Need some help in 3D surface plotting...

phanikumar.ds · March 12, 2018, 1:19pm

Hi All,

I am trying to 3D surface plot the data from a .csv file. there is already
a reference plot drawn with this data (seems it was done by some windows
app) and I am trying to do the same with linux (in fact on Raspberry Pi)
with matplot library.

I have attached the .csv file for reference.

Original plot (with some microsoft tool) is as below.

and when I plot the same data with matplotlib, the plot is as below.

Seems the plotting is ok, but for the layer of light orange patches - not
sure, what is causing this. My python code is as below. Let me know if you
have any suggestion for me.

from mpl_toolkits.mplot3d import Axes3D
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import numpy as np
import csv

X = []
Y = []
Z = []

#Read the selected file
with open ('Plasma.csv', 'r') as csvfile:
plots = csv.reader (csvfile, delimiter=',')
for row in plots:
X.append(float(row[0]))
Y.append(float(row[1]))
Z.append(float(row[2]))

#Getting ready for the dispaly
fig = plt.figure()
ax = fig.gca(projection='3d')

#Set the labels...
ax.set_xlabel('X (mm)')
ax.set_ylabel('Y (mm)')
ax.set_zlabel('CPD (mV)')

#Setting the places properly...
tmp_planes = ax.zaxis._PLANES
ax.zaxis._PLANES = (tmp_planes[2], tmp_planes[3],
tmp_planes[0], tmp_planes[1],
tmp_planes[4],tmp_planes[5])

# Make data.
X, Y = np.meshgrid(X, Y)

#Plot
surf = ax.plot_surface(X, Y, Z, cmap=cm.coolwarm, linewidth=0)

plt.show()

With best regards,
Phani.
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system · March 12, 2018, 4:17pm

Hi Phani,

Please find attached a modified version of your script that should help
(hopefully). It produces the attached PNG. I think that your problem is
how to reshape your data before feeding them to the 3d plotting routine.

Besides, I am no mplot3d expert, but I wonder if there would be a way to
set the z-axis on the left **without** relying on private attributes
(this is often very **not** future-proof as such features can be changed
without warning in a future version of the library).

Best,
Adrien

Hi All,

I am trying to 3D surface plot the data from a .csv file. there is
already a reference plot drawn with this data (seems it was done by some
windows app) and I am trying to do the same with linux (in fact on
Raspberry Pi) with matplot library.

I have attached the .csv file for reference.

Original plot (with some microsoft tool) is as below.

and when I plot the same data with matplotlib, the plot is as below.

Seems the plotting is ok, but for the layer of light orange patches -
not sure, what is causing this. My python code is as below. Let me know
if you have any suggestion for me.

from mpl_toolkits.mplot3d import Axes3D
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import numpy as np
import csv

X =
Y =
Z =

#Read the selected file
with open ('Plasma.csv', 'r') as csvfile:
plots = csv.reader (csvfile, delimiter=',')
for row in plots:
X.append(float(row[0]))
Y.append(float(row[1]))
Z.append(float(row[2]))

#Getting ready for the dispaly
fig = plt.figure()
ax = fig.gca(projection='3d')

#Set the labels...
ax.set_xlabel('X (mm)')
ax.set_ylabel('Y (mm)')
ax.set_zlabel('CPD (mV)')

#Setting the places properly...
tmp_planes = ax.zaxis._PLANES
ax.zaxis._PLANES = (tmp_planes[2], tmp_planes[3],
tmp_planes[0], tmp_planes[1],
tmp_planes[4],tmp_planes[5])

# Make data.
X, Y = np.meshgrid(X, Y)

#Plot
surf = ax.plot_surface(X, Y, Z, cmap=cm.coolwarm, linewidth=0)

plt.show()

With best regards,
Phani.

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···

On 03/12/2018 06:19 AM, Phani Kumar wrote:

phanikumar.ds · March 13, 2018, 10:49am

Hi Adrien,

Thanks a lot. I tried your suggestion and initial got

root at phani:/home/pi/SampleExample# python Trial1.py
Traceback (most recent call last):
  File "Trial1.py", line 46, in <module>
    surf = ax.plot_surface(xx, yy, zz, cmap="inferno")
  File "/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/axes3d.py",
line 1637, in plot_surface
    polyc = art3d.Poly3DCollection(polys, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/art3d.py",
line 476, in __init__
    PolyCollection.__init__(self, verts, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py", line
799, in __init__
    Collection.__init__(self, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py", line
107, in __init__
    cm.ScalarMappable.__init__(self, norm, cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 197, in
__init__
    self.cmap = get_cmap(cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 163, in
get_cmap
    % (name, ', '.join(cmap_d.keys())))
ValueError: Colormap inferno is not recognized. Possible values are:
Spectral, summer, coolwarm, Wistia_r, pink_r, Set1, Set2, Set3, brg_r,
Dark2, prism, PuOr_r, afmhot_r, terrain_r, PuBuGn_r, RdPu, gist_ncar_r,
gist_yarg_r, Dark2_r, YlGnBu, RdYlBu, hot_r, gist_rainbow_r, gist_stern,
PuBu_r, cool_r, cool, gray, copper_r, Greens_r, GnBu, gist_ncar, spring_r,
gist_rainbow, gist_heat_r, Wistia, OrRd_r, CMRmap, bone, gist_stern_r,
RdYlGn, Pastel2_r, spring, terrain, YlOrRd_r, Set2_r, winter_r, PuBu,
RdGy_r, spectral, rainbow, flag_r, jet_r, RdPu_r, gist_yarg, BuGn, Paired_r,
hsv_r, bwr, cubehelix, Greens, PRGn, gist_heat, spectral_r, Paired, hsv,
Oranges_r, prism_r, Pastel2, Pastel1_r, Pastel1, gray_r, jet, Spectral_r,
gnuplot2_r, gist_earth, YlGnBu_r, copper, gist_earth_r, Set3_r, OrRd,
gnuplot_r, ocean_r, brg, gnuplot2, PuRd_r, bone_r, BuPu, Oranges, RdYlGn_r,
PiYG, CMRmap_r, YlGn, binary_r, gist_gray_r, Accent, BuPu_r, gist_gray,
flag, bwr_r, RdBu_r, BrBG, Reds, Set1_r, summer_r, GnBu_r, BrBG_r, Reds_r,
RdGy, PuRd, Accent_r, Blues, autumn_r, autumn, cubehelix_r, nipy_spectral_r,
ocean, PRGn_r, Greys_r, pink, binary, winter, gnuplot, RdYlBu_r, hot,
YlOrBr, coolwarm_r, rainbow_r, Purples_r, PiYG_r, YlGn_r, Blues_r, YlOrBr_r,
seismic, Purples, seismic_r, RdBu, Greys, BuGn_r, YlOrRd, PuOr, PuBuGn,
nipy_spectral, afmhot
root at bitscope:/home/pi/SampleExample#

So I thought the color scheme "inferno" is not supported (or may be not
installed in my pi). So I changed it to "coolwarm" and I see the image as
below.

<http://matplotlib.1069221.n5.nabble.com/file/t5142/plasma.png>

Though this is way better than my initial version, still I see only 2 color
combination... may be I need to check with color schemes provided in the
error message.

Thanks a lot any way. Also let me know if you think any suitable color
scheme for this kind of gradient.

Will check with you on other technical questions after I finish this.

Thanks again,

With best regards,
Phani.

···

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ben.v.root · March 13, 2018, 1:29pm

The error message means you have an old version of matplotlib. Inferno was
added in version 1.5. We are currently at verson 2.2.1 (supposedly will be
released today?). I would also wonder if your install of numpy is old as
well. Chances are, you are hitting on some old forgotten bug. Could you try
updating your packages?

···

On Tue, Mar 13, 2018 at 6:49 AM, phanids <phanikumar.ds at gmail.com> wrote:

Hi Adrien,

Thanks a lot. I tried your suggestion and initial got

root at phani:/home/pi/SampleExample# python Trial1.py
Traceback (most recent call last):
  File "Trial1.py", line 46, in <module>
    surf = ax.plot_surface(xx, yy, zz, cmap="inferno")
  File "/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/axes3d.py",
line 1637, in plot_surface
    polyc = art3d.Poly3DCollection(polys, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/art3d.py",
line 476, in __init__
    PolyCollection.__init__(self, verts, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py", line
799, in __init__
    Collection.__init__(self, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py", line
107, in __init__
    cm.ScalarMappable.__init__(self, norm, cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 197, in
__init__
    self.cmap = get_cmap(cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 163, in
get_cmap
    % (name, ', '.join(cmap_d.keys())))
ValueError: Colormap inferno is not recognized. Possible values are:
Spectral, summer, coolwarm, Wistia_r, pink_r, Set1, Set2, Set3, brg_r,
Dark2, prism, PuOr_r, afmhot_r, terrain_r, PuBuGn_r, RdPu, gist_ncar_r,
gist_yarg_r, Dark2_r, YlGnBu, RdYlBu, hot_r, gist_rainbow_r, gist_stern,
PuBu_r, cool_r, cool, gray, copper_r, Greens_r, GnBu, gist_ncar, spring_r,
gist_rainbow, gist_heat_r, Wistia, OrRd_r, CMRmap, bone, gist_stern_r,
RdYlGn, Pastel2_r, spring, terrain, YlOrRd_r, Set2_r, winter_r, PuBu,
RdGy_r, spectral, rainbow, flag_r, jet_r, RdPu_r, gist_yarg, BuGn,
Paired_r,
hsv_r, bwr, cubehelix, Greens, PRGn, gist_heat, spectral_r, Paired, hsv,
Oranges_r, prism_r, Pastel2, Pastel1_r, Pastel1, gray_r, jet, Spectral_r,
gnuplot2_r, gist_earth, YlGnBu_r, copper, gist_earth_r, Set3_r, OrRd,
gnuplot_r, ocean_r, brg, gnuplot2, PuRd_r, bone_r, BuPu, Oranges, RdYlGn_r,
PiYG, CMRmap_r, YlGn, binary_r, gist_gray_r, Accent, BuPu_r, gist_gray,
flag, bwr_r, RdBu_r, BrBG, Reds, Set1_r, summer_r, GnBu_r, BrBG_r, Reds_r,
RdGy, PuRd, Accent_r, Blues, autumn_r, autumn, cubehelix_r,
nipy_spectral_r,
ocean, PRGn_r, Greys_r, pink, binary, winter, gnuplot, RdYlBu_r, hot,
YlOrBr, coolwarm_r, rainbow_r, Purples_r, PiYG_r, YlGn_r, Blues_r,
YlOrBr_r,
seismic, Purples, seismic_r, RdBu, Greys, BuGn_r, YlOrRd, PuOr, PuBuGn,
nipy_spectral, afmhot
root at bitscope:/home/pi/SampleExample#

So I thought the color scheme "inferno" is not supported (or may be not
installed in my pi). So I changed it to "coolwarm" and I see the image as
below.

<http://matplotlib.1069221.n5.nabble.com/file/t5142/plasma.png>

Though this is way better than my initial version, still I see only 2 color
combination... may be I need to check with color schemes provided in the
error message.

Thanks a lot any way. Also let me know if you think any suitable color
scheme for this kind of gradient.

Will check with you on other technical questions after I finish this.

Thanks again,

With best regards,
Phani.

--
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vincent.adrien · March 13, 2018, 3:16pm

Hi Phani,

I would make the same analysis and suggestion as Ben about the error that you got.

About the color map, any rather recent version of Matplotlib (let's say 1.5.3+ or 2+) should have a list of color maps close to the list here:
https://matplotlib.org/tutorials/colors/colormaps.html
A few of them may be missing if you are not using Matplotlib 2.2+, but that is really a few of them.

As your data seem to have only values of the same sign, I would advise for any sequential color scheme rather than a diverging one like "coolwarm" (except if the mid-range value has a very specific meaning that you would want to emphasize). The point of the "viridis" family? ("viridis", "inferno", "plasma", "magma", and recently "cividis") is to be perceptually uniform, which should thus be felt quite the same in color or gray scale printing, as well as by colorblind people.

Best,
Adrien

···

On March 13, 2018 6:29:07 AM PDT, Benjamin Root <ben.v.root at gmail.com> wrote:

The error message means you have an old version of matplotlib. Inferno
was
added in version 1.5. We are currently at verson 2.2.1 (supposedly will
be
released today?). I would also wonder if your install of numpy is old
as
well. Chances are, you are hitting on some old forgotten bug. Could you
try
updating your packages?

On Tue, Mar 13, 2018 at 6:49 AM, phanids <phanikumar.ds at gmail.com> >wrote:

Hi Adrien,

Thanks a lot. I tried your suggestion and initial got

root at phani:/home/pi/SampleExample# python Trial1.py
Traceback (most recent call last):
  File "Trial1.py", line 46, in <module>
    surf = ax.plot_surface(xx, yy, zz, cmap="inferno")
  File

"/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/axes3d.py",

line 1637, in plot_surface
    polyc = art3d.Poly3DCollection(polys, *args, **kwargs)
  File

"/usr/lib/python2.7/dist-packages/mpl_toolkits/mplot3d/art3d.py",

line 476, in __init__
    PolyCollection.__init__(self, verts, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py",

line

799, in __init__
    Collection.__init__(self, **kwargs)
  File "/usr/lib/python2.7/dist-packages/matplotlib/collections.py",

line

107, in __init__
    cm.ScalarMappable.__init__(self, norm, cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 197,

in

__init__
    self.cmap = get_cmap(cmap)
  File "/usr/lib/python2.7/dist-packages/matplotlib/cm.py", line 163,

in

get_cmap
    % (name, ', '.join(cmap_d.keys())))
ValueError: Colormap inferno is not recognized. Possible values are:
Spectral, summer, coolwarm, Wistia_r, pink_r, Set1, Set2, Set3,

brg_r,

Dark2, prism, PuOr_r, afmhot_r, terrain_r, PuBuGn_r, RdPu,

gist_ncar_r,

gist_yarg_r, Dark2_r, YlGnBu, RdYlBu, hot_r, gist_rainbow_r,

gist_stern,

PuBu_r, cool_r, cool, gray, copper_r, Greens_r, GnBu, gist_ncar,

spring_r,

gist_rainbow, gist_heat_r, Wistia, OrRd_r, CMRmap, bone,

gist_stern_r,

RdYlGn, Pastel2_r, spring, terrain, YlOrRd_r, Set2_r, winter_r, PuBu,
RdGy_r, spectral, rainbow, flag_r, jet_r, RdPu_r, gist_yarg, BuGn,
Paired_r,
hsv_r, bwr, cubehelix, Greens, PRGn, gist_heat, spectral_r, Paired,

hsv,

Oranges_r, prism_r, Pastel2, Pastel1_r, Pastel1, gray_r, jet,

Spectral_r,

gnuplot2_r, gist_earth, YlGnBu_r, copper, gist_earth_r, Set3_r, OrRd,
gnuplot_r, ocean_r, brg, gnuplot2, PuRd_r, bone_r, BuPu, Oranges,

RdYlGn_r,

PiYG, CMRmap_r, YlGn, binary_r, gist_gray_r, Accent, BuPu_r,

gist_gray,

flag, bwr_r, RdBu_r, BrBG, Reds, Set1_r, summer_r, GnBu_r, BrBG_r,

Reds_r,

RdGy, PuRd, Accent_r, Blues, autumn_r, autumn, cubehelix_r,
nipy_spectral_r,
ocean, PRGn_r, Greys_r, pink, binary, winter, gnuplot, RdYlBu_r, hot,
YlOrBr, coolwarm_r, rainbow_r, Purples_r, PiYG_r, YlGn_r, Blues_r,
YlOrBr_r,
seismic, Purples, seismic_r, RdBu, Greys, BuGn_r, YlOrRd, PuOr,

PuBuGn,

nipy_spectral, afmhot
root at bitscope:/home/pi/SampleExample#

So I thought the color scheme "inferno" is not supported (or may be

not

installed in my pi). So I changed it to "coolwarm" and I see the

image as

below.

<http://matplotlib.1069221.n5.nabble.com/file/t5142/plasma.png>

Though this is way better than my initial version, still I see only 2

color

combination... may be I need to check with color schemes provided in

the

error message.

Thanks a lot any way. Also let me know if you think any suitable

color

scheme for this kind of gradient.

Will check with you on other technical questions after I finish this.

Thanks again,

With best regards,
Phani.

--
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f28077.html
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phanikumar.ds · March 15, 2018, 9:54am

Hi Benjamin, Adrien,

You guys are awesome !!!

//Earlier versions
root at phani:/home/pi/SampleExample# python -c 'import matplotlib; print
matplotlib.__version__'
*1.4.2 *

root at phani:/home/pi/SampleExample# python -c "import numpy; print
(numpy.__version__)"
*1.8.2*

did *python -mpip install -U matplotlib* for update and then

root at phani:/home/pi/SampleExample# python -c 'import matplotlib; print
matplotlib.__version__'
*2.2.0*

root at phani:/home/pi/SampleExample# python -c "import numpy; print
(numpy.__version__)"
*1.14.2*

But when I run it, I get below warning message...

root at phani:/home/pi/SampleExample# python Trial1.py

*/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_gtk3.py:181:
Warning: Source ID 7 was not found when attempting to remove it
GLib.source_remove(self._idle_draw_id)*

1. Still the plotting happens (attached). Googling says there is nothing to
worry about the warning. Do you have any suggestion for me?

2. Is there any way I can set the grid color to light blue (as in the
original image)? May be it helps in better highlighting the plot (than which
is currently white).

3. In original image, also there is a "shade" of the plot on X - axis. Is
there any way we can get the shade? Basically it would help to find the
range more exactly as the X-Axis would have the scale.

4. This python script, I am calling from QT. Is there any way, I can call
matplotlib libraries from QT itself?

Thanks a lot,

With best regards,
Phani.

<http://matplotlib.1069221.n5.nabble.com/file/t5142/plasma.png>

···

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system · March 15, 2018, 7:38pm

Hi Phani,

1. The warning may be simply related to the backend that you are using.
You could give a shot to other backends if there are avalaible on your
setup. See for example the lines:

mpl.use("Qt5Agg")  # or TkAgg or any other available backend
import matplotlib.pyplot as plt

at the top in the attached file `example_v2.png`.

2. For the edge line color, please have a look at the call of
`ax.plot_surface` in that script. You can indeed pass keyword arguments
like "edgecolor" or "linewidth".

3. I am not sure of what you mean about the shade on the x-axis.

4. I am out of my depth there :/.

Also I realized that the trick to pin the z-axis labels onto the left
side produces weird grid lines for that axis. Maybe Ben would have a
better solution (i.e. a real one...), but in the meantime, I suggested
another workaround in the script, which leads to the attached PNG.

Best,
Adrien

Hi Benjamin, Adrien,

You guys are awesome !!!

//Earlier versions
root at phani:/home/pi/SampleExample# python -c 'import matplotlib; print
matplotlib.__version__'
*1.4.2 *

root at phani:/home/pi/SampleExample# python -c "import numpy; print
(numpy.__version__)"
*1.8.2*

did *python -mpip install -U matplotlib* for update and then

root at phani:/home/pi/SampleExample# python -c 'import matplotlib; print
matplotlib.__version__'
*2.2.0*

root at phani:/home/pi/SampleExample# python -c "import numpy; print
(numpy.__version__)"
*1.14.2*

But when I run it, I get below warning message...

root at phani:/home/pi/SampleExample# python Trial1.py

*/usr/local/lib/python2.7/dist-packages/matplotlib/backends/backend_gtk3.py:181:
Warning: Source ID 7 was not found when attempting to remove it
GLib.source_remove(self._idle_draw_id)*

1. Still the plotting happens (attached). Googling says there is nothing to
worry about the warning. Do you have any suggestion for me?

2. Is there any way I can set the grid color to light blue (as in the
original image)? May be it helps in better highlighting the plot (than which
is currently white).

3. In original image, also there is a "shade" of the plot on X - axis. Is
there any way we can get the shade? Basically it would help to find the
range more exactly as the X-Axis would have the scale.

4. This python script, I am calling from QT. Is there any way, I can call
matplotlib libraries from QT itself?

Thanks a lot,

With best regards,
Phani.

<http://matplotlib.1069221.n5.nabble.com/file/t5142/plasma.png>

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On 03/15/2018 02:54 AM, phanids wrote: