Can anyone explain this?? >>> N.max(Zdat) #this is numpy.max function 1302.73592859 >>> zdat,x,y = m.transform_scalar (Zdat,lons,lats,nx,ny,returnxy=True,order=0) >>> N.max(zdat) 0.0 >>> In this case, Zdat is my original array sent to my plotting function. It seems to lose all it's data when I run transform_scalar. I've tried it with order=1 as well, with the same result. Am I missing something? I'm having a really hard time getting basemap to work using either imshow or contourf. Any help would be greatly appreciated. Thanks!
John wrote: > Can anyone explain this?? > > >>> N.max(Zdat) #this is numpy.max function > 1302.73592859 > >>> zdat,x,y = > m.transform_scalar(Zdat,lons,lats,nx,ny,returnxy=True,order=0) > >>> N.max (zdat) > 0.0 > >>> > > In this case, Zdat is my original array sent to my plotting function. > It seems to lose all it's data when I run transform_scalar. I've tried > it with order=1 as well, with the same result. Am I missing something? > > I'm having a really hard time getting basemap to work using either > imshow or contourf. Any help would be greatly appreciated. > > Thanks! John: I'll need more info about the Zdat array. It should be a 2-D array on a lat/lon grid whose longitudes (the 2nd dimension) are given by the 1-d array lons, and whose latitudes (the first dimension) are given by the 1-d array lats. lats and lons should be given in degrees. transform_scalar should then return an array of shape (ny,nx) on a regular grid in map projection coordinates. Note that to use contourf you don't have to use transform_scalar, you can just plot the data on the original lat/lon grid. Below is the transform_scalar docstring for reference: def transform_scalar(self,datin,lons,lats,nx,ny,returnxy=False,checkbounds=False,order=1,masked=False): """ interpolate a scalar field (datin) from a lat/lon grid with longitudes = lons and latitudes = lats to a (ny,nx) native map projection grid. Typically used to transform data to map projection coordinates so it can be plotted on the map with imshow. lons, lats must be rank-1 arrays containing longitudes and latitudes (in degrees) of datin grid in increasing order (i.e. from dateline eastward, and South Pole northward). For non-cylindrical projections (those other than cylindrical equidistant, mercator and miller) lons must fit within range -180 to 180. if returnxy=True, the x and y values of the native map projection grid are also returned. If checkbounds=True, values of lons and lats are checked to see that they lie within the map projection region. Default is False. If checkbounds=False, points outside map projection region will be clipped to values on the boundary if masked=False. If masked=True, the return value will be a masked array with those points masked. The order keyword can be 0 for nearest-neighbor interpolation, or 1 for bilinear interpolation (default 1).""" -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-124 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
Jeff, Thanks for the quick reply, below is my plotting code. Here are the answers to your question about my arrray: >>> type(Zdat); type(zdat) <type 'numpy.ndarray'> <type 'numpy.ndarray'> >>> shape(Zdat); shape(zdat) (180, 360) (596, 596) >>> shape(lons); shape(x) (360,) (596, 596) >>> shape(lats); shape(y) (180,) (596, 596) I would like to use contourf, but ultimately I want to plot the log(zdat), and since my data have so many null or zero values, I can't get that to work with contourf, whereas imshow seems to handle it. Thanks!! PLOTTING FUNCTION HERE: def fp_plot(datain): from matplotlib.toolkits.basemap import Basemap, shiftgrid Zdat=datain; n,m=N.shape(Zdat) lons=N.array([i-179.5 for i in range(m)]) lats=N.array([i-89.5 for i in range(n)]) print "The array is bounded: %s : %s lat, %s : %s lon " % (N.min(lats), N.max(lats),N.min(lons),N.max(lons)) # Set up basmap. m = Basemap(llcrnrlon=-180.,llcrnrlat=-90.,urcrnrlon=180.,urcrnrlat=90.0 ,\ rsphere=(6378137.00,6356752.3142),\ resolution='l',area_thresh=1000.,projection='npstere',\ lat_1=80.,lon_0=0., boundinglat=40.) # transform to nx x ny regularly spaced native projection grid nx = int((m.xmax-m.xmin)/20000.)+1; ny = int((m.ymax-m.ymin)/20000.)+1 zdat,x,y = m.transform_scalar(Zdat,lons,lats,nx,ny,returnxy=True) # create the figure. fig=figure(figsize=(12,8)) # add an axes, leaving room for colorbar on the right. ax = fig.add_axes([0.1,0.1,0.7,0.7]) # plot image over map with imshow. Want to use this, but no success yet. anorm=normalize(.015*N.max(zdat),0.95*N.max(zdat)); # Draw flexpart output m.imshow(x,y,zdat) # Draw map components m.drawcoastlines() m.drawcountries() m.drawstates() meridians=arange(-170.,180.,20.) m.drawmeridians(meridians,labels=[1,1,0,0]) paralles=arange(-85.,85.,5.) m.drawparallels(paralles, labels=[0,0,0,1]); show(); Now, to answer your question, Zdat, or datain is a numpy array with the following characteristics:
John wrote: > Jeff, > > Thanks for the quick reply, below is my plotting code. Here are the > answers to your question about my arrray: > > >>> type(Zdat); type(zdat) > <type 'numpy.ndarray'> > <type 'numpy.ndarray'> > >>> shape(Zdat); shape(zdat) > (180, 360) > (596, 596) > >>> shape(lons); shape(x) > (360,) > (596, 596) > >>> shape(lats); shape(y) > (180,) > (596, 596) > > I would like to use contourf, but ultimately I want to plot the > log(zdat), and since my data have so many null or zero values, I can't > get that to work with contourf, whereas imshow seems to handle it. > > Thanks!! > > > > PLOTTING FUNCTION HERE: > > def fp_plot(datain): > from matplotlib.toolkits.basemap import Basemap, shiftgrid > > Zdat=datain; > n,m=N.shape(Zdat) > lons=N.array([i-179.5 for i in range(m)]) > lats=N.array([i-89.5 for i in range(n)]) > print "The array is bounded: %s : %s lat, %s : %s lon " % > (N.min(lats),N.max(lats),N.min(lons),N.max(lons)) > # Set up basmap. > m = > Basemap(llcrnrlon=-180.,llcrnrlat=-90.,urcrnrlon=180.,urcrnrlat= 90.0,\ > rsphere=(6378137.00,6356752.3142),\ > resolution='l',area_thresh=1000.,projection='npstere',\ > lat_1=80.,lon_0=0., boundinglat=40.) > # transform to nx x ny regularly spaced native projection grid > nx = int((m.xmax-m.xmin)/20000.)+1; ny = int((m.ymax-m.ymin)/20000.)+1 > zdat,x,y = m.transform_scalar(Zdat,lons,lats,nx,ny,returnxy=True) > # create the figure. > fig=figure(figsize=(12,8)) > # add an axes, leaving room for colorbar on the right. > ax = fig.add_axes([0.1,0.1,0.7,0.7]) > > # plot image over map with imshow. Want to use this, but no > success yet. > anorm=normalize(.015*N.max(zdat),0.95*N.max(zdat)); > # Draw flexpart output > m.imshow(x,y,zdat) > > # Draw map components > m.drawcoastlines() > m.drawcountries() > m.drawstates() > meridians=arange(-170.,180.,20.) > m.drawmeridians(meridians,labels=[1,1,0,0]) > paralles=arange(-85.,85.,5.) > m.drawparallels(paralles, labels=[0,0,0,1]); show(); > > Now, to answer your question, Zdat, or datain is a numpy array with > the following characteristics: > > > > > John: Looks like some of your message got cut off. Just a few comments so far: 1) you don't need the llcrnrlat,llcrnrlon,urcrnrlat,urcrnrlon args when creating a Basemap instance with projection='npstere'. They should just be ignored though, so I don't think this is the problem. 2) what exactly happens when you run this script? Do you just get an array of zeros for zdat? 3) what happens when you use contourf? It should work just as well as imshow, and would save you the extra interpolation step. pcolor is another option that would not require interpolation. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-124 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
No, it didn't get cut off, I just decided to move that section forward before the code and forgot to delete that line ;) Okay, let's see... 1) Yes, I've left them in for the moment since I saw that they will be ignored, and I'm playing with different projections... seems it doesn't hurt. 2) Yes, it would appear zdat is an array of 0.0 3) With contourf, I get a mismatch... not sure where: ValueError: shape mismatch: objects cannot be broadcast to a single shape File "c:\Python\mod\plotPickle.py", line 30, in <module> fp_plot(z); File "c:\Python\mod\plotf.py", line 55, in fp_plot m.contourf(lons,lats,Zdat) File "c:\Python25\Lib\site-packages\matplotlib\toolkits\basemap\basemap.py", line 2436, in contourf xymask = NX.logical_or(NX.greater(x,1.e20),NX.greater(y,1.e20)) Here is the information about the numpy.arrays I'm using: >>> N.shape(lons);N.shape(lats);N.shape(Zdat) (360,) (180,) (180, 360) I tried: m.contourf(lons,lats,Zdat.transose()) as well, and receive the same error. Thanks again!
Also, I don't know if it's related, but I'm getting this Error / Warning: UnboundLocalError: local variable 'pylab' referenced before assignment Traceback: File "c:\Python25\lib\site-packages\matplotlib\toolkits\basemap\basemap.py", line 2232, in imshow ax = pylab.gca() As my script calls the various basemap.py methods(imshow, drawcoastlines, drawcountries, etc.)
John wrote: > No, it didn't get cut off, I just decided to move that section forward > before the code and forgot to delete that line ;) > > Okay, let's see... > > 1) Yes, I've left them in for the moment since I saw that they will be > ignored, and I'm playing with different projections... seems it > doesn't hurt. > > 2) Yes, it would appear zdat is an array of 0.0 > > 3) With contourf, I get a mismatch... not sure where: > ValueError: shape mismatch: objects cannot be broadcast to a single shape > File "c:\Python\mod\plotPickle.py", line 30, in <module> > fp_plot(z); > File "c:\Python\mod\plotf.py", line 55, in fp_plot > m.contourf(lons,lats,Zdat) > File > "c:\Python25\Lib\site-packages\matplotlib\toolkits\basemap\basemap.py", > line 2436, in contourf > xymask = NX.logical_or(NX.greater(x,1.e20),NX.greater(y,1.e20)) > > Here is the information about the numpy.arrays I'm using: > >>> N.shape(lons);N.shape(lats);N.shape(Zdat) > (360,) > (180,) > (180, 360) > > I tried: m.contourf(lons,lats,Zdat.transose()) as well, and receive > the same error. > > Thanks again! Try adding this just before the contourf call lons, lats = numpy.meshgrid(lons, lats) x, y = m(lons, lats) # map is the Basemap instance then use cs = m.contourf(x,y,zdat) x,y have to be in map projection coordinates, and they must be 2D. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-124 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
Shoot, still getting the error discussed above: ValueError: shape mismatch: objects cannot be broadcast to a single shapeFile "c:07円_jfb\Programming\Python\mod_flexpart\plotPickle.py", line 30, in <module> fp_plot(z); File "c:07円_jfb\Programming\Python\mod_flexpart\plotflex.py", line 55, in fp_plot cs = m.contourf(x,y,zdat) File "c:\Python25\Lib\site-packages\matplotlib\toolkits\basemap\basemap.py", line 2439, in contourf mask = NX.logical_or(ma.getmaskarray(data),xymask) What seems strange, is that after following your instructions: nx = int((m.xmax-m.xmin)/20000.)+1; ny = int((m.ymax-m.ymin)/20000.)+1 zdat,x,y = m.transform_scalar(Zdat,lons,lats,nx,ny,returnxy=True) lons, lats = N.meshgrid(lons, lats) x, y = m(lons, lats) # map is the Basemap instance cs = m.contourf(x,y,zdat) The shape of my zdat no longer fits?? >>> print [N.shape(i) for i in [x,y,zdat]] [(180, 360), (180, 360), (596, 596)]
Hold on, see my errors, trying again....
Well, it seems like I'm making progress, but it's stll not the plot I'm hoping to produce. Something seems strange. First, it does create a contourf plot, but I really need to take log(zdata) and use imshow (which seems to handly the INF issue, wheras contourf crashes). On another issue though, once the image is created, when I draw the map components it covers the image entirely.. so I just see coastlines, meridians, etc on a whilte background as if I had never plotted the data. Thanks for helping with this! I'm really trying to make a movement with my colleagues away from matlab, but I need to have things operating more smoothly... lately it hasn't been going so well. This is a great product you've made!
John wrote: > Well, it seems like I'm making progress, but it's stll not the plot > I'm hoping to produce. Something seems strange. First, it does create > a contourf plot, but I really need to take log(zdata) and use imshow > (which seems to handly the INF issue, wheras contourf crashes). On > another issue though, once the image is created, when I draw the map > components it covers the image entirely.. so I just see coastlines, > meridians, etc on a whilte background as if I had never plotted the data. > > Thanks for helping with this! I'm really trying to make a movement > with my colleagues away from matlab, but I need to have things > operating more smoothly... lately it hasn't been going so well. This > is a great product you've made! John: I think you need to send a self-contained script that triggers the error you are seeing. -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-124 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
John, We actually have the facility for using a log color scale directly, including handling out-of-range values, but I confess I am having a little trouble with it. I can't pursue it right now, but probably can do so this evening. It looks like the problem is a bug, but I am not sure. Eric
John, Attached is a script illustrating how to make contourf plots with a log colorscale. I made some improvements in svn, as noted in the script, but you can still do it with the regular mpl release. All of this should carry through to basemap with no changes in basemap. Eric John wrote: > Well, it seems like I'm making progress, but it's stll not the plot I'm > hoping to produce. Something seems strange. First, it does create a > contourf plot, but I really need to take log(zdata) and use imshow > (which seems to handly the INF issue, wheras contourf crashes). On > another issue though, once the image is created, when I draw the map > components it covers the image entirely.. so I just see coastlines, > meridians, etc on a whilte background as if I had never plotted the data. > > Thanks for helping with this! I'm really trying to make a movement with > my colleagues away from matlab, but I need to have things operating more > smoothly... lately it hasn't been going so well. This is a great product > you've made! > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Thanks Eric... Just a question, I've noticed that if I put enough resolution in lev_exp (ie. lev_exp=arange(0,log10(z.max()),0.15) #or more is even nicer! Then the file size gets quite large due to all the colors. Any suggestions? I know its a separate issue... -john
John wrote: > Thanks Eric... > > Just a question, I've noticed that if I put enough resolution in lev_exp > (ie. lev_exp=arange(0,log10(z.max()),0.15) #or more is even nicer! Then > the file size gets quite large due to all the colors. Any suggestions? I > know its a separate issue... > > -john I don't have any suggestions for reducing file size. What backend are you using? Eric
The default, TkAgg. I've tried the others as I have some strange behavior with TkAgg, but they don't work at all... In fact, I think I'll start another thread, because the problem I have is now predictable... I would be interested to see if there's a solution...