[issue] spectrum generation

[inesboxexa]

Hi Alan,

I started to get the following error recently:

In f_saving_spectra_details (line 16)
! Running pre-processing and generating representative spectra...
Warning: Error occurred while executing the listener callback for event FastMethods defined for class TotalSpectrum:
Error using num2str (line 45)
Input to num2str must be numeric.

Error in f_saving_spectra_details>@(src,canUseFastMethods)disp(['! Using fast Methods? A: ',num2str(canUseFastMethods)]) (line 36)
addlistener(spectrumGeneration, 'FastMethods', @(src, canUseFastMethods)disp(['! Using fast Methods? A: ' num2str(canUseFastMethods)]));

Error in PostProcessing/setUpFastMethods (line 159)
notify(this, 'FastMethods', BooleanEventData(canUseFastMethods));

Error in TotalSpectrum/process (line 26)
[canUseFastMethods, workflow] = this.setUpFastMethods(dataRepresentation);

Error in f_saving_spectra_details (line 57)
totalSpectrum = spectrumGeneration.process(data); % create total spectrum

In PostProcessing/setUpFastMethods (line 159)
In TotalSpectrum/process (line 26)
In f_saving_spectra_details (line 57)
com.alanmrace.JSpectralAnalysis.Spectrum@5a6482a9
Error using TotalSpectrum/process (line 33)
Java exception occurred:
java.lang.ArrayIndexOutOfBoundsException: -1

at com.alanmrace.JSpectralAnalysis.zerofilling.InterpolationRebinZeroFilling.interpLinear(InterpolationRebinZeroFilling.java:95)

at com.alanmrace.JSpectralAnalysis.zerofilling.InterpolationRebinZeroFilling.process(InterpolationRebinZeroFilling.java:45)

at com.alanmrace.JSpectralAnalysis.PreprocessingWorkflow.process(PreprocessingWorkflow.java:32)

at com.alanmrace.JSpectralAnalysis.spectralrepresentation.MultithreadedSpectralRepresentationGeneration.createSpectrumList(MultithreadedSpectralRepresentationGeneration.java:85)

at com.alanmrace.JSpectralAnalysis.spectralrepresentation.MultithreadedSpectralRepresentationGeneration.generateTotalSpectrum(MultithreadedSpectralRepresentationGeneration.java:103)

Error in f_saving_spectra_details (line 57)
totalSpectrum = spectrumGeneration.process(data); % create total spectrum

This is the code that I'm running:

addJARsToClassPath()
preprocessing = PreprocessingWorkflow;
preprocessing.loadWorkflow(preprocessing_file);

    parser = ImzMLParser([filesToProcess(file_index).folder filesep filesToProcess(file_index).name]);
    parser.parse; % parse the imzML file
    
    % Total Spectrum
    
    spectrumGeneration = TotalSpectrum();
    spectrumGeneration.setPreprocessingWorkflow(preprocessing); % set preprocessing workflow

    addlistener(spectrumGeneration, 'FastMethods', @(src, canUseFastMethods)disp(['! Using fast Methods? A: ' num2str(canUseFastMethods)]));        
    
    data = DataOnDisk(parser);
    totalSpectrum = spectrumGeneration.process(data); % create total spectrum
    totalSpectrum = totalSpectrum.get(1);

Is it anything you changed recently? Or is it my fault? I just updated Java but that didn't solve it.

Thank you,
Teresa