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update snirf_specification.md
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Implement changes to the measurementLists similar to those made in change request #157 on the measurementList.
Update the presence of measurementLists.
Reorder the descriptions of measurementLists for consistency.
Revise the table of contents to include measurementLists.
Update the format summary to include measurementLists.
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@sreekanthkura7
sreekanthkura7 committed Aug 21, 2024
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73 changes: 36 additions & 37 deletions snirf_specification.md
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Expand Up @@ -30,6 +30,18 @@ Shared Near Infrared Spectroscopy Format (SNIRF) Specification
* [data.measurementList.dataTypeIndex](#nirsidatajmeasurementlistkdatatypeindex)
* [data.measurementList.sourcePower](#nirsidatajmeasurementlistksourcepower)
* [data.measurementList.detectorGain](#nirsidatajmeasurementlistkdetectorgain)
* [data.measurementLists](#nirsidatajmeasurementlists)
* [data.measurementLists.sourceIndex](#nirsidatajmeasurementlistssourceindex)
* [data.measurementLists.detectorIndex](#nirsidatajmeasurementlistsdetectorindex)
* [data.measurementLists.wavelengthIndex](#nirsidatajmeasurementlistswavelengthindex)
* [data.measurementLists.wavelengthActual](#nirsidatajmeasurementlistswavelengthactual)
* [data.measurementLists.wavelengthEmissionActual](#nirsidatajmeasurementlistswavelengthemissionactual)
* [data.measurementLists.dataType](#nirsidatajmeasurementlistsdatatype)
* [data.measurementLists.dataUnit](#nirsidatajmeasurementlistsdataunit)
* [data.measurementLists.dataTypeLabel](#nirsidatajmeasurementlistsdatatypelabel)
* [data.measurementLists.dataTypeIndex](#nirsidatajmeasurementlistsdatatypeindex)
* [data.measurementLists.sourcePower](#nirsidatajmeasurementlistssourcepower)
* [data.measurementLists.detectorGain](#nirsidatajmeasurementlistsdetectorgain)
* [stim](#nirsistimj)
* [stim.name](#nirsistimjname)
* [stim.data](#nirsistimjdata)
Expand Down Expand Up @@ -170,6 +182,18 @@ Note that this table serves as machine-readable schema for the SNIRF format. Its
|            `dataTypeIndex`            | * Data type index for a given channel  |   `<i>`  * |
|            `sourcePower`              | * Source power for a given channel  |   `<f>`    |
|            `detectorGain`             | * Detector gain for a given channel  |   `<f>`    |
|        `measurementLists`            | * source-detector information     |  `{.}` * |
|            `sourceIndex`              | * Source index for each channel |   `[<i>,...]`* |
|            `detectorIndex`            | * Detector index for each channel |   `[<i>,...]`* |
|            `wavelengthIndex`          | * Wavelength index for each channel |   `[<i>,...]`* |
|            `wavelengthActual`         | * Actual wavelength for each channel |   `[<f>,...]`  |
|            `wavelengthEmissionActual` | * Actual emission wavelength for each channel|   `[<f>,...]`  |
|            `dataType`                 | * Data type for each channel |   `[<i>,...]`* |
|            `dataUnit`                 | * SI unit for each channel |   `["s",...]`  |
|            `dataTypeLabel`            | * Data type name for each channel |   `["s",...]` |
|            `dataTypeIndex`            | * Data type index for each channel |   `[<i>,...]`* |
|            `sourcePower`              | * Source power for each channel |   `[<f>,...]`  |
|            `detectorGain`             | * Detector gain for each channel |   `[<f>,...]`  |
|     `stim{i}`                         | * Root-group for stimulus measurements       |  `{i}`    |
|         `name`                        | * Name of the stimulus data     |   `"s"`  + |
|         `data`                        | * Data stream of the stimulus channel | `[[<f>,...]]` +|
Expand Down Expand Up @@ -538,7 +562,7 @@ As described below, optional variables `probe.sourceLabels` and
label for sources and detectors.

#### /nirs(i)/data(j)/measurementLists
* **Presence**: optional
* **Presence**: required if measurementList is not present
* **Type**: group
* **Location**: `/nirs(i)/data(j)/measurementLists`

Expand All @@ -553,102 +577,77 @@ The arrays of `measurementLists` are:
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/sourceIndex`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Source indices for each channel.
Source indices for each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/detectorIndex
* **Presence**: required if measurementLists is present
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/detectorIndex`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Detector indices for each channel.
Detector indices for each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/wavelengthIndex
* **Presence**: required if measurementLists is present
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/wavelengthIndex`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Index of the "nominal" wavelength (in `probe.wavelengths`) per channel.
Index of the "nominal" wavelength (in `probe.wavelengths`) for each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/wavelengthActual
* **Presence**: optional
* **Type**: numeric 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/wavelengthActual`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Actual (measured) wavelength in nm, if available, for the source in each channel.
Actual (measured) wavelength in nm, if available, for the source in each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/wavelengthEmissionActual
* **Presence**: optional
* **Type**: numeric 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/wavelengthEmissionActual`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Actual (measured) emission wavelength in nm, if available, for the source in each channel.
Actual (measured) emission wavelength in nm, if available, for the source in each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/dataType
* **Presence**: required if measurementLists is present
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/dataType`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. See Appendix for list of possible values.
A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. See Appendix for list of possible values.

#### /nirs(i)/data(j)/measurementLists/dataUnit
* **Presence**: optional
* **Type**: string 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/dataUnit`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. International System of Units (SI units) identifier for each channel.
International System of Units (SI units) identifier for each channel. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/dataTypeLabel
* **Presence**: optional
* **Type**: string 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/dataTypeLabel`

Data-type label. Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.
Data-type label. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/dataTypeIndex
* **Presence**: required if measurementLists is present
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/dataTypeIndex`

Data-type specific parameter indices. Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Note that the Time Domain and Diffuse Correlation Spectroscopy data types have two additional parameters and so `dataTimeIndex` must be a 2-D array with 2 columns that index the additional parameters.
Data-type specific parameter indices. A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Note that the Time Domain and Diffuse Correlation Spectroscopy data types have two additional parameters and so `dataTimeIndex` must be a 2-D array with 2 columns that index the additional parameters.

#### /nirs(i)/data(j)/measurementLists/sourcePower
* **Presence**: optional
* **Type**: numeric 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/sourcePower`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Units are optionally defined in `metaDataTags`.
A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Units are optionally defined in `metaDataTags`.

#### /nirs(i)/data(j)/measurementLists/detectorGain
* **Presence**: optional
* **Type**: numeric 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/detectorGain`

Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Units are optionally defined in `metaDataTags`.

#### /nirs(i)/data(j)/measurementLists/moduleIndex
* **Presence**: optional
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/moduleIndex`

Index of a repeating module. Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/sourceModuleIndex
* **Presence**: optional
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/sourceModuleIndex`

Index of the module that contains the source of the channel.
This index must be used together with `detectorModuleIndex`, and
can not be used when `moduleIndex` presents. Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.

#### /nirs(i)/data(j)/measurementLists/detectorModuleIndex
* **Presence**: optional
* **Type**: integer 1-D array
* **Location**: `/nirs(i)/data(j)/measurementLists/detectorModuleIndex`

Index of the module that contains the detector of the channel.
This index must be used together with `sourceModuleIndex`, and
can not be used when `moduleIndex` presents. Must be 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`.
A 1-D array with length equal to the size of the second dimension of `/nirs(i)/data(j)/dataTimeSeries`. Units are optionally defined in `metaDataTags`.

#### /nirs(i)/stim(j)
* **Presence**: optional
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