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pints.py
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pints.py
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from __future__ import print_function
# ---- System Libraries ---- #
from builtins import zip
from builtins import str
from builtins import range
import sys
import os
import datetime
import time
import platform
# Check for PyQt6 (native mac M1 compatibility), otherwise continue using PyQt5
import importlib
PyQt6_spec = importlib.util.find_spec("PyQt6")
if PyQt6_spec != None:
from PyQt6 import QtCore, QtGui, QtWidgets, uic
else:
from PyQt5 import QtCore, QtGui, QtWidgets, uic
from collections import defaultdict
# ---- Math Libraries ---- #
import scipy as sp
import scipy.signal as spsg
import numpy as np
import math
from pyfftw.interfaces import scipy_fftpack as fftw
# ---- Plotting Libraries ---- #
import matplotlib as mpl;
mpl.use("Qt5Agg")
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg as FigureCanvas,
NavigationToolbar2QT as NavigationToolbar)
import matplotlib.pyplot as plt; plt.style.use('ggplot')
# ---- Data Classes ---- #
from magiqdataclasses import *
# ---- Simulation Libraries ---- #
import pygamma as pg
from simclasses import *
qtCreatorFile = "pints/ui/PINTS.ui"
Ui_MainWindow, QtBaseClass = uic.loadUiType(qtCreatorFile)
# ---- Main Application Class ---- #
class MyApp(QtWidgets.QWidget, Ui_MainWindow):
def __init__(self):
QtWidgets.QWidget.__init__(self)
Ui_MainWindow.__init__(self)
self.setupUi(self)
# Bind buttons to methods in each tab
self.setBindings('Simulate')
self.setBindings('Load Experiment')
self.setBindings('Edit Metabolites')
self.setBindings('Plot')
self.setBindings('Export')
self.setBindings('EditCST')
self.setBindings('Guess')
# Setup for plotting in the "Plot Metabolites" and "Generate Guess File" Tabs
self.canvas = [None]*3
self.toolbar = [None]*3
self.setPlot('Plot')
self.setPlot('Guess')
def setBindings(self, tab):
if tab == 'Simulate':
self.confirmSimParamsButton.clicked.connect(self.confirmSimParams)
self.calibrationMetaboliteComboBox.setCurrentIndex(35)
self.calibrationMetaboliteComboBox_bruker.setCurrentIndex(35)
self.calibrationMetaboliteComboBox_laser.setCurrentIndex(35)
self.loadBrukerDataBrowseButton.clicked.connect(self.loadBrukerData)
self.workingDirectory_bruker = os.path.expanduser('~')
self.loadBrukerDataLoadButton.clicked.connect(self.loadBrukerParams)
self.loadBrukerDataLoadButton.setEnabled(False)
self.runSimulationButton.setEnabled(False)
self.runSimulationButton.clicked.connect(self.runSimulation)
elif tab == 'Load Experiment':
self.filenameBrowseButton.clicked.connect(self.chooseExperimentFile)
self.filenameConfirmButton.clicked.connect(self.loadExperimentFile)
self.filenameConfirmButton.setEnabled(False)
self.specExpButton.clicked.connect(self.specExp)
self.specExpButton.setEnabled(False)
elif tab == 'Edit Metabolites':
self.editMetabOKButton.clicked.connect(self.saveMetabInfo)
self.editMetabOKButton.setEnabled(False)
self.loadMetabConfirmButton.clicked.connect(self.loadMetabInfoFile)
self.loadMetabConfirmButton.setEnabled(False)
self.loadMetabBrowseButton.clicked.connect(self.chooseMetabInfoFile)
self.loadMetabBrowseButton.setEnabled(False)
elif tab == 'Plot':
self.plotButton.clicked.connect(self.plot)
self.plotButton.setEnabled(False)
elif tab == 'Export':
self.plotButton.clicked.connect(self.plot)
self.outputFilenameConfirmButton_rawTime.clicked.connect(self.setOutputFile_rawTime)
self.outputFilenameConfirmButton_rawTime.setEnabled(False)
self.outputFilenameConfirmButton_rawFreq.clicked.connect(self.setOutputFile_rawFreq)
self.outputFilenameConfirmButton_rawFreq.setEnabled(False)
self.outputFilenameConfirmButton_dat.clicked.connect(self.setOutputFile_dat)
self.outputFilenameConfirmButton_dat.setEnabled(False)
self.exportButton_rawTime.clicked.connect(self.export_rawTime)
self.exportButton_rawTime.setEnabled(False)
self.exportButton_rawFreq.clicked.connect(self.export_rawFreq)
self.exportButton_rawFreq.setEnabled(False)
self.exportButton_dat.clicked.connect(self.export_dat)
self.exportButton_dat.setEnabled(False)
elif tab == 'EditCST':
self.cstOKButton.clicked.connect(self.saveCSTInfo)
self.cstOKButton.setEnabled(False)
self.cstLoadButton.clicked.connect(self.loadCSTInfo)
self.cstLoadButton.setEnabled(False)
self.cstFilenameConfirmButton.clicked.connect(self.setCSTFile)
self.cstFilenameConfirmButton.setEnabled(False)
self.genCSTButton.clicked.connect(self.genCST)
self.genCSTButton.setEnabled(False)
elif tab == 'Guess':
self.filenameBrowseButton_dat.clicked.connect(self.chooseDATFile)
self.filenameBrowseButton_dat.setEnabled(False)
self.filenameConfirmButton_dat.clicked.connect(self.loadDATFile)
self.filenameConfirmButton_dat.setEnabled(False)
self.plotGESButton.clicked.connect(self.plotGES)
self.plotGESButton.setEnabled(False)
self.gesFilenameConfirmButton.clicked.connect(self.setGESFile)
self.gesFilenameConfirmButton.setEnabled(False)
self.genGESButton.clicked.connect(self.genGES)
self.genGESButton.setEnabled(False)
# ---- Methods for Simulate Tab ---- #
def loadBrukerData(self):
prev = str(self.loadBrukerDataLineEdit.text())
self.loadBrukerDataLineEdit.setText(str(QtWidgets.QFileDialog.getExistingDirectory(self, 'Open Bruker Data Directory', self.workingDirectory_bruker)))
if str(self.loadBrukerDataLineEdit.text()) == '':
if str(prev) == '':
self.loadBrukerDataLineEdit.setText(str(prev))
self.loadBrukerDataLoadButton.setEnabled(False)
self.T3Button.setEnabled(True)
self.T7Button.setEnabled(True)
self.T9Button.setEnabled(True)
self.dwellTimeInput_sim.setEnabled(True)
self.acqLengthInput_sim.setEnabled(True)
self.echoTimeInput_sim.setEnabled(True)
self.sLASERradioButton.setEnabled(True)
self.sLASERradioButton_bruker.setEnabled(True)
self.LASERradioButton.setEnabled(False)
else:
self.loadBrukerDataLoadButton.setEnabled(True)
self.T3Button.setEnabled(False)
self.T7Button.setEnabled(False)
self.T9Button.setEnabled(False)
self.dwellTimeInput_sim.setEnabled(False)
self.acqLengthInput_sim.setEnabled(False)
self.echoTimeInput_sim.setEnabled(False)
self.sLASERradioButton.setEnabled(False)
self.sLASERradioButton_bruker.setEnabled(False)
self.LASERradioButton.setEnabled(False)
self.workingDirectory_bruker = os.path.abspath(os.path.join(os.path.expanduser(str(prev)), os.pardir))
def loadBrukerParams(self):
file_dir = str(self.loadBrukerDataLineEdit.text())
data = BrukerFID(file_dir)
self.sLASERradioButton.setChecked(False)
self.sLASERradioButton_bruker.setChecked(True)
self.LASERradioButton.setChecked(False)
# Experiment Info
b0 = float(data.header['PVM_FrqRef']['value'][0])
# This if-statement is just a sanity check.
if b0 > 350:
self.T3Button.setChecked(False)
self.T7Button.setChecked(False)
self.T9Button.setChecked(True)
elif b0 > 200:
self.T3Button.setChecked(False)
self.T7Button.setChecked(True)
self.T9Button.setChecked(False)
else:
self.T3Button.setChecked(True)
self.T7Button.setChecked(False)
self.T9Button.setChecked(False)
dt = float(data.header['PVM_DigDw']['value']) / 1000
self.dwellTimeInput_sim.setText(str(dt))
acqt = dt * int(data.header['PVM_DigNp']['value'])
self.acqLengthInput_sim.setText(str(acqt))
digshift = int(data.header['PVM_DigShift']['value'])
self.digShiftInput_bruker.setText(str(digshift))
te = float(data.header['PVM_EchoTime']['value'])
self.echoTimeInput_sim.setText(str(te))
te1 = int(float(data.header['TE1']['value']))
te2 = int(float(data.header['TE2']['value']))
self.TE1_bruker.setText(str(te1))
self.TE2_bruker.setText(str(te2))
# sLASER Pulse Info
# | Pulse Structure (pulse length, pulse bandwith, flip angle, excitation, ~, ~, ~, ~, ~, amplitude, shape)
# Excitation
ep = data.header['VoxPul1']['value'].replace('(','').replace(' ','').replace(')','').split(',')
epn = data.header['VoxPul1Enum']['value'].replace('>','').replace('<','')
self.excPulse_bruker = {'name': epn, 'params': ep}
plen = float(ep[0]) * 1000
self.excPulseLength_bruker.setText(str(plen))
pamp = float(ep[-2]) / 10
self.excAmpMin_bruker.setText(str(0))
self.excAmpMax_bruker.setText(str(pamp))
# Refocussing
rp = data.header['VoxPul2']['value'].replace('(','').replace(' ','').replace(')','').split(',')
rpn = data.header['VoxPul2Enum']['value'].replace('>','').replace('<','')
self.rfcPulse_bruker = {'name': rpn, 'params': rp}
plen = float(rp[0]) * 1000
self.afpPulseLengthInput_bruker.setText(str(plen))
pamp = float(rp[-2]) / 10
self.afpAmpMin_bruker.setText(str(0))
self.afpAmpMax_bruker.setText(str(pamp))
# Editing Pulse Info
# --- TBD ---
def fit_sin(self, tt, yy):
'''Fit sin to the input time sequence, and return fitting parameters "amp", "omega", "phase", "offset", "freq", "period" and "fitfunc"'''
tt = np.array(tt)
yy = np.array(yy)
ff = np.fft.fftfreq(len(tt), (tt[1]-tt[0])) # assume uniform spacing
Fyy = abs(np.fft.fft(yy))
guess_freq = abs(ff[np.argmax(Fyy[1:])+1]) # excluding the zero frequency "peak", which is related to offset
guess_amp = np.std(yy) * 2.**0.5
guess_offset = np.mean(yy)
guess = np.array([guess_amp, 2.*np.pi*guess_freq, 0., guess_offset])
popt, pcov = sp.optimize.curve_fit(self.sinfunc, tt, yy, p0=guess)
A, w, p, c = popt
f = w/(2.*np.pi)
fitfunc = lambda t: A * np.sin(w*t + p) + c
return {"amp": A, "omega": w, "phase": p, "offset": c, "freq": f, "period": 1./f, "fitfunc": fitfunc, "maxcov": np.max(pcov), "rawres": (guess,popt,pcov)}
def sinfunc(self, t, A, w, p, c):
return A * np.sin(w*t + p) + c
def logs_func(self, x, A, B, K, s):
return A + (K - A)/(1 + np.exp(-B*(x-s)))
def confirmSimParams(self):
if self.sLASERradioButton_bruker.isChecked():
if self.T7Button.isChecked():
self.sim_experiment = Experiment('slaser_bruker', 297.2)
elif self.T3Button.isChecked():
self.sim_experiment = Experiment('slaser_bruker', 123.3)
elif self.T9Button.isChecked():
self.sim_experiment = Experiment('slaser_bruker', 400.2)
self.sim_experiment.name = 'semi-LASER (Bruker)'
if 'Calculated' in self.excPulse_bruker['name']:
self.sim_experiment.inpulse90file = 'pints/pulses/rect.exc'
else:
self.sim_experiment.inpulse90file = 'pints/pulses/'+self.excPulse_bruker['name']+'.exc'
self.sim_experiment.inpulse180file = 'pints/pulses/'+self.rfcPulse_bruker['name']+'.inv'
elif self.sLASERradioButton.isChecked():
if self.T7Button.isChecked():
self.sim_experiment = Experiment('slaser', 297.2)
elif self.T3Button.isChecked():
self.sim_experiment = Experiment('slaser', 123.3)
elif self.T9Button.isChecked():
self.sim_experiment = Experiment('slaser', 400.2)
self.sim_experiment.name = 'semi-LASER'
elif self.LASERradioButton.isChecked():
if self.T7Button.isChecked():
self.sim_experiment = Experiment('laser', 297.2)
elif self.T3Button.isChecked():
self.sim_experiment = Experiment('laser', 123.3)
elif self.T9Button.isChecked():
self.sim_experiment = Experiment('laser', 400.2)
self.sim_experiment.name = 'LASER'
self.sim_experiment.author = platform.node()
self.sim_experiment.date = datetime.datetime.now().strftime("%Y_%m_%d")
self.sim_experiment.description = 'Density-matrix simulations of metabolites using PyGAMMA and metabolite parameters from V. Govindaraju et. al, NMR Biomed. 2000;13:129-153'
self.sim_experiment.type = 'PINTS'
self.insysfiles = [
'alanine.sys',
'aspartate.sys',
'choline_1-CH2_2-CH2.sys',
'choline_N(CH3)3_a.sys',
'choline_N(CH3)3_b.sys',
'creatine_N(CH3).sys',
'creatine_X.sys',
'd-glucose-alpha.sys',
'd-glucose-beta.sys',
'eth.sys',
'gaba.sys',
'glutamate.sys',
'glutamine.sys',
'glutathione_cysteine.sys',
'glutathione_glutamate.sys',
'glutathione_glycine.sys',
'glycine.sys',
'gpc_7-CH2_8-CH2.sys',
'gpc_glycerol.sys',
'gpc_N(CH3)3_a.sys',
'gpc_N(CH3)3_b.sys',
'lactate.sys',
'myoinositol.sys',
'naa_acetyl.sys',
'naa_aspartate.sys',
'naag_acetyl.sys',
'naag_aspartyl.sys',
'naag_glutamate.sys',
'pcho_N(CH3)3_a.sys',
'pcho_N(CH3)3_b.sys',
'pcho_X.sys',
'pcr_N(CH3).sys',
'pcr_X.sys',
'peth.sys',
'scyllo-inositol.sys',
'taurine.sys']
if self.sim_experiment.b0 == 123.3:
self.macromolecules = [
'MM09',
'MM12',
'MM14',
'MM16',
'MM20',
'MM21',
'MM23',
'MM26',
'MM30',
'MM31',
'MM37',
'MM38',
'MM40' ]
# From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215417/
self.macromolecules_data = self.tree()
self.macromolecules_data['MM09'] = Macromolecule('MM09', 0.90, 'L', 21.20, 0.72, 0)
self.macromolecules_data['MM12'] = Macromolecule('MM12', 1.21, 'L', 19.16, 0.28, 0)
self.macromolecules_data['MM14'] = Macromolecule('MM14', 1.38, 'L', 15.90, 0.38, 0)
self.macromolecules_data['MM16'] = Macromolecule('MM16', 1.63, 'L', 07.50, 0.05, 0)
self.macromolecules_data['MM20'] = Macromolecule('MM20', 2.01, 'L', 29.03, 0.45, 0)
self.macromolecules_data['MM21'] = Macromolecule('MM21', 2.09, 'L', 20.53, 0.36, 0)
self.macromolecules_data['MM23'] = Macromolecule('MM23', 2.25, 'L', 17.89, 0.36, 0)
self.macromolecules_data['MM26'] = Macromolecule('MM26', 2.61, 'L', 05.30, 0.04, 0)
self.macromolecules_data['MM30'] = Macromolecule('MM30', 2.96, 'L', 14.02, 0.20, 0)
self.macromolecules_data['MM31'] = Macromolecule('MM31', 3.11, 'L', 17.89, 0.11, 0)
self.macromolecules_data['MM37'] = Macromolecule('MM37', 3.67, 'L', 33.52, 0.64, 0)
self.macromolecules_data['MM38'] = Macromolecule('MM38', 3.80, 'L', 11.85, 0.07, 0)
self.macromolecules_data['MM40'] = Macromolecule('MM40', 3.96, 'L', 37.48, 1.00, 0)
else:
self.macromolecules = [ 'lm1',
'lm2',
'lm3',
'lm4',
'lm5',
'lm6',
'lm7',
'lm8',
'lm9',
'lm10',
'lm11',
'lm12',
'lm13',
'lm14' ]
self.macromolecules_data = self.tree()
self.macromolecules_data['lm1'] = Macromolecule('lm1', 0.9457810, 'L', 50.72009, 3.5501260, -1.13820100)
self.macromolecules_data['lm2'] = Macromolecule('lm2', 1.4757810, 'L', 54.12614, 2.8557010, 0.054570260)
self.macromolecules_data['lm3'] = Macromolecule('lm3', 1.7057810, 'L', 68.32043, 3.9072800, -0.06015777)
self.macromolecules_data['lm4'] = Macromolecule('lm4', 2.1157810, 'L', 96.43580, 4.7191390, -0.09620739)
self.macromolecules_data['lm5'] = Macromolecule('lm5', 2.3157810, 'L', 69.70896, 2.7845620, -0.57759460)
self.macromolecules_data['lm6'] = Macromolecule('lm6', 3.0157810, 'L', 42.72932, 1.0176800, -0.65827850)
self.macromolecules_data['lm7'] = Macromolecule('lm7', 3.9854041, 'L', 29.64625, 1.2094070, 0.288971500)
self.macromolecules_data['lm8'] = Macromolecule('lm8', 7.1257810, 'L', 274.4760, 4.0466410, 0.302700400)
self.macromolecules_data['lm9'] = Macromolecule('lm9', 7.8557810, 'L', 37.37627, 1.3135740, 0.020221810)
self.macromolecules_data['lm10'] = Macromolecule('lm10', 2.6557810, 'L', 121.4557, 2.3499680, -0.58261020)
self.macromolecules_data['lm11'] = Macromolecule('lm11', 1.2357810, 'L', 30.68139, 0.7444791, -1.13820100)
self.macromolecules_data['lm12'] = Macromolecule('lm12', -0.628240, 'L', 1789.202, 21.518780, -3.65296700)
self.macromolecules_data['lm13'] = Macromolecule('lm13', 3.2957810, 'L', 109.4958, 1.6655390, 0.163575600)
self.macromolecules_data['lm14'] = Macromolecule('lm14', 3.7057810, 'L', 169.6304, 4.8735330, -1.35431900)
self.sim_experiment.obs_iso = '1H'
try:
self.sim_experiment.acq_time = float(self.acqLengthInput_sim.text())
self.sim_experiment.dwell_time = float(self.dwellTimeInput_sim.text())
self.sim_experiment.TE = float(self.echoTimeInput_sim.text())
if self.sLASERradioButton_bruker.isChecked():
self.sim_experiment.TE1 = float(self.TE1_bruker.text())
self.sim_experiment.TE2 = float(self.TE2_bruker.text())
self.sim_experiment.PULSE_90_LENGTH = float(self.excPulseLength_bruker.text())*10**(-6)
self.sim_experiment.PULSE_180_LENGTH = float(self.afpPulseLengthInput_bruker.text())*10**(-6)
self.sim_experiment.RF_OFFSET = float(self.rfOffsetInput_bruker.text())
amin = int(np.floor(float(self.excAmpMin_bruker.text()))); amax = int(np.ceil(float(self.excAmpMax_bruker.text())))
self.sim_experiment.A_90s = np.linspace(amin, amax, (amax-amin)*10 + 1)
amin = int(np.floor(float(self.afpAmpMin_bruker.text()))); amax = int(np.ceil(float(self.afpAmpMax_bruker.text())))
self.sim_experiment.A_180s = np.linspace(amin, amax, (amax-amin)*10 + 1)
self.sim_experiment.DigShift = int(self.digShiftInput_bruker.text())*self.sim_experiment.dwell_time
# Editing Pulse Info
# --- TBD ---
elif self.sLASERradioButton.isChecked():
self.sim_experiment.PULSE_90_LENGTH = float(self.slrPulseLengthInput.text())*10**(-6)
self.sim_experiment.fudge_factor = int(self.fudgeFactorInput.text())
self.sim_experiment.PULSE_180_LENGTH = float(self.afpPulseLengthInput.text())*10**(-6)
self.sim_experiment.RF_OFFSET = float(self.rfOffsetInput.text())
self.sim_experiment.A_90s = np.linspace(int(self.slrAmpMinInput.text()), int(self.slrAmpMaxInput.text()), (int(self.slrAmpMaxInput.text())-int(self.slrAmpMinInput.text()))*10 + 1)
self.sim_experiment.A_180s = np.linspace(int(self.afpAmpMinInput.text()), int(self.afpAmpMaxInput.text()), (int(self.afpAmpMaxInput.text())-int(self.afpAmpMinInput.text()))*10 + 1)
elif self.LASERradioButton.isChecked():
self.sim_experiment.PULSE_90_LENGTH = float(self.ahpPulseLengthInput_laser.text())*10**(-6)
self.sim_experiment.PULSE_180_LENGTH = float(self.afpPulseLengthInput_laser.text())*10**(-6)
self.sim_experiment.RF_OFFSET = float(self.rfOffsetInput_laser.text())
self.sim_experiment.A_90s = np.linspace(int(self.ahpAmpMinInput_laser.text()), int(self.ahpAmpMaxInput_laser.text()), (int(self.ahpAmpMaxInput_laser.text())-int(self.ahpAmpMinInput_laser.text()))*10 + 1)
self.sim_experiment.A_180s = np.linspace(int(self.afpAmpMinInput_laser.text()), int(self.afpAmpMaxInput_laser.text()), (int(self.afpAmpMaxInput_laser.text())-int(self.afpAmpMinInput_laser.text()))*10 + 1)
self.sim_experiment.tolppm = float(self.tolppmInput.text())
self.sim_experiment.tolpha = float(self.tolphaInput.text())
self.sim_experiment.ppmlo = float(self.ppmloInput.text()) - self.sim_experiment.RF_OFFSET
self.sim_experiment.ppmhi = float(self.ppmhiInput.text()) - self.sim_experiment.RF_OFFSET
self.simConsole.clear()
self.simConsole.append('Confirming simulation experiment parameters ...')
self.simConsole.append(' | b0: ' + str(self.sim_experiment.b0) + ' MHz')
self.simConsole.append(' | observed species: ' + str(self.sim_experiment.obs_iso))
self.simConsole.append(' | gyratio: ' + str(self.sim_experiment.getGyratio()) + ' MHz/mT')
self.simConsole.append(' | dwell time: ' + str(self.sim_experiment.dwell_time) + ' sec')
self.simConsole.append(' | acqusition time: ' + str(self.sim_experiment.acq_time) + ' sec')
self.simConsole.append(' | TE: ' + str(self.sim_experiment.TE) + ' msec')
self.simConsole.append(' | A_90s: ' + str(np.array(self.sim_experiment.A_90s)))
self.simConsole.append(' | A_180s: ' + str(np.array(self.sim_experiment.A_180s)))
self.simConsole.append(' | rf_offset: ' + str(self.sim_experiment.RF_OFFSET) + ' ppm')
self.confirmSimParamsButton.setEnabled(False)
self.runSimulationButton.setEnabled(True)
except Exception as e:
self.simConsole.append('\nERROR: ' + str(e) + '\n>> Please check your simulation parameters.\n')
def runSimulation(self):
self.runSimulationButton.setEnabled(False)
self.simProgressBar.setMaximum(int(np.size(self.insysfiles)) + 2)
self.simProgressBar.setValue(0)
if self.sLASERradioButton_bruker.isChecked():
# Create a new simulations results file
self.save_dir_sim = 'pints/experiments/sLASER_sim_bruker_' \
+ datetime.datetime.now().strftime("%Y_%m_%d_%H%M%S") \
+ '_TE' + str(self.sim_experiment.TE)
if self.T7Button.isChecked():
self.save_dir_sim += '_7T/'
elif self.T3Button.isChecked():
self.save_dir_sim += '_3T/'
elif self.T9Button.isChecked():
self.save_dir_sim += '_9T/'
if not os.path.exists(self.save_dir_sim):
os.makedirs(self.save_dir_sim)
self.sim_results = open(self.save_dir_sim + 'sLASER_sim_results.txt', 'w')
# Write parameters in file
self.sim_results.write(';PINTS for FITMAN Simulation Output\n')
self.sim_results.write(';Experiment Information\n')
self.sim_results.write(';---------------------------------------------------------------------------\n')
self.sim_results.write(';Name: ' + self.sim_experiment.name + '\n')
self.sim_results.write(';Created: ' + self.sim_experiment.date + '\n')
self.sim_results.write(';Comment: ' + self.sim_experiment.description + '\n')
self.sim_results.write(';PI: ' + self.sim_experiment.author + '\n')
self.sim_results.write(';b0: ' + str(self.sim_experiment.b0) + '\n')
self.sim_results.write(';' + str(int(np.size(self.insysfiles)+int(np.size(self.macromolecules)))) + ' Metabolites: ' + str(self.insysfiles).replace('[','').replace(']','').replace('\'','').replace('.sys',''))
if self.macroIncludeButton.isChecked(): self.sim_results.write(', ' + str(self.macromolecules).replace('[','').replace(']','').replace('\'',''))
self.sim_results.write('\n')
self.sim_results.write(';Simulation Results\n')
self.sim_results.write(';---------------------------------------------------------------------------\n')
# Set up for calibration experiments
insysfile = str(self.calibrationMetaboliteComboBox.currentText()) + '.sys'
if self.sim_experiment.b0 == 123.3:
insysfile = 'pints/metabolites/3T_' + insysfile
elif self.sim_experiment.b0 == 297.2:
insysfile = 'pints/metabolites/7T_' + insysfile
elif self.sim_experiment.b0 == 400.2:
insysfile = 'pints/metabolites/9.4T_' + insysfile
print('')
print(insysfile)
spin_system = pg.spin_system()
spin_system.read(insysfile)
for i in range(spin_system.spins()):
spin_system.PPM(i, spin_system.PPM(i) - self.sim_experiment.RF_OFFSET)
# Run the 180 calibration
self.simConsole.append('\n1. 180-degree calibration sLASER (w/ ideal 90, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
A180_calibration_data = []
for A_180 in self.sim_experiment.A_180s:
TE = self.sim_experiment.TE * 1E-3
TE1 = self.sim_experiment.TE1 * 1E-3
TE2 = self.sim_experiment.TE2 * 1E-3
# build 90 degree pulse
pulse_dur_90 = 0
# build 180 degree pulse
A_180, pulse180, pulse_dur_180, Ureal180 = self.slaser_build180(self.sim_experiment.inpulse180file, A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'bruker')
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1/2.0 - pulse_dur_90/2.0 - pulse_dur_180/2.0
delay2 = TE1/2.0 + TE2/2.0 - pulse_dur_180
delay3 = TE2 - pulse_dur_180
delay4 = delay2
delay5 = TE1/2.0 - pulse_dur_180 + self.sim_experiment.DigShift
# TE_fill = TE - 2.*TE1 - 2.*TE2
# delay1 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay2 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay3 = TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay4 = TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay5 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + self.sim_experiment.DigShift
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = pg.Ixpuls(spin_system, sigma0, self.sim_experiment.obs_iso, 90.0) # apply ideal 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
# acquire
mx = pg.TTable1D(ACQ.table(sigma0))
# binning to remove degenerate peaks
outf, outa, outp = self.binning_code(mx, self.sim_experiment.b0, spin_system, self.sim_experiment.obs_iso, self.sim_experiment.tolppm, self.sim_experiment.tolpha, self.sim_experiment.ppmlo, self.sim_experiment.ppmhi, self.sim_experiment.RF_OFFSET)
metab_calib180 = self.apply_metab_properties(str(self.calibrationMetaboliteComboBox.currentText()), A_180, outf, outa, outp, insysfile)
lb = 15 if (self.sim_experiment.b0 == 297.2 or self.sim_experiment.b0 == 400.2) else 6
f, spectra = metab_calib180.getSpec(TE, self.sim_experiment.b0, self.sim_experiment.getTime(), 0, 1, 0, 0, lb, self.sim_experiment.getFs())
A180_calibration_data.append(np.real(spectra)[np.argmax(np.abs(spectra))])
# Fit a logistic function
initial_guess_A = np.amin(A180_calibration_data)
initial_guess_B = np.abs(np.amax(A180_calibration_data)-np.amin(A180_calibration_data))/np.abs(A180_calibration_data[np.argmax(A180_calibration_data)]-A180_calibration_data[np.argmin(A180_calibration_data)])
initial_guess_K = np.amax(A180_calibration_data)
initial_guess_s = self.sim_experiment.A_180s[np.argmin(A180_calibration_data)]
fit_x = self.sim_experiment.A_180s
fit_y = np.pad(A180_calibration_data[np.argmin(A180_calibration_data):], (np.size(A180_calibration_data[:np.argmin(A180_calibration_data)]), 0), 'constant', constant_values=(np.amin(A180_calibration_data),0))
params, params_covariance = sp.optimize.curve_fit(self.logs_func, fit_x, fit_y, p0=[initial_guess_A,initial_guess_B,initial_guess_K, initial_guess_s])#, bounds=([-np.inf, 0, 0, 0], [0, np.inf, np.inf, self.sim_experiment.A_180s[-1]]))
self.simConsole.append(' | A + (K - A)/(1 + np.exp(-B*x)): ')
self.simConsole.append(' | A0 = ' + str(initial_guess_A) + ', B0 = ' + str(initial_guess_B) + ', K0 = ' + str(initial_guess_K) + ', s0 = ' + str(initial_guess_s))
self.simConsole.append(' | A = ' + str(params[0]) + ', B = ' + str(params[1]) + ', K = ' + str(params[2]) + ', s = ' + str(params[3]))
A180_calibration_data_init = self.logs_func(self.sim_experiment.A_180s, initial_guess_A, initial_guess_B, initial_guess_K, initial_guess_s)
A180_calibration_data_fitted = self.logs_func(self.sim_experiment.A_180s, params[0], params[1], params[2], params[3])
# save results
if self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()] + int(self.sim_experiment.A_180s[-1]/6) < self.sim_experiment.A_180s[-1]:
self.sim_experiment.A_180 = self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()] + int(self.sim_experiment.A_180s[-1]/6) # pad to be sure of adiabicity
else:
self.sim_experiment.A_180 = self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()]
plt.figure()
plt.plot(self.sim_experiment.A_180s, A180_calibration_data, '.', color='blue')
plt.plot(self.sim_experiment.A_180s, A180_calibration_data_init, color='green')
plt.plot(self.sim_experiment.A_180s, A180_calibration_data_fitted, color='red')
plt.plot(self.sim_experiment.A_180, A180_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_180s)-self.sim_experiment.A_180)).argmin()], 'x', color='black')
plt.text(self.sim_experiment.A_180, A180_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_180s)-self.sim_experiment.A_180)).argmin()]*1.2, str(self.sim_experiment.A_180), rotation='vertical', color='black')
plt.title('180-degree calibration sLASER (w/ ideal 90, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
plt.xlabel('A_180 [mT]')
plt.ylabel('Signal Intensity'); plt.ylim([np.amin(A180_calibration_data) + 0.25*np.amin(A180_calibration_data),np.amax(A180_calibration_data) + 0.25*np.amax(A180_calibration_data)])
plt.savefig(self.save_dir_sim + '180-DEGREE-CALIBRATION' + '_' + str(self.sim_experiment.PULSE_180_LENGTH) + 'secAFP.pdf')
plt.close()
# update progress bar
self.simProgressBar.setValue(1)
self.simConsole.append(' | CALIBRATED 180 AFP AMPLITUDE: ' + str(self.sim_experiment.A_180))
self.slaser_build180(self.sim_experiment.inpulse180file, self.sim_experiment.A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, True, 'bruker')
# Run the 90 calibration
self.simConsole.append('\n2. 90-degree calibration sLASER (w/ AFP 180, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
A90_calibration_data = []
for A_90 in self.sim_experiment.A_90s:
TE = self.sim_experiment.TE * 1E-3
TE1 = self.sim_experiment.TE1 * 1E-3
TE2 = self.sim_experiment.TE2 * 1E-3
# build 90 degree pulse
A_90, pulse90, pulse_dur_90, peak_to_end_90, Ureal90 = self.slaser_build90(self.sim_experiment.inpulse90file, A_90, self.sim_experiment.PULSE_90_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'bruker')
# build 180 degree pulse
A_180, pulse180, pulse_dur_180, Ureal180 = self.slaser_build180(self.sim_experiment.inpulse180file, A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'bruker')
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1/2.0 - pulse_dur_90/2.0 - pulse_dur_180/2.0
delay2 = TE1/2.0 + TE2/2.0 - pulse_dur_180
delay3 = TE2 - pulse_dur_180
delay4 = delay2
delay5 = TE1/2.0 - pulse_dur_180 + self.sim_experiment.DigShift
# TE_fill = TE - 2.*TE1 - 2.*TE2
# delay1 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 - pulse_dur_90/2.0
# delay2 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay3 = TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay4 = TE2/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0
# delay5 = TE1/2.0 - pulse_dur_180/2.0 + TE_fill/8.0 + self.sim_experiment.DigShift
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = Ureal90.evolve(sigma0) # apply 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
# acquire
mx = pg.TTable1D(ACQ.table(sigma0))
# binning to remove degenerate peaks
outf, outa, outp = self.binning_code(mx, self.sim_experiment.b0, spin_system, self.sim_experiment.obs_iso, self.sim_experiment.tolppm, self.sim_experiment.tolpha, self.sim_experiment.ppmlo, self.sim_experiment.ppmhi, self.sim_experiment.RF_OFFSET)
metab_calib90 = self.apply_metab_properties(str(self.calibrationMetaboliteComboBox.currentText()), A_90, outf, outa, outp, insysfile)
lb = 15 if (self.sim_experiment.b0 == 297.2 or self.sim_experiment.b0 == 400.2) else 6
f, spectra = metab_calib90.getSpec(TE, self.sim_experiment.b0, self.sim_experiment.getTime(), 0, 1, 0, 0, lb, self.sim_experiment.getFs())
A90_calibration_data.append(np.real(spectra)[np.argmax(np.abs(spectra))])
# Fit a sine function
fitted_sine = self.fit_sin(self.sim_experiment.A_90s, A90_calibration_data)
params = [fitted_sine[key] for key in fitted_sine.keys()]
self.simConsole.append(' | A * sin(w*x + p) + c:')
self.simConsole.append(' | A = ' + str(params[0]) + ', w = ' + str(params[1]) + ', p = ' + str(params[2]) + ', c = ' + str(params[3]))
A90_calibration_data_fitted = self.sinfunc(self.sim_experiment.A_90s, params[0], params[1], params[2], params[3])
# save results
self.sim_experiment.A_90 = self.sim_experiment.A_90s[np.argmax(A90_calibration_data_fitted)]
plt.figure()
plt.plot(self.sim_experiment.A_90s, A90_calibration_data, '.', color='blue')
plt.plot(self.sim_experiment.A_90s, A90_calibration_data_fitted, color='red')
plt.plot(self.sim_experiment.A_90, A90_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_90s)-self.sim_experiment.A_90)).argmin()], 'x', color='black')
plt.text(self.sim_experiment.A_90, A90_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_90s)-self.sim_experiment.A_90)).argmin()]*1.2, str(self.sim_experiment.A_90), rotation='vertical', color='black')
plt.title('90-degree calibration sLASER (w/ AFP 180, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
plt.xlabel('A_90 [mT]')
plt.ylabel('Signal Intensity'); plt.ylim([np.amin(A90_calibration_data) + 0.25*np.amin(A90_calibration_data),np.amax(A90_calibration_data) + 0.25*np.amax(A90_calibration_data)])
plt.savefig(self.save_dir_sim + '90-DEGREE-CALIBRATION' + '_' + str(self.sim_experiment.PULSE_180_LENGTH) + 'secAFP.pdf')
plt.close()
self.simConsole.append(' | CALIBRATED 90 SLR AMPLITUDE: ' + str(self.sim_experiment.A_90))
self.slaser_build90(self.sim_experiment.inpulse90file, self.sim_experiment.A_90, self.sim_experiment.PULSE_90_LENGTH, self.sim_experiment.getGyratio(), spin_system, True, 'bruker')
elif self.sLASERradioButton.isChecked():
# Create a new simulations results file
self.save_dir_sim = 'pints/experiments/sLASER_sim_siemens_' \
+ datetime.datetime.now().strftime("%Y_%m_%d_%H%M%S") \
+ '_TE' + str(self.sim_experiment.TE)
if self.T7Button.isChecked():
self.save_dir_sim += '_7T/'
elif self.T3Button.isChecked():
self.save_dir_sim += '_3T/'
elif self.T9Button.isChecked():
self.save_dir_sim += '_9T/'
if not os.path.exists(self.save_dir_sim):
os.makedirs(self.save_dir_sim)
self.sim_results = open(self.save_dir_sim + 'sLASER_sim_results.txt', 'w')
# Write parameters in file
self.sim_results.write(';PINTS for FITMAN Simulation Output\n')
self.sim_results.write(';Experiment Information\n')
self.sim_results.write(';---------------------------------------------------------------------------\n')
self.sim_results.write(';Name: ' + self.sim_experiment.name + '\n')
self.sim_results.write(';Created: ' + self.sim_experiment.date + '\n')
self.sim_results.write(';Comment: ' + self.sim_experiment.description + '\n')
self.sim_results.write(';PI: ' + self.sim_experiment.author + '\n')
self.sim_results.write(';b0: ' + str(self.sim_experiment.b0) + '\n')
self.sim_results.write(';' + str(int(np.size(self.insysfiles)+int(np.size(self.macromolecules)))) + ' Metabolites: ' + str(self.insysfiles).replace('[','').replace(']','').replace('\'','').replace('.sys',''))
if self.macroIncludeButton.isChecked(): self.sim_results.write(', ' + str(self.macromolecules).replace('[','').replace(']','').replace('\'',''))
self.sim_results.write('\n')
self.sim_results.write(';Simulation Results\n')
self.sim_results.write(';---------------------------------------------------------------------------\n')
# Set up for calibration experiments
insysfile = str(self.calibrationMetaboliteComboBox.currentText()) + '.sys'
if self.sim_experiment.b0 == 123.3:
insysfile = 'pints/metabolites/3T_' + insysfile
elif self.sim_experiment.b0 == 297.2:
insysfile = 'pints/metabolites/7T_' + insysfile
elif self.sim_experiment.b0 == 400.2:
insysfile = 'pints/metabolites/9.4T_' + insysfile
print('')
print(insysfile)
spin_system = pg.spin_system()
spin_system.read(insysfile)
for i in range(spin_system.spins()):
spin_system.PPM(i, spin_system.PPM(i) - self.sim_experiment.RF_OFFSET)
# Run the 180 calibration
self.simConsole.append('\n1. 180-degree calibration sLASER (w/ ideal 90, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
A180_calibration_data = []
for A_180 in self.sim_experiment.A_180s:
TE = self.sim_experiment.TE
TE1 = float((TE * 0.31) / 1000.0)
TE3 = float((TE * 0.31) / 1000.0)
TE2 = float(TE/1000.0 - TE1 - TE3)
TE_fill = TE/1000.0 - TE1 - TE2 - TE3
# build 90 degree pulse
peak_to_end_90 = 0
# build 180 degree pulse
A_180, pulse180, pulse_dur_180, Ureal180 = self.slaser_build180(self.sim_experiment.inpulse180file, A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'siemens')
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1/2.0 + TE_fill/8.0 - pulse_dur_180/2.0 - peak_to_end_90
delay2 = TE1/2.0 + TE_fill/8.0 + TE2/4.0 + TE_fill/8.0 - pulse_dur_180
delay3 = TE2/4.0 + TE_fill/8.0 + TE2/4.0 + TE_fill/8.0 - pulse_dur_180
delay4 = TE2/4.0 + TE_fill/8.0 + TE3/2.0 + TE_fill/8.0 - pulse_dur_180
delay5 = TE3/2.0 + TE_fill/8.0 - pulse_dur_180/2.0
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = pg.Ixpuls(spin_system, sigma0, self.sim_experiment.obs_iso, 90.0) # apply ideal 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
# acquire
mx = pg.TTable1D(ACQ.table(sigma0))
# binning to remove degenerate peaks
outf, outa, outp = self.binning_code(mx, self.sim_experiment.b0, spin_system, self.sim_experiment.obs_iso, self.sim_experiment.tolppm, self.sim_experiment.tolpha, self.sim_experiment.ppmlo, self.sim_experiment.ppmhi, self.sim_experiment.RF_OFFSET)
metab_calib180 = self.apply_metab_properties(str(self.calibrationMetaboliteComboBox.currentText()), A_180, outf, outa, outp, insysfile)
lb = 15 if (self.sim_experiment.b0 == 297.2 or self.sim_experiment.b0 == 400.2) else 6
f, spectra = metab_calib180.getSpec(TE, self.sim_experiment.b0, self.sim_experiment.getTime(), 0, 1, 0, 0, lb, self.sim_experiment.getFs())
A180_calibration_data.append(np.real(spectra)[np.argmax(np.abs(spectra))])
# Fit a logistic function
initial_guess_A = np.amin(A180_calibration_data)
initial_guess_B = np.abs(np.amax(A180_calibration_data)-np.amin(A180_calibration_data))/np.abs(A180_calibration_data[np.argmax(A180_calibration_data)]-A180_calibration_data[np.argmin(A180_calibration_data)])
initial_guess_K = np.amax(A180_calibration_data)
initial_guess_s = self.sim_experiment.A_180s[np.argmin(A180_calibration_data)]
fit_x = self.sim_experiment.A_180s
fit_y = np.pad(A180_calibration_data[np.argmin(A180_calibration_data):], (np.size(A180_calibration_data[:np.argmin(A180_calibration_data)]), 0), 'constant', constant_values=(np.amin(A180_calibration_data),0))
params, params_covariance = sp.optimize.curve_fit(self.logs_func, fit_x, fit_y, p0=[initial_guess_A,initial_guess_B,initial_guess_K, initial_guess_s])#, bounds=([-np.inf, 0, 0, 0], [0, np.inf, np.inf, self.sim_experiment.A_180s[-1]]))
self.simConsole.append(' | A + (K - A)/(1 + np.exp(-B*x)): ')
self.simConsole.append(' | A0 = ' + str(initial_guess_A) + ', B0 = ' + str(initial_guess_B) + ', K0 = ' + str(initial_guess_K) + ', s0 = ' + str(initial_guess_s))
self.simConsole.append(' | A = ' + str(params[0]) + ', B = ' + str(params[1]) + ', K = ' + str(params[2]) + ', s = ' + str(params[3]))
A180_calibration_data_init = self.logs_func(self.sim_experiment.A_180s, initial_guess_A, initial_guess_B, initial_guess_K, initial_guess_s)
A180_calibration_data_fitted = self.logs_func(self.sim_experiment.A_180s, params[0], params[1], params[2], params[3])
# save results
if self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()] + int(self.sim_experiment.A_180s[-1]/6) < self.sim_experiment.A_180s[-1]:
self.sim_experiment.A_180 = self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()] + int(self.sim_experiment.A_180s[-1]/6) # pad to be sure of adiabicity
else:
self.sim_experiment.A_180 = self.sim_experiment.A_180s[(np.abs(np.asarray(fit_y)-params[2])).argmin()]
plt.figure()
plt.plot(self.sim_experiment.A_180s, A180_calibration_data, '.', color='blue')
plt.plot(self.sim_experiment.A_180s, A180_calibration_data_init, color='green')
plt.plot(self.sim_experiment.A_180s, A180_calibration_data_fitted, color='red')
plt.plot(self.sim_experiment.A_180, A180_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_180s)-self.sim_experiment.A_180)).argmin()], 'x', color='black')
plt.text(self.sim_experiment.A_180, A180_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_180s)-self.sim_experiment.A_180)).argmin()]*1.2, str(self.sim_experiment.A_180), rotation='vertical', color='black')
plt.title('180-degree calibration sLASER (w/ ideal 90, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
plt.xlabel('A_180 [mT]')
plt.ylabel('Signal Intensity'); plt.ylim([np.amin(A180_calibration_data) + 0.25*np.amin(A180_calibration_data),np.amax(A180_calibration_data) + 0.25*np.amax(A180_calibration_data)])
plt.savefig(self.save_dir_sim + '180-DEGREE-CALIBRATION' + '_' + str(self.sim_experiment.PULSE_180_LENGTH) + 'secAFP.pdf')
plt.close()
# update progress bar
self.simProgressBar.setValue(1)
self.simConsole.append(' | CALIBRATED 180 AFP AMPLITUDE: ' + str(self.sim_experiment.A_180))
self.slaser_build180(self.sim_experiment.inpulse180file, self.sim_experiment.A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, True, 'siemens')
# Run the 90 calibration
self.simConsole.append('\n2. 90-degree calibration sLASER (w/ AFP 180, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
A90_calibration_data = []
for A_90 in self.sim_experiment.A_90s:
TE = self.sim_experiment.TE
TE1 = float((TE * 0.31) / 1000.0)
TE3 = float((TE * 0.31) / 1000.0)
TE2 = float(TE/1000.0 - TE1 - TE3)
TE_fill = TE/1000.0 - TE1 - TE2 - TE3
# build 90 degree pulse
A_90, pulse90, pulse_dur_90, peak_to_end_90, Ureal90 = self.slaser_build90(self.sim_experiment.inpulse90file, A_90, self.sim_experiment.PULSE_90_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'siemens')
# build 180 degree pulse
A_180, pulse180, pulse_dur_180, Ureal180 = self.slaser_build180(self.sim_experiment.inpulse180file, self.sim_experiment.A_180, self.sim_experiment.PULSE_180_LENGTH, self.sim_experiment.getGyratio(), spin_system, False, 'siemens')
H = pg.Hcs(spin_system) + pg.HJ(spin_system)
D = pg.Fm(spin_system, self.sim_experiment.obs_iso)
ac = pg.acquire1D(pg.gen_op(D), H, self.sim_experiment.dwell_time)
ACQ = ac
delay1 = TE1/2.0 + TE_fill/8.0 - pulse_dur_180/2.0 - peak_to_end_90
delay2 = TE1/2.0 + TE_fill/8.0 + TE2/4.0 + TE_fill/8.0 - pulse_dur_180
delay3 = TE2/4.0 + TE_fill/8.0 + TE2/4.0 + TE_fill/8.0 - pulse_dur_180
delay4 = TE2/4.0 + TE_fill/8.0 + TE3/2.0 + TE_fill/8.0 - pulse_dur_180
delay5 = TE3/2.0 + TE_fill/8.0 - pulse_dur_180/2.0
Udelay1 = pg.prop(H, delay1)
Udelay2 = pg.prop(H, delay2)
Udelay3 = pg.prop(H, delay3)
Udelay4 = pg.prop(H, delay4)
Udelay5 = pg.prop(H, delay5)
sigma0 = pg.sigma_eq(spin_system) # init
sigma1 = Ureal90.evolve(sigma0) # apply 90-degree pulse
sigma0 = pg.evolve(sigma1, Udelay1)
sigma1 = Ureal180.evolve(sigma0) # apply AFP1
sigma0 = pg.evolve(sigma1, Udelay2)
sigma1 = Ureal180.evolve(sigma0) # apply AFP2
sigma0 = pg.evolve(sigma1, Udelay3)
sigma1 = Ureal180.evolve(sigma0) # apply AFP3
sigma0 = pg.evolve(sigma1, Udelay4)
sigma1 = Ureal180.evolve(sigma0) # apply AFP4
sigma0 = pg.evolve(sigma1, Udelay5)
# acquire
mx = pg.TTable1D(ACQ.table(sigma0))
# binning to remove degenerate peaks
outf, outa, outp = self.binning_code(mx, self.sim_experiment.b0, spin_system, self.sim_experiment.obs_iso, self.sim_experiment.tolppm, self.sim_experiment.tolpha, self.sim_experiment.ppmlo, self.sim_experiment.ppmhi, self.sim_experiment.RF_OFFSET)
metab_calib90 = self.apply_metab_properties(str(self.calibrationMetaboliteComboBox.currentText()), A_90, outf, outa, outp, insysfile)
lb = 15 if (self.sim_experiment.b0 == 297.2 or self.sim_experiment.b0 == 400.2) else 6
f, spectra = metab_calib90.getSpec(TE, self.sim_experiment.b0, self.sim_experiment.getTime(), 0, 1, 0, 0, lb, self.sim_experiment.getFs())
A90_calibration_data.append(np.real(spectra)[np.argmax(np.abs(spectra))])
# Fit a sine function
fitted_sine = self.fit_sin(self.sim_experiment.A_90s, A90_calibration_data)
params = [fitted_sine[key] for key in fitted_sine.keys()]
self.simConsole.append(' | A * sin(w*x + p) + c:')
self.simConsole.append(' | A = ' + str(params[0]) + ', w = ' + str(params[1]) + ', p = ' + str(params[2]) + ', c = ' + str(params[3]))
A90_calibration_data_fitted = self.sinfunc(self.sim_experiment.A_90s, params[0], params[1], params[2], params[3])
# save results
self.sim_experiment.A_90 = self.sim_experiment.A_90s[np.argmax(A90_calibration_data_fitted)]
plt.figure()
plt.plot(self.sim_experiment.A_90s, A90_calibration_data, '.', color='blue')
plt.plot(self.sim_experiment.A_90s, A90_calibration_data_fitted, color='red')
plt.plot(self.sim_experiment.A_90, A90_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_90s)-self.sim_experiment.A_90)).argmin()], 'x', color='black')
plt.text(self.sim_experiment.A_90, A90_calibration_data[(np.abs(np.asarray(self.sim_experiment.A_90s)-self.sim_experiment.A_90)).argmin()]*1.2, str(self.sim_experiment.A_90), rotation='vertical', color='black')
plt.title('90-degree calibration sLASER (w/ AFP 180, ' + str(self.calibrationMetaboliteComboBox.currentText()) + ') experiment')
plt.xlabel('A_90 [mT]')
plt.ylabel('Signal Intensity'); plt.ylim([np.amin(A90_calibration_data) + 0.25*np.amin(A90_calibration_data),np.amax(A90_calibration_data) + 0.25*np.amax(A90_calibration_data)])
plt.savefig(self.save_dir_sim + '90-DEGREE-CALIBRATION' + '_' + str(self.sim_experiment.PULSE_180_LENGTH) + 'secAFP.pdf')
plt.close()
self.simConsole.append(' | CALIBRATED 90 SLR AMPLITUDE: ' + str(self.sim_experiment.A_90))
self.slaser_build90(self.sim_experiment.inpulse90file, self.sim_experiment.A_90, self.sim_experiment.PULSE_90_LENGTH, self.sim_experiment.getGyratio(), spin_system, True, 'siemens')
elif self.LASERradioButton.isChecked():
# Create a new simulations results file
self.save_dir_sim = 'pints/experiments/LASER_sim_' \
+ datetime.datetime.now().strftime("%Y_%m_%d_%H%M%S") \
+ '_TE' + str(self.sim_experiment.TE)
if self.T7Button.isChecked():
self.save_dir_sim += '_7T/'
elif self.T3Button.isChecked():
self.save_dir_sim += '_3T/'
elif self.T9Button.isChecked():
self.save_dir_sim += '_9T/'
if not os.path.exists(self.save_dir_sim):