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AlanRace / imzMLConverter

Tool for converting mass spectrometry data to the imzML format.
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[issue] trying to convert grd into imzml #7

Closed inesboxexa closed 3 years ago

inesboxexa commented 3 years ago

Hi Alan,

I was trying to use this converter to go from grd to imzml using the code below:

C:\Users\tm6\Documents\GitHub\jimzMLConverter\target>java -jar jimzMLConverter-2.1.0.jar imzML -p "X:\Teresa\BEIS biofilms project sims data\Biofilm 1\ToF\GRD ToF\biofilm 1 tof negative1.properties.txt" "X:\Teresa\BEIS biofilms project sims data\Biofilm 1\ToF\GRD ToF\biofilm 1 tof negative1.itm.grd"

But I got the following error:

Mar 31, 2021 1:43:32 PM com.alanmrace.jimzmlconverter.MainCommand convert INFO: Converting file X:\Teresa\BEIS biofilms project sims data\Biofilm 1\ToF\GRD ToF\biofilm 1 tof negative1.itm.grd Mar 31, 2021 1:43:32 PM com.alanmrace.jimzmlconverter.MainCommand convert INFO: Detected ION-TOF GRD file Mar 31, 2021 1:43:32 PM com.alanmrace.jimzmlparser.obo.OBOTerm parse INFO: Unknown value-type encountered 'value-type:xsd\:dateTime "The allowed value-type for this CV term."' @ MS:1000747 Mar 31, 2021 1:43:32 PM com.alanmrace.jimzmlparser.obo.OBOTerm parse INFO: Unknown value-type encountered 'value-type:xsd\:dateTime "The allowed value-type for this CV term."' @ MS:1002435 Exception in thread "main" java.lang.NullPointerException: Cannot invoke "com.alanmrace.jimzmlconverter.IONTOF.IONTOFProperty.getIntegerValue()" because "xDimension" is null at com.alanmrace.jimzmlconverter.GRDToImzMLConverter.setPropertiesFile(GRDToImzMLConverter.java:98) at com.alanmrace.jimzmlconverter.MainCommand.convert(MainCommand.java:287) at com.alanmrace.jimzmlconverter.MainCommand.main(MainCommand.java:186)

Do you know what this means? Does it give us a clue on what is wrong with the grd file?

Thank you, Teresa

AlanRace commented 3 years ago

Hi Teresa, Yes that definitely helps. The problem is that the converter/parser expects certain properties in the .properties.txt file to contain:

Registration.Raster.StageRaster.TotalResolution.X
Registration.Raster.StageRaster.TotalResolution.Y

It seems like the properties file that you supplied doesn't contain these properties any more, and instead there are now:

Acquisition.#1.Raster.TotalResolution.X 256 256 256
Acquisition.#1.Raster.TotalResolution.Y 256 256 256

To get things moving, I'd suggest adding two new lines to the properties.txt file:

Registration.Raster.StageRaster.TotalResolution.X   256 256 256
Registration.Raster.StageRaster.TotalResolution.Y   256 256 256

Replace 256 with however many pixels are in the X and Y direction in the image.

Hope that helps,

Alan

inesboxexa commented 3 years ago

Hi Alan,

Thank you very much - this has solved it.

Best, Teresa