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add 3d viz + move notebooks to analysis/

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mickypaganini committed Apr 21, 2017
1 parent 8edd99f commit ce41feb9c6e4c95397131e8a5535b8c7c91ed2ba
Showing with 2,300 additions and 3,793 deletions.
  1. +4 −0 .gitignore
  2. 0 { → analysis}/feats1d.py
  3. 0 { → analysis}/firstlook.ipynb
  4. +270 −0 analysis/ndap.py
  5. +2,026 −0 analysis/secondlook.ipynb
  6. +0 −3,793 secondlook.ipynb
@@ -1,3 +1,6 @@
# images
*.png

# hdf5 files
*.hdf
*.h5
@@ -93,3 +96,4 @@ ENV/

# Rope project settings
.ropeproject

File renamed without changes.
File renamed without changes.
@@ -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()

Large diffs are not rendered by default.

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