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-commits@xxxxxxx
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
Re: r27018 - /branches/nmrglue/test_suite/system_tests/nmrglue.py