Re: r27012 - /branches/nmrglue/test_suite/system_tests/nmrglue.py -- December 08, 2014

Hi Edward.

I think I will have to leave the implementation in relax.

Time goes away from pursuing the analysis, and goes into rather annoying
stuff.

The idea is simple.
Load one or two spectrum.
Plot the contour, or histogram.
Or make a correlation plot of the two spectra.

Store the data.

Storing the axis plots is a different question.
http://stackoverflow.com/questions/7290370/store-and-reload-matplotlib-pyplot-object

I cannot actually do it at the moment.
So essentially, it just storing a numpy array


2014-12-08 13:59 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

Hi Troels,

I didn't notice that the shape was not preserved.  To store the numpy
shape, this is also not a problem as XML has attributes.  For example
'type' is the attribute already used to determine what we do with the
data in relax.  We simply add a new 'shape' attribute and read this
then reshape when loading the data.  If at any point you need help for
implementing any of the XML stuff, just say and I can do a few things
in your branch.

Regards,

Edward


On 8 December 2014 at 13:40,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Mon Dec  8 13:40:52 2014
New Revision: 27012

URL: http://svn.gna.org/viewcvs/relax?rev=27012&view=rev
Log:
Try to decode the numpy array as base64 string.

This shows, that the shape of the data is lost after decoding.

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=27012&r1=27011&r2=27012&view=diff

==============================================================================

--- branches/nmrglue/test_suite/system_tests/nmrglue.py (original)
+++ branches/nmrglue/test_suite/system_tests/nmrglue.py Mon Dec  8

13:40:52 2014

@@ -21,7 +21,8 @@

###############################################################################


 # Python module imports.
-from numpy import concatenate, save
+import base64
+from numpy import concatenate, float32, float64, frombuffer, save
 from os import path, sep
 from tempfile import mkdtemp

@@ -364,6 +365,9 @@
         dic  = cdp.nmrglue_dic[sp_id]
         udic  = cdp.nmrglue_udic[sp_id]
         data = cdp.nmrglue_data[sp_id]
+        s = base64.b64encode(data)
+        cdp.nmrglue_data[sp_id] = s
+        print("Type of encoding is:", type(cdp.nmrglue_data[sp_id]))

         # Try storing the numpy array, and print size
         data_numpy = ds.tmpdir + sep + 'data.npy'
@@ -379,6 +383,8 @@
         dirpath = ds.tmpdir

         print("Shape of data is %ix%i"%(data.shape[0], data.shape[1]))
+        print("dtype of data is", data.dtype)
+        print("Type of data[0][0]: ", type(data[0][0]))

         # Save the results.
         self.interpreter.state.save('state', dir=dirpath,

compress_type=1, force=True)

@@ -393,6 +399,20 @@
         # Load the state again.
         self.interpreter.state.load(dirpath+sep+'state')

+        # Decode
+        print("Decoding")
+        r = base64.decodestring(cdp.nmrglue_data[sp_id])
+        q = frombuffer(r,dtype=float32)
+        cdp.nmrglue_data[sp_id] = q
+        print("Type of decoded is:", type(cdp.nmrglue_data[sp_id]))
+        print("Shape of numpy array is:", cdp.nmrglue_data[sp_id].shape)
+
+        # Test data.
+        print("Testing data array.")
+        print("Shape of data is %ix%i, and of cdp.nmrglue_data is

%ix%i"%(data.shape[0], data.shape[1], cdp.nmrglue_data[sp_id].shape[0],
cdp.nmrglue_data[sp_id].shape[1]))

+        self.assertEqual(data, cdp.nmrglue_data[sp_id])
+
+        print("Testing dics.")
         # Make tests that they are the same.
         self.assertEqual(dic, cdp.nmrglue_dic[sp_id])
         for id in dic:


_______________________________________________
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


_______________________________________________
relax (http://www.nmr-relax.com)

This is the relax-devel mailing list
relax-devel@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-devel

Re: r27012 - /branches/nmrglue/test_suite/system_tests/nmrglue.py

Header

Content

Related Messages