Problem with .png files?

Community matplotlib-users
1

There appears to be a problem with .png files that matplotlib creates.
Some programs (like GIMP and xv) do not identify them as png
files and cannot display them.

··· 

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2

Bill:

I do not have that problem using mpl-0.90.1 or svn which I checked out and installed yesterday. I have gimp-2.2.17 and have no problems opening them on my linux system or my two XP systems at work. The issue I do find is that when I specify the DPI in the savefig command, it does not properly get encoded into the png, although the size of the graphic is set accordingly. So maybe that is a clue to what's happening to you. You are saving them as "something.png", right ?

Wayne

Bill Dandreta wrote:

···

There appears to be a problem with .png files that matplotlib creates. Some programs (like GIMP <http://www.gimp.org/&gt; and xv) <http://www.trilon.com/xv/&gt; do not identify them as png files and cannot display them.

3

Wayne E. Harlan wrote:

Bill:

I do not have that problem using mpl-0.90.1 or svn which I checked out
and installed yesterday. I have gimp-2.2.17 and have no problems
opening them on my linux system or my two XP systems at work. The
issue I do find is that when I specify the DPI in the savefig command,
it does not properly get encoded into the png, although the size of
the graphic is set accordingly. So maybe that is a clue to what's
happening to you. You are saving them as "something.png", right ?

I discovered the problem, xv and gimp were compiled without png support.

Thanks for your input.

···

--
Bill

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4

Bill Dandreta wrote:

There appears to be a problem with .png files that matplotlib creates. Some programs (like GIMP <http://www.gimp.org/&gt; and xv) <http://www.trilon.com/xv/&gt; do not identify them as png files and cannot display them.

Would you be more specific, please? I can't reproduce the problem. I don't have xv, but on my ubuntu feisty machine the "file" command and gimp both recognize mpl-generated png files (using Agg backend).

Do you have mpl-generated png files that are recognized by some display programs but not by gimp and xv? If so, what are the programs that recognize them? What version of mpl was used, and what backend? Please provide an example.

Eric

5

Eric Firing wrote:

Bill Dandreta wrote:

There appears to be a problem with .png files that matplotlib
creates. Some programs (like GIMP <http://www.gimp.org/&gt; and xv)
<http://www.trilon.com/xv/&gt; do not identify them as png files and
cannot display them.

Would you be more specific, please? I can't reproduce the problem. I
don't have xv, but on my ubuntu feisty machine the "file" command and
gimp both recognize mpl-generated png files (using Agg backend).

Do you have mpl-generated png files that are recognized by some
display programs but not by gimp and xv? If so, what are the programs
that recognize them? What version of mpl was used, and what backend?
Please provide an example.

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

···

--
Bill

wjdandreta@...872...

Gentoo Linux X86_64 2.6.20-gentoo-r8

Reclaim Your Inbox with http://www.mozilla.org/products/thunderbird/

All things cometh to he who waiteth as long as he who waiteth worketh like hell while he waiteth.

6

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

Thanks,

Wayne

Bill Dandreta wrote:

···

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

7

I'll look into this. I actually made a similar fix on another project I used to work on... It should be theoretically possible, barring any roadblocks from how matplotlib is doing things.

Cheers,
Mike

Wayne E. Harlan wrote:

···

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

Thanks,

Wayne

Bill Dandreta wrote:

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

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Michael Droettboom
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Space Telescope Science Institute
Operated by AURA for NASA

8

This is now added in SVN, and only for the Agg backend(s). It won't work with some of the other ways to save PNG files, such as Gdk, Wx (non-Agg) and Cairo. If anyone was any thoughts about how to support saving the resolution in those backends, please share.

Also note that resolution is saved in "dots per meter" in PNG files, so rounding error makes things slightly off -- for instance, 100 dpi is shows up as 99.999998 dpi in the GIMP.

Cheers,
Mike

Michael Droettboom wrote:

···

I'll look into this. I actually made a similar fix on another project I used to work on... It should be theoretically possible, barring any roadblocks from how matplotlib is doing things.

Cheers,
Mike

Wayne E. Harlan wrote:

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

Thanks,

Wayne

Bill Dandreta wrote:

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

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Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

9

Wayne E. Harlan wrote:

I would like to follow up on my first response to Bill. It probably
should be a new thread, but I'll start here. When png files are saved
with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72
(default ?). As I understand it, the dpi setting in the graphics file
tells the application opening it how big to display it. When I use
savefig with a DPI=300 and the plot figure I am saving was created with
figsize=(6,4.5) I expect the figure to open in word or swriter at the
size I specified (6" by 4.5") with the appropriate number of pixels.
However, at present, that does not happen. The number of pixels in the
figure is correct but I have to resize it manually to get the right
size. Can this be fixed ?

This info may or may not be useful. If I save a plot with savefig()
without specifying a figsize, sometimes the figure gets clipped. What
gets saved is the portion of the image that show() displays. I
determined experimentally that figsize=(13,10) causes show() to open the
image at full screen size and so far using that size saves an unclipped
image.

···

--
Bill

wjdandreta@...872...

Gentoo Linux X86_64 2.6.20-gentoo-r8

Reclaim Your Inbox with http://www.mozilla.org/products/thunderbird/

All things cometh to he who waiteth as long as he who waiteth worketh like hell while he waiteth.

10

Bill Dandreta wrote:

Wayne E. Harlan wrote:

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

This info may or may not be useful. If I save a plot with savefig()
without specifying a figsize, sometimes the figure gets clipped. What
gets saved is the portion of the image that show() displays. I
determined experimentally that figsize=(13,10) causes show() to open the
image at full screen size and so far using that size saves an unclipped
image.

Is this with 0.90.1 or a SVN version? What backend are you using?

Cheers,
Mike

···

--
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

11

Not quite. The figure opens at the correct size in the gimp but all I see is background - no plot stuff.

Wayne

Michael Droettboom wrote:

···

This is now added in SVN, and only for the Agg backend(s). It won't work with some of the other ways to save PNG files, such as Gdk, Wx (non-Agg) and Cairo. If anyone was any thoughts about how to support saving the resolution in those backends, please share.

Also note that resolution is saved in "dots per meter" in PNG files, so rounding error makes things slightly off -- for instance, 100 dpi is shows up as 99.999998 dpi in the GIMP.

Cheers,
Mike

Michael Droettboom wrote:

I'll look into this. I actually made a similar fix on another project I used to work on... It should be theoretically possible, barring any roadblocks from how matplotlib is doing things.

Cheers,
Mike

Wayne E. Harlan wrote:

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

Thanks,

Wayne

Bill Dandreta wrote:

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

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12

Hmmm. I'm very surprised that this change could cause that. All it does is add an additional metadata chunk to the PNG file, which shouldn't have any affect on the image data itself. simple_plot.py works fine for me in GIMP 2.0.5 both before and after this change. Can you verify that this plot was working before the change to save the resolution in the PNG file? If so, can you send me the source for your plot and the PNG file? Also, what version of libpng are you using? (pkg-config --version libpng should display this on most recent Linux distros).

Cheers,
Mike

Wayne E. Harlan wrote:

···

Not quite. The figure opens at the correct size in the gimp but all I see is background - no plot stuff.

Wayne

Michael Droettboom wrote:

This is now added in SVN, and only for the Agg backend(s). It won't work with some of the other ways to save PNG files, such as Gdk, Wx (non-Agg) and Cairo. If anyone was any thoughts about how to support saving the resolution in those backends, please share.

Also note that resolution is saved in "dots per meter" in PNG files, so rounding error makes things slightly off -- for instance, 100 dpi is shows up as 99.999998 dpi in the GIMP.

Cheers,
Mike

Michael Droettboom wrote:

I'll look into this. I actually made a similar fix on another project I used to work on... It should be theoretically possible, barring any roadblocks from how matplotlib is doing things.

Cheers,
Mike

Wayne E. Harlan wrote:

I would like to follow up on my first response to Bill. It probably should be a new thread, but I'll start here. When png files are saved with a DPI=300 argument, and I open them in the Gimp, the dpi is only 72 (default ?). As I understand it, the dpi setting in the graphics file tells the application opening it how big to display it. When I use savefig with a DPI=300 and the plot figure I am saving was created with figsize=(6,4.5) I expect the figure to open in word or swriter at the size I specified (6" by 4.5") with the appropriate number of pixels. However, at present, that does not happen. The number of pixels in the figure is correct but I have to resize it manually to get the right size. Can this be fixed ?

Thanks,

Wayne

Bill Dandreta wrote:

I resolved the problem. It was unrelated to mpl. xv and gimp were
complied w/o png support. Recompiling with png support resolved the problem.

-------------------------------------------------------------------------

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Still grepping through log files to find problems? Stop.
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--
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

13

Michael Droettboom wrote:

Bill Dandreta wrote:

This info may or may not be useful. If I save a plot with savefig()
without specifying a figsize, sometimes the figure gets clipped. What
gets saved is the portion of the image that show() displays. I
determined experimentally that figsize=(13,10) causes show() to open the
image at full screen size and so far using that size saves an unclipped
image.

Is this with 0.90.1 or a SVN version? What backend are you using?

dev-python/matplotlib
     Installed versions: 0.90.1 (01:40:48 06/08/07) (doc examples gtk tk)

dev-lang/python
     Installed versions: 2.4.4-r5 (2.4) (19:12:16 09/23/07) (berkdb
-bootstrap -build doc examples gdbm ipv6 ncurses -nocxx -nothreads
readline ssl tk -ucs2)

$ pkg-config --version libpng
0.21

~/.matplotlib/matplotlibrc:
backend : GTKAgg
numerix : numpy
units : True

···

--
Bill

wjdandreta@...872...

Gentoo Linux X86_64 2.6.20-gentoo-r8

Reclaim Your Inbox with http://www.mozilla.org/products/thunderbird/

All things cometh to he who waiteth as long as he who waiteth worketh like hell while he waiteth.

14

Michael:

I tried a complete checkout for comparison (3929). In the meantime, my libpng is 1.2.18 (installed from source as is everything - this is an LFS/BLFS system.) Yes, the plot was working before the change and I can send you some png's from that if you need to see them, or I can backtrack to 0.90.1 and repeat this. Please bear in mind that the plot displays (and always has) quite correctly on screen - it's just the saved file that consists of just background. I have attached the script, the resulting png and a saved screenshot from the Gimp. Attachments are gzipped.

Wayne

Michael Droettboom wrote:

FilterResponse.py.gz (1.92 KB)

FilterResponses.png.gz (456 Bytes)

ScreenShot.png.gz (54.8 KB)

···

Hmmm. I'm very surprised that this change could cause that. All it does is add an additional metadata chunk to the PNG file, which shouldn't have any affect on the image data itself. simple_plot.py works fine for me in GIMP 2.0.5 both before and after this change. Can you verify that this plot was working before the change to save the resolution in the PNG file? If so, can you send me the source for your plot and the PNG file? Also, what version of libpng are you using? (pkg-config --version libpng should display this on most recent Linux distros).

15

Unfortunately, I'm not able to reproduce this here with the .py you attached. Both SVN r3926 (before the PNG resolution change) and SVN r3927 (after the PNG resolution change) work for me. Are you comparing those two SVN revisions, or SVN vs. 0.90.1?

I can confirm that the PNG you attached is all white and fully transparent.

Just for information, my machine (RHEL4) has libpng 1.2.7.

Can you send a copy of your matplotlibrc? Also, can you save out a .raw image? (If you rename it to foo.rgba, you can display these images with the ImageMagick command "display -size 1800x1200 -depth 8 foo.rgba") That would help determine whether the problem is in the PNG-writing code or something higher up.

Cheers,
Mike

Wayne E. Harlan wrote:

···

Michael:

I tried a complete checkout for comparison (3929). In the meantime, my libpng is 1.2.18 (installed from source as is everything - this is an LFS/BLFS system.) Yes, the plot was working before the change and I can send you some png's from that if you need to see them, or I can backtrack to 0.90.1 and repeat this. Please bear in mind that the plot displays (and always has) quite correctly on screen - it's just the saved file that consists of just background. I have attached the script, the resulting png and a saved screenshot from the Gimp. Attachments are gzipped.

Wayne

Michael Droettboom wrote:

Hmmm. I'm very surprised that this change could cause that. All it does is add an additional metadata chunk to the PNG file, which shouldn't have any affect on the image data itself. simple_plot.py works fine for me in GIMP 2.0.5 both before and after this change. Can you verify that this plot was working before the change to save the resolution in the PNG file? If so, can you send me the source for your plot and the PNG file? Also, what version of libpng are you using? (pkg-config --version libpng should display this on most recent Linux distros).
  
--
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA