[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