From 57453d0ffc5488991ba9e302cf7d809b7d191208 Mon Sep 17 00:00:00 2001
From: ryanhammonds <ryan.hammonds@utexas.edu>
Date: Tue, 5 Jan 2021 19:34:42 -0800
Subject: [PATCH 1/2] plotly figures for t1w

---
 pynets/reports/plotting.py | 58 ++++++++++++++++++++++++++++++++++++++
 requirements.txt           |  1 +
 2 files changed, 59 insertions(+)
 create mode 100644 pynets/reports/plotting.py

diff --git a/pynets/reports/plotting.py b/pynets/reports/plotting.py
new file mode 100644
index 00000000..4344158e
--- /dev/null
+++ b/pynets/reports/plotting.py
@@ -0,0 +1,58 @@
+"""Plotting functions to embed into html reports."""
+
+import nibabel as nib
+import os
+import numpy as np
+import plotly.graph_objs as go
+from plotly.subplots import make_subplots
+
+
+def plot_t1w(t1w):
+    """Plot t1w images using plotly.
+
+    Parameters
+    ----------
+    t1w : str
+        Path to a t1w image.
+
+    Returns
+    -------
+    fig : plotly.graph_objs.Figure
+        A plotly figure that is ready-to-embed using the to_html method.
+    """
+
+    # Load data from file
+    t1w_arr = nib.load(t1w).get_fdata()
+
+    # Space out z-slices
+    z_max = np.shape(t1w_arr)[2]
+    pad = 30
+    z_slices = np.linspace(pad, z_max-pad, num=21, dtype=int)
+
+    # Init figure
+    nrows = 3
+    ncols = 7
+    fig = make_subplots(nrows, ncols, vertical_spacing=0.005, horizontal_spacing=0.005)
+
+    # Get subplot positions
+    fig_idxs = [(row, col) for row in range(1, nrows+1)
+                for col in range(1, ncols+1)]
+
+    for idx, z_slice in enumerate(z_slices):
+
+        # Slice and rotate the t1w array
+        img_slice = np.rot90(t1w_arr[:, :, z_slice], k=3)
+
+        # Get subplot coords
+        x_coord, y_coord = fig_idxs[idx]
+
+        fig.add_trace(go.Heatmap(z=img_slice, showscale=False, colorscale="gray"),
+                      x_coord, y_coord)
+
+        # Update axes
+        fig.update_xaxes(showticklabels=False, row=x_coord, col=y_coord)
+        fig.update_yaxes(showticklabels=False, row=x_coord, col=y_coord)
+
+    fig.update_layout(width=800, height=500)
+
+    return fig
diff --git a/requirements.txt b/requirements.txt
index cedd103e..66e76a79 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -36,3 +36,4 @@ git+https://github.com/dPys/nilearn.git@enh/parc_conn
 git+https://github.com/dPys/deepbrain.git@master
 urllib3>=1.25.4
 mplcyberpunk>=0.1.11
+plotly>=4.14.1

From e7d579f0a2475ad468498b6999d645dd22061021 Mon Sep 17 00:00:00 2001
From: ryanhammonds <ryan.hammonds@utexas.edu>
Date: Thu, 7 Jan 2021 18:49:46 -0800
Subject: [PATCH 2/2] plotly figures for segs

---
 pynets/reports/plotting.py | 51 ++++++++++++++++++++++++--------------
 1 file changed, 33 insertions(+), 18 deletions(-)

diff --git a/pynets/reports/plotting.py b/pynets/reports/plotting.py
index 4344158e..d187f769 100644
--- a/pynets/reports/plotting.py
+++ b/pynets/reports/plotting.py
@@ -7,13 +7,17 @@
 from plotly.subplots import make_subplots
 
 
-def plot_t1w(t1w):
+def plot_t1w_with_segs(t1w, wm, csf):
     """Plot t1w images using plotly.
 
     Parameters
     ----------
     t1w : str
         Path to a t1w image.
+    wm : str
+        Path to wm image.
+    csf : str
+        Path to csf image.
 
     Returns
     -------
@@ -23,11 +27,8 @@ def plot_t1w(t1w):
 
     # Load data from file
     t1w_arr = nib.load(t1w).get_fdata()
-
-    # Space out z-slices
-    z_max = np.shape(t1w_arr)[2]
-    pad = 30
-    z_slices = np.linspace(pad, z_max-pad, num=21, dtype=int)
+    wm_arr = nib.load(wm).get_fdata()
+    csf_arr = nib.load(csf).get_fdata()
 
     # Init figure
     nrows = 3
@@ -38,21 +39,35 @@ def plot_t1w(t1w):
     fig_idxs = [(row, col) for row in range(1, nrows+1)
                 for col in range(1, ncols+1)]
 
-    for idx, z_slice in enumerate(z_slices):
+    # Plot segs
+    _add_overlay(fig, t1w_arr, "gray", 1.0, fig_idxs)
+    _add_overlay(fig, wm_arr, "ice", 0.5, fig_idxs)
+    _add_overlay(fig, csf_arr, "ice", 0.5, fig_idxs)
 
-        # Slice and rotate the t1w array
-        img_slice = np.rot90(t1w_arr[:, :, z_slice], k=3)
+    fig.update_layout(width=800, height=500)
 
-        # Get subplot coords
-        x_coord, y_coord = fig_idxs[idx]
+    return fig
 
-        fig.add_trace(go.Heatmap(z=img_slice, showscale=False, colorscale="gray"),
-                      x_coord, y_coord)
 
-        # Update axes
-        fig.update_xaxes(showticklabels=False, row=x_coord, col=y_coord)
-        fig.update_yaxes(showticklabels=False, row=x_coord, col=y_coord)
+def _add_overlay(fig, data_arr, colorscale, opacity, fig_idxs):
+    """Add an overlay to the figure."""
 
-    fig.update_layout(width=800, height=500)
+    # Space out z_slices
+    z_max = np.shape(data_arr)[2]
+    pad = 30
+    z_slices = np.linspace(pad, z_max-pad, num=21, dtype=int)
 
-    return fig
+    for idx, z_slice in enumerate(z_slices):
+
+        # Get subplot position
+        x_pos, y_pos = fig_idxs[idx]
+
+        # Don't plot if array is all zeros
+        if np.mean(data_arr[:, :, z_slice]) > 0:
+
+            fig.add_trace(go.Heatmap(z=np.rot90(data_arr[:, :, z_slice], k=3), showscale=False,
+                                     colorscale=colorscale, opacity=opacity),
+                          x_pos, y_pos)
+
+        fig.update_xaxes(showticklabels=False, row=x_pos, col=y_pos)
+        fig.update_yaxes(showticklabels=False, row=x_pos, col=y_pos)