Hi Troels, Do you think it would be worth created a simple system test which just calls the setup_plot_correlation() method, just to test more code paths?
Regards, Edward On 8 December 2014 at 16:21, <tlin...@nmr-relax.com> wrote: > Author: tlinnet > Date: Mon Dec 8 16:21:20 2014 > New Revision: 27018 > > URL: http://svn.gna.org/viewcvs/relax?rev=27018&view=rev > Log: > Added systemtest Nmrglue.plot_plot_correlation, which shows how nmrglue could > be used for a correlation plot of all intensities > in a spectrum. > > io.file_list: Is used to quickly assemble a long list of filenames in a > directory: > spectrum.nmrglue_read: is used to read the data. > > The numpy arrays for all spectrums in the two methods are then concatenated. > Then the intensities are plotted against each other. > > This shows how the intensities are modulated. > > 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/test_suite/system_tests/nmrglue.py > > 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=27018&r1=27017&r2=27018&view=diff > ============================================================================== > --- branches/nmrglue/test_suite/system_tests/nmrglue.py (original) > +++ branches/nmrglue/test_suite/system_tests/nmrglue.py Mon Dec 8 16:21:20 > 2014 > @@ -22,7 +22,7 @@ > > # Python module imports. > import base64 > -from numpy import concatenate, float32, float64, frombuffer, save > +from numpy import array, concatenate, float32, float64, frombuffer, save > from os import path, sep > from tempfile import mkdtemp > > @@ -98,6 +98,20 @@ > plt.show() > > > + def plot_plot_correlation(self): > + """Plot data for correlation plot. > + > + The data is from systemtest -s Relax_disp.test_repeat_cpmg > + U{task #7826<https://gna.org/task/index.php?7826>}. Write an python > class for the repeated analysis of dispersion data. > + """ > + > + # Call setup function. > + self.setup_plot_correlation() > + > + # Show > + plt.show() > + > + > def plot_plot_hist_cpmg(self): > """Plot the plot_hist function in pipe_control. > > @@ -178,6 +192,100 @@ > > # Set a new title. > ax.set_title("CPMG Spectrum") > + > + > + def setup_plot_correlation(self): > + """Setup data for correlation plot. > + > + The data is from systemtest -s Relax_disp.test_repeat_cpmg > + U{task #7826<https://gna.org/task/index.php?7826>}. Write an python > class for the repeated analysis of dispersion data. > + """ > + > + # Define base path to files. > + base_path = status.install_path + > sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'repeated_analysis'+sep+'SOD1' > + > + # Define folder to all ft files. > + ft2_folder_1 = base_path +sep+ 'cpmg_disp_sod1d90a_060518' +sep+ > 'cpmg_disp_sod1d90a_060518_normal.fid' +sep+ 'ft2_data' > + ft2_folder_2 = base_path +sep+ 'cpmg_disp_sod1d90a_060521' +sep+ > 'cpmg_disp_sod1d90a_060521_normal.fid' +sep+ 'ft2_data' > + > + # Get the file list matching a glob pattern for the reference. > + ref_500 = '128_*_FT.ft2' > + ref_500_id = 'ref_500' > + ref_600 = '128_*_FT.ft2' > + ref_600_id = 'ref_600' > + > + # Get the file lists. > + self.interpreter.io.file_list(glob=ref_500, dir=ft2_folder_1, > id=ref_500_id) > + self.interpreter.io.file_list(glob=ref_600, dir=ft2_folder_2, > id=ref_600_id) > + > + # Then get the file list for method. > + met_500 = '126_*_MDD.ft2' > + met_500_id = 'met_500' > + met_600 = '126_*_MDD.ft2' > + met_600_id = 'met_600' > + > + # Get the file lists. > + self.interpreter.io.file_list(glob=met_500, dir=ft2_folder_1, > id=met_500_id) > + self.interpreter.io.file_list(glob=met_600, dir=ft2_folder_2, > id=met_600_id) > + > + # Read the spectra. > + # First loop over the glob id. > + ids_ref = [] > + ids_met = [] > + for io_id in cdp.io_ids: > + # Get the directory > + io_dir = cdp.io_dir[io_id] > + > + # Then loop over the file_roots: > + for i, froot in enumerate(cdp.io_file_root[io_id]): > + # Get the basename > + bname = cdp.io_basename[io_id][i] > + > + # Form new nmrglue id. > + ng_id = froot + '_' + io_id > + > + # Assign ids to list. > + if 'ref_' in ng_id: > + ids_ref.append(ng_id) > + elif 'met_' in ng_id: > + ids_met.append(ng_id) > + > + # Read the spectrum data. > + self.interpreter.spectrum.nmrglue_read(file=bname, > dir=io_dir, nmrglue_id=ng_id) > + > + # Create an empty reference array. > + np_arr_ref = array([]) > + > + # Loop over id ref: > + for ng_id in ids_ref: > + data = cdp.nmrglue_data[ng_id] > + data_flat = data.flatten() > + print(ng_id, data.shape, data_flat.shape) > + np_arr_ref = concatenate( (np_arr_ref, data_flat) ) > + > + # Create an empty method array. > + np_arr_met = array([]) > + > + # Loop over id ref: > + for ng_id in ids_met: > + data = cdp.nmrglue_data[ng_id] > + data_flat = data.flatten() > + print(ng_id, data.shape, data_flat.shape) > + np_arr_met = concatenate( (np_arr_met, data_flat) ) > + > + # Create correlation plot. > + fig = plt.figure() > + ax = fig.add_subplot(111) > + > + line = array( [np_arr_ref.min(), np_arr_ref.max()] ) > + > + ax.plot(np_arr_ref, np_arr_met, '+', label='corr') > + ax.plot(line, line, 'r-', label='corr') > + > + # Set text. > + ax.set_xlabel("All spectrum intensities for reference") > + ax.set_ylabel("All spectrum intensities for method") > + ax.set_title("Correlation plot") > > > def setup_plot_hist_cpmg(self, show=False): > > > _______________________________________________ > 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
