Hi,
These patches have now been applied and committed. The commit
messages are still not up to standard - I had to manually add '.' to
the end of most sentences. As for the code, it is not quite
functional yet. I can see that lib.software.nmrpipe is not
constructing the intensity_data structure correctly for use in the
pipe_control.spectrum module. The spectrum name is not needed in this
structure. And the 'intensity' element should be a list when multiple
columns are present. For example one element of the list would be:
['HE1', 'NE1', ':62@NE1', [1851056.0, 2000000.0]]
For single entries, it doesn't matter if it is a list or single
element as pipe_control.spectrum.read() converts this anyway.
One question I have is, how should the user interact with the
spectrum.read_intensities user function? Obviously they will need to
give a list of spectrum IDs (or a single value). We should check that
this matches the number of Z_A columns (you don't need to do anything
as the pipe_control.spectrum.read() function already has this check).
Now, does the user need to say which columns the data is in, or can we
always automatically determine this? If we can do this for the user,
which I think we can, then we should throw a RelaxError if int_col is
given by the user. And int_col should not be sent into the
lib.software.nmrpipe.read_list_intensity_seriestab() function. Then
we can automatically pull out all of the data from the seriesTab file
and return it to lib.software.nmrpipe in the above format. The
pipe_control.spectrum.read() function will handle the rest correctly.
So in pipe_control.spectrum.read(), you don't need to loop over the
spectra. As soon as the code in the format == 'seriestab' block
creates a data structure as above, with a spin ID string in the 3rd
position, everything will just function correctly.
I have also noticed that we currently don't test the reading of a
NMRPipe seriesTab file containing multiple intensity data columns. I
think for this we should create a second system test, very similar to
the current Peak_lists.test_read_peak_list_NMRPipe_seriesTab test.
Maybe it could be called
Peak_lists.test_read_peak_list_NMRPipe_seriesTab_multi? This is the
ultimate aim for the seriesTab reading and it must be tested. I think
that we are now quite close to being able to read your intensity data.
Cheers,
Edward
On 20 July 2013 18:39, Troels E. Linnet
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Follow-up Comment #37, sr #3043 (project relax):
Made corrections
(file #18372, file #18373)
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File name: seriestab.tar.gz Size:1 KB
File name: spectrum.tar.gz Size:1 KB
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Re: [sr #3043] Support for NMRPipe seriesTab format *.ser