name: core.nwb.base id: core.nwb.base imports: - hdmf-common.base - hdmf-common.table - nwb.language default_prefix: core.nwb.base/ classes: NWBData: name: NWBData description: An abstract data type for a dataset. is_a: Data attributes: name: name: name range: string required: true tree_root: true TimeSeriesReferenceVectorData: name: TimeSeriesReferenceVectorData description: 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. is_a: VectorData attributes: name: name: name range: string required: true tree_root: true Image: name: Image description: 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)). is_a: NWBData attributes: name: name: name range: string required: true resolution: name: resolution description: Pixel resolution of the image, in pixels per centimeter. range: float32 description: name: description description: Description of the image. range: text array: name: array range: Image__Array tree_root: true Image__Array: name: Image__Array is_a: Arraylike attributes: x: name: x range: numeric required: true y: name: y range: numeric required: true r, g, b: name: r, g, b range: numeric required: false minimum_cardinality: 3 maximum_cardinality: 3 r, g, b, a: name: r, g, b, a range: numeric required: false minimum_cardinality: 4 maximum_cardinality: 4 ImageReferences: name: ImageReferences description: Ordered dataset of references to Image objects. is_a: NWBData attributes: name: name: name range: string required: true array: name: array range: ImageReferences__Array tree_root: true ImageReferences__Array: name: ImageReferences__Array is_a: Arraylike attributes: num_images: name: num_images range: Image required: true NWBContainer: name: NWBContainer description: An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers. is_a: Container attributes: name: name: name range: string required: true tree_root: true NWBDataInterface: name: NWBDataInterface description: An abstract data type for a generic container storing collections of data, as opposed to metadata. is_a: NWBContainer attributes: name: name: name range: string required: true tree_root: true TimeSeries: name: TimeSeries description: General purpose time series. is_a: NWBDataInterface attributes: name: name: name range: string required: true description: name: description description: Description of the time series. range: text comments: name: comments description: 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. range: text data: name: data description: 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. multivalued: false range: TimeSeries__data required: true starting_time: name: starting_time description: 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. multivalued: false range: TimeSeries__starting_time required: false timestamps: name: timestamps description: Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. multivalued: true range: float64 required: false control: name: control description: 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. multivalued: true range: uint8 required: false control_description: name: control_description description: Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0. multivalued: true range: text required: false sync: name: sync description: 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. multivalued: false range: TimeSeries__sync required: false tree_root: true TimeSeries__data: name: TimeSeries__data description: 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: name: name ifabsent: string(data) range: string required: true equals_string: data conversion: name: conversion description: 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. range: float32 offset: name: offset description: 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. range: float32 resolution: name: resolution description: 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. range: float32 unit: name: unit description: 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'. range: text continuity: name: continuity description: 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. range: text array: name: array range: TimeSeries__data__Array TimeSeries__data__Array: name: TimeSeries__data__Array is_a: Arraylike attributes: num_times: name: num_times range: AnyType required: true num_DIM2: name: num_DIM2 range: AnyType required: false num_DIM3: name: num_DIM3 range: AnyType required: false num_DIM4: name: num_DIM4 range: AnyType required: false TimeSeries__starting_time: name: TimeSeries__starting_time description: 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. attributes: name: name: name ifabsent: string(starting_time) range: string required: true equals_string: starting_time rate: name: rate description: Sampling rate, in Hz. range: float32 unit: name: unit description: Unit of measurement for time, which is fixed to 'seconds'. range: text value: name: value range: float64 required: true TimeSeries__sync: name: TimeSeries__sync description: 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. attributes: name: name: name ifabsent: string(sync) range: string required: true equals_string: sync ProcessingModule: name: ProcessingModule description: A collection of processed data. is_a: NWBContainer attributes: name: name: name range: string required: true description: name: description description: Description of this collection of processed data. range: text nwb_data_interface: name: nwb_data_interface description: Data objects stored in this collection. multivalued: true range: NWBDataInterface required: false dynamic_table: name: dynamic_table description: Tables stored in this collection. multivalued: true range: DynamicTable required: false tree_root: true Images: name: Images description: 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. is_a: NWBDataInterface attributes: name: name: name range: string required: true description: name: description description: Description of this collection of images. range: text Image: name: Image description: Images stored in this collection. multivalued: true range: Image required: true order_of_images: name: order_of_images description: 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. multivalued: false range: Images__order_of_images required: false tree_root: true Images__order_of_images: name: Images__order_of_images description: 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. is_a: ImageReferences attributes: name: name: name ifabsent: string(order_of_images) range: string required: true equals_string: order_of_images