import scipy
import scipy.io as sio
from pathlib import Path
import numpy as np
import numpy as np
lipari = list(np.genfromtxt('lipari.csv', skip_header=0))
ii=0
for index in lipari:
lipari[ii]='rgb('+str(index[0])+','+str(index[1])+','+str(index[2])+')'
ii+=1
invlipari=list(reversed(lipari))
navia = list(np.genfromtxt('navia.csv', skip_header=0))
ii=0
for index in navia:
navia[ii]='rgb('+str(index[0])+','+str(index[1])+','+str(index[2])+')'
ii+=1
data_dir = Path("../../../data/06-MT-01-qMT")
b0map_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/b0mapMAT.mat')
b0map = np.array(b0map_mat["b0mapMAT"])
b1map_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/b1mapMAT.mat')
b1map = np.array(b1map_mat["b1mapMAT"])
r1map_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/r1mapMAT.mat')
r1map = np.array(r1map_mat["r1mapMAT"])
mtdata_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/mtdataMAT.mat')
mtdata = np.array(mtdata_mat["mtdataMAT"])
mask_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/maskMAT.mat')
mask = np.array(mask_mat["maskMAT"])
Fmap_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/FmapMAT.mat')
Fmap = np.array(Fmap_mat["FmapMAT"])
kfmap_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/kfmapMAT.mat')
kfmap = np.array(kfmap_mat["kfmapMAT"])
T2fmap_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/T2fmapMAT.mat')
T2fmap = np.array(T2fmap_mat["T2f"])
T2rmap_mat = scipy.io.loadmat(data_dir / 'qMT_tutorial-ISMRM2022-main' / 'results/realData/T2rmapMAT.mat')
T2rmap = np.array(T2rmap_mat["T2r"])
import matplotlib.pyplot as plt
from PIL import Image
from matplotlib.image import imread
import scipy.io
import plotly
from plotly.subplots import make_subplots
import plotly.graph_objs as go
import numpy as np
from plotly import __version__
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
config={'showLink': False, 'displayModeBar': False}
# PYTHON CODE
from plotly import tools
xAxis = np.arange(0,88)
yAxis = np.arange(0,128)
b0map = np.multiply(b0map,mask)
b1map = np.multiply(b1map,mask)
r1map = np.multiply(r1map,mask)
mtdata_angle = np.multiply(mtdata[:,:,:,0].reshape((88,128)),mask)
Fmap = np.multiply(Fmap,mask)
kfmap = np.multiply(kfmap,mask)
T2fmap = np.multiply(T2fmap,mask)
T2rmap = np.multiply(T2rmap,mask)
trace1 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(b0map,3),
zmin=-30,
zmax=30,
colorscale='RdBu',
colorbar=dict(title = "B<sub>0</sub> (Hz)", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=True,
name = 'B<sub>0</sub> (Hz)')
trace2 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(b1map,3),
zmin=0.7,
zmax=1.3,
colorscale='RdBu',
colorbar=dict(title = "B<sub>1</sub>", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=False,
name = 'B<sub>1</sub> values')
trace3 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(r1map,3),
zmin=0.5,
zmax=1.5,
colorscale=invlipari,
colorbar=dict(title = "R<sub>1</sub> (s<sup>-1</sup>)", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=False,
name = 'R<sub>1</sub> (s<sup>-1</sup>)')
trace4 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(mtdata_angle,3),
zmin=0.5,
zmax=1,
colorscale='Portland',
colorbar=dict(title = "MT", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=False,
name = 'MT (angle 142)')
trace5 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(Fmap,3),
zmin=0.05,
zmax=0.3,
colorscale='Portland',
colorbar=dict(title = "F", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=True,
name = 'F')
trace6 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(kfmap,3),
colorscale='Portland',
colorbar=dict(title = "k<sub>f</sub> (s<sup>-1</sup>)", thickness=35,
tickfont=dict(family='Times New Roman', size=15), ypad=1),
visible=False,
name = 'k<sub>f</sub> (s<sup>-1</sup>)')
trace7 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(T2fmap,3),
zmin=0,
zmax=0.05,
colorscale=navia,
colorbar=dict(title = "T<sub>2f</sub> (ms)", thickness=35,
tickfont=dict(family='Times New Roman', size=15)),
visible=False,
name = 'T<sub>2f</sub> (ms)')
trace8 = go.Heatmap(x = xAxis,
y = yAxis,
z=np.rot90(T2rmap,3),
zmin=5e-6,
zmax=25e-6,
colorscale=navia,
colorbar=dict(title = "T<sub>2r</sub> (s)", thickness=35, ticklen=7,
tickfont=dict(family='Times New Roman', size=15)),
visible=False,
name = 'T<sub>2r</sub> (μs)')
data1=[trace1, trace2, trace3, trace4]
data2=[trace5, trace6, trace7, trace8]
updatemenus = list([
dict(active=0,
x = 0.2,
xanchor = 'left',
y = -0.15,
yanchor = 'bottom',
direction = 'up',
font=dict(
family='Times New Roman',
size=16
),
buttons=list([
dict(label = 'B0 map',
method = 'update',
args = [{'visible': [True, False, False, False]},
]),
dict(label = 'B1 map',
method = 'update',
args = [{'visible': [False, True, False, False]},
]),
dict(label = 'R1 map',
method = 'update',
args = [{'visible': [False, False, True, False]},
]),
dict(label = 'MT data',
method = 'update',
args = [{'visible': [False, False, False, True]},
])
]),
)
])
layout1 = dict(
width=345,
height=345,
margin = dict(
t=40,
r=50,
b=10,
l=50),
annotations=[
dict(
x=0.5,
y=1.15,
showarrow=False,
text='Input maps',
font=dict(
family='Times New Roman',
size=26
),
xref='paper',
yref='paper'
)
],
xaxis = dict(range = [0,85], autorange = False,
showgrid = False, zeroline = False, showticklabels = False,
ticks = '', domain=[0, 1]),
yaxis = dict(range = [0,127], autorange = False,
showgrid = False, zeroline = False, showticklabels = False,
ticks = '', domain=[0, 1]),
showlegend = False,
autosize = False,
updatemenus=updatemenus
)
fig = dict(data=data1,layout=layout1)
iplot(fig, filename = 'basic-heatmap', config = config)Loading...
updatemenus = list([
dict(active=0,
x = 0.2,
xanchor = 'left',
y = -0.15,
yanchor = 'bottom',
direction = 'up',
font=dict(
family='Times New Roman',
size=16),
buttons=list([
dict(label = 'F map',
method = 'update',
args = [{'visible': [True, False, False, False]},
]),
dict(label = 'kf map',
method = 'update',
args = [{'visible': [False, True, False, False]},
]),
dict(label = 'T2f map',
method = 'update',
args = [{'visible': [False, False, True, False]},
]),
dict(label = 'T2r map',
method = 'update',
args = [{'visible': [False, False, False, True]},
])
]),
)
])
layout2 = dict(
width=345,
height=345,
margin = dict(
t=40,
r=50,
b=10,
l=50),
annotations=[
dict(
x=0.5,
y=1.15,
showarrow=False,
text='Fitted maps',
font=dict(
family='Times New Roman',
size=26
),
xref='paper',
yref='paper'
)
],
xaxis = dict(range = [0,85], autorange = False,
showgrid = False, zeroline = False, showticklabels = False,
ticks = '', domain=[0, 1]),
yaxis = dict(range = [0,127], autorange = False,
showgrid = False, zeroline = False, showticklabels = False,
ticks = '', domain=[0, 1]),
showlegend = False,
autosize = False,
updatemenus=updatemenus
)
fig = dict(data=data2,layout=layout2)
iplot(fig, filename = 'basic-heatmap', config = config)Loading...