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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
The text was updated successfully, but these errors were encountered:
Hi Teresa, Yes that definitely helps. The problem is that the converter/parser expects certain properties in the .properties.txt file to contain:
.properties.txt
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:
properties.txt
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.
256
Hope that helps,
Alan
Sorry, something went wrong.
Thank you very much - this has solved it.
Best, Teresa
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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
The text was updated successfully, but these errors were encountered: