Hi Troels, Unfortunately you committed too much here. It should only be the system test, but it includes changes to the relax library and the pipe control package. Could you revert and try again?
Cheers, Edward On 27 November 2014 at 17:57, <tlin...@nmr-relax.com> wrote: > 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() > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > relax-comm...@gna.org > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
