interactive example: interactive_2d

This example shows how to use nmrglue and matplotlib to create a simple interactive environment for examining a 2D spectrum from a NMRPipe file.

[source code]

#! /usr/bin/env python
# Create contour plots of a 2D NMRPipe spectrum

import nmrglue as ng
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm

# plot parameters
cmap = matplotlib.cm.Blues_r    # contour map (colors to use for contours)
contour_start   = 30000     # contour level start value
contour_num     = 20        # number of contour levels
contour_factor  = 1.20      # scaling factor between contour levels

# calculate contour levels
cl = [contour_start*contour_factor**x for x in xrange(contour_num)]

# read in the data from a NMRPipe file
dic,data = ng.pipe.read("../../common_data/2d_pipe/test.ft2")

# make ppm scales
uc_13c = ng.pipe.make_uc(dic,data,dim=1)
ppm_13c = uc_13c.ppm_scale()
uc_15n = ng.pipe.make_uc(dic,data,dim=0)
ppm_15n = uc_15n.ppm_scale()

# create the figure
fig = plt.figure()
ax = fig.add_subplot(111)

# plot the contours
etup = (ppm_13c[0],ppm_13c[-1],ppm_15n[0],ppm_15n[-1])
ax.contour(data,cl,cmap=cmap,extent=etup)

# decorate the axes
ax.set_ylabel("15N (ppm)")
ax.set_xlabel("13C (ppm)")
ax.set_title("Protein 2D NCa Spectrum")
ax.set_xlim(70,40)
ax.set_ylim(135,100)

# start interactive session, script ends when window is closed
plt.show()