ProjectiveGeometry23 0.1.0__tar.gz

projectivegeometry23-0.1.0/LICENSE

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projectivegeometry23-0.1.0/MANIFEST.in

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+include README.md
+include LICENSE
+recursive-include ProjectiveGeometry23 *.py

projectivegeometry23-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ProjectiveGeometry23
+Version: 0.1.0
+Summary: Projective geometry in 2D and 3D with homogeneous and Plücker coordinates, projection matrices, and visualization.
+Home-page: https://github.com/aaichert/ProjectiveGeometry23
+Author: Andre Aichert
+Author-email: aaichert@gmail.com
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Provides-Extra: svg
+Requires-Dist: svg_snip; extra == "svg"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# ProjectiveGeometry23
+## Projective Geometry of Two- and Three-space
+
+`ProjectiveGeometry23` is a collection of numpy-based utilities for projective geometry of real two- and three-space, including homogeneous coordinates of point, lines and planes, Plücker coordinates and projection matrices.
+
+The package has been converted from an existing C++ implementation [LibProjectiveGeometry](https://github.com/aaichert/LibProjectiveGeometry), which is well-tested and obviously faster.
+
+The main use of this code is for the visualization or X-Ray source-detector geometries but applied generally to geometric computer vision problems. 
+
+Features:
+ - Computing with points, lines and planes
+ - Plücker coordinates, Plücker matrices
+ - Projection matrices, intrinsic and extrinsic parameters
+ - Decomposition of projection matrices, backprojection
+ - Visualization of X-Ray source-detector geometries
+ - (WIP) estimation based on direct linear transform, X-ray calibraion
+
+General recommendation for better readibility of outputs:
+
+```py
+from rich import print
+np.set_printoptions(suppress=True)
+```
+
+Example of an interactive visualization, using the optional `svg_snip` package:
+
+```py
+from svg_snip.Jupyter import CanvasWithOverlay
+from svg_snip.Composer import Composer
+import svg_snip.Elements as e2d
+import svg_snip.Elements3D as e3d
+
+from ProjectiveGeometry23.homography import rotation_x, rotation_z, scale
+from ProjectiveGeometry23.svg_utils import svg_source_detector, svg_world_geometry
+    
+vis = CanvasWithOverlay(int(target.image_size[0]), int(target.image_size[1]))
+
+# World transformation
+ax, az = 0.5, 0.5
+s = 0.2
+
+def handle_draw(vis):
+    global ax
+    global az
+    x,y = vis.mouse_state.pos()
+    svg = Composer((vis.w, vis.h))
+
+    svg.add(svg_world_geometry)
+    svg.add(svg_source_detector, projection=target,
+            draw_on_detector=svg_world_geometry,
+            label_source='C0', label_detector='I0(u,v)')
+
+    svg.add(e2d.star, x=x, y=y, size=8,
+        fill="red" if vis.mouse_state.clicked else "blue")
+
+    svg.add(e2d.text, x=10, y=20, content=f'ax={ax:.3} az={az:.3}')
+            
+    T = scale(s) @ rotation_x(ax) @ rotation_z(az)
+    raw_svg_code = svg.render(P=target.P@T)
+    vis.html_overlay.value = raw_svg_code
+    
+    if vis.mouse_state.clicked:
+        az += vis.mouse_state.dx * 0.01
+        ax += vis.mouse_state.dy * 0.01
+    
+vis.handle_draw = handle_draw
+
+vis.display()
+
+```
+
+![source_detector_geometry.png](source_detector_geometry.png)
+
+## Installation
+
+### Using pip
+You can install `ProjectiveGeometry23` using pip:
+
+```bash
+pip install ProjectiveGeometry23
+```
+
+
+### Using `setup.py`
+
+```sh
+git clone https://github.com/aaichert/ProjectiveGeometry23
+cd ProjectiveGeometry23
+python setup.py install
+```
+
+### Testing and Publication on PyPy
+
+Two useful code snippets
+
+```bash
+python -m unittest discover tests
+```
+
+```bash
+python setup.py sdist bdist_wheel
+pip install twine
+twine upload dist/*
+```
+
+### References
+
+1. LibProjectiveGeometry (c++). GitHub https://github.com/aaichert/EpipolarConsistency/tree/master/code/LibProjectiveGeometry
+2. Hartley, Richard, and Andrew Zisserman. Multiple view geometry in computer vision. Cambridge university press, 2003. https://www.robots.ox.ac.uk/~vgg/hzbook/
+3. Coxeter, Harold Scott Macdonald. Projective geometry. Springer Science & Business Media, 2003.
+4. Stolfi, Jorge. "Oriented projective geometry." Proceedings of the third annual symposium on Computational geometry. 1987.

projectivegeometry23-0.1.0/ProjectiveGeometry23/__init__.py

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+# This file makes ProjectiveGeometry23 a Python package.

projectivegeometry23-0.1.0/ProjectiveGeometry23/central_projection.py

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+"""
+Linear projection from real projective three-space to real projective two-space.
+Representations of a pinhole camera as Projection matrix optionally with additional information of image size and pixelation.
+
+Author: André Aichert
+Date: June 22, 2023
+"""
+
+import numpy as np
+import scipy
+
+
+# recommended:
+# from rich import print
+# np.set_printoptions(suppress=True)
+
+class ProjectionMatrix:
+    def __init__(self, P, image_size=(400, 300), pixel_spacing=1.0):
+        """Pinhole projection model as 3x4 projection matrix with optional
+        information of detector size and pixel spacing [mm per px]."""
+        self.P = np.array(P).reshape((3, 4))
+        self.image_size = np.array(image_size)
+        self.pixel_spacing = pixel_spacing
+
+
+    @classmethod
+    def perspective_look_at(cls, eye, center=np.array([0, 0, 0]), image_size=(400, 300), fovy_rad=0.5, pixel_spacing=1.0):
+        """Create a ProjectionMatrix that looks at a center point from and eye point given field-of-view and image size.
+
+        Extrinsic parameters as rotation matix R and translation vector t:
+        - eye: Position [X,Y,Z] of the camera (camera center)
+        - center: Point the camera is looking at (target position)
+        
+        Intrinsic parameters of a pinhole camera as a 3x3 matrix K.
+        - fovy_rad: Field of view angle in radians (vertical)
+        - image_size: Width and height of the image sensor
+
+        Returns ProjectionMatrix P=K[R t] with given image_size
+        
+        TODO: optional pixel_spacing should probably affect intrinsics
+        """
+        # Up vector defining the camera's orientation
+        up=np.array([0, 1, 0])
+        
+        # Intrinsics
+        w, h = image_size
+        tanfov2 = 2 * np.tan(0.5 * fovy_rad)
+        fx, fy = h / tanfov2, h / tanfov2
+        cx, cy = 0.5 * w, 0.5 * h
+
+        K = np.array([[fx, 0, cx],
+                      [0, fy, cy],
+                      [0, 0, 1]])
+
+        # Extrinsics
+        fwd = (center - eye) / np.linalg.norm(center - eye)
+        left = np.cross(up, fwd)
+        left /= np.linalg.norm(left)
+        new_up = np.cross(fwd, left)
+
+        R = np.array([left, new_up, -fwd])
+        t = -R.dot(eye)
+        
+        # Compose projection matrix
+        P = np.zeros((3, 4))
+        P[:, :3] = K @ R
+        P[:, 3] = K @ t
+        
+        return cls(P, image_size, pixel_spacing)
+
+    def to_dict(self):
+        return {
+            "P": self.P.tolist(),
+            "image_size": self.image_size.to_dict(),
+            "pixel_spacing": self.pixel_spacing
+        }
+
+    def to_ompl(self, with_geometry=True):
+        def f2str(f):
+            return np.format_float_positional(f, trim='-')
+        s = "; ".join([" ".join([f2str(x) for x in row]) for row in self.P])
+        if with_geometry:
+            return f'#> spacing="{self.pixel_spacing}" detector_size_px="{self.image_size}"\n[{s}]'
+        else:
+            return f'[{s}]'
+        
+    @classmethod
+    def from_dict(cls, data):
+        return cls(
+            data["P"],
+            np.array(data["image_size"]),
+            data["pixel_spacing"]
+        )
+
+    def to_json(self):
+        return json.dumps(self.to_dict(), indent=2)
+
+    @classmethod
+    def from_json(cls, json_str):
+        data = json.loads(json_str)
+        return cls.from_dict(data)
+
+    def __repr__(self):
+        return f"ProjectionMatrix:\n{self.P}\nImage Size: {self.image_size}\nPixel Spacing: {self.pixel_spacing}"
+
+    def principal_ray(self):
+        return self.P[2][0:3]
+
+    def normalize(self):
+        norm_m3 = np.linalg.norm(self.principal_ray())
+        detM = np.linalg.det(self.P[0:3, 0:3])
+        if detM < 0:
+            norm_m3 *= -1;
+        self.P /= norm_m3
+
+    def getCenterOfProjection(self):
+        _, _, V = np.linalg.svd(self.P)
+        C = V[-1, :4]
+        if C[3] < -1e-12 or C[3] > 1e-12:
+            C = C / C[3]  # By definition: Camera centers are always positive points.
+        return C.reshape(-1, 1)
+
+    def getPrincipalPoint(self):
+        pp = self.P[:3, :3] @ self.P[2, :3].T
+        return pp / pp[2]
+
+    def getPrincipalRay(self):
+        m3 = self.P[2, :3]
+        if np.linalg.norm(m3) > 1e-12:
+            m3 = m3 / np.linalg.norm(m3)
+        return m3.reshape(-1, 1)
+
+    def getFocalLengthPx(self):
+        """Compute the focal length in pixels (diagonal entries of K in P=K[R t] )."""
+        self.normalize()
+        
+        m1 = self.P[0, :3]
+        m2 = self.P[1, :3]
+        m3 = self.P[2, :3]
+
+        U = np.cross(m3, m2) / np.linalg.norm(np.cross(m3, m2))
+        V = np.cross(m3, m1) / np.linalg.norm(np.cross(m3, m1))
+
+        focal_length_u_px = np.dot(m1, np.cross(V, m3))
+        # focal_length_v_px = np.dot(m2, np.cross(U, m3))  # should be identical
+
+        return focal_length_u_px
+
+    def getDetectorAxisDirections(self):
+        """Compute the two three-points where the image u- and v-axes meet infinity. Scaled to world coordinates."""
+        self.normalize()
+        
+        m1 = self.P[0, :3]
+        m2 = self.P[1, :3]
+        m3 = self.P[2, :3]
+
+        U = np.append(np.cross(m3, m2) / np.linalg.norm(np.cross(m3, m2)), 0)
+        V = np.append(np.cross(m3, m1) / np.linalg.norm(np.cross(m3, m1)), 0)
+
+        return U, V
+
+    def getDetectorAxisDirectionsPx(self):
+        """Compute the two three-points where the image u- and v-axes
+        meet infinity. Scaled to pixels."""
+        U, V = getDetectorAxisDirections()
+        return U * self.pixel_spacing, V * self.pixel_spacing
+
+    def getDetectorPlane(self, imageVPointsUp=False):
+        """ Decomposes the projection matrix to compute the equation of the
+        image/detector plane. Assumes rectangular pixels. This is identical to
+        the principal place shifted by the focal length. For left-handed
+        coordinate systems, set imageVPointsUp to True.
+        Returns the image detector plane in Hessian normal form and a boolean
+        indicating whether imageVPointsUp appears to be set correctly. """
+        # TODO: alternative (that won't know when handedness is off)
+        # focal_length_u_mm = self.getFocalLength() * self.pixel_spacing
+        K, R, t, appears_flipped = self.decomposition(imageVPointsUp)
+        focal_length_u_mm = K[0, 0] * self.pixel_spacing
+        principal_plane = self.P[2, :4].copy()
+        principal_plane /= np.linalg.norm(principal_plane[:3])
+        principal_plane[3] -= focal_length_u_mm
+        return principal_plane, appears_flipped
+
+    def decomposition(self, imageVPointsUp = False):
+        """Decompose Projection Matrix into K[R|t] using RQ-decomposition.
+        Returns K, R, t and a boolean indicating if R is left-handed.
+        For right-handed world coordinates implies imageVPointsUp is wrong."""
+        # Compute RQ decomposition of leftmost 3x3 sub-matrix of P
+        R, Q = scipy.linalg.rq(self.P[:3, :3].copy())
+        K = R
+        R = Q
+        # make diagonal of K positive
+        S = np.eye(3)
+        if K[0, 0] < 0:
+            S[0, 0] = -1
+        if K[1, 1] < 0:
+            S[1, 1] = -1
+        if imageVPointsUp:
+            S[1, 1] *= -1
+        if K[2, 2] < 0:
+            S[2, 2] = -1
+        K = K @ S
+        R = S @ R
+        # Force zero elements in K
+        K[1, 0] = K[2, 0] = K[2, 1] = 0
+        # Scale
+        K *= 1.0 / K[2, 2]
+        t = np.linalg.solve(K, self.P[:3, 3])
+        # EXPLANATION of appears_flipped:
+        # In oriented projective geometry, for a visible point x=P*X the
+        # homogeneous coordinate will be positive. A negative homogeneous
+        # coordinate implies "behind the camera". You can thus change the
+        # direction in which a camera is facing by a multiplication of the
+        # projection matrix with -1.
+        # This is relevant for the decomposition, because in practice, the
+        # coordinate system can be left-handed. In this case, the image
+        # "rotation" matrix has negative determinant. This may actually be the
+        # case, e.g. for the way pixels are stored in a BMP file, some window
+        # coordinates or Siemens 'Leonardo' style raw images. In most cases,
+        # though, that means you got the oriantation wrong.
+        # You can check using sourceDetectorGeometry. Only if your pixel
+        # spacing and imageVPointsUp values are correct, will the image plane
+        # and detector origin be on the opposite side of the object w.r.t.
+        # source position (as it should be... duh).
+        appears_flipped = np.linalg.det(R) > 0
+        return K, R, t, appears_flipped
+
+    def pseudoinverse(self):
+        return np.linalg.pinv(self.P)
+
+    def backproject(self, x):
+        """Compute Plücker Coordinates of a backprojection for a 2D image point x in homogeneous coordinates.
+        if x is a list, make sure to convert o a column vector np.array(x).reshape(-1, 1)."""
+        Pinv = self.pseudoinverse()
+        return Pinv @ x
+
+    def computeFundamentalMatrix(self, P1):
+        """Compute fundamental matrix from two projection matrices. Pseudoinverse-based implementation"""
+        if isinstance(P1, ProjectionMatrix):
+            P1 = P1.P
+        C0 = self.getCenterOfProjection()
+        e1 = P1 @ C0
+        e1 = e1.flatten() / np.linalg.norm(e1)
+        e1x = np.array([[     0, +e1[2], -e1[1]],
+                        [-e1[2],      0, +e1[0]],
+                        [+e1[1], -e1[0],      0]])
+        P0plus = self.pseudoinverse()
+
+        return  np.dot(np.dot(e1x, P1), P0plus)

projectivegeometry23-0.1.0/ProjectiveGeometry23/estimation.py

@@ -0,0 +1,71 @@
+"""
+Direct Linear Transformation (DLT)
+Author: André Aichert
+Date: June 22, 2023
+"""
+
+
+import numpy as np
+
+def dlt_normalization(p2d, p3d, matches):
+    """Normalization of 2D and 3D point clouds. Input assumed to have homogeneous coordinate 1.
+    Purpose: De-mean and scale to +/- sqtr(2), sqrt(3) respectively. """
+    # Compute mean
+    mean2d = np.array([0, 0])
+    mean3d = np.array([0, 0, 0])
+    for i, j in matches:
+        mean2d += p2d[i][:2]
+        mean3d += p3d[j][:3]
+    mean2d /= len(match)
+    mean3d /= len(match)
+
+    # Compute size
+    s2d = 0
+    s3d = 0
+    for i, j in matches:
+        s2d += np.linalg.norm(p2d[i][:2] - mean2d)
+        s3d += np.linalg.norm(p3d[j][:3] - mean3d)
+    s2d *= np.sqrt(2) / len(match)
+    s3d *= np.sqrt(3) / len(match)
+
+    # Compose normalization matrices
+    normalization_2d = np.matmul(scale(s2d, s2d), translation(-mean2d[0], -mean2d[1]))
+    normalization_3d = np.matmul(scale(s3d, s3d, s3d), translation(-mean3d[0], -mean3d[1], -mean3d[2]))
+
+    return normalization_2d, normalization_3d
+
+
+def dlt(x, X, match=None):
+    """Direct Linear Transformation (DLT) for projection matrices."""
+    # Optional match parameter
+    if not match and len(X) == len(x):
+        match = {i: i for i in range(len(X))}
+
+    # Check for insufficient data
+    if len(match) < 6:
+        return np.zeros((3, 4))
+
+    # Normalization of input data
+    N_px, N_mm = dlt_normalization(x, X, match)
+
+    # Build homogeneous system matrix from point matches
+    A = np.zeros((2 * len(match), 12))
+    for k, (key, value) in enumerate(match.items()):
+        # Normalize input points
+        x_norm = np.dot(N_px, x[key])
+        X_norm = np.dot(N_mm, X[value])
+        # Write two rows in A (we get two independent equations from one point match)
+        A[2 * k, 4:8] = x_norm[2] * X_norm
+        A[2 * k + 1, 0:4] = -x_norm[2] * X_norm
+        A[2 * k, 8:12] = -x_norm[1] * X_norm
+        A[2 * k + 1, 8:12] = x_norm[0] * X_norm
+
+    # Solve and reshape
+    _, _, V = np.linalg.svd(A)
+    p = V[-1] / V[-1, -1]
+    P_norm = p.reshape((3, 4))
+
+    # Denormalize
+    P = np.dot(np.dot(np.linalg.inv(N_px), P_norm), N_mm)
+    P /= np.linalg.norm(P[:, :3], axis=0)
+    return P