Re: [matplotlib-devel] Misalignment imshow vs. grid lines

2012-10-30 Thread Nicolas Rougier 


Sorry, I was too fast in my reply.

When I save the figure, the png output is ok while the pdf is displaying some 
kind of interpolation with the image.

import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

n = 16
fig = plt.figure(figsize=(6,6))
Z = np.array(([0,1]*(n//2) + [1,0]*(n//2))*(n//2)).reshape(n,n)
plt.imshow(Z, interpolation='none', cmap=plt.cm.gray, extent=[0,n,0,n], 
alpha=.25)
plt.xticks(np.arange(0,n), [])
plt.yticks(np.arange(0,n), [])
plt.grid(ls='solid')
plt.savefig('pylab-grid.png')
plt.savefig('pylab-grid.pdf')
plt.show()





Just for the record, "Skim", "Preview" and "Adobe Reader" on OSX do not give 
the same output on the saved pdf.
"Adobe Reader" displays the expected result (same as saved png) while "Preview" 
and "Skim" are apparently trying to make some (bad) interpolation of the 
checkboard image.


Nicolas


On Oct 30, 2012, at 7:52 , Nicolas Rougier wrote:

> 
> 
> You're right. Using 'none' interpolation seems to solve the problem. Good to 
> know !
> 
> One last question, why is the 'none' interpolation restricted to Agg/PS/pdf ?
> 
> 
> Nicolas
> 
> 
> 
> On Oct 30, 2012, at 6:53 , Jae-Joon Lee wrote:
> 
>> On Tue, Oct 30, 2012 at 12:25 AM, Nicolas Rougier
>>  wrote:
>>> 
>>> 
>>> Thanks for testing.
>>> 
>>> If I zoom at any line cross, the lines are definitely at the wrong place 
>>> for me.
>> 
>> As  jules hummon commented, I see lines in right places when I zoom in.
>> 
>>> As for screen aliasing I'm not sure since both the png and pdf seems to be 
>>> wrong in my case.
>> 
>> It still can be some aliasing-related issue. Note that with
>> interpolation="nearest", the images are rasterized with given dpi even
>> if you save the figure as pdf.
>> The agg backend tries to adjust the location of lines and images so
>> that they are well-aligned with the pixels, and the issue seems to be
>> related with that behavior.
>> 
>> In my case, using interpolation="none" worked out okay. So give it a try.
>> 
>> Regards,
>> 
>> -JJ
>> 
>> 
>>> Weird !
>>> 
>>> 
>>> Nicolas
>>> 
>>> 
>>> On Oct 29, 2012, at 15:40 , jules hummon wrote:
>>> 
 Nicolas
 
 I get that too, (with your script and various things in my work).
 But if you zoom in, the lines are in the right place.   Is it
 some kind of screen aliasing?
 
 Jules
 
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Re: [matplotlib-devel] Misalignment imshow vs. grid lines

2012-10-30 Thread Phil Elson 
Thanks for making this so easy to reproduce. It is so much easier when
there is a small, self contained, correct example!

Initially I was thinking that the problem was some kind of snapping issue
with the ticks, but it turns out, if you change the interpolation scheme to
"none", you get perfect alignment:


import numpy as np
import matplotlib.pyplot as plt

n = 16
fig = plt.figure(figsize=(10,10))

Z = np.zeros((n, n))
Z[::2, ::2] = 1
Z[1::2, 1::2] = 1

# pick the interpolation you want:
interp = 'nearest'
interp = 'none'

plt.imshow(Z, interpolation=interp,
cmap='gray', extent=[0, n, 0, n],
alpha=0.25)

plt.xticks(np.arange(n))
plt.yticks(np.arange(n))
plt.grid(ls='solid')

plt.show()



I haven't considered where to go from this point, but I wanted to let you
know about this option.

Thanks,

Phil



On 30 October 2012 07:10, Nicolas Rougier  wrote:

>
>
> Sorry, I was too fast in my reply.
>
> When I save the figure, the png output is ok while the pdf is displaying
> some kind of interpolation with the image.
>
> import numpy as np
> import matplotlib
> matplotlib.use('Agg')
> import matplotlib.pyplot as plt
>
> n = 16
> fig = plt.figure(figsize=(6,6))
> Z = np.array(([0,1]*(n//2) + [1,0]*(n//2))*(n//2)).reshape(n,n)
> plt.imshow(Z, interpolation='none', cmap=plt.cm.gray, extent=[0,n,0,n],
> alpha=.25)
> plt.xticks(np.arange(0,n), [])
> plt.yticks(np.arange(0,n), [])
> plt.grid(ls='solid')
> plt.savefig('pylab-grid.png')
> plt.savefig('pylab-grid.pdf')
> plt.show()
>
>
>
>
>
> Just for the record, "Skim", "Preview" and "Adobe Reader" on OSX do not
> give the same output on the saved pdf.
> "Adobe Reader" displays the expected result (same as saved png) while
> "Preview" and "Skim" are apparently trying to make some (bad) interpolation
> of the checkboard image.
>
>
> Nicolas
>
>
> On Oct 30, 2012, at 7:52 , Nicolas Rougier wrote:
>
> >
> >
> > You're right. Using 'none' interpolation seems to solve the problem.
> Good to know !
> >
> > One last question, why is the 'none' interpolation restricted to
> Agg/PS/pdf ?
> >
> >
> > Nicolas
> >
> >
> >
> > On Oct 30, 2012, at 6:53 , Jae-Joon Lee wrote:
> >
> >> On Tue, Oct 30, 2012 at 12:25 AM, Nicolas Rougier
> >>  wrote:
> >>>
> >>>
> >>> Thanks for testing.
> >>>
> >>> If I zoom at any line cross, the lines are definitely at the wrong
> place for me.
> >>
> >> As  jules hummon commented, I see lines in right places when I zoom in.
> >>
> >>> As for screen aliasing I'm not sure since both the png and pdf seems
> to be wrong in my case.
> >>
> >> It still can be some aliasing-related issue. Note that with
> >> interpolation="nearest", the images are rasterized with given dpi even
> >> if you save the figure as pdf.
> >> The agg backend tries to adjust the location of lines and images so
> >> that they are well-aligned with the pixels, and the issue seems to be
> >> related with that behavior.
> >>
> >> In my case, using interpolation="none" worked out okay. So give it a
> try.
> >>
> >> Regards,
> >>
> >> -JJ
> >>
> >>
> >>> Weird !
> >>>
> >>>
> >>> Nicolas
> >>>
> >>>
> >>> On Oct 29, 2012, at 15:40 , jules hummon wrote:
> >>>
>  Nicolas
> 
>  I get that too, (with your script and various things in my work).
>  But if you zoom in, the lines are in the right place.   Is it
>  some kind of screen aliasing?
> 
>  Jules
> 
> 
> --
>  The Windows 8 Center - In partnership with Sourceforge
>  Your idea - your app - 30 days.
>  Get started!
>  http://windows8center.sourceforge.net/
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> what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/
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> >>>
> >>>
> >>>
> --
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> >>> Your idea - your app - 30 days.
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> >
> >
> >
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>
>
>

Re: [matplotlib-devel] Misalignment imshow vs. grid lines

2012-10-30 Thread Maciek Dems 
In reply to message from Nicolas Rougier, dated Tuesday 30 of October 2012, 
on subject "Re: [matplotlib-devel] Misalignment imshow vs. grid lines"
> You're right. Using 'none' interpolation seems to solve the problem. Good
> to know !

Unfortunately it does not! It only makes problem less pronounced, but still 
present. Furthermore pcolor is also affected, similarly to imshow, however, 
the misalignment is usually no more than one pixel (although in some 
applications it is still unacceptable).

I guess that the problem is with truncation errors in some calculations...

Here are some test scripts and sample results. Mind that the misalignment 
depend randomly on zoom factor and the position of the image.

The scripts:

# test_imshow.py
# --
import numpy as np
import matplotlib.pyplot as plt

n = 16
fig = plt.figure(figsize=(10,10))

Z = np.ones((n, n))
Z[::2, ::2] = 2
Z[1::2, 1::2] = 2

def test(interp, sub):
plt.subplot(sub)

plt.imshow(Z, interpolation=interp,
cmap='gray', extent=[0, n, 0, n], vmin=0)

plt.xticks(np.arange(n))
plt.yticks(np.arange(n))
plt.grid(ls='solid')
plt.title(interp)

test('nearest', 121)
test('none', 122)

plt.show()



# test_pcolor.py
# --
import numpy as np
import matplotlib.pyplot as plt

n = 16
fig = plt.figure(figsize=(10,10))

Z = np.ones((n, n))
Z[::2, ::2] = 2
Z[1::2, 1::2] = 2

plt.pcolor(np.arange(n+1), np.arange(n+1), Z,
cmap='gray', vmin=0)

plt.xticks(np.arange(n))
plt.yticks(np.arange(n))
plt.grid(ls='solid')

plt.show()



The results (some manual zooming) are attached and also available here:
http://dems.art.pl/files/imshow.png
http://dems.art.pl/files/pcolor.png

-- 
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Re: [matplotlib-devel] Misalignment imshow vs. grid lines

2012-10-30 Thread Nicolas Rougier 


Yep, I can confirm this but the story is a bit different on my side since the 
.png is wrong but not the .pdf (only ok with Acrobat Reader though):

import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

n = 16
fig = plt.figure(figsize=(6,6))
Z = np.zeros((n,n))
Z[::2,::2] = Z[1::2,1::2] = 1
plt.imshow(Z, interpolation='none', cmap=plt.cm.gray, extent=[0,n,0,n], 
alpha=0.25)
plt.xticks(np.arange(0,n), []), plt.yticks(np.arange(0,n), [])
plt.grid(ls='solid')
delta = 0.01
plt.xlim(1-delta,1+delta), plt.ylim(1-delta,1+delta)
plt.savefig('pylab-grid.png')
plt.savefig('pylab-grid.pdf')


Nicolas




On Oct 30, 2012, at 10:59 , Maciek Dems wrote:

> In reply to message from Nicolas Rougier, dated Tuesday 30 of October 2012, 
> on subject "Re: [matplotlib-devel] Misalignment imshow vs. grid lines"
> > You're right. Using 'none' interpolation seems to solve the problem. Good
> > to know !
>  
> Unfortunately it does not! It only makes problem less pronounced, but still 
> present. Furthermore pcolor is also affected, similarly to imshow, however, 
> the misalignment is usually no more than one pixel (although in some 
> applications it is still unacceptable).
>  
> I guess that the problem is with truncation errors in some calculations...
>  
> Here are some test scripts and sample results. Mind that the misalignment 
> depend randomly on zoom factor and the position of the image.
>  
> The scripts:
>  
> # test_imshow.py
> # --
> import numpy as np
> import matplotlib.pyplot as plt
>  
> n = 16
> fig = plt.figure(figsize=(10,10))
>  
> Z = np.ones((n, n))
> Z[::2, ::2] = 2
> Z[1::2, 1::2] = 2
>  
> def test(interp, sub):
> plt.subplot(sub)
> 
> plt.imshow(Z, interpolation=interp,
> cmap='gray', extent=[0, n, 0, n], vmin=0)
>  
> plt.xticks(np.arange(n))
> plt.yticks(np.arange(n))
> plt.grid(ls='solid')
> plt.title(interp)
>  
> test('nearest', 121)
> test('none', 122)
>  
> plt.show()
>  
>  
>  
> # test_pcolor.py
> # --
> import numpy as np
> import matplotlib.pyplot as plt
>  
> n = 16
> fig = plt.figure(figsize=(10,10))
>  
> Z = np.ones((n, n))
> Z[::2, ::2] = 2
> Z[1::2, 1::2] = 2
>  
> plt.pcolor(np.arange(n+1), np.arange(n+1), Z,
> cmap='gray', vmin=0)
>  
> plt.xticks(np.arange(n))
> plt.yticks(np.arange(n))
> plt.grid(ls='solid')
>  
> plt.show()
>  
>  
>  
> The results (some manual zooming) are attached and also available here:
> http://dems.art.pl/files/imshow.png
> http://dems.art.pl/files/pcolor.png
>  
> -- 
> Maciek Dems http://dems.art.pl/en
> --
> Everyone hates slow websites. So do we.
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Re: [matplotlib-devel] Delaying rc3 (again)

2012-10-30 Thread Phil Elson 
> Given the severe weather approaching this area, I
won't have a chance to test and get out an 1.2.0rc3 candidate until at
least Thursday.

Very pleased to see that you have weathered the storm and are back
githubbing!

There are no more PRs in the 1.2.x milestone (
https://github.com/matplotlib/matplotlib/issues?milestone=4&page=1&state=open)
so I think we are in a good state to take a cut at any point.
I would be happy enough to spend the afternoon preparing a release
candidate 3 (though other than tagging and running tests on as many
architectures as possible, I'm not familiar with what is involved) if that
would help? If you would rather wait, I don't think it is a big problem,
the important thing to know is that we are on firm ground and the v1.2.x
branch is in a fantastic state for release.

To everyone who has helped us with testing or bug finding/squashing for
this release so far: Thank you for your hard work and commitment - it
really does make the release so much better as a result.

All the best,

Phil







On 29 October 2012 19:10, Michael Droettboom  wrote:

> Just a quick note: Given the severe weather approaching this area, I
> won't have a chance to test and get out an 1.2.0rc3 candidate until at
> least Thursday.
>
> Mike
>
>
> --
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Re: [matplotlib-devel] Delaying rc3 (again)

2012-10-30 Thread Michael Droettboom 
Agreed!  Thanks to everyone for their hard work.  I think this has 
shaped up to be a great release.


I'm fortunate to have power and connectivity today, so I was able to get 
a release tested, tagged and uploaded.


To our binary builders: as able, it would be great to put the binaries 
up (or send them to me to do so), and then I'll make an announcement on 
matplotlib-users.  I really intend (barring any really serious issues) 
this to be the last rc before the 1.2.0 final.


Thanks again,
Mike

On 10/30/2012 11:28 AM, Phil Elson wrote:

> Given the severe weather approaching this area, I
won't have a chance to test and get out an 1.2.0rc3 candidate until at
least Thursday.

Very pleased to see that you have weathered the storm and are back 
githubbing!


There are no more PRs in the 1.2.x milestone 
(https://github.com/matplotlib/matplotlib/issues?milestone=4&page=1&state=open) 
so I think we are in a good state to take a cut at any point.
I would be happy enough to spend the afternoon preparing a release 
candidate 3 (though other than tagging and running tests on as many 
architectures as possible, I'm not familiar with what is involved) if 
that would help? If you would rather wait, I don't think it is a big 
problem, the important thing to know is that we are on firm ground and 
the v1.2.x branch is in a fantastic state for release.


To everyone who has helped us with testing or bug finding/squashing 
for this release so far: Thank you for your hard work and commitment - 
it really does make the release so much better as a result.


All the best,

Phil







On 29 October 2012 19:10, Michael Droettboom > wrote:


Just a quick note: Given the severe weather approaching this area, I
won't have a chance to test and get out an 1.2.0rc3 candidate until at
least Thursday.

Mike


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Re: [matplotlib-devel] Delaying rc3 (again)

2012-10-30 Thread Russell E. Owen 
In article <[email protected]>,
 Michael Droettboom  
 wrote:

> Agreed!  Thanks to everyone for their hard work.  I think this has 
> shaped up to be a great release.
> 
> I'm fortunate to have power and connectivity today, so I was able to get 
> a release tested, tagged and uploaded.
> 
> To our binary builders: as able, it would be great to put the binaries 
> up (or send them to me to do so), and then I'll make an announcement on 
> matplotlib-users.  I really intend (barring any really serious issues) 
> this to be the last rc before the 1.2.0 final.
> 
> Thanks again,
> Mike

The Mac binaries are now up. This time it built perfectly on MacOS X 
10.4; thanks to the folks that worked so hard fixing those build 
problems.

The 32-bit version is not well tested because I have neither inkscape 
nor ghostscript installed on that ancient system, but it passes the 
tests that it can run under those circumstances.

The 64-bit version passes all tests except 2 knownfail and 3 skipped.

-- Russell

P.S. I had to build the 64-bit version twice. The first time I tried to 
build it using the same directory of code that I used to build 32-bit 
version. I first deleted the "build" and "dist" subdirectories and ran 
"python setup.py clean", then built as usual. There were no errors or 
warnings during the build, but the unit tests would not run on the 
results -- complaining of missing modules.

So I built again using a freshly unpacked code directory and that worked 
just fine.

I'm pretty sure I've seen this problem before, but keep forgetting to 
ask about it.

Is this a bug somewhere (e.g. in matplotlib's setup.py or somewhere in 
python) or is there some better way to clear out a python code directory?


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Re: [matplotlib-devel] Delaying rc3 (again)

2012-10-30 Thread Christoph Gohlke 

On 10/30/2012 8:54 AM, Michael Droettboom wrote:
> Agreed!  Thanks to everyone for their hard work.  I think this has
> shaped up to be a great release.
>
> I'm fortunate to have power and connectivity today, so I was able to get
> a release tested, tagged and uploaded.
>
> To our binary builders: as able, it would be great to put the binaries
> up (or send them to me to do so), and then I'll make an announcement on
> matplotlib-users.  I really intend (barring any really serious issues)
> this to be the last rc before the 1.2.0 final.
>
> Thanks again,
> Mike
>

Looks good: all tests pass on Python 2.6 to 3.3, 32 and 64 bit, on my 
Windows system.

However, the agg_buffer_to_array.py example crashes under some 
circumstances. See 
. Can anyone 
reproduce the crash?

Christoph

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[matplotlib-devel] Fwd: Delaying rc3 (again)

2012-10-30 Thread Damon McDougall 
Whoops! I copied in the users mailing list by accident. Stupid iPhone gmail
app is stupid.

I might have possibly ruined the rc3 surprise. Sorry about that.

-- Forwarded message --
From: *Damon McDougall*
Date: Tuesday, October 30, 2012
Subject: [matplotlib-devel] Delaying rc3 (again)
To: "Russell E. Owen" 
Cc: "[email protected]" <
[email protected]>


On Tuesday, October 30, 2012, Russell E. Owen wrote:

> In article <[email protected]>,
>  Michael Droettboom 
>  wrote:
>
> > Agreed!  Thanks to everyone for their hard work.  I think this has
> > shaped up to be a great release.
> >
> > I'm fortunate to have power and connectivity today, so I was able to get
> > a release tested, tagged and uploaded.
> >
> > To our binary builders: as able, it would be great to put the binaries
> > up (or send them to me to do so), and then I'll make an announcement on
> > matplotlib-users.  I really intend (barring any really serious issues)
> > this to be the last rc before the 1.2.0 final.
> >
> > Thanks again,
> > Mike
>
> The Mac binaries are now up. This time it built perfectly on MacOS X
> 10.4; thanks to the folks that worked so hard fixing those build
> problems.
>
> The 32-bit version is not well tested because I have neither inkscape
> nor ghostscript installed on that ancient system, but it passes the
> tests that it can run under those circumstances.
>
> The 64-bit version passes all tests except 2 knownfail and 3 skipped.
>
> -- Russell
>
> P.S. I had to build the 64-bit version twice. The first time I tried to
> build it using the same directory of code that I used to build 32-bit
> version. I first deleted the "build" and "dist" subdirectories and ran
> "python setup.py clean", then built as usual. There were no errors or
> warnings during the build, but the unit tests would not run on the
> results -- complaining of missing modules.
>
> So I built again using a freshly unpacked code directory and that worked
> just fine.
>
> I'm pretty sure I've seen this problem before, but keep forgetting to
> ask about it.
>
> Is this a bug somewhere (e.g. in matplotlib's setup.py or somewhere in
> python) or is there some better way to clear out a python code directory?
>

Yes! I'm sending you a virtual high five! Thanks for thy Russell.


-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom



-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom
--
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