De Pauw Antoine wrote: > Thanks Jeff, > > This seems to work with csv file types, and I've been experimenting a bit > with it > > However, when I try to implement this with my original code (with binary > files), I get an error like that one: > > Traceback (most recent call last): > File "C:\Python25\Projects\FigPlot\FigPlot.py", line 39, in <module> > x,y = map(Lon,Lat) > TypeError: 'numpy.ndarray' object is not callable > > I think this is coming from the fact I use array objects to store values... > could you confirm it? >
Antoine: It looks like you the object map is not a Basemap instance, but a numpy array. Try putting 'print type(map)' just ahead of this statement to verify this. I suspect your re-using the name 'map' in your code, overwriting the Basemap class instance. -Jeff > Also, I'll see if it is possible to invert color scale and mask everything > under a certain value > > Thanks very much for your help! > > Antoine De Pauw > Collaborateur de recherches, Informatique - Research collaborator, IT > Laboratoire de chimie quantique et photophysique - Quantum chemistry and > photophysics laboratory > Université Libre de Bruxelles - ULB > > > -----Original Message----- > From: Jeff Whitaker [mailto:[EMAIL PROTECTED] > Sent: jeudi 11 septembre 2008 14:10 > To: De Pauw Antoine > Cc: 'Matplotlib Users' > Subject: Re: [Matplotlib-users] Information request > > De Pauw Antoine wrote: > >> Hi Jeff, >> >> I have put the code online with a sample of the data here: >> >> http://snipplr.com/view/8307/map-plotting-python-code-temporary/ >> >> I hope you'll be able to give me some advice as it is quite difficult for >> someone new in python and scientific computation >> >> Antoine De Pauw >> Collaborateur de recherches, Informatique - Research collaborator, IT >> Laboratoire de chimie quantique et photophysique - Quantum chemistry and >> photophysics laboratory >> Université Libre de Bruxelles - ULB >> >> > > Antoine: I may have the size of the pixels wrong, and lat/lon > transposed, but this is the general idea: > > from mpl_toolkits.basemap import Basemap > import matplotlib.pyplot as plt > import numpy as np > lats = []; lons = []; data = [] > for line in open('pixels.dat'): > linesplit = line.split(',') > lons.append(float(linesplit[1])) > lats.append(float(linesplit[0])) > data.append(float(linesplit[2])) > map = > Basemap(projection='mill',llcrnrlat=min(lats)-5,urcrnrlat=max(lats)+5,\ > > urcrnrlon=max(lons)+5,llcrnrlon=min(lons)-5,resolution='l') > x,y = map(lons,lats) > plt.scatter(x,y,s=25,c=data,marker='s',edgecolor="None",cmap=plt.cm.jet) > plt.colorbar(shrink=0.6) > map.drawcoastlines() > plt.show() > > -Jeff > > >> -----Original Message----- >> From: Jeff Whitaker [mailto:[EMAIL PROTECTED] >> Sent: mercredi 10 septembre 2008 16:45 >> To: Antoine De Pauw >> Cc: Matplotlib Users >> Subject: Re: Information request >> >> Antoine De Pauw wrote: >> >> >>> Thanks Jeff, >>> >>> In fact my points are arranged in three unsorted arrays, with a simple >>> >>> >> scheme (thats why I couldn't plot them with imshow and others) >> >> >>> arrays: >>> >>> [lat][lon][val] >>> [-10][ 17][0.3] >>> [ 37][ 23][3.7] >>> ... ... ... >>> >>> and so for many rows... >>> >>> what I have to do is looping through my arrays like that >>> >>> while i < rowcount: >>> plot_to_map(lat[i],lon[i],val[i]) >>> >>> it is evidently an idea of how it could be done easily but my knowledge >>> > of > >>> >>> >> these libraries is too weak for me to figure out how to do it >> >> >>> my data comes from huge binary files but is extremely simple, so it would >>> >>> >> be really easy for anyone to help me as the problem itself is how to put >> unsorted points on the map with latitude and longitude coordinates >> >> >> Antoine: You haven't said if your data forms a rectangular array. If >> so, you can build a 2-d array from the input file and plot it with >> imshow. If not, you can still plug the elements into a 2-d masked >> array, leaving the missing pixels masked. You say the points are >> 'unsorted', does that mean they are randomly distributed and do not form >> a rectangular grid? >> >> It would really be much easier to help if you gave us more information, >> such as how the data is structured, what the pixel footprint is, etc. >> Perhaps you could post the binary file on an ftp site somewhere with >> code to read it. >> >> Also, please hit 'reply all' when replying, so the matplotlib users >> mailing list is CC'ed. >> >> -Jeff >> >> >>>> Antoine De Pauw wrote: >>>> >>>> >>>>> Sir, >>>>> >>>>> I'm sorry, as english is not my mothertongue and it is sometimes >>>>> >>>>> >> difficult to be understandable. >> >> >>>>> All is in the script I gave to you initially, except the point drawing >>>>> >>>>> >> code which would be useless as it is proven not to work (I dont know the >> method to do it). >> >> >>>>> What I have is a map, and a set of pixels I have to put on it with >>>>> >>>>> >> geographic coordinates. >> >> >>>>> I cannot find the right method to put colour pixels on the map, that's >>>>> >>>>> >> the problem. >> >> >>>>> I have that map in miller projection, and three arrays containing >>>>> >>>>> >> respectively latitude, longitude and satellite measured value. >> >> >>>>> What I need to obtain is something approximately like this: >>>>> >>>>> > http://www.oma.be/BIRA-IASB/Molecules/SO2archive/info/background/so2sc200703 > >> _00_lr.gif but with the basemap toolkit. >> >> >>>>> So, my question is: how could I do to plot a coloured pixel at >>>>> >>>>> >> coordinates lat:lon on that map? If I have just the method to project a >> geographic coordinate on the map and put a coloured pixel at the right >> place, all is done and I just have to loop my arrays... Also, I would have >> to implement some antialiasing on the map. >> >> >>>>> >>>>> >>>>> >>>> Antoine: >>>> >>>> Are the pixels arranged on a regular grid - or are they randomly >>>> distributed? If they are on a grid, it's easy (using pcolor or imshow). >>>> > > >>>> If you could send me your data I may be able to get you started. >>>> >>>> (I'm cc'ing the matplotlib list so others can join in the discussion). >>>> >>>> >>>> -Jeff >>>> >>>> >>>>> If this is not possible to do it in a simple and explainable way, >>>>> > please > >>>>> >>>>> >> tell me and I'll continue using matlab or searching for the bit of code >> which will save me >> >> >>>>> Anyway, I have to thank you for your interest to help me.. >>>>> >>>>> Many thanks, >>>>> >>>>> Antoine De Pauw >>>>> >>>>> >>>>> >>>>> >>>>>> Antoine De Pauw wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Hi, and thanks for the answer >>>>>>> >>>>>>> In fact, what I do is reading a binary file to obtain 3 arrays >>>>>>> >>>>>>> >> (Lat,Lon,Val) describing geographic points which are associated by index >> (like point 1 is Lat[0]:Lon[0] with value Val[0]) >> >> >>>>>>> What I need to do is to plot some points on the map (miller >>>>>>> > projection > >>>>>>> >>>>>>> >> for most) based on latitude and longitude, to obtain a colour map (points >> are unordered, it is from IASI satellite computations) >> >> >>>>>>> I'm able to create a map, draw simple things on it, etc but the >>>>>>> >>>>>>> >> problem I have is any method I try for plotting points is failing, either >> pcolor, pcolormesh, imshow, etc. >> >> >>>>>>> When I found your post on that mailing list, I figured out that you >>>>>>> >>>>>>> >> might have the experience and skills to easily explain to me how to >> manipulate these points and plot them on the map, as there's like no help >> > on > >> the web except standard examples... >> >> >>>>>>> Please tell me if this is possible for you to give me some tips, or >>>>>>> > if > >>>>>>> >>>>>>> >> it takes too much of your time just advice me some lectures >> >> >>>>>>> Best regards, >>>>>>> >>>>>>> De Pauw Antoine >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> Antoine: It would really help to have a script demonstrating your >>>>>> problem. It sounds to me like you want to plot markers representing a >>>>>> > > >>>>>> set of points - for that you should use the scatter method. pcolor, >>>>>> pcolormesh and friends are for plotting gridded data. >>>>>> >>>>>> -Jeff >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> De Pauw Antoine wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Dear sir, >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I’m currently trying to improve our plotting tools here at >>>>>>>>> > the > >>>>>>>>> >>>>>>>>> >> “Quantum >> >> >>>>>>>>> Chemistry and Photophysics” section of the Université Libre >>>>>>>>> > de > >>>>>>>>> >>>>>>>>> >> >> >>>>>>>>> Bruxelles, and I ran, after many time passed at searching for a >>>>>>>>> solution, on an explanation from you here: >>>>>>>>> >>>>>>>>> >>>>>>>>> >> http://www.nabble.com/Re:-matplotlib-basemap-question-tt17759370.html >> >> >>>>>>>>> >>>>>>>>> >>>>>>>>> It seems that you could help me find a solution, as I cannot plot >>>>>>>>> >>>>>>>>> >> any >> >> >>>>>>>>> points on maps. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Could you please tell me what I could do to plot data in a simple >>>>>>>>> >>>>>>>>> >> way, >> >> >>>>>>>>> assuming I have 3 unordered arrays containing respectively >>>>>>>>> > latitude, > >>>>>>>>> >>>>>>>>> >> >> >>>>>>>>> longitude and values to plot? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Some tips would be very nice from you as any method I have tried so >>>>>>>>> >>>>>>>>> >> far >> >> >>>>>>>>> give me some errors… >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thank you very much in advance, >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> PS: I give you the code I’m using currently, missing the >>>>>>>>> >>>>>>>>> >> plotting part >> >> >>>>>>>>> >>>>>>>>> >>>>>>>>> from mpl_toolkits.basemap import Basemap >>>>>>>>> >>>>>>>>> from numpy import * >>>>>>>>> >>>>>>>>> from scipy.io.numpyio import fread >>>>>>>>> >>>>>>>>> import matplotlib.pyplot as plt >>>>>>>>> >>>>>>>>> import numpy as np >>>>>>>>> >>>>>>>>> import os >>>>>>>>> >>>>>>>>> import sys >>>>>>>>> >>>>>>>>> import array >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> fileName="c:/20080821.b56" >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> print('preparing map') >>>>>>>>> >>>>>>>>> map = >>>>>>>>> >>>>>>>>> >>>>>>>>> > Basemap(projection='mill',lat_0=0,lon_0=0,resolution='i',area_thresh=30000.) > >> >> >>>>>>>>> map.drawcoastlines(0.5,antialiased=1) >>>>>>>>> >>>>>>>>> map.drawmapboundary() >>>>>>>>> >>>>>>>>> #map.drawmeridians(np.arange(-180,180,60),linewidth=0.5, >>>>>>>>> labels=np.arange(-180,180,60), labelstyle="+/-") >>>>>>>>> >>>>>>>>> #map.drawparallels(np.arange(-90,90,30), linewidth=0.5, >>>>>>>>> labels=np.arange(-180,180,30), labelstyle="+/-") >>>>>>>>> >>>>>>>>> print('reading binary data') >>>>>>>>> >>>>>>>>> nbreligne=long(os.stat(fileName)[6])/(8*int(fileName[-2:])) >>>>>>>>> >>>>>>>>> Lat=zeros(nbreligne) >>>>>>>>> >>>>>>>>> Lon=zeros(nbreligne) >>>>>>>>> >>>>>>>>> Val=zeros(nbreligne) >>>>>>>>> >>>>>>>>> rawfile=fromfile(open(fileName,'rb'),'d',-1) >>>>>>>>> >>>>>>>>> Lat=rawfile[0:nbreligne] >>>>>>>>> >>>>>>>>> Lon=rawfile[nbreligne:nbreligne*2] >>>>>>>>> >>>>>>>>> Val=rawfile[nbreligne*21:nbreligne*22] >>>>>>>>> >>>>>>>>> print('shifting latitudes and projecting to map') >>>>>>>>> >>>>>>>>> i=0 >>>>>>>>> >>>>>>>>> while i < nbreligne: >>>>>>>>> >>>>>>>>> if(Lon[i]>180): >>>>>>>>> >>>>>>>>> print(Lon[i]) >>>>>>>>> >>>>>>>>> Lon[i]-=360 >>>>>>>>> >>>>>>>>> print(Lon[i]) >>>>>>>>> >>>>>>>>> i+=1 >>>>>>>>> >>>>>>>>> print('plotting data') >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> #plotting code comes here >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> Antoine: If you send me a self-contained script that produces the >>>>>>>> problem you see, I can help you debug it. As it stands now, I have >>>>>>>> >>>>>>>> >> very >> >> >>>>>>>> little to work with - it could be your plotting commands, or it >>>>>>>> > could > >>>>>>>> >>>>>>>> >> be >> >> >>>>>>>> your data. >>>>>>>> >>>>>>>> -Jeff >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> print('saving map') >>>>>>>>> >>>>>>>>> plt.savefig("testfig.png",dpi=600) >>>>>>>>> >>>>>>>>> print('done') >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> *Antoine De Pauw* >>>>>>>>> Collaborateur de recherches, Informatique - Research collaborator, >>>>>>>>> >>>>>>>>> >> IT >> >> >>>>>>>>> Laboratoire de chimie quantique et photophysique - Quantum >>>>>>>>> > chemistry > >>>>>>>>> >>>>>>>>> >> and >> >> >>>>>>>>> photophysics laboratory >>>>>>>>> *Université Libre de Bruxelles - ULB <http://ww.ulb.ac.be/>* >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Jeffrey S. Whitaker Phone : (303)497-6313 >>>>>>>> Meteorologist FAX : (303)497-6449 >>>>>>>> NOAA/OAR/PSD R/PSD1 Email : [EMAIL PROTECTED] >>>>>>>> 325 Broadway Office : Skaggs Research Cntr 1D-113 >>>>>>>> Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> Jeffrey S. Whitaker Phone : (303)497-6313 >>>>>> NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449 >>>>>> 325 Broadway Boulder, CO, USA 80305-3328 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> -- >>>> Jeffrey S. Whitaker Phone : (303)497-6313 >>>> NOAA/OAR/CDC R/PSD1 FAX : (303)497-6449 >>>> 325 Broadway Boulder, CO, USA 80305-3328 >>>> >>>> >>>> >>>> >>>> >>> >>> >> >> > > > -- Jeffrey S. 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