Generics.yml

- resample:
    desc: Resample an Image to Match the Space of Another Image
    params: [source, target, ...]

- slices:
    desc: Extract an ordered series of 2D slices from a 3D or 4D object
    params: [x, ...]
    return: A list of 2D matrices, each containing a slice from the input object

- ndim:
    desc: Extract the number of dimensions of an object
    params: [x, ...]
    return: The number of dimensions of the input object `x`

- dim_of:
    desc: Get the length of a given dimension of an object
    params: [x, axis]
    return: An integer representing the length of the specified axis

- which_dim:
    desc: Find Dimensions of a Given Axis
    params: [x, axis]
    return: An integer representing the dimension of the specified axis for the given object

- add_dim:
    desc: Add a Dimension to an Object
    params: [x, n]
    return: An updated dimensioned object with the new dimension added

- drop_dim:
    desc: Drop a Dimension from an Object
    params: [x, dimnum]
    return: An updated dimensioned object with the specified dimension removed

- space:
    desc: Extract Geometric Properties of an Image
    params: [x, ...]
    return: An object representing the geometric space of the image, of type NeuroSpace

- split_fill:
    desc: Fill Disjoint Sets of Values with the Output of a Function
    params: [x, fac, FUN]
    return: A new object in which the original values have been replaced by the output of the function

- map_values:
    desc: Maps values from one set to another using a user-supplied lookup table
    params: [x, lookup]

- split_scale:
    desc: Centers and/or scales the row-subsets of a numeric matrix or matrix-like object
    params: [x, f, center, scale]

- split_reduce:
    desc: Summarizes subsets of a numeric matrix or matrix-like object by first splitting the object by row and then applying a summary function
    params: [x, fac, FUN]

- spacing:
    desc: Extracts the voxel dimensions of an image
    params: [x]

- bounds:
    desc: Extracts the spatial bounds (origin + dim * spacing) of an image represented by the input object
    params: [x]

- axes:
    desc: Extracts image axes
    params: [x]

- origin:
    desc: Extracts image origin
    params: [x]

- centroid:
    desc: Returns the centroid of an object
    params: [x, ...]

- centroids:
    desc: Returns a matrix of centroids of an object
    params: [x, ...]

- trans:
    desc: Extracts image coordinate transformation
    params: [x]

- inverse_trans:
    desc: Extracts inverse image coordinate transformation
    params: [x]

- read_elements:
    desc: Read a sequence of elements from an input source
    params: [x, num_elements]
    return: Elements as a vector

- read_columns:
    desc: Read a set of column vector from an input source
    params: [x, column_indices]
    return: Matrix consisting of the requested column vectors

- write_elements:
    desc: Write a sequence of elements from an input source
    params: [x, els]

- write_vol:
    desc: Write a 3D image volume to disk
    params: [x, file_name, format, data_type]
    details: Output format will be inferred from file extension

- write_vec:
    desc: Write a 4D image vector to disk
    params: [x, file_name, format, data_type, extra_args]

- reorient:
    desc: Remap the grid-to-world coordinates mapping of an image
    params: [x, orient]
    return: Reoriented space

- index_to_grid:
    desc: Convert 1D indices to n-dimensional grid coordinates
    params: [x, idx]
    return: Matrix of grid coordinates

- index_to_coord:
    desc: Convert 1D indices to n-dimensional real world coordinates
    params: [x, idx]
    return: Matrix of real coordinates

- coord_to_index:
    desc: Convert n-dimensional real world coordinates to 1D indices
    params: [x, coords]
    return: Vector of indices

- coord_to_grid:
    desc: Convert n-dimensional real world coordinates to grid coordinates
    params: [x, coords]
    return: Matrix of grid coordinates

- grid_to_coord:
    desc: Convert N-dimensional grid coordinate coordinates to real world coordinates
    params: [x, coords]
    return: Matrix of real coordinates

- grid_to_grid:
    desc: Convert voxel coordinates in the reference space (LPI) to native array space
    params: [x, vox]
    return: Matrix of native voxel coordinates

- grid_to_index:
    desc: Convert N-dimensional grid coordinate to 1D indices
    params: [x, coords]
    return: Vector of indices

- sub_vector:
    desc: Extract a sub-vector from a NeuroVec object
    params: [x, i, extra_args]
    return: NeuroVec object that is a sub-sequence of the supplied object

- scale_series:
    desc: Scale (center and/or normalize by standard deviation) each series of a 4D image
    params: [x, center, scale]

- as.sparse:
    desc: Convert to from dense to sparse representation
    params:

- slice:
    desc: Extract a 2D slice from an image volume
    params: [x, zlevel, along, orientation, ...]

- render:
    desc: Map an image intensities to an image with color values
    params: [x, width, height, colmap, ...]

- render_slice:
    desc: Render a slice at z coordinate
    params: [x, zpos, width, height, colmap, ...]

- perm_mat:
    desc: Extract permutation matrix associated with an image
    return: an N x N permutation matrix, where N is the dimensionality of the image
    params: [x, ...]

- concat:
    desc: Concatenate two objects in the time dimension
    return: a temporally concatenated object
    params: [x, y, ...]

- conn_comp:
    desc: Find connected components in an image
    params: [x, ...]
- voxels:
    desc: Extract voxel coordinates
    params: [x, ...]
- file_matches:
    desc: Test whether a file name conforms to the given FileFormat instance
    return: TRUE for match, FALSE otherwise
    params: [x, file_name]
- header_file_matches:
    desc: Test whether a file name conforms to the given FileFormat instance (header file only)

- header_file_matches:
    desc: Test whether a file name conforms to the given FileFormat instance (header file only)
    return: TRUE for match, FALSE otherwise
    params: [x, file_name]

- data_file_matches:
    desc: Test whether a file name conforms to the given FileFormat instance (data file only)
    return: TRUE for match, FALSE otherwise
    params: [x, file_name]

- header_file:
    desc: Get the name of the header file, given a file name and a FileFormat instance
    return: the correct header name
    params: [x, file_name]

- data_file:
    desc: Get the name of the data file, given a file name and a FileFormat instance
    return: the correct header name
    params: [x, file_name]

- strip_extension:
    desc: Strip extension from file name, given a FileFormat instance
    return: file_name without extension
    params: [x, file_name]

- read_meta_info:
    desc: Read image meta info given a file and a FileFormat instance
    params: [x, file_name]

- embed_kernel:
    desc: Position kernel in a position in image space
    params: [x, sp, center_voxel, ...]


- resample: [source, target]
- slices: [x]
- ndim: [x]
- dim_of: [x, axis]
- which_dim: [x, axis]
- add_dim: [x, n]
- drop_dim: [x, dimnum]
- space: [x]
- split_fill: [x, fac, FUN]
- map_values: [x, lookup]
- split_scale: [x, f, center, scale]
- split_reduce: [x, fac, FUN]
- spacing: [x]
- bounds: [x]
- axes: [x]
- origin: [x]
- centroid: [x]
- centroids: [x]
- trans: [x]
- inverse_trans: [x]
- read_elements: [x, num_elements]
- read_columns: [x, column_indices]
- write_elements: [x, els]
- write_vol: [x, file_name, format, data_type]
- write_vec: [x, file_name, format, data_type, extra_args]
- reorient: [x, orient]
- index_to_grid: [x, idx]
- index_to_coord: [x, idx]
- coord_to_index: [x, coords]
- coord_to_grid: [x, coords]
- grid_to_coord: [x, coords]
- grid_to_grid: [x, vox]
- grid_to_index: [x, coords]
- sub_vector: [x, i, extra_args]
- scale_series: [x, center, scale]
- as_sparse: []
- slice: [x, zlevel, along, orientation]
- render: [x, width, height, colmap]
- render_slice: [x, zpos, width, height, colmap]
- perm_mat: [x]
- concat: [x, y]
- conn_comp: [x]
- voxels: [x]
- file_matches: [x, file_name]
- header_file_matches: [x, file_name]
- data_file_matches: [x, file_name]
- header_file: [x, file_name]
- data_file: [x, file_name]
- strip_extension: [x, file_name]
- read_meta_info: [x, file_name]
- embed_kernel: [x, sp, center_voxel]