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FakeReader: add support for populating channel wavelengths and instrument #4272

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FakeReader: add support for populating channel wavelengths and instrument #4272

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@sbesson sbesson commented Feb 6, 2025

See discussion at ome/omero-py#443

This extends the FakeReader logic to be able to populate additional metadata:

  • channel wavelengths (both emission & excitation): using a set of channel specific keys similar to how channel colors and channel names are set
  • instrument: using a single boolean withInstrument key

With these changes, the following fake file should include channel wavelengths and an instrument

showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=490nm&withInstrument=true.fake" -omexml-only -nopix

Up for discussion is the naming of the wavelength key as we have a mixture of supported styles - see https://bio-formats.readthedocs.io/en/latest/developers/generating-test-images.html#key-value-pairs. I started with a minimal version, alternatives would be:

  • emissionWavelength_x / excitationWavelength_x (like physicalSizeX)
  • EmissionWavelength_x / ExcitationWavelength_x (like PositionX_x)
  • ChannelEmissionWavelength_x / ChannelExcitationWavelength_x (like ChannelName_x)

@sbesson
FakeReader: add support for populating channel wavelengths
1f3a5e3 
Similarly to channel colors, this introduces new indexed key/value
pairs allowing to fill arrays and set the emission and excitation
wavelength of the channels in the OME metadata
@sbesson
FakeReader: add support for populating instrument metadata
0f47e17 
This metadata is already populated in the case of SPW fake files.
Adds a new boolean key withInstrument allowing to use
XMLMockObjects.createInstrument() to add an instrument to the
OME metadata
@jburel
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jburel commented Feb 6, 2025

I ran several tests successfully

No unit

./showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=490&withInstrument=true.fake" -omexml-only -nopix  
<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
   <Instrument ID="Instrument:0">
      <Microscope LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="Upright"/>
      <Laser FrequencyMultiplication="30" ID="LightSource:0" LaserMedium="Alexandrite" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" PockelCell="false" Power="200.0" PowerUnit="mW" RepetitionRate="30.0" RepetitionRateUnit="aHz" SerialNumber="0123456789" Tuneable="false" Type="Dye" Wavelength="200.0" WavelengthUnit="nm"/>
      <Arc ID="LightSource:1" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789" Type="HgXe"/>
      <Filament ID="LightSource:2" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789" Type="Halogen"/>
      <LightEmittingDiode ID="LightSource:3" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789"/>
      <Laser FrequencyMultiplication="30" ID="LightSource:4" LaserMedium="Alexandrite" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" PockelCell="false" Power="200.0" PowerUnit="mW" RepetitionRate="30.0" RepetitionRateUnit="aHz" SerialNumber="0123456789" Tuneable="false" Type="Dye" Wavelength="200.0" WavelengthUnit="nm"/>
      <Detector AmplificationGain="0.0" Gain="1.0" ID="Detector:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Offset="2.0" SerialNumber="0123456789" Type="CCD" Voltage="100" VoltageUnit="V" Zoom="3.0"/>
      <Objective CalibratedMagnification="1.0" Correction="UV" ID="Objective:0" Immersion="Oil" Iris="true" LensNA="0.5" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" NominalMagnification="1.5" SerialNumber="0123456789" WorkingDistance="1.0" WorkingDistanceUnit="µm"/>
      <FilterSet ID="FilterSet:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789"/>
      <Filter ID="Filter:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="LongPass">
         <TransmittanceRange CutIn="200.0" CutInTolerance="1.0" CutInToleranceUnit="nm" CutInUnit="nm" CutOut="300.0" CutOutTolerance="1.0" CutOutToleranceUnit="nm" CutOutUnit="nm" Transmittance="0.5"/>
      </Filter>
      <Filter ID="Filter:1" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="LongPass">
         <TransmittanceRange CutIn="200.0" CutInTolerance="1.0" CutInToleranceUnit="nm" CutInUnit="nm" CutOut="300.0" CutOutTolerance="1.0" CutOutToleranceUnit="nm" CutOutUnit="nm" Transmittance="0.5"/>
      </Filter>
      <Dichroic ID="Dichroic:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789"/>
   </Instrument>
   <Image ID="Image:0" Name="test">
      <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint8">
         <Channel EmissionWavelength="457.0" EmissionWavelengthUnit="nm" ExcitationWavelength="360.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel EmissionWavelength="528.0" EmissionWavelengthUnit="nm" ExcitationWavelength="490.0" ExcitationWavelengthUnit="nm" ID="Channel:0:1" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel ID="Channel:0:2" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <MetadataOnly/>
      </Pixels>
   </Image>
</OME>

Different unit

./showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=490Å&withInstrument=true.fake" -omexml-only -nopix 
<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
   <Instrument ID="Instrument:0">
      <Microscope LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="Upright"/>
      <Laser FrequencyMultiplication="30" ID="LightSource:0" LaserMedium="Alexandrite" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" PockelCell="false" Power="200.0" PowerUnit="mW" RepetitionRate="30.0" RepetitionRateUnit="aHz" SerialNumber="0123456789" Tuneable="false" Type="Dye" Wavelength="200.0" WavelengthUnit="nm"/>
      <Arc ID="LightSource:1" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789" Type="HgXe"/>
      <Filament ID="LightSource:2" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789" Type="Halogen"/>
      <LightEmittingDiode ID="LightSource:3" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Power="200.0" PowerUnit="mW" SerialNumber="0123456789"/>
      <Laser FrequencyMultiplication="30" ID="LightSource:4" LaserMedium="Alexandrite" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" PockelCell="false" Power="200.0" PowerUnit="mW" RepetitionRate="30.0" RepetitionRateUnit="aHz" SerialNumber="0123456789" Tuneable="false" Type="Dye" Wavelength="200.0" WavelengthUnit="nm"/>
      <Detector AmplificationGain="0.0" Gain="1.0" ID="Detector:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" Offset="2.0" SerialNumber="0123456789" Type="CCD" Voltage="100" VoltageUnit="V" Zoom="3.0"/>
      <Objective CalibratedMagnification="1.0" Correction="UV" ID="Objective:0" Immersion="Oil" Iris="true" LensNA="0.5" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" NominalMagnification="1.5" SerialNumber="0123456789" WorkingDistance="1.0" WorkingDistanceUnit="µm"/>
      <FilterSet ID="FilterSet:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789"/>
      <Filter ID="Filter:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="LongPass">
         <TransmittanceRange CutIn="200.0" CutInTolerance="1.0" CutInToleranceUnit="nm" CutInUnit="nm" CutOut="300.0" CutOutTolerance="1.0" CutOutToleranceUnit="nm" CutOutUnit="nm" Transmittance="0.5"/>
      </Filter>
      <Filter ID="Filter:1" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789" Type="LongPass">
         <TransmittanceRange CutIn="200.0" CutInTolerance="1.0" CutInToleranceUnit="nm" CutInUnit="nm" CutOut="300.0" CutOutTolerance="1.0" CutOutToleranceUnit="nm" CutOutUnit="nm" Transmittance="0.5"/>
      </Filter>
      <Dichroic ID="Dichroic:0" LotNumber="9876543210" Manufacturer="Manufacturer" Model="Model" SerialNumber="0123456789"/>
   </Instrument>
   <Image ID="Image:0" Name="test">
      <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint8">
         <Channel EmissionWavelength="457.0" EmissionWavelengthUnit="nm" ExcitationWavelength="360.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel EmissionWavelength="528.0" EmissionWavelengthUnit="nm" ExcitationWavelength="490.0" ExcitationWavelengthUnit="Å" ID="Channel:0:1" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel ID="Channel:0:2" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <MetadataOnly/>
      </Pixels>
   </Image>
</OME>

Invalid unit

./showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=490kkk&withInstrument=true.fake" -omexml-only -nopix 
Exception in thread "main" java.lang.RuntimeException: Invalid wavelength: 490kkk
	at loci.formats.in.FakeReader.parseWavelength(FakeReader.java:1527)
	at loci.formats.in.FakeReader.initFile(FakeReader.java:776)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)
	at loci.formats.ImageReader.setId(ImageReader.java:864)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1048)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1159)

invalid value

./showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=-10k&withInstrument=true.fake" -omexml-only -nopix 
Exception in thread "main" java.lang.RuntimeException: Invalid wavelength: -10k
	at loci.formats.in.FakeReader.parseWavelength(FakeReader.java:1527)
	at loci.formats.in.FakeReader.initFile(FakeReader.java:776)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)
	at loci.formats.ImageReader.setId(ImageReader.java:864)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1048)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1159)

@jburel
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jburel commented Feb 6, 2025

Due to the number of parameters potentially added to generate a fake file, I will vote to keep the name as short as possible while being clear. The current keys used are explicit enough

@jburel
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jburel commented Feb 6, 2025

Without instrument (default is false)

./showinf "test&sizeC=3&emission_0=457nm&emission_1=528nm&excitation_0=360nm&excitation_1=20km&withInstrument=false.fake" -omexml-only -nopix 
<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
   <Image ID="Image:0" Name="test">
      <Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint8">
         <Channel EmissionWavelength="457.0" EmissionWavelengthUnit="nm" ExcitationWavelength="360.0" ExcitationWavelengthUnit="nm" ID="Channel:0:0" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel EmissionWavelength="528.0" EmissionWavelengthUnit="nm" ExcitationWavelength="20.0" ExcitationWavelengthUnit="km" ID="Channel:0:1" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <Channel ID="Channel:0:2" SamplesPerPixel="1">
            <LightPath/>
         </Channel>
         <MetadataOnly/>
      </Pixels>
   </Image>
</OME>

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