# Prepare Python environment
import numpy as np
import scipy.io as sio
from pathlib import Path
from contextlib import contextmanager
import sys, os
from pathlib import Path
@contextmanager
def suppress_stdout():
with open(os.devnull, "w") as devnull:
old_stdout = sys.stdout
sys.stdout = devnull
try:
yield
finally:
sys.stdout = old_stdout
import os
from pathlib import Path
def find_myst_yml_directories(start_dir=None):
"""
Recursively search for directories containing myst.yml file.
Args:
start_dir (str or Path): Starting directory (defaults to current directory)
Returns:
list: List of full paths to directories containing myst.yml
"""
if start_dir is None:
start_dir = Path.cwd()
else:
start_dir = Path(start_dir)
myst_dirs = []
def _search_directory(current_dir):
# Check if myst.yml exists in current directory
myst_file = current_dir / "myst.yml"
if myst_file.exists():
myst_dirs.append(str(current_dir.resolve()))
# Don't search subdirectories if we found myst.yml here
return
# Recursively search all subdirectories
for item in current_dir.iterdir():
if item.is_dir():
try:
_search_directory(item)
except (PermissionError, OSError):
# Skip directories we can't access
continue
_search_directory(start_dir)
return myst_dirs
def find_myst_yml_directories_upwards(start_dir=None):
"""
Search for myst.yml in current directory, if not found go to parent and repeat.
Args:
start_dir (str or Path): Starting directory (defaults to current directory)
Returns:
str or None: Full path of directory containing myst.yml, or None if not found
"""
if start_dir is None:
current_dir = Path.cwd()
else:
current_dir = Path(start_dir)
# Keep going up until we reach the filesystem root
while current_dir != current_dir.parent: # Stop at root
myst_file = current_dir / "myst.yml"
if myst_file.exists():
return str(current_dir.resolve())
# Move to parent directory
current_dir = current_dir.parent
return None
with suppress_stdout():
repo_path = Path(find_myst_yml_directories_upwards())
print(repo_path)
data_req_path = repo_path / "binder" / "data_requirement.json"
data_path = repo_path / "data"
dataset_path = data_path / "qmrlab-mooc"
data_dir = dataset_path / "03-T2" / "03-T2"
data_file = "multiexpo_T2_image.mat"
#Load either archived or generated plot variables
mat_contents = sio.loadmat(data_dir / data_file)
# Get MATLAB data
# Input MET2 data with different TE values
ME_TE_1 = mat_contents['ME_TE_1']
ME_TE_2 = mat_contents['ME_TE_2']
ME_TE_3 = mat_contents['ME_TE_3']
ME_TE_4 = mat_contents['ME_TE_4']
ME_TE_4 = mat_contents['ME_TE_4']
# Output MWF, IEW and MW maps from qMRLab simulation
MWF_map = mat_contents['MWF']
T2MW_map = mat_contents['T2MW']
T2IEW_map = mat_contents['T2IEW']
## Plot
import matplotlib.pyplot as plt
import chart_studio.plotly as py
import plotly.graph_objs as go
import numpy as np
from chart_studio.plotly import plot
from IPython.display import display, HTML
from plotly import tools
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
config = {'showLink': False, 'displayModeBar': False}
xAxis = np.arange(0, MWF_map.shape[1])
yAxis = np.arange(0, MWF_map.shape[0])
trace1 = go.Heatmap(x=xAxis,
y=yAxis,
z=ME_TE_1,
colorscale='Gray',
showscale=False,
visible=False,
name='Signal')
trace2 = go.Heatmap(x=xAxis,
y=yAxis,
z=ME_TE_2,
colorscale='Gray',
showscale=False,
visible=False,
name='Signal')
trace3 = go.Heatmap(x=xAxis,
y=yAxis,
z=ME_TE_3,
colorscale='Gray',
showscale=False,
visible=True,
name='Signal')
trace4 = go.Heatmap(x=xAxis,
y=yAxis,
z=ME_TE_4,
colorscale='Gray',
visible=False,
showscale=False,
name='Signal')
trace5 = go.Heatmap(x=xAxis,
y=yAxis,
z=MWF_map,
colorscale='Portland',
xaxis='x2',
yaxis='y2',
visible=True,
name='MWF',
zmin=25,
zmax=55)
trace6 = go.Heatmap(x=xAxis,
y=yAxis,
z=T2IEW_map,
colorscale='Portland',
xaxis='x2',
yaxis='y2',
visible=False,
name='T2 IEW (ms)',
zmin=40,
zmax=100)
trace7 = go.Heatmap(x=xAxis,
y=yAxis,
z=T2MW_map,
colorscale='Portland',
xaxis='x2',
yaxis='y2',
visible=False,
name='T2 MW (ms)',
zmin=15,
zmax=40)
data = [trace1, trace2, trace3, trace4, trace5, trace6, trace7]
updatemenus = [
dict(
active=2,
x=0.12,
xanchor='left',
y=-0.15,
yanchor='bottom',
direction='up',
font=dict(family='Times New Roman', size=16),
buttons=[
dict(label='12.8 ms',
method='update',
args=[{'visible': [True, False, False, False, trace5['visible'], trace6['visible'], trace7['visible']]}]),
dict(label='128 ms',
method='update',
args=[{'visible': [False, True, False, False, trace5['visible'], trace6['visible'], trace7['visible']]}]),
dict(label='256 ms',
method='update',
args=[{'visible': [False, False, True, False, trace5['visible'], trace6['visible'], trace7['visible']]}]),
dict(label='384 ms',
method='update',
args=[{'visible': [False, False, False, True, trace5['visible'], trace6['visible'], trace7['visible']]}])
],
),
dict(
x=0.7,
xanchor='left',
y=-0.15,
yanchor='bottom',
direction='up',
font=dict(family='Times New Roman', size=16),
buttons=[
dict(label='MWF',
method='update',
args=[{'visible': [trace1['visible'], trace2['visible'], trace3['visible'], trace4['visible'], True, False, False]},
{'annotations': [
dict(
x=0.19,
y=1.15,
showarrow=False,
text='MET2w',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=0.85,
y=1.15,
showarrow=False,
text='MWF map',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=1.17,
y=1.15,
showarrow=False,
text='T<sub>2</sub> (ms)',
font=dict(family='Times New Roman', size=26),
xref='paper',
yref='paper'
),
dict(
x=0.02,
y=-0.15,
showarrow=False,
text='TE:',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
]}]),
dict(label='T2 IEW',
method='update',
args=[{'visible': [trace1['visible'], trace2['visible'], trace3['visible'], trace4['visible'], False, True, False]},
{'annotations': [
dict(
x=0.19,
y=1.15,
showarrow=False,
text='MET2w',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=0.95,
y=1.25,
showarrow=False,
text='T2 map for<br>Intra/Extracellular Water',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=1.17,
y=1.15,
showarrow=False,
text='T<sub>2</sub> (ms)',
font=dict(family='Times New Roman', size=26),
xref='paper',
yref='paper'
),
dict(
x=0.02,
y=-0.15,
showarrow=False,
text='TE:',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
]}]),
dict(label='T2 MW',
method='update',
args=[{'visible': [trace1['visible'], trace2['visible'], trace3['visible'], trace4['visible'], False, False, True]},
{'annotations': [
dict(
x=0.19,
y=1.15,
showarrow=False,
text='MET2w',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=0.86,
y=1.25,
showarrow=False,
text='T2 map for<br>Myelin Water',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
dict(
x=1.17,
y=1.15,
showarrow=False,
text='T<sub>2</sub> (ms)',
font=dict(family='Times New Roman', size=26),
xref='paper',
yref='paper'
),
dict(
x=0.02,
y=-0.15,
showarrow=False,
text='TE:',
font=dict(family='Times New Roman', size=22),
xref='paper',
yref='paper'
),
]}])
],
),
]
layout = dict(
width=728,
height=448.5,
margin=dict(
t=90,
r=140,
b=90,
l=30),
annotations=[
dict(
x=0.19,
y=1.15,
showarrow=False,
text='MET2w',
font=dict(
family='Times New Roman',
size=22
),
xref='paper',
yref='paper'
),
dict(
x=0.85,
y=1.15,
showarrow=False,
text='MWF map', # Default title, will change with dropdown selection
font=dict(
family='Times New Roman',
size=22
),
xref='paper',
yref='paper'
),
dict(
x=1.17,
y=1.15,
showarrow=False,
text='T<sub>2</sub> (ms)',
font=dict(
family='Times New Roman',
size=26
),
xref='paper',
yref='paper'
),
dict(
x=0.02,
y=-0.15,
showarrow=False,
text='TE:',
font=dict(
family='Times New Roman',
size=22
),
xref='paper',
yref='paper'
),
],
xaxis=dict(range=[0, xAxis[-1]], autorange=False,
showgrid=False, zeroline=False, showticklabels=False,
ticks='', domain=[0, 0.5]), # First plot domain
yaxis=dict(range=[0, yAxis[-1]], autorange=False,
showgrid=False, zeroline=False, showticklabels=False,
ticks='', domain=[0, 1]),
xaxis2=dict(range=[0, xAxis[-1]], autorange=False,
showgrid=False, zeroline=False, showticklabels=False,
ticks='', domain=[0.5, 1]), # Second plot domain
yaxis2=dict(range=[0, yAxis[-1]], autorange=False,
showgrid=False, zeroline=False, showticklabels=False,
ticks='', domain=[0, 1], anchor='x2'),
showlegend=False,
autosize=False,
updatemenus=updatemenus
)
fig = dict(data=data, layout=layout)
iplot(fig, filename='ir_fig_2.html', config=config)
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