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[FIX] Rename channels.tsv column: orientation_component to component #1417

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merged 9 commits into from
Feb 15, 2023
Merged

[FIX] Rename channels.tsv column: orientation_component to component #1417

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3ce3b37
Fix orientation_component column to component
sjeung Feb 13, 2023
8ce4d4d
Rename orientation_component to component
sjeung Feb 13, 2023
069c36b
Wording change in IMU channel description in nirs
sjeung Feb 13, 2023
7275ca7
Merge pull request #1 from sjeung/master
sjeung Feb 13, 2023
a700bbb
Correct table fence
sjeung Feb 14, 2023
7636a87
Enhance description for component column
sjeung Feb 14, 2023
c5fc777
Remove orientation component from nirs.yaml
sjeung Feb 14, 2023
8a83e67
Remove trailing space
sjeung Feb 14, 2023
b0f6058
Reduce cell padding
sjeung Feb 14, 2023
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24 changes: 12 additions & 12 deletions src/modality-specific-files/near-infrared-spectroscopy.md
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Expand Up @@ -206,18 +206,18 @@ Any of the channel types defined in other BIDS specification MAY be used here as
As several of these data types are commonly acquired using NIRS devices they are included as an example at the base of the table.
Note that upper-case is REQUIRED.

| **Keyword** | **Description** |
| --------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| NIRSCWAMPLITUDE | Continuous wave amplitude measurements. Equivalent to dataType 001 in SNIRF. |
| NIRSCWFLUORESCENSEAMPLITUDE | Continuous wave fluorescence amplitude measurements. Equivalent to dataType 051 in SNIRF. |
| NIRSCWOPTICALDENSITY | Continuous wave change in optical density measurements. Equivalent to dataTypeLabel dOD in SNIRF. |
| NIRSCWHBO | Continuous wave oxygenated hemoglobin (oxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbO in SNIRF. |
| NIRSCWHBR | Continuous wave deoxygenated hemoglobin (deoxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbR in SNIRF. |
| NIRSCWMUA | Continuous wave optical absorption measurements. Equivalent to dataTypeLabel mua in SNIRF. |
| ACCEL | Accelerometer channel, one channel for each orientation. An extra column `component` for the axis of the orientation MUST be added to the `*_channels.tsv` file (x, y or z). |
| GYRO | Gyrometer channel, one channel for each orientation. An extra column `component` for the axis of the orientation MUST be added to the `*_channels.tsv` file (x, y or z). |
| MAGN | Magnetomenter channel, one channel for each orientation. An extra column `component` for the axis of the orientation MUST be added to the `*_channels.tsv` file (x, y or z). |
| MISC | Miscellaneous |
| **Keyword** | **Description** |
| --------------------------- | -----------------------------------------------------------------------------------------------------------------------------------------------------------|
| NIRSCWAMPLITUDE | Continuous wave amplitude measurements. Equivalent to dataType 001 in SNIRF. |
| NIRSCWFLUORESCENSEAMPLITUDE | Continuous wave fluorescence amplitude measurements. Equivalent to dataType 051 in SNIRF. |
| NIRSCWOPTICALDENSITY | Continuous wave change in optical density measurements. Equivalent to dataTypeLabel dOD in SNIRF. |
| NIRSCWHBO | Continuous wave oxygenated hemoglobin (oxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbO in SNIRF. |
| NIRSCWHBR | Continuous wave deoxygenated hemoglobin (deoxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbR in SNIRF. |
| NIRSCWMUA | Continuous wave optical absorption measurements. Equivalent to dataTypeLabel mua in SNIRF. |
| ACCEL | Accelerometer channel, one channel for each spatial axis. An extra column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). |
| GYRO | Gyrometer channel, one channel for each spatial axis. An extra column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). |
| MAGN | Magnetomenter channel, one channel for each spatial axis. An extra column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). |
| MISC | Miscellaneous |

### Example `*_channels.tsv`

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15 changes: 11 additions & 4 deletions src/schema/objects/columns.yaml
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Expand Up @@ -308,16 +308,23 @@ onset:
acquired data point.
type: number
unit: s
orientation_component:
name: orientation_component
display_name: Orientation Component
component:
name: component
display_name: Component
description: |
Description of the orientation of the channel.
Description of the spatial axis or label of quaternion component associated with the channel.
For example, `x`,`y`,`z` for position channels,
or `quat_x`, `quat_y`, `quat_z`, `quat_w` for quaternion orientation channels.
type: string
enum:
- x
- y
- z
- quat_x
- quat_y
- quat_z
- quat_w
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- n/a
pathology:
name: pathology
display_name: Pathology
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4 changes: 2 additions & 2 deletions src/schema/rules/checks/nirs.yaml
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Expand Up @@ -44,14 +44,14 @@ ShortChannelCountReq:
checks:
- sidecar.ShortChannelCount == count(associations.channels.short_channel, true)

OrientationComponent:
Component:
selectors:
- datatype == "nirs"
- suffix == "channels"
- extension == ".tsv"
- intersect(columns.type, ["ACCEL", "GYRO", "MAGN"])
checks:
- columns.orientation_component != null
- columns.component != null

RequiredChannels:
selectors:
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2 changes: 1 addition & 1 deletion src/schema/rules/tabular_data/nirs.yaml
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Expand Up @@ -21,7 +21,7 @@ nirsChannels:
sampling_frequency:
level: optional
level_addendum: required if `SamplingFrequency` is `n/a` in `_nirs.json`
orientation_component:
component:
level: optional
level_addendum: required if `type` is `ACCEL`, `GYRO` or `MAGN`
wavelength_actual: optional
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