Author: tlinnet
Date: Thu Nov 27 17:57:00 2014
New Revision: 26790
URL: http://svn.gna.org/viewcvs/relax?rev=26790&view=rev
Log:
Added systemtest Nmrglue.xtest_plot_contour to test the functionality of
contour plotting.
Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to
nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion:
https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html
Modified:
branches/nmrglue/lib/software/nmrglue.py
branches/nmrglue/pipe_control/nmrglue.py
branches/nmrglue/test_suite/system_tests/nmrglue.py
Modified: branches/nmrglue/lib/software/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/software/nmrglue.py?rev=26790&r1=26789&r2=26790&view=diff
==============================================================================
--- branches/nmrglue/lib/software/nmrglue.py (original)
+++ branches/nmrglue/lib/software/nmrglue.py Thu Nov 27 17:57:00 2014
@@ -23,13 +23,90 @@
"""Module for the wrapper functions around the nmrglue module."""
# Python module imports.
-from re import search, split
+from numpy import arange
+import matplotlib.pyplot as plt
+import matplotlib.cm
# relax module imports.
from extern import nmrglue
from lib.errors import RelaxError
from lib.io import get_file_path
from lib.spectrum.objects import Nmrglue_data
+
+
+def contour_plot(spectrum_id=None, contour_start=30000., contour_num=20,
contour_factor=1.20, ppm=True, show=False):
+ """Plot the spectrum as contour plot.
+
+ @keyword spectrum_id: The spectrum identification string.
+ @type spectrum_id: str or list of str
+ @keyword contour_start: Contour level start value
+ @type contour_start: float
+ @keyword contour_num: Number of contour levels
+ @type contour_num: int
+ @keyword contour_factor: Scaling factor between contour levels
+ @type contour_factor: float
+ @keyword ppm: A flag which if True will make the plot in
ppm scale. Else it is in points.
+ @type ppm: bool
+ @keyword show: A flag which if True will make a call to
matplotlib.pyplot.show().
+ @type show: bool
+ @return: The matplotlib.axes.AxesSubplot class, which
can be manipulated to add additional text to the axis.
+ @rtype: matplotlib.axes.AxesSubplot
+ """
+
+ # Extract the data.
+ dic = cdp.ngdata[spectrum_id].dic
+ udic = cdp.ngdata[spectrum_id].udic
+ data = cdp.ngdata[spectrum_id].data
+
+ # Setup plot parameters
+ # contour map (colors to use for contours)
+ cmap = matplotlib.cm.Blues_r
+
+ # Calculate contour levels
+ cl = contour_start * contour_factor ** arange(contour_num)
+
+ # Create the figure
+ fig = plt.figure()
+ ax = fig.add_subplot(111)
+
+ # Plot the contours
+
+ # Plot in ppm scale
+ if ppm:
+ # make ppm scales
+ uc_dim1 = nmrglue.pipe.make_uc(dic, data, dim=1)
+ ppm_dim1 = uc_dim1.ppm_scale()
+ ppm_dim1_0, ppm_dim1_1 = uc_dim1.ppm_limits()
+ uc_dim0 = nmrglue.pipe.make_uc(dic, data, dim=0)
+ ppm_dim0 = uc_dim0.ppm_scale()
+ ppm_dim0_0, ppm_dim0_1 = uc_dim0.ppm_limits()
+
+ ax.contour(data, cl, cmap=cmap, extent=(ppm_dim1_0, ppm_dim1_1,
ppm_dim0_0, ppm_dim0_1))
+
+ # Decorate
+ ax.set_ylabel("%s (ppm)"%udic[0]['label'])
+ ax.set_xlabel("%s (ppm)"%udic[1]['label'])
+ ax.set_title("Spectrum")
+ lim_dim1 = [ppm_dim1_0, ppm_dim1_1]
+ lim_dim0 = [ppm_dim0_0, ppm_dim0_1]
+ ax.set_xlim(max(lim_dim1), min(lim_dim1))
+ ax.set_ylim(max(lim_dim0), min(lim_dim0))
+
+ else:
+ # Plot in points.
+ ax.contour(data, cl, cmap=cmap, extent=(0, data.shape[1] - 1, 0,
data.shape[0] - 1))
+
+ # Decorate
+ ax.set_ylabel("%s (points)"%udic[0]['label'])
+ ax.set_xlabel("%s (points)"%udic[1]['label'])
+ ax.set_title("Spectrum")
+
+ # If show.
+ if show:
+ plt.show()
+
+ # Return ax
+ return ax
def read_spectrum(file=None, dir=None):
Modified: branches/nmrglue/pipe_control/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/pipe_control/nmrglue.py?rev=26790&r1=26789&r2=26790&view=diff
==============================================================================
--- branches/nmrglue/pipe_control/nmrglue.py (original)
+++ branches/nmrglue/pipe_control/nmrglue.py Thu Nov 27 17:57:00 2014
@@ -24,7 +24,7 @@
# relax module imports.
from lib.errors import RelaxError
-from lib.software.nmrglue import read_spectrum
+from lib.software.nmrglue import contour_plot, read_spectrum
from pipe_control.pipes import check_pipe
from pipe_control.spectrum import add_spectrum_id, check_spectrum_id, delete
@@ -72,3 +72,29 @@
# Store the data.
add_nmrglue_data(spectrum_id=spectrum_id, nmrglue_data=nmrglue_data)
+
+
+def plot_contour(spectrum_id=None, contour_start=30000., contour_num=20,
contour_factor=1.20, ppm=True, show=False):
+ """Plot the spectrum as contour plot.
+
+ @keyword spectrum_id: The spectrum identification string.
+ @type spectrum_id: str or list of str
+ @keyword contour_start: Contour level start value
+ @type contour_start: float
+ @keyword contour_num: Number of contour levels
+ @type contour_num: int
+ @keyword contour_factor: Scaling factor between contour levels
+ @type contour_factor: float
+ @keyword ppm: A flag which if True will make the plot in
ppm scale. Else it is in points.
+ @type ppm: bool
+ @keyword show: A flag which if True will make a call to
matplotlib.pyplot.show().
+ @type show: bool
+ @return: The matplotlib.axes.AxesSubplot class, which
can be manipulated to add additional text to the axis.
+ @rtype: matplotlib.axes.AxesSubplot
+ """
+
+ # Call the contour plot.
+ ax = contour_plot(spectrum_id=spectrum_id, contour_start=contour_start,
contour_num=contour_num, contour_factor=contour_factor, ppm=ppm, show=show)
+
+ return ax
+
Modified: branches/nmrglue/test_suite/system_tests/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py?rev=26790&r1=26789&r2=26790&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/nmrglue.py (original)
+++ branches/nmrglue/test_suite/system_tests/nmrglue.py Thu Nov 27 17:57:00
2014
@@ -26,6 +26,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
+from pipe_control.nmrglue import plot_contour
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
from extern import nmrglue
@@ -82,3 +83,27 @@
# Assert the version to be 0.4.
self.assertEqual(ng_vers, '0.4')
+
+
+ def xtest_plot_contour(self):
+ """Test the plot_contour function in pipe_control.
+ This is from the
U{tutorial<http://jjhelmus.github.io/nmrglue/current/examples/plot_2d_spectrum.html>}."""
+
+ # Read the spectrum.
+ fname = 'freq_real.ft2'
+ sp_id = 'test'
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ds.ng_test,
spectrum_id=sp_id)
+
+ # Call the pipe_control function and get the return axis.
+ ax = plot_contour(spectrum_id=sp_id, ppm=True, show=False)
+
+ # Set new limits.
+ ax.set_xlim(30, 0)
+ ax.set_ylim(15, -20)
+
+ # add some labels
+ ax.text(25.0, 0.0, "Test", size=8, color='r')
+
+ # Now show
+ import matplotlib.pyplot as plt
+ plt.show()
r26790 - in /branches/nmrglue: lib/software/nmrglue.py pipe_control/nmrglue.py test_suite/system_tests/nmrglue.py