Descriptions for quantities and sub-sections in transmission plugin

[ka-sarthak]

Below you can find the tree structure of the UVVisTransmission measurement class, TransmissionSpectrophotometer class, and TransmissionSample class. We need concise descriptions for each quantity and sub-section in them.

Some descriptions are already available (these are italicized), but they are mere suggestions. Feel free to suggest better ones.

Ideally, the description should be 1-2 lines long and clear to understand.

UVVisTransmission measurement class

• method (str)
• user (str)
  • description: Name of the analyst/user
• subsection: UVVisTransmissionResult
  • transmittance (list[float])
  • absorbance (list[float])
  • wavelength (list[float])
• subsection: TransmissionSettings
  • ordinate_type (MEnum(['%T', 'A']))
  • sample_beam_position (MEnum(['Front', 'Rear']))
  • common_beam_mask (int)
  • common_beam_depolarizer (bool)
  • polarizer_angle (float)
  • subsection: Accessory
    • polarizer (bool)
      • description: True if the polarizer is used, else False.
    • aperture (float)
  • subsection: Monochromator
    • monochromator_change_point (list[float])
    • subsection: SlitWidth
      • description: Slit width value over a wavelength range.
      • slit_width_servo (bool)
        • description: True if slit width servo is on, i.e., the slit width varies over the wavelength range, else False.
  • subsection: Lamp
    • d2_lamp (bool)
    • tungsten_lamp (bool)
    • lamp_change_point (list[float])
  • subsection: Detector
    • module (MEnum(['three detector module', '150-mm integrating sphere']))
    • detector_change_point (list[float])
    • subsection: NIRGain
      • description: NIR gain over a wavelength range.
    • subsection: IntegrationTime
      • description: Integration time over a wavelength range.
  • subsection: Attenuator
    • sample (int)
      • description: Sample beam attenuation in %
    • reference (int)
      • description: Reference beam attenuation in %

TransmissionSpectrophotometer instrument class

• serial_number (str)
• software_version (str)

TranmissionSample sample class

• name (str)
• lab_id (str)
  • description: Sample ID.
• chemical_composition (str)
• length (float)
  • description: Length (or thickness) of the sample in mm.
• orientation (str) description: Crystallographic orientation of the sample.

[ahm531]

Hi Sarthak, Here are some descriptions added to the quantities. I am also attaching a page from the help page of the PerkinElmer instrument software from which I got most of the text. Here is the file

UVVisTransmission measurement class

• method (str)
  • description: Measurement technique used.
• user (str)
  • description: Name of the analyst/user
• subsection: UVVisTransmissionResult
  • transmittance (list[float])
    • description: List of transmittance values (%).
  • absorbance (list[float])
    • description: List of absorbance values.
  • wavelength (list[float])
    • description: List of wavelength values (nm).
• subsection: TransmissionSettings
  • ordinate_type (MEnum(['%T', 'A']))
    • description: Specifies whether the ordinate (y-axis) of the measurement data is displayed as percent transmittance (%T) or absorbance (A).
  • sample_beam_position (MEnum(['Front', 'Rear']))
    • description: Position of the sample beam: either the front or the back of the sample chamber.
  • common_beam_mask (int)
    • description: Beam mask settings: 100% means the mask is fully open and 100% of the beam passes. 0% means the mask is closed and no light passes.
  • common_beam_depolarizer (bool)
    • description: Optional accessory used to depolarize the radiation coming from the monochromator (True if used, , else False).
  • polarizer_angle (float)
    • description: Angle of the polarizer in degrees.
  • subsection: Accessory
    • polarizer (bool)
      • description: Optional accessory to polarize or depolarize the light beam entering the sample (True if used, else False).
    • aperture (float)
      • description: Diameter of the aperture in millimeters.
  • subsection: Monochromator
    • monochromator_change_point (list[float])
      • description: The wavelength at which the monochromator changes settings.
    • subsection: SlitWidth
      • description: Slit width value in nm.
      • slit_width_servo (bool)
        • description: True if slit width servo is on, i.e. the system monitors the reference beam energy and adjusts the slits to avoid over-saturation of the detectors.
  • subsection: Lamp
    • d2_lamp (bool)
      • description: True when the deuterium lamp is used (typically covers UV ranges from approximately 160 nm to 400 nm).
    • tungsten_lamp (bool)
      • description: True when the tungsten lamp is used (typically covering the visible to near-infrared range from about 320 nm to 2500 nm).
    • lamp_change_point (list[float])
      • description: The wavelength at which beams are switched between deuterium and tungsten lamps.
  • subsection: Detector
    • module (MEnum(['three detector module', '150-mm integrating sphere']))
      • description: Type of detector module used.
    • detector_change_point (list[float])
      • description: The wavelength at which the detector module changes.
    • subsection: NIRGain
      • description: The gain factor for the detector.
      • description: NIR gain over a wavelength range.
    • subsection: IntegrationTime
      • description: Integration time over a wavelength range.
  • subsection: Attenuator
    • sample (int)
      • description: Sample beam attenuation in %
    • reference (int)
      • description: Reference beam attenuation in %

TransmissionSpectrophotometer instrument class

• serial_number (str)
  • description: Spectrophotometer serial number.
• software_version (str)
  • description: Software version used by the spectrophotometer.

TranmissionSample sample class

• name (str)
  • description: Descriptive name of the sample
• lab_id (str)
  • description: An ID string that is unique at least for the lab that produced this sample.
• chemical_composition (str)
  • description: Chemical composition of the sample
• length (float)
  • description: Length (or thickness) of the sample in mm.
• orientation (str) description: Crystallographic orientation of the sample.

[ka-sarthak]

@ahm531 Great work! Thanks a lot for your input and sharing the file from Perkin Elmer.

Some question:

• Is the polarizer_angle the one for the Accessory.polarizer. If that's the case, then we can move this quantity into the Accessory sub-section. Can you comment on this?
• The description for Accessory.polarizer includes "Optional accessory to polarize or depolarize the light beam". This is a bit confusing. Do you mean that two Accessories can be added to either polarize (using a polarizer) or depolarize (using a depolarizer) the light beam? In this case, do you think we should move common_beam_depolarizer to this sub-section?

Some remarks:

• common_beam_polarizer is actually common_beam_depolarizer. This is a typo in my comment above, will edit it there. But I think you wrote the correct description anyways!
• I think the descriptions should be unit-agnostic. I myself am a culprit of adding something like Length (or thickness) of the sample in mm. But given that one toggle the units on the GUI, and the conversion is taken care by NOMAD, puting the units in description gives a false notion to the user that they should always stick with this unit. On other hand, specifying that a certain dimensionless quantity is a percentage or ratio in the description is totally reasonable.

[ka-sarthak]

@budschi @ahm531 Is there a need to specify the detector materials used in Detector sub-section? In the Perkin Elmer help guide, they write "The instrument uses a single detector (photomultiplier for UV/Vis and PbS or InGaAs for NIR)"

[ahm531]

Is the polarizer_angle the one for the Accessory.polarizer. If that's the case, then we can move this quantity into the Accessory sub-section. Can you comment on this?

• I guess so. It also confused me at first that they were separated.

The description for Accessory.polarizer includes "Optional accessory to polarize or depolarize the light beam". This is a bit confusing. Do you mean that two Accessories can be added to either polarize (using a polarizer) or depolarize (using a depolarizer) the light beam? In this case, do you think we should move common_beam_depolarizer to this sub-section?

There is one accessory that can either polarize or depolarize the light. see here

• I also quote from the manual "The optional depolarizer/polarizer mounts inside the sample chamber. It is used to polarize or depolarize the light beam entering the sample. A switch on the accessory sets it to depolarizer or polarizer".
• I don't think the common_beam_depolarizer (CBD) should be moved to this subsection. The CBD is installed inside the spectrometer and works on the common light beam coming from the source (before it is separated into the reference beam and the sample beam in the sample compartment) The polarizer/depolarizer is installed in the sample compartment.

[ahm531]

@budschi @ahm531 Is there a need to specify the detector materials used in Detector sub-section? In the Perkin Elmer help guide, they write "The instrument uses a single detector (photomultiplier for UV/Vis and PbS or InGaAs for `NIR)"

I think the individual types of detectors are standard. However, for generality, I guess there should be another module in this list module (MEnum(['three detector module', '150-mm integrating sphere']). The three detector module is only available in Lambda 1050. However, the instrument versions have only two detectors (I'm not sure what that mode would be called).

[ahm531]

Just checked one of my ASC files (Lambda 950) it has the following line (25) about the detector: CommonBeamDepol,RBeamAtt,SBeamAtt,**uv/vis/nir detector**

Do you think we should also include this in the module quantity?

[ka-sarthak]

I guess so. It also confused me at first that they were separated.

@ahm531 Nice, so there's a connection between the two.

I also quote from the manual "The optional depolarizer/polarizer mounts inside the sample chamber. It is used to polarize or depolarize the light beam entering the sample. A switch on the accessory sets it to depolarizer or polarizer".

I don't think the common_beam_depolarizer (CBD) should be moved to this subsection. The CBD is installed inside the spectrometer and works on the common light beam coming from the source (before it is separated into the reference beam and the sample beam in the sample compartment) The polarizer/depolarizer is installed in the sample compartment.

Okay, this is now much clearer to me. CBD is always present and is not an optional accessory per se. The accessory on the other hand allows to both polarize and depolarize the light. In this case, we should have quantities that handle both these options in the accessory.

Just checked one of my ASC files (Lambda 950) it has the following line (25) about the detector: CommonBeamDepol,RBeamAtt,SBeamAtt,**uv/vis/nir detector**

Do you think we should also include this in the module quantity?

The other detector module you mention is the uv/vis/nir detector, right? In the reader, we set three-detector-module when uv/vis/nir detector is found in line 25. Here's the code. Let me know your thoughts on this.

[hirokitanaka-ikz]

@ka-sarthak @ahm531 Hi, concerning the polarizers and depolarizers, I know that some devices have a depolarizer inside, so-called common beam depolarizer (we can activate and deactivate it). Perkin Elmer offers two options: common beam depolarizer or polarizer/depolarizer drive accessory (https://resources.perkinelmer.com/lab-solutions/resources/docs/prd-006991A-04-LAMBDA650-1050PolarizerDepolarizerOptions.pdf). Our Lambda1050 does not have it but the polarizer/depolarizer drive accessory instead.

[ahm531]

@ka-sarthak Both Lambda 950 and 1050 measure the same range (175-3300 nm) covering UV/Vis/NIR light.

• Lambda 950 uses two detectors (PMT and PbS) for good performance.

• Lambda 1050 has a "three detector module" with PMT, PbS and InGaAs. This additional detector (InGaAs) makes it much better at picking up weak signals in the near infrared (NIR) region (about 900-1700 nm).

Now, translating uv/vis/nir detector to three-detector module doesn't seem accurate, especially since the Lambda 950 doesn't have three detectors. The term "three-detector module" is specific to the configuration of the Lambda 1050. However, I don't have solution to this at the moment, but would be happy to discuss and compare the asc files from both instruments.

Also, having the three-detector module would mean that there are two wavelength change points when someone is measuring from 175 nm to 3300 nm. I'm wondering if this is accounted for in the code (or planned).

[ka-sarthak]

@ahm531 @hirokitanaka-ikz Thank you both for sharing detailed differences in detector between the two instruments. We should make the schema adaptable to the two versions for instrument.

Here are some points from my side:

• Use EnumEditQuantity for detector_module which gives us a dropdown menu to select the module. Here we can add uv/vis/nir, uv/vis/nir three-detector-module, 150mm Sphere Based on the name of the instrument taken from the .asc file (Lambda 1050 or Lambda 950), the respective detector module will be selected. Add the information about the individual detector (for eg., Three detector module has PMT, InGaAs, and PbS detectors) in the descriptions of the module.

• @ahm531 the number of detector change point is variable, and depends on the data file. So in case of normal detector, there will be only one change point, in case of three-detector module, there will be two change points.

• @hirokitanaka-ikz As you pointed out in the guide, they mention that CBD is an optional accessory along with Polarizer/Depolarizer (or Pol/Depol). Should we add both these in the accessory sub-section?

• move polarizer_angle to the accessory sub-section under Pol/Depol. @hirokitanaka-ikz is this polarizer angle related to the polarizer inside the sample chamber (Pol/Depol)?

[ka-sarthak]

Thanks for making this discussion lively! Let's find some time this week to finalize on these points.