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 / "01" / "figure_6.pkl"
with open(filename, 'rb') as f:
TR_range, TI_lowres, TI_highres, T1_mean, T1_std, data_mean, data_std, data_noiseless = pickle.load(f)
config={'showLink': False, 'displayModeBar': False}
init_notebook_mode(connected=True)
data1 = [dict(
visible = False,
x = np.squeeze(np.asarray(TI_lowres[ii,:])),
y = np.squeeze(np.asarray(data_mean[ii,:])),
error_y=dict(
type='data',
color = ('rgb(22, 96, 167)'),
array=np.squeeze(np.asarray(data_std[ii,:])),
visible=True
),
line = dict(
color = ('rgb(22, 96, 167)'),
dash = 'dot'),
mode = 'markers',
name = 'Monte Carlo simulated signal',
text = 'Monte Carlo simulated signal',
hoverinfo = 'x+y+text') for ii in range(len(TR_range))]
data1[28]['visible'] = True
data2 = [dict(
visible = False,
x = np.squeeze(np.asarray(TI_highres[ii,:])),
y = np.squeeze(np.asarray(data_noiseless[ii,:])),
line = dict(
color = ('rgb(247, 152, 19)'),
),
name = 'Noiseless signal',
text = 'Noiseless signal',
hoverinfo = 'x+y+text') for ii in range(len(TR_range))]
data2[28]['visible'] = True
data_meanT1 = [dict(
visible = False,
x = TR_range,
y = T1_mean,
name = 'Mean T<sub>1</sub> (s)',
text = 'Mean T<sub>1</sub> (s)',
hoverinfo = 'x+y+text',
xaxis='x2',
yaxis='y2') for ii in range(len(TR_range))]
data_meanT1[15]['visible'] = True
data_stdT1 = [dict(
visible = False,
x = TR_range,
y = T1_std,
line = dict(
color = ('rgb(222, 22, 22)'),
),
name = 'STD T<sub>1</sub> (s)',
text = 'STD T<sub>1</sub> (s)',
hoverinfo = 'x+y+text',
xaxis='x2',
yaxis='y3') for ii in range(len(TR_range))]
data_stdT1[28]['visible'] = True
data = data2 + data1 + data_meanT1 + data_stdT1
steps = []
for i in range(len(TR_range)):
step = dict(
method = 'restyle',
args = ['visible', [False] * len(data1)],
label = str(TR_range[i])
)
step['args'][1][i] = True # Toggle i'th trace to "visible"
steps.append(step)
sliders = [dict(
x = 0,
y = -0.02,
active = 28,
currentvalue = {"prefix": "TR value (ms): <b>"},
pad = {"t": 50, "b": 10},
steps = steps
)]
layout = go.Layout(
width=540,
height=540,
margin = dict(
t=0,
r=25,
b=100,
l=75),
annotations=[
dict(
x=0.5004254919715793,
y=-0.17,
showarrow=False,
text='Inversion Time – TI (ms)',
font=dict(
family='Times New Roman',
size=26
),
xref='paper',
yref='paper'
),
dict(
x=-0.15,
y=0.5,
showarrow=False,
text='Signal (magnitude)',
font=dict(
family='Times New Roman',
size=26
),
textangle=-90,
xref='paper',
yref='paper'
),
dict(
x=0.76,
y=0.77,
showarrow=False,
text='<b>TR (ms)<b>',
font=dict(
family='Times New Roman',
size=14
),
xref='paper',
yref='paper'
),
dict(
x=0.40,
y=0.35,
showarrow=False,
text='<b>Mean T<sub>1</sub> (ms)<b>',
font=dict(
family='Times New Roman',
size=14
),
textangle=-90,
xref='paper',
yref='paper'
),
dict(
x=1.00,
y=0.35,
showarrow=False,
text='<b>STD T<sub>1</sub> (ms)<b>',
font=dict(
family='Times New Roman',
size=14
),
textangle=-90,
xref='paper',
yref='paper'
)
],
xaxis=dict(
autorange=False,
range=[0, 5000],
showgrid=False,
linecolor='black',
linewidth=2
),
yaxis=dict(
autorange=False,
range=[0, 1],
showgrid=False,
linecolor='black',
linewidth=2
),
xaxis2=dict(
domain=[0.5, 0.90],
anchor='y2',
mirror = True,
side='top',
ticks='inside',
showline=True,
),
yaxis2=dict(
autorange=False,
range=[500, 1300],
domain=[0.05, 0.65],
anchor='x2',
mirror = True,
ticks='inside',
showline=True,
),
yaxis3=dict(
autorange=False,
range=[0, 190],
domain=[0.05, 0.65],
anchor='x2',
overlaying='y2',
side='right',
ticks='inside',
),
legend=dict(
x=0.3,
y=1.35,
traceorder='normal',
font=dict(
family='Times New Roman',
size=12,
color='#000'
),
bordercolor='#000000',
borderwidth=2
),
sliders=sliders,
plot_bgcolor='white'
)
fig = dict(data=data, layout=layout)
iplot(fig, filename = 'ir_fig_6.html', config = config)
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