Author: tlinnet
Date: Sun Dec 7 23:43:05 2014
New Revision: 27006
URL: http://svn.gna.org/viewcvs/relax?rev=27006&view=rev
Log:
Fix to systemtest of Nmrglue.
This is after changing spectrum_id to nmrglue_id, and for change of storing
data in cdp.
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/
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=27006&r1=27005&r2=27006&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/nmrglue.py (original)
+++ branches/nmrglue/test_suite/system_tests/nmrglue.py Sun Dec 7 23:43:05
2014
@@ -21,8 +21,8 @@
###############################################################################
# Python module imports.
-from numpy import concatenate
-from os import sep
+from numpy import concatenate, save
+from os import path, sep
from tempfile import mkdtemp
# relax module imports.
@@ -139,10 +139,10 @@
# 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)
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ds.ng_test,
nmrglue_id=sp_id)
# Call the pipe_control function and get the return axis.
- ax = plot_contour(spectrum_id=sp_id, ppm=True, show=show)
+ ax = plot_contour(nmrglue_id=sp_id, ppm=True, show=show)
# Set new limits.
ax.set_xlim(30, 0)
@@ -170,10 +170,10 @@
# Read the spectrum.
fname = '128_0_FT.ft2'
sp_id = file_root(fname)
- self.interpreter.spectrum.nmrglue_read(file=fname, dir=ft2_folder_1,
spectrum_id=sp_id)
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ft2_folder_1,
nmrglue_id=sp_id)
# Call the pipe_control function and get the return axis.
- ax = plot_contour(spectrum_id=sp_id, contour_start=200000.,
contour_num=20, contour_factor=1.20, ppm=True, show=show)
+ ax = plot_contour(nmrglue_id=sp_id, contour_start=200000.,
contour_num=20, contour_factor=1.20, ppm=True, show=show)
# Set a new title.
ax.set_title("CPMG Spectrum")
@@ -195,12 +195,12 @@
# Read the spectrum.
fname = '128_0_FT.ft2'
sp_id = file_root(fname)
- self.interpreter.spectrum.nmrglue_read(file=fname, dir=ft2_folder_1,
spectrum_id=sp_id)
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ft2_folder_1,
nmrglue_id=sp_id)
# Extract the data.
- dic = cdp.ngdata[sp_id].dic
- udic = cdp.ngdata[sp_id].udic
- data = cdp.ngdata[sp_id].data
+ dic = cdp.nmrglue_dic[sp_id]
+ udic = cdp.nmrglue_udic[sp_id]
+ data = cdp.nmrglue_data[sp_id]
# Plot the histogram.
kwargs = {'bins': 3000, 'range': None, 'normed': False,
'facecolor':'green', 'alpha':0.75}
@@ -225,11 +225,11 @@
basename_list, file_root_list =
get_file_list(glob_pattern=ft2_glob_pat, dir=ft2_folder_1)
# Read the spectra.
- self.interpreter.spectrum.nmrglue_read(file=basename_list,
dir=ft2_folder_1, spectrum_id=file_root_list)
+ self.interpreter.spectrum.nmrglue_read(file=basename_list,
dir=ft2_folder_1, nmrglue_id=file_root_list)
# Extract the data.
- data_0 = cdp.ngdata[file_root_list[0]].data
- data_1 = cdp.ngdata[file_root_list[1]].data
+ data_0 = cdp.nmrglue_data[file_root_list[0]]
+ data_1 = cdp.nmrglue_data[file_root_list[1]]
# First flatten arrays, and then merge them.
data = concatenate( (data_0.flatten(), data_1.flatten() ) )
@@ -245,15 +245,15 @@
# 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)
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ds.ng_test,
nmrglue_id=sp_id)
# Test that the spectrum id has been stored.
- self.assertEqual(cdp.spectrum_ids[0], sp_id)
+ self.assertEqual(cdp.nmrglue_ids[0], sp_id)
# Extract the data.
- dic = cdp.ngdata[sp_id].dic
- udic = cdp.ngdata[sp_id].udic
- data = cdp.ngdata[sp_id].data
+ dic = cdp.nmrglue_dic[sp_id]
+ udic = cdp.nmrglue_udic[sp_id]
+ data = cdp.nmrglue_data[sp_id]
# Test the data.
self.assertEqual(udic[0]['label'], '15N')
@@ -292,15 +292,15 @@
basename_list, file_root_list = cdp.io_basename[ft2_glob_pat],
cdp.io_file_root[ft2_glob_pat]
# First test that expected RelaxErrors are raised.
- self.assertRaises(RelaxError,
self.interpreter.spectrum.nmrglue_read, file=basename_list, dir=ft2_folder_1,
spectrum_id='test')
- self.assertRaises(RelaxError,
self.interpreter.spectrum.nmrglue_read, file='128_0_FT.ft2',
dir=ft2_folder_1, spectrum_id=file_root_list)
+ self.assertRaises(RelaxError,
self.interpreter.spectrum.nmrglue_read, file=basename_list, dir=ft2_folder_1,
nmrglue_id='test')
+ self.assertRaises(RelaxError,
self.interpreter.spectrum.nmrglue_read, file='128_0_FT.ft2',
dir=ft2_folder_1, nmrglue_id=file_root_list)
# Read the spectra.
- self.interpreter.spectrum.nmrglue_read(file=basename_list,
dir=ft2_folder_1, spectrum_id=file_root_list)
+ self.interpreter.spectrum.nmrglue_read(file=basename_list,
dir=ft2_folder_1, nmrglue_id=file_root_list)
# Test that the spectrum id has been stored.
- self.assertEqual(cdp.spectrum_ids[0], file_root_list[0])
- self.assertEqual(cdp.spectrum_ids[1], file_root_list[1])
+ self.assertEqual(cdp.nmrglue_ids[0], file_root_list[0])
+ self.assertEqual(cdp.nmrglue_ids[1], file_root_list[1])
def test_plot_contour(self):
@@ -351,34 +351,56 @@
# 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)
+ self.interpreter.spectrum.nmrglue_read(file=fname, dir=ds.ng_test,
nmrglue_id=sp_id)
+
+ # Get the file size.
+ data_size_file = path.getsize(ds.ng_test + sep + fname)
+ print("Filesize of .ft2 file is: %i"%(data_size_file) )
# Test that the spectrum id has been stored.
- self.assertEqual(cdp.spectrum_ids[0], sp_id)
+ self.assertEqual(cdp.nmrglue_ids[0], sp_id)
# Extract the data.
- dic = cdp.ngdata[sp_id].dic
- udic = cdp.ngdata[sp_id].udic
- data = cdp.ngdata[sp_id].data
+ dic = cdp.nmrglue_dic[sp_id]
+ udic = cdp.nmrglue_udic[sp_id]
+ data = cdp.nmrglue_data[sp_id]
+
+ # Try storing the numpy array, and print size
+ data_numpy = ds.tmpdir + sep + 'data.npy'
+ print("Storing numpy array to: %s"%data_numpy)
+ save(data_numpy, data)
+ data_numpy_size = path.getsize(data_numpy)
+ print("Filesize of .npy file is: %i"%(data_numpy_size) )
+
+ # Delete the large data array, for faster saving.
+ cdp.nmrglue_data[sp_id] = 0
# Store the directory path, before reset of the controller.
dirpath = ds.tmpdir
- cdp.hello = "HELLO WORLD"
- print(cdp)
- print(type(cdp.ngdata))
- print(type(cdp.ngdata[sp_id]))
+ print("Shape of data is %ix%i"%(data.shape[0], data.shape[1]))
# Save the results.
self.interpreter.state.save('state', dir=dirpath, compress_type=1,
force=True)
+ # Get the file size.
+ state_size_file = path.getsize(dirpath + sep + 'state.bz2')
+ print("Filesize of state file is %i"%(state_size_file) )
+
# Reset of the controller.
self.interpreter.reset()
# Load the state again.
self.interpreter.state.load(dirpath+sep+'state')
- print(cdp.hello)
+ # Make tests that they are the same.
+ self.assertEqual(dic, cdp.nmrglue_dic[sp_id])
+ for id in dic:
+ self.assertEqual(dic[id], cdp.nmrglue_dic[sp_id][id])
+
+ self.assertEqual(udic, cdp.nmrglue_udic[sp_id])
+ for id in udic:
+ self.assertEqual(udic[id], cdp.nmrglue_udic[sp_id][id])
def test_version(self):
r27006 - /branches/nmrglue/test_suite/system_tests/nmrglue.py