#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (c) 2017-2020 Johan Berglund
# BlochBuster is distributed under the terms of the GNU General Public License
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
BlochBuster is a nuclear magnetic resonance Bloch equation simulator written in Python.
It simulates magnetization vectors based on the Bloch equations, including precession, relaxation, and excitation.
BlochBuster outputs animated gif or mp4 files, which can be 3D plots of the magnetization vectors, plots of transverse and longitudinal magnetization, or pulse sequence diagrams.
Input paramaters are provided by human readable configuration files.
The animations are made using ffmpeg.
'''
import mpl_toolkits.mplot3d.art3d as art3d
from mpl_toolkits.mplot3d import proj3d
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.patches import Circle, Rectangle
from matplotlib.patches import FancyArrowPatch
import numpy as np
from numbers import Number
import scipy.integrate as integrate
from scipy.stats import norm
import os.path
import shutil
import argparse
import yaml
import FFMPEGwriter
colors = { 'bg': [1,1,1],
'circle': [0,0,0,.03],
'axis': [.5,.5,.5],
'text': [.05,.05,.05],
'spoilText':[.5,0,0],
'RFtext': [0,.5,0],
'Gtext': [80/256,80/256,0],
'comps': [ [.3,.5,.2],
[.1,.4,.5],
[.5,.3,.2],
[.5,.4,.1],
[.4,.1,.5],
[.6,.1,.3]],
'boards': { 'w1': [.5,0,0],
'Gx': [0,.5,0],
'Gy': [0,.5,0],
'Gz': [0,.5,0]
},
'kSpacePos': [1, .5, 0]
}
class Arrow3D(FancyArrowPatch):
'''Matplotlib FancyArrowPatch for 3D rendering.'''
def __init__(self, xs, ys, zs, *args, **kwargs):
FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
self._verts3d = xs, ys, zs
def draw(self, renderer):
xs3d, ys3d, zs3d = self._verts3d
xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
FancyArrowPatch.draw(self, renderer)
def plotFrame3D(config, vectors, frame, output):
'''Creates a plot of magnetization vectors in a 3D view.
Args:
config: configuration dictionary.
vectors: numpy array of size [nx, ny, nz, nComps, nIsochromats, 3, nFrames].
frame: which frame to plot.
output: specification of desired output (dictionary from config).
Returns:
plot figure.
'''
nx, ny, nz, nComps, nIsoc = vectors.shape[:5]
# Create 3D axes
if nx*ny*nz==1 or config['collapseLocations']:
aspect = .952 # figure aspect ratio
elif nz==1 and ny==1 and nx>1:
aspect = 0.6
elif nz==1 and nx>1 and ny>1:
aspect = .75
else:
aspect = 1
figSize = 5 # figure size in inches
canvasWidth = figSize
canvasHeight = figSize*aspect
fig = plt.figure(figsize=(canvasWidth, canvasHeight), dpi=output['dpi'])
axLimit = max(nx,ny,nz)/2+.5
if config['collapseLocations']:
axLimit = 1.0
ax = fig.gca(projection='3d', xlim=(-axLimit,axLimit), ylim=(-axLimit,axLimit), zlim=(-axLimit,axLimit), fc=colors['bg'])
if nx*ny*nz>1 and not config['collapseLocations']:
azim = -78 # azimuthal angle of x-y-plane
ax.view_init(azim=azim) #ax.view_init(azim=azim, elev=elev)
ax.set_axis_off()
width = 1.65 # to get tight cropping
height = width/aspect
left = (1-width)/2
bottom = (1-height)/2
if nx*ny*nz==1 or config['collapseLocations']: # shift to fit legend
left += .035
bottom += -.075
else:
bottom += -.085
ax.set_position([left, bottom, width, height])
if output['drawAxes']:
# Draw axes circles
for i in ["x", "y", "z"]:
circle = Circle((0, 0), 1, fill=True, lw=1, fc=colors['circle'])
ax.add_patch(circle)
art3d.pathpatch_2d_to_3d(circle, z=0, zdir=i)
# Draw x, y, and z axes
ax.plot([-1, 1], [0, 0], [0, 0], c=colors['axis'], zorder=-1) # x-axis
ax.text(1.08, 0, 0, r'$x^\prime$', horizontalalignment='center', color=colors['text'])
ax.plot([0, 0], [-1, 1], [0, 0], c=colors['axis'], zorder=-1) # y-axis
ax.text(0, 1.12, 0, r'$y^\prime$', horizontalalignment='center', color=colors['text'])
ax.plot([0, 0], [0, 0], [-1, 1], c=colors['axis'], zorder=-1) # z-axis
ax.text(0, 0, 1.05, r'$z$', horizontalalignment='center', color=colors['text'])
# Draw title:
fig.text(.5, 1, config['title'], fontsize=14, horizontalalignment='center', verticalalignment='top', color=colors['text'])
# Draw time
time = config['tFrames'][frame%(len(config['t'])-1)] # frame time [msec]
time_text = fig.text(0, 0, 'time = %.1f msec' % (time), color=colors['text'], verticalalignment='bottom')
# TODO: put isochromats in this order from start
order = [int((nIsoc-1)/2-abs(m-(nIsoc-1)/2)) for m in range(nIsoc)]
thres = 0.075*axLimit # threshold on vector magnitude for shrinking
if 'rotate' in output:
rotFreq = output['rotate'] * 1e-3 # coordinate system rotation relative resonance frequency [kHz]
rotMat = rotMatrix(2 * np.pi * rotFreq * time, 2) # rotation matrix for rotating coordinate system
pos = [0,0,0]
# Draw magnetization vectors
for z in range(nz):
for y in range(ny):
for x in range(nx):
for c in range(nComps):
for m in range(nIsoc):
col = colors['comps'][(c) % len(colors['comps'])]
M = vectors[x,y,z,c,m,:3,frame]
if not config['collapseLocations']:
pos = vectors[x,y,z,c,m,3:,frame]/config['locSpacing']
if 'rotate' in output:
M = np.dot(M, rotMat) # rotate vector relative to coordinate system
Mnorm = np.linalg.norm(M)
alpha = 1.-2*np.abs((m+.5)/nIsoc-.5)
if Mnorm>thres:
arrowScale = 20
else:
arrowScale = 20*Mnorm/thres # Shrink arrowhead close to origo
ax.add_artist(Arrow3D( [pos[0], pos[0]+M[0]],
[-pos[1], -pos[1]+M[1]],
[-pos[2], -pos[2]+M[2]],
mutation_scale=arrowScale,
arrowstyle='-|>', shrinkA=0, shrinkB=0, lw=2,
color=col, alpha=alpha,
zorder=order[m]+nIsoc*int(100*(1-Mnorm))))
# Draw "spoiler" and "FA-pulse" text
fig.text(1, .94, config['RFtext'][frame], fontsize=14, alpha=config['RFalpha'][frame],
color=colors['RFtext'], horizontalalignment='right', verticalalignment='top')
fig.text(1, .88, config['Gtext'][frame], fontsize=14, alpha=config['Galpha'][frame],
color=colors['Gtext'], horizontalalignment='right', verticalalignment='top')
fig.text(1, .82, config['spoiltext'], fontsize=14, alpha=config['spoilAlpha'][frame],
color=colors['spoilText'], horizontalalignment='right', verticalalignment='top')
# Draw legend:
for c in range(nComps):
col = colors['comps'][(c) % len(colors['comps'])]
ax.plot([0, 0], [0, 0], [0, 0], '-', lw=2, color=col, alpha=1.,
label=config['components'][c]['name'])
handles, labels = ax.get_legend_handles_labels()
leg = fig.legend([plt.Line2D((0, 1), (0, 0), lw=2, color=colors['comps'][(c) %
len(colors['comps'])]) for c, handle in enumerate(
handles)], labels, loc=2, bbox_to_anchor=[
-.025, .94])
leg.draw_frame(False)
for text in leg.get_texts():
text.set_color(colors['text'])
return fig
def plotFrameMT(config, signal, frame, output):
'''Creates a plot of transversal or longituinal magnetization over time.
Args:
config: configuration dictionary.
signal: numpy array of size [nComps, 3, nFrames].
frame: which frame to plot up to.
output: specification of desired output (dictionary from config).
Returns:
plot figure.
'''
if output['type'] not in ['xy', 'z']:
raise Exception('output "type" must be 3D, kspace, psd, xy (transversal) or z (longitudinal)')
# create diagram
xmin, xmax = output['tRange']
if output['type'] == 'xy':
if 'abs' in output and not output['abs']:
ymin, ymax = -1, 1
else:
ymin, ymax = 0, 1
elif output['type'] == 'z':
ymin, ymax = -1, 1
fig = plt.figure(figsize=(5, 2.7), facecolor=colors['bg'], dpi=output['dpi'])
ax = fig.gca(xlim=(xmin, xmax), ylim=(ymin, ymax), fc=colors['bg'])
for side in ['bottom', 'right', 'top', 'left']:
ax.spines[side].set_visible(False) # remove default axes
ax.grid()
plt.title(config['title'], color=colors['text'])
plt.xlabel('time[ms]', horizontalalignment='right', color=colors['text'])
if output['type'] == 'xy':
if 'abs' in output and not output['abs']:
ax.xaxis.set_label_coords(1.1, .475)
plt.ylabel('$M_x, M_y$', rotation=0, color=colors['text'])
else: # absolute value of transversal magnetization
ax.xaxis.set_label_coords(1.1, .1)
plt.ylabel('$|M_{xy}|$', rotation=0, color=colors['text'])
elif output['type'] == 'z':
ax.xaxis.set_label_coords(1.1, .475)
plt.ylabel('$M_z$', rotation=0, color=colors['text'])
ax.yaxis.set_label_coords(-.07, .95)
plt.tick_params(axis='y', labelleft='off')
plt.tick_params(axis='x', colors=colors['text'])
ax.xaxis.set_ticks_position('none') # tick markers
ax.yaxis.set_ticks_position('none')
# draw x and y axes as arrows
bbox = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
width, height = bbox.width, bbox.height # get width and height of axes object
hw = 1/25*(ymax-ymin) # manual arrowhead width and length
hl = 1/25*(xmax-xmin)
yhw = hw/(ymax-ymin)*(xmax-xmin) * height/width # compute matching arrowhead length and width
yhl = hl/(xmax-xmin)*(ymax-ymin) * width/height
ax.arrow(xmin, 0, (xmax-xmin)*1.05, 0, fc=colors['text'], ec=colors['text'], lw=1, head_width=hw, head_length=hl, clip_on=False, zorder=100)
ax.arrow(xmin, ymin, 0, (ymax-ymin)*1.05, fc=colors['text'], ec=colors['text'], lw=1, head_width=yhw, head_length=yhl, clip_on=False, zorder=100)
# Draw magnetization vectors
nComps = signal.shape[0]
if output['type'] == 'xy':
for c in range(nComps):
col = colors['comps'][c % len(colors['comps'])]
if 'abs' in output and not output['abs']: # real and imag part of transversal magnetization
ax.plot(config['tFrames'][:frame+1], signal[c,0,:frame+1], '-', lw=2, color=col)
col = colors['comps'][c+nComps+1 % len(colors['comps'])]
ax.plot(config['tFrames'][:frame+1], signal[c,1,:frame+1], '-', lw=2, color=col)
else: # absolute value of transversal magnetization
ax.plot(config['tFrames'][:frame+1], np.linalg.norm(signal[c,:2,:frame+1], axis=0), '-', lw=2, color=col)
# plot sum component if both water and fat (special case)
if all(key in [comp['name'] for comp in config['components']] for key in ['water', 'fat']):
col = colors['comps'][nComps % len(colors['comps'])]
if 'abs' in output and not output['abs']: # real and imag part of transversal magnetization
ax.plot(config['tFrames'][:frame+1], np.mean(signal[:,0,:frame+1],0), '-', lw=2, color=col)
col = colors['comps'][2*nComps+1 % len(colors['comps'])]
ax.plot(config['tFrames'][:frame+1], np.mean(signal[:,1,:frame+1],0), '-', lw=2, color=col)
else: # absolute value of transversal magnetization
ax.plot(config['tFrames'][:frame+1], np.linalg.norm(np.mean(signal[:,:2,:frame+1],0), axis=0), '-', lw=2, color=col)
elif output['type'] == 'z':
for c in range(nComps):
col = colors['comps'][(c) % len(colors['comps'])]
ax.plot(config['tFrames'][:frame+1], signal[c,2,:frame+1], '-', lw=2, color=col)
return fig
def plotFrameKspace(config, frame, output):
'''Creates a plot of k-space position for the given frame.
Args:
config: configuration dictionary.
frame: which frame to plot.
output: specification of desired output (dictionary from config).
Returns:
plot figure.
'''
#TODO: support for 3D k-space
kmax = 1/(2*config['locSpacing'])
xmin, xmax = -kmax, kmax
ymin, ymax = -kmax, kmax
fig = plt.figure(figsize=(5, 5), facecolor=colors['bg'], dpi=output['dpi'])
ax = fig.gca(xlim=(xmin, xmax), ylim=(ymin, ymax), fc=colors['bg'])
for side in ['bottom', 'right', 'top', 'left']:
ax.spines[side].set_color(colors['text'])
ax.grid()
plt.title(config['title'], color=colors['text'])
plt.xlabel('$k_x$ [m$^{-1}$]', horizontalalignment='right', color=colors['text'])
plt.ylabel('$k_y$ [m$^{-1}$]', rotation=0, color=colors['text'])
plt.tick_params(axis='y', colors=colors['text'])
plt.tick_params(axis='x', colors=colors['text'])
frameTime = config['tFrames'][frame]%config['TR']
kx, ky, kz = 0, 0, 0
for i, event in enumerate(config['events']):
firstFrame, lastFrame = getEventFrames(config, i)
if event['t'] < frameTime:
dur = min(frameTime, config['t'][lastFrame])-config['t'][firstFrame]
if 'spoil' in event and event['spoil']:
kx, ky, kz = 0, 0, 0
kx += gyro * event['Gx'] * dur / 1e3
ky += gyro * event['Gy'] * dur / 1e3
kz += gyro * event['Gz'] * dur / 1e3
else:
break
ax.plot(kx, ky, '.', markersize=10, color=colors['kSpacePos'])
return fig
def plotFramePSD(config, frame, output):
'''Creates a plot of the pulse sequence diagram.
Args:
config: configuration dictionary.
frame: which frame to indicate by vertical line.
output: specification of desired output (dictionary from config).
Returns:
plot figure.
'''
if 'fig' in output:
fig, timeLine = output['fig']
else:
xmin, xmax = output['tRange']
ymin, ymax = 0, 5
fig = plt.figure(figsize=(5, 5), facecolor=colors['bg'], dpi=output['dpi'])
ax = fig.gca(xlim=(xmin, xmax), ylim=(ymin, ymax), fc=colors['bg'])
for side in ['bottom', 'right', 'top', 'left']:
ax.spines[side].set_visible(False) # remove default axes
plt.title(config['title'], color=colors['text'])
plt.xlabel('time[ms]', horizontalalignment='right', color=colors['text'])
plt.tick_params(axis='y', labelleft='off')
plt.tick_params(axis='x', colors=colors['text'])
ax.xaxis.set_ticks_position('none') # tick markers
ax.yaxis.set_ticks_position('none')
# draw x axis as arrow
bbox = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
width, height = bbox.width, bbox.height # get width and height of axes object
hw = 1/25*(ymax-ymin) # manual arrowhead width and length
hl = 1/25*(xmax-xmin)
yhw = hw/(ymax-ymin)*(xmax-xmin) * height/width # compute matching arrowhead length and width
yhl = hl/(xmax-xmin)*(ymax-ymin) * width/height
ax.arrow(xmin, 0, (xmax-xmin)*1.05, 0, fc=colors['text'], ec=colors['text'], lw=1, head_width=hw, head_length=hl, clip_on=False, zorder=100)
boards = {'w1': {'ypos': 4}, 'Gx': {'ypos': 3}, 'Gy': {'ypos': 2}, 'Gz': {'ypos': 1}}
for board in boards:
boards[board]['signal'] = [0]
t = [0]
for event in config['events']:
for board in boards:
boards[board]['signal'].append(boards[board]['signal'][-1]) # end of previous event:
boards[board]['signal'].append(event[board]) # start of this event:
t.append(event['t']) # end of previous event:
t.append(event['t']) # start of this event:
boards['w1']['scale'] = 0.48 / np.max([np.abs(w) for w in boards['w1']['signal'] if np.abs(w) < 50])
if 'gmax' not in output:
output['gmax'] = np.max(np.abs(np.concatenate((boards['Gx']['signal'], boards['Gy']['signal'], boards['Gz']['signal']))))
boards['Gx']['scale'] = boards['Gy']['scale'] = boards['Gz']['scale'] = 0.48 / output['gmax']
for board in ['w1', 'Gx', 'Gy', 'Gz']:
ax.plot(t, boards[board]['ypos'] + np.array(boards[board]['signal']) * boards[board]['scale'], lw=1, color=colors['boards'][board])
ax.plot([xmin, xmax], [boards[board]['ypos'], boards[board]['ypos']], color=colors['text'], lw=1, clip_on=False, zorder=100)
ax.text(0, boards[board]['ypos'], board, fontsize=14,
color=colors['text'], horizontalalignment='right', verticalalignment='center')
# plot vertical time line:
timeLine, = ax.plot([config['tFrames'][frame]%config['TR'], config['tFrames'][frame]%config['TR']], [0, 5], color=colors['text'], lw=1, clip_on=False, zorder=100)
output['fig'] = fig, timeLine
timeLine.set_xdata([config['tFrames'][frame]%config['TR'], config['tFrames'][frame]%config['TR']])
fig.canvas.draw()
return fig
# Apply spoiling of the transversal magnetization
def spoil(M):
'''Spoil the transversal magnetization in magnetization vector.
Args:
M: magnetization vector, numpy array of size 3.
Returns:
spoiled magnetization vector, numpy array of size 3.
'''
return np.array([0, 0, M[2]])
def derivs(M, t, Meq, w, w1, T1, T2):
'''Bloch equations in rotating frame.
Args:
w: Larmor frequency :math:`2\\pi\\gamma B_0` [kRad / s].
w1 (complex): B1 rotation frequency :math:`2\\pi\\gamma B_1` [kRad / s].
T1: longitudinal relaxation time.
T2: transverse relaxation time.
M: magnetization vector.
Meq: equilibrium magnetization.
t: time vector (needed for scipy.integrate.odeint).
Returns:
integrand :math:`\\frac{dM}{dt}`
'''
dMdt = np.zeros_like(M)
dMdt[0] = -M[0]/T2+M[1]*w+M[2]*w1.real
dMdt[1] = -M[0]*w-M[1]/T2+M[2]*w1.imag
dMdt[2] = -M[0]*w1.real-M[1]*w1.imag+(Meq-M[2])/T1
return dMdt
def getEventFrames(config, i):
'''Get first and last frame of event i in config['events'] in terms of config['t']
Args:
config: configuration dictionary.
i: event index
Returns:
firstFrame: index of first frame in terms of config['t']
lastFrame: index of last frame in terms of config['t']
'''
try:
firstFrame = np.where(config['t']==config['events'][i]['t'])[0][0]
except IndexError:
print('Event time not found in time vector')
raise
if i < len(config['events'])-1:
nextEventTime = config['events'][i+1]['t']
else:
nextEventTime = config['TR']
try:
lastFrame = np.where(config['t']==nextEventTime)[0][0]
except IndexError:
print('Event time not found in time vector')
raise
return firstFrame, lastFrame
def applyPulseSeq(config, Meq, M0, w, T1, T2, pos0, v, D):
'''Simulate magnetization vector during nTR (+nDummies) applications of pulse sequence.
Args:
config: configuration dictionary.
Meq: equilibrium magnetization along z axis.
M0: initial state of magnetization vector, numpy array of size 3.
w: Larmor frequency :math:`2\\pi\\gamma B_0` [kRad/s].
T1: longitudinal relaxation time.
T2: transverse relaxation time.
pos0: position (x,y,z) of magnetization vector at t=0 [m].
v: velocity (x,y,z) of spins [mm/s]
D: diffusivity (x,y,z) of spins [:math:`mm^2/s`]
Returns:
magnetization vector over time, numpy array of size [6, nFrames]. 1:3 are magnetization, 4:6 are position
'''
M = np.zeros([len(config['t']), 3])
M[0] = M0 # Initial state
pos = np.tile(pos0, [len(config['t']), 1]) # initial position
if np.linalg.norm(D) > 0: # diffusion contribution
for frame in range(1,len(config['t'])):
dt = config['t'][frame] - config['t'][frame-1]
for dim in range(3):
pos[frame][dim] = pos[frame-1][dim] + norm.rvs(scale=np.sqrt(D[dim]*dt*1e-9)) # standard deviation in meters
if config['t'][frame]==0: # reset position for t=0
pos[:frame+1] += np.tile(pos0 - pos[frame], [frame+1, 1])
if np.linalg.norm(v) > 0: # velocity contribution
pos += np.outer(config['t'], v) * 1e-6
for rep in range(-config['nDummies'], config['nTR']): # dummy TRs get negative frame numbers
TRstartFrame = rep * config['nFramesPerTR']
for i, event in enumerate(config['events']):
firstFrame, lastFrame = getEventFrames(config, i)
firstFrame += TRstartFrame
lastFrame += TRstartFrame
M0 = M[firstFrame]
if 'spoil' in event and event['spoil']: # Spoiler event
M0 = spoil(M0)
# frequency due to w plus any gradients
# (use position at firstFrame, i.e. approximate no motion during frame)
wg = w
wg += 2*np.pi*gyro*event['Gx']*pos[firstFrame, 0]/1000 # [kRad/s]
wg += 2*np.pi*gyro*event['Gy']*pos[firstFrame, 1]/1000 # [kRad/s]
wg += 2*np.pi*gyro*event['Gz']*pos[firstFrame, 2]/1000 # [kRad/s]
w1 = event['w1'] * np.exp(1j * np.radians(event['phase']))
t = config['t'][firstFrame:lastFrame+1]
if len(t)==0:
raise Exception("Corrupt config['events']")
M[firstFrame:lastFrame+1] = integrate.odeint(derivs, M0, t, args=(Meq, wg, w1, T1, T2)) # Solve Bloch equation
return np.concatenate((M, pos),1).transpose()
def simulateComponent(config, component, Meq, M0=None, pos=None):
''' Simulate nIsochromats magnetization vectors per component with uniform distribution of Larmor frequencies.
Args:
config: configuration dictionary.
component: component specification from config.
Meq: equilibrium magnetization along z axis.
M0: initial state of magnetization vector, numpy array of size 3.
pos: position (x,y,z) of magnetization vector [m].
Returns:
component magnetization vectors over time, numpy array of size [nIsochromats, 6, nFrames]. 1:3 are magnetization, 4:6 are position.
'''
if not M0:
M0 = [0, 0, Meq] # Default initial state is equilibrium magnetization
if not pos:
pos = [0, 0, 0]
v = [component['vx'], component['vy'], component['vz']]
D = [component['Dx'], component['Dy'], component['Dz']]
# Shifts in ppm for dephasing vectors:
isochromats = [(2*i+1-config['nIsochromats'])/2*config['isochromatStep']+component['CS'] for i in range(0, config['nIsochromats'])]
comp = np.empty((config['nIsochromats'],6,len(config['t'])))
for m, isochromat in enumerate(isochromats):
w = config['w0']*isochromat*1e-6 # Demodulated frequency [kRad / s]
comp[m,:,:] = applyPulseSeq(config, Meq, M0, w, component['T1'], component['T2'], pos, v, D)
return comp
def getText(config):
''' Get opacity and display text pulseSeq event text flashes in 3D plot and store in config.
Args:
config: configuration dictionary.
'''
# Setup display text related to pulseSeq events:
config['RFtext'] = np.full([len(config['t'])], '', dtype=object)
config['Gtext'] = np.full([len(config['t'])], '', dtype=object)
config['spoiltext'] = 'spoiler'
config['RFalpha'] = np.zeros([len(config['t'])])
config['Galpha'] = np.zeros([len(config['t'])])
config['spoilAlpha'] = np.zeros([len(config['t'])])
for rep in range(config['nTR']):
TRstartFrame = rep * config['nFramesPerTR']
for i, event in enumerate(config['events']):
firstFrame, lastFrame = getEventFrames(config, i)
firstFrame += TRstartFrame
lastFrame += TRstartFrame
if 'RFtext' in event:
config['RFtext'][firstFrame:] = event['RFtext']
config['RFalpha'][firstFrame:lastFrame+1] = 1.0
if any('{}text'.format(g) in event for g in ['Gx', 'Gy', 'Gz']): # gradient event
Gtext = ''
for g in ['Gx', 'Gy', 'Gz']:
if '{}text'.format(g) in event:
Gtext += ' ' + event['{}text'.format(g)]
config['Gtext'][firstFrame:] = Gtext
config['Galpha'][firstFrame:lastFrame+1] = 1.0
if 'spoil' in event and event['spoil']:
config['spoilAlpha'][firstFrame] = 1.0
def roundEventTime(time):
''' Round off time to certain precision.
Args:
time: time to be rounded [ms]
Returns:
rounded time
'''
return np.round(time, decimals=6) # nanosecond precision should be enough
def addEventsToTimeVector(t, pulseSeq):
''' Read event times from pulseSeq struct and add to input time vector.
Args:
t: input time vector [ms]
pulseSeq: pulse sequence struct of events with event times [ms]
Returns:
Array of unique sorted set of times in input time vector and event times.
'''
t = list(t)
for event in pulseSeq:
t.append(event['t'])
return np.unique(roundEventTime(np.array(t)))
def calculateFA(B1, dur):
''' Calculate flip angle for given B1 waveform and duration.
Args:
B1: vector of B1 amplitudes [uT]
dur: duration of pulse [ms]
Returns:
Pulse flip angle
'''
dwell = dur / len(B1)
FA = 0
for b in B1:
FA += 360*(dwell * gyro * np.real(b) * 1e-6)
return FA
def loadGradfromFile(filename):
''' Read gradient waveform from file and return as list. The file is expected to contain a yaml list of the gradient in mT/m, or a field 'grad' holding such a list.
Args:
filename: filename of gradient yaml file.
Returns:
Gradient waveform as a list
'''
with open(filename, 'r') as f:
try:
grad = yaml.safe_load(f)
except yaml.YAMLError as exc:
raise Exception('Error reading gradient file {}'.format(filename)) from exc
if 'grad' in grad:
grad = grad['grad']
if isinstance(grad, list) and len(grad)>0 and isinstance(grad[0], Number):
return grad
else:
raise Exception('Error reading gradient file {}. File must contain a yaml list of numbers.'.format(filename))
def isNumList(obj):
''' Check if object is non-empty list of numbers.
Args:
obj: object to be checked
Returns:
true or false
'''
return isinstance(obj, list) and len(obj)>0 and isinstance(obj[0], Number)
def RFfromStruct(RF):
''' Read RF pulse from struct and return as array.
Args:
RF: list of the RF amplitude, or a struct with key 'amp' and optionally 'phase', each containing a list of equal length. amp is the RF amplitude [uT], and 'phase' is RF phase modulation [degrees].
Returns:
RF pulse as a (possibly complex) numpy array
'''
if isNumList(RF):
B1 = np.array(RF)
elif 'amp' in RF and isNumList(RF['amp']):
B1 = np.array(RF['amp'])
if 'phase' in RF:
if not isNumList(RF['phase']):
raise Exception("'phase' of RF struct must be numerical list")
elif len(RF['phase']) != len(B1):
raise Exception("'amp' and 'phase' of RF struct must have equal length")
B1 = B1 * np.exp(1j*np.radians(RF['phase']))
else:
raise Exception('Unknown format of RF struct')
return B1
def loadRFfromFile(filename):
''' Read RF pulse from file and return as array. The file is expected to contain a yaml list of the RF amplitude, or a list containing two lists, where the second holds the RF phase in degrees.
Args:
filename: filename of RF yaml file.
Returns:
RF pulse as a numpy array (complex if phase was given)
'''
with open(filename, 'r') as f:
try:
RFstruct = yaml.safe_load(f)
except yaml.YAMLError as exc:
raise Exception('Error reading RF file {}'.format(filename)) from exc
return RFfromStruct(RFstruct)
def checkPulseSeq(config):
''' Check/verify pulse sequence given by config.
Args:
config: configuration dictionary.
'''
if 'pulseSeq' not in config:
config['pulseSeq'] = []
allowedKeys = ['t', 'spoil', 'dur', 'FA', 'B1', 'phase', 'Gx', 'Gy', 'Gz']
for event in config['pulseSeq']:
for item in event.keys(): # allowed keys
if item not in allowedKeys:
raise Exception('PulseSeq key "{}" not supported'.format(item))
if not 't' in event:
raise Exception('All pulseSeq events must have an event time "t"')
if not any([key in event for key in ['FA', 'B1', 'Gx', 'Gy', 'Gz', 'spoil']]):
raise Exception('Empty events not allowed')
if event['t'] > config['TR']:
raise Exception('pulseSeq event t exceeds TR')
if 'spoil' in event: # Spoiler event
if not event['spoil']:
raise Exception('Spoiler event must have spoil: true')
if any([key not in ['t', 'spoil'] for key in event]):
raise Exception('Spoiler event should only have event time t and spoil: true')
event['spoiltext'] = 'spoiler'
else:
if 'dur' not in event:
raise Exception('All pulseSeq events except spoiler events must have a duration dur [msec]')
if roundEventTime(event['dur'])==0:
raise Exception('Event duration is too short')
if (event['t'] + event['dur']) > config['TR']:
raise Exception('pulseSeq event t+dur exceeds TR')
if 'phase' in event:
if not isinstance(event['phase'], Number):
raise Exception('Event phase [degrees] must be numeric')
if not ('FA' in event or 'B1' in event):
raise Exception('Only RF events can have a phase')
if 'FA' in event or 'B1' in event: # RF-pulse event (possibly with gradient)
# combinations not allowed:
if 'B1' in event and not 'dur' in event:
raise Exception('RF-pulse must provide "dur" along with "B1"')
if 'B1' in event:
if isinstance(event['B1'], Number):
event['B1'] = np.array([event['B1']])
elif isinstance(event['B1'], str):
event['B1'] = loadRFfromFile(event['B1'])
else:
event['B1'] = RFfromStruct(event['B1'])
# calculate FA prescribed by B1
if 'B1' in event:
calcFA = calculateFA(event['B1'], event['dur'])
# calculate B1 or scale it to get prescribed FA
if 'FA' in event:
if 'B1' not in event:
event['B1'] = np.array([event['FA']/(event['dur'] * 360 * gyro * 1e-6)])
else:
event['B1'] = event['B1'] * event['FA'] / calcFA # scale B1 to get prescribed FA
else:
event['FA'] = calcFA
event['w1'] = [2 * np.pi * gyro * B1 * 1e-6 for B1 in event['B1']] # kRad / s
event['RFtext'] = str(int(abs(event['FA'])))+u'\N{DEGREE SIGN}'+'-pulse'
if any([key in event for key in ['Gx', 'Gy', 'Gz']]): # Gradient (no RF)
if not ('dur' in event and event['dur']>0):
raise Exception('Gradient must have a specified duration>0 (dur [ms])')
for g in ['Gx', 'Gy', 'Gz']:
if g in event:
if isinstance(event[g], dict) and 'file' in event[g] and 'amp' in event[g]:
grad = loadGradfromFile(event[g]['file'])
event[g] = list(np.array(grad) / np.max(grad) * event[g]['amp'])
elif not isinstance(event[g], Number) and not (isinstance(event[g], list) and len(event[g])>0):
raise Exception('Unknown type {} for B1'.format(type(event[g])))
# Sort pulseSeq according to event time
config['pulseSeq'] = sorted(config['pulseSeq'], key=lambda event: event['t'])
# split any pulseSeq events with array values into separate events
config['separatedPulseSeq'] = []
for event in config['pulseSeq']:
arrLengths = [len(event[key]) for key in ['w1', 'Gx', 'Gy', 'Gz'] if key in event and isinstance(event[key], list)]
if len(arrLengths) > 0: # arrays in event
arrLength = np.max(arrLengths)
if len(set(arrLengths))==2 and 1 in set(arrLengths):
# extend any singleton arrays to full length
for key in ['w1', 'Gx', 'Gy', 'Gz']:
if key in event and isinstance(event[key], list) and len(event[key])==1:
event[key] *= arrLength
elif len(set(arrLengths))>1:
raise Exception('If w1, Gx, Gy, Gz of an event are provided as lists, equal length is required')
for i, t in enumerate(np.linspace(event['t'], event['t'] + event['dur'], arrLength, endpoint=False)):
subDur = event['dur'] / arrLength
subEvent = {'t': t, 'dur': subDur}
if i==0 and spoil in event:
subEvent['spoil'] = event['spoil']
for key in ['w1', 'Gx', 'Gy', 'Gz', 'phase', 'RFtext']:
if key in event:
if type(event[key]) is list:
if i < len(event[key]):
subEvent[key] = event[key][i]
else:
raise Exception('Length of {} does not match other event properties'.format(key))
else:
subEvent[key] = event[key]
if key in ['Gx', 'Gy', 'Gz']:
subEvent['{}text'.format(key)] = '{}: {:2.0f} mT/m'.format(key, subEvent[key])
config['separatedPulseSeq'].append(subEvent)
else:
for key in ['Gx', 'Gy', 'Gz']:
if key in event:
event['{}text'.format(key)] = '{}: {:2.0f} mT/m'.format(key, event[key])
config['separatedPulseSeq'].append(event)
# Sort separatedPulseSeq according to event time
config['separatedPulseSeq'] = sorted(config['separatedPulseSeq'], key=lambda event: event['t'])
def emptyEvent():
''' Creates empty pulse sequence event.
Returns:
"empty" pulse sequence event
'''
return {'w1': 0, 'Gx': 0, 'Gy': 0, 'Gz': 0, 'phase': 0, 'spoil': False}
def mergeEvent(event, event2merge, t):
''' Merge events by adding w1, Gx, Gy, Gz, phase and updating event texts. Also update event time t.
Args:
event: original event
event2merge: event to be merged
t: new event time
Returns:
Merged event
'''
for channel in ['w1', 'Gx', 'Gy', 'Gz', 'phase']:
if channel in event2merge:
event[channel] += event2merge[channel]
for text in ['RFtext', 'Gxtext', 'Gytext', 'Gztext', 'spoilText']:
if text in event2merge:
event[text] = event2merge[text]
if 'spoil' in event2merge:
event['spoil'] = True
else:
event['spoil'] = False
event['t'] = t
return event
def detachEvent(event, event2detach, t):
''' Detach events by subtracting w1, Gx, Gy, Gz, phase and removing event texts. Also update event time t.
Args:
event: original event
event2detach: event to be detached
t: new event time
Returns:
Detached event
'''
for channel in ['w1', 'Gx', 'Gy', 'Gz', 'phase']:
if channel in event2detach:
event[channel] -= event2detach[channel]
for text in ['RFtext', 'Gxtext', 'Gytext', 'Gztext', 'spoilText']:
if text in event and text in event2detach and event[text]==event2detach[text]:
del event[text]
event['t'] = t
return event
def getPrescribedTimeVector(config, nTR):
''' Get time vector of animations prescribed by 'speed', 'TR', 'fps', and 'maxRFspeed' in config.
Args:
config: configuration dictionary
nTR: number of TR:s in time vector
Returns:
Time vector prescribed by config
'''
speedEvents = config['speed'] + [event for event in config['pulseSeq'] if any(['FA' in event, 'B1' in event])]
speedEvents = sorted(speedEvents, key=lambda event: event['t'])
kernelTime = np.array([])
t = 0
dt = 1e3 / config['fps'] * config['speed'][0]['speed'] # Animation time resolution [msec]
for event in speedEvents:
kernelTime = np.concatenate((kernelTime, np.arange(t, event['t'], dt)), axis=None)
t = max(t, event['t'])
if 'speed' in event:
dt = 1e3 / config['fps'] * event['speed'] # Animation time resolution [msec]
if 'FA' in event or 'B1' in event:
RFdt = min(dt, 1e3 / config['fps'] * config['maxRFspeed']) # Time resolution during RF [msec]
kernelTime = np.concatenate((kernelTime, np.arange(event['t'], event['t'] + event['dur'], RFdt)), axis=None)
t = event['t'] + event['dur']
kernelTime = np.concatenate((kernelTime, np.arange(t, config['TR'], dt)), axis=None)
timeVec = np.array([])
for rep in range(nTR): # Repeat time vector for each TR
timeVec = np.concatenate((timeVec, kernelTime + rep * config['TR']), axis=None)
return np.unique(roundEventTime(timeVec))
def setupPulseSeq(config):
''' Check and setup pulse sequence given by config. Set clock and store in config.
Args:
config: configuration dictionary.
'''
checkPulseSeq(config)
# Create non-overlapping events, each with constant w1, Gx, Gy, Gz, including empty "relaxation" events
config['events'] = []
ongoingEvents = []
newEvent = emptyEvent() # Start with empty "relaxation event"
newEvent['t'] = 0
for i, event in enumerate(config['separatedPulseSeq']):
eventTime = roundEventTime(event['t'])
# Merge any events starting simultaneously:
if eventTime==newEvent['t']:
newEvent = mergeEvent(newEvent, event, eventTime)
else:
config['events'].append(dict(newEvent))
newEvent = mergeEvent(newEvent, event, eventTime)
if 'dur' in event: # event is ongoing unless no 'dur', i.e. spoiler event
ongoingEvents.append(event)
# sort ongoing events according to event end time:
sorted(ongoingEvents, key=lambda event: event['t'] + event['dur'], reverse=False)
if event is config['separatedPulseSeq'][-1]:
nextEventTime = roundEventTime(config['TR'])
else:
nextEventTime = roundEventTime(config['separatedPulseSeq'][i+1]['t'])
for stoppingEvent in [event for event in ongoingEvents[::-1] if roundEventTime(event['t'] + event['dur']) <= nextEventTime]:
config['events'].append(dict(newEvent))
newEvent = detachEvent(newEvent, stoppingEvent, roundEventTime(stoppingEvent['t'] + stoppingEvent['dur']))
ongoingEvents.pop()
config['events'].append(dict(newEvent))
# Set clock vector
config['kernelClock'] = getPrescribedTimeVector(config, 1)
config['kernelClock'] = addEventsToTimeVector(config['kernelClock'], config['events'])
if config['kernelClock'][-1] == config['TR']:
config['kernelClock'] = config['kernelClock'][:-1]
config['nFramesPerTR'] = len(config['kernelClock'])
config['t'] = np.array([])
for rep in range(-config['nDummies'], config['nTR']): # Repeat time vector for each TR (dummy TR:s get negative time)
config['t'] = np.concatenate((config['t'], roundEventTime(config['kernelClock'] + rep * config['TR'])), axis=None)
config['t'] = np.concatenate((config['t'], roundEventTime(config['nTR'] * config['TR'])), axis=None) # Add end time to time vector
config['kernelClock'] = np.concatenate((config['kernelClock'], config['TR']), axis=None) # Add end time to kernel clock
def arrangeLocations(slices, config, key='locations'):
''' Check and setup locations or M0. Set nx, ny, and nz and store in config.
Args:
slices: (nested) list of M0 or locations (spatial distribution of Meq).
config: configuration dictionary.
key: pass 'locations' for Meq distribution, and 'M0' for M0 distribution.
'''
if key not in ['M0', 'locations']:
raise Exception('Argument "key" must be "locations" or "M0", not {}'.format(key))
if not isinstance(slices, list):
raise Exception('Expected list in config "{}", not {}'.format(key, type(slices)))
if not isinstance(slices[0], list):
slices = [slices]
if not isinstance(slices[0][0], list):
slices = [slices]
if key=='M0' and not isinstance(slices[0][0][0], list):
slices = [slices]
if 'nz' not in config:
config['nz'] = len(slices)
elif len(slices)!=config['nz']:
raise Exception('Config "{}": number of slices do not match'.format(key))
if 'ny' not in config:
config['ny'] = len(slices[0])
elif len(slices[0])!=config['ny']:
raise Exception('Config "{}": number of rows do not match'.format(key))
if 'nx' not in config:
config['nx'] = len(slices[0][0])
elif len(slices[0][0])!=config['nx']:
raise Exception('Config "{}": number of elements do not match'.format(key))
if key=='M0' and len(slices[0][0][0])!=3:
raise Exception('Config "{}": inner dimension must be of length 3'.format(key))
return slices
def checkConfig(config):
''' Check and setup config.
Args:
config: configuration dictionary.
'''
if any([key not in config for key in ['TR', 'B0', 'speed', 'output']]):
raise Exception('Config must contain "TR", "B0", "speed", and "output"')
if 'title' not in config:
config['title'] = ''
config['TR'] = roundEventTime(config['TR'])
if 'nTR' not in config:
config['nTR'] = 1
if 'nDummies' not in config:
config['nDummies'] = 0
if 'nIsochromats' not in config:
config['nIsochromats'] = 1
if 'isochromatStep' not in config:
if config['nIsochromats']>1:
raise Exception('Please specify "isochromatStep" [ppm] in config')
else:
config['isochromatStep']=0
if 'components' not in config:
config['components'] = [{}]
for comp in config['components']:
for (key, default) in [('name', ''),
('CS', 0),
('T1', np.inf),
('T2', np.inf),
('vx', 0),
('vy', 0),
('vz', 0),
('Dx', 0),
('Dy', 0),
('Dz', 0)]:
if key not in comp:
comp[key] = default
config['nComps'] = len(config['components'])
if 'locSpacing' not in config:
config['locSpacing'] = 0.001 # distance between locations [m]
if 'fps' not in config:
config['fps'] = 15 # Frames per second in animation (<=15 should be supported by powepoint)
config['w0'] = 2*np.pi*gyro*config['B0'] # Larmor frequency [kRad/s]
# check speed prescription
if isinstance(config['speed'], Number):
config['speed'] = [{'t': 0, 'speed': config['speed']}]
elif isinstance(config['speed'], list):
for event in config['speed']:
if not ('t' in event and 'speed' in event):
raise Exception("Each item in 'speed' list must have field 't' [msec] and 'speed'")
if event['t']>=config['TR']:
raise Exception("Specified speed change must be within TR.")
if not 0 in [event['t'] for event in config['speed']]:
raise Exception("Speed at time 0 must be specified.")
else:
raise Exception("Config 'speed' must be a number or a list")
config['speed'] = sorted(config['speed'], key=lambda event: event['t'])
if 'maxRFspeed' not in config:
config['maxRFspeed'] = 0.001
elif not isinstance(config['maxRFspeed'], Number):
raise Exception("Config 'maxRFspeed' must be numeric")
setupPulseSeq(config)
### Arrange locations ###
if not 'collapseLocations' in config:
config['collapseLocations'] = False
if not 'locations' in config:
config['locations'] = arrangeLocations([[[1]]], config)
else:
if isinstance(config['locations'], dict):
for comp in iter(config['locations']):
config['locations'][comp] = arrangeLocations(config['locations'][comp], config)
elif isinstance(config['locations'], list):
locs = config['locations']
config['locations'] = {}
for comp in [n['name'] for n in config['components']]:
config['locations'][comp] = arrangeLocations(locs, config)
else:
raise Exception('Config "locations" should be list or components dict')
for (FOV, n) in [('FOVx', 'nx'), ('FOVy', 'ny'), ('FOVz', 'nz')]:
if FOV not in config:
config[FOV] = config[n]*config['locSpacing'] #FOV in m
if 'M0' in config:
if isinstance(config['M0'], dict):
for comp in iter(config['M0']):
config['M0'][comp] = arrangeLocations(config['M0'][comp], config, 'M0')
elif isinstance(config['M0'], list):
M0 = config['M0']
config['M0'] = {}
for comp in [n['name'] for n in config['components']]:
config['M0'][comp] = arrangeLocations(M0, config, 'M0')
else:
raise Exception('Config "M0" should be list or components dict')
# check output
for output in config['output']:
if 'tRange' in output:
if not len(output['tRange'])==2:
raise Exception('Output "tRange" expected to be 2-tuple')
elif output['type']=='psd':
output['tRange'] = [0, config['TR']]
else:
output['tRange'] = [0, config['nTR'] * config['TR']]
if 'dpi' not in output:
output['dpi'] = 100
if 'freeze' not in output:
output['freeze'] = []
elif not isinstance(output['freeze'], list):
output['freeze'] = [output['freeze']]
if output['type']=='3D':
if 'drawAxes' not in output:
output['drawAxes'] = config['nx']*config['ny']*config['nz'] == 1
if 'background' not in config:
config['background'] = {}
if 'color' not in config['background']:
config['background']['color'] = 'black'
if config['background']['color'] not in ['black', 'white']:
raise Exception('Only "black" and "white" supported as background colors')
def rotMatrix(angle, axis):
'''Get 3D rotation matrix.
Args:
angle: rotation angle in radians.
axis: axis of rotation (0, 1, or 2).
Returns:
rotation matrix, numpy array of size [3, 3]
'''
c, s = np.cos(angle), np.sin(angle)
R = np.array([[1,0,0], [0,c,-s], [0,s,c]])
return np.roll(np.roll(R, axis, axis=0), axis, axis=1)
def spherical2cartesian(spherical):
'''Convert 3D vector from spherical to Cartesian coordinates.
Args:
spherical: 3-tuple holding vector length, polar, and azimuthal angle
Returns:
Cartesian vector, list of size 3
'''
r, polar, azim = spherical
M = np.dot(np.dot(np.array([0, 0, r]), rotMatrix(np.radians(azim), 1)), rotMatrix(np.radians(polar), 2))
return list(M)
def resampleOnPrescribedTimeFrames(vectors, config):
''' Resample (interpolate) given vectors corresponding to time vector config['t'] on time vector config['tFrames]. Also resample text and alpha channels in config similiarly.
Args:
vectors: magnetization vectors of shape [nx, ny, nz, nComps, nIsochromats, 3, len(config['t'])]
Returns:
resampled magnetization vectors of shape [nx, ny, nz, nComps, nIsochromats, 3, len(config['tFrames'])]
'''
config['tFrames'] = getPrescribedTimeVector(config, config['nTR'])
newShape = list(vectors.shape)
newShape[6] = len(config['tFrames'])
resampledVectors = np.zeros(newShape)
for x in range(newShape[0]):
for y in range(newShape[1]):
for z in range(newShape[2]):
for c in range(newShape[3]):
for i in range(newShape[4]):
for dim in range(newShape[5]):
resampledVectors[x,y,z,c,i,dim,:] = np.interp(config['tFrames'], config['t'], vectors[x,y,z,c,i,dim,:])
# resample text alpha channels:
for channel in ['RFalpha', 'Galpha', 'spoilAlpha']:
alphaVector = np.zeros([len(config['tFrames'])])
for i in range(len(alphaVector)):
if i == len(alphaVector)-1:
ks = np.where(config['t']>=config['tFrames'][i])[0]
else:
ks = np.where(np.logical_and(config['t']>=config['tFrames'][i], config['t']<config['tFrames'][i+1]))[0]
alphaVector[i] = np.max(config[channel][ks])
config[channel] = alphaVector
# resample text:
for text in ['RFtext', 'Gtext']:
textVector = np.full([len(config['tFrames'])], '', dtype=object)
for i in range(len(textVector)):
k = np.where(config['t']>=config['tFrames'][i])[0][0]
textVector[i] = config[text][k]
config[text] = textVector
return resampledVectors
def fadeTextFlashes(config, fadeTime=1.0):
''' Modify text alpha channels such that the text flashes fade
Args:
config: configuration dictionary.
fadeTime: time of fade in seconds
'''
decay = 1.0/(config['fps'] * fadeTime) # alpha decrease per frame
for channel in ['RFalpha', 'Galpha', 'spoilAlpha']:
for i in range(1, len(config[channel])):
if config[channel][i]==0:
config[channel][i] = max(0, config[channel][i-1]-decay)
def run(configFile, leapFactor=1, gifWriter='ffmpeg'):
''' Main program. Read and setup config, simulate magnetization vectors and write animated gif.
Args:
configFile: YAML file specifying configuration.
leapFactor: Skip frame factor for faster processing and smaller filesize.
gifWriter: external program to write gif. Must be "ffmpeg" or "imagemagick"/"convert".
'''
# Check if gifWriter exists
gifWriter = gifWriter.lower()
if gifWriter == 'ffmpeg':
if not shutil.which('ffmpeg'):
raise Exception('FFMPEG not found')
elif gifWriter in ['imagemagick', 'convert']:
if not shutil.which('convert'):
raise Exception('ImageMagick (convert) not found')
else:
raise Exception('Argument gifWriter must be "ffmpeg" or "imagemagick"/"convert"')
# Set global constants
global gyro
gyro = 42577. # Gyromagnetic ratio [kHz/T]
# Read configuration file
with open(configFile, 'r') as f:
try:
config = yaml.safe_load(f)
except yaml.YAMLError as exc:
raise Exception('Error reading config file') from exc
### Setup config correctly ###
checkConfig(config)
if config['background']['color'] == 'black':
for i in ['bg', 'axis', 'text', 'circle']:
colors[i][:3] = list(map(lambda x: 1-x, colors[i][:3]))
### Simulate ###
vectors = np.empty((config['nx'],config['ny'],config['nz'],config['nComps'],config['nIsochromats'],6,len(config['t'])))
for z in range(config['nz']):
for y in range(config['ny']):
for x in range(config['nx']):
for c, component in enumerate(config['components']):
if component['name'] in config['locations']:
try:
Meq = config['locations'][component['name']][z][y][x]
except:
raise Exception('Is the "location" matrix shape equal for all components?')
elif isinstance(config['locations'], list):
Meq = config['locations'][z][y][x]
else:
Meq = 0.0
if 'M0' in config and component['name'] in config['M0']:
try:
M0 = spherical2cartesian(config['M0'][component['name']][z][y][x])
except:
raise Exception('Is the "M0" matrix shape equal for all components?')
elif 'M0' in config and isinstance(config['M0'], list):
M0 = spherical2cartesian(config['M0'][z][y][x])
else:
M0 = None
pos = [(x+.5-config['nx']/2)*config['locSpacing'],
(y+.5-config['ny']/2)*config['locSpacing'],
(z+.5-config['nz']/2)*config['locSpacing']]
vectors[x,y,z,c,:,:,:] = simulateComponent(config, component, Meq, M0, pos)
### Animate ###
getText(config) # prepare text flashes for 3D plot
vectors = resampleOnPrescribedTimeFrames(vectors, config)
fadeTextFlashes(config)
delay = int(100/config['fps']*leapFactor) # Delay between frames in ticks of 1/100 sec
outdir = './out'
for output in config['output']:
if output['file']:
if output['type'] in ['xy', 'z']:
signal = np.sum(vectors[:,:,:,:,:,:3,:], (0,1,2,4)) # sum over space and isochromats
if 'normalize' in output and output['normalize']:
for c, comp in enumerate([n['name'] for n in config['components']]):
signal[c,:] /= np.sum(config['locations'][comp])
signal /= np.max(np.abs(signal)) # scale signal relative to maximum
if 'scale' in output:
signal *= output['scale']
if gifWriter == 'ffmpeg':
ffmpegWriter = FFMPEGwriter.FFMPEGwriter(config['fps'])
else:
tmpdir = './tmp'
if os.path.isdir(tmpdir):
rmTmpDir = input('Temporary folder "{}" already exists. Delete(Y/N)?'.format(tmpdir))
if rmTmpDir.upper() == 'Y':
shutil.rmtree(tmpdir)
else:
raise Exception('No files written.')
os.makedirs(tmpdir, exist_ok=True)
os.makedirs(outdir, exist_ok=True)
outfile = os.path.join(outdir, output['file'])
output['freezeFrames'] = []
for t in output['freeze']:
output['freezeFrames'].append(np.argmin(np.abs(config['tFrames'] - t)))
for frame in range(0, len(config['tFrames']), leapFactor):
# Use only every leapFactor frame in animation
if output['type'] == '3D':
fig = plotFrame3D(config, vectors, frame, output)
elif output['type'] == 'kspace':
fig = plotFrameKspace(config, frame, output)
elif output['type'] == 'psd':
fig = plotFramePSD(config, frame, output)
elif output['type'] in ['xy', 'z']:
fig = plotFrameMT(config, signal, frame, output)
plt.draw()
filesToSave = []
if frame in output['freezeFrames']:
filesToSave.append('{}_{}.png'.format('.'.join(outfile.split('.')[:-1]), str(frame).zfill(4)))
if gifWriter == 'ffmpeg':
ffmpegWriter.addFrame(fig)
else: # use imagemagick: save frames temporarily
filesToSave.append(os.path.join(tmpdir, '{}.png'.format(str(frame).zfill(4))))
for file in filesToSave:
print('Saving frame {}/{} as "{}"'.format(frame+1, len(config['tFrames']), file))
plt.savefig(file, facecolor=plt.gcf().get_facecolor())
plt.close()
if gifWriter == 'ffmpeg':
ffmpegWriter.write(outfile)
else: # use imagemagick
print('Creating animated gif "{}"'.format(outfile))
compress = '-layers Optimize'
os.system(('convert {} -delay {} {}/*png {}'.format(compress, delay, tmpdir, outfile)))
shutil.rmtree(tmpdir)
def parseAndRun():
''' Command line parser. Parse command line and run main program. '''
# Initiate command line parser
parser = argparse.ArgumentParser(description='Simulate magnetization vectors using Bloch equations and create animated gif')
parser.add_argument('--configFile', '-c',
help="Name of configuration text file",
type=str,
default='')
parser.add_argument('--leapFactor', '-l',
help="Leap factor for smaller filesize and fewer frames per second",
type=int,
default=1)
# Parse command line
args = parser.parse_args()
# Run main program
run(args.configFile, args.leapFactor)
if __name__ == '__main__':
parseAndRun()
