add example code notebooks

topics/resources/notebooks/05/nominals/social-media.csv

+id,gender,pref_service,age,happiness
+0,female,Facebook,35,happy
+1,female,Facebook,51,very happy
+2,female,Facebook,43,sad
+3,female,Facebook,27,very sad
+4,female,Facebook,18,very sad
+5,female,Facebook,54,happy
+6,female,Facebook,57,neutral
+7,female,Facebook,18,sad
+8,female,Facebook,65,very sad
+9,female,Facebook,34,very sad
+10,female,Facebook,79,sad
+11,female,Instagram,32,very sad
+12,female,Instagram,24,very sad
+13,female,Instagram,37,sad
+14,female,Instagram,28,very sad
+15,female,Instagram,28,sad
+16,female,Instagram,28,very happy
+17,female,Instagram,26,very sad
+18,female,Instagram,32,sad
+19,female,Instagram,33,very happy
+20,female,Instagram,30,sad
+21,female,Instagram,42,very happy
+22,female,Instagram,18,sad
+23,female,Instagram,23,neutral
+24,female,Instagram,34,sad
+25,female,Instagram,18,sad
+26,female,Mastodon,39,happy
+27,female,Mastodon,31,very happy
+28,female,Mastodon,23,neutral
+29,female,Mastodon,30,very sad
+30,female,Mastodon,20,very happy
+31,female,Mastodon,18,neutral
+32,female,Twitter,46,neutral
+33,female,Twitter,47,very happy
+34,female,Twitter,36,sad
+35,female,Twitter,35,very happy
+36,female,Twitter,18,neutral
+37,female,Twitter,24,sad
+38,female,Twitter,29,neutral
+39,female,Twitter,38,very sad
+40,female,Twitter,53,happy
+41,female,Twitter,28,neutral
+42,female,Other,21,neutral
+43,female,Other,39,neutral
+44,female,Other,28,very sad
+45,male,Facebook,19,very happy
+46,male,Facebook,58,happy
+47,male,Facebook,27,neutral
+48,male,Facebook,32,very sad
+49,male,Facebook,24,sad
+50,male,Facebook,45,very happy
+51,male,Facebook,56,neutral
+52,male,Facebook,34,very sad
+53,male,Facebook,46,neutral
+54,male,Facebook,33,happy
+55,male,Facebook,75,very happy
+56,male,Facebook,63,neutral
+57,male,Facebook,31,happy
+58,male,Instagram,31,happy
+59,male,Instagram,35,sad
+60,male,Instagram,30,very happy
+61,male,Instagram,21,very sad
+62,male,Instagram,26,neutral
+63,male,Instagram,33,sad
+64,male,Instagram,31,sad
+65,male,Instagram,20,sad
+66,male,Instagram,31,neutral
+67,male,Instagram,19,very sad
+68,male,Instagram,18,sad
+69,male,Mastodon,27,sad
+70,male,Mastodon,34,very happy
+71,male,Mastodon,29,neutral
+72,male,Twitter,54,neutral
+73,male,Twitter,58,happy
+74,male,Twitter,40,very happy
+75,male,Twitter,27,neutral
+76,male,Twitter,34,neutral
+77,male,Twitter,18,very sad
+78,male,Twitter,35,sad
+79,male,Twitter,34,happy
+80,male,Twitter,37,very happy
+81,male,Twitter,49,very happy
+82,male,Twitter,18,very sad
+83,male,Twitter,45,sad
+84,male,Twitter,28,happy
+85,male,Twitter,45,very sad
+86,male,Twitter,37,happy
+87,male,Twitter,22,very happy
+88,male,Twitter,46,very happy
+89,male,Other,22,neutral
+90,male,Other,34,very sad
+91,male,Other,23,very sad
+92,male,Other,24,very happy
+93,nonbinary,Mastodon,26,very sad
+94,nonbinary,Other,48,neutral
+95,prefer not to say,Twitter,44,neutral

topics/resources/notebooks/05/numerical-categorical/social-media.csv

+id,gender,pref_service,age,happiness
+0,female,Facebook,35,happy
+1,female,Facebook,51,very happy
+2,female,Facebook,43,sad
+3,female,Facebook,27,very sad
+4,female,Facebook,18,very sad
+5,female,Facebook,54,happy
+6,female,Facebook,57,neutral
+7,female,Facebook,18,sad
+8,female,Facebook,65,very sad
+9,female,Facebook,34,very sad
+10,female,Facebook,79,sad
+11,female,Instagram,32,very sad
+12,female,Instagram,24,very sad
+13,female,Instagram,37,sad
+14,female,Instagram,28,very sad
+15,female,Instagram,28,sad
+16,female,Instagram,28,very happy
+17,female,Instagram,26,very sad
+18,female,Instagram,32,sad
+19,female,Instagram,33,very happy
+20,female,Instagram,30,sad
+21,female,Instagram,42,very happy
+22,female,Instagram,18,sad
+23,female,Instagram,23,neutral
+24,female,Instagram,34,sad
+25,female,Instagram,18,sad
+26,female,Mastodon,39,happy
+27,female,Mastodon,31,very happy
+28,female,Mastodon,23,neutral
+29,female,Mastodon,30,very sad
+30,female,Mastodon,20,very happy
+31,female,Mastodon,18,neutral
+32,female,Twitter,46,neutral
+33,female,Twitter,47,very happy
+34,female,Twitter,36,sad
+35,female,Twitter,35,very happy
+36,female,Twitter,18,neutral
+37,female,Twitter,24,sad
+38,female,Twitter,29,neutral
+39,female,Twitter,38,very sad
+40,female,Twitter,53,happy
+41,female,Twitter,28,neutral
+42,female,Other,21,neutral
+43,female,Other,39,neutral
+44,female,Other,28,very sad
+45,male,Facebook,19,very happy
+46,male,Facebook,58,happy
+47,male,Facebook,27,neutral
+48,male,Facebook,32,very sad
+49,male,Facebook,24,sad
+50,male,Facebook,45,very happy
+51,male,Facebook,56,neutral
+52,male,Facebook,34,very sad
+53,male,Facebook,46,neutral
+54,male,Facebook,33,happy
+55,male,Facebook,75,very happy
+56,male,Facebook,63,neutral
+57,male,Facebook,31,happy
+58,male,Instagram,31,happy
+59,male,Instagram,35,sad
+60,male,Instagram,30,very happy
+61,male,Instagram,21,very sad
+62,male,Instagram,26,neutral
+63,male,Instagram,33,sad
+64,male,Instagram,31,sad
+65,male,Instagram,20,sad
+66,male,Instagram,31,neutral
+67,male,Instagram,19,very sad
+68,male,Instagram,18,sad
+69,male,Mastodon,27,sad
+70,male,Mastodon,34,very happy
+71,male,Mastodon,29,neutral
+72,male,Twitter,54,neutral
+73,male,Twitter,58,happy
+74,male,Twitter,40,very happy
+75,male,Twitter,27,neutral
+76,male,Twitter,34,neutral
+77,male,Twitter,18,very sad
+78,male,Twitter,35,sad
+79,male,Twitter,34,happy
+80,male,Twitter,37,very happy
+81,male,Twitter,49,very happy
+82,male,Twitter,18,very sad
+83,male,Twitter,45,sad
+84,male,Twitter,28,happy
+85,male,Twitter,45,very sad
+86,male,Twitter,37,happy
+87,male,Twitter,22,very happy
+88,male,Twitter,46,very happy
+89,male,Other,22,neutral
+90,male,Other,34,very sad
+91,male,Other,23,very sad
+92,male,Other,24,very happy
+93,nonbinary,Mastodon,26,very sad
+94,nonbinary,Other,48,neutral
+95,prefer not to say,Twitter,44,neutral

topics/resources/notebooks/05/ordinals/generosity.csv

+"experience","faith","cause","values"
+"not at all","not at all","not at all","not at all"
+"not at all","not at all","not at all","not at all"
+"not at all","not at all","not at all","not at all"
+"not at all","not at all","not at all","a little"
+"not at all","not at all","not at all","a little"
+"not at all","not at all","not at all","a little"
+"not at all","not at all","a little","neutral"
+"not at all","not at all","a little","neutral"
+"a little","not at all","neutral","a little"
+"a little","not at all","a little","a little"
+"a little","not at all","a little","a little"
+"a little","not at all","a little","a little"
+"a little","not at all","a little","strongly"
+"a little","not at all","a little","strongly"
+"a little","not at all","strongly","strongly"
+"a little","not at all","very strongly","strongly"
+"a little","not at all","neutral","very strongly"
+"a little","a little","strongly","strongly"
+"a little","a little","strongly","strongly"
+"a little","a little","strongly","strongly"
+"neutral","neutral","neutral","neutral"
+"neutral","neutral","neutral","neutral"
+"neutral","neutral","neutral","neutral"
+"neutral","neutral","neutral","neutral"
+"neutral","neutral","neutral","neutral"
+"neutral","neutral","strongly","neutral"
+"neutral","neutral","neutral","very strongly"
+"strongly","a little","strongly","strongly"
+"strongly","a little","strongly","strongly"
+"strongly","a little","strongly","very strongly"
+"strongly","a little","strongly","very strongly"
+"strongly","a little","very strongly","very strongly"
+"strongly","strongly","very strongly","very strongly"
+"strongly","strongly","very strongly","very strongly"
+"very strongly","strongly","very strongly","very strongly"
+"very strongly","very strongly","very strongly","very strongly"
+"very strongly","very strongly","very strongly","very strongly"

topics/resources/notebooks/10/Plotting in 3D - Vispy.ipynb

+%% Cell type:code id: tags:
+
+``` python
+%matplotlib inline
+```
+
+%% Cell type:code id: tags:
+
+``` python
+import numpy as np
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import vispy
+from vispy import app, visuals, scene
+from vispy.visuals.transforms import STTransform
+from vispy.util.filter import gaussian_filter
+
+print(vispy.sys_info())
+```
+
+%% Cell type:markdown id: tags:
+
+# 3D line with Matplotlib and VisPy
+
+%% Cell type:code id: tags:
+
+``` python
+# Prepare data.
+n = 60
+x = np.sin(np.linspace(-2, 2, n) * np.pi)
+y = np.cos(np.linspace(-2, 2, n) * np.pi)
+z = np.linspace(-2, 2, n)
+
+# Create a matplotlib figure manually.
+fig = plt.figure()
+
+# Add a 3D axes subplot.
+ax = fig.add_subplot(projection='3d')
+ax.plot(x, y, z)
+plt.show()
+```
+
+%% Cell type:code id: tags:
+
+``` python
+# Prepare data.
+n = 60
+x = np.sin(np.linspace(-2, 2, n) * np.pi)
+y = np.cos(np.linspace(-2, 2, n) * np.pi)
+z = np.linspace(-2, 2, n)
+
+# Combine x, y and z into a numpy matrix. 
+pos = np.c_[x, y, z]
+
+# Build visuals.
+Plot3D = scene.visuals.create_visual_node(visuals.LinePlotVisual)
+
+# Build canvas.
+canvas = scene.SceneCanvas(keys='interactive', title='plot3d')
+
+# Add a ViewBox to let the user zoom/rotate.
+view = canvas.central_widget.add_view()
+view.camera = 'turntable'
+view.camera.fov = 45
+view.camera.distance = 6
+
+# Plot.
+Plot3D(pos, width=2.0, color='red',
+       edge_color='w', symbol='o', face_color=(0.2, 0.2, 1, 0.8),
+       parent=view.scene)
+canvas.show()
+app.run()
+```
+
+%% Cell type:markdown id: tags:
+
+# 3D surface with Matplotlib and VisPy
+
+%% Cell type:code id: tags:
+
+``` python
+# https://matplotlib.org/gallery/mplot3d/surface3d.html
+fig = plt.figure(figsize=(6, 6))
+ax = fig.add_subplot(projection='3d')
+
+# Make data.
+x = np.arange(-5, 5, 0.25)
+y = np.arange(-5, 5, 0.25)
+
+# Combine coordinate vectors into coordinate matrices.
+xx, yy = np.meshgrid(x, y)
+
+# Compute the surface equation.
+r = np.sqrt(xx**2 + yy**2)
+z = np.sin(r)
+
+# Plot the surface.
+surf = ax.plot_surface(xx, yy, z, cmap=mpl.cm.coolwarm)
+
+# Customize the z axis.
+ax.set_zlim(-1, 1)
+
+plt.show()
+```
+
+%% Cell type:code id: tags:
+
+``` python
+# Prepare the data.
+n = 250
+x = np.linspace(-5, 5, n)
+y = np.linspace(-5, 5, n)
+x, y = np.meshgrid(x, y)
+r = np.sqrt(x**2 + y**2)
+z = np.sin(r) * 100
+
+# Build the canvas.
+canvas = scene.SceneCanvas(keys='interactive', bgcolor='w')
+
+# Set up the camera.
+view = canvas.central_widget.add_view()
+view.camera = scene.TurntableCamera(up='z', fov=60, scale_factor=2)
+
+# Build the visuals.
+p1 = scene.visuals.SurfacePlot(z=z, color=(0.3, 0.3, 1, 1))
+p1.transform = scene.transforms.MatrixTransform()
+p1.transform.scale([1/249., 1/249., 1/249.])
+p1.transform.translate([-0.5, -0.5, 0])
+view.add(p1)
+xax = scene.Axis(pos=[[-0.5, -0.5], [0.5, -0.5]], tick_direction=(0, -1),
+                 font_size=16, axis_color='k', tick_color='k', text_color='k',
+                 parent=view.scene, axis_label='x')
+xax.transform = scene.STTransform(translate=(0, 0, -0.2))
+yax = scene.Axis(pos=[[-0.5, -0.5], [-0.5, 0.5]], tick_direction=(-1, 0),
+                 font_size=16, axis_color='k', tick_color='k', text_color='k',
+                 parent=view.scene, axis_label='y')
+yax.transform = scene.STTransform(translate=(0, 0, -0.2))
+
+# Add a 3D axis to keep us oriented.
+axis = scene.visuals.XYZAxis(parent=view.scene)
+
+canvas.show()
+app.run()
+```

topics/resources/notebooks/10/vispy-isosurface-mri.py

+# Simplified version of: http://api.vispy.org/en/v0.4.0/examples/basics/scene/volume.html
+
+import sys
+import numpy as np
+from vispy import app, scene
+
+
+# Prepare canvas.
+canvas = scene.SceneCanvas(keys='interactive', size=(800, 600))
+
+# Set up a viewbox to display the image with interactive pan/zoom.
+view = canvas.central_widget.add_view()
+
+# Load MRI data.
+mri = np.load('./mri.npz')['data']
+mri = np.flipud(np.rollaxis(mri, 1))
+surface = scene.visuals.Isosurface(mri,
+                                   # Choose level to visualise as surface.
+                                   level=mri.mean(),
+                                   color=(0.5, 0.6, 1, 1),
+                                   shading='smooth',
+                                   parent=view.scene)
+
+surface.transform = scene.transforms.STTransform(translate=(-100, -100, -100))
+
+cam = scene.cameras.TurntableCamera(parent=view.scene, fov=60, distance=300,
+                                    name='Turntable', elevation=90, azimuth=-80)
+view.camera = cam
+
+
+if __name__ == '__main__':
+    canvas.show()
+    if sys.flags.interactive == 0:
+        app.run()

topics/resources/notebooks/10/vispy-isosurface.py

+# http://api.vispy.org/en/v0.4.0/examples/basics/scene/isosurface.html
+
+import sys
+import numpy as np
+from vispy import app, scene
+
+
+# Create a canvas with a 3D viewport.
+canvas = scene.SceneCanvas()
+view = canvas.central_widget.add_view()
+
+
+# Define a scalar field from which we will generate an isosurface.
+def psi(i, j, k, offset=(25, 25, 50)):
+    x = i-offset[0]
+    y = j-offset[1]
+    z = k-offset[2]
+    th = np.arctan2(z, (x**2+y**2)**0.5)
+    r = (x**2 + y**2 + z**2)**0.5
+    a0 = 1
+    ps = ((1./81.) * 1./(6.*np.pi)**0.5 * (1./a0)**(3/2) * (r/a0)**2 *
+          np.exp(-r/(3*a0)) * (3 * np.cos(th)**2 - 1))
+    return ps
+
+
+data = np.abs(np.fromfunction(psi, (50, 50, 100)))
+
+# Create isosurface visual.
+surface = scene.visuals.Isosurface(data, level=data.max()/4.,
+                                   color=(0.5, 0.6, 1, 1), shading='smooth',
+                                   parent=view.scene)
+surface.transform = scene.transforms.STTransform(translate=(-25, -25, -50))
+
+# Add a 3D axis to keep us oriented.
+axis = scene.visuals.XYZAxis(parent=view.scene)
+
+# Use a 3D camera.
+# Manual bounds; Mesh visual does not provide bounds yet.
+# Note how you can set bounds before assigning the camera to the viewbox.
+cam = scene.TurntableCamera(elevation=30, azimuth=30)
+cam.set_range((-10, 10), (-10, 10), (-10, 10))
+view.camera = cam
+
+
+if __name__ == '__main__':
+    canvas.show()
+    if sys.flags.interactive == 0:
+        app.run()