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Re: [Matplotlib-users] How to create a movie?? (from matlab code) I figured the error , now how to stop the animation and put colormaps
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From: Gousios G. <gg...@wi...> - 2012-01-24 15:20:41
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Στις 24/01/2012 01:31 μμ, ο/η Gousios George έγραψε: > Στις 23/01/2012 08:39 μμ, ο/η Tony Yu έγραψε: >> >> >> 2012/1/23 Gousios George <gg...@wi... >> <mailto:gg...@wi...>> >> >> Στις 23/01/2012 08:10 μμ, ο/η Benjamin Root έγραψε: >>> 2012/1/23 Gousios George <gg...@wi... >>> <mailto:gg...@wi...>> >>> >>> Στις 23/01/2012 07:48 μμ, ο/η Tony Yu έγραψε: >>>> >>>> >>>> 2012/1/23 Gousios George <gg...@wi... >>>> <mailto:gg...@wi...>> >>>> >>>> Στις 23/01/2012 06:52 μμ, ο/η Tony Yu έγραψε: >>>>> >>>>> >>>>> 2012/1/23 Gousios George <gg...@wi... >>>>> <mailto:gg...@wi...>> >>>>> >>>>> Στις 21/01/2012 07:43 μμ, ο/η Gousios George έγραψε: >>>>>> Στις 21/01/2012 07:05 μμ, ο/η Tony Yu έγραψε: >>>>>>> >>>>>>> >>>>>>> On Sat, Jan 21, 2012 at 11:31 AM, Gousios George >>>>>>> <gg...@wi... >>>>>>> <mailto:gg...@wi...>> wrote: >>>>>>> >>>>>>> Στις 21/01/2012 04:54 μμ, ο/η Tony Yu έγραψε: >>>>>>>> >>>>>>>> >>>>>>>> On Sat, Jan 21, 2012 at 9:07 AM, Gousios >>>>>>>> George <gg...@wi... >>>>>>>> <mailto:gg...@wi...>> wrote: >>>>>>>> >>>>>>>> Hello , i have the following code in >>>>>>>> matlab and trying to do it in >>>>>>>> matplotlib. >>>>>>>> >>>>>>>> I have this code in matlab (in a >>>>>>>> function showGraphs): >>>>>>>> ... >>>>>>>> m = size(myList, 3); >>>>>>>> for k = 1:m >>>>>>>> g = myList(:, :, k); >>>>>>>> image(g + 1) >>>>>>>> axis off >>>>>>>> axis square >>>>>>>> M(k) = getframe; >>>>>>>> end; >>>>>>>> >>>>>>>> and in another file (another function): >>>>>>>> ... >>>>>>>> M = showGraphs(grids) >>>>>>>> movie(M, 1) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> I did so far: >>>>>>>> >>>>>>>> def showGraphs(data): >>>>>>>> data=sc.array([data]) >>>>>>>> n=sc.shape(data)[2] >>>>>>>> for k in range(n): >>>>>>>> mydata=data[:,:,k] >>>>>>>> #plt.imshow(mydata+1) -->> >>>>>>>> this doesn't work >>>>>>>> >>>>>>>> Also ,in order to do the animation : >>>>>>>> >>>>>>>> grids=...(result from another function) >>>>>>>> result=showGraph(grids) >>>>>>>> fig=plt.figure() >>>>>>>> ani=animation.FuncAnimation(fig,result,interval=30,blit=True) >>>>>>>> plt.show() >>>>>>>> >>>>>>>> Right now the program says "TypeError: >>>>>>>> 'NoneType' object is not >>>>>>>> callable" (it has errors in the >>>>>>>> animation call) >>>>>>>> >>>>>>>> What should be my approach to this in >>>>>>>> order to have the animation? >>>>>>>> >>>>>>>> Thank you! >>>>>>>> >>>>>>>> >>>>>>>> You're getting that error because the >>>>>>>> second argument to FuncAnimation (`result` >>>>>>>> in your example) should be a function (not >>>>>>>> always; see example 2 linked below). Right >>>>>>>> now, if your `showGraphs` function is >>>>>>>> defined in full, it returns a value of >>>>>>>> None, which gets saved to `result` (hence >>>>>>>> the error). >>>>>>>> >>>>>>>> You should take a look at some of the image >>>>>>>> animation examples (ex1 >>>>>>>> <http://matplotlib.sourceforge.net/examples/animation/dynamic_image.html>, >>>>>>>> ex2 >>>>>>>> <http://matplotlib.sourceforge.net/examples/animation/dynamic_image2.html>). >>>>>>>> >>>>>>>> -Tony >>>>>>>> >>>>>>> >>>>>>> I did now : >>>>>>> >>>>>>> >>>>>>> def showGraphs(data): >>>>>>> data=sc.array([data]) >>>>>>> n=sc.shape(data)[2] >>>>>>> ims=[] >>>>>>> >>>>>>> for k in range(n): >>>>>>> mydata=data[:,:,k] >>>>>>> im=plt.imshow(mydata+1) >>>>>>> ims.append([im]) >>>>>>> return ims >>>>>>> >>>>>>> and now it gives me "TypeError: Invalid >>>>>>> dimensions for image data. >>>>>>> >>>>>>> >>>>>>> Please post short, but executable examples when >>>>>>> possible. I'm not sure what your data looks >>>>>>> like, but your call to `sc.array` is strange >>>>>>> (I'm not sure why you have square brackets, >>>>>>> which effectively adds an unnecessary dimension >>>>>>> to your data). >>>>>>> >>>>>>> The code attached below should work. >>>>>>> >>>>>>> Cheers, >>>>>>> -Tony >>>>>>> >>>>>>> import numpy as np >>>>>>> import matplotlib.pyplot as plt >>>>>>> from matplotlib.animation import ArtistAnimation >>>>>>> >>>>>>> >>>>>>> fig = plt.figure() >>>>>>> >>>>>>> def showGraphs(data): >>>>>>> data = np.asarray(data) # unnecessary in >>>>>>> this example >>>>>>> n = np.shape(data)[2] >>>>>>> >>>>>>> ims = [] >>>>>>> #for mydata in np.rollaxis(data, -1): >>>>>>> for k in range(n): >>>>>>> mydata = data[:, :, k] >>>>>>> im = plt.imshow(mydata) >>>>>>> ims.append([im]) >>>>>>> return ims >>>>>>> >>>>>>> # 5 frames of a random 20 x 20 image >>>>>>> data = np.random.uniform(size=(20, 20, 5)) >>>>>>> ims = showGraphs(data) >>>>>>> >>>>>>> ani = ArtistAnimation(fig, ims) >>>>>>> plt.show() >>>>>> Now,it gives me 2 figures (why 2?) but >>>>>> empty.(maybe i didn't convert right the matlab >>>>>> code below?) >>>>>> The data in the showGraphs function is the result >>>>>> from this function (in matlab): >>>>>> ......... >>>>>> grids = zeros(n, n, t + 1); >>>>>> grids(:, :, 1) = rest; >>>>>> for i = 2:(t + 1) >>>>>> Extended = extendLat1(rest); >>>>>> rest = applyExtended(Extended); >>>>>> grids(:, :, i) = rest; >>>>>> end; >>>>>> >>>>>> And i did this in python: >>>>>> >>>>>> grids=sc.zeros((area,area,t+1)) >>>>>> rest=grids[:,:,0] >>>>>> for i in range(1,t): >>>>>> extended=extend(rest) >>>>>> rest=apply_extend(extended) >>>>>> grids[:,:,i]=rest >>>>>> return grids >>>>>> >>>>>> Thanks for helping! >>>>>> >>>>> Any help?Thanks! >>>>> >>>>> Sorry, but could you be a bit clearer: >>>>> * Did the example I provide work for you? >>>>> * Assuming it did, are you essentially replacing >>>>> `data` in my example with `grids` in this most recent >>>>> example? >>>>> * I don't get 2 figures: are you asking about the code >>>>> from my last message? >>>>> * Please provide a minimal, *executable* example >>>>> >>>>> -Tony >>>> Ok,i 'll try! >>>> >>>> 1) Yes,your example works fine. >>>> 2) Yes,i return grids from another function (work) doing : >>>> >>>> grids=work(area,...,time) >>>> result=showGraphs(grids) >>>> ani=ArtistAnimation(fig,result) >>>> plt.show() >>>> >>>> The contents of the work function are shown above. >>>> I just want to make sure that i have done the >>>> conversion from matlab right. >>>> Maybe the problem is somewhere else? >>>> >>>> Thank you. >>>> >>>> >>>> Did you get 2 figures with my original example, or just in >>>> your modified code? If it's only in your modified code, >>>> then there's something you're not showing which is creating >>>> the extra figure. >>>> >>>> Unfortunately, the `work` function you showed in the >>>> previous message is not executable (`apply_extend`, >>>> `extend`, etc. aren't defined), which it makes it very >>>> difficult to debug. If my code snippet worked for you, then >>>> the only difference is in how you've defined `grids`---do >>>> you know how it's different? >>>> >>>> -Tony >>>> >>> Ok,i am sending you the whole code of the program. (forget >>> the names of the functions i showed you so far , i use other >>> names). >>> >>> EMPTY=0 #empty cell >>> TREE=1 #tree cell >>> BURNING=2 #burning cell >>> probTree=0.8 #probability of tree >>> probBurning=0.001 #a tree ignites with this probability >>> even if no neighbor is burning >>> probLighting=0.0001 #chance that a tree been hit from light >>> probResistBurn=0.3 #chance that a tree does not burn even >>> if it's neighbor burns >>> t=20 >>> area=50 >>> >>> >>> def spread(cell,N,E,S,W): >>> >>> if cell==EMPTY: >>> return EMPTY >>> elif cell==BURNING: >>> return EMPTY >>> else: >>> if (N==BURNING or E==BURNING or S==BURNING or >>> W==BURNING): >>> if (sc.rand()<probResistBurn): >>> return TREE >>> else: >>> return BURNING >>> elif (sc.rand()<probLighting *(1-probResistBurn)): >>> return BURNING >>> else: >>> return TREE >>> >>> def extend(lat): >>> lat = sc.matrix(lat) >>> extendRows= sc.vstack([lat[-1,:], lat, lat[0,:]]) >>> extendLat=sc.hstack([extendRows[:,-1], extendRows, >>> extendRows[:,0]]) >>> return extendLat >>> >>> def apply_extend(matr): >>> #matr = sc.matrix(matr) >>> matr=sc.array([matr]) >>> area=sc.shape(matr)[0] >>> final=sc.zeros((area,area)) >>> for i in range(1,area): >>> for j in range(1,area): >>> cell=matr[i,j] >>> N=matr[i-1,j] >>> E=matr[i,j+1] >>> S=matr[i+1,j] >>> W=matr[i,j-1] >>> final[i-1,j-1]=spread(cell,N,E,S,W) >>> return final >>> >>> def >>> fire(area,probTree,probBurning,probLighting,probResistBurn,t): >>> >>> trees_or_burns=sc.rand(area,area)<probTree # tree or a >>> burning tree >>> burns=trees_or_burns*(sc.rand(area,area)<probBurning) >>> # burning tree >>> trees=trees_or_burns-burns >>> # tree >>> empties=sc.ones((area,area))-trees_or_burns >>> # empty cell >>> >>> forest=empties*EMPTY + trees*TREE + burns*BURNING #the >>> whole forest >>> >>> grids=sc.zeros((area,area,t+1)) >>> forest=grids[:,:,0] >>> for i in range(1,): >>> extended_forest=extend(forest) >>> forest=apply_extend(extended_forest) >>> grids[:,:,i]=forest >>> return grids >>> >>> def Graph(data): >>> data=sc.array(data) >>> n=sc.shape(data)[2] >>> ims=[] >>> for i in range(n): >>> mydata=data[:,:,i] >>> im=plt.imshow(mydata) >>> >>> ims.append([im]) >>> return ims >>> >>> >>> if __name__=="__main__": >>> >>> grids=fire(area,probTree,probBurning,probLighting,probResistBurn,t) >>> result=Graph(grids) >>> fig=plt.figure() >>> >>> #ani=animation.FuncAnimation(fig,result,interval=30,blit=True,repeat_delay=1000) >>> ani=ArtistAnimation(fig,result) >>> plt.show() >>> >>> Also, i am sending you the code in matlab : >>> >>> >>> >>> In Graph(), you call "plt.imshow()", which will create a new >>> figure automatically if one doesn't exist already. Change >>> fig=plt.figure() to fig=plt.gcf() >>> >>> Ben Root >>> >> Ok,now it shows me only one figure but it's full of blue color >> and doesn't do anything. >> Thanks >> >> Actually, it's plotting your data correctly. If you print out the >> values of `mydata` in the `Graph` loop, you'll see that everything is >> zero. >> >> -Tony > You are right they are all zeros!I don't unsderstand.. > > I am not sure if the function extend causes the problem. > > The extend function from matlab is : > > function extlat = extendLat1(lat); > extendRows = [lat(end, :); lat; lat(1, :)]; > extlat = [extendRows(:, end) extendRows extendRows(:, 1)]; > > I tested my version and i am sure that it gives the right results.But > here,in matlab it has "lat" as argument . In python i create "lat = > sc.matrix(lat)" .I think this is right?? > > Also , the function apply_extend in matlab is: > > function newmat = applyExtended(matExt); > n = size(matExt, 1) - 2; > newmat = zeros(n); > for i = 2:(n + 1) > for j = 2:(n + 1) > site = matExt(i, j); > N = matExt(i - 1, j); > E = matExt(i, j + 1); > S = matExt(i + 1, j); > W = matExt(i, j - 1); > newmat(i - 1, j - 1) = spread(site, N, E, S, W); > end; > end; > > I think i have done it right. > > Also ,the function fire in matlab : > > function grids = fire(n, probTree, probBurning, chanceLightning, > chanceImmune, t); > > global EMPTY TREE BURNING probLightning probImmune > EMPTY = 0; TREE = 1; BURNING = 2; > probLightning = chanceLightning; > probImmune = chanceImmune; > > treesOrBurns = (rand(n) < probTree); > > burns = treesOrBurns .* (rand(n) < probBurning); > > trees = treesOrBurns - burns; > > empties = 1 - treesOrBurns; > > forest = empties * EMPTY + trees * TREE + burns * BURNING; > > grids = zeros(n, n, t + 1); > grids(:, :, 1) = forest; > for i = 2:(t + 1) > forestExtended = extendLat1(forest); > forest = applyExtended(forestExtended); > grids(:, :, i) = forest; > end; > > > Could someone figure where am i doing wrong?(i have the whole code of > mine above). > > Thanks! > Ok, i figured the error! It was at the "forest=grids[:,:,0]".It should be "grids[:,:,0]=forest". Now i want to ask 2 questions. 1) How to stop the animation??It should stop when the simulation ends but now it starts all over again. 2) How to use colormaps ,because i didn't understand from here <http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps> or here <http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps>. And how can i put specific colors for specific values.For example for my value "EMPTY->color white",TREE->color green. Thank you! |
