prtools 2.0.0__tar.gz → 2.0.1__tar.gz

{prtools-2.0.0/prtools.egg-info → prtools-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: prtools
-Version: 2.0.0
+Version: 2.0.1
 Summary: Utility functions for image-based phase retrieval
 Author: Andy Kee
 License: MIT License

{prtools-2.0.0 → prtools-2.0.1}/prtools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '2.0.0'
+__version__ = '2.0.1'
 
 
 from prtools._array_api import use
@@ -55,6 +55,7 @@ from prtools.shape import (
     circle,
     hexagon,
     rectangle,
+    ellipse,
     spider,
     sin,
     waffle

{prtools-2.0.0 → prtools-2.0.1}/prtools/shape.py

@@ -219,6 +219,68 @@ def rectangle(shape, width, height, shift=(0, 0), angle=0, antialias=True,
     return rect
 
 
+def ellipse(shape, xradius, yradius, shift=(0,0), angle=0, antialias=True,
+            indexing='ij'):
+    """Draw an ellipse
+
+    Parameters
+    ----------
+    shape : array_like
+        Size of output in pixels (nrows, ncols)
+    xradius : float
+        Semi-axis of the ellipse in pixels in the x (horizontal) direction.
+    yradius : float
+        Semi-axis of the ellipse in pixels in the y (vertical) direction.
+    shift : (2,) array_like, optional
+        How far to shift center in float (rows, cols). Default is (0, 0).
+    angle : float, optional
+        Rotation of the ellipse in degrees counterclockwise from horizontal.
+        Default is 0.
+    antialias : bool, optional
+        If True (default), the shape edges are antialiased.
+    indexing : {'ij', 'xy'}, optional
+        Matrix ('ij', default) or cartesian ('xy') indexing of output.
+
+    Returns
+    -------
+    ndarray
+
+    Examples
+    --------
+    .. plot::
+        :include-source:
+        :context: reset
+        :scale: 50
+
+        >>> ell = prtools.ellipse(shape=(256, 256), xradius=100, yradius=50)
+        >>> plt.imshow(ell, cmap='gray')
+
+    .. plot::
+        :include-source:
+        :context: reset
+        :scale: 50
+
+        >>> ell = prtools.ellipse(shape=(256, 256), xradius=100, yradius=50, angle=30)
+        >>> plt.imshow(ell, cmap='gray')
+
+    """
+    a, b = yradius, xradius
+    rr, cc = mesh(shape, shift, angle, indexing=indexing)
+
+    rho = np.sqrt((rr / a)**2 + (cc / b)**2)
+    grad = np.sqrt((rr / a**2)**2 + (cc / b**2)**2)
+
+    with np.errstate(divide='ignore', invalid='ignore'):
+        dist = (1 - rho) * rho / grad
+    dist = np.where(grad == 0, 1.0, dist)  # center is always interior
+    ell = np.clip(dist + 0.5, 0.0, 1.0)
+
+    if not antialias:
+        ell[ell > 0] = 1
+
+    return ell
+
+
 def spider(shape, width, angle=0, shift=(0, 0), antialias=True, indexing='ij'):
     """Draw a spider
 
@@ -261,10 +323,6 @@ def spider(shape, width, angle=0, shift=(0, 0), antialias=True, indexing='ij'):
     return 1 - rectangle(shape, len, width, shift, angle, antialias, indexing)
 
 
-def ellipse():
-    pass
-
-
 def gauss(shape, sigma, shift=(0, 0), indexing='ij'):
     """Generate a 2D Gaussian function.
 

{prtools-2.0.0 → prtools-2.0.1}/prtools/zernike.py

@@ -14,7 +14,7 @@ def zernike(mask, index, normalize=True, order='noll', rho=None, theta=None):
         Binary mask defining the extent to compute the Zernike polynomial
         over.
     index : int
-        Noll Zernike index as defined in [1]
+        Zernike mode index
     normalize : bool, optional
         If True (default), the output is normalized according to [1]. If False,
         the output value ranges [-1, 1] over the mask.
@@ -112,8 +112,8 @@ def zernike_compose(mask, coeffs, normalize=True, order='noll', rho=None, theta=
     mask : array_like
         Binary mask defining the extent to compute the Zernike polynomial over.
     coeffs : array_like
-        List of coefficients corresponding to Zernike indices (Noll ordering)
-        used to create the OPD.
+        List of coefficients corresponding to Zernike indices used to create
+        the OPD.
     normalize : bool, optional
         If True (default), the output is normalized according to [1]. If False,
         the output value ranges [-1, 1] over the mask.
@@ -177,7 +177,7 @@ def zernike_basis(mask, modes, vectorize=False, normalize=True, order='noll',
     mask : array_like
         Binary mask defining the extent to compute the Zernike polynomial over.
     modes : array_like
-        List of modes (Noll ordering) to return.
+        List of modes to return.
     vectorize : bool, optional
         If True, the output is returned as a
         ``(length(modes), modes.shape[0]*modes.shape[1])`` array If False
@@ -228,11 +228,11 @@ def zernike_fit(opd, mask, modes, normalize=True, order='noll', rho=None,
     Parameters
     ----------
     opd : array_like
-        OPD to fit.
+        OPD to fit. NaN values in ``opd`` are excluded from the fit.
     mask : array_like
         Binary mask defining the extent to compute the Zernike basis over.
     modes : array_like
-        List of modes (Noll ordering) to fit.
+        List of modes to fit.
     normalize : bool, optional
         If True (default), the output is normalized according to [1]. If False,
         the output value ranges [-1, 1] over the mask.
@@ -271,14 +271,16 @@ def zernike_fit(opd, mask, modes, normalize=True, order='noll', rho=None,
     [1] Noll, RJ. Zernike polynomials and atmospheric turbulence. J Opt Soc Am 66, 207-211  (1976).
 
     """
-    opd = np.asarray(opd)
+    opd = np.asarray(opd).ravel()
     mask = np.asarray(mask)
-
     basis = zernike_basis(mask, modes, True, normalize, order, rho, theta)
+    
+    # valid data includes all non-NaN values inside the mask
+    valid = np.isfinite(opd) & mask.ravel().astype(bool)
+    
+    coeff, *_ = np.linalg.lstsq(basis[:, valid].T, opd[valid], rcond=None)
 
-    basis = np.linalg.pinv(basis)
-
-    return np.einsum('ij,i->j', basis, opd.ravel())
+    return coeff
 
 
 def zernike_remove(opd, mask, modes, order='noll', rho=None, theta=None):
@@ -291,7 +293,7 @@ def zernike_remove(opd, mask, modes, order='noll', rho=None, theta=None):
     mask : array_like
         Binary mask defining the extent to compute the Zernike basis over.
     modes : array_like
-        List of modes (Noll ordering) to remove.
+        List of modes to remove.
     order : {'noll', 'fringe', 'ansi'}, optional
         Zernike ordering scheme. Default is 'noll'.
     rho : array_like, optional

{prtools-2.0.0 → prtools-2.0.1/prtools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: prtools
-Version: 2.0.0
+Version: 2.0.1
 Summary: Utility functions for image-based phase retrieval
 Author: Andy Kee
 License: MIT License