multi-view example notebook: don't prune registration edges and perfo…

…rm affine registration
histopathology · Sep 4, 2024 · e93af95 · e93af95
1 parent 359c013
commit e93af95
Showing 1 changed file with 34 additions and 13 deletions.
diff --git a/notebooks/stitching_multi_view.ipynb b/notebooks/stitching_multi_view.ipynb
@@ -34,7 +34,7 @@
     "%matplotlib notebook\n",
     "\n",
     "# the package napari-stitcher is required for visualization with napari\n",
-    "VISUALIZE_USING_NAPARI = False\n",
+    "VISUALIZE_USING_NAPARI = True\n",
     "\n",
     "if VISUALIZE_USING_NAPARI:\n",
     "    import napari\n",
@@ -188,21 +188,48 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# import skimage.registration\n",
+    "registration.register?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "from multiview_stitcher import registration\n",
     "\n",
     "with dask.diagnostics.ProgressBar():\n",
     "\n",
+    "    # phase shift registration\n",
     "    params = registration.register(\n",
-    "        # [msi_utils.get_sim_from_msim(msim) for msim in msims],\n",
     "        msims,\n",
     "        registration_binning={'z': 2, 'y': 8, 'x': 8},\n",
     "        reg_channel_index=0,\n",
     "        transform_key='affine_manual',\n",
+    "        new_transform_key='translation_registered',\n",
+    "        pre_registration_pruning_method=None,\n",
+    "        groupwise_resolution_kwargs={\n",
+    "            'transform': 'translation',\n",
+    "        }\n",
     "    )\n",
-    "    \n",
-    "for msim, param in zip(msims, params):\n",
-    "    msi_utils.set_affine_transform(msim, param, transform_key='affine_registered', base_transform_key='affine_manual')"
+    "\n",
+    "    # affine registration\n",
+    "    params = registration.register(\n",
+    "        msims,\n",
+    "        registration_binning={'z': 2, 'y': 8, 'x': 8},\n",
+    "        reg_channel_index=0,\n",
+    "        transform_key='translation_registered',\n",
+    "        new_transform_key='affine_registered',\n",
+    "        pre_registration_pruning_method=None,\n",
+    "        pairwise_reg_func=registration.registration_ANTsPy,\n",
+    "        pairwise_reg_func_kwargs={\n",
+    "            'transform_types': ['Rigid', 'Affine'],\n",
+    "        },\n",
+    "        groupwise_resolution_kwargs={\n",
+    "            'transform': 'affine',\n",
+    "        }\n",
+    "    )"
    ]
   },
   {
@@ -223,16 +250,10 @@
     "    viewer = napari.Viewer(ndisplay=3)\n",
     "\n",
     "    lds = viewer_utils.create_image_layer_tuples_from_msims(\n",
-    "        msims, transform_key='affine_manual', n_colors=4,\n",
-    "        name_prefix='pre-registered view',\n",
-    "        contrast_limits=[0, 1000],\n",
-    "        )\n",
-    "    mlayers = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, do_link_layers=True)\n",
-    "\n",
-    "    lds = viewer_utils.create_image_layer_tuples_from_msims(\n",
     "        msims, transform_key='affine_registered', n_colors=4,\n",
     "        name_prefix='registered view',\n",
     "        contrast_limits=[0, 1000],\n",
+    "        positional_cmaps=False,\n",
     "        )\n",
     "    rlayers = viewer_utils.add_image_layer_tuples_to_viewer(viewer, lds, do_link_layers=True)"
    ]