# Prepare Python environment
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 / "04-B1-02-AFI" / "04-B1-02-AFI"
data_file = "fig2.mat"
#Load either archived or generated plot variables
mat_contents = sio.loadmat(data_dir / data_file)
params = mat_contents["params"]
Nex_range = mat_contents["Nex_range"][0]
signal1_analytical = mat_contents["signal1_analytical"]
signal2_analytical = mat_contents["signal2_analytical"]
signal1_blochsim = mat_contents["signal1_blochsim"]
signal2_blochsim = mat_contents["signal2_blochsim"]
## Plot
# PYTHON CODE
# Module imports
import matplotlib.pyplot as plt
import chart_studio.plotly as py
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
# PYTHON CODE
init_notebook_mode(connected=True)
data1_1 = [dict(
visible = False,
line=dict(color='royalblue', dash='dash'),
x = params["EXC_FA"][0][0][0],
y = abs(np.squeeze(np.asarray(signal1_analytical[ii]))),
name = 'S<sub>1</sub>: Analytical Solution',
text = 'S<sub>1</sub>: Analytical Solution',
hoverinfo = 'x+y+text') for ii in range(len(Nex_range))]
data1_1[7]['visible'] = True
data1_2 = [dict(
visible = False,
line=dict(color='firebrick', dash='dash'),
x = params["EXC_FA"][0][0][0],
y = abs(np.squeeze(np.asarray(signal2_analytical[ii]))),
name = 'S<sub>2</sub>: Analytical Solution',
text = 'S<sub>2</sub>: Analytical Solution',
hoverinfo = 'x+y+text') for ii in range(len(Nex_range))]
data1_2[7]['visible'] = True
data2_1 = [dict(
visible = False,
line=dict(color='royalblue'),
x = params["EXC_FA"][0][0][0],
y = abs(np.squeeze(np.asarray(signal1_blochsim[ii]))),
name = 'S<sub>1</sub>: Bloch Simulation',
text = 'S<sub>1</sub>: Bloch Simulation',
hoverinfo = 'x+y+text') for ii in range(len(Nex_range))]
data2_1[7]['visible'] = True
data2_2 = [dict(
visible = False,
line=dict(color='firebrick'),
x = params["EXC_FA"][0][0][0],
y = abs(np.squeeze(np.asarray(signal2_blochsim[ii]))),
name = 'S<sub>2</sub>: Bloch Simulation',
text = 'S<sub>2</sub>: Bloch Simulation',
hoverinfo = 'x+y+text') for ii in range(len(Nex_range))]
data2_2[7]['visible'] = True
data = data1_1 + data2_1 + data1_2 + data2_2
steps = []
for i in range(len(Nex_range)):
step = dict(
method = 'restyle',
args = ['visible', [False] * len(data1_1)],
label = str(Nex_range[i])
)
step['args'][1][i] = True # Toggle i'th trace to "visible"
steps.append(step)
sliders = [dict(
x = 0,
y = -0.02,
active = 5,
currentvalue = {"prefix": "n<sup>th</sup> TR1-TR2: <b>"},
pad = {"t": 50, "b": 10},
steps = steps)]
layout = go.Layout(
width=580,
height=450,
margin=go.layout.Margin(
l=80,
r=40,
b=60,
t=10,
),
annotations=[
dict(
x=0.5004254919715793,
y=-0.18,
showarrow=False,
text='Excitation Flip Angle (°)',
font=dict(
family='Times New Roman',
size=22
),
xref='paper',
yref='paper'
),
dict(
x=-0.15,
y=0.5,
showarrow=False,
text='Signal',
font=dict(
family='Times New Roman',
size=22
),
textangle=-90,
xref='paper',
yref='paper'
),
],
xaxis=dict(
autorange=False,
range=[0, params['EXC_FA'][0][0][0][-1]],
showgrid=False,
linecolor='black',
linewidth=2
),
yaxis=dict(
autorange=True,
showgrid=False,
linecolor='black',
linewidth=2
),
legend=dict(
x=0.5,
y=0.9,
traceorder='normal',
font=dict(
family='Times New Roman',
size=12,
color='#000'
),
bordercolor='#000000',
borderwidth=2
),
sliders=sliders
)
fig = dict(data=data, layout=layout)
iplot(fig, filename = 'basic-line', config = config)Loading...