Re: [Tutor] Plotting with python

[Oscar Benjamin]

On 31 October 2015 at 00:00, Terry Carroll  wrote:
> If you were going to get started doing some simple plotting with Python 2.7
> (in my case, I'm simply plotting temperature against time-of-day) what would
> you use?
>
>  - matplotlib [1]
>  - gnuplot [2]
>  - something else entirely?

I'd use matplotlib.

> Assume no substantial familiarity with the underlying plotting software, let
> alone the Python bindings.
>
> The only thing I can think of that might be special is to specify the
> upper/lower bounds of the plot; for example, in my case, I know the
> temperatures vary between somewhere around 70-78 degrees F., so I'd want the
> Y-axis to go, say 60-90, not arbitrarily start at zero; but I suspect this
> is a pretty standard thing in almost any plotting package.

This is straightforward in most plotting packages. Here's a simple
example of doing it in matplotlib:

#!/usr/bin/env python3

import matplotlib.pyplot as plt

times = [0, 1, 2, 3, 4, 5]  # hours
temperatures = [68, 70, 75, 73, 72, 71] # Fahrenheit

fig = plt.figure(figsize=(5, 4))
ax = fig.add_axes([0.15, 0.15, 0.70, 0.70])
ax.plot(times, temperatures)
ax.set_xlabel('Time (hours)')
ax.set_ylabel(r'Temp ($^{\circ}\mathrm{F}$)')
ax.set_title('Temperature vs time')

plt.show()

--
Oscar
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Re: [Tutor] Plotting with python

[Laura Creighton]

I'd use matplotlib, unless the ultimate goal is to render onto a
webpage.  Then I would use bokeh. 

http://bokeh.pydata.org/en/latest/

Laura
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[Tutor] Plotting with python

[Terry Carroll]

If you were going to get started doing some simple plotting with Python 
2.7 (in my case, I'm simply plotting temperature against time-of-day) what 
would you use?


 - matplotlib [1]
 - gnuplot [2]
 - something else entirely?


Assume no substantial familiarity with the underlying plotting software, 
let alone the Python bindings.


The only thing I can think of that might be special is to specify the 
upper/lower bounds of the plot; for example, in my case, I know the 
temperatures vary between somewhere around 70-78 degrees F., so I'd want 
the Y-axis to go, say 60-90, not arbitrarily start at zero; but I suspect 
this is a pretty standard thing in almost any plotting package.


[1] http://matplotlib.org/api/pyplot_api.html
[2] http://gnuplot-py.sourceforge.net/
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Re: [Tutor] Plotting with python

[Mark Lawrence]

On 31/10/2015 00:00, Terry Carroll wrote:

If you were going to get started doing some simple plotting with Python
2.7 (in my case, I'm simply plotting temperature against time-of-day)
what would you use?

  - matplotlib [1]
  - gnuplot [2]
  - something else entirely?

Assume no substantial familiarity with the underlying plotting software,
let alone the Python bindings.

The only thing I can think of that might be special is to specify the
upper/lower bounds of the plot; for example, in my case, I know the
temperatures vary between somewhere around 70-78 degrees F., so I'd want
the Y-axis to go, say 60-90, not arbitrarily start at zero; but I
suspect this is a pretty standard thing in almost any plotting package.

[1] http://matplotlib.org/api/pyplot_api.html
[2] http://gnuplot-py.sourceforge.net/



matplotlib, I gave up gnuplot in favour of it maybe 15 years ago and 
have never looked back.


--
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.

Mark Lawrence

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Re: [Tutor] Plotting with python

[Martin A. Brown]

>> If you were going to get started doing some simple plotting with Python
>> 2.7 (in my case, I'm simply plotting temperature against time-of-day)
>> what would you use?
>>
>>  - matplotlib [1]
>>  - gnuplot [2]
>>  - something else entirely?
>>
>> Assume no substantial familiarity with the underlying plotting software,
>> let alone the Python bindings.
>>
>> The only thing I can think of that might be special is to specify the
>> upper/lower bounds of the plot; for example, in my case, I know the
>> temperatures vary between somewhere around 70-78 degrees F., so I'd want
>> the Y-axis to go, say 60-90, not arbitrarily start at zero; but I
>> suspect this is a pretty standard thing in almost any plotting package.
>>
>> [1] http://matplotlib.org/api/pyplot_api.html
>> [2] http://gnuplot-py.sourceforge.net/
>
> matplotlib, I gave up gnuplot in favour of it maybe 15 years ago and have 
> never
> looked back.

I think my transition was later and I'm modestly bilingual with 
these tools.  However, in principle, I agree with Mark--IF you are 
primarily using Python as your tool for massaging and exploring 
data.

If you are, then I might add one more suggestion.  There's a project 
called 'IPython' [0] which has built a very nicely extended and 
richer interactive interface to the Python interpreter.  You can use 
IPython as a replacement for the Python interactive shell.  I have 
for years, and it's wonderful (even though, I also use the 
interactive shell that ships with the system supplied Python I use).

Why am I talking about IPython?  Aside from other benefits, the 
IPython Notebook [1] is directly useful to those who are also 
matplotlib users, because it allows you to record an entire analysis 
session, display graphics inline (see macro "%matplotlib inline") 
and then later, share the data explorations in a web browser.

N.B. I have not found any running, public IPython Notebooks.  This 
doesn't surprise me, because of the security risks of allowing just 
anybody access to a Python instance is like letting strangers into 
your kitchen.  They might eat all of your food, or try to crack that 
safe behind the portrait in the dining room.

  http://calebmadrigal.com/graph-ipython-notebook/

So, if I were in your shoes, starting today, I'd install IPython and 
matplotlib and then fire up the IPython Notebook on my local 
machine, type '%matplotlib inline' and start trying to display my 
data.  One nice feature of matplotlib is that it autoscales by 
default.  So, if all of your values (temperature) are within the 
range you want to display, you don't need to mess with the axes.

See their tutorial:

  http://matplotlib.org/users/pyplot_tutorial.html

Good luck and enjoy!

-Martin

 [0] http://ipython.org/
 [1] http://ipython.org/notebook.html

-- 
Martin A. Brown
http://linux-ip.net/
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Re: [Tutor] plotting in python

[stm atoc]

The output of the print len(Conc[0]), len(z) is 100 3600.
Now I changed Conc[0] to Conc[1], and the output is: 100 100
But still I need to see from Concentration from 0.


On Thu, Dec 1, 2011 at 5:26 AM, Asokan Pichai paso...@talentsprint.com wrote:
 On Thu, Dec 1, 2011 at 2:38 AM, stm atoc stm.at...@googlemail.com wrote:
 Hi there,

 I have a question regarding plotting with Python.

 I have the following python script:

 [SNIPPED]
 plot(Conc[0],z)

 [SNIPPED]
 ---So, What would you suggest?

 What is the output of
 print len(Conc[0]), len(z)

 You may insert that line above the plot and see

 Asokan Pichai
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Re: [Tutor] plotting in python

[Andreas Perstinger]

[Please don't top-post. Put your answers below the text you cite.]

On 2011-12-01 09:01, stm atoc wrote:

The output of the print len(Conc[0]), len(z) is 100 3600.
Now I changed Conc[0] to Conc[1], and the output is: 100 100


So, you've changed the line

print len(Conc[0]), len(z)

to

print len(Conc[1]), len(z)

and the only thing that changed in the output is the length of z which 
is calculated independently of Conc in your script?


This would be very strange.

Does your script run if you use Conc[1] (or some other indexes) 
instead of Conc[0] when you call the plot-function?
If yes, it's very likely that you have the wrong data in Conc[0]. 
But that's impossible to tell without your data file (ourtest_out.list).


Bye, Andreas
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Re: [Tutor] plotting in python

[Andreas Perstinger]

[Still top-posting :-( ]

On 2011-12-01 11:13, stm atoc wrote:

Well, I did also change the line in the python script to this:

plot(Conc[0],z,'r-',label='initial')
plot(Conc[1],z,'b-',label='after 20s')

to see both Conc[0] and [1].


And did it work?


I will send the output data attaches to this email  (ourtest_out.list).

I wonder if this way is fine.


I'm not sure about the policy regarding attachements on this list but I 
think it would have been better to provide a link than attach it.


Anyways, I've reduced your original script, did a test run and it works 
as expected (at least it shows a plot):


import numpy
import matplotlib.pyplot as pyplot

with open(ourtest_out.list, r) as f:
z = numpy.array([float(v) for v in f.readline().split()[1:]])

a = numpy.loadtxt(ourtest_out.list, skiprows=3)
N = 100
Conc = a[1:, N+1:]

print len(Conc[0]) == len(z)

pyplot.figure()
pyplot.plot(Conc[0], z)
pyplot.show()

Do you still get an error?

Bye, Andreas
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Re: [Tutor] plotting in python

[stm atoc]

For previous script that I have written, I had trouble having one plot
for all data at the same time and I could see two line for Conc[0] and
Conc[1] separately. Now, even I modified Conc = a[1:, N+1:] to  Conc =
a[0:, N+1:], still one plot is created...which is pretty good and no
error!

Thank you so much,
Sue

On Thu, Dec 1, 2011 at 12:39 PM, Andreas Perstinger
andreas.perstin...@gmx.net wrote:
 [Still top-posting :-( ]


 On 2011-12-01 11:13, stm atoc wrote:

 Well, I did also change the line in the python script to this:

 plot(Conc[0],z,'r-',label='initial')
 plot(Conc[1],z,'b-',label='after 20s')

 to see both Conc[0] and [1].


 And did it work?


 I will send the output data attaches to this email  (ourtest_out.list).

 I wonder if this way is fine.


 I'm not sure about the policy regarding attachements on this list but I
 think it would have been better to provide a link than attach it.

 Anyways, I've reduced your original script, did a test run and it works as
 expected (at least it shows a plot):

 import numpy
 import matplotlib.pyplot as pyplot

 with open(ourtest_out.list, r) as f:
    z = numpy.array([float(v) for v in f.readline().split()[1:]])

 a = numpy.loadtxt(ourtest_out.list, skiprows=3)
 N = 100
 Conc = a[1:, N+1:]

 print len(Conc[0]) == len(z)

 pyplot.figure()
 pyplot.plot(Conc[0], z)
 pyplot.show()

 Do you still get an error?

 Bye, Andreas
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[Tutor] plotting in python

[stm atoc]

Hi there,

I have a question regarding plotting with Python.

I have the following python script:

# coding: utf-8
from pylab import *
import numpy

filename='ourtest_out.list'

fh=open(filename)
line=fh.readline()
fh.close

z=array([ float(val) for val in line.split()[1:] ])


a = numpy.loadtxt(filename,skiprows=3)
N=100
t = a[:,0]
nu = a[0:,1:N+1]
#Conc = a[1:,N+1:]
Conc = a[1:,N+1:]

levels=arange(-10,1)
levels=levels[-3]-levels
t=t/360.

figure()
plot(Conc[0],z)

xlabel('C')
ylabel('z')
#show()
savefig('Conc.png')
close()

#nu
figure()
lw = 2.0 #linewidth
dpi = 96

levels=arange(-10,1)
levels=levels[-3]-levels
plot(nu[0],z)
xlabel('nu')
ylabel('z')
savefig('nu.png')
close()


However, once I run the program (run.py)

I have error like this:

---
ValueErrorTraceback (most recent call last)
/Users/…./run.py in module()
 24
 25 figure()
--- 26 plot(Conc[0],z)
 27
 28 xlabel('C')

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/pyplot.py
in plot(*args, **kwargs)
   2284 ax.hold(hold)
   2285 try:
- 2286 ret = ax.plot(*args, **kwargs)
   2287 draw_if_interactive()
   2288 finally:

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in plot(self, *args, **kwargs)
   3781 lines = []
   3782
- 3783 for line in self._get_lines(*args, **kwargs):
   3784 self.add_line(line)
   3785 lines.append(line)

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _grab_next_args(self, *args, **kwargs)
315 return
316 if len(remaining) = 3:
-- 317 for seg in self._plot_args(remaining, kwargs):
318 yield seg
319 return

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _plot_args(self, tup, kwargs)
292 x = np.arange(y.shape[0], dtype=float)
293
-- 294 x, y = self._xy_from_xy(x, y)
295
296 if self.command == 'plot':

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _xy_from_xy(self, x, y)
232 y = np.atleast_1d(y)
233 if x.shape[0] != y.shape[0]:
-- 234 raise ValueError(x and y must have same first dimension)
235 if x.ndim  2 or y.ndim  2:
236 raise ValueError(x and y can be no greater than 2-D)

ValueError: x and y must have same first dimension


---So, What would you suggest?
Thanks in advance,
Sue
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Re: [Tutor] plotting in python

[Wayne Werner]

On Wed, Nov 30, 2011 at 3:08 PM, stm atoc stm.at...@googlemail.com wrote:

 Hi there,

 I have a question regarding plotting with Python.

 snip
 ValueError: x and y must have same first dimension


It looks like  something is wrong with the data that you're trying to plot.
Specifically, the data that you're trying to plot has the wrong dimensions
(like it says).

An example:

# 2d space:
x = [(1, 1), (2, 2), (3,3)]
y = [(1,1,1), (2,2,2), (3,3,3)]

x is a series of points in 2 dimensions, and y is a series in 3. If your
data really is supposed to look like that then you'll need to pad or trim
the data so you've got the correct dimensions.

HTH,
Wayne
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Re: [Tutor] plotting in python

[Emile van Sebille]

On 11/30/2011 1:08 PM stm atoc said...

Hi there,

I have a question regarding plotting with Python.

I have the following python script:

# coding: utf-8
from pylab import *
import numpy

filename='ourtest_out.list'

fh=open(filename)
line=fh.readline()
fh.close

z=array([ float(val) for val in line.split()[1:] ])


a = numpy.loadtxt(filename,skiprows=3)
N=100
t = a[:,0]
nu = a[0:,1:N+1]
#Conc = a[1:,N+1:]
Conc = a[1:,N+1:]

levels=arange(-10,1)
levels=levels[-3]-levels
t=t/360.

figure()
plot(Conc[0],z)

xlabel('C')
ylabel('z')
#show()
savefig('Conc.png')
close()

#nu
figure()
lw = 2.0 #linewidth
dpi = 96

levels=arange(-10,1)
levels=levels[-3]-levels
plot(nu[0],z)
xlabel('nu')
ylabel('z')
savefig('nu.png')
close()


However, once I run the program (run.py)

I have error like this:

---
ValueErrorTraceback (most recent call last)
/Users/…./run.py inmodule()
  24
  25 figure()
---  26 plot(Conc[0],z)
  27
  28 xlabel('C')

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/pyplot.py
in plot(*args, **kwargs)
2284 ax.hold(hold)
2285 try:
-  2286 ret = ax.plot(*args, **kwargs)
2287 draw_if_interactive()
2288 finally:

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in plot(self, *args, **kwargs)
3781 lines = []
3782
-  3783 for line in self._get_lines(*args, **kwargs):
3784 self.add_line(line)
3785 lines.append(line)

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _grab_next_args(self, *args, **kwargs)
 315 return
 316 if len(remaining)= 3:
--  317 for seg in self._plot_args(remaining, kwargs):
 318 yield seg
 319 return

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _plot_args(self, tup, kwargs)
 292 x = np.arange(y.shape[0], dtype=float)
 293
--  294 x, y = self._xy_from_xy(x, y)
 295
 296 if self.command == 'plot':

/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
in _xy_from_xy(self, x, y)
 232 y = np.atleast_1d(y)
 233 if x.shape[0] != y.shape[0]:
--  234 raise ValueError(x and y must have same first dimension)
 235 if x.ndim  2 or y.ndim  2:
 236 raise ValueError(x and y can be no greater than 2-D)

ValueError: x and y must have same first dimension


---So, What would you suggest?


Looking over the traceback and code, it would appear the error is saying 
that there is an inconsistency with the arguments expected vs the 
arguments passed, which appears in this case to relate to ...


plot(Conc[0],z)

... which derives its parameters from the two lines ...

z=array([ float(val) for val in line.split()[1:] ])

... and ...

a = numpy.loadtxt(filename,skiprows=3)


So, I'd conclude that I'd need a better understanding of how to use the 
functions plot, array and numpy.loadtext.  Neither plot nor array are 
python builtins nor defined within your script, so they're likely 
brought in from ...


from pylab import *

... which is generally not something you want to do except when first 
starting to experiment and learn a new module, and then I'd keep things 
to the interactive interpreter for testing and discovery.  This form of 
import is generally thought of as polluting the namespace and may allow 
library specific names to mask python builtins.  For example. suppose a 
module 'xyz' contains a special 'print' function.  Executing 'from xyz 
import *' would shadow the python builtin print function essentially 
making it inaccessible.  It's possible (although unlikely in the case of 
pylab specifically) that any python builtins that are used in your 
script have been replaced with pylab versions.  A better technique is to 
simply import pylab and refer to its functions as pylab.xyz so that no 
ambiguity is possible.


So, read up on pylab, find their support list [1], and follow up there. 
 We focus mainly on getting you far enough along with python basics and 
generally leave specific library support to the library authors and 
support groups.


HTH

Emile


[1] start at http://www.scipy.org/Mailing_Lists

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Re: [Tutor] plotting in python

[Asokan Pichai]

On Thu, Dec 1, 2011 at 2:38 AM, stm atoc stm.at...@googlemail.com wrote:
 Hi there,

 I have a question regarding plotting with Python.

 I have the following python script:

[SNIPPED]
 plot(Conc[0],z)

[SNIPPED]
 ---So, What would you suggest?

What is the output of
print len(Conc[0]), len(z)

You may insert that line above the plot and see

Asokan Pichai
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[Tutor] plotting with python

[Bala subramanian]

Friends,
I am not sure if this forum is appropriate to ask question about a
particular package. After getting suggestions from some of you for python
based plotting, I have just started with matplotlib. I am bit confused with
the relation between matplotlib and pylab.

In the matplotlib homepage, example plots are shown with both *
matplotlib.pyplot* and* pylab*. Inaddition within matplotlib, there is a
module called *matplotlib.pylab*

i) matplotlib and pylab - both are same or different modules ?. Is there
any advantage of using one over the other ?

ii) Is it like i can plot the graphs with both matplotlib and pylab ?

iii) can some kindly show me an example of ploting multy Y axes plot, ie
NXY.

Thanks in advance,
Bala
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Re: [Tutor] plotting with python

[Kent Johnson]

On Fri, Mar 27, 2009 at 7:46 AM, Bala subramanian
bala.biophys...@gmail.com wrote:
 Friends,
 I am not sure if this forum is appropriate to ask question about a
 particular package. After getting suggestions from some of you for python
 based plotting, I have just started with matplotlib. I am bit confused with
 the relation between matplotlib and pylab.

 In the matplotlib homepage, example plots are shown with both
 matplotlib.pyplot and pylab. Inaddition within matplotlib, there is a module
 called matplotlib.pylab

 i) matplotlib and pylab - both are same or different modules ?. Is there
 any advantage of using one over the other ?

 ii) Is it like i can plot the graphs with both matplotlib and pylab ?

IIUC, pylab is part of matplotlib. It provides a simplified,
functional (not object-oriented) interface to matplotlib. Using
matplotlib directly gives you more control over the result.

 iii) can some kindly show me an example of ploting multy Y axes plot, ie NXY.
Take a look at the gallery for something similar to what you want.
Clicking on a gallery image will show you a larger image and the code
that created it.
http://matplotlib.sourceforge.net/gallery.html

Kent
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Re: [Tutor] plotting with python

[greg whittier]

matplotlib and pylab are two APIs to the same library.  Using
matplotlib is a more object-oriented, pythonic API.  pylab is modeled
after the Matlab plotting functions to make it easier for those coming
from that environment.

There's a matplotlib mailing list and you can often figure out what
you need from perusing the examples and the thumbnail gallery.  In
your case, I think
http://matplotlib.sourceforge.net/examples/api/two_scales.html is what
you want.

On Fri, Mar 27, 2009 at 7:46 AM, Bala subramanian
bala.biophys...@gmail.com wrote:
 Friends,
 I am not sure if this forum is appropriate to ask question about a
 particular package. After getting suggestions from some of you for python
 based plotting, I have just started with matplotlib. I am bit confused with
 the relation between matplotlib and pylab.

 In the matplotlib homepage, example plots are shown with both
 matplotlib.pyplot and pylab. Inaddition within matplotlib, there is a module
 called matplotlib.pylab

 i) matplotlib and pylab - both are same or different modules ?. Is there
 any advantage of using one over the other ?

 ii) Is it like i can plot the graphs with both matplotlib and pylab ?

 iii) can some kindly show me an example of ploting multy Y axes plot, ie
 NXY.

 Thanks in advance,
 Bala


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