add 3d viz + move notebooks to analysis/

.gitignore

@@ -1,3 +1,6 @@
+# images
+*.png
+
 # hdf5 files
 *.hdf
 *.h5
@@ -93,3 +96,4 @@ ENV/
 
 # Rope project settings
 .ropeproject
+

analysis/ndap.py

@@ -0,0 +1,270 @@
+from mpl_toolkits.mplot3d import axes3d
+import matplotlib.pyplot as plt
+from matplotlib import rcParams
+import numpy as np
+rcParams['axes.labelsize'] = 14
+rcParams['axes.titlesize'] = 16
+rcParams['xtick.labelsize'] = 14
+rcParams['ytick.labelsize'] = 14
+rcParams['legend.fontsize'] = 14
+rcParams['font.family'] = 'serif'
+rcParams['font.serif'] = ['Computer Modern Roman']
+rcParams['text.usetex'] = True
+rcParams['grid.alpha'] = 0.0
+
+def make_element():
+    """ A element consists of a bunch of planes/surfaces..."""
+
+    element = {
+        "top"    : np.asarray( [[[0,1],[0,1]], [[0,0],[1,1]], [[1,1],[1,1]]] ),
+        "bottom" : np.asarray( [[[0,1],[0,1]], [[0,0],[1,1]], [[0,0],[0,0]]] ),
+        "left"   : np.asarray( [[[0,0],[0,0]], [[0,1],[0,1]], [[0,0],[1,1]]] ),
+        "right"  : np.asarray( [[[1,1],[1,1]], [[0,1],[0,1]], [[0,0],[1,1]]] ),
+        "front"  : np.asarray( [[[0,1],[0,1]], [[0,0],[0,0]], [[0,0],[1,1]]] ),
+        "back"   : np.asarray( [[[0,1],[0,1]], [[1,1],[1,1]], [[0,0],[1,1]]] )
+    }
+
+    return element
+
+def apply_spacing(l, m, n, spacing=(None, 0,0,0)):
+    """Position of array elements in relation to each other."""
+
+    recipe, l_f, m_f, n_f = spacing
+    if recipe not in [None, 'even', 'l', 'm', 'n']:
+        raise TypeError("BAD")
+
+    if recipe is None:
+        return (0,0,0)
+    elif recipe == 'even':
+        return (l*l_f, m*m_f, n*n_f)
+    elif recipe == 'l':
+        return (l*l_f, l*m_f, l*n_f)
+    elif recipe == 'm':
+        return (m*l_f, m*m_f, m*n_f)
+    elif recipe == 'n':
+        return (n*l_f, n*m_f, n*n_f)
+    else:
+        raise TypeError("Unknown recipe[%s]" % recipe)
+
+def text_coords(array, l, m, n):
+    return "[%d,%d,%d]" % (l, m, n)
+
+def text_values(array, l, m, n):
+    return str(array[l,m, n])
+
+class NDArrayPlotter(object):
+
+    def __init__(
+        self, 
+        array,
+        color="blue",
+        alpha="0.6",
+        scale=(1, 1, 1),
+        spacing=(None, 0,0,0)
+    ):
+        self.defaults_ = {
+            "color":    color,
+            "alpha":    alpha,
+            "scale":    scale,
+            "spacing":  spacing
+        }
+        self.reset(array)
+
+    def reset(self, array):
+        self.array_ = array
+
+        self.set_color(self.defaults_["color"])
+        self.set_alpha(self.defaults_["alpha"])
+        self.set_spacing(self.defaults_["spacing"])
+        self.set_scale(self.defaults_["scale"])
+
+    def set_color(self, color):
+        self.colors = np.zeros(self.array_.shape, dtype=('a10'))
+        self.colors[:] = color
+
+        return self.colors
+
+    def set_alpha(self, alpha):
+        self.alphas = np.empty(self.array_.shape, dtype=np.float32)
+        self.alphas[:] = alpha
+
+        return self.alphas
+
+    def set_scale(self, scale):
+        self.scale = scale
+
+        return self.scale
+
+    def set_spacing(self, spacing):
+        self.spacing = spacing
+
+        return self.spacing
+
+    def render(self, array=None, text=None, azim=-15, elev=15):
+
+        if not array:
+            array = self.array_
+
+        if array.shape != self.array_.shape:
+            reset(array)
+
+        fig = plt.figure(figsize=(10,10), dpi=120)
+        ax = fig.add_subplot(111, projection='3d')
+
+        element = make_element()
+
+        for l in xrange(0, array.shape[0]):
+            for m in xrange(0, array.shape[1]):
+                for n in xrange(0, array.shape[2]):
+
+                    # Extract settings that apply to all sides of the element
+                    alpha = self.alphas[l, m, n]
+                    color = self.colors[l, m, n]
+
+                    relative_pos = apply_spacing(l, m, n, self.spacing)
+
+                    for side in element:
+                        (Ls, Ms, Ns) = (
+                            self.scale[0]*(element[side][0] + l ) +relative_pos[0],
+                            self.scale[1]*(element[side][1] + m ) +relative_pos[1],
+                            self.scale[2]*(element[side][2] + n ) +relative_pos[2]
+                        )
+                        ax.plot_surface(
+                            Ls, Ns, Ms,
+                            rstride=1, cstride=1,
+                            alpha=alpha,
+                            color=color,
+                            edgecolors=(0, 0, 0, 0.5),
+                            linewidth=0.2
+                        )
+
+                    if text:
+
+                        elmt_label = text(array, l, m, n)
+
+                        elmt_center_coord = np.asarray([l,m,n])
+                        elmt_center_coord = elmt_center_coord*np.asarray(self.scale) \
+                                         + np.asarray(relative_pos)
+                        elmt_center_coord = elmt_center_coord + np.asarray(self.scale)/2.0
+
+                        elmt_label_coord = elmt_center_coord
+
+                        ax.text(
+                            elmt_label_coord[0], elmt_label_coord[2], elmt_label_coord[1], 
+                            elmt_label,
+                            horizontalalignment='center', verticalalignment='center',
+                            zdir='y'
+                        )
+
+        # highest = 0                         # Make it look cubic
+        # for size in array.shape:
+        #     if size > highest:
+        #         highest = size
+        # ax.set_xlim((0,highest))
+        # ax.set_ylim((0,highest))
+        # ax.set_zlim((0,highest))
+
+
+        #ax.set_title(r"ND array(\textbf{\emph{l}}, \textbf{\emph{m}}, \textbf{\emph{n}}) = %dD %s" % (array.ndim, str(array.shape)))
+
+        plt.gca().invert_zaxis()
+
+        #
+        #   This is a crazy way to print axis-labels...
+        #
+        # x = l
+        # y = n
+        # z = m
+        L, M, N = array.shape
+        L_scl,  M_scl,  N_scl  = np.asarray(self.scale)
+        L_skew, M_skew, N_skew = apply_spacing(L_scl, M_scl, N_scl, self.spacing)
+
+        axis_label_format = r"$\leftarrow$ \textbf{\emph{%s}} $\rightarrow$"
+
+        #laxis_label = axis_label_format % "l" 
+        #maxis_label = axis_label_format % "m" 
+        #naxis_label = axis_label_format % "n" 
+
+        # ax.text(
+        #     (L_scl*(L+L_skew))/2.0, -0.5, (M_scl*(M+M_skew))+0.5,
+        #     laxis_label, zdir='x', horizontalalignment='center', verticalalignment='center'
+        # )
+        # ax.text(
+        #     0, -0.5, (M_scl*(M+M_skew))/2.0, 
+        #     maxis_label, zdir='z', horizontalalignment='center', verticalalignment='center'
+        # )
+        # ax.text(
+        #     0, (N_scl*(N+N_skew))/2.0, -0.5, 
+        #     naxis_label, zdir='y', 
+        # )
+        plt.axis('off')
+
+        """
+        ax.set_xlabel('l') 
+        ax.set_ylabel('n')
+        ax.set_zlabel('m')
+        # Get rid of the ticks
+        ax.set_xticks([])
+        ax.set_yticks([])
+        ax.set_zticks([])
+        # Get rid of the panes
+        ax.w_xaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
+        ax.w_yaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
+        ax.w_zaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
+        # Get rid of the spines
+        ax.w_xaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
+        ax.w_yaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
+        ax.w_zaxis.line.set_color((1.0, 1.0, 1.0, 0.0))
+        """
+        #
+        # End of crazy crazy way to print axis-labels
+        #
+
+        ax.view_init(azim=azim, elev=elev)
+
+        return (fig, ax)
+
+def main():
+
+
+    """
+    colors = plotter.colors
+    colors[:] = "#00FF00"
+    colors[ 0,  :, :] = "#FF0000"
+    colors[-1,  :, :] = "#FF0000"
+    colors[ :,  0, :] = "#FF0000"
+    colors[ :, -1, :] = "#FF0000"
+    colors[ :,  :, 0] = "#FF0000"
+    colors[ :,  :,-1] = "#FF0000"
+    alphas = plotter.alphas
+    alphas[:] = 0.3
+    alphas[ 0,  :, :] = 0.05
+    alphas[-1,  :, :] = 0.05
+    alphas[ :,  0, :] = 0.05
+    alphas[ :, -1, :] = 0.05
+    alphas[ :,  :, 0] = 0.05
+    alphas[ :,  :,-1] = 0.05
+    alphas = plotter.alphas
+    alphas[:] = 0.05
+    colors = plotter.set_color("#0000FF")
+    colors[:,1,1] = "#FF0000"
+    alphas[:,1,1] = 0.75
+    colors[1,:,1] = "#FF0000"
+    alphas[1,:,1] = 0.75
+    """
+    subject = np.arange(0,9).reshape((1,3,3))
+    plotter = NDArrayPlotter(subject, spacing=('even', 0.2,0.2,0.2))
+
+    colors = plotter.set_color("#FFFF00")
+    alphas = plotter.set_alpha(0.2)
+
+    colors[:,1,:] = "#FF0000"
+    colors[:,0,:] = "#00FF00"
+    colors[:,2,:] = "#0000FF"
+
+    (fig_coord, ax_coors) = plotter.render(text=text_coords)
+    (fig_values, ax_value) = plotter.render(text=text_values)
+    plt.show()
+
+if __name__ == "__main__":
+    main()