Merge pull request #493 from oesteban/enh/notebook-components

ENH: Show registration reportlets inline within Jupyter notebooks

Author: oesteban

niworkflows/viz/__init__.py

@@ -1,9 +1,6 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from __future__ import absolute_import, division, print_function, unicode_literals
-
 from .plots import plot_carpet
 from .utils import SVGNS
 
-__all__ = ['plot_carpet', 'SVGNS']
+__all__ = ["plot_carpet", "SVGNS"]

niworkflows/viz/notebook.py

@@ -0,0 +1,62 @@
+"""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
+
+
+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."""
+    from IPython.display import SVG, display as _disp
+
+    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,
+                ),
+            )
+        )
+    )