PlotBasics: Difference between revisions

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Line 31: Line 31:
they are fun.   
they are fun.   
<source lang="Python">
<source lang="Python">
# initialize arrays and read in data from the web
SN_list = ['']        
# list of names
SN_list = ['']
z_array = np.array([])
z_array = np.array([])
mod_array = np.array([])
mod_array = np.array([])
Line 46: Line 44:
     moderr_array = np.append(moderr_array,np.float64(moderr))   
     moderr_array = np.append(moderr_array,np.float64(moderr))   
f.close()
f.close()
<\source>
</source>


 
Now to the plotting.
# First we close whatever windows we might have:
First we close whatever windows we might have:
<source lang="Python">
plt.close()
plt.close()
</source>


# Now let us plot some points
Now let us plot some points:
<source lang="Python">
plt.plot(z_array, mod_array)
plt.plot(z_array, mod_array)
 
</source>
# Notice it is a mess, by default it connects the lines
Notice it is a mess; by default it connects the lines.
# We close the window with plt.close()
We will close it and start over.
temp=raw_input("hit enter to show next plot")
<source lang="Python">
plt.close()
plt.close()
</source>


# We clearly need axes lables
We clearly needs a title and axes labels
<source lang="Python">
plt.title("Union2 SN Cosmology Data")
plt.xlabel('z', fontsize=20)
plt.xlabel('z', fontsize=20)
# But we want a Greek Letter, so we can put some LaTeX syle code with the r command:
</source>
 
But we want a Greek Letter, so we can put some LaTeX syle code with the r command:
<source lang="Python">
plt.ylabel(r'$\mu=m-M$', fontsize=20)
plt.ylabel(r'$\mu=m-M$', fontsize=20)
plt.title("Union2 SN Cosmology Data")
</source>
# Now we add a format string, as follows:
 
Now we add a format string to the plot command:
<source lang="Python">
plt.plot(z_array, mod_array,'ro')
plt.plot(z_array, mod_array,'ro')
Now this looks better, we have red circles
</source>
temp=raw_input("hit enter to show next plot")
 
Now this looks better, we have red circles
 
Now we start a new plot:
<source lang="Python">
plt.close()
plt.close()



Revision as of 14:44, 31 October 2011

3 Ways to plot

There are three ways to go about plotting in matplotlib.

1. You can use the pylab environment

2. You can use the matplotlib.pyplot environment, with plotting commands and functions.

3. You can define plot objects, and then use the pyplot methods on those objects.

The last way gives you most control, but the other two are somewhat easier. We will give examples using the last two ways here.

Supernova Cosmology Example

  1. We will import the pyplot and numpy packages
import numpy as np
import matplotlib.pyplot as plt


We are going to download data from the internet so

import urllib

Begin by reading the Union2 SN cosmology data from LBL, because they are fun.

SN_list = ['']          
z_array = np.array([])
mod_array = np.array([])
moderr_array = np.array([])
f = urllib.urlopen('http://supernova.lbl.gov/Union/figures/SCPUnion2_mu_vs_z.txt')
for line in f:
    if line[0] == '#': continue    # Ignore anything that starts with a #
    SN, z, mod, moderr = line.split()
    SN_list.append(SN)
    z_array = np.append(z_array,np.float64(z))
    mod_array = np.append(mod_array,np.float64(mod))
    moderr_array = np.append(moderr_array,np.float64(moderr))   
f.close()

Now to the plotting. First we close whatever windows we might have:

plt.close()

Now let us plot some points:

plt.plot(z_array, mod_array)

Notice it is a mess; by default it connects the lines. We will close it and start over.

plt.close()

We clearly needs a title and axes labels

plt.title("Union2 SN Cosmology Data")
plt.xlabel('z', fontsize=20)

But we want a Greek Letter, so we can put some LaTeX syle code with the r command:

plt.ylabel(r'$\mu=m-M$', fontsize=20)

Now we add a format string to the plot command:

plt.plot(z_array, mod_array,'ro')

Now this looks better, we have red circles

Now we start a new plot: <source lang="Python"> plt.close()


  1. Now let's plot with the error bars

plt.errorbar(z_array, mod_array, yerr=moderr_array, fmt='.')

  1. And putting lables and colors we can do:

plt.xlabel(r'$z$', fontsize=20) plt.ylabel(r'$\mu=m-M$', fontsize=20) plt.title("Union2 SN Cosmology Data") plt.errorbar(z_array, mod_array, yerr=moderr_array, fmt='.', capsize=0,

   elinewidth=1.0, ecolor=(0.6,0.0,1.0), color='green' )
  1. Notice that colors can be specified in the format commond, on in a color command.
  2. They can be given via an RGB tuple, a name, or a single number between 0 and 1 for
  3. gray scale.
  1. Now we can save it as a pdf, or most other formats, with:
  2. plt.savefig('Union2_plot1.pdf', format="pdf", transparent=True, bbox_inches='tight')

temp=raw_input("hit enter to show next plot") plt.close()

  1. Now there are a lot of points, so let's figure our what our distribution is in z

plt.hist(z_array, 25)

  1. And slap a label on it

plt.xlabel(r'$z$', fontsize=20)

temp=raw_input("hit enter to show next plot") plt.close()

  1. Now, let's find the real distance from the distance modulus.
  2. To do this we will define a function and a constant

def distance_Mly(m,z):

   return 0.0000326 * (10**(m/5)) / (1.0 + z)

c = 299792.458 # km/s

  1. Now:

d_array = distance_Mly(mod_array,z_array)

  1. Now we will calculate the error bars in the distance, both ways:

d_error_plus = distance_Mly((mod_array+moderr_array),z_array) - d_array d_error_minus = d_array - distance_Mly((mod_array-moderr_array),z_array)

  1. And plot the graph with asymetrical horizontal error bars, and lables
  2. Notice the different color formats that can be used.

plt.errorbar(d_array, c*z_array, xerr=(d_error_minus,d_error_plus), fmt='s',

   capsize=5, elinewidth=1.0, color=(0.4,0.0,1.0), ecolor='aqua', barsabove=True)

plt.ylabel('cz (km/s)', fontsize=15, color='0.0') plt.xlabel('Distance (Mly)', fontsize=10, color='g') plt.title("Union2 SN Cosmology Data", color=(0.4,0.0,1.0))

temp=raw_input("hit enter to show next plot") plt.close()

  1. Now we will plot with a second vertical and horizontal axis

plt.errorbar(d_array/1000.0, c*z_array, xerr=(d_error_minus/1000.0,d_error_plus/1000.0), fmt='.',

   capsize=0, elinewidth=1.0, color=(0.4,0.0,1.0), ecolor='aqua', barsabove=True)
  1. Now we make room for each axis

plt.subplots_adjust(right=0.875, top=0.8)

plt.ylabel('cz (km/s)', fontsize=15, color='aqua') plt.xlabel('Distance (Gly)', fontsize=15, color='aqua') axes1_range = np.array( plt.axis() ) # get the default axes and convert to n array print(axes1_range)

axes2_range = 1.0*axes1_range # Don't forget, we need to make it copy it. axes2_range[0:2] = 1000*axes1_range[0:2]/3.26 # set second y-axis to z axes2_range[2:4] = axes1_range[2:4]/c # set second y-axis to z print(axes2_range)

  1. now we switch to the second axis

temp=raw_input("hit enter to show next plot") plt.twinx() # This swaps the Y axis plt.ylabel('z', fontsize=15, color='r') # I am not sure why this has to be before plt.twiny() plt.twiny() # This swaps the X axis plt.xlabel('Distance (Mpc)', fontsize=15, color='purple') plt.axis(axes2_range, axisbg='#d0,1f,ff') plt.title("Union2 SN Cosmology Data", color=(0.4,0.0,1.0), x=0.5, y=1.15)