iblatlas.streamlines.utils

Functions

`get_mask`	Generate a mask to plot results onto
`project_points_onto_flatmap`	Projects 3D points with associated values onto a 2D flatmap.
`project_volume_onto_flatmap`	Projects a 3D volume onto a 2D flatmap by aggregating values along streamline paths.
`validate_aggr`	Validates if the provided aggregation type is valid.
`xyz_to_depth`	For a given xyz coordinates return the depth from the surface of the cortex.

xyz_to_depth(xyz, per=True, res_um=25)[source]

For a given xyz coordinates return the depth from the surface of the cortex. The depth is returned as a percentage if per=True and in um if per=False. Note the lookup will only work for xyz cooordinates that are in the Isocortex of the Allen volume. If coordinates outside of this region are given then the depth is returned as nan.

Parameters:

xyz (numpy.array) – An (n, 3) array of Cartesian coordinates. The order is ML, AP, DV and coordinates should be given in meters relative to bregma.
per (bool) – Whether to do the lookup in percentage from the surface of the cortex or depth in um from the surface of the cortex.
res_um (float or int) – The resolution of the brain atlas to do the depth lookup

Returns:

numpy.array
The depths from the surface of the cortex for each cartesian coordinate. If the coordinate does not lie within
the Isocortex, depth value returned is nan

get_mask(volume='annotation', br=None)[source]

Generate a mask to plot results onto

Parameters:

volumestr, optional: The type of volume to project. Options are: - ‘image’: Projects the anatomical image using max intensity. - ‘annotation’: Projects the labeled regions and maps them to RGB colors. - ‘boundary’: Projects labeled regions and extracts anatomical boundaries. Default is ‘annotation’.
brBrainRegions, optional: An instance of the BrainRegions If None, a default BrainRegions is initialized.

Returns:

imgnp.ndarray: The resulting 2D flatmap projection image, either grayscale, RGB, or binary mask, depending on the selected volume type.

validate_aggr(aggr: str) → None[source]

Validates if the provided aggregation type is valid.

Parameters:

aggrstr: The aggregation method to validate (e.g., ‘mean’, ‘sum’).

Raises:

AssertionError: If the aggregation type is not one of the allowed values.

project_volume_onto_flatmap(vol: ndarray, res_um: int = 25, aggr: str = 'mean', plot: bool = True, cmap: str = 'viridis', clevels: tuple = None, ax: Axes = None) → ndarray[source]

Projects a 3D volume onto a 2D flatmap by aggregating values along streamline paths.

Parameters:

volnp.ndarray: A 3D numpy array representing the volume data to be projected.
res_umint: The resolution of the volume. Must be one of 10, 25 or 50.
aggrstr, optional: The aggregation method (‘sum’, ‘count’, ‘mean’, etc.), default is ‘mean’.
plotbool, optional: Whether to plot the resulting projection, default is True.
cmapstr, optional: The colormap to use for the plot, default is ‘viridis’.
clevelstuple, optional: The color limits to use for the plot, default is None.
axmatplotlib.axes.Axes, optional: The axes on which to plot, default is None.

Returns:

np.ndarray: The projected 2D array onto the flatmap.
matplotlib.figure.Figure: Matplotlib figure object if plot=True, otherwise None.
matplotlib.axes.Axes: Matplotlib axes object if plot=True, otherwise None.

project_points_onto_flatmap(xyz: ndarray, values: ndarray, res_um: int = 25, aggr: str = 'mean', plot: bool = True, cmap: str = 'viridis', clevels: tuple = None, ax: Axes = None) → ndarray[source]

Projects 3D points with associated values onto a 2D flatmap.

Parameters:

xyznp.ndarray: An array containing xyz coordinates of the points to be projected. xyz values should be given in metres
valuesnp.ndarray: A 1D array of values to associate with the points.
resint: The resolution to load the corresponding streamline paths.
aggrstr, optional: The aggregation method (‘sum’, ‘count’, ‘mean’, etc.), default is ‘mean’.
plotbool, optional: Whether to plot the resulting projection, default is True.
cmapstr, optional: The colormap to use for the plot, default is ‘viridis’.
clevelstuple, optional: The color limits to use for the plot, default is None.
axmatplotlib.axes.Axes, optional: The axes on which to plot, default is None.

Returns:

np.ndarray: The projected 2D array onto the flatmap.
matplotlib.figure.Figure: Matplotlib figure object if plot=True, otherwise None.
matplotlib.axes.Axes: Matplotlib axes object if plot=True, otherwise None.