Merge branch 'logo'

doc/logo/Makefile

@@ -0,0 +1,11 @@
+.PHONY: logo
+
+logo: green_orange_snake.png snake_logo.svg
+	inkscape --export-png=scikits_image_logo.png --export-dpi=100 \
+		     --export-area-drawing --export-background-opacity=1 \
+			 snake_logo.svg
+	python shrink_logo.py
+
+green_orange_snake.png:
+	python scikits_image_logo.py --no-plot
+

doc/logo/scikits_image_logo.py

@@ -0,0 +1,226 @@
+"""
+Script to draw scikits.image logo using Scipy logo as stencil. The easiest
+starting point is the `plot_colorized_logo`; the "if-main" demonstrates its use.
+
+Original snake image from pixabay [1]_
+
+.. [1] http://pixabay.com/en/snake-green-toxic-close-yellow-3237/
+"""
+import numpy as np
+import matplotlib.pyplot as plt
+import scipy.misc
+
+import scikits.image.io as sio
+import scikits.image.filter as imfilt
+
+import scipy_logo
+
+
+# Utility functions
+# =================
+
+def get_edges(img):
+    edge = np.empty(img.shape)
+    if len(img.shape) == 3:
+        for i in range(3):
+            edge[:, :, i] = imfilt.sobel(img[:, :, i])
+    else:
+        edge = imfilt.sobel(img)
+    edge = rescale_intensity(edge)
+    return edge
+
+def rescale_intensity(img):
+    i_range = float(img.max() - img.min())
+    img = (img - img.min()) / i_range * 255
+    return np.uint8(img)
+
+def colorize(img, color, whiten=False):
+    """Return colorized image from gray scale image
+
+    Parameters
+    ----------
+    img : N x M array
+        grayscale image
+    color : length-3 sequence of floats
+        RGB color spec. Float values should be between 0 and 1.
+    whiten : bool
+        If True, a color value less than 1 increases the image intensity.
+    """
+    color = np.asarray(color)[np.newaxis, np.newaxis, :]
+    img = img[:, :, np.newaxis]
+    if whiten:
+        # truncate and stretch intensity range to enhance contrast
+        img = np.clip(img, 80, 255)
+        img = rescale_intensity(img)
+        return np.uint8(color * (255 - img) + img)
+    else:
+        return np.uint8(img * color)
+
+
+def prepare_axes(ax):
+    plt.sca(ax)
+    ax.xaxis.set_visible(False)
+    ax.yaxis.set_visible(False)
+    for spine in ax.spines.itervalues():
+        spine.set_visible(False)
+
+
+_rgb_stack = np.ones((1, 1, 3), dtype=bool)
+def gray2rgb(arr):
+    """Return RGB image from a grayscale image.
+
+    Expand h x w image to h x w x 3 image where color channels are simply copies
+    of the grayscale image.
+    """
+    return arr[:, :, np.newaxis] * _rgb_stack
+
+
+# Logo generating classes
+# =======================
+
+class LogoBase(object):
+
+    def __init__(self):
+        self.logo = scipy_logo.ScipyLogo(radius=self.radius)
+        self.mask_1 = self.logo.get_mask(self.img.shape, 'upper left')
+        self.mask_2 = self.logo.get_mask(self.img.shape, 'lower right')
+        self.edges = get_edges(self.img)
+        # truncate and stretch intensity range to enhance contrast
+        self.edges = np.clip(self.edges, 0, 100)
+        self.edges = rescale_intensity(self.edges)
+
+
+    def _crop_image(self, img):
+        w = 2 * self.radius
+        x, y = self.origin
+        return img[y:y+w, x:x+w]
+
+    def get_canvas(self):
+        return 255 * np.ones(self.img.shape, dtype=np.uint8)
+
+    def plot_curve(self, **kwargs):
+        self.logo.plot_snake_curve(**kwargs)
+
+
+class SnakeLogo(LogoBase):
+
+    def __init__(self):
+        self.radius = 250
+        self.origin = (420, 0)
+        img = sio.imread('data/snake_pixabay.jpg')        
+        img = self._crop_image(img)
+
+        img = img.astype(float) * 1.1
+        img[img > 255] = 255
+        self.img = img.astype(np.uint8)
+
+        LogoBase.__init__(self)
+
+
+snake_color = SnakeLogo()
+snake = SnakeLogo()
+# turn RGB image into gray image
+snake.img = np.mean(snake.img, axis=2)
+snake.edges = np.mean(snake.edges, axis=2)
+
+
+# Demo plotting functions
+# =======================
+
+def plot_colorized_logo(logo, color, edges='light', switch=False, whiten=False):
+    """Convenience function to plot artificially colored logo.
+
+    Parameters
+    ----------
+    logo : subclass of LogoBase
+    color : length-3 sequence of floats
+        RGB color spec. Float values should be between 0 and 1.
+    edges : {'light'|'dark'}
+        Specifies whether Sobel edges are drawn light or dark
+    switch : bool
+        If False, the image is drawn on the southeast half of the Scipy curve
+        and the edge image is drawn on northwest half.
+    whiten : bool
+        If True, a color value less than 1 increases the image intensity.
+    """
+    if not hasattr(color[0], '__iter__'):
+        color = [color] * 2
+    if not hasattr(whiten, '__iter__'):
+        whiten = [whiten] * 2
+    img = gray2rgb(logo.get_canvas())
+    mask_img = gray2rgb(logo.mask_2)
+    mask_edge = gray2rgb(logo.mask_1)
+    if switch:
+        mask_img, mask_edge = mask_edge, mask_img
+    if edges == 'dark':
+        lg_edge = colorize(255 - logo.edges, color[0], whiten=whiten[0])
+    else:
+        lg_edge = colorize(logo.edges, color[0], whiten=whiten[0])
+    lg_img = colorize(logo.img, color[1], whiten=whiten[1])
+    img[mask_img] = lg_img[mask_img]
+    img[mask_edge] = lg_edge[mask_edge]
+    logo.plot_curve(lw=5, color='w')
+    plt.imshow(img)
+
+
+def red_light_edges(logo, **kwargs):
+    plot_colorized_logo(logo, (1, 0, 0), edges='light', **kwargs)
+
+
+def red_dark_edges(logo, **kwargs):
+    plot_colorized_logo(logo, (1, 0, 0), edges='dark', **kwargs)
+
+def blue_light_edges(logo, **kwargs):
+    plot_colorized_logo(logo, (0.35, 0.55, 0.85), edges='light', **kwargs)
+
+
+def blue_dark_edges(logo, **kwargs):
+    plot_colorized_logo(logo, (0.35, 0.55, 0.85), edges='dark', **kwargs)
+
+
+def green_orange_light_edges(logo, **kwargs):
+    colors = ((0.6, 0.8, 0.3), (1, 0.5, 0.1))
+    plot_colorized_logo(logo, colors, edges='light', **kwargs)
+
+def green_orange_dark_edges(logo, **kwargs):
+    colors = ((0.6, 0.8, 0.3), (1, 0.5, 0.1))
+    plot_colorized_logo(logo, colors, edges='dark', **kwargs)
+
+
+if __name__ == '__main__':
+
+    import sys
+    plot = False
+    if len(sys.argv) < 2 or sys.argv[1] != '--no-plot':
+        plot = True
+
+        print "Run with '--no-plot' flag to generate logo silently."
+
+    def plot_all():
+        plotters = (red_light_edges, red_dark_edges,
+                    blue_light_edges, blue_dark_edges,
+                    green_orange_light_edges, green_orange_dark_edges)
+
+        f, axes_array = plt.subplots(nrows=2, ncols=len(plotters))
+        for plot, ax_col in zip(plotters, axes_array.T):
+                prepare_axes(ax_col[0])
+                plot(snake)
+                prepare_axes(ax_col[1])
+                plot(snake, whiten=True)
+        plt.tight_layout()
+
+    def plot_snake():
+
+        f, ax = plt.subplots()
+        prepare_axes(ax)
+        green_orange_dark_edges(snake, whiten=(False, True))
+        plt.savefig('green_orange_snake.png', bbox_inches='tight')
+
+    if plot:
+        plot_all()
+
+    plot_snake()
+
+    if plot:
+        plt.show()
+

doc/logo/scipy_logo.py

@@ -0,0 +1,262 @@
+"""
+Code used to trace Scipy logo.
+"""
+import numpy as np
+import matplotlib.pyplot as plt
+import scikits.image.io as imgio
+from scipy.misc import lena
+import matplotlib.nxutils as nx
+
+
+class SymmetricAnchorPoint(object):
+    """Anchor point in a parametric curve with symmetric handles
+
+    Parameters
+    ----------
+    pt : length-2 sequence
+        (x, y) coordinates of anchor point
+    theta : float
+        angle of control handle
+    length : float
+        half-length of symmetric control handle. Each control point is `length`
+        distance away from the anchor point.
+    use_degrees : bool
+        If True, convert input `theta` from degrees to radians.
+    """
+
+    def __init__(self, pt, theta, length, use_degrees=False):
+        self.pt = pt
+        if use_degrees:
+            theta = theta * np.pi / 180
+        self.theta = theta
+        self.length = length
+
+    def control_points(self):
+        """Return control points for symmetric handles
+
+        The first point is in the direction of theta and the second is directly
+        opposite. For example, if `theta = 0`, then the first `p1` will be
+        directly to the right of the anchor point, and `p2` will be directly
+        to the left.
+        """
+        theta = self.theta
+        offset = self.length * np.array([np.cos(theta), np.sin(theta)])
+        p1 = self.pt + offset
+        p2 = self.pt - offset
+        return p1, p2
+
+    def __repr__(self):
+        v = (self.pt, self.theta * 180/np.pi, self.length)
+        return 'SymmetricAnchorPoint(pt={0}, theta={1}, length={2})'.format(*v)
+
+
+def curve_from_anchor_points(pts):
+    """Return curve from a list of SymmetricAnchorPoints"""
+    assert len(pts) > 1
+    bezier_pts = []
+    for anchor in pts:
+        c1, c2 = anchor.control_points()
+        bezier_pts.extend([c2, anchor.pt, c1])
+    # clip control points from ends
+    bezier_pts = bezier_pts[1:-1]
+    x, y = [], []
+    # every third point is an anchor point
+    for i in range(0, len(bezier_pts)-1, 3):
+        xi, yi = cubic_curve(*bezier_pts[i:i+4])
+        x.append(xi)
+        y.append(yi)
+    return np.hstack(x), np.hstack(y)
+
+
+def cubic_curve(p0, p1, p2, p3, npts=20):
+    """Return points on a cubic Bezier curve
+
+    Parameters
+    ----------
+    p0, p3 : length-2 sequences
+        end points of curve
+    p1, p2 : length-2 sequences
+        control points of curve
+    npts : int
+        number of points to return (including end points)
+
+    Returns
+    -------
+    x, y : arrays
+        points on cubic curve
+    """
+    t = np.linspace(0, 1, npts)[:, np.newaxis]
+    # cubic bezier curve from http://en.wikipedia.org/wiki/Bezier_curve
+    b = (1-t)**3 * p0 + 3*t*(1-t)**2 * p1 + 3*t**2*(1-t) * p2 + t**3 * p3
+    x, y = b.transpose()
+    return x, y
+
+
+class Circle(object):
+
+    def __init__(self, center, radius):
+        self.center = center
+        self.radius = radius
+
+    def point_from_angle(self, angle):
+        r = self.radius
+        # `angle` can be a scalar or 1D array: transpose twice for best results
+        pts = r * np.array((np.cos(angle), np.sin(angle))).T + self.center
+        return pts.T
+
+    def plot(self, **kwargs):
+        ax = kwargs.pop('ax', plt.gca())
+        fc = kwargs.pop('fc', 'none')
+        c = plt.Circle(self.center, self.radius, fc=fc, **kwargs)
+        ax.add_patch(c)
+
+
+class ScipyLogo(object):
+    """Object to generate scipy logo
+
+    Parameters
+    ----------
+    center : length-2 array
+        the Scipy logo will be centered on this point.
+    radius : float
+        radius of logo
+    """
+
+    CENTER = np.array((254, 246))
+    RADIUS = 252.0
+    THETA_START = 2.58
+    THETA_END = -0.368
+
+    def __init__(self, center=None, radius=None):
+        if center is None:
+            if radius is None:
+                center = self.CENTER
+            else:
+                center = np.array((radius, radius))
+        self.center = center
+        if radius is None:
+            radius = self.RADIUS
+        self.radius = radius
+
+
+        # calculate end points of curve so that it lies exactly on circle
+        logo_circle = Circle(self.CENTER, self.RADIUS)
+        s_start = logo_circle.point_from_angle(self.THETA_START)
+        s_end = logo_circle.point_from_angle(self.THETA_END)
+
+        self.circle = Circle(self.center, self.radius)
+        # note that angles are clockwise because of inverted y-axis
+        self._anchors = [SymmetricAnchorPoint(*t, use_degrees=True)
+                         for t in [(s_start,    -37, 90),
+                                   ((144, 312),   7, 20),
+                                   ((205, 375),  52, 50),
+                                   ((330, 380), -53, 60),
+                                   ((290, 260),-168, 50),
+                                   ((217, 245),-168, 50),
+                                   ((182, 118), -50, 60),
+                                   ((317, 125),  53, 60),
+                                   ((385, 198),  10, 20),
+                                   (s_end,      -25, 60)]]
+        # normalize anchors so they have unit radius and are centered at origin
+        for a in self._anchors:
+            a.pt = (a.pt - self.CENTER) / self.RADIUS
+            a.length = a.length / self.RADIUS
+
+    def snake_anchors(self):
+        """Return list of SymmetricAnchorPoints defining snake curve"""
+        anchors = []
+        for a in self._anchors:
+            pt = self.radius * a.pt + self.center
+            length = self.radius * a.length
+            anchors.append(SymmetricAnchorPoint(pt, a.theta, length))
+        return anchors
+
+    def snake_curve(self):
+        """Return x, y coordinates of snake curve"""
+        return curve_from_anchor_points(self.snake_anchors())
+
+    def plot_snake_curve(self, **kwargs):
+        ax = kwargs.pop('ax', plt.gca())
+        x, y = self.snake_curve()
+        ax.plot(x, y, 'k', **kwargs)
+
+    def plot_circle(self, **kwargs):
+        self.circle.plot(**kwargs)
+
+    def plot_image(self, **kwargs):
+        ax = kwargs.pop('ax', plt.gca())
+        img = imgio.imread('data/scipy.png')
+        ax.imshow(img, **kwargs)
+
+    def get_mask(self, shape, region):
+        """
+        Parameters
+        ----------
+        region : {'upper left', 'lower right'}
+        """
+        if region == 'upper left':
+            theta = np.linspace(self.THETA_END, self.THETA_START - 2 * np.pi)
+        elif region == 'lower right':
+            theta = np.linspace(self.THETA_END, self.THETA_START)
+        else:
+            msg = "Expected 'upper left' or 'lower right'; got %s" % region
+            raise ValueError(msg)
+        xy_circle = self.circle.point_from_angle(theta).T
+        x, y = self.snake_curve()
+        xy_curve = np.array((x, y)).T
+        xy_poly = np.vstack((xy_curve, xy_circle))
+
+        h, w = shape[:2]
+        y_img, x_img = np.mgrid[:h, :w]
+        xy_points = np.column_stack((x_img.flat, y_img.flat))
+
+        mask = nx.points_inside_poly(xy_points, xy_poly)
+        return mask.reshape((h, w))
+
+
+def plot_scipy_trace():
+    plt.figure()
+    logo = ScipyLogo()
+    logo.plot_snake_curve()
+    logo.plot_circle()
+    logo.plot_image()
+    plot_anchors(logo.snake_anchors())
+
+
+def plot_anchors(anchors, color='r', alpha=0.7):
+    for a in anchors:
+        c = a.control_points()
+        x, y = np.transpose(c)
+        plt.plot(x, y, 'o-', color=color, mfc='w', mec=color, alpha=alpha)
+        plt.plot(a.pt[0], a.pt[1], 'o', color=color, alpha=alpha)
+
+
+def plot_snake_overlay():
+    plt.figure()
+    logo = ScipyLogo((670, 250), 250)
+    logo.plot_snake_curve()
+    logo.plot_circle()
+    img = imgio.imread('data/snake_pixabay.jpg')
+    #mask = logo.get_mask(img.shape, 'upper left')
+    #img[mask] = 255
+    plt.imshow(img)
+
+
+def plot_lena_overlay():
+    plt.figure()
+    logo = ScipyLogo((300, 300), 180)
+    logo.plot_snake_curve()
+    logo.plot_circle()
+    img = lena()
+    #mask = logo.get_mask(img.shape, 'upper left')
+    #img[mask] = 255
+    plt.imshow(img)
+
+
+if __name__ == '__main__':
+    plot_scipy_trace()
+    plot_snake_overlay()
+    plot_lena_overlay()
+
+    plt.show()
+

doc/logo/shrink_logo.py

@@ -0,0 +1,16 @@
+from scikits.image import io, transform
+
+s = 0.7
+
+img = io.imread('scikits_image_logo.png')
+h, w, c = img.shape
+
+print "\nScaling down logo by %.1fx..." % s
+
+img = transform.homography(img, [[s, 0, 0],
+                                 [0, s, 0],
+                                 [0, 0, 1]],
+                           output_shape=(int(h*s), int(w*s), 4),
+                           order=3)
+
+io.imsave('scikits_image_logo_small.png', img)

doc/logo/snake_logo.svg

@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="744.09448819"
+   height="1052.3622047"
+   id="svg2"
+   version="1.1"
+   inkscape:version="0.48.1 r9760"
+   sodipodi:docname="snake_logo.svg">
+  <defs
+     id="defs4" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
+     inkscape:pageopacity="0.0"
+     inkscape:pageshadow="2"
+     inkscape:zoom="0.98994949"
+     inkscape:cx="161.85782"
+     inkscape:cy="843.24881"
+     inkscape:document-units="px"
+     inkscape:current-layer="layer1"
+     showgrid="false"
+     inkscape:window-width="1280"
+     inkscape:window-height="722"
+     inkscape:window-x="0"
+     inkscape:window-y="24"
+     inkscape:window-maximized="1" />
+  <metadata
+     id="metadata7">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title />
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1">
+    <image
+       sodipodi:absref="/home/stefan/src/scikits_image_logo/green_orange_snake.png"
+       xlink:href="green_orange_snake.png"
+       y="6.4703732"
+       x="8.8462782"
+       id="image3147"
+       height="132.30446"
+       width="132.30446" />
+    <g
+       id="g3158"
+       transform="translate(-105.05586,-195.43585)">
+      <text
+         sodipodi:linespacing="125%"
+         id="text3150"
+         y="278.58533"
+         x="261.22247"
+         style="font-size:24px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#4d4d4d;fill-opacity:1;stroke:none;font-family:Verdana;-inkscape-font-specification:Verdana"
+         xml:space="preserve"><tspan
+           style="font-size:70px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:Ubuntu;-inkscape-font-specification:Ubuntu"
+           y="278.58533"
+           x="261.22247"
+           id="tspan3152"
+           sodipodi:role="line">scikits-image</tspan></text>
+      <text
+         sodipodi:linespacing="125%"
+         id="text3154"
+         y="306.86957"
+         x="262.52374"
+         style="font-size:24px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill:#4d4d4d;fill-opacity:1;stroke:none;font-family:Verdana;-inkscape-font-specification:Verdana"
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+           x="262.52374"
+           id="tspan3156"
+           sodipodi:role="line">image processing in python</tspan></text>
+    </g>
+  </g>
+</svg>

doc/source/conf.py

@@ -123,7 +123,7 @@ html_title = 'scikits.image v%s docs' % version
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = "scikits_image_logo_small.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

doc/source/themes/agogo/static/agogo.css_t

@@ -584,7 +584,7 @@ pre {
     background-color: {{ theme_codebgcolor }};
     color: {{ theme_codetextcolor }};
     line-height: 120%;
-    border: 1px solid #ac9;
+    border: 0px solid #ac9;
     border-left: none;
     border-right: none;
 }