG output
from Agg and Cairo is slightly different: Agg's point has 4 solid
pixel, while Cairo's has 4 pixel with random shade.

Postscript output has the same problem.  The "pixel" in an EPS file
generated by mpl is significantly bigger than that from another
drawing program I used.

The problem occurs in all my plotting scripts, e.g., this basic one:

[CODE]
import numpy as np

x=np.arange(100)
y=np.random.randn(100)

ioff()
fig=gcf()
fig.clf()

ax=fig.add_axes(0.15,0.1,0.8, 0.85)
ax.plot(x,y,"k,")

ion()
fig.canvas.draw()
[/CODE]

Here is how I identify the problem:
1. use the above script to plot on screen
2. savefig("plot.png")
3. open plot.png in GIMP and check the pixel size.

I also attached the two PNG files generated with Agg and Cairo backends.


On Sun, Feb 5, 2012 at 6:45 AM, Jae-Joon Lee<lee.j.j...@gmail.com>  wrote:
How are you plotting your points.

If you use *plot*, there is a *markersize* parameter.
If you use *scatter*, the third argument controls the marker size.

But you may actually complaining about other issues, e.g.,
antialiasing, etc. So, if above are not your answer, please post a
complete example and describe your problem in more detail.

Regards,

-JJ


On Sat, Feb 4, 2012 at 2:15 PM, Chris<plut...@gmail.com>  wrote:
I noticed this a few years back, but left it aside because most of the
time I can live with it.  Recently I need to make a few plots
containing a few million points, and 4 pixels for a point is a
disaster.  So my question is why the pixel marker size is set at 4
pixels?  And is there anyway to change it to a single pixel?

Thanks,
Chris
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