Color in 3d plots

This may be a dumb question, however i have been scratching
my head trying to figure out how to plot a 3 dimensional plot with with a
colour map different from the elevation(Z) parameter.

An example of this done in Matlab would be

[X,Y,Z] = peaks(30);

C=Z’% could be anything other than Z
as long as it has the same dimensions

surf(X,Y,Z,C)

axis([-3 3 -3 3
-10 5])

Is this possible with matplotlib ‘0.99.1’

If so how do i go about doing this is there some
sample code?

Mike Alger, M.A.Sc

malger@…2153…

I have been looking at this for
the past day and in am pretty sure I could replace the instance of polyc by the
“cmap if statements” my colour array and I should be able to get close
to what I want. However I am new to both python & mpl, and I am not
entirely sure in how I would go about testing my hypothesis. Furthermore I am
also relatively new to submitting fixes to open-source projects so I have lots
of questions about how I would go about suggesting a modification.

1.)
can I just modify
the file in the C:\python26\Lib\site-packages\mpl-toolkits\mplot3d\axes3d.py
file to do my tests?

a.
Also, where are
these files usually kept in a linux environment ?

b.
What do I do with
the. pyc files with the same name? are they re-complied automatically when I
call the function externally?

2.)
Is this
capability already built in with the colour argument ? if so how do I
properly call it?

3.)
If I do make a
modification should it be as a separate function with the additional variable
or should I try to stuff the new capability into the old function

4.)
is there a clean
easy to follow tutorial for submitting changes via svn or can I rely on someone
else to do the final commit?

I have attached the function in
question for reference to save others from digging down into their python
directories

Again thanks for taking your
time to help me figure this out

Mike Alger

< Code>

def plot_surface(self, X,
Y, Z, *args, **kwargs):

‘’’

Create a surface plot.

By default it will be colored in shades of a solid color,

but it also supports color mapping by supplying the cmap

argument.

========== ================================================

Argument Description

========== ================================================

X, Y, Data values as numpy.arrays

Z

rstride Array row stride (step size)

cstride Array column stride (step size)

color Color of the surface patches

cmap A colormap for the surface patches.

========== ================================================

‘’’

had_data = self.has_data()

rows, cols = Z.shape

tX, tY, tZ = np.transpose(X), np.transpose(Y), np.transpose(Z)

rstride = kwargs.pop(‘rstride’, 10)

cstride = kwargs.pop(‘cstride’, 10)

color = kwargs.pop(‘color’, ‘b’)

color = np.array(colorConverter.to_rgba(color))

cmap = kwargs.get(‘cmap’, None)

polys = []

normals = []

avgz = []

for rs in np.arange(0, rows-1, rstride):

for cs in np.arange(0, cols-1, cstride):

ps = []

corners = []

for a, ta in [(X, tX), (Y, tY), (Z, tZ)]:

ztop = a[rs][cs:min(cols, cs+cstride+1)]

zleft = ta[min(cols-1, cs+cstride)][rs:min(rows, rs+rstride+1)]

zbase = a[min(rows-1, rs+rstride)][cs:min(cols, cs+cstride+1):]

zbase = zbase[::-1]

zright = ta[cs][rs:min(rows, rs+rstride+1):]

zright = zright[::-1]

corners.append([ztop[0], ztop[-1], zbase[0], zbase[-1]])

z = np.concatenate((ztop, zleft, zbase, zright))

ps.append(z)

The construction leaves the array with duplicate points, which

are removed here.

ps = zip(*ps)

lastp = np.array([])

ps2 = []

avgzsum = 0.0

for p in ps:

if p != lastp:

ps2.append§

lastp = p

avgzsum += p[2]

polys.append(ps2)

avgz.append(avgzsum / len(ps2))

v1 = np.array(ps2[0]) - np.array(ps2[1])

v2 = np.array(ps2[2]) - np.array(ps2[0])

normals.append(np.cross(v1, v2))

polyc = art3d.Poly3DCollection(polys, *args, **kwargs) ## this is where a
modification could be made to allow for a separate colour matrix

if cmap is not None:

polyc.set_array(np.array(avgz))

polyc.set_linewidth(0)

else:

colors = self._shade_colors(color, normals)

polyc.set_facecolors(colors)

self.add_collection(polyc)

self.auto_scale_xyz(X, Y, Z, had_data)

return polyc

···

From: Mike Alger
[mailto:mike.alger@…2879…]
Sent: November-23-09 3:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: [Matplotlib-users] Color in 3d plots

This may be a dumb question, however I have been scratching my head trying to figure out how to plot
a 3 dimensional plot with with a colour map different from the elevation(Z)
parameter.

An example of this done in Matlab would be

[X,Y,Z] = peaks(30);

C=Z’% could be anything other than Z
as long as it has the same dimensions

surf(X,Y,Z,C)

axis([-3 3 -3 3
-10 5])

Is this possible with matplotlib ‘0.99.1’

If so how do i go about doing this is there some
sample code?

Mike Alger, M.A.Sc

malger@…2153…

After a weekend of no replies I
managed to figure a way out myself

As this was “left to the reader
as an exercise” I will leave the integration or improvement of this solution as
an exercise to the next reader

What I have done is basically
cloned the plot surface function and replaced the avgz variable with a
reference to the “colors” parameter i have added to the function call.

This code doesn’t center things
perfectly with respect to the grid (for some reason a 40x40 grid turns into
39x39 grid in the function) again this is something else that could be improved,
however I am happy with it and a one pixel shift won’t be missed in my plots. I
also have no real clue as to what the following comments was about

The

construction leaves the array with duplicate points, which

are removed

here.

but it is probably related to
my non centered plots.

What follows is the modified function
:

def plot_surface2(self,
X, Y, Z, colors, *args, **kwargs):

‘’’

Create a surface plot.

By default it will be
colored in shades of a solid color,

but it also supports
color mapping by supplying the cmap

argument.

···

==========

Argument Description

==========

X, Y, Data values
as numpy.arrays

Z

colors an array
the same size as z that contains a separate color data

rstride Array row
stride (step size)

cstride Array column
stride (step size)

color Color of the
surface patches

cmap A colormap
for the surface patches.

==========

‘’’

had_data =
self.has_data()

rows, cols = Z.shape

tX, tY, tZ =
np.transpose(X), np.transpose(Y), np.transpose(Z)

rstride =
kwargs.pop(‘rstride’, 10)

cstride =
kwargs.pop(‘cstride’, 10)

color =
kwargs.pop(‘color’, ‘b’)

color =
np.array(colorConverter.to_rgba(color))

cmap =
kwargs.get(‘cmap’, None)

polys = []

normals = []

avgz = []

for rs in np.arange(0,
rows-1, rstride):

for cs in
np.arange(0, cols-1, cstride):

ps = []

corners = []

for a, ta in
[(X, tX), (Y, tY), (Z, tZ)]:

ztop =
a[rs][cs:min(cols, cs+cstride+1)]

zleft =
ta[min(cols-1, cs+cstride)][rs:min(rows, rs+rstride+1)]

zbase =
a[min(rows-1, rs+rstride)][cs:min(cols, cs+cstride+1):]

zbase =
zbase[::-1]

zright =
ta[cs][rs:min(rows, rs+rstride+1):]

zright =
zright[::-1]

corners.append([ztop[0], ztop[-1], zbase[0], zbase[-1]])

z =
np.concatenate((ztop, zleft, zbase, zright))

ps.append(z)

The

construction leaves the array with duplicate points, which

are removed

here.

ps = zip(*ps)

lastp =
np.array([])

ps2 = []

avgzsum = 0.0

for p in ps:

if p !=
lastp:

ps2.append§

lastp =
p

avgzsum
+= p[2]

polys.append(ps2)

##################################

Begin of changes

##################################

#avgz.append(avgzsum
/ len(ps2))

avgz.append(colors[rs][cs])

##################################

end of changes

##################################

v1 =
np.array(ps2[0]) - np.array(ps2[1])

v2 =
np.array(ps2[2]) - np.array(ps2[0])

normals.append(np.cross(v1, v2))

polyc =
art3d.Poly3DCollection(polys, *args, **kwargs)

if cmap is not None:

polyc.set_array(np.array(colors))

polyc.set_array(np.array(avgz))

polyc.set_linewidth(0)

else:

colors =
self._shade_colors(color, normals)

polyc.set_facecolors(colors)

self.add_collection(polyc)

self.auto_scale_xyz(X,
Y, Z, had_data)

return polyc

From: Mike Alger [mailto:malger@…2153…]
Sent: November-25-09 8:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] Color in 3d plots

I have been looking at this for the
past day and in am pretty sure I could replace the instance of polyc by the
“cmap if statements” my colour array and I should be able to get close to what
I want. However I am new to both python & mpl, and I am not entirely sure
in how I would go about testing my hypothesis. Furthermore I am also relatively
new to submitting fixes to open-source projects so I have lots of questions
about how I would go about suggesting a modification.

1.)
can I just modify
the file in the C:\python26\Lib\site-packages\mpl-toolkits\mplot3d\axes3d.py
file to do my tests?

a.
Also, where are
these files usually kept in a linux environment ?

b.
What do I do with
the. pyc files with the same name? are they re-complied automatically when I
call the function externally?

2.)
Is this capability
already built in with the colour argument ? if so how do I properly call it?

3.)
If I do make a
modification should it be as a separate function with the additional variable
or should I try to stuff the new capability into the old function

4.)
is there a clean
easy to follow tutorial for submitting changes via svn or can I rely on someone
else to do the final commit?

I have attached the function in
question for reference to save others from digging down into their python
directories

Again thanks for taking your
time to help me figure this out

Mike Alger

< Code>

def plot_surface(self, X,
Y, Z, *args, **kwargs):

‘’’

Create a surface plot.

By default it will be colored in shades of a solid color,

but it also supports color mapping by supplying the cmap

argument.

========== ================================================

Argument Description

========== ================================================

X, Y, Data values as numpy.arrays

Z

rstride Array row stride (step size)

cstride Array column stride (step size)

color Color of the surface patches

cmap A colormap for the surface patches.

========== ================================================

‘’’

had_data = self.has_data()

rows, cols = Z.shape

tX, tY, tZ = np.transpose(X), np.transpose(Y), np.transpose(Z)

rstride = kwargs.pop(‘rstride’, 10)

cstride = kwargs.pop(‘cstride’, 10)

color = kwargs.pop(‘color’, ‘b’)

color = np.array(colorConverter.to_rgba(color))

cmap = kwargs.get(‘cmap’, None)

polys = []

normals = []

avgz = []

for rs in np.arange(0, rows-1, rstride):

for cs in np.arange(0, cols-1, cstride):

ps = []

corners = []

for a, ta in [(X, tX), (Y, tY), (Z, tZ)]:

ztop = a[rs][cs:min(cols, cs+cstride+1)]

zleft = ta[min(cols-1, cs+cstride)][rs:min(rows, rs+rstride+1)]

zbase = a[min(rows-1, rs+rstride)][cs:min(cols, cs+cstride+1):]

zbase = zbase[::-1]

zright = ta[cs][rs:min(rows, rs+rstride+1):]

zright = zright[::-1]

corners.append([ztop[0], ztop[-1], zbase[0], zbase[-1]])

z = np.concatenate((ztop, zleft, zbase, zright))

ps.append(z)

The construction leaves the array with duplicate points, which

are removed here.

ps = zip(*ps)

lastp = np.array([])

ps2 = []

avgzsum = 0.0

for p in ps:

if p != lastp:

ps2.append§

lastp = p

avgzsum += p[2]

polys.append(ps2)

avgz.append(avgzsum / len(ps2))

v1 = np.array(ps2[0]) - np.array(ps2[1])

v2 = np.array(ps2[2]) - np.array(ps2[0])

normals.append(np.cross(v1, v2))

polyc = art3d.Poly3DCollection(polys, *args, **kwargs) ## this is where a
modification could be made to allow for a separate colour matrix

if cmap is not None:

polyc.set_array(np.array(avgz))

polyc.set_linewidth(0)

else:

colors = self._shade_colors(color, normals)

polyc.set_facecolors(colors)

self.add_collection(polyc)

self.auto_scale_xyz(X, Y, Z, had_data)

return polyc

From: Mike Alger
[mailto:mike.alger@…2879…]
Sent: November-23-09 3:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: [Matplotlib-users] Color in 3d plots

This may be a dumb question, however I have been scratching my head trying to figure out how to plot
a 3 dimensional plot with with a colour map different from the elevation(Z)
parameter.

An example of this done in Matlab would be

[X,Y,Z] = peaks(30);

C=Z’% could be anything other than Z
as long as it has the same dimensions

surf(X,Y,Z,C)

axis([-3 3 -3 3
-10 5])

Is this possible with matplotlib ‘0.99.1’

If so how do i go about doing this is there some
sample code?

Mike Alger, M.A.Sc

malger@…2153…

After a weekend of no replies I managed to figure a way out myself

Hey Mike, sorry for the radio silence. mpl is a big project and no
one developer is equipped to answer questions about everything. We
currently have only one active developer (Reinier) working on the 3D
stuff. I've CCd him, and hopefully he can take a look at your patch.

3.) If I do make a modification should it be as a separate function with
the additional variable or should I try to stuff the new capability into the
old function

4.) is there a clean easy to follow tutorial for submitting changes via
svn or can I rely on someone else to do the final commit?

In general, if the new functionality is close to the old, we'd like to
see it incorporated into the existing API, perhaps with a new keyword
argument. We have some documentation on how to contribute to mpl at
http://matplotlib.sourceforge.net/devel/coding_guide.html; see also
the FAQ http://matplotlib.sourceforge.net/faq/howto_faq.html#contributing-howto

As this was “left to the reader as an exercise” I will leave the integration
or improvement of this solution as an exercise to the next reader

What I have done is basically cloned the plot surface function and replaced
the avgz variable with a reference to the “colors” parameter i have added to
the function call.

This code doesn’t center things perfectly with respect to the grid (for
some reason a 40x40 grid turns into 39x39 grid in the function) again this
is something else that could be improved, however I am happy with it and a
one pixel shift won’t be missed in my plots. I also have no real clue as to
what the following comments was about

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

but it is probably related to my non centered plots.

What follows is the modified function :

def plot_surface2(self, X, Y, Z, colors, *args, **kwargs):

What will be most helpful is an "svn diff", as explained in the coding
guide and FAQ linked above, with an example (included in the diff)
that shows the before and after behavior. That way even an naive
developer can appreciate the before and after changes and commit the
code if the original developer responsible for that part of the code
base is not available. The ideal situation is "apply this patch
generated from an svn diff and run example so_and_so.py to see the
plot with and without the patch". As explained in the FAQ, if you
don't get proper attention here on the mailing list, please post a bug
or patch on the sourceforge tracker so we don't lose it -- sometimes
our inattention is not due to lack of interest but to lack of time,
and a report filed on the tracker helps us not lose the thread.

Thanks for the help!

JDH

···

On Mon, Nov 30, 2009 at 8:06 PM, Mike Alger <malger@...2153...> wrote:

Sorry i was getting a bit frustrated by checking every day and seeing other problems getting solved relativly fast, again i understand its a big project, and i do appreciate your time, i hope i didn`t come off as a complete jerk.

I figured since my suggested change would affect how others would interact with the existing function i should defer some interface design decisions to someone more familiar with the API and the interface philosophy before i would start suggesting my hacks to the code to get it to do what i want. again, i would love to build this functionality into the existing code, and it think it could be done via a good choice of kwargs parameters. Again i know how i can do this for my particular solution but how this should be done to minimize the effect on other users of the code i am not sure.

thanks again for the response, i was going a bit crazy as i saw MPL as the perfect solution as it does just about everything i need except that one tiny variation in the surface command and i didn't want to rule it out its use in a user interface project i have work on in the coming months because of it.

Mike

···

----- Original Message -----
From: John Hunter <jdh2358@...287...>
Date: Monday, November 30, 2009 11:26 pm
Subject: Re: [Matplotlib-users] Color in 3d plots
To: Mike Alger <malger@...2153...>
Cc: matplotlib-users@lists.sourceforge.net, Reinier Heeres <reinier@...2885......>

On Mon, Nov 30, 2009 at 8:06 PM, Mike Alger <malger@...2153...> wrote:
> After a weekend of no replies I managed to figure a way out myself

Hey Mike, sorry for the radio silence. mpl is a big project and no
one developer is equipped to answer questions about everything. We
currently have only one active developer (Reinier) working on the 3D
stuff. I've CCd him, and hopefully he can take a look at your patch.

>
> 3.) If I do make a modification should it be as a separate
function with
> the additional variable or should I try to stuff the new capability
into the
> old function
>
> 4.) is there a clean easy to follow tutorial for submitting
changes via
> svn or can I rely on someone else to do the final commit?

In general, if the new functionality is close to the old, we'd like to
see it incorporated into the existing API, perhaps with a new keyword
argument. We have some documentation on how to contribute to mpl at
http://matplotlib.sourceforge.net/devel/coding_guide.html; see also
the FAQ http://matplotlib.sourceforge.net/faq/howto_faq.html#contributing-howto

> As this was “left to the reader as an exercise” I will leave the integration
> or improvement of this solution as an exercise to the next reader
>
> What I have done is basically cloned the plot surface function and replaced
> the avgz variable with a reference to the “colors” parameter i have
added to
> the function call.
>
> This code doesn’t center things perfectly with respect to the grid
(for
> some reason a 40x40 grid turns into 39x39 grid in the function)
again this
> is something else that could be improved, however I am happy with it
and a
> one pixel shift won’t be missed in my plots. I also have no real
clue as to
> what the following comments was about
>
>
>
> # The construction leaves the array with duplicate points,
> which
>
> # are removed here.
>
>
>
> but it is probably related to my non centered plots.
>
> What follows is the modified function :
>
> def plot_surface2(self, X, Y, Z, colors, *args, **kwargs):

What will be most helpful is an "svn diff", as explained in the coding
guide and FAQ linked above, with an example (included in the diff)
that shows the before and after behavior. That way even an naive
developer can appreciate the before and after changes and commit the
code if the original developer responsible for that part of the code
base is not available. The ideal situation is "apply this patch
generated from an svn diff and run example so_and_so.py to see the
plot with and without the patch". As explained in the FAQ, if you
don't get proper attention here on the mailing list, please post a bug
or patch on the sourceforge tracker so we don't lose it -- sometimes
our inattention is not due to lack of interest but to lack of time,
and a report filed on the tracker helps us not lose the thread.

Thanks for the help!

JDH

Hi Mike,

Sorry for the slow reply, but I put support for this in the
development version in SVN. It can also do a bit of shading to make
the surface look more structured.

Note that the fact that a 40x40 grid turns into 39x39 squares is
expected behavior: the code assumes the 40 points are the *edges* of
the patches. There are only 39 patches between 40 points.

Regards,
Reinier

···

On Tue, Dec 1, 2009 at 3:06 AM, Mike Alger <malger@...2153...> wrote:

After a weekend of no replies I managed to figure a way out myself

As this was “left to the reader as an exercise” I will leave the integration
or improvement of this solution as an exercise to the next reader

What I have done is basically cloned the plot surface function and replaced
the avgz variable with a reference to the “colors” parameter i have added to
the function call.

This code doesn’t center things perfectly with respect to the grid (for
some reason a 40x40 grid turns into 39x39 grid in the function) again this
is something else that could be improved, however I am happy with it and a
one pixel shift won’t be missed in my plots. I also have no real clue as to
what the following comments was about

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

but it is probably related to my non centered plots.

What follows is the modified function :

def plot_surface2(self, X, Y, Z, colors, *args, **kwargs):

    &#39;&#39;&#39;

    Create a surface plot\.

    By default it will be colored in shades of a solid color,

    but it also supports color mapping by supplying the \*cmap\*

    argument\.

    ==========  ================================================

    Argument    Description

    ==========  ================================================

    \*X\*, \*Y\*,   Data values as numpy\.arrays

    \*Z\*

    \*colors\*   an array the same size as z that contains a separate

color data

    \*rstride\*   Array row stride \(step size\)

    \*cstride\*   Array column stride \(step size\)

    \*color\*     Color of the surface patches

    \*cmap\*      A colormap for the surface patches\.

    ==========  ================================================

    &#39;&#39;&#39;

    had\_data = self\.has\_data\(\)

    rows, cols = Z\.shape

    tX, tY, tZ = np\.transpose\(X\), np\.transpose\(Y\), np\.transpose\(Z\)

    rstride = kwargs\.pop\(&#39;rstride&#39;, 10\)

    cstride = kwargs\.pop\(&#39;cstride&#39;, 10\)

    color = kwargs\.pop\(&#39;color&#39;, &#39;b&#39;\)

    color = np\.array\(colorConverter\.to\_rgba\(color\)\)

    cmap = kwargs\.get\(&#39;cmap&#39;, None\)

    polys = \[\]

    normals = \[\]

    avgz = \[\]

    for rs in np\.arange\(0, rows\-1, rstride\):

        for cs in np\.arange\(0, cols\-1, cstride\):

            ps = \[\]

            corners = \[\]

            for a, ta in \[\(X, tX\), \(Y, tY\), \(Z, tZ\)\]:

                ztop = a\[rs\]\[cs:min\(cols, cs\+cstride\+1\)\]

                zleft = ta\[min\(cols\-1, cs\+cstride\)\]\[rs:min\(rows,

rs+rstride+1)]

                zbase = a\[min\(rows\-1, rs\+rstride\)\]\[cs:min\(cols,

cs+cstride+1):]

                zbase = zbase\[::\-1\]

                zright = ta\[cs\]\[rs:min\(rows, rs\+rstride\+1\):\]

                zright = zright\[::\-1\]

                corners\.append\(\[ztop\[0\], ztop\[\-1\], zbase\[0\], zbase\[\-1\]\]\)

                z = np\.concatenate\(\(ztop, zleft, zbase, zright\)\)

                ps\.append\(z\)

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

            ps = zip\(\*ps\)

            lastp = np\.array\(\[\]\)

            ps2 = \[\]

            avgzsum = 0\.0

            for p in ps:

                if p \!= lastp:

                    ps2\.append\(p\)

                    lastp = p

                    avgzsum \+= p\[2\]

            polys\.append\(ps2\)

            \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#

            Begin of changes

##################################

            \#avgz\.append\(avgzsum / len\(ps2\)\)

avgz.append(colors[rs][cs])

            \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#

            end of changes

##################################

            v1 = np\.array\(ps2\[0\]\) \- np\.array\(ps2\[1\]\)

            v2 = np\.array\(ps2\[2\]\) \- np\.array\(ps2\[0\]\)

            normals\.append\(np\.cross\(v1, v2\)\)

    polyc = art3d\.Poly3DCollection\(polys, \*args, \*\*kwargs\)

    if cmap is not None:

     \#  polyc\.set\_array\(np\.array\(colors\)\)

        polyc\.set\_array\(np\.array\(avgz\)\)

        polyc\.set\_linewidth\(0\)

    else:

        colors = self\.\_shade\_colors\(color, normals\)

        polyc\.set\_facecolors\(colors\)

    self\.add\_collection\(polyc\)

    self\.auto\_scale\_xyz\(X, Y, Z, had\_data\)

    return polyc

From: Mike Alger [mailto:malger@…2153…]
Sent: November-25-09 8:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] Color in 3d plots

I have been looking at this for the past day and in am pretty sure I could
replace the instance of polyc by the “cmap if statements” my colour array
and I should be able to get close to what I want. However I am new to both
python & mpl, and I am not entirely sure in how I would go about testing my
hypothesis. Furthermore I am also relatively new to submitting fixes to
open-source projects so I have lots of questions about how I would go about
suggesting a modification.

1.) can I just modify the file in the
C:\python26\Lib\site-packages\mpl-toolkits\mplot3d\axes3d.py file to do my
tests?

a. Also, where are these files usually kept in a linux environment ?

b. What do I do with the. pyc files with the same name? are they
re-complied automatically when I call the function externally?

2.) Is this capability already built in with the colour argument ? if so
how do I properly call it?

3.) If I do make a modification should it be as a separate function with
the additional variable or should I try to stuff the new capability into the
old function

4.) is there a clean easy to follow tutorial for submitting changes via
svn or can I rely on someone else to do the final commit?

I have attached the function in question for reference to save others from
digging down into their python directories

Again thanks for taking your time to help me figure this out

Mike Alger

< Code>

def plot_surface(self, X, Y, Z, *args, **kwargs):

    &#39;&#39;&#39;

    Create a surface plot\.

    By default it will be colored in shades of a solid color,

    but it also supports color mapping by supplying the \*cmap\*

    argument\.

    ==========  ================================================

    Argument    Description

    ==========  ================================================

    \*X\*, \*Y\*,   Data values as numpy\.arrays

    \*Z\*

    \*rstride\*   Array row stride \(step size\)

    \*cstride\*   Array column stride \(step size\)

    \*color\*     Color of the surface patches

    \*cmap\*      A colormap for the surface patches\.

    ==========  ================================================

    &#39;&#39;&#39;

    had\_data = self\.has\_data\(\)

    rows, cols = Z\.shape

    tX, tY, tZ = np\.transpose\(X\), np\.transpose\(Y\), np\.transpose\(Z\)

    rstride = kwargs\.pop\(&#39;rstride&#39;, 10\)

    cstride = kwargs\.pop\(&#39;cstride&#39;, 10\)

    color = kwargs\.pop\(&#39;color&#39;, &#39;b&#39;\)

    color = np\.array\(colorConverter\.to\_rgba\(color\)\)

    cmap = kwargs\.get\(&#39;cmap&#39;, None\)

    polys = \[\]

    normals = \[\]

    avgz = \[\]

    for rs in np\.arange\(0, rows\-1, rstride\):

        for cs in np\.arange\(0, cols\-1, cstride\):

            ps = \[\]

            corners = \[\]

            for a, ta in \[\(X, tX\), \(Y, tY\), \(Z, tZ\)\]:

                ztop = a\[rs\]\[cs:min\(cols, cs\+cstride\+1\)\]

                zleft = ta\[min\(cols\-1, cs\+cstride\)\]\[rs:min\(rows,

rs+rstride+1)]

                zbase = a\[min\(rows\-1, rs\+rstride\)\]\[cs:min\(cols,

cs+cstride+1):]

                zbase = zbase\[::\-1\]

                zright = ta\[cs\]\[rs:min\(rows, rs\+rstride\+1\):\]

                zright = zright\[::\-1\]

                corners\.append\(\[ztop\[0\], ztop\[\-1\], zbase\[0\], zbase\[\-1\]\]\)

                z = np\.concatenate\(\(ztop, zleft, zbase, zright\)\)

                ps\.append\(z\)

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

            ps = zip\(\*ps\)

            lastp = np\.array\(\[\]\)

            ps2 = \[\]

            avgzsum = 0\.0

            for p in ps:

                if p \!= lastp:

                    ps2\.append\(p\)

                    lastp = p

                    avgzsum \+= p\[2\]

            polys\.append\(ps2\)

            avgz\.append\(avgzsum / len\(ps2\)\)

            v1 = np\.array\(ps2\[0\]\) \- np\.array\(ps2\[1\]\)

            v2 = np\.array\(ps2\[2\]\) \- np\.array\(ps2\[0\]\)

            normals\.append\(np\.cross\(v1, v2\)\)

    polyc = art3d\.Poly3DCollection\(polys, \*args, \*\*kwargs\) \#\# this is

where a modification could be made to allow for a separate colour matrix

    if cmap is not None:

        polyc\.set\_array\(np\.array\(avgz\)\)

        polyc\.set\_linewidth\(0\)

    else:

        colors = self\.\_shade\_colors\(color, normals\)

        polyc\.set\_facecolors\(colors\)

    self\.add\_collection\(polyc\)

    self\.auto\_scale\_xyz\(X, Y, Z, had\_data\)

    return polyc

</Code>

From: Mike Alger [mailto:mike.alger@…2879…]
Sent: November-23-09 3:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: [Matplotlib-users] Color in 3d plots

This may be a dumb question, however I have been scratching my head trying
to figure out how to plot a 3 dimensional plot with with a colour map
different from the elevation(Z) parameter.

An example of this done in Matlab would be

[X,Y,Z] = peaks(30);

C=Z'% could be anything other than Z as long as it has the same dimensions

surf(X,Y,Z,C)

axis([-3 3 -3 3 -10 5])

Is this possible with matplotlib '0.99.1'

If so how do i go about doing this is there some sample code?

Mike Alger, M.A.Sc

malger@...2153...

------------------------------------------------------------------------------
Join us December 9, 2009 for the Red Hat Virtual Experience,
a free event focused on virtualization and cloud computing.
Attend in-depth sessions from your desk. Your couch. Anywhere.
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_______________________________________________
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Tel: +31 6 10852639

I had a hunch that was the case but wasn`t entirely sure, and to be honest
3d plot functions have always been a black box for me and i have never
really thought about what exactly gets plotted in 3d plot until now

Thanks again
Reinier i will take a look at the SVN A.S.A.P.

Mike

···

-----Original Message-----
From: Reinier Heeres [mailto:reinier@…2663…]
Sent: December-09-09 7:17 PM
To: Mike Alger
Cc: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] Color in 3d plots

Hi Mike,

Sorry for the slow reply, but I put support for this in the
development version in SVN. It can also do a bit of shading to make
the surface look more structured.

Note that the fact that a 40x40 grid turns into 39x39 squares is
expected behavior: the code assumes the 40 points are the *edges* of
the patches. There are only 39 patches between 40 points.

Regards,
Reinier

On Tue, Dec 1, 2009 at 3:06 AM, Mike Alger <malger@...2153...> wrote:

After a weekend of no replies I managed to figure a way out myself

As this was “left to the reader as an exercise” I will leave the

integration

or improvement of this solution as an exercise to the next reader

What I have done is basically cloned the plot surface function and

replaced

the avgz variable with a reference to the “colors” parameter i have added

to

the function call.

This code doesn’t center things perfectly with respect to the grid (for
some reason a 40x40 grid turns into 39x39 grid in the function) again this
is something else that could be improved, however I am happy with it and a
one pixel shift won’t be missed in my plots. I also have no real clue as

to

what the following comments was about

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

but it is probably related to my non centered plots.

What follows is the modified function :

def plot_surface2(self, X, Y, Z, colors, *args, **kwargs):

    &#39;&#39;&#39;

    Create a surface plot\.

    By default it will be colored in shades of a solid color,

    but it also supports color mapping by supplying the \*cmap\*

    argument\.

    ==========  ================================================

    Argument    Description

    ==========  ================================================

    \*X\*, \*Y\*,   Data values as numpy\.arrays

    \*Z\*

    \*colors\*   an array the same size as z that contains a separate

color data

    \*rstride\*   Array row stride \(step size\)

    \*cstride\*   Array column stride \(step size\)

    \*color\*     Color of the surface patches

    \*cmap\*      A colormap for the surface patches\.

    ==========  ================================================

    &#39;&#39;&#39;

    had\_data = self\.has\_data\(\)

    rows, cols = Z\.shape

    tX, tY, tZ = np\.transpose\(X\), np\.transpose\(Y\), np\.transpose\(Z\)

    rstride = kwargs\.pop\(&#39;rstride&#39;, 10\)

    cstride = kwargs\.pop\(&#39;cstride&#39;, 10\)

    color = kwargs\.pop\(&#39;color&#39;, &#39;b&#39;\)

    color = np\.array\(colorConverter\.to\_rgba\(color\)\)

    cmap = kwargs\.get\(&#39;cmap&#39;, None\)

    polys = \[\]

    normals = \[\]

    avgz = \[\]

    for rs in np\.arange\(0, rows\-1, rstride\):

        for cs in np\.arange\(0, cols\-1, cstride\):

            ps = \[\]

            corners = \[\]

            for a, ta in \[\(X, tX\), \(Y, tY\), \(Z, tZ\)\]:

                ztop = a\[rs\]\[cs:min\(cols, cs\+cstride\+1\)\]

                zleft = ta\[min\(cols\-1, cs\+cstride\)\]\[rs:min\(rows,

rs+rstride+1)]

                zbase = a\[min\(rows\-1, rs\+rstride\)\]\[cs:min\(cols,

cs+cstride+1):]

                zbase = zbase\[::\-1\]

                zright = ta\[cs\]\[rs:min\(rows, rs\+rstride\+1\):\]

                zright = zright\[::\-1\]

                corners\.append\(\[ztop\[0\], ztop\[\-1\], zbase\[0\],

zbase[-1]])

                z = np\.concatenate\(\(ztop, zleft, zbase, zright\)\)

                ps\.append\(z\)

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

            ps = zip\(\*ps\)

            lastp = np\.array\(\[\]\)

            ps2 = \[\]

            avgzsum = 0\.0

            for p in ps:

                if p \!= lastp:

                    ps2\.append\(p\)

                    lastp = p

                    avgzsum \+= p\[2\]

            polys\.append\(ps2\)

            \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#

            Begin of changes

##################################

            \#avgz\.append\(avgzsum / len\(ps2\)\)

avgz.append(colors[rs][cs])

            \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#

            end of changes

##################################

            v1 = np\.array\(ps2\[0\]\) \- np\.array\(ps2\[1\]\)

            v2 = np\.array\(ps2\[2\]\) \- np\.array\(ps2\[0\]\)

            normals\.append\(np\.cross\(v1, v2\)\)

    polyc = art3d\.Poly3DCollection\(polys, \*args, \*\*kwargs\)

    if cmap is not None:

     \#  polyc\.set\_array\(np\.array\(colors\)\)

        polyc\.set\_array\(np\.array\(avgz\)\)

        polyc\.set\_linewidth\(0\)

    else:

        colors = self\.\_shade\_colors\(color, normals\)

        polyc\.set\_facecolors\(colors\)

    self\.add\_collection\(polyc\)

    self\.auto\_scale\_xyz\(X, Y, Z, had\_data\)

    return polyc

From: Mike Alger [mailto:malger@…2153…]
Sent: November-25-09 8:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: Re: [Matplotlib-users] Color in 3d plots

I have been looking at this for the past day and in am pretty sure I could
replace the instance of polyc by the “cmap if statements” my colour array
and I should be able to get close to what I want. However I am new to both
python & mpl, and I am not entirely sure in how I would go about testing

my

hypothesis. Furthermore I am also relatively new to submitting fixes to
open-source projects so I have lots of questions about how I would go

about

suggesting a modification.

1.) can I just modify the file in the
C:\python26\Lib\site-packages\mpl-toolkits\mplot3d\axes3d.py file to do my
tests?

a. Also, where are these files usually kept in a linux environment ?

b. What do I do with the. pyc files with the same name? are they
re-complied automatically when I call the function externally?

2.) Is this capability already built in with the colour argument ? if

so

how do I properly call it?

3.) If I do make a modification should it be as a separate function

with

the additional variable or should I try to stuff the new capability into

the

old function

4.) is there a clean easy to follow tutorial for submitting changes via
svn or can I rely on someone else to do the final commit?

I have attached the function in question for reference to save others from
digging down into their python directories

Again thanks for taking your time to help me figure this out

Mike Alger

< Code>

def plot_surface(self, X, Y, Z, *args, **kwargs):

    &#39;&#39;&#39;

    Create a surface plot\.

    By default it will be colored in shades of a solid color,

    but it also supports color mapping by supplying the \*cmap\*

    argument\.

    ==========  ================================================

    Argument    Description

    ==========  ================================================

    \*X\*, \*Y\*,   Data values as numpy\.arrays

    \*Z\*

    \*rstride\*   Array row stride \(step size\)

    \*cstride\*   Array column stride \(step size\)

    \*color\*     Color of the surface patches

    \*cmap\*      A colormap for the surface patches\.

    ==========  ================================================

    &#39;&#39;&#39;

    had\_data = self\.has\_data\(\)

    rows, cols = Z\.shape

    tX, tY, tZ = np\.transpose\(X\), np\.transpose\(Y\), np\.transpose\(Z\)

    rstride = kwargs\.pop\(&#39;rstride&#39;, 10\)

    cstride = kwargs\.pop\(&#39;cstride&#39;, 10\)

    color = kwargs\.pop\(&#39;color&#39;, &#39;b&#39;\)

    color = np\.array\(colorConverter\.to\_rgba\(color\)\)

    cmap = kwargs\.get\(&#39;cmap&#39;, None\)

    polys = \[\]

    normals = \[\]

    avgz = \[\]

    for rs in np\.arange\(0, rows\-1, rstride\):

        for cs in np\.arange\(0, cols\-1, cstride\):

            ps = \[\]

            corners = \[\]

            for a, ta in \[\(X, tX\), \(Y, tY\), \(Z, tZ\)\]:

                ztop = a\[rs\]\[cs:min\(cols, cs\+cstride\+1\)\]

                zleft = ta\[min\(cols\-1, cs\+cstride\)\]\[rs:min\(rows,

rs+rstride+1)]

                zbase = a\[min\(rows\-1, rs\+rstride\)\]\[cs:min\(cols,

cs+cstride+1):]

                zbase = zbase\[::\-1\]

                zright = ta\[cs\]\[rs:min\(rows, rs\+rstride\+1\):\]

                zright = zright\[::\-1\]

                corners\.append\(\[ztop\[0\], ztop\[\-1\], zbase\[0\],

zbase[-1]])

                z = np\.concatenate\(\(ztop, zleft, zbase, zright\)\)

                ps\.append\(z\)

            \# The construction leaves the array with duplicate points,

which

            \# are removed here\.

            ps = zip\(\*ps\)

            lastp = np\.array\(\[\]\)

            ps2 = \[\]

            avgzsum = 0\.0

            for p in ps:

                if p \!= lastp:

                    ps2\.append\(p\)

                    lastp = p

                    avgzsum \+= p\[2\]

            polys\.append\(ps2\)

            avgz\.append\(avgzsum / len\(ps2\)\)

            v1 = np\.array\(ps2\[0\]\) \- np\.array\(ps2\[1\]\)

            v2 = np\.array\(ps2\[2\]\) \- np\.array\(ps2\[0\]\)

            normals\.append\(np\.cross\(v1, v2\)\)

    polyc = art3d\.Poly3DCollection\(polys, \*args, \*\*kwargs\) \#\# this is

where a modification could be made to allow for a separate colour matrix

    if cmap is not None:

        polyc\.set\_array\(np\.array\(avgz\)\)

        polyc\.set\_linewidth\(0\)

    else:

        colors = self\.\_shade\_colors\(color, normals\)

        polyc\.set\_facecolors\(colors\)

    self\.add\_collection\(polyc\)

    self\.auto\_scale\_xyz\(X, Y, Z, had\_data\)

    return polyc

</Code>

From: Mike Alger [mailto:mike.alger@…2879…]
Sent: November-23-09 3:42 PM
To: matplotlib-users@lists.sourceforge.net
Subject: [Matplotlib-users] Color in 3d plots

This may be a dumb question, however I have been scratching my head trying
to figure out how to plot a 3 dimensional plot with with a colour map
different from the elevation(Z) parameter.

An example of this done in Matlab would be

[X,Y,Z] = peaks(30);

C=Z'% could be anything other than Z as long as it has the same dimensions

surf(X,Y,Z,C)

axis([-3 3 -3 3 -10 5])

Is this possible with matplotlib '0.99.1'

If so how do i go about doing this is there some sample code?

Mike Alger, M.A.Sc

malger@...2153...

----------------------------------------------------------------------------
--

Join us December 9, 2009 for the Red Hat Virtual Experience,
a free event focused on virtualization and cloud computing.
Attend in-depth sessions from your desk. Your couch. Anywhere.
http://p.sf.net/sfu/redhat-sfdev2dev
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

--
Reinier Heeres
Tel: +31 6 10852639