Fixed weird bug w.r.t. ipynbs created in VS Code, switched ode to odeint

talks/matlab_vs_python/bloch/bloch.ipynb

 %% Cell type:markdown id: tags:
 
 Imports
 
 %% Cell type:code id: tags:
 
 ``` python
 import numpy as np
-from scipy.integrate import ode
+from scipy.integrate import ode, solve_ivp
 import matplotlib.pyplot as plt
 ```
 
 %% Cell type:markdown id: tags:
 
 # Define the Bloch equation
 
 $$\frac{d\vec{M}}{dt} = \vec{M}\times \vec{B} - \frac{M_x + M_y}{T2} - \frac{M_z - M_0}{T1}$$
 
 In this section:
 - define a function
 - numpy functions like np.cross
 
 %% Cell type:code id: tags:
 
 ``` python
 # define bloch equation
-def bloch_ode(t, M, T1, T2):
+def bloch(t, M, T1, T2):
     # get effective B-field at time t
     B = B_eff(t)
     # cross product of M and B, add T1 and T2 relaxation terms
     return np.array([M[1]*B[2] - M[2]*B[1] - M[0]/T2,
                      M[2]*B[0] - M[0]*B[2] - M[1]/T2,
                      M[0]*B[1] - M[1]*B[0] - (M[2]-1)/T1])
     # alternatively
     #return np.cross(M,B) - np.array([M[0]/T2, M[1]/T2, (M[2]-1)/T1])
 ```
 
 %% Cell type:markdown id: tags:
 
 # Define the pulse sequence
 
 We work in the rotating frame, so we only need the amplitude envelope of the RF pulse
 
 Typically, B1 excitation fields point in the x- and/or y-directions
 Gradient fields point in the z-direction
 
 In this simple example, a simple sinc-pulse excitation pulse is applied for 1 ms along the x-axis
 then a gradient is turned on for 1.5 ms after that.
 
 In this section:
 - constants such as np.pi
 - functions like np.sinc
 
 %% Cell type:code id: tags:
 
 ``` python
 # define effective B-field
 def B_eff(t):
     # Do nothing for 0.25 ms
     if t < 0.25:
         return np.array([0, 0, 0])
     # Sinc RF along x-axis and slice-select gradient on for 1.00 ms
     elif t < 1.25:
         return np.array([np.pi*np.sinc((t-0.75)*4), 0, np.pi])
     # Do nothing for 0.25 ms
     elif t < 1.50:
         return np.array([0, 0, 0])
     # Slice refocusing gradient on for 1.50 ms
     # Half the area of the slice-select gradient lobe
     elif t < 3.00:
         return np.array([0, 0, -(1/3)*np.pi])
     # Pulse sequence finished
     else:
         return np.array([0, 0, 0])
 ```
 
 %% Cell type:markdown id: tags:
 
 # Plot the pulse sequence
 
 In this section:
 - unpacking return values
 - unwanted return values
 - list comprehension
 - basic plotting
 
 %% Cell type:code id: tags:
 
 ``` python
 # Create 2 vertical subplots
 _, ax = plt.subplots(2, 1, figsize=(12,12))
 
 # Get pulse sequence B-fields from 0 - 5 ms
 pulseq = [B_eff(t) for t in np.linspace(0,5,1000)]
 pulseq = np.array(pulseq)
 
 # Plot RF
 ax[0].plot(pulseq[:,0])
 ax[0].set_ylabel('B1')
 
 # Plot gradient
 ax[1].plot(pulseq[:,2])
 ax[1].set_ylabel('Gradient')
 ```
 
 %% Cell type:markdown id: tags:
 
 # Integrate ODE
 
-This uses a Runge-Kutta variant called the "Dormand-Prince method"
+This uses a Runge-Kutta variant called the "Dormand-Prince method" by default. Other ode integration methods are available.
 
 In this section:
-- list of arrays
 - ode solvers
-- list appending
+- lambdas (anonymous functions)
 
 %% Cell type:code id: tags:
 
 ``` python
 # Set the initial conditions
-# time (t) = 0
 # equilibrium magnetization (M) = (0, 0, 1)
-t = [0]
-M = [np.array([0, 0, 1])]
+M = [0, 0, 1]
 
-# Set integrator time-step
-dt= 0.005
+# Set time interval for integration
+t = [0, 5]
 
-# Set up ODE integrator object
-r = ode(bloch_ode)
-
-# Choose the integrator method
-r.set_integrator('dopri5')
-
-# Pass in initial values
-r.set_initial_value(M[0], t[0])
+# Set max step size
+dt = 0.005
 
 # Set T1 and T2
 T1, T2 = 1500, 50
-r.set_f_params(T1, T2)
 
-# Integrate by looping over time, moving dt by step size each iteration
-# Append new time point and Magnetisation vector at every step to t and M
-while r.successful() and r.t < 5:
-    t.append(r.t + dt)
-    M.append(r.integrate(t[-1]))
+# Integrate ODE
+# In Scipy 1.2.0, the first argument to solve_ivp must be a function that takes exactly 2 arguments
+sol = solve_ivp(lambda t, M : bloch(t, M, T1, T2), t, M, max_step=dt)
 
-# Convert M to 2-D numpy array from list of arrays
-M = np.array(M)
+# Grab output
+t = sol.t
+M = sol.y
 ```
 
 %% Cell type:markdown id: tags:
 
 # Plot Results
 
 In this section:
 - more plotting
 
 %% Cell type:code id: tags:
 
 ``` python
 # Create single axis
 _, ax = plt.subplots(figsize=(12,12))
 
 # Plot x, y and z components of Magnetisation
-ax.plot(t, M[:,0], label='Mx')
-ax.plot(t, M[:,1], label='My')
-ax.plot(t, M[:,2], label='Mz')
+ax.plot(t, M[0,:], label='Mx')
+ax.plot(t, M[1,:], label='My')
+ax.plot(t, M[2,:], label='Mz')
 
 # Add legend and grid
 ax.legend()
 ax.grid()
 ```

talks/matlab_vs_python/partial_fourier/partial_fourier.ipynb

@@ -2,9 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "Imports"
    ]
@@ -22,9 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Load data\n",
     "\n",
@@ -57,9 +53,7 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# 6/8 Partial Fourier sampling\n",
     "\n",
@@ -91,9 +85,7 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Estimate phase\n",
     "\n",
@@ -130,9 +122,7 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# POCS reconstruction\n",
     "\n",
@@ -192,9 +182,7 @@
   },
   {
    "cell_type": "markdown",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Display error and plot reconstruction\n",
     "\n",
@@ -252,9 +240,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3-final"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
\ No newline at end of file
+}