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Merge pull request #482 from NeurodataWithoutBorders/schema-260-release
add schema files and update default version
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,264 @@ | ||
| datasets: | ||
| - neurodata_type_def: NWBData | ||
| neurodata_type_inc: Data | ||
| doc: An abstract data type for a dataset. | ||
|
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||
| - neurodata_type_def: TimeSeriesReferenceVectorData | ||
| neurodata_type_inc: VectorData | ||
| default_name: timeseries | ||
| dtype: | ||
| - name: idx_start | ||
| dtype: int32 | ||
| doc: Start index into the TimeSeries 'data' and 'timestamp' datasets of the referenced | ||
| TimeSeries. The first dimension of those arrays is always time. | ||
| - name: count | ||
| dtype: int32 | ||
| doc: Number of data samples available in this time series, during this epoch | ||
| - name: timeseries | ||
| dtype: | ||
| target_type: TimeSeries | ||
| reftype: object | ||
| doc: The TimeSeries that this index applies to | ||
| doc: Column storing references to a TimeSeries (rows). For each TimeSeries this | ||
| VectorData column stores the start_index and count to indicate the range in time | ||
| to be selected as well as an object reference to the TimeSeries. | ||
|
|
||
| - neurodata_type_def: Image | ||
| neurodata_type_inc: NWBData | ||
| dtype: numeric | ||
| dims: | ||
| - - x | ||
| - y | ||
| - - x | ||
| - y | ||
| - r, g, b | ||
| - - x | ||
| - y | ||
| - r, g, b, a | ||
| shape: | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - 3 | ||
| - - null | ||
| - null | ||
| - 4 | ||
| doc: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the | ||
| third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or | ||
| (x, y, (r, g, b, a)). | ||
| attributes: | ||
| - name: resolution | ||
| dtype: float32 | ||
| doc: Pixel resolution of the image, in pixels per centimeter. | ||
| required: false | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of the image. | ||
| required: false | ||
|
|
||
| - neurodata_type_def: ImageReferences | ||
| neurodata_type_inc: NWBData | ||
| dtype: | ||
| target_type: Image | ||
| reftype: object | ||
| dims: | ||
| - num_images | ||
| shape: | ||
| - null | ||
| doc: Ordered dataset of references to Image objects. | ||
|
|
||
| groups: | ||
| - neurodata_type_def: NWBContainer | ||
| neurodata_type_inc: Container | ||
| doc: An abstract data type for a generic container storing collections of data and | ||
| metadata. Base type for all data and metadata containers. | ||
|
|
||
| - neurodata_type_def: NWBDataInterface | ||
| neurodata_type_inc: NWBContainer | ||
| doc: An abstract data type for a generic container storing collections of data, | ||
| as opposed to metadata. | ||
|
|
||
| - neurodata_type_def: TimeSeries | ||
| neurodata_type_inc: NWBDataInterface | ||
| doc: General purpose time series. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| default_value: no description | ||
| doc: Description of the time series. | ||
| required: false | ||
| - name: comments | ||
| dtype: text | ||
| default_value: no comments | ||
| doc: Human-readable comments about the TimeSeries. This second descriptive field | ||
| can be used to store additional information, or descriptive information if the | ||
| primary description field is populated with a computer-readable string. | ||
| required: false | ||
| datasets: | ||
| - name: data | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - num_DIM2 | ||
| - - num_times | ||
| - num_DIM2 | ||
| - num_DIM3 | ||
| - - num_times | ||
| - num_DIM2 | ||
| - num_DIM3 | ||
| - num_DIM4 | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - null | ||
| doc: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension | ||
| should always represent time. This can also be used to store binary data | ||
| (e.g., image frames). This can also be a link to data stored in an external file. | ||
| attributes: | ||
| - name: conversion | ||
| dtype: float32 | ||
| default_value: 1.0 | ||
| doc: Scalar to multiply each element in data to convert it to the specified 'unit'. | ||
| If the data are stored in acquisition system units or other units | ||
| that require a conversion to be interpretable, multiply the data by 'conversion' | ||
| to convert the data to the specified 'unit'. e.g. if the data acquisition system | ||
| stores values in this object as signed 16-bit integers (int16 range | ||
| -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data | ||
| acquisition system gain is 8000X, then the 'conversion' multiplier to get from | ||
| raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9. | ||
| required: false | ||
| - name: offset | ||
| dtype: float32 | ||
| default_value: 0.0 | ||
| doc: Scalar to add to the data after scaling by 'conversion' to finalize its coercion | ||
| to the specified 'unit'. Two common examples of this include (a) data stored in an | ||
| unsigned type that requires a shift after scaling to re-center the data, | ||
| and (b) specialized recording devices that naturally cause a scalar offset with | ||
| respect to the true units. | ||
| required: false | ||
| - name: resolution | ||
| dtype: float32 | ||
| default_value: -1.0 | ||
| doc: Smallest meaningful difference between values in data, stored in the specified | ||
| by unit, e.g., the change in value of the least significant bit, or a larger | ||
| number if signal noise is known to be present. If unknown, use -1.0. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| doc: Base unit of measurement for working with the data. Actual stored values are | ||
| not necessarily stored in these units. To access the data in these units, | ||
| multiply 'data' by 'conversion' and add 'offset'. | ||
| - name: continuity | ||
| dtype: text | ||
| doc: Optionally describe the continuity of the data. Can be "continuous", "instantaneous", or | ||
| "step". For example, a voltage trace would be "continuous", because samples | ||
| are recorded from a continuous process. An array of lick times would be "instantaneous", | ||
| because the data represents distinct moments in time. Times of image presentations would be | ||
| "step" because the picture remains the same until the next timepoint. This field is optional, | ||
| but is useful in providing information about the underlying data. It may inform the way this | ||
| data is interpreted, the way it is visualized, and what analysis methods are applicable. | ||
| required: false | ||
| - name: starting_time | ||
| dtype: float64 | ||
| doc: Timestamp of the first sample in seconds. When timestamps are uniformly | ||
| spaced, the timestamp of the first sample can be specified and all subsequent | ||
| ones calculated from the sampling rate attribute. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: rate | ||
| dtype: float32 | ||
| doc: Sampling rate, in Hz. | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for time, which is fixed to 'seconds'. | ||
| - name: timestamps | ||
| dtype: float64 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Timestamps for samples stored in data, in seconds, relative to the | ||
| common experiment master-clock stored in NWBFile.timestamps_reference_time. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: interval | ||
| dtype: int32 | ||
| value: 1 | ||
| doc: Value is '1' | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for timestamps, which is fixed to 'seconds'. | ||
| - name: control | ||
| dtype: uint8 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Numerical labels that apply to each time point in data for the purpose of | ||
| querying and slicing data by these values. If present, the length of this | ||
| array should be the same size as the first dimension of data. | ||
| quantity: '?' | ||
| - name: control_description | ||
| dtype: text | ||
| dims: | ||
| - num_control_values | ||
| shape: | ||
| - null | ||
| doc: Description of each control value. Must be present if control is present. | ||
| If present, control_description[0] should describe time points where control == 0. | ||
| quantity: '?' | ||
| groups: | ||
| - name: sync | ||
| doc: Lab-specific time and sync information as provided directly from hardware | ||
| devices and that is necessary for aligning all acquired time information to | ||
| a common timebase. The timestamp array stores time in the common timebase. | ||
| This group will usually only be populated in TimeSeries that are | ||
| stored external to the NWB file, in files storing raw data. Once timestamp | ||
| data is calculated, the contents of 'sync' are mostly for archival purposes. | ||
| quantity: '?' | ||
|
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||
| - neurodata_type_def: ProcessingModule | ||
| neurodata_type_inc: NWBContainer | ||
| doc: A collection of processed data. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of this collection of processed data. | ||
| groups: | ||
| - neurodata_type_inc: NWBDataInterface | ||
| doc: Data objects stored in this collection. | ||
| quantity: '*' | ||
| - neurodata_type_inc: DynamicTable | ||
| doc: Tables stored in this collection. | ||
| quantity: '*' | ||
|
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||
| - neurodata_type_def: Images | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Images | ||
| doc: A collection of images with an optional way to specify the order of the images | ||
| using the "order_of_images" dataset. An order must be specified if the images are | ||
| referenced by index, e.g., from an IndexSeries. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of this collection of images. | ||
| datasets: | ||
| - neurodata_type_inc: Image | ||
| doc: Images stored in this collection. | ||
| quantity: '+' | ||
| - name: order_of_images | ||
| neurodata_type_inc: ImageReferences | ||
| doc: Ordered dataset of references to Image objects stored in the parent group. | ||
| Each Image object in the Images group should be stored once and only once, so | ||
| the dataset should have the same length as the number of images. | ||
| quantity: '?' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,124 @@ | ||
| groups: | ||
| - neurodata_type_def: SpatialSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: "Direction, e.g., of gaze or travel, or position. The TimeSeries::data field\ | ||
| \ is a 2D array storing position or direction relative to some reference frame.\ | ||
| \ Array structure: [num measurements] [num dimensions]. Each SpatialSeries has\ | ||
| \ a text dataset reference_frame that indicates the zero-position, or the zero-axes\ | ||
| \ for direction. For example, if representing gaze direction, 'straight-ahead'\ | ||
| \ might be a specific pixel on the monitor, or some other point in space. For\ | ||
| \ position data, the 0,0 point might be the top-left corner of an enclosure, as\ | ||
| \ viewed from the tracking camera. The unit of data will indicate how to interpret\ | ||
| \ SpatialSeries values." | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - x | ||
| - - num_times | ||
| - x,y | ||
| - - num_times | ||
| - x,y,z | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - 1 | ||
| - - null | ||
| - 2 | ||
| - - null | ||
| - 3 | ||
| doc: 1-D or 2-D array storing position or direction relative to some reference frame. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: meters | ||
| doc: Base unit of measurement for working with the data. The default value | ||
| is 'meters'. Actual stored values are not necessarily stored in these units. | ||
| To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. | ||
| required: false | ||
| - name: reference_frame | ||
| dtype: text | ||
| doc: Description defining what exactly 'straight-ahead' means. | ||
| quantity: '?' | ||
|
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| - neurodata_type_def: BehavioralEpochs | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralEpochs | ||
| doc: TimeSeries for storing behavioral epochs. The objective of this and the other | ||
| two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is | ||
| to provide generic hooks for software tools/scripts. This allows a tool/script | ||
| to take the output one specific interface (e.g., UnitTimes) and plot that data | ||
| relative to another data modality (e.g., behavioral events) without having to | ||
| define all possible modalities in advance. Declaring one of these interfaces means | ||
| that one or more TimeSeries of the specified type is published. These TimeSeries | ||
| should reside in a group having the same name as the interface. For example, if | ||
| a BehavioralTimeSeries interface is declared, the module will have one or more | ||
| TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs | ||
| should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries | ||
| is for continuous data. | ||
| groups: | ||
| - neurodata_type_inc: IntervalSeries | ||
| doc: IntervalSeries object containing start and stop times of epochs. | ||
| quantity: '*' | ||
|
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| - neurodata_type_def: BehavioralEvents | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralEvents | ||
| doc: TimeSeries for storing behavioral events. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a> | ||
| for more details. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing behavioral events. | ||
| quantity: '*' | ||
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| - neurodata_type_def: BehavioralTimeSeries | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralTimeSeries | ||
| doc: TimeSeries for storing Behavoioral time series data. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a> | ||
| for more details. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing continuous behavioral data. | ||
| quantity: '*' | ||
|
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| - neurodata_type_def: PupilTracking | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: PupilTracking | ||
| doc: Eye-tracking data, representing pupil size. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing time series data on pupil size. | ||
| quantity: '+' | ||
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| - neurodata_type_def: EyeTracking | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: EyeTracking | ||
| doc: Eye-tracking data, representing direction of gaze. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing data measuring direction of gaze. | ||
| quantity: '*' | ||
|
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| - neurodata_type_def: CompassDirection | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: CompassDirection | ||
| doc: With a CompassDirection interface, a module publishes a SpatialSeries object | ||
| representing a floating point value for theta. The SpatialSeries::reference_frame | ||
| field should indicate what direction corresponds to 0 and which is the direction | ||
| of rotation (this should be clockwise). The si_unit for the SpatialSeries should | ||
| be radians or degrees. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing direction of gaze travel. | ||
| quantity: '*' | ||
|
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| - neurodata_type_def: Position | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Position | ||
| doc: Position data, whether along the x, x/y or x/y/z axis. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing position data. | ||
| quantity: '+' |
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