# Prepare Python environment
import scipy.io as sio
import numpy as np
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 / "06-MT-03-MTsat" / "06-MT-03-MTsat"
data_file = "fig1_mtsat.mat"
#Load either archived or generated plot variables
mat_contents = sio.loadmat(data_dir / data_file)
MTsats = mat_contents["MTsats"][0]
MTRs = mat_contents["MTRs"][0]
T1s = mat_contents["T1s"][0]
T1f = mat_contents["T1_range"][0]
# Plot Figure 1
# Module imports
import matplotlib.pyplot as plt
import plotly as py
import plotly.graph_objs as go
import numpy as np
from plotly import __version__
from plotly.subplots import make_subplots
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
config={'showLink': False, 'displayModeBar': False}
init_notebook_mode(connected=True)
# PYTHON CODE
init_notebook_mode(connected=True)
# The polling here is to ensure that plotly.js has already been loaded before
# setting display alignment in order to avoid a race condition.
## Setup for plots
fig = make_subplots(rows=1, cols=3, horizontal_spacing = 0.1)
fig.add_trace(
go.Scatter(
x=T1f,
y=MTRs,
hoverinfo = 'y',
showlegend=False
), row= 1, col=1
)
fig.add_trace(
go.Scatter(
x=T1f,
y=T1s,
hoverinfo = 'y',
showlegend=False
), row= 1, col=2
)
fig.add_trace(
go.Scatter(
x=T1f,
y=MTsats,
hoverinfo = 'y',
showlegend=False
), row= 1, col=3
)
layout = go.Layout(
width=900,
height=250,
margin=go.layout.Margin(
l=200,
r=30,
b=60,
t=00,
),
annotations=[
dict(
x=0.51,
y=-0.3,
showarrow=False,
text='T1f (s)',
font=dict(
family='Times New Roman',
size=22
),
textangle=0,
xref='paper',
yref='paper'
),
dict(
x=0.92,
y=-0.3,
showarrow=False,
text='T1f (s)',
font=dict(
family='Times New Roman',
size=22
),
textangle=0,
xref='paper',
yref='paper'
),
dict(
x=0.1,
y=-0.3,
showarrow=False,
text='T1f (s)',
font=dict(
family='Times New Roman',
size=22
),
textangle=0,
xref='paper',
yref='paper'
),
dict(
x=-0.08,
y=0.5,
showarrow=False,
text='MTR',
font=dict(
family='Times New Roman',
size=22
),
textangle=-90,
xref='paper',
yref='paper'
),
dict(
x=0.285,
y=0.5,
showarrow=False,
text='T<sub>1</sub> (s)',
font=dict(
family='Times New Roman',
size=22
),
textangle=-90,
xref='paper',
yref='paper'
),
dict(
x=0.685,
y=0.5,
showarrow=False,
text='MTsat (%)',
font=dict(
family='Times New Roman',
size=22
),
textangle=-90,
xref='paper',
yref='paper'
),
],
xaxis=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2
),
yaxis=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2,
range=[50,70]
),
xaxis2=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2,
range=[0.7,1.3]
),
yaxis2=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2,
range=[0.7,1.3]
),
xaxis3=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2
),
yaxis3=dict(
showgrid=True,
gridcolor='rgb(169,169,169)',
linecolor='black',
linewidth=2,
range=[5,7]
),
)
fig.update_layout(layout)
plot(fig, filename = 'mtsatt1.html', config = config)
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'mtsatt1.html'