pulse2percept.utils¶
Various utility and helper functions.
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pulse2percept.utils.
bisect
(y_target, func, args=None, kwargs=None, x_lo=0, x_hi=1, x_tol=1e-06, y_tol=0.001, max_iter=100)[source]¶ Binary search (bisection method) to find
x
value that givesy_target
For a function
y = func(x, *args, **kwargs)
, returnsx_opt
for whichfunc(x_opt, *args, **kwargs)
is approximately equal toy_target
.New in version 0.7.
Parameters: - y_target (float) – Target y value
- args, kwargs (func,) – The function to call along with its positional and keyword arguments
- x_hi (x_lo,) – Lower and upper bounds on
x
- x_tol (float, optional) – Search will stop if the range of candidate
x
values is smaller thanx_tol
- y_tol (float, optional) – Search will stop if
y
is withiny_tol
ofy_target
- max_iter (int, optional) – Maximum number of iterations to run
Returns: x_opt (float) – The x value such that func(x_opt) $approx$ y_target
Notes
- Assumes
func
is a monotonously increasing function ofx
. - Does not require
x_lo
andx_hi
to have opposite signs as in the conventional bisection method.
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pulse2percept.utils.
cached
(f)[source]¶ Cached property decorator
Decorator can be added to the property of a class to maintain a cache. This is useful when computing the property is computationall expensive. The property will only be computed on first call, and subsequent calls will refer to the cached result.
Important
When making use of a cached property, the class should also maintain a
_cache_active
flag set to True or False.New in version 0.7.
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pulse2percept.utils.
center_image
(img, loc=None)[source]¶ Center the image foreground
This function shifts the center of mass (CoM) to the image center. The background of the image is assumed to be black (0 grayscale).
New in version 0.7.
Parameters: - img (ndarray) – A 2D NumPy array representing a (height, width) grayscale image, or a 3D NumPy array representing a (height, width, channels) RGB image
- loc ((col, row), optional) – The pixel location at which to center the CoM. By default, shifts the CoM to the image center.
Returns: img (ndarray) – A copy of the image centered at
loc
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pulse2percept.utils.
center_vector
(vec, newlen)[source]¶ Returns the center
newlen
portion of a vector.Adapted from
scipy.signal.signaltools._centered
: github.com/scipy/scipy/blob/v0.18.0/scipy/signal/signaltools.py#L236-L243
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pulse2percept.utils.
circ_r2_score
(y_true, y_pred)[source]¶ Calculate circular R² (the coefficient of determination)
The best possible score is 1.0, lower values are worse.
New in version 0.7.
Parameters: - y_true (array-like) – Ground truth (correct) target values.
- y_pred (array-like) – Estimated target values.
Returns: z (float) – The R² score
Notes
- If the ground-truth data has zero variance, R² will be zero.
- This is not a symmetric function
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pulse2percept.utils.
conv
(data, kernel, mode='full', method='fft')[source]¶ Convoles data with a kernel using either FFT or sparse convolution
This function convolves data with a kernel, relying either on the fast Fourier transform (FFT) or a sparse convolution function.
Parameters: - data (array_like) – First input, typically the data array
- kernel (array_like) – Second input, typically the kernel
- mode (str {'full', 'valid', 'same'}, optional, default: 'full') –
A string indicating the size of the output:
full
:- The output is the full discrete linear convolution of the inputs.
valid
:- The output consists only of those elements that do not rely on zero-padding.
same
:- The output is the same size as
data
, centered with respect to the ‘full’ output.
- method (str {'fft', 'sparse'}, optional, default: 'fft') –
A string indicating the convolution method:
fft
:- Use the fast Fourier transform (FFT).
sparse
:- Use the sparse convolution.
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class
pulse2percept.utils.
Curcio1990Transform
[source]¶ Converts between visual angle and retinal eccentricity [Curcio1990]
-
static
dva2ret
(xdva)[source]¶ Convert degrees of visual angle (dva) to retinal eccentricity (um)
Assumes that one degree of visual angle is equal to 280 um on the retina [Curcio1990].
-
static
ret2dva
(xret)[source]¶ Convert retinal eccentricity (um) to degrees of visual angle (dva)
Assumes that one degree of visual angle is equal to 280 um on the retina [Curcio1990]
-
static
-
class
pulse2percept.utils.
Data
(data, axes=None, metadata=None)[source]¶ N-dimensional data container
New in version 0.6.
Parameters:
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pulse2percept.utils.
delta_angle
(source_angle, target_angle, hi=6.283185307179586)[source]¶ Returns the signed difference between two angles (rad)
The difference is calculated as target_angle - source_angle. The difference will thus be positive if target_angle > source_angle.
New in version 0.7.
Parameters: - target_angle (source_angle,) – Input arrays with circular data in the range [0, hi]
- hi (float, optional) – Sets the upper bounds of the range (e.g., 2*np.pi or 360). Lower bound is always 0
Returns: The signed difference target_angle - source_angle in [0, hi]
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class
pulse2percept.utils.
deprecated
(alt_func=None, deprecated_version=None, removed_version=None)[source]¶ Decorator to mark deprecated functions and classes with a warning.
See also
Adapted from https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/utils/deprecation.py.
Parameters:
-
exception
pulse2percept.utils.
FreezeError
[source]¶ Exception class used to raise when trying to add attributes to Frozen Classes of type Frozen do not allow for new attributes to be set outside the constructor.
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
class
pulse2percept.utils.
Frozen
[source]¶ “Frozen” classes (and subclasses) do not allow for new class attributes to be set outside the constructor. On attempting to add a new attribute, the class will raise a FreezeError.
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pulse2percept.utils.
gamma
(n, tau, tsample, tol=0.01)[source]¶ Returns the impulse response of
n
cascaded leaky integratorsThis function calculates the impulse response of
n
cascaded leaky integrators with constant of proportionality 1/tau
: y = (t/theta).^(n-1).*exp(-t/theta)/(theta*factorial(n-1))Parameters: - n (int) – Number of cascaded leaky integrators
- tau (float) – Decay constant of leaky integration (seconds). Equivalent to the inverse of the constant of proportionality.
- tsample (float) – Sampling time step (seconds).
- tol (float) – Cut the kernel to size by ignoring function values smaller
than a fraction
tol
of the peak value.
-
class
pulse2percept.utils.
Grid2D
(x_range, y_range, step=1, grid_type='rectangular')[source]¶ 2D spatial grid
This class generates a two-dimensional mesh grid from a range of x, y values and provides an iterator to loop over elements.
New in version 0.6.
Parameters: - x_range ((x_min, x_max)) – A tuple indicating the range of x values (includes end points)
- y_range (tuple, (y_min, y_max)) – A tuple indicating the range of y values (includes end points)
- step (int, double, tuple) – Step size. If int or double, the same step will apply to both x and y ranges. If a tuple, it is interpreted as (x_step, y_step).
- grid_type ({'rectangular', 'hexagonal'}) – The grid type
Notes
- The grid uses Cartesian indexing (
indexing='xy'
for NumPy’smeshgrid
function). This implies that the grid’s shape will be (number of y coordinates) x (number of x coordinates). - If a range is zero, the step size is irrelevant.
Examples
You can iterate through a grid as if it were a list:
>>> grid = Grid2D((0, 1), (2, 3)) >>> for x, y in grid: ... print(x, y) 0.0 2.0 1.0 2.0 0.0 3.0 1.0 3.0
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plot
(transform=None, autoscale=True, zorder=1, ax=None)[source]¶ Plot the extension of the grid
Parameters: - transform (function, optional) – A coordinate transform to be applied to the (x,y) coordinates of
the grid (e.g.,
Curcio1990Transform.dva2ret
) - autoscale (bool, optional) – Whether to adjust the x,y limits of the plot to fit the implant
- zorder (int, optional) – The Matplotlib zorder at which to plot the grid
- ax (matplotlib.axes._subplots.AxesSubplot, optional) – A Matplotlib axes object. If None, will either use the current axes (if exists) or create a new Axes object
- transform (function, optional) – A coordinate transform to be applied to the (x,y) coordinates of
the grid (e.g.,
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pulse2percept.utils.
parfor
(func, in_list, out_shape=None, n_jobs=-1, engine='joblib', scheduler='threading', func_args=[], func_kwargs={})[source]¶ Parallel for loop for NumPy arrays
Parameters: - func (callable) – The function to apply to each item in the array. Must have the form:
func(arr, idx, *args, *kwargs) where arr is an ndarray and idx is an
index into that array (a tuple). The Return of
func
needs to be one item (e.g. float, int) per input item. - in_list (list) – All legitimate inputs to the function to operate over.
- out_shape (int or tuple of ints, optional) – If set, output will be reshaped accordingly. The new shape should be compatible with the original shape. If an integer, then the result will be a 1-D array of that length. One shape dimension can be -1. In this case, the value is inferred from the length of the array and remaining dimensions.
- n_jobs (integer, optional, default: 1) – The number of jobs to perform in parallel. -1 to use all cpus
- engine (str, optional, default: 'joblib') – {‘dask’, ‘joblib’, ‘serial’} The last one is useful for debugging – runs the code without any parallelization.
- scheduler (str, optional, default: 'threading') – Which scheduler to use (irrelevant for ‘serial’ engine): - ‘threading’: a scheduler backed by a thread pool - ‘multiprocessing’: a scheduler backed by a process pool
- *func_args (list, optional) – Positional arguments to
func
- **func_kwargs (dict, optional) – Keyword arguments to
func
Returns: ndarray – NumPy array of identical shape to
arr
Note
Equivalent to pyAFQ version (blob e20eaa0 from June 3, 2016): https://github.com/arokem/pyAFQ/blob/master/AFQ/utils/parallel.py
- func (callable) – The function to apply to each item in the array. Must have the form:
func(arr, idx, *args, *kwargs) where arr is an ndarray and idx is an
index into that array (a tuple). The Return of
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class
pulse2percept.utils.
PrettyPrint
[source]¶ An abstract class that provides a way to prettyprint all class attributes, inspired by scikit-learn.
Classes deriving from PrettyPrint are required to implement a
_pprint_params
method that returns a dictionary containing all the attributes to prettyprint.Examples
>>> from pulse2percept.utils import PrettyPrint >>> class MyClass(PrettyPrint): ... def __init__(self, a, b): ... self.a = a ... self.b = b ... ... def _pprint_params(self): ... return {'a': self.a, 'b': self.b} >>> MyClass(1, 2) MyClass(a=1, b=2)
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pulse2percept.utils.
r2_score
(y_true, y_pred)[source]¶ Calculate R² (the coefficient of determination)
The
r2_score
function computes the coefficient of determination, usually denoted as R².The best possible score is 1.0, lower values are worse.
It represents the proportion of variance (of y) that has been explained by the independent variables in the model. It provides an indication of goodness of fit and therefore a measure of how well unseen samples are likely to be predicted by the model.
If \(\hat{y}_i\) is the predicted value of the \(i\)-th sample and \(y_i\) is the corresponding true value for total \(n\) samples, the estimated R² is defined as:
\[R^2(y, \hat{y}) = 1 - \frac{\sum_{i=1}^{n} (y_i - \hat{y}_i)^2}{\sum_{i=1}^{n} (y_i - \bar{y})^2}\]where \(\bar{y} = \frac{1}{n} \sum_{i=1}^{n} y_i\) and \(\sum_{i=1}^{n} (y_i - \hat{y}_i)^2 = \sum_{i=1}^{n} \epsilon_i^2\).
Note that
r2_score
calculates unadjusted R² without correcting for bias in sample variance of y.New in version 0.7.
Parameters: - y_true (array-like) – Ground truth (correct) target values.
- y_pred (array-like) – Estimated target values.
Returns: z (float) – The R² score
Notes
- If the ground-truth data has zero variance, R² will be zero.
- This is not a symmetric function
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class
pulse2percept.utils.
RetinalCoordTransform
[source]¶ Base class for a retinal coordinate transform
A template
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pulse2percept.utils.
scale_image
(img, scaling_factor)[source]¶ Scale the image foreground
This function scales the image foreground by a factor. The background of the image is assumed to be black (0 grayscale).
New in version 0.7.
Parameters: - img (ndarray) – A 2D NumPy array representing a (height, width) grayscale image, or a 3D NumPy array representing a (height, width, channels) RGB image
- scaling_factor (float) – Factory by which to scale the image
Returns: img (ndarray) – A copy of the scaled image
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pulse2percept.utils.
shift_image
(img, shift_cols, shift_rows)[source]¶ Shift the image foreground
This function shifts the center of mass (CoM) of the image by the specified number of rows and columns. The background of the image is assumed to be black (0 grayscale).
New in version 0.7.
Parameters: - img (ndarray) – A 2D NumPy array representing a (height, width) grayscale image, or a 3D NumPy array representing a (height, width, channels) RGB image
- shift_cols (float) – Number of columns by which to shift the CoM. Positive: to the right, negative: to the left
- shift_rows (float) – Number of rows by which to shift the CoM. Positive: downward, negative: upward
Returns: img (ndarray) – A copy of the shifted image
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pulse2percept.utils.
trim_image
(img, tol=0)[source]¶ Remove any black border around the image
New in version 0.7.
Parameters: - img (ndarray) – A 2D NumPy array representing a (height, width) grayscale image, or a 3D NumPy array representing a (height, width, channels) RGB image. If an alpha channel is present, the image will first be blended with black.
- tol (float, optional) – Any pixels with gray levels > tol will be trimmed.
- return_coords (bool, optional) – If True, will also return the row and column coordinates of the retained image
Returns: img (ndarray) – A copy of the image with trimmed borders.
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pulse2percept.utils.
unique
(a, tol=1e-06, return_index=False)[source]¶ Find the unique elements of a sorted 1D array
Special case of
numpy.unique
(array is flat, sortened) with a tolerance leveltol
.New in version 0.7.
Parameters: - a (array_like) – Input array: must be sorted, and will be flattened if it is not already 1-D.
- tol (float, optional) – If the difference between two elements in the array is smaller than
tol
, the two elements are considered equal. - return_index (bool, optional) – If True, also return the indices of
a
that result in the unique array.
Returns: - unique (ndarray) – The sorted unique values
- unique_indices (ndarray, optional) – The indices of the first occurrences of the unique values in the
original array. Only provided if
return_index
is True.
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class
pulse2percept.utils.
Watson2014DisplaceTransform
[source]¶ - Converts between visual angle and retinal eccentricity using RGC
- displacement [Watson2014]
Converts from eccentricity (defined as distance from a visual center) in degrees of visual angle (dva) to microns on the retina using Eqs. 5, A5, and A6 in [Watson2014].
In a central retinal zone, the retinal ganglion cell (RGC) bodies are displaced centrifugally some distance from the inner segments of the cones to which they are connected through the bipolar cells, and thus from their receptive field. The displacement function is described in Eq. 5 of [Watson2014].
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dva2ret
(xdva, ydva)[source]¶ Converts dva to retinal coords
Parameters: ydva (xdva,) – x,y coordinates in dva Returns: xret, yret (double or array-like) – Corresponding x,y coordinates in microns
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static
watson_displacement
(r, meridian='temporal')[source]¶ Ganglion cell displacement function
Implements the ganglion cell displacement function described in Eq. 5 of [Watson2014].
Parameters: - r (double|array-like) – Eccentricity in degrees of visual angle (dva)
- meridian ('temporal' or 'nasal') –
Returns: - The displacement in dva experienced by ganglion cells at eccentricity
r
.
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class
pulse2percept.utils.
Watson2014Transform
[source]¶ Converts between visual angle and retinal eccentricity [Watson2014]
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static
dva2ret
(r_deg)[source]¶ Converts visual angles (deg) into retinal distances (um)
This function converts degrees of visual angle into a retinal distance from the optic axis (um) using Eq. A5 in [Watson2014].
Parameters: r_dva (double or array-like) – Eccentricity in degrees of visual angle (dva) Returns: r_um (double or array-like) – Eccentricity in microns
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static
ret2dva
(r_um)[source]¶ Converts retinal distances (um) to visual angles (deg)
This function converts an eccentricity measurement on the retinal surface(in micrometers), measured from the optic axis, into degrees of visual angle using Eq. A6 in [Watson2014].
Parameters: r_um (double or array-like) – Eccentricity in microns Returns: r_dva (double or array-like) – Eccentricity in degrees of visual angle (dva)
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static