[Matplotlib-users] best way to browse images
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
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Re: [Matplotlib-users] best way to browse images
What is happening is that you are not telling the image to redraw, so you
are only seeing it refresh for other reasons. Try adding a fig.draw() call
prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan jsla...@cfa.harvard.edu
wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
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Re: [Matplotlib-users] best way to browse images
Also, you aren't updating first after the first call, so it is constantly
making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu wrote:
What is happening is that you are not telling the image to redraw, so you
are only seeing it refresh for other reasons. Try adding a fig.draw() call
prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
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Re: [Matplotlib-users] best way to browse images
Hi Ben,
Sorry, in my little example, I left out a few things. I do update first
after the first call. And I do call draw() after other calls. So here is
a more accurate representation of what I do:
first = True
fig = plt.figure()
for file in files:
hdu = fits.open(file)
image = hdu[0].data
hdu.close()
if first:
ax = fig,add_subplot(1,1,1)
im = ax.imshow(image)
plt.show()
first = False
else:
im.set_data(image)
plt.draw()
ans = raw_input('continue?')
if ans == 'n':
break
Jon
On Tue, Oct 14, 2014 at 10:42 AM, Benjamin Root ben.r...@ou.edu wrote:
Also, you aren't updating first after the first call, so it is
constantly making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu wrote:
What is happening is that you are not telling the image to redraw, so you
are only seeing it refresh for other reasons. Try adding a fig.draw() call
prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
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--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
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Re: [Matplotlib-users] best way to browse images
Hmm. I just saw that you suggest fig.draw(). Is there a difference with
plt.draw()?
Jon
On Tue, Oct 14, 2014 at 11:20 AM, Slavin, Jonathan jsla...@cfa.harvard.edu
wrote:
Hi Ben,
Sorry, in my little example, I left out a few things. I do update first
after the first call. And I do call draw() after other calls. So here is
a more accurate representation of what I do:
first = True
fig = plt.figure()
for file in files:
hdu = fits.open(file)
image = hdu[0].data
hdu.close()
if first:
ax = fig,add_subplot(1,1,1)
im = ax.imshow(image)
plt.show()
first = False
else:
im.set_data(image)
plt.draw()
ans = raw_input('continue?')
if ans == 'n':
break
Jon
On Tue, Oct 14, 2014 at 10:42 AM, Benjamin Root ben.r...@ou.edu wrote:
Also, you aren't updating first after the first call, so it is
constantly making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu wrote:
What is happening is that you are not telling the image to redraw, so
you are only seeing it refresh for other reasons. Try adding a fig.draw()
call prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push
notifications.
Take corrective actions from your mobile device.
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--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
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Re: [Matplotlib-users] best way to browse images
Only if there are multiple figures (plt.draw() operates on the current
active figure, while fig.draw() explicitly operates upon that figure).
Another possibility is that the bottleneck truly is the IO. Depending on
exactly how fits work, it might be lazily loading data for you, so the test
without the display of the images might not actually be loading any data
into memory.
Ben Root
On Tue, Oct 14, 2014 at 11:22 AM, Slavin, Jonathan jsla...@cfa.harvard.edu
wrote:
Hmm. I just saw that you suggest fig.draw(). Is there a difference with
plt.draw()?
Jon
On Tue, Oct 14, 2014 at 11:20 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi Ben,
Sorry, in my little example, I left out a few things. I do update first
after the first call. And I do call draw() after other calls. So here is
a more accurate representation of what I do:
first = True
fig = plt.figure()
for file in files:
hdu = fits.open(file)
image = hdu[0].data
hdu.close()
if first:
ax = fig,add_subplot(1,1,1)
im = ax.imshow(image)
plt.show()
first = False
else:
im.set_data(image)
plt.draw()
ans = raw_input('continue?')
if ans == 'n':
break
Jon
On Tue, Oct 14, 2014 at 10:42 AM, Benjamin Root ben.r...@ou.edu wrote:
Also, you aren't updating first after the first call, so it is
constantly making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu wrote:
What is happening is that you are not telling the image to redraw, so
you are only seeing it refresh for other reasons. Try adding a fig.draw()
call prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is
generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push
notifications.
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--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
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Re: [Matplotlib-users] best way to browse images
I've found that, for big images, the *first* draw is very slow, due to the
intensity scaling of the image, which happens at full resolution. Panning
and zooming afterwards is fast because the intensity scaling is cached, but
changing the data array or updating the norm kwarg is slow again. I made
ModestImage (https://github.com/ChrisBeaumont/mpl-modest-image) to deal
with this -- it dynamically downsamples images to screen resolution. This
makes the first draw after updating the data or norm much faster, while
slowing down subsequent redraws. Perhaps this could help you out?
cheers,
chris
On Tue, Oct 14, 2014 at 12:08 PM, Benjamin Root ben.r...@ou.edu wrote:
Only if there are multiple figures (plt.draw() operates on the current
active figure, while fig.draw() explicitly operates upon that figure).
Another possibility is that the bottleneck truly is the IO. Depending on
exactly how fits work, it might be lazily loading data for you, so the test
without the display of the images might not actually be loading any data
into memory.
Ben Root
On Tue, Oct 14, 2014 at 11:22 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hmm. I just saw that you suggest fig.draw(). Is there a difference with
plt.draw()?
Jon
On Tue, Oct 14, 2014 at 11:20 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi Ben,
Sorry, in my little example, I left out a few things. I do update first
after the first call. And I do call draw() after other calls. So here is
a more accurate representation of what I do:
first = True
fig = plt.figure()
for file in files:
hdu = fits.open(file)
image = hdu[0].data
hdu.close()
if first:
ax = fig,add_subplot(1,1,1)
im = ax.imshow(image)
plt.show()
first = False
else:
im.set_data(image)
plt.draw()
ans = raw_input('continue?')
if ans == 'n':
break
Jon
On Tue, Oct 14, 2014 at 10:42 AM, Benjamin Root ben.r...@ou.edu wrote:
Also, you aren't updating first after the first call, so it is
constantly making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu
wrote:
What is happening is that you are not telling the image to redraw, so
you are only seeing it refresh for other reasons. Try adding a fig.draw()
call prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is
generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to
do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push
notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
___
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Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
[Matplotlib-users] v1.4.1rc1
I am happy to announce that I have tagged a release candidate for 1.4.1. This is a bug-fix release which fixes most of the bug that popped up in 1.4.0 including: - setup.py does not die when freetype is not installed - reverts the changes to interactive plotting so `ion` will work as expected - sundry unicode fixes (looking up user folders, importing seaborn/pandas/networkx with macosx backend - fixed boxplot regressions The tarball is available from github, sourceforge and can be install via pip install matplotlib==1.4.1rc1 Tom -- Thomas Caswell tcasw...@gmail.com -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] best way to browse images
Hi Chris,
Thanks for that tip. I'll give it a try. They are big images (2048 x
2048) so it seems like your suggestion should work.
Jon
On Tue, Oct 14, 2014 at 12:18 PM, Chris Beaumont cbeaum...@cfa.harvard.edu
wrote:
I've found that, for big images, the *first* draw is very slow, due to the
intensity scaling of the image, which happens at full resolution. Panning
and zooming afterwards is fast because the intensity scaling is cached, but
changing the data array or updating the norm kwarg is slow again. I made
ModestImage (https://github.com/ChrisBeaumont/mpl-modest-image) to deal
with this -- it dynamically downsamples images to screen resolution. This
makes the first draw after updating the data or norm much faster, while
slowing down subsequent redraws. Perhaps this could help you out?
cheers,
chris
On Tue, Oct 14, 2014 at 12:08 PM, Benjamin Root ben.r...@ou.edu wrote:
Only if there are multiple figures (plt.draw() operates on the current
active figure, while fig.draw() explicitly operates upon that figure).
Another possibility is that the bottleneck truly is the IO. Depending on
exactly how fits work, it might be lazily loading data for you, so the test
without the display of the images might not actually be loading any data
into memory.
Ben Root
On Tue, Oct 14, 2014 at 11:22 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hmm. I just saw that you suggest fig.draw(). Is there a difference
with plt.draw()?
Jon
On Tue, Oct 14, 2014 at 11:20 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi Ben,
Sorry, in my little example, I left out a few things. I do update
first after the first call. And I do call draw() after other calls. So
here is a more accurate representation of what I do:
first = True
fig = plt.figure()
for file in files:
hdu = fits.open(file)
image = hdu[0].data
hdu.close()
if first:
ax = fig,add_subplot(1,1,1)
im = ax.imshow(image)
plt.show()
first = False
else:
im.set_data(image)
plt.draw()
ans = raw_input('continue?')
if ans == 'n':
break
Jon
On Tue, Oct 14, 2014 at 10:42 AM, Benjamin Root ben.r...@ou.edu
wrote:
Also, you aren't updating first after the first call, so it is
constantly making new axes and recalling imshow().
Ben Root
On Tue, Oct 14, 2014 at 10:41 AM, Benjamin Root ben.r...@ou.edu
wrote:
What is happening is that you are not telling the image to redraw, so
you are only seeing it refresh for other reasons. Try adding a fig.draw()
call prior to the raw_input() call.
Cheers!
Ben Root
On Tue, Oct 14, 2014 at 10:03 AM, Slavin, Jonathan
jsla...@cfa.harvard.edu wrote:
Hi all,
In my work lately I have often wanted to browse through a series of
images. This means displaying the image(s), looking at it/them and then
continuing. I have coded this in a few different ways, but it is
generally
pretty slow -- which is to say that the image display takes more than a
couple seconds (~4) after I tell it to continue to the next image. I
tested the loop without image display and it was a factor of ~80 times
faster than it was with image display, so it's doesn't have anything to
do
with reading the images from disk. My latest approach is basically:
first = True
fig = plt.figure()
for file in imagefiles:
# read in image data (fits files)
if first:
ax = fig.add_suplot(1,1,1)
im = ax.imshow(image)
else:
im.set_data(image)
ans = raw_input('continue?')
if ans == 'n':
break
Is there a more efficient way to do this?
Regards,
Jon
--
Jonathan D. Slavin Harvard-Smithsonian CfA
jsla...@cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
fax: (617) 496-7577USA
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Re: [Matplotlib-users] wind vector plot from grb2 files
So, you need to know what tools to use to read in grib2 data? There are two particular grib readers that I am familiar with: PyNIO and pygrib2. PyNIO actually isn't a grib reader, as much as a swiss army knife of file readers. It is very similar to the netcdf4 interface, so if you are familiar with that, then PyNIO is very nice in that respect. Unfortunately, PyNIO is not available through pypi. You have to go directly to their website, sign up and download it directly from them. Oh, and may god have mercy on your soul if you have to build from source for either PyNIO or pygrib2... try the binaries if possible. Ben Root On Tue, Oct 14, 2014 at 1:09 AM, Sourav Chatterjee srv@gmail.com wrote: Can somebody help me to plot the wind vectors in spstere projection reading data from a grb2 file *without using Dataset (netcdf4*)? Thanks Sourav -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
