pynwb.image module
- class pynwb.image.ImageSeries(name, data=None, unit=None, format=None, external_file=None, starting_frame=None, bits_per_pixel=None, dimension=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, offset=0.0, device=None)[source]
Bases:
TimeSeries
General image data that is common between acquisition and stimulus time series. The image data can be stored in the HDF5 file or it will be stored as an external image file.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. Can be 3D or 4D. The first dimension must be time (frame). The second and third dimensions represent x and y. The optional fourth dimension represents z. Either data or external_file must be specified (not None), but not both. If data is not specified, data will be set to an empty 3D array.unit (
str
) – The unit of measurement of the image data, e.g., values between 0 and 255. Required when data is specified. If unit (and data) are not specified, then unit will be set to “unknown”.format (
str
) – Format of image. Three types - 1) Image format; tiff, png, jpg, etc. 2) external 3) raw.external_file (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Path or URL to one or more external file(s). Field only present if format=external. Either external_file or data must be specified (not None), but not both.starting_frame (
Iterable
) – Each entry is a frame number that corresponds to the first frame of each file listed in external_file within the full ImageSeries.bits_per_pixel (
int
) – DEPRECATED: Number of bits per image pixeldimension (
Iterable
) – Number of pixels on x, y, (and z) axes.resolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valueoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.device (
Device
) – Device used to capture the images/video.
- DEFAULT_DATA = array([], shape=(0, 0, 0), dtype=uint8)
- property bits_per_pixel
- property device
Device used to capture the images/video.
- property dimension
Number of pixels on x, y, (and z) axes.
- property external_file
Path or URL to one or more external file(s). Field only present if format=external. Either external_file or data must be specified (not None), but not both.
- property format
Format of image. Three types - 1) Image format; tiff, png, jpg, etc. 2) external 3) raw.
- namespace = 'core'
- neurodata_type = 'ImageSeries'
- property starting_frame
Each entry is a frame number that corresponds to the first frame of each file listed in external_file within the full ImageSeries.
- class pynwb.image.IndexSeries(name, data, unit, indexed_timeseries=None, indexed_images=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, offset=0.0)[source]
Bases:
TimeSeries
Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored somewhere, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced ImageSeries, and the timestamps array indicates when that image was displayed.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. Must be 1D, where the first dimension must be time (frame)unit (
str
) – The base unit of measurement (should be SI unit)indexed_timeseries (
TimeSeries
) – Link to TimeSeries containing images that are indexed.indexed_images (
Images
) – Link to Images object containing an ordered set of images that are indexed. The Images object must contain a ‘ordered_images’ dataset specifying the order of the images in the Images type.resolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valueoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.
- property indexed_timeseries
Link to TimeSeries containing images that are indexed.
- namespace = 'core'
- neurodata_type = 'IndexSeries'
- class pynwb.image.ImageMaskSeries(name, masked_imageseries, data=None, unit=None, format=None, external_file=None, starting_frame=None, bits_per_pixel=None, dimension=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, offset=0.0, device=None)[source]
Bases:
ImageSeries
An alpha mask that is applied to a presented visual stimulus. The data[] array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it’s explicitly changed.
- Parameters:
name (
str
) – The name of this TimeSeries datasetmasked_imageseries (
ImageSeries
) – Link to ImageSeries that mask is applied to.data (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. Can be 3D or 4D. The first dimension must be time (frame). The second and third dimensions represent x and y. The optional fourth dimension represents z. Either data or external_file must be specified (not None), but not both. If data is not specified, data will be set to an empty 3D array.unit (
str
) – The unit of measurement of the image data, e.g., values between 0 and 255. Required when data is specified. If unit (and data) are not specified, then unit will be set to “unknown”.format (
str
) – Format of image. Three types - 1) Image format; tiff, png, jpg, etc. 2) external 3) raw.external_file (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Path or URL to one or more external file(s). Field only present if format=external. Either external_file or data must be specified (not None), but not both.starting_frame (
Iterable
) – Each entry is a frame number that corresponds to the first frame of each file listed in external_file within the full ImageSeries.bits_per_pixel (
int
) – DEPRECATED: Number of bits per image pixeldimension (
Iterable
) – Number of pixels on x, y, (and z) axes.resolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valueoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.device (
Device
) – Device used to capture the mask data. This field will likely not be needed. The device used to capture the masked ImageSeries data should be stored in the ImageSeries.
- property masked_imageseries
Link to ImageSeries that mask is applied to.
- namespace = 'core'
- neurodata_type = 'ImageMaskSeries'
- class pynwb.image.OpticalSeries(name, distance, field_of_view, orientation, data=None, unit=None, format=None, external_file=None, starting_frame=None, bits_per_pixel=None, dimension=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, device=None, offset=0.0)[source]
Bases:
ImageSeries
Image data that is presented or recorded. A stimulus template movie will be stored only as an image. When the image is presented as stimulus, additional data is required, such as field of view (eg, how much of the visual field the image covers, or how what is the area of the target being imaged). If the OpticalSeries represents acquired imaging data, orientation is also important.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdistance (
float
) – Distance from camera/monitor to target/eye.field_of_view (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Width, height and depth of image, or imaged area (meters).orientation (
str
) – Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.data (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Images presented to subject, either grayscale or RGB. May be 3D or 4D. The first dimension must be time (frame). The second and third dimensions represent x and y. The optional fourth dimension must be length 3 and represents the RGB value for color images. Either data or external_file must be specified, but not both.unit (
str
) – The unit of measurement of the image data, e.g., values between 0 and 255. Required when data is specified. If unit (and data) are not specified, then unit will be set to “unknown”.format (
str
) – Format of image. Three types - 1) Image format; tiff, png, jpg, etc. 2) external 3) raw.external_file (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Path or URL to one or more external file(s). Field only present if format=external. Either external_file or data must be specified (not None), but not both.starting_frame (
Iterable
) – Each entry is a frame number that corresponds to the first frame of each file listed in external_file within the full ImageSeries.bits_per_pixel (
int
) – DEPRECATED: Number of bits per image pixeldimension (
Iterable
) – Number of pixels on x, y, (and z) axes.resolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuedevice (
Device
) – Device used to capture the images/video.offset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.
- property distance
Distance from camera/monitor to target/eye.
- property field_of_view
Width, height and depth of image, or imaged area (meters).
- property orientation
Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.
- namespace = 'core'
- neurodata_type = 'OpticalSeries'
- class pynwb.image.GrayscaleImage(name, data, resolution=None, description=None)[source]
Bases:
Image
- Parameters:
name (
str
) – The name of this imagedata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Data of grayscale image. Must be 2D where the dimensions represent x and y.resolution (
float
) – pixels / cmdescription (
str
) – description of image
- namespace = 'core'
- neurodata_type = 'GrayscaleImage'
- class pynwb.image.RGBImage(name, data, resolution=None, description=None)[source]
Bases:
Image
- Parameters:
name (
str
) – The name of this imagedata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Data of color image. Must be 3D where the first and second dimensions represent x and y. The third dimension has length 3 and represents the RGB value.resolution (
float
) – pixels / cmdescription (
str
) – description of image
- namespace = 'core'
- neurodata_type = 'RGBImage'
- class pynwb.image.RGBAImage(name, data, resolution=None, description=None)[source]
Bases:
Image
- Parameters:
name (
str
) – The name of this imagedata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – Data of color image with transparency. Must be 3D where the first and second dimensions represent x and y. The third dimension has length 4 and represents the RGBA value.resolution (
float
) – pixels / cmdescription (
str
) – description of image
- namespace = 'core'
- neurodata_type = 'RGBAImage'