ENH: Show registration reportlets inline within Jupyter notebooks

Add a little wrapper around our registration reportlet to allow them to
render (and flicker) within a notebook.
Created for nipy/nitransforms#93.

Author: oesteban

niworkflows/viz/notebook.py

@@ -0,0 +1,51 @@
+"""Visualization component for Jupyter Notebooks."""
+from pathlib import Path
+import numpy as np
+import nibabel as nb
+from .utils import compose_view, plot_registration, cuts_from_bbox
+from IPython.display import SVG, display as _disp
+
+
+def display(
+    fixed_image,
+    moving_image,
+    contour=None,
+    cuts=None,
+    fixed_label="F",
+    moving_label="M",
+):
+    """Plot the flickering panels to show a registration process."""
+    if isinstance(fixed_image, (str, Path)):
+        fixed_image = nb.load(str(fixed_image))
+    if isinstance(moving_image, (str, Path)):
+        moving_image = nb.load(str(moving_image))
+
+    if cuts is None:
+        n_cuts = 7
+        if contour is not None:
+            if isinstance(contour, (str, Path)):
+                contour = nb.load(str(contour))
+            cuts = cuts_from_bbox(contour, cuts=n_cuts)
+        else:
+            hdr = fixed_image.header.copy()
+            hdr.set_data_dtype('uint8')
+            mask_nii = nb.Nifti1Image(
+                np.ones(fixed_image.shape, dtype='uint8'),
+                fixed_image.affine, hdr)
+            cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
+
+    # Call composer
+    _disp(SVG(compose_view(
+        plot_registration(fixed_image, 'fixed-image',
+                          estimate_brightness=True,
+                          cuts=cuts,
+                          label=fixed_label,
+                          contour=contour,
+                          compress=False),
+        plot_registration(moving_image, 'moving-image',
+                          estimate_brightness=True,
+                          cuts=cuts,
+                          label=moving_label,
+                          contour=contour,
+                          compress=False),
+    )))

niworkflows/viz/utils.py

@@ -3,6 +3,7 @@
 """Helper tools for visualization purposes"""
 from pathlib import Path
 from shutil import which
+from tempfile import TemporaryDirectory
 import subprocess
 import base64
 import re
@@ -327,10 +328,15 @@ def plot_registration(anat_nii, div_id, plot_params=None,
 
 
 def compose_view(bg_svgs, fg_svgs, ref=0, out_file='report.svg'):
-    """
-    Composes the input svgs into one standalone svg and inserts
-    the CSS code for the flickering animation
-    """
+    """Compose the input svgs into one standalone svg with CSS flickering animation."""
+    out_file = Path(out_file).absolute()
+    out_file.write_text("\n".join(
+        _compose_view(bg_svgs, fg_svgs, ref=ref)
+    ))
+    return str(out_file)
+
+
+def _compose_view(bg_svgs, fg_svgs, ref=0):
 
     if fg_svgs is None:
         fg_svgs = []
@@ -379,11 +385,12 @@ def compose_view(bg_svgs, fg_svgs, ref=0, out_file='report.svg'):
     fig.root.attrib.pop("width")
     fig.root.attrib.pop("height")
     fig.root.set("preserveAspectRatio", "xMidYMid meet")
-    out_file = Path(out_file).absolute()
-    fig.save(str(out_file))
 
-    # Post processing
-    svg = out_file.read_text().splitlines()
+    with TemporaryDirectory() as tmpdirname:
+        out_file = Path(tmpdirname) / "tmp.svg"
+        fig.save(str(out_file))
+        # Post processing
+        svg = out_file.read_text().splitlines()
 
     # Remove <?xml... line
     if svg[0].startswith("<?xml"):
@@ -398,8 +405,7 @@ def compose_view(bg_svgs, fg_svgs, ref=0, out_file='report.svg'):
 .foreground-svg:hover { animation-play-state: running;}
 </style>""" % tuple([uuid4()] * 2))
 
-    out_file.write_text("\n".join(svg))
-    return str(out_file)
+    return svg
 
 
 def transform_to_2d(data, max_axis):