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Hello all 

Can any one explain me how can I use griddata in matplotlib for 2-d interpolation of polar to cartesian co-ordinates.
I have two 1D arrays r and theta of 128 and 64 cells respectively
I have a 2D array temperature T(r,theta) with (128, 64) cells. I would like to have Tnew(200,200) cells in cartesian coordinates x = r*cos(th) and y = r*sin(th)

for the same I use

Tnew = griddata(x,y,T,xi,yi) .... 

and x = outer(r,cos(th)) and y=outer(r,sin(th))
where xi,yi = mgrid[x.min():x.max():200j,y.min():y.max():200j]


I get a ValueError suggesting that griddata does not like to have 2D arrays of x and y 

How can I get this to work?

Regards
Bhargav Vaidya
 

Hi all,

After trying several ways around this problem, I've found a solution
that is pretty straightforward and produces nice results.  The problem
I'm referring to is that when I saved my figures as encapsulated
PostScript for inclusion in a LaTeX document, the figures came out
missing certain text when the document is converted to pdf (e.g. using
dvipdf on the dvi file or ps2pdf on the ps file created using dvips).  

One solution is to set the rcParams['text.usetex'] = True, but that
leads to a different font (serif) used for the numbers and for the axis
labels (there are ways around that also...)  But the best way that I've
found is to save the figures as pdf and then convert them to eps by
using pdftops with the -eps flag.  You do lose transparency that way,
but the figure, including text, looks good.  You can also use the
convert command from the ImageMagick package to do the pdf to eps
conversion, which maintains the transparency at the cost of a worse
looking figure (bitmapped) overall.

It'd be nice to know exactly why this problem occurs in the first place.
I assume it has to do with the interaction of pdf with some fonts used
in mathtext.

Jon 
-- 
______________________________________________________________
Jonathan D. Slavin              Harvard-Smithsonian CfA
js...@cf...         60 Garden Street, MS 83
phone: (617) 496-7981           Cambridge, MA 02138-1516
 cell: (781) 363-0035           USA
______________________________________________________________

I could already answer one question by myself about the top margin in
gridspec.

'''1) I would like to reduce the top margin. For that I though I can do
something like this:
gs = gridspec.GridSpec(2, 1, width_ratios=[2,1])

- gs.update(bottom=0.2, left=0.2, hspace=0.05)
+ gs.update(bottom=0.2, left=0.2, hspace=0.05, top=0.1)

But I get an error ""ValueError: bottom cannot be >= top"". This
limitation is not clear to me, why is this so?'''


So if I want a top margin of 0.1*figure height I would have to specify
	>>> top = 0.9
So "top" is the absolute distance of the top plot edge from the lower
figure edge. 1.0 would make the plot extend to the top edge.

Looking back I must say that
http://matplotlib.sourceforge.net/api/gridspec_api.html#matplotlib.gridspec.GridSpecBase
is not very helpful. And it is very counter-intuitive to the Axes
dimension specification with location lower left and width/height
	>>> plt.axes([0.1, 0.1, 0.8, 0.8])

To clarify I created a small illustration.

On Tue, Aug 16, 2011 at 7:12 PM, Andre' Walker-Loud <wal...@gm...>wrote:

> Hi All,
>
> A question for a possible new feature for Matplotlib.
>
> First, in case there is a way to do it currently:
>
> I often find myself plotting data with errorbars, and I would like to be
> able to modify the marker, or marker size of each individual point
> separately.  A (seemingly to me) natural way to do this would allow
>
> marker
> markersize
> markerfacecolor
> markeredgecolor
>
> etc accept arrays, as well as a single kwarg.  As far as I can tell, if I
> have a set of data, and I want to make the markers with different sizes, the
> only way to do this is have a loop that calls each data point individually
> and assigns the marker features.
>

That's how I would do it right now.


>
> 1 - am I mistaken?  and if so, could someone instruct me how to achieve my
> goal
>
> 2 - does anyone else find this feature desirable?  If so, could this be
> added to Matplotlib?  I have not the coding experience to attempt this
> myself - but I imagine the simplest thing to do would be check if the
> marker, ms, etc are given single kwargs, or arrays.  If single, everything
> happens as now.  If array, then check the len of the array against the len
> of the data, and if the same, match the entries.
>
>
I personally would love to see more consistent support for features like
this across all plotting and collection types.  However, there are some
issues that prevent making this an easy fix.  The primary issue is
distinguishing user intent with respect to colors.  Right now, a user could
specify color as a string or a rgb tuple.  Now, if we accept an array of
those things, it becomes harder to determine the user's intent.

The way forward, I think, is some sort of decorator library (dbook.py?) that
provides a common set of methods that all plotting and collection functions
could use to consistently prepare input data.

I encourage you to file a feature request on github, but for now, the best
way seems to be looping the errorbar call.

Cheers,
Ben Root

Hi,

I want to have two plots above each other with shared y-axis. For this I
am using gridspec to adjust the vertical distance between the graphs.

Attached is a .pdf with the current results. Two problems:

1) I would like to reduce the top margin. For that I though I can do
something like this:
gs = gridspec.GridSpec(2, 1, width_ratios=[2,1])

- gs.update(bottom=0.2, left=0.2, hspace=0.05)
+ gs.update(bottom=0.2, left=0.2, hspace=0.05, top=0.1)

But I get an error ""ValueError: bottom cannot be >= top"". This
limitation is not clear to me, why is this so?


2) I want to make a shared y-axis label. I found this page:
http://www.scipy.org/Cookbook/Matplotlib/Multiple_Subplots_with_One_Axis_Label
But any additional axis I put before the gridspec axis is not shown in
the end. Is there a special procedure that can be used together with
gridspec?





Below the code I use for the figure:

################################
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec

# Import data into numpy ndarray
tung = np.loadtxt('tungsten_profiles_leveled.txt')
insu = np.loadtxt('insulator_profiles_leveled.txt')
   
fig_width_pt = 270 
fig_height_pt = 220
inches_per_pt = 1.0/72.27               # Convert pt to inches
fig_width = fig_width_pt*inches_per_pt  # width in inches
fig_height =fig_height_pt*inches_per_pt       # height in inches
fig_size = [fig_width,fig_height]

# Settings for fitting LaTeX style
plt.rc('font',**{'family':'serif','serif':['Computer Modern Roman']})
params = {'backend': 'ps',
          'text.latex.preamble': [r"\usepackage{upgreek}"],
          'axes.labelsize': 10,
          'text.fontsize': 10,
          'legend.fontsize': 8,
          'xtick.labelsize': 8,
          'ytick.labelsize': 8,
          'text.usetex': True,
          'figure.figsize': fig_size,
          'axes.unicode_minus': True}
plt.rcParams.update(params)

#######
plt.figure(1)
plt.clf()

gs = gridspec.GridSpec(2, 1, width_ratios=[2,1])
gs.update(bottom=0.2, left=0.2, hspace=0.05, top=0.1)

ax1 = plt.subplot(gs[0])
plt.ylabel(r'Height (nm)', labelpad = 12)
for i in range(len(tung[:][0])/2):
    ax1.plot(tung[:,i*2]*1e6-0.3, tung[:,1+i*2]*1e9,linewidth=1)
plt.ylim(-1,11)
plt.yticks([0, 2, 4, 6, 8, 10])
leg = ax1.legend(('Profile 1', 'Profile 2', 'Profile 3', 'Profile 4',
                  'Profile 5', 'Profile 6', 'Profile 7'),
                  shadow=True, loc = (1.1,-0.5))
plt.setp(ax1.get_xticklabels(), visible=False)
ax1.annotate(r'\bf Tungsten', xy=(0,10),
                xycoords='data',   # <-- check webpage for different
coordinate systems
                horizontalalignment='left', verticalalignment='top',
                fontsize=10)

ax2 = plt.subplot(gs[1], sharex = ax1)
for i in range(len(insu[:][0])/2):
    ax2.plot(insu[:,i*2]*1e6-0.3, insu[:,1+i*2]*1e9,linewidth=1)
plt.xlim(-0.1,2.1)
plt.ylim(-1,11)
plt.yticks([0, 2, 4, 6, 8, 10])
plt.xlabel(r'Position ($\upmu$m)', labelpad = 12)
plt.ylabel(r'Height (nm)', labelpad = 12) # r for raw
ax2.annotate(r'\bf Insulator', xy=(0,10),
                xycoords='data',   # <-- check webpage for different
coordinate systems
                horizontalalignment='left', verticalalignment='top',
                fontsize=10)


#plt.show()
plt.savefig('line_profiles.pdf')

Hey guys,


I was hoping someone could provide a hint for how I should go about correcting this. As you can see, locations for the inline labels for 
contours in this image are unfortunately chosen, and they overlap with one another. If I set manual to 'True' then I get this weird behavior 
where I can only choose labels in the top left grid and nothing is shownin any of the other grids.

I am using a 2x2 Image Grid (I get the same problem when using gridspec instead of image grid), and loadingcontour data (2x2 array) from a file.

Thanks for your help,
Ron

Thanks a lot John and Benjamin for your help.

The Proxy Artist approach fits the bill perfectly.

I used the following code to make a legend from my color_lut lookup table.


# Lookup table for color
col_lut = dict(Bistris7p2 = "burlywood", Cit7p2 = "c",APhosph8p0 = "m",
Acetate5p5 = "k",Borate8p5 = "y",Mes6p7 = "c",Hep8p2 = "g",ATris9p0 = "r")

for key,value in col_lut.items():
    legend_box.append(Rectangle((0,0),1,1,fc="%s" % value))
    legend_text.append(key)
ax.legend(legend_box, legend_text)


Hari


On Wed, Aug 17, 2011 at 7:23 PM, John Hunter <jd...@gm...> wrote:

> On Wed, Aug 17, 2011 at 5:30 PM, hari jayaram <ha...@gm...> wrote:
> > Thanks for your email Ben. Sorry I am still lost.
> >
> > I dont understand what the handles type is . In my example I guess the
> > handles are an array of circles representing each x,y,z point.I am still
> a
> > little lost since the plot autmatically plots my 3 arrays
> > The color of each circle is arbitrary and stored a the color array.
> > Even after looking at the examples I dont know how to construct
> > my plt.legend() call.
>
> Take a look at the proxy artist section of the legend guide and see if
> that helps
>
>
> http://matplotlib.sourceforge.net/users/legend_guide.html#using-proxy-artist
>
> JDH
>

cool,

On Wed, Aug 17, 2011 at 5:15 PM, Benjamin Root <ben...@ou...> wrote:
> On Wed, Aug 17, 2011 at 7:01 PM, Mathew Yeates <mat...@gm...> wrote:
>>
>> Here is how to do it
>>    display=mainwindow.get_display()
>>    screen = gtk.gdk.Display.get_default_screen(display)
>>    x,y=mainwindow.get_pointer()
>>    s,x,y,m = display.get_pointer()
>>    gtk.gdk.Display.warp_pointer(display, screen,x+1,y)
>>
>
> Ok, glad that works for you.  For reference, the email I was referring to is
> here:
>
> http://www.mail-archive.com/mat...@li.../msg08321.html
>
> The toolkit offers a bunch of other tools for scripting out interaction, in
> case anybody cares about that sort of thing. (actually, might be a good idea
> to consider adding stuff like that to the testing suite...)
>
> Ben Root
>
>

On Wed, Aug 17, 2011 at 7:01 PM, Mathew Yeates <mat...@gm...> wrote:

> Here is how to do it
>    display=mainwindow.get_display()
>    screen = gtk.gdk.Display.get_default_screen(display)
>    x,y=mainwindow.get_pointer()
>    s,x,y,m = display.get_pointer()
>    gtk.gdk.Display.warp_pointer(display, screen,x+1,y)
>
>
Ok, glad that works for you.  For reference, the email I was referring to is
here:

http://www.mail-archive.com/mat...@li.../msg08321.html

The toolkit offers a bunch of other tools for scripting out interaction, in
case anybody cares about that sort of thing. (actually, might be a good idea
to consider adding stuff like that to the testing suite...)

Ben Root

Here is how to do it
    display=mainwindow.get_display()
    screen = gtk.gdk.Display.get_default_screen(display)
    x,y=mainwindow.get_pointer()
    s,x,y,m = display.get_pointer()
    gtk.gdk.Display.warp_pointer(display, screen,x+1,y)

On Wed, Aug 17, 2011 at 11:53 PM, Mathew Yeates <mat...@gm...> wrote:
> I'm looking for something like
> ---------
> display = gdk_display_get_default ();
>    screen = gdk_display_get_default_screen (display);
>
>    /* get cursor position */
>    gdk_display_get_pointer (display, NULL, &x, &y, NULL);
>
>    /* set new cusor position */
>    x += xadd;
>    y += yadd;
>    gdk_display_warp_pointer (display, screen, x, y);
>
> On Wed, Aug 17, 2011 at 11:52 PM, Benjamin Root <ben...@ou...> wrote:
>>
>>
>> On Wednesday, August 17, 2011, Mathew Yeates <mat...@gm...> wrote:
>>> Does anyone have an example showing how to change the cursor position
>>> using the key pad instead of the mouse?
>>>
>>>
>>> -Mathew
>>>
>>
>> Are you talking about externally to mpl or within mpl?  I have some code
>> from a couple of months ago that automated graph interaction that allowed me
>> to exactly reproduce various actions so I could profile the execution.
>>
>> It uses the Gtk accessibility framework to control the mouse.
>>
>> Ben Root
>