# Prepare Python environment

import scipy.io as sio
import numpy as np
from pathlib import Path

data_dir = Path("../../../data/06-MT-03-MTsat")
data_file = "sim2.mat"

#Load either archived or generated plot variables
mat_contents = sio.loadmat(data_dir / data_file)

Mz_after = mat_contents["Mz_after"][0]
delta_Mz_T1relax = mat_contents["delta_Mz_T1relax"][0]
Mz_before = mat_contents["Mz_before"][0]
M0_remainingTR_free =  mat_contents["M0_remainingTR_free"][0]
delta_Mz_T1relax_remaining =  mat_contents["delta_Mz_T1relax_remaining"][0]

x=np.arange(1,len(Mz_before)+1)
y1 = (1-(Mz_after-delta_Mz_T1relax)/Mz_before)*100
y2=(1-(M0_remainingTR_free-delta_Mz_T1relax_remaining)/Mz_before)*100
y3=(1-(Mz_after-delta_Mz_T1relax)/Mz_before)*100+(1-(M0_remainingTR_free-delta_Mz_T1relax_remaining)/Mz_before)*100

# 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=1, horizontal_spacing = 0.1)

fig.add_trace(
        go.Scatter(
        x=x,
        y=y1,
        hoverinfo = 'y',
        visible=True,
        name='MTsat contribution from MT pulse event'
        )
    )

fig.add_trace(
        go.Scatter(
        x=x,
        y=y2,
        hoverinfo = 'y',
        visible=True,
        name='MTsat contribution from cross-relaxation event'
        )
    )

fig.add_trace(
        go.Scatter(
        x=x,
        y=y3,
        hoverinfo = 'y',
        visible=True,
        name='Total MTsat for TR'
        )
    )

layout = go.Layout(
    width=600,
    height=500,
    margin=go.layout.Margin(
        l=60,
        r=30,
        b=60,
        t=60,
    ),
    legend={
        "x": 0.3,
        "y": 0.9,
        "xref": "paper",
        "yref": "paper",
    },
    xaxis=dict(
        showgrid=True,
        gridcolor='rgb(169,169,169)',
        linecolor='black',
        linewidth=2,
        title='Repetition #'
    ),
    yaxis=dict(
        showgrid=True,
        gridcolor='rgb(169,169,169)',
        linecolor='black',
        linewidth=2,
        title="\"MTsat\" (%)"
    ),
)

fig.update_layout(layout)

iplot(fig, filename = 'fig4.html', config = config)