How to create a movie?? (from matlab code)

���� 21/01/2012 07:43 ��, �/� Gousios George ������:

���� 21/01/2012 07:05 ��, �/� Tony Yu ������:

          ���� 21/01/2012 04:54

��, �/� Tony Yu ������:

                    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, ex2).

                    -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!

···
      On Sat, Jan 21, 2012 at 11:31 AM, > > Gousios George <ggeo1@...3830...> > >           wrote:
                  On Sat, Jan 21, 2012 at > > > > 9:07 AM, Gousios George <ggeo1@...3830...> > > > >                       wrote:

2012/1/23 Gousios George <ggeo1@…3830…>

Στις 21/01/2012 07:43 μμ, ο/η Gousios George έγραψε:

Στις 21/01/2012 07:05 μμ, ο/η Tony Yu έγραψε:

          Στις 21/01/2012 04:54

μμ, ο/η Tony Yu έγραψε:

                    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, ex2).

                    -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

···
      On Sat, Jan 21, 2012 at 11:31 AM, > > > Gousios George <ggeo1@...3830...> > > >           wrote:
                  On Sat, Jan 21, 2012 at > > > > > 9:07 AM, Gousios George <ggeo1@...3830...> > > > > >                       wrote:

���� 23/01/2012 06:52 ��, �/� Tony Yu ������:

2012/1/23 Gousios George <ggeo1@…3830…>

        ���� 21/01/2012 07:43

��, �/� Gousios George ������:

          ���� 21/01/2012 07:05 ��, �/� Tony

Yu ������:

                  ����

21/01/2012 04:54 ��, �/� Tony Yu ������:

                            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, ex2).

                            -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.
···
              On Sat, Jan 21, 2012 at 11:31 > > > > AM, Gousios George <ggeo1@...3830...> > > > >                   wrote:
                          On Sat, Jan 21, > > > > > > 2012 at 9:07 AM, Gousios George <ggeo1@...3830...> > > > > > >                               wrote:

2012/1/23 Gousios George <ggeo1@…3830…>

Στις 23/01/2012 06:52 μμ, ο/η Tony Yu έγραψε:

2012/1/23 Gousios George <ggeo1@…3830…>

        Στις 21/01/2012 07:43

μμ, ο/η Gousios George έγραψε:

          Στις 21/01/2012 07:05 μμ, ο/η Tony

Yu έγραψε:

                  Στις

21/01/2012 04:54 μμ, ο/η Tony Yu έγραψε:

                            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, ex2).

                            -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

···
              On Sat, Jan 21, 2012 at 11:31 > > > > > AM, Gousios George <ggeo1@...3830...> > > > > >                   wrote:
                          On Sat, Jan 21, > > > > > > > 2012 at 9:07 AM, Gousios George <ggeo1@...3934...0...> > > > > > > >                               wrote:

���� 23/01/2012 07:48 ��, �/� Tony Yu ������:

2012/1/23 Gousios George <ggeo1@…3830…>

        ���� 23/01/2012 06:52

��, �/� Tony Yu ������:

2012/1/23 Gousios George <ggeo1@…3830…>

                    ����

21/01/2012 07:43 ��, �/� Gousios George ������:

                      ���� 21/01/2012 07:05

��, �/� Tony Yu ������:

                              ���� 21/01/2012 04:54 ��, �/� Tony Yu

������:

                                        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, ex2).

                                        -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� :
···
                          On Sat, Jan 21, > > > > > > 2012 at 11:31 AM, Gousios George <ggeo1@...3830...> > > > > > >                               wrote:
                                      On Sat, > > > > > > > > Jan 21, 2012 at 9:07 AM, > > > > > > > > Gousios George <ggeo1@...3830...> > > > > > > > >                                           wrote:

2012/1/23 Gousios George <ggeo1@…3830…>

Στις 23/01/2012 07:48 μμ, ο/η Tony Yu έγραψε:

2012/1/23 Gousios George <ggeo1@…3830…>

        Στις 23/01/2012 06:52

μμ, ο/η Tony Yu έγραψε:

2012/1/23 Gousios George <ggeo1@…3830…>

                    Στις

21/01/2012 07:43 μμ, ο/η Gousios George έγραψε:

                      Στις 21/01/2012 07:05

μμ, ο/η Tony Yu έγραψε:

                              Στις 21/01/2012 04:54 μμ, ο/η Tony Yu

έγραψε:

                                        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, ex2).

                                        -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

···
                          On Sat, Jan 21, > > > > > > > 2012 at 11:31 AM, Gousios George <ggeo1@...3935...30...> > > > > > > >                               wrote:
                                      On Sat, > > > > > > > > > Jan 21, 2012 at 9:07 AM, > > > > > > > > > Gousios George <ggeo1@...3830...> > > > > > > > > >                                           wrote:

���� 23/01/2012 08:10 ��, �/� Benjamin Root ������:

2012/1/23 Gousios George <ggeo1@…3830…>

        ���� 23/01/2012 07:48

��, �/� Tony Yu ������:

2012/1/23 Gousios George <ggeo1@…3830…>

                    ����

23/01/2012 06:52 ��, �/� Tony Yu ������:

                            2012/1/23 Gousios

George <ggeo1@…3830…>

                                ���� 21/01/2012 07:43 ��, �/�

Gousios George ������:

                                  ����

21/01/2012 07:05 ��, �/� Tony Yu
������:

                                          ����

21/01/2012 04:54 ��, �/�
Tony Yu ������:

                                                  On

Sat, Jan 21, 2012

                                                    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, ex2).

                                                    -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
···
                                      On Sat, > > > > > > > > Jan 21, 2012 at 11:31 AM, > > > > > > > > Gousios George <ggeo1@...3830...> > > > > > > > >                                           wrote:

at 9:07 AM, > > > > > > > > > > Gousios George <ggeo1@…3830…> > > > > > > > > > > wrote:

2012/1/23 Gousios George <ggeo1@…3830…>

Στις 23/01/2012 08:10 μμ, ο/η Benjamin Root έγραψε:

2012/1/23 Gousios George <ggeo1@…3830…>

        Στις 23/01/2012 07:48

μμ, ο/η Tony Yu έγραψε:

2012/1/23 Gousios George <ggeo1@…3830…>

                    Στις

23/01/2012 06:52 μμ, ο/η Tony Yu έγραψε:

                            2012/1/23 Gousios

George <ggeo1@…3830…>

                                Στις 21/01/2012 07:43 μμ, ο/η

Gousios George έγραψε:

                                  Στις

21/01/2012 07:05 μμ, ο/η Tony Yu
έγραψε:

                                          Στις

21/01/2012 04:54 μμ, ο/η
Tony Yu έγραψε:

                                                  On

Sat, Jan 21, 2012

                                                    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, ex2).

                                                    -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

···
                                      On Sat, > > > > > > > > > Jan 21, 2012 at 11:31 AM, > > > > > > > > > Gousios George <ggeo1@...3830...> > > > > > > > > >                                           wrote:

at 9:07 AM, > > > > > > > > > > > Gousios George <ggeo1@…3830…> > > > > > > > > > > > wrote:

���� 23/01/2012 08:39 ��, �/� Tony Yu ������:

2012/1/23 Gousios George <ggeo1@…3830…>

        ���� 23/01/2012 08:10

��, �/� Benjamin Root ������:

2012/1/23 Gousios George <ggeo1@…3830…>

                    ����

23/01/2012 07:48 ��, �/� Tony Yu ������:

                            2012/1/23 Gousios

George <ggeo1@…3830…>

                                ���� 23/01/2012 06:52 ��, �/� Tony

Yu ������:

                                        2012/1/23

Gousios George <ggeo1@…3830…>

                                            ����

21/01/2012 07:43 ��, �/�
Gousios George ������:

                                              ���� 21/01/2012 07:05

��, �/� Tony Yu
������:

                                                  On

Sat, Jan 21, 2012

                                                      ����

21/01/2012
04:54 ��, �/�
Tony Yu
������:

                                                      On

Sat, Jan 21,
2012 at 9:07
AM, Gousios
George <ggeo1@…3830…>
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 +
                                                      � � 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, ex2).

                                                      -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!
···

at 11:31 AM, > > > > > > > > > > Gousios George <ggeo1@…3830…> > > > > > > > > > > wrote: