Example Scripts: Difference between revisions
(Created page with "=Example Scripts for Various MVAPACK Patterns= ''Note: Patterns may be sensitive to file location and path variables.'' ===Example 1: 1D NMR Processing to Matrix Export=== '''''%%''''' indicates comment line. All lines can be copied and pasted to terminal. <code> %% Start file extraction from 1D NMR files located in nmrdata sub directory filenames = glob("nmrdata/*"); [F.data, F.parms] = loadnmr(filenames); %% Apply apodization and zero fills apodizationWindowFunction...") |
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<code> | <code> | ||
%% Start file extraction from 1D NMR files located in nmrdata sub directory | %% Start file extraction from 1D NMR files located in nmrdata sub directory<br> | ||
filenames = glob("nmrdata/*"); | filenames = glob("nmrdata/*");<br> | ||
[F.data, F.parms] = loadnmr(filenames); | [F.data, F.parms] = loadnmr(filenames);<br> | ||
%% Apply apodization and zero fills | %% Apply apodization and zero fills<br> | ||
apodizationWindowFunction = @expwindow); | apodizationWindowFunction = @expwindow);<br> | ||
F.data = apodize(F.data, F.parms, apodizationWindowFunction); | F.data = apodize(F.data, F.parms, apodizationWindowFunction);<br> | ||
zeroFills = 2; | zeroFills = 2;<br> | ||
F.data = zerofill(F.data, F.parms, 2); | F.data = zerofill(F.data, F.parms, 2);<br> | ||
%% Fourier transform and phase | %% Fourier transform and phase<br> | ||
[S.data,S.ppm] = nmrft(F.data,F.parms); | [S.data,S.ppm] = nmrft(F.data,F.parms);<br> | ||
phaseObjective = @simplex_entropy; | phaseObjective = @simplex_entropy;<br> | ||
[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseObjective); | [S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseObjective);<br> | ||
%% Remove unreal portion and align spectra | %% Remove unreal portion and align spectra<br> | ||
X.data = realnmr(S.data, F.parms); | X.data = realnmr(S.data, F.parms);<br> | ||
X.ppm = S.ppm; | X.ppm = S.ppm;<br> | ||
X.data = icoshift(X.data, X.ppm); | X.data = icoshift(X.data, X.ppm);<br> | ||
%% Save matrix as csv | %% Save matrix as csv<br> | ||
csvwrite("DataMatrix.csv", X.data); | csvwrite("DataMatrix.csv", X.data);<br> | ||
csvwrite("ChemicalShiftsData.csv", X.ppm); | csvwrite("ChemicalShiftsData.csv", X.ppm);<br> | ||
</code> | |||
Latest revision as of 23:34, 12 August 2024
Example Scripts for Various MVAPACK Patterns
Note: Patterns may be sensitive to file location and path variables.
Example 1: 1D NMR Processing to Matrix Export
%% indicates comment line. All lines can be copied and pasted to terminal.
%% Start file extraction from 1D NMR files located in nmrdata sub directory
filenames = glob("nmrdata/*");
[F.data, F.parms] = loadnmr(filenames);
%% Apply apodization and zero fills
apodizationWindowFunction = @expwindow);
F.data = apodize(F.data, F.parms, apodizationWindowFunction);
zeroFills = 2;
F.data = zerofill(F.data, F.parms, 2);
%% Fourier transform and phase
[S.data,S.ppm] = nmrft(F.data,F.parms);
phaseObjective = @simplex_entropy;
[S.data, S.phc0, S.phc1] = autophase(S.data, F.parms, phaseObjective);
%% Remove unreal portion and align spectra
X.data = realnmr(S.data, F.parms);
X.ppm = S.ppm;
X.data = icoshift(X.data, X.ppm);
%% Save matrix as csv
csvwrite("DataMatrix.csv", X.data);
csvwrite("ChemicalShiftsData.csv", X.ppm);