from repo2data.repo2data import Repo2Data
import os
import pickle
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
from IPython.display import display, HTML
from plotly import tools
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_ROOT = dataset_path / "qmrlab-t1-book" / "t1-book-neurolibre"
filename = DATA_ROOT / "02" / 'figure_5.pkl'
with open(filename, 'rb') as f:
params, data_mean, data_mean_div_sin, data_mean_div_tan, data_std, data_std_div_sin, data_std_div_tan, params_highres, signal_WM, signal_WM_div_sin, signal_WM_div_tan = pickle.load(f)
config={'showLink': False, 'displayModeBar': False}
init_notebook_mode(connected=True)
data1 = dict(
visible = True,
x = params_highres["EXC_FA"],
y = signal_WM,
name = 'Analytical Solutions',
text = params["EXC_FA"],
mode = 'lines',
line = dict(
color = ('rgb(0, 0, 0)'),
dash = 'dot'),
hoverinfo='none')
data2 = dict(
visible = True,
x = signal_WM_div_tan,
y = signal_WM_div_sin,
name = 'Analytical Solutions',
text = params_highres["EXC_FA"],
mode = 'lines',
xaxis='x2',
yaxis='y2',
line = dict(
color = ('rgb(0, 0, 0)'),
dash = 'dot'
),
hoverinfo='none',
showlegend=False)
data3 = dict(
visible = True,
x = params["EXC_FA"],
y = data_mean,
name = 'Nonlinear Form - Noisy',
text = ["Flip angle: " + str(x) + "°" for x in params["EXC_FA"]],
mode = 'markers',
hoverinfo = 'y+text',
line = dict(
color = ('rgb(22, 96, 167)'),
),
error_y=dict(
type='data',
array=data_std,
visible=True,
color = ('rgb(142, 192, 240)')
))
data4 = dict(
visible = True,
x = data_mean_div_tan,
y = data_mean_div_sin,
name = 'Linear Form - Noisy',
text = ["Flip angle: " + str(x) + "°" for x in params["EXC_FA"]],
mode = 'markers',
xaxis='x2',
yaxis='y2',
hoverinfo = 'x+y+text',
line = dict(
color = ('rgb(205, 12, 24)'),
),
error_x=dict(
type='data',
array=data_std_div_tan,
visible=True,
color = ('rgb(248, 135, 142)')
),
error_y=dict(
type='data',
array=data_std_div_sin,
visible=True,
color = ('rgb(248, 135, 142)')
))
data = [data1, data2, data3, data4]
layout = go.Layout(
width=580,
height=450,
margin=go.layout.Margin(
l=80,
r=80,
b=60,
t=60,
),
annotations=[
dict(
x=0.5004254919715793,
y=-0.14,
showarrow=False,
text='Excitation Flip Angle (<i>θ<sub>n</sub></i>)',
font=dict(
family='Times New Roman',
size=22,
color=('rgb(21, 91, 158)')
),
xref='paper',
yref='paper'
),
dict(
x=-0.17,
y=0.5,
showarrow=False,
text='Signal (<i>S<sub>n</sub></i>)',
font=dict(
family='Times New Roman',
size=22,
color=('rgb(21, 91, 158)')
),
textangle=-90,
xref='paper',
yref='paper'
),
dict(
x=0.5004254919715793,
y=1.15,
showarrow=False,
text='<i>S<sub>n</sub></i> / tan(<i>θ<sub>n</sub></i>)',
font=dict(
family='Times New Roman',
size=22,
color=('rgb(169, 10, 20)')
),
xref='paper',
yref='paper'
),
dict(
x=1.16,
y=0.5,
showarrow=False,
text='<i>S<sub>n</sub></i> / sin(<i>θ<sub>n</sub></i>)',
font=dict(
family='Times New Roman',
size=22,
color=('rgb(169, 10, 20)')
),
xref='paper',
yref='paper',
textangle=-90,
),
],
xaxis=dict(
autorange=False,
range=[params['EXC_FA'][0], params['EXC_FA'][-1]],
showgrid=False,
linecolor='black',
linewidth=2
),
yaxis=dict(
autorange=True,
showgrid=False,
linecolor='black',
linewidth=2
),
xaxis2=dict(
autorange=False,
range=[0, 1],
showgrid=False,
mirror=True,
overlaying= 'x',
anchor= 'y2',
side= 'top',
linecolor='black',
linewidth=2
),
yaxis2=dict(
autorange=False,
range=[0, 1],
showgrid=False,
overlaying= 'y',
anchor= 'x',
side= 'right',
linecolor='black',
linewidth=2
),
legend=dict(
x=0.32,
y=0.98,
traceorder='normal',
font=dict(
family='Times New Roman',
size=12,
color='#000'
),
bordercolor='#000000',
borderwidth=2
),
plot_bgcolor='white'
)
fig = dict(data=data, layout=layout)
iplot(fig, filename = 'vfa_fig_5.html', config = config)
Loading...