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[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema #998

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Feb 4, 2022
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[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema #998

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b2232ad
remove extra double quotes from examples in columns.yml
Remi-Gau Feb 3, 2022
6ecac66
update example highlighting and add double quotes for JSON keys or va…
Remi-Gau Feb 3, 2022
badd3c2
update example and JSON keys and values highlighting in metadata.yml
Remi-Gau Feb 3, 2022
7d27299
Apply suggestions from code review
Remi-Gau Feb 3, 2022
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Remi-Gau Feb 4, 2022
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24 changes: 12 additions & 12 deletions src/schema/objects/columns.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ duration:
name: duration
description: |
Duration of the event (measured from onset) in seconds.
Must always be either zero or positive (or `"n/a"` if unavailable).
Must always be either zero or positive (or `n/a` if unavailable).
A "duration" value of zero implies that the delta function or event is so
short as to be effectively modeled as an impulse.
anyOf:
Expand Down Expand Up @@ -188,7 +188,7 @@ mapping:
material:
name: material
description: |
Material of the electrode (for example, `"Tin"`, `"Ag/AgCl"`, `"Gold"`).
Material of the electrode (for example, `Tin`, `Ag/AgCl`, `Gold`).
type: string
metabolite_parent_fraction:
name: metabolite_parent_fraction
Expand Down Expand Up @@ -269,7 +269,7 @@ participant_id:
plasma_radioactivity:
name: plasma_radioactivity
description: |
Radioactivity in plasma, in unit of plasma radioactivity (for example, `"kBq/mL"`).
Radioactivity in plasma, in unit of plasma radioactivity (for example, `kBq/mL`).
type: number
# reference column for channels.tsv files for EEG data
reference__eeg:
Expand All @@ -283,7 +283,7 @@ reference__eeg:
reference__ieeg:
name: reference
description: |
Specification of the reference (for example, 'mastoid', 'ElectrodeName01', 'intracranial', 'CAR', 'other', 'n/a').
Specification of the reference (for example, `mastoid`, `ElectrodeName01`, `intracranial`, `CAR`, `other`, `n/a`).
If the channel is not an electrode channel (for example, a microphone channel) use `n/a`.
anyOf:
- type: string
Expand All @@ -300,7 +300,7 @@ response_time:
description: |
Response time measured in seconds.
A negative response time can be used to represent preemptive responses and
"n/a" denotes a missed response.
`n/a` denotes a missed response.
anyOf:
- type: number
unit: s
Expand Down Expand Up @@ -387,7 +387,7 @@ software_filters:
name: software_filters
description: |
List of temporal and/or spatial software filters applied
(for example, "SSS", `"SpatialCompensation"`).
(for example, `SSS`, `SpatialCompensation`).
Note that parameters should be defined in the general MEG sidecar .json file.
Indicate `n/a` in the absence of software filters applied.
anyOf:
Expand All @@ -408,8 +408,8 @@ status:
name: status
description: |
Data quality observed on the channel.
A channel is considered `"bad"` if its data quality is compromised by excessive noise.
If quality is unknown, then a value of `"n/a"` may be used.
A channel is considered `bad` if its data quality is compromised by excessive noise.
If quality is unknown, then a value of `n/a` may be used.
Description of noise type SHOULD be provided in `[status_description]`.
type: string
enum:
Expand All @@ -432,7 +432,7 @@ stim_file:
(under the root folder of the dataset; with optional subfolders).
The values under the `stim_file` column correspond to a path relative to
`/stimuli`.
For example `"images/cat03.jpg"` will be translated to `"/stimuli/images/cat03.jpg"`.
For example `images/cat03.jpg` will be translated to `/stimuli/images/cat03.jpg`.
type: string
format: stimuli_relative
strain:
Expand Down Expand Up @@ -461,8 +461,8 @@ trial_type:
description: |
Primary categorisation of each trial to identify them as instances of the
experimental conditions.
For example: for a response inhibition task, it could take on values "go" and
"no-go" to refer to response initiation and response inhibition experimental
For example: for a response inhibition task, it could take on values `go` and
`no-go` to refer to response initiation and response inhibition experimental
conditions.
type: string
trigger:
Expand Down Expand Up @@ -544,7 +544,7 @@ whole_blood_radioactivity:
name: whole_blood_radioactivity
description: |
Radioactivity in whole blood samples,
in unit of radioactivity measurements in whole blood samples (for example, `"kBq/mL"`).
in unit of radioactivity measurements in whole blood samples (for example, `kBq/mL`).
type: number
x:
name: x
Expand Down
36 changes: 18 additions & 18 deletions src/schema/objects/entities.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ acquisition:
resolution.
In such case two files could have the following names:
`sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
the user is free to choose any other label than highres and lowres as long
the user is free to choose any other label than `highres` and `lowres` as long
as they are consistent across subjects and sessions.
In case different sequences are used to record the same modality
(for example, RARE and FLASH for T1w)
(for example, `RARE` and `FLASH` for T1w)
this field can also be used to make that distinction.
At what level of detail to make the distinction (for example,
just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
just between `RARE` and `FLASH`, or between `RARE`, `FLASH`, and `FLASHsubsampled`)
remains at the discretion of the researcher.
type: string
format: label
Expand All @@ -32,7 +32,7 @@ ceagent:
The `ce-<label>` key/value can be used to distinguish
sequences using different contrast enhanced images.
The label is the name of the contrast agent.
The key `ContrastBolusIngredient` MAY also be added in the JSON file,
The key `"ContrastBolusIngredient"` MAY also be added in the JSON file,
with the same label.
type: string
format: label
Expand Down Expand Up @@ -82,9 +82,9 @@ echo:
If files belonging to an entity-linked file collection are acquired at different
echo times, the `_echo-<index>` key/value pair MUST be used to distinguish
individual files.
This entity represents the `EchoTime` metadata field. Please note that the `<index>`
This entity represents the `"EchoTime"` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the
`EchoTime` value which needs to be stored in the field `EchoTime` of the separate
`"EchoTime"` value which needs to be stored in the field `"EchoTime"` of the separate
JSON file.
type: string
format: index
Expand All @@ -95,9 +95,9 @@ flip:
If files belonging to an entity-linked file collection are acquired at different
flip angles, the `_flip-<index>` key/value pair MUST be used to distinguish
individual files.
This entity represents the `FlipAngle` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
value which needs to be stored in the field `FlipAngle` of the separate JSON file.
This entity represents the `"FlipAngle"` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `"FlipAngle"`
value which needs to be stored in the field `"FlipAngle"` of the separate JSON file.
type: string
format: index
hemisphere:
Expand All @@ -119,9 +119,9 @@ inversion:
If files belonging to an entity-linked file collection are acquired at different
inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
individual files.
This entity represents the `InversionTime` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
value which needs to be stored in the field `InversionTime` of the separate JSON file.
This entity represents the `"InversionTime` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `"InversionTime"`
value which needs to be stored in the field `"InversionTime"` of the separate JSON file.
type: string
format: index
label:
Expand Down Expand Up @@ -151,7 +151,7 @@ mtransfer:
If files belonging to an entity-linked file collection are acquired at different
magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
distinguish individual files.
This entity represents the `MTState` metadata field. Allowed label values for this
This entity represents the `"MTState"` metadata field. Allowed label values for this
entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
respectively.
type: string
Expand All @@ -172,7 +172,7 @@ part:

Phase images MAY be in radians or in arbitrary units.
The sidecar JSON file MUST include the units of the `phase` image.
The possible options are `rad` or `arbitrary`.
The possible options are `"rad"` or `"arbitrary"`.

When there is only a magnitude image of a given type, the `part` key MAY be
omitted.
Expand All @@ -190,7 +190,7 @@ processing:
a file that was a result of particular processing performed on the device.

This is useful for files produced in particular by Elekta's MaxFilter
(for example, sss, tsss, trans, quat or mc),
(for example, `sss`, `tsss`, `trans`, `quat` or `mc`),
which some installations impose to be run on raw data because of active
shielding software corrections before the MEG data can actually be
exploited.
Expand All @@ -201,7 +201,7 @@ reconstruction:
entity: rec
description: |
The `rec-<label>` key/value can be used to distinguish
different reconstruction algorithms (for example ones using motion
different reconstruction algorithms (for example `MoCo` for the ones using motion
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This feels like common enough occurrence in scanners output to add it by name as an example

correction).
type: string
format: label
Expand All @@ -220,7 +220,7 @@ resolution:
entity: res
description: |
Resolution of regularly sampled N-dimensional data.
MUST have a corresponding `Resolution` metadata field to provide
MUST have a corresponding `"Resolution"` metadata field to provide
interpretation.

This entity is only applicable to derivative data.
Expand Down Expand Up @@ -350,7 +350,7 @@ tracer:
description: |
The `trc-<label>` key/value can be used to distinguish
sequences using different tracers.
The key `TracerName` MUST also be included in the associated JSON file,
The key `"TracerName"` MUST also be included in the associated JSON file,
although the label may be different.
type: string
format: label
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