[Matplotlib-users] matshow unequal element sizes
Hi all, I am trying to draw a heatmap using matshow, which I then save as a PDF. If I then zoom in in the PDF, I notice that different rows have different sizes, and different columns have different sizes. It seems that some rows/columns have twice the height/width as other rows/columns. Attached is a screenshot of part of the PDF after zooming in. Is there some way to force all rows / columns to have the same height/width? Best, -Michiel. attachment: image.PNG-- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow unequal element sizes
By default (when interpolation=nearest) matplotlib is performing nearest neighbor interpolation on the image to the request PDF dpi before storing it in the file. This results in rows and columns of unequal size because the ratio from the original image to the destination resolution is likely not integral. You can set interpolation=none, which will pass the original image as-is on to the file, but then we can't control the interpolation mode (since there's no way to tell the PDF viewer what sort of interpolation to perform), so that (usually) will result in bicubic interpolation, which is probably not what you want. Mike On 06/06/2013 05:52 AM, Michiel de Hoon wrote: Hi all, I am trying to draw a heatmap using matshow, which I then save as a PDF. If I then zoom in in the PDF, I notice that different rows have different sizes, and different columns have different sizes. It seems that some rows/columns have twice the height/width as other rows/columns. Attached is a screenshot of part of the PDF after zooming in. Is there some way to force all rows / columns to have the same height/width? Best, -Michiel. -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow unequal element sizes
Thanks! Using pcolor indeed solved the problem. Now my rows and columns are all nice and even. Best, -Michiel. From: Benjamin Root ben.r...@ou.edu To: Michael Droettboom md...@stsci.edu Cc: Matplotlib Users matplotlib-users@lists.sourceforge.net Sent: Friday, June 7, 2013 1:40 AM Subject: Re: [Matplotlib-users] matshow unequal element sizes On Thu, Jun 6, 2013 at 10:14 AM, Michael Droettboom md...@stsci.edu wrote: By default (when interpolation=nearest) matplotlib is performing nearest neighbor interpolation on the image to the request PDF dpi before storing it in the file. This results in rows and columns of unequal size because the ratio from the original image to the destination resolution is likely not integral. You can set interpolation=none, which will pass the original image as-is on to the file, but then we can't control the interpolation mode (since there's no way to tell the PDF viewer what sort of interpolation to perform), so that (usually) will result in bicubic interpolation, which is probably not what you want. Mike From experience, it seems that pcolor() or pcolormesh() works best for pdf's because it saves the polygons. You might need some tweaking to get it exactly right, but at least the pdf viewer won't smudge it all out. Cheers! Ben Root -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users-- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] matshow / imshow with date-axis
Hi, is it possible to perform a surface plot a NxM matrix with date-axes? Similar to plot_date for 1D-Plots. The dates are available as an N-sized (or M-sized) array of float values. At the moment, I am using imshow or matshow for the color plots, but the only way I found to manipulate the axes is the 'extent' keyword argument, which is not sufficient in this context. Any hints? Micha -- View this message in context: http://old.nabble.com/matshow---imshow-with-date-axis-tp28068228p28068228.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow / imshow with date-axis
On Monday 29 March 2010 13:56:51 Atomfried wrote: Hi, is it possible to perform a surface plot a NxM matrix with date-axes? Similar to plot_date for 1D-Plots. The dates are available as an N-sized (or M-sized) array of float values. At the moment, I am using imshow or matshow for the color plots, but the only way I found to manipulate the axes is the 'extent' keyword argument, which is not sufficient in this context. Any hints? Micha Hi Micha, Did you already set the date-xaxis by hand? - for axes 'ax' using e.g. ax.xaxis_date(tz=None) ax.yaxis_date(tz=None) I would hope that extent and this together yield your aim, but I'm not so familiar with date-axes. Kind regards, Mattthias -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow / imshow with date-axis
Hi Matthias, Thanks for the help. The problem is, however, that the 'extent' parameter only manipulates the range of the (integer) values on the axis. Before setting the *axis_date property, I need to set the axes data to arrays of (non-equidistant) floats. Best Regards, Micha Matthias Michler wrote: Did you already set the date-xaxis by hand? - for axes 'ax' using e.g. ax.xaxis_date(tz=None) ax.yaxis_date(tz=None) -- View this message in context: http://old.nabble.com/matshow---imshow-with-date-axis-tp28068228p28070890.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow
On Thu, Sep 17, 2009 at 2:49 AM, Bala subramanian
bala.biophys...@gmail.com wrote:
Friends,
I have a matrix data and i used matshow() function to plot. The plot is
attached.
1) After plotting the data, i used xticks() function to change the x-axis
tick labels from x1 to x12 ( figure attached). Similarly I want to change
the y-axis tick labels into as A,B and C, instead of 0,1,2 (in the attached
figure) but when i use yticks() function as below, it dosent happen, instead
it changes the plot.
yticks( arange(3), ('A','B','C'))
Can you post a complete code (a simplified version that reproduces the
problem)? I have done some simple tests but it worked as expected.
Also, please report the version number of your mpl installation.
2) I used the colormap cm.autumn to create the plot. Suppose if i want to
generate the same plot with green,black, red combination, how should i
specify the colors in matshow.
If none of the mpl's colormaps fits your need, you need to create your
own colormap.
Maybe the links below will be helpful.
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps
-JJ
Thanks in advance.
Bala
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[Matplotlib-users] matshow
Friends,
I have a matrix data and i used matshow() function to plot. The plot is
attached.
1) After plotting the data, i used xticks() function to change the x-axis
tick labels from x1 to x12 ( figure attached). Similarly I want to change
the y-axis tick labels into as A,B and C, instead of 0,1,2 (in the attached
figure) but when i use yticks() function as below, it dosent happen, instead
it changes the plot.
yticks( arange(3), ('A','B','C'))
2) I used the colormap *cm.autumn* to create the plot. Suppose if i want to
generate the same plot with green,black, red combination, how should i
specify the colors in matshow.
Thanks in advance.
Bala
attachment: test.png--
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Re: [Matplotlib-users] matshow?
Thanks again Eric for the updated matshow(). I apologise for repeating: Since it has been decided (has it?) that matshow will retain the feature that a new figure is created (with aspect ratio matching the matrix), then if one adds a colorbar (a typical thing to do), the matrix height is smaller than the colorbar, which is not visually appealing. Also, it is fairly common to desire combining a matrix visualisation with other plots, and hence the new figure becomes an issue. Of course, I guess one could use Axes.matshow() now to avoid the above. If that is to be the case, fine. One very minor thing to note: the new matshow() is missing ticks on the lower x-axis. Thanks again for the excellent support for a function that clearly a lot of people are using. Cheers, Suresh - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow?
Fernando Perez wrote:
[...]
Frankly, I don't care how it's done: I wrote matshow long ago, back
when axis('scaled') didn't exist in the first place. If the same
result can be achieved by other means that are cleaner, I'm sure John
will accept a patch.
One of the matshow anomalies is that it is a pylab function only instead
of a wrapper for an Axes method, so I made a new Axes.matshow(), and a
temporary matshow1() pylab function that calls it. Differences between
matshow() and matshow1():
1) The latter labels the *centers* of the squares representing the
matrix elements, starting from zero. Tick values are consequently integers.
2) matshow1 uses the same function as matshow (figaspect()) to determine
the window dimensions, but keeps the matrix elements square when they
would be stretched in matshow. I can change this back to the matshow
behavior if desired.
All I need regularly in my work is the ability to plot a matrix such
that both the axis AND the enclosing figure (which determines the size
of the resulting EPS files for publications or talks) have the aspect
ratio of the actual matrix. How that result is achieved is really
immaterial to me.
I suspect that what you would actually prefer is better automated figure
sizing so that it would always nicely enclose the axes with their
labels, titles, etc., correct? There is nothing magic about having the
actual aspect ratio of the figure exactly match that of the axes box?
(Not that I can easily achieve the nice wrapping result--this is just to
clarify the ideal.)
matshow does what I need so I use it, but I have no particular
attachment to the code other than the fact that it happens to work
correctly. That's a bonus in my book.
Absolutely!
Another anomaly of matshow (presently preserved in matshow1) is the
returnall kwarg; this seems like the sort of thing that should either be
supported by all pylab functions, or by none. The argument for none is
that one can easily use gcf() and gca() to get the other two arguments.
Do you want to keep the returnall kwarg?
Eric
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[Matplotlib-users] matshow?
Why does pylab.matshow() create a new figure by default when no other standard pylab function I know of does that? It seems very inconsistent for no particular gain, since as always figure();matshow(m) will achieve that result if that is what is desired. --bb - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] matshow?
On 3/17/07, Bill Baxter [EMAIL PROTECTED] wrote:
A pox on matplotlib's default reply-to-sender!
Resending my reply that went to Fernando alone below.
On 3/17/07, Fernando Perez [EMAIL PROTECTED] wrote:
On 3/16/07, Bill Baxter [EMAIL PROTECTED] wrote:
Why does pylab.matshow() create a new figure by default when no other
standard pylab function I know of does that? It seems very
inconsistent for no particular gain, since as always
figure();matshow(m) will achieve that result if that is what is
desired.
No: matshow has to create a figure with a non-standard size so that
the final figure has the same aspect ratio as the array being
displayed. If you call figure() first, the figure has already been
created.
The code:
# Extract actual aspect ratio of array and make appropriately sized
figure
w,h = figaspect(arr)
fig = figure(fignum,figsize=(w,h))
I guess that makes sense.
Personally I'd rather have consistency. I'm not sure why matshow() in
particular needs to have the window shape match the image shape.
Why not just do axis('scaled') within the confines of the window you have?
Tried it out, it seems to work pretty well, and seems more consistent
with the way other things work in pylab.
def mymatshow(*args,**kw):
Display an array as a matrix in a new figure window.
The origin is set at the upper left hand corner and rows (first dimension
of the array) are displayed horizontally. The aspect ratio of the figure
window is that of the array, as long as it is possible to fit it within
your screen with no stretching. If the window dimensions can't accomodate
this (extremely tall/wide arrays), some stretching will inevitably occur.
Tick labels for the xaxis are placed on top by default.
matshow() calls imshow() with args and **kwargs, but by default it sets
interpolation='nearest' (unless you override it). All other arguments and
keywords are passed to imshow(), so see its docstring for further details.
Special keyword arguments which are NOT passed to imshow():
- fignum(None): by default, matshow() creates a new figure window with
automatic numbering. If fignum is given as an integer, the created
figure will use this figure number. Because of how matshow() tries to
set the figure aspect ratio to be the one of the array, if you provide
the number of an already existing figure, strange things may happen.
- returnall(False): by default, the return value is a figure instance.
With 'returnall=True', a (figure, axes, image) tuple is returned.
Example usage:
def samplemat(dims):
aa = zeros(dims)
for i in range(min(dims)):
aa[i,i] = i
return aa
dimlist = [(12,12),(128,64),(64,512),(2048,256)]
for d in dimlist:
fig, ax, im = matshow(samplemat(d))
show()
# Preprocess args for our purposes
arr = asarray(args[0])
# Extract unique keywords we can't pass to imshow
kw = kw.copy()
fignum = popd(kw,'fignum',None)
retall = popd(kw,'returnall',False)
# Extract actual aspect ratio of array and make appropriately sized figure
w,h = figaspect(arr)
#fig = figure(fignum,figsize=(w,h))
fig = gcf()
cla()
ax = fig.add_axes([0.15, 0.09, 0.775, 0.775])
axis('scaled')
ax.xaxis.tick_top()
ax.title.set_y(1.05) # raise it up a bit for tick top
kw['aspect'] = 'auto'
# imshow call: use 'lower' origin (we'll flip axes later)
kw['origin'] = 'lower'
# Unless overridden, don't interpolate
kw.setdefault('interpolation','nearest')
# All other keywords go through to imshow.
im = ax.imshow(*args,**kw)
gci._current = im
# set the x and y lim to equal the matrix dims
nr,nc = arr.shape[:2]
ax.set_xlim((0,nc))
ax.set_ylim((nr,0))
draw_if_interactive()
if retall:
return fig, ax, im
else:
return fig
--bb
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