Data Reduction Datacube

AlanRace / SpectralAnalysis

Software for the analysis and interactive exploration of spectral imaging data

https://alanrace.github.io/SpectralAnalysis/

Apache License 2.0

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Data Reduction Datacube #9

Closed educhicano closed 4 years ago

educhicano commented 5 years ago

Hi Alan, I'm trying to perform a clustering over my imzML images and then save the cluster of interest in a new imzML file but when I try to do it by using Datacube reduction (Process Separately option), SpectralAnalysis/Matlab shows an error when imzML is selected as Output: No constructor 'com.alanmrace.jimzmlparser.imzML.ImzML' with matching signature found. How can I solve it? Thanks in advance!

AlanRace commented 5 years ago

Hey, Are you using the latest version of SpectralAnalysis? The line in DatacubeReduction.m that says com.alanmrace.jimzmlparser.imzML.ImzML should instead be com.alanmrace.jimzmlparser.imzml.ImzML. This should have already been updated in the latest version - could you please check?

Thanks,

Alan

educhicano commented 5 years ago

Hi again, yes, i've downloaded the last version today, but i've downloaded the windows version, not the source. I've tried to see the DatacubeReduction.m file but i cant open it neither Matlab nor anything else. Attached I send you the DatacubeReduction.m file i've here (change the extension to see it ;)) DatacubeReduction.txt

AlanRace commented 5 years ago

Hi again, Can you try the latest version of SpectralAnalysis (v1.2.1, https://github.com/AlanRace/SpectralAnalysis/releases/tag/v1.2.1)?

Alan

educhicano commented 5 years ago

Hi! I've tried with v1.2.1 and now java is giving java_error me the following error

AlanRace commented 5 years ago

Okay now it looks like the issue is that the data you are trying to load is either too large for your PC, or is too large for your current MATLAB settings. You can increase the amount of java heap memory by following the instructions on the links provided here , depending on which MATLAB version you are using.

educhicano commented 5 years ago

Hi again Alan. Thanks for your time! I've changed java heap memory from 384MB to the maximum allowed, 8121MB but the error continues. The imzML file and associated ibd file I'm trying to cluster and save are 6380KB and 266876KB respectively, so, its not a huge dataset like other I've here (more than 3gb). I'm using Matlab2015b java_heap

AlanRace commented 4 years ago

Hello, Can you tell me exactly what settings you used when trying to perform DatacubeReduction? It may be because of the large amount of empty space in the data that it is failing with the memory issues. Did you just try and create the datacube for a single region of interest?

Thanks,

Alan

AlanRace commented 4 years ago

Hello again, This should now be fixed in the latest version of SpectralAnalysis. I believe the problem was with Bruker data and the absolute coordinate system (rather than relative) resulting in large images.

Thanks,

Alan