From d92947557150b61102e98d584d91644c20589216 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 16 Jul 2025 13:59:53 -0400
Subject: [PATCH 01/29] Add basic controls to define warp points

---
 large_image/tilesource/jupyter.py | 68 ++++++++++++++++++++++++++++---
 1 file changed, 62 insertions(+), 6 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 4020473ad..b103a012e 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -91,7 +91,10 @@ class IPyLeafletMixin:
 
     def __init__(self, *args, **kwargs) -> None:
         self._jupyter_server_manager = None
-        self._map = Map(ts=self)
+        self._map = Map(
+            ts=self,
+            editWarp=kwargs.get('editWarp', False),
+        )
         if ipyleafletPresent:
             self.to_map = self._map.to_map
             self.from_map = self._map.from_map
@@ -167,7 +170,9 @@ def __init__(
             self, *, ts: Optional[IPyLeafletMixin] = None,
             metadata: Optional[dict] = None, url: Optional[str] = None,
             gc: Optional[Any] = None, id: Optional[str] = None,
-            resource: Optional[str] = None) -> None:
+            resource: Optional[str] = None,
+            editWarp: bool = False,
+    ) -> None:
         """
         Specify the large image to be used with the IPyLeaflet Map.  One of (a)
         a tile source, (b) metadata dictionary and tile url, (c) girder client
@@ -187,6 +192,9 @@ def __init__(
         self._layer = self._map = self._metadata = self._frame_slider = None
         self._frame_histograms: Optional[dict[int, Any]] = None
         self._ts = ts
+        self._edit_warp = editWarp
+        if self._edit_warp:
+            self.warp_points = dict(src=[], dst=[])
         if (not url or not metadata) and gc and (id or resource):
             fileId = None
             if id is None:
@@ -282,7 +290,7 @@ def make_map(
         Create an ipyleaflet map given large_image metadata, an optional
         ipyleaflet layer, and the center of the tile source.
         """
-        from ipyleaflet import Map, basemaps, projections
+        from ipyleaflet import FullScreenControl, Map, basemaps, projections
         from ipywidgets import VBox
 
         try:
@@ -351,11 +359,60 @@ def make_map(
         self._map = m
         children.append(m)
 
-        self.add_region_indicator()
+        if self._edit_warp:
+            children.append(self.add_warp_editor())
+        else:
+            # Only add region indicator if not using warp editor so that
+            # the map doesn't have conflicting on_interaction callbacks
+            self.add_region_indicator()
+        self._map.add(FullScreenControl())
+        return VBox(children)
+
+    def add_warp_editor(self):
+        from ipyleaflet import DivIcon, Marker
+        from ipywidgets import VBox, Label
+
+        help_text = Label('To begin editing a warp, click on the image to place reference points.')
+        children = [help_text]
+        marker_style = (
+            'border-radius: 50%; position: relative;'
+            'height: 16px; width: 16px; top: -8px; left: -8px;'
+            'text-align: center; font-size: 11px;'
+        )
+
+        def handle_drag(event):
+            old = [round(v) for v in event.get('old')]
+            new = [round(v) for v in event.get('new')]
+            marker_title = event.get('owner').title
+            group_name = marker_title[:3]
+            index = int(marker_title[3:])
+            self.warp_points[group_name][index] = new
+            if group_name == 'dst' and self.warp_points['src'][index] is None:
+                self.warp_points['src'][index] = old
+                html = f'<div style="background-color: #ff6a5e; {marker_style}">{index}</div>'
+                icon = DivIcon(html=html, icon_size=[0, 0])
+                marker = Marker(location=old, draggable=True, icon=icon, title=f'src {index}')
+                marker.observe(handle_drag, 'location')
+                self._map.add(marker)
+
+        def handle_interaction(**kwargs):
+            if kwargs.get('type') == 'click':
+                coords = kwargs.get('coordinates')
+                index = len(self.warp_points['src'])
+                html = f'<div style="background-color: #19a7ff; {marker_style}">{index}</div>'
+                icon = DivIcon(html=html, icon_size=[0, 0])
+                marker = Marker(location=coords, draggable=True, icon=icon, title=f'dst {index}')
+                marker.observe(handle_drag, 'location')
+                self._map.add(marker)
+                self.warp_points['src'].append(None)
+                self.warp_points['dst'].append(coords)
+                help_text.value = 'After placing reference points, you can drag them to start defining the warp.'
+
+        self._map.on_interaction(handle_interaction)
         return VBox(children)
 
     def add_region_indicator(self):
-        from ipyleaflet import FullScreenControl, GeomanDrawControl, Popup
+        from ipyleaflet import GeomanDrawControl, Popup
         from ipywidgets import HTML
 
         metadata = self._metadata
@@ -440,7 +497,6 @@ def handle_draw(target, action, geo_json):
         draw_control.on_draw(handle_draw)
         self._map.on_interaction(handle_interaction)
         self._map.add(draw_control)
-        self._map.add(FullScreenControl())
 
     @property
     def layer(self) -> Any:

From bc564d23929c9e1d49a93af415b8af61961e7f03 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 16 Jul 2025 14:54:51 -0400
Subject: [PATCH 02/29] Add display of json and yaml schemas with warp points

---
 large_image/tilesource/jupyter.py | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index b103a012e..9419980c8 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -21,6 +21,7 @@
 import os
 import threading
 import weakref
+import yaml
 from typing import Any, Optional, Union, cast
 from urllib.parse import parse_qs, quote, urlencode, urlparse, urlunparse
 
@@ -370,16 +371,34 @@ def make_map(
 
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
-        from ipywidgets import VBox, Label
+        from ipywidgets import Accordion, HTML, Label, VBox
 
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
-        children = [help_text]
+        yaml_schema = HTML('yaml')
+        json_schema = HTML('json')
+        schemas = Accordion(children=[yaml_schema, json_schema], titles=('YAML', 'JSON'))
+        schemas.layout.display = 'none'
+        children = [help_text, schemas]
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
             'text-align: center; font-size: 11px;'
         )
 
+        def update_schemas():
+            help_text.value = 'Reference the schemas below to use this warp with the MultiFileTileSource (either as YAML or JSON).'
+            schema = dict(sources=[
+                dict(
+                    #  TODO: is there a better way to get the path value?
+                    path=str(self._ts._initValues[0][0]),
+                    z=0, position=dict(x=0, y=0, warp=self.warp_points)
+                )
+            ])
+            json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
+            yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
+            schemas.layout.display = 'block'
+
+
         def handle_drag(event):
             old = [round(v) for v in event.get('old')]
             new = [round(v) for v in event.get('new')]
@@ -394,6 +413,7 @@ def handle_drag(event):
                 marker = Marker(location=old, draggable=True, icon=icon, title=f'src {index}')
                 marker.observe(handle_drag, 'location')
                 self._map.add(marker)
+            update_schemas()
 
         def handle_interaction(**kwargs):
             if kwargs.get('type') == 'click':
@@ -406,7 +426,8 @@ def handle_interaction(**kwargs):
                 self._map.add(marker)
                 self.warp_points['src'].append(None)
                 self.warp_points['dst'].append(coords)
-                help_text.value = 'After placing reference points, you can drag them to start defining the warp.'
+                help_text.value = 'After placing reference points, you can drag them to define the warp.'
+                schemas.layout.display = 'none'
 
         self._map.on_interaction(handle_interaction)
         return VBox(children)

From cade572434304eadcfc4b9a0e0f7a75a375106bb Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Mon, 21 Jul 2025 14:56:29 -0400
Subject: [PATCH 03/29] Only show matched points in schemas

---
 large_image/tilesource/jupyter.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 9419980c8..782b6f932 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -387,11 +387,15 @@ def add_warp_editor(self):
 
         def update_schemas():
             help_text.value = 'Reference the schemas below to use this warp with the MultiFileTileSource (either as YAML or JSON).'
+            matched_points = {
+                k: [point for index, point in enumerate(v) if self.warp_points.get('src')[index] and self.warp_points.get('dst')[index]]
+                for k, v in self.warp_points.items()
+            }
             schema = dict(sources=[
                 dict(
                     #  TODO: is there a better way to get the path value?
                     path=str(self._ts._initValues[0][0]),
-                    z=0, position=dict(x=0, y=0, warp=self.warp_points)
+                    z=0, position=dict(x=0, y=0, warp=matched_points)
                 )
             ])
             json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
@@ -427,7 +431,6 @@ def handle_interaction(**kwargs):
                 self.warp_points['src'].append(None)
                 self.warp_points['dst'].append(coords)
                 help_text.value = 'After placing reference points, you can drag them to define the warp.'
-                schemas.layout.display = 'none'
 
         self._map.on_interaction(handle_interaction)
         return VBox(children)

From 0936694dbd54b7254a728b6706e5e117ca1a71e3 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Mon, 21 Jul 2025 18:26:12 -0400
Subject: [PATCH 04/29] First pass at applying transform via multi source

---
 large_image/tilesource/jupyter.py | 78 +++++++++++++++++++++++++++----
 1 file changed, 70 insertions(+), 8 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 782b6f932..fd955b08b 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -161,6 +161,10 @@ def iplmap(self) -> Any:
             """
             return self._map.map
 
+    @property
+    def warp_points(self):
+        return self._map.warp_points
+
 
 class Map:
     """
@@ -190,7 +194,7 @@ def __init__(
         :param resource: a girder resource path of an item or file that exists
             on the girder client.
         """
-        self._layer = self._map = self._metadata = self._frame_slider = None
+        self._layer = self._map = self._metadata = self.frame_selector = None
         self._frame_histograms: Optional[dict[int, Any]] = None
         self._ts = ts
         self._edit_warp = editWarp
@@ -371,14 +375,16 @@ def make_map(
 
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
-        from ipywidgets import Accordion, HTML, Label, VBox
+        from ipywidgets import Accordion, Checkbox, HTML, Label, VBox
 
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
+        transform_checkbox = Checkbox(description='Show Transformed', value=True)
+        transform_checkbox.layout.display = 'none'
         yaml_schema = HTML('yaml')
         json_schema = HTML('json')
         schemas = Accordion(children=[yaml_schema, json_schema], titles=('YAML', 'JSON'))
         schemas.layout.display = 'none'
-        children = [help_text, schemas]
+        children = [transform_checkbox, help_text, schemas]
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
@@ -401,7 +407,8 @@ def update_schemas():
             json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
             yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
             schemas.layout.display = 'block'
-
+            transform_checkbox.layout.display = 'block'
+            self.update_warp(transform_checkbox.value)
 
         def handle_drag(event):
             old = [round(v) for v in event.get('old')]
@@ -432,6 +439,10 @@ def handle_interaction(**kwargs):
                 self.warp_points['dst'].append(coords)
                 help_text.value = 'After placing reference points, you can drag them to define the warp.'
 
+        def toggle_transform(event):
+            self.update_warp(event.get('new'))
+
+        transform_checkbox.observe(toggle_transform, names=['value'])
         self._map.on_interaction(handle_interaction)
         return VBox(children)
 
@@ -575,7 +586,21 @@ def from_map(self, coordinate: Union[list[float], tuple[float, float]]) -> tuple
             return transf.transform(x, y)
         return x, self._metadata['sizeY'] - y
 
+    def update_warp(self, show_warp):
+        current_frame = self.frame_selector.currentFrame if self.frame_selector is not None else 0
+        if show_warp and len(self.warp_points.get('src')):
+            matched_points = {
+                k: [point for index, point in enumerate(v) if self.warp_points.get('src')[index] and self.warp_points.get('dst')[index]]
+                for k, v in self.warp_points.items()
+            }
+            self.update_layer_query(frame=current_frame, style=dict(warp=matched_points))
+        else:
+            self.update_layer_query(frame=current_frame, style=dict())
+
     def update_frame(self, frame, style, **kwargs):
+        self.update_layer_query(frame=frame, style=style)
+
+    def update_layer_query(self, frame, style, **kwargs):
         if self._layer:
             parsed_url = urlparse(self._layer.url)
             query = parsed_url.query
@@ -640,6 +665,21 @@ def default(self, obj):
         return json.JSONEncoder.default(self, obj)
 
 
+multi_source = None
+def _lazyImportMultiSource():
+    """
+    Import the large_image_source_multi module. This is only needed when editWarp is used.
+    """
+    global multi_source
+
+    if multi_source is None:
+        try:
+            import large_image_source_multi as multi_source
+        except ImportError:
+            msg = 'large_image_source_multi module not found.'
+            raise TileSourceError(msg)
+
+
 def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:
     import tornado.httpserver
     import tornado.netutil
@@ -666,6 +706,20 @@ def ports(self) -> tuple[int, ...]:
         def port(self) -> int:
             return self.ports[0]
 
+        def get_warp_source(self, warp):
+            if multi_source is None:
+                _lazyImportMultiSource()
+            #  TODO: is there a better way to get the path value?
+            path = str(self.tile_source._initValues[0][0])
+            return multi_source.open(dict(sources=[
+                dict(
+                    path=path,
+                    position=dict(
+                        x=0, y=0, warp=warp
+                    )
+                )
+            ]))
+
     manager = RequestManager(tile_source)
     # NOTE: set `ports` manually after launching server
 
@@ -705,12 +759,20 @@ def get(self) -> None:
             z = int(self.get_argument('z'))
             frame = int(self.get_argument('frame', default='0'))
             style = self.get_argument('style', default=None)
-            if style:
-                manager.tile_source.style = json.loads(style)  # type: ignore[attr-defined]
+            warp = None
             encoding = self.get_argument('encoding', 'PNG')
+            if style:
+                style = json.loads(style)
+                warp = style.get('warp')
+                if warp is None:
+                    manager.tile_source.style = style  # type: ignore[attr-defined]
             try:
-                tile_binary = manager.tile_source.getTile(  # type: ignore[attr-defined]
-                    x, y, z, encoding=encoding, frame=frame)
+                if warp is not None:
+                    tile_binary = manager.get_warp_source(warp).getTile(  # type: ignore[attr-defined]
+                        x, y, z, encoding=encoding, frame=frame)
+                else:
+                    tile_binary = manager.tile_source.getTile(  # type: ignore[attr-defined]
+                        x, y, z, encoding=encoding, frame=frame)
             except TileSourceXYZRangeError as e:
                 self.clear()
                 self.set_status(404)

From 0b94c4cbf2fc06db3a8ec5393687e0fb8e895e0a Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 09:08:42 -0400
Subject: [PATCH 05/29] Correct coordinate ordering for warp points

---
 large_image/tilesource/jupyter.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index fd955b08b..61ff0aa04 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -410,15 +410,18 @@ def update_schemas():
             transform_checkbox.layout.display = 'block'
             self.update_warp(transform_checkbox.value)
 
+        def convert_coordinate(coord):
+            return [coord[1], coord[0]]
+
         def handle_drag(event):
             old = [round(v) for v in event.get('old')]
             new = [round(v) for v in event.get('new')]
             marker_title = event.get('owner').title
             group_name = marker_title[:3]
             index = int(marker_title[3:])
-            self.warp_points[group_name][index] = new
+            self.warp_points[group_name][index] = convert_coordinate(new)
             if group_name == 'dst' and self.warp_points['src'][index] is None:
-                self.warp_points['src'][index] = old
+                self.warp_points['src'][index] = convert_coordinate(old)
                 html = f'<div style="background-color: #ff6a5e; {marker_style}">{index}</div>'
                 icon = DivIcon(html=html, icon_size=[0, 0])
                 marker = Marker(location=old, draggable=True, icon=icon, title=f'src {index}')
@@ -436,7 +439,7 @@ def handle_interaction(**kwargs):
                 marker.observe(handle_drag, 'location')
                 self._map.add(marker)
                 self.warp_points['src'].append(None)
-                self.warp_points['dst'].append(coords)
+                self.warp_points['dst'].append(convert_coordinate(coords))
                 help_text.value = 'After placing reference points, you can drag them to define the warp.'
 
         def toggle_transform(event):

From aeed1eabcb43be0a8acd5056461b16da059c5763 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 10:00:49 -0400
Subject: [PATCH 06/29] Allow a user to add a reference image and control
 opacity

---
 large_image/tilesource/jupyter.py | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 61ff0aa04..baa128086 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -95,6 +95,7 @@ def __init__(self, *args, **kwargs) -> None:
         self._map = Map(
             ts=self,
             editWarp=kwargs.get('editWarp', False),
+            reference=kwargs.get('reference'),
         )
         if ipyleafletPresent:
             self.to_map = self._map.to_map
@@ -176,7 +177,7 @@ def __init__(
             metadata: Optional[dict] = None, url: Optional[str] = None,
             gc: Optional[Any] = None, id: Optional[str] = None,
             resource: Optional[str] = None,
-            editWarp: bool = False,
+            editWarp: bool = False, reference: Optional[IPyLeafletMixin] = None,
     ) -> None:
         """
         Specify the large image to be used with the IPyLeaflet Map.  One of (a)
@@ -198,6 +199,8 @@ def __init__(
         self._frame_histograms: Optional[dict[int, Any]] = None
         self._ts = ts
         self._edit_warp = editWarp
+        self._reference = reference
+        self._reference_layer = None
         if self._edit_warp:
             self.warp_points = dict(src=[], dst=[])
         if (not url or not metadata) and gc and (id or resource):
@@ -296,7 +299,7 @@ def make_map(
         ipyleaflet layer, and the center of the tile source.
         """
         from ipyleaflet import FullScreenControl, Map, basemaps, projections
-        from ipywidgets import VBox
+        from ipywidgets import FloatSlider, VBox
 
         try:
             default_zoom = metadata['levels'] - metadata['sourceLevels']
@@ -361,6 +364,26 @@ def make_map(
             m.fit_bounds(bounds=[[0, 0], [metadata['sizeY'], metadata['sizeX']]])
         if self._geospatial:
             m.add_layer(layer)
+
+        if self._reference is not None:
+            default_opacity = 0.5
+            self._reference_layer = self._reference.as_leaflet_layer()
+            self._reference_layer.opacity = default_opacity
+            m.add_layer(self._reference_layer)
+
+            def update_reference_opacity(event):
+                self._reference_layer.opacity = event.get('new', default_opacity)
+
+            reference_slider = FloatSlider(
+                description='Reference Opacity',
+                value=default_opacity, step=0.1,
+                min=0, max=1,
+                readout_format='.1f',
+                style={'description_width': 'initial'}
+            )
+            reference_slider.observe(update_reference_opacity, names=['value'])
+            children.append(reference_slider)
+
         self._map = m
         children.append(m)
 

From 40b2021b78f7678e199f454b9541d56a227f8726 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 10:07:33 -0400
Subject: [PATCH 07/29] Fix formatting

---
 large_image/tilesource/jupyter.py | 105 ++++++++++++++++--------------
 1 file changed, 57 insertions(+), 48 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index baa128086..c61c9c145 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -21,11 +21,11 @@
 import os
 import threading
 import weakref
-import yaml
 from typing import Any, Optional, Union, cast
 from urllib.parse import parse_qs, quote, urlencode, urlparse, urlunparse
 
 import numpy as np
+import yaml
 
 import large_image
 from large_image.exceptions import TileSourceError, TileSourceXYZRangeError
@@ -379,7 +379,7 @@ def update_reference_opacity(event):
                 value=default_opacity, step=0.1,
                 min=0, max=1,
                 readout_format='.1f',
-                style={'description_width': 'initial'}
+                style={'description_width': 'initial'},
             )
             reference_slider.observe(update_reference_opacity, names=['value'])
             children.append(reference_slider)
@@ -398,7 +398,7 @@ def update_reference_opacity(event):
 
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
-        from ipywidgets import Accordion, Checkbox, HTML, Label, VBox
+        from ipywidgets import HTML, Accordion, Checkbox, Label, VBox
 
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
         transform_checkbox = Checkbox(description='Show Transformed', value=True)
@@ -415,17 +415,21 @@ def add_warp_editor(self):
         )
 
         def update_schemas():
-            help_text.value = 'Reference the schemas below to use this warp with the MultiFileTileSource (either as YAML or JSON).'
+            help_text.value = (
+                'Reference the schemas below to use this warp with '
+                'the MultiFileTileSource (either as YAML or JSON).'
+            )
             matched_points = {
-                k: [point for index, point in enumerate(v) if self.warp_points.get('src')[index] and self.warp_points.get('dst')[index]]
+                k: [point for index, point in enumerate(v) if self.warp_points.get(
+                    'src')[index] and self.warp_points.get('dst')[index]]
                 for k, v in self.warp_points.items()
             }
             schema = dict(sources=[
                 dict(
                     #  TODO: is there a better way to get the path value?
                     path=str(self._ts._initValues[0][0]),
-                    z=0, position=dict(x=0, y=0, warp=matched_points)
-                )
+                    z=0, position=dict(x=0, y=0, warp=matched_points),
+                ),
             ])
             json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
             yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
@@ -463,7 +467,9 @@ def handle_interaction(**kwargs):
                 self._map.add(marker)
                 self.warp_points['src'].append(None)
                 self.warp_points['dst'].append(convert_coordinate(coords))
-                help_text.value = 'After placing reference points, you can drag them to define the warp.'
+                help_text.value = (
+                    'After placing reference points, you can drag them to define the warp.'
+                )
 
         def toggle_transform(event):
             self.update_warp(event.get('new'))
@@ -616,7 +622,8 @@ def update_warp(self, show_warp):
         current_frame = self.frame_selector.currentFrame if self.frame_selector is not None else 0
         if show_warp and len(self.warp_points.get('src')):
             matched_points = {
-                k: [point for index, point in enumerate(v) if self.warp_points.get('src')[index] and self.warp_points.get('dst')[index]]
+                k: [point for index, point in enumerate(v) if self.warp_points.get(
+                    'src')[index] and self.warp_points.get('dst')[index]]
                 for k, v in self.warp_points.items()
             }
             self.update_layer_query(frame=current_frame, style=dict(warp=matched_points))
@@ -692,6 +699,8 @@ def default(self, obj):
 
 
 multi_source = None
+
+
 def _lazyImportMultiSource():
     """
     Import the large_image_source_multi module. This is only needed when editWarp is used.
@@ -706,45 +715,46 @@ def _lazyImportMultiSource():
             raise TileSourceError(msg)
 
 
-def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:
-    import tornado.httpserver
-    import tornado.netutil
-    import tornado.web
+class RequestManager:
+    def __init__(self, tile_source: IPyLeafletMixin) -> None:
+        self._tile_source_ = weakref.ref(tile_source)
+        self._ports = ()
 
-    class RequestManager:
-        def __init__(self, tile_source: IPyLeafletMixin) -> None:
-            self._tile_source_ = weakref.ref(tile_source)
-            self._ports = ()
+    @property
+    def tile_source(self) -> IPyLeafletMixin:
+        return cast(IPyLeafletMixin, self._tile_source_())
 
-        @property
-        def tile_source(self) -> IPyLeafletMixin:
-            return cast(IPyLeafletMixin, self._tile_source_())
+    @tile_source.setter
+    def tile_source(self, source: IPyLeafletMixin) -> None:
+        self._tile_source_ = weakref.ref(source)
 
-        @tile_source.setter
-        def tile_source(self, source: IPyLeafletMixin) -> None:
-            self._tile_source_ = weakref.ref(source)
+    @property
+    def ports(self) -> tuple[int, ...]:
+        return self._ports
 
-        @property
-        def ports(self) -> tuple[int, ...]:
-            return self._ports
+    @property
+    def port(self) -> int:
+        return self.ports[0]
+
+    def get_warp_source(self, warp):
+        if multi_source is None:
+            _lazyImportMultiSource()
+        #  TODO: is there a better way to get the path value?
+        path = str(self.tile_source._initValues[0][0])
+        return multi_source.open(dict(sources=[
+            dict(
+                path=path,
+                position=dict(
+                    x=0, y=0, warp=warp,
+                ),
+            ),
+        ]))
 
-        @property
-        def port(self) -> int:
-            return self.ports[0]
-
-        def get_warp_source(self, warp):
-            if multi_source is None:
-                _lazyImportMultiSource()
-            #  TODO: is there a better way to get the path value?
-            path = str(self.tile_source._initValues[0][0])
-            return multi_source.open(dict(sources=[
-                dict(
-                    path=path,
-                    position=dict(
-                        x=0, y=0, warp=warp
-                    )
-                )
-            ]))
+
+def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:
+    import tornado.httpserver
+    import tornado.netutil
+    import tornado.web
 
     manager = RequestManager(tile_source)
     # NOTE: set `ports` manually after launching server
@@ -793,12 +803,11 @@ def get(self) -> None:
                 if warp is None:
                     manager.tile_source.style = style  # type: ignore[attr-defined]
             try:
+                source = manager.tile_source
                 if warp is not None:
-                    tile_binary = manager.get_warp_source(warp).getTile(  # type: ignore[attr-defined]
-                        x, y, z, encoding=encoding, frame=frame)
-                else:
-                    tile_binary = manager.tile_source.getTile(  # type: ignore[attr-defined]
-                        x, y, z, encoding=encoding, frame=frame)
+                    source = manager.get_warp_source(warp)
+                tile_binary = source.getTile(  # type: ignore[attr-defined]
+                    x, y, z, encoding=encoding, frame=frame)
             except TileSourceXYZRangeError as e:
                 self.clear()
                 self.set_status(404)

From 6ad03398be801bb3dfb6d75ca091d4bfa4b4cd16 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 11:58:32 -0400
Subject: [PATCH 08/29] Fix typing

---
 large_image/tilesource/jupyter.py | 91 ++++++++++++++++++-------------
 1 file changed, 53 insertions(+), 38 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index c61c9c145..93950577d 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -30,6 +30,7 @@
 import large_image
 from large_image.exceptions import TileSourceError, TileSourceXYZRangeError
 from large_image.tilesource.utilities import JSONDict
+from large_image.widgets.components import FrameSelector
 
 ipyleafletPresent = importlib.util.find_spec('ipyleaflet') is not None
 ipyvuePresent = importlib.util.find_spec('ipyvue') is not None
@@ -166,6 +167,11 @@ def iplmap(self) -> Any:
     def warp_points(self):
         return self._map.warp_points
 
+    @property
+    def image_path(self):
+        #  TODO: is there a better way to get the path value?
+        return str(self._initValues[0][0])  # type: ignore[attr-defined]
+
 
 class Map:
     """
@@ -195,14 +201,15 @@ def __init__(
         :param resource: a girder resource path of an item or file that exists
             on the girder client.
         """
-        self._layer = self._map = self._metadata = self.frame_selector = None
+        self._layer = self._map = self._metadata = None
+        self.frame_selector: Optional[FrameSelector] = None
         self._frame_histograms: Optional[dict[int, Any]] = None
         self._ts = ts
         self._edit_warp = editWarp
         self._reference = reference
         self._reference_layer = None
         if self._edit_warp:
-            self.warp_points = dict(src=[], dst=[])
+            self.warp_points: dict[str, list[Optional[list[int]]]] = dict(src=[], dst=[])
         if (not url or not metadata) and gc and (id or resource):
             fileId = None
             if id is None:
@@ -341,8 +348,6 @@ def make_map(
         children: list[Any] = []
         frames = metadata.get('frames')
         if frames is not None and ipyvuePresent and aiohttpPresent:
-            from large_image.widgets.components import FrameSelector
-
             self.frame_selector = FrameSelector()
             self.frame_selector.imageMetadata = metadata
             self.frame_selector.updateFrameCallback = self.update_frame
@@ -368,11 +373,13 @@ def make_map(
         if self._reference is not None:
             default_opacity = 0.5
             self._reference_layer = self._reference.as_leaflet_layer()
-            self._reference_layer.opacity = default_opacity
-            m.add_layer(self._reference_layer)
+            if self._reference_layer is not None:
+                self._reference_layer.opacity = default_opacity
+                m.add_layer(self._reference_layer)
 
             def update_reference_opacity(event):
-                self._reference_layer.opacity = event.get('new', default_opacity)
+                if self._reference_layer is not None:
+                    self._reference_layer.opacity = event.get('new', default_opacity)
 
             reference_slider = FloatSlider(
                 description='Reference Opacity',
@@ -415,20 +422,16 @@ def add_warp_editor(self):
         )
 
         def update_schemas():
+            if self._ts is None:
+                return
             help_text.value = (
                 'Reference the schemas below to use this warp with '
                 'the MultiFileTileSource (either as YAML or JSON).'
             )
-            matched_points = {
-                k: [point for index, point in enumerate(v) if self.warp_points.get(
-                    'src')[index] and self.warp_points.get('dst')[index]]
-                for k, v in self.warp_points.items()
-            }
             schema = dict(sources=[
                 dict(
-                    #  TODO: is there a better way to get the path value?
-                    path=str(self._ts._initValues[0][0]),
-                    z=0, position=dict(x=0, y=0, warp=matched_points),
+                    path=self._ts.image_path,
+                    z=0, position=dict(x=0, y=0, warp=self.get_matched_warp_points()),
                 ),
             ])
             json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
@@ -453,7 +456,8 @@ def handle_drag(event):
                 icon = DivIcon(html=html, icon_size=[0, 0])
                 marker = Marker(location=old, draggable=True, icon=icon, title=f'src {index}')
                 marker.observe(handle_drag, 'location')
-                self._map.add(marker)
+                if self._map is not None:
+                    self._map.add(marker)
             update_schemas()
 
         def handle_interaction(**kwargs):
@@ -464,7 +468,8 @@ def handle_interaction(**kwargs):
                 icon = DivIcon(html=html, icon_size=[0, 0])
                 marker = Marker(location=coords, draggable=True, icon=icon, title=f'dst {index}')
                 marker.observe(handle_drag, 'location')
-                self._map.add(marker)
+                if self._map is not None:
+                    self._map.add(marker)
                 self.warp_points['src'].append(None)
                 self.warp_points['dst'].append(convert_coordinate(coords))
                 help_text.value = (
@@ -475,7 +480,8 @@ def toggle_transform(event):
             self.update_warp(event.get('new'))
 
         transform_checkbox.observe(toggle_transform, names=['value'])
-        self._map.on_interaction(handle_interaction)
+        if self._map is not None:
+            self._map.on_interaction(handle_interaction)
         return VBox(children)
 
     def add_region_indicator(self):
@@ -618,14 +624,24 @@ def from_map(self, coordinate: Union[list[float], tuple[float, float]]) -> tuple
             return transf.transform(x, y)
         return x, self._metadata['sizeY'] - y
 
+    def get_matched_warp_points(self):
+        src = self.warp_points.get('src')
+        dst = self.warp_points.get('dst')
+        if src is None or dst is None:
+            return {}
+        return {
+            k: [
+                point for index, point in enumerate(v)
+                if len(src) > index and src[index] and
+                len(dst) > index and dst[index]
+            ]
+            for k, v in self.warp_points.items()
+        }
+
     def update_warp(self, show_warp):
         current_frame = self.frame_selector.currentFrame if self.frame_selector is not None else 0
-        if show_warp and len(self.warp_points.get('src')):
-            matched_points = {
-                k: [point for index, point in enumerate(v) if self.warp_points.get(
-                    'src')[index] and self.warp_points.get('dst')[index]]
-                for k, v in self.warp_points.items()
-            }
+        matched_points = self.get_matched_warp_points()
+        if show_warp and len(matched_points):
             self.update_layer_query(frame=current_frame, style=dict(warp=matched_points))
         else:
             self.update_layer_query(frame=current_frame, style=dict())
@@ -677,9 +693,10 @@ async def fetch(url):
                     async with session.get(url) as response:
                         self._frame_histograms[frame] = await response.json()  # type: ignore
                         # rewrite whole object for watcher
-                        self.frame_selector.frameHistograms = (
-                            self._frame_histograms.copy()  # type: ignore
-                        )
+                        if self.frame_selector is not None and self._frame_histograms is not None:
+                            self.frame_selector.frameHistograms = (
+                                self._frame_histograms.copy()  # type: ignore
+                            )
 
             asyncio.ensure_future(fetch(histogram_url))
 
@@ -737,18 +754,16 @@ def port(self) -> int:
         return self.ports[0]
 
     def get_warp_source(self, warp):
-        if multi_source is None:
-            _lazyImportMultiSource()
-        #  TODO: is there a better way to get the path value?
-        path = str(self.tile_source._initValues[0][0])
-        return multi_source.open(dict(sources=[
-            dict(
-                path=path,
-                position=dict(
-                    x=0, y=0, warp=warp,
+        _lazyImportMultiSource()
+        if multi_source is not None and self.tile_source is not None:
+            return multi_source.open(dict(sources=[
+                dict(
+                    path=self.tile_source.image_path,
+                    position=dict(
+                        x=0, y=0, warp=warp,
+                    ),
                 ),
-            ),
-        ]))
+            ]))
 
 
 def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:

From 03d60c7f214868cc780b9dc8e1efca3ea7355ae0 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 12:33:44 -0400
Subject: [PATCH 09/29] Invert Y axis from map coordinates

---
 large_image/tilesource/jupyter.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 93950577d..6a48196fb 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -440,8 +440,11 @@ def update_schemas():
             transform_checkbox.layout.display = 'block'
             self.update_warp(transform_checkbox.value)
 
-        def convert_coordinate(coord):
-            return [coord[1], coord[0]]
+        def convert_coordinate(map_coord):
+            y, x = map_coord
+            if self._ts is not None:
+                y = self._ts.sizeY - y
+            return [x, y]
 
         def handle_drag(event):
             old = [round(v) for v in event.get('old')]

From 5bcb3500644a57bcb104b110a81b49e1222f2b80 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 13:51:12 -0400
Subject: [PATCH 10/29] Set width and height of warped multi source

---
 large_image/tilesource/jupyter.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 6a48196fb..611748723 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -759,14 +759,18 @@ def port(self) -> int:
     def get_warp_source(self, warp):
         _lazyImportMultiSource()
         if multi_source is not None and self.tile_source is not None:
-            return multi_source.open(dict(sources=[
-                dict(
-                    path=self.tile_source.image_path,
-                    position=dict(
-                        x=0, y=0, warp=warp,
+            return multi_source.open(dict(
+                sources=[
+                    dict(
+                        path=self.tile_source.image_path,
+                        position=dict(
+                            x=0, y=0, warp=warp,
+                        ),
                     ),
-                ),
-            ]))
+                ],
+                width=self.tile_source.sizeX,
+                height=self.tile_source.sizeY,
+            ))
 
 
 def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:

From 586c88d1a56e342196874fb611132d48b9c58346 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 22 Jul 2025 16:17:08 -0400
Subject: [PATCH 11/29] Don't allow warp editor mode if source path does not
 exist

---
 large_image/tilesource/jupyter.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 611748723..2a9bdeddd 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -167,11 +167,6 @@ def iplmap(self) -> Any:
     def warp_points(self):
         return self._map.warp_points
 
-    @property
-    def image_path(self):
-        #  TODO: is there a better way to get the path value?
-        return str(self._initValues[0][0])  # type: ignore[attr-defined]
-
 
 class Map:
     """
@@ -403,10 +398,20 @@ def update_reference_opacity(event):
         self._map.add(FullScreenControl())
         return VBox(children)
 
+    def warp_editor_validate_source(self):
+        if self._ts is None:
+            msg = 'Warp editor mode not allowed; source is not defined.'
+            raise TileSourceError(msg)
+
+        if not os.path.exists(str(self._ts.largeImagePath)):  # type: ignore[attr-defined]
+            msg = 'Warp editor mode not allowed; source file does not exist.'
+            raise TileSourceError(msg)
+
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
         from ipywidgets import HTML, Accordion, Checkbox, Label, VBox
 
+        self.warp_editor_validate_source()
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
         transform_checkbox = Checkbox(description='Show Transformed', value=True)
         transform_checkbox.layout.display = 'none'
@@ -430,7 +435,7 @@ def update_schemas():
             )
             schema = dict(sources=[
                 dict(
-                    path=self._ts.image_path,
+                    path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
                     z=0, position=dict(x=0, y=0, warp=self.get_matched_warp_points()),
                 ),
             ])
@@ -443,7 +448,7 @@ def update_schemas():
         def convert_coordinate(map_coord):
             y, x = map_coord
             if self._ts is not None:
-                y = self._ts.sizeY - y
+                y = self._ts.sizeY - y   # type: ignore[attr-defined]
             return [x, y]
 
         def handle_drag(event):
@@ -762,7 +767,7 @@ def get_warp_source(self, warp):
             return multi_source.open(dict(
                 sources=[
                     dict(
-                        path=self.tile_source.image_path,
+                        path=str(self.tile_source.largeImagePath),
                         position=dict(
                             x=0, y=0, warp=warp,
                         ),

From c1ad0201c618f41b75a56df619152f709d6d40c9 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Mon, 28 Jul 2025 16:48:42 -0400
Subject: [PATCH 12/29] Create both src and dst point on click

---
 large_image/tilesource/jupyter.py | 42 +++++++++++++++++--------------
 1 file changed, 23 insertions(+), 19 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 2a9bdeddd..33d788402 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -451,35 +451,39 @@ def convert_coordinate(map_coord):
                 y = self._ts.sizeY - y   # type: ignore[attr-defined]
             return [x, y]
 
+        def create_reference_point_pair(coord):
+            converted = convert_coordinate(coord)
+            index = len(self.warp_points['src'])
+            self.warp_points['src'].append(converted)
+            self.warp_points['dst'].append(converted)
+
+            for group_name, color in [
+                ('src', '#ff6a5e'), ('dst', '#19a7ff'),
+            ]:
+                html = f'<div style="background-color: {color}; {marker_style}">{index}</div>'
+                icon = DivIcon(html=html, icon_size=[0, 0])
+                marker = Marker(
+                    location=coord,
+                    draggable=True,
+                    icon=icon,
+                    title=f'{group_name} {index}',
+                )
+                marker.observe(handle_drag, 'location')
+                if self._map is not None:
+                    self._map.add(marker)
+
         def handle_drag(event):
-            old = [round(v) for v in event.get('old')]
             new = [round(v) for v in event.get('new')]
             marker_title = event.get('owner').title
             group_name = marker_title[:3]
             index = int(marker_title[3:])
             self.warp_points[group_name][index] = convert_coordinate(new)
-            if group_name == 'dst' and self.warp_points['src'][index] is None:
-                self.warp_points['src'][index] = convert_coordinate(old)
-                html = f'<div style="background-color: #ff6a5e; {marker_style}">{index}</div>'
-                icon = DivIcon(html=html, icon_size=[0, 0])
-                marker = Marker(location=old, draggable=True, icon=icon, title=f'src {index}')
-                marker.observe(handle_drag, 'location')
-                if self._map is not None:
-                    self._map.add(marker)
             update_schemas()
 
         def handle_interaction(**kwargs):
             if kwargs.get('type') == 'click':
-                coords = kwargs.get('coordinates')
-                index = len(self.warp_points['src'])
-                html = f'<div style="background-color: #19a7ff; {marker_style}">{index}</div>'
-                icon = DivIcon(html=html, icon_size=[0, 0])
-                marker = Marker(location=coords, draggable=True, icon=icon, title=f'dst {index}')
-                marker.observe(handle_drag, 'location')
-                if self._map is not None:
-                    self._map.add(marker)
-                self.warp_points['src'].append(None)
-                self.warp_points['dst'].append(convert_coordinate(coords))
+                create_reference_point_pair(kwargs.get('coordinates'))
+                update_schemas()
                 help_text.value = (
                     'After placing reference points, you can drag them to define the warp.'
                 )

From 772c49d018e489d90b221ea9ba4ad9160998df5c Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Mon, 28 Jul 2025 16:50:08 -0400
Subject: [PATCH 13/29] Use `noCache=False` on warped multi source

---
 large_image/tilesource/jupyter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 33d788402..8637d5302 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -779,7 +779,7 @@ def get_warp_source(self, warp):
                 ],
                 width=self.tile_source.sizeX,
                 height=self.tile_source.sizeY,
-            ))
+            ), noCache=False)
 
 
 def launch_tile_server(tile_source: IPyLeafletMixin, port: int = 0) -> Any:

From a837250efdb7d0473dae7c4c197a762f6e423864 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 29 Jul 2025 11:44:45 -0400
Subject: [PATCH 14/29] Add buttons to copy schemas to clipboard

---
 large_image/tilesource/jupyter.py | 49 +++++++++++++++++++++++++------
 1 file changed, 40 insertions(+), 9 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 8637d5302..93e8c49f0 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -19,6 +19,8 @@
 import importlib.util
 import json
 import os
+import re
+import time
 import threading
 import weakref
 from typing import Any, Optional, Union, cast
@@ -409,7 +411,8 @@ def warp_editor_validate_source(self):
 
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
-        from ipywidgets import HTML, Accordion, Checkbox, Label, VBox
+        from IPython.display import Javascript
+        from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
 
         self.warp_editor_validate_source()
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
@@ -417,15 +420,46 @@ def add_warp_editor(self):
         transform_checkbox.layout.display = 'none'
         yaml_schema = HTML('yaml')
         json_schema = HTML('json')
-        schemas = Accordion(children=[yaml_schema, json_schema], titles=('YAML', 'JSON'))
+        copy_yaml_button = Button(description='Copy YAML', icon='fa-copy')
+        copy_json_button = Button(description='Copy JSON', icon='fa-copy')
+        yaml_box = VBox(children=[copy_yaml_button, yaml_schema])
+        json_box = VBox(children=[copy_json_button, json_schema])
+        schemas = Accordion(children=[yaml_box, json_box], titles=('YAML', 'JSON'))
         schemas.layout.display = 'none'
-        children = [transform_checkbox, help_text, schemas]
+        schema_copy_output = Output()
+        schema_copy_output.layout.display = 'none'
+        children = [transform_checkbox, help_text, schemas, schema_copy_output]
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
             'text-align: center; font-size: 11px;'
         )
 
+        def get_schema():
+            return dict(sources=[
+                dict(
+                    path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
+                    z=0, position=dict(x=0, y=0, warp=self.get_matched_warp_points()),
+                ),
+            ])
+
+        def copy_schema(button):
+            content = ''
+            schema = get_schema()
+            desc = button.description
+            if 'YAML' in desc:
+                content = yaml.dump(schema)
+            elif 'JSON' in desc:
+                content = json.dumps(schema)
+            copy_js = Javascript(f"navigator.clipboard.writeText('{re.escape(content)}')")
+            schema_copy_output.clear_output()
+            schema_copy_output.append_display_data(copy_js)
+            button.description = 'Copied!'
+            button.icon = 'fa-check'
+            time.sleep(2)
+            button.description = desc
+            button.icon = 'fa-copy'
+
         def update_schemas():
             if self._ts is None:
                 return
@@ -433,12 +467,7 @@ def update_schemas():
                 'Reference the schemas below to use this warp with '
                 'the MultiFileTileSource (either as YAML or JSON).'
             )
-            schema = dict(sources=[
-                dict(
-                    path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
-                    z=0, position=dict(x=0, y=0, warp=self.get_matched_warp_points()),
-                ),
-            ])
+            schema = get_schema()
             json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
             yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
             schemas.layout.display = 'block'
@@ -492,6 +521,8 @@ def toggle_transform(event):
             self.update_warp(event.get('new'))
 
         transform_checkbox.observe(toggle_transform, names=['value'])
+        copy_yaml_button.on_click(copy_schema)
+        copy_json_button.on_click(copy_schema)
         if self._map is not None:
             self._map.on_interaction(handle_interaction)
         return VBox(children)

From e2a2140798beb822795f068771921d305f296d3d Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 29 Jul 2025 13:37:55 -0400
Subject: [PATCH 15/29] Allow removal of point pairs with double-click events

---
 large_image/tilesource/jupyter.py | 43 +++++++++++++++++--------------
 1 file changed, 23 insertions(+), 20 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 93e8c49f0..d29a03fca 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -429,6 +429,7 @@ def add_warp_editor(self):
         schema_copy_output = Output()
         schema_copy_output.layout.display = 'none'
         children = [transform_checkbox, help_text, schemas, schema_copy_output]
+        markers = {'src': [], 'dst': []}
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
@@ -439,7 +440,7 @@ def get_schema():
             return dict(sources=[
                 dict(
                     path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
-                    z=0, position=dict(x=0, y=0, warp=self.get_matched_warp_points()),
+                    z=0, position=dict(x=0, y=0, warp=self.warp_points),
                 ),
             ])
 
@@ -478,7 +479,7 @@ def convert_coordinate(map_coord):
             y, x = map_coord
             if self._ts is not None:
                 y = self._ts.sizeY - y   # type: ignore[attr-defined]
-            return [x, y]
+            return [int(x), int(y)]
 
         def create_reference_point_pair(coord):
             converted = convert_coordinate(coord)
@@ -497,10 +498,26 @@ def create_reference_point_pair(coord):
                     icon=icon,
                     title=f'{group_name} {index}',
                 )
+                marker.on_dblclick(lambda **e: remove_reference_point_pair(marker))
                 marker.observe(handle_drag, 'location')
+                markers[group_name].append(marker)
                 if self._map is not None:
                     self._map.add(marker)
 
+        def remove_reference_point_pair(marker):
+            index = int(marker.title[3:])
+            for group_name in ['src', 'dst']:
+                del self.warp_points[group_name][index]
+                if self._map is not None:
+                    self._map.remove(markers[group_name][index])
+                del markers[group_name][index]
+                # reset indices of remaining markers
+                for i, m in enumerate(markers[group_name]):
+                    m.title = f'{group_name} {i}'
+                    html = re.sub(r'>\d+<', f'>{i}<', m.icon.html)
+                    m.icon = DivIcon(html=html, icon_size=[0, 0])
+            update_schemas()
+
         def handle_drag(event):
             new = [round(v) for v in event.get('new')]
             marker_title = event.get('owner').title
@@ -514,7 +531,8 @@ def handle_interaction(**kwargs):
                 create_reference_point_pair(kwargs.get('coordinates'))
                 update_schemas()
                 help_text.value = (
-                    'After placing reference points, you can drag them to define the warp.'
+                    'After placing reference points, you can drag them to define the warp. '
+                    'You may also double-click any point to remove the point pair.'
                 )
 
         def toggle_transform(event):
@@ -667,25 +685,10 @@ def from_map(self, coordinate: Union[list[float], tuple[float, float]]) -> tuple
             return transf.transform(x, y)
         return x, self._metadata['sizeY'] - y
 
-    def get_matched_warp_points(self):
-        src = self.warp_points.get('src')
-        dst = self.warp_points.get('dst')
-        if src is None or dst is None:
-            return {}
-        return {
-            k: [
-                point for index, point in enumerate(v)
-                if len(src) > index and src[index] and
-                len(dst) > index and dst[index]
-            ]
-            for k, v in self.warp_points.items()
-        }
-
     def update_warp(self, show_warp):
         current_frame = self.frame_selector.currentFrame if self.frame_selector is not None else 0
-        matched_points = self.get_matched_warp_points()
-        if show_warp and len(matched_points):
-            self.update_layer_query(frame=current_frame, style=dict(warp=matched_points))
+        if show_warp and len(self.warp_points['src']):
+            self.update_layer_query(frame=current_frame, style=dict(warp=self.warp_points))
         else:
             self.update_layer_query(frame=current_frame, style=dict())
 

From 6c76080ee4dc047d38a765756010fba5af30fece Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 29 Jul 2025 14:25:31 -0400
Subject: [PATCH 16/29] Refactor to split complex function

---
 large_image/tilesource/jupyter.py | 156 +++++++++++++++++-------------
 1 file changed, 90 insertions(+), 66 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index d29a03fca..a01e17d5a 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -20,8 +20,8 @@
 import json
 import os
 import re
-import time
 import threading
+import time
 import weakref
 from typing import Any, Optional, Union, cast
 from urllib.parse import parse_qs, quote, urlencode, urlparse, urlunparse
@@ -207,6 +207,7 @@ def __init__(
         self._reference_layer = None
         if self._edit_warp:
             self.warp_points: dict[str, list[Optional[list[int]]]] = dict(src=[], dst=[])
+            self._warp_widgets: dict = dict()
         if (not url or not metadata) and gc and (id or resource):
             fileId = None
             if id is None:
@@ -409,44 +410,30 @@ def warp_editor_validate_source(self):
             msg = 'Warp editor mode not allowed; source file does not exist.'
             raise TileSourceError(msg)
 
-    def add_warp_editor(self):
-        from ipyleaflet import DivIcon, Marker
-        from IPython.display import Javascript
-        from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
+    def get_warp_schema(self):
+        return dict(sources=[
+            dict(
+                path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
+                z=0, position=dict(x=0, y=0, warp=self.warp_points),
+            ),
+        ])
 
-        self.warp_editor_validate_source()
-        help_text = Label('To begin editing a warp, click on the image to place reference points.')
-        transform_checkbox = Checkbox(description='Show Transformed', value=True)
-        transform_checkbox.layout.display = 'none'
-        yaml_schema = HTML('yaml')
-        json_schema = HTML('json')
-        copy_yaml_button = Button(description='Copy YAML', icon='fa-copy')
-        copy_json_button = Button(description='Copy JSON', icon='fa-copy')
-        yaml_box = VBox(children=[copy_yaml_button, yaml_schema])
-        json_box = VBox(children=[copy_json_button, json_schema])
-        schemas = Accordion(children=[yaml_box, json_box], titles=('YAML', 'JSON'))
-        schemas.layout.display = 'none'
-        schema_copy_output = Output()
-        schema_copy_output.layout.display = 'none'
-        children = [transform_checkbox, help_text, schemas, schema_copy_output]
-        markers = {'src': [], 'dst': []}
-        marker_style = (
-            'border-radius: 50%; position: relative;'
-            'height: 16px; width: 16px; top: -8px; left: -8px;'
-            'text-align: center; font-size: 11px;'
-        )
+    def convert_warp_coordinate(self, map_coord):
+        y, x = map_coord
+        if self._ts is not None:
+            y = self._ts.sizeY - y   # type: ignore[attr-defined]
+        return [int(x), int(y)]
 
-        def get_schema():
-            return dict(sources=[
-                dict(
-                    path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
-                    z=0, position=dict(x=0, y=0, warp=self.warp_points),
-                ),
-            ])
+    def toggle_warp_transform(self, event):
+        self.update_warp(event.get('new'))
 
-        def copy_schema(button):
+    def copy_warp_schema(self, button):
+        from IPython.display import Javascript
+
+        schema_copy_output = self._warp_widgets.get('copy_output')
+        if schema_copy_output is not None:
             content = ''
-            schema = get_schema()
+            schema = self.get_warp_schema()
             desc = button.description
             if 'YAML' in desc:
                 content = yaml.dump(schema)
@@ -461,28 +448,71 @@ def copy_schema(button):
             button.description = desc
             button.icon = 'fa-copy'
 
-        def update_schemas():
-            if self._ts is None:
-                return
-            help_text.value = (
-                'Reference the schemas below to use this warp with '
-                'the MultiFileTileSource (either as YAML or JSON).'
-            )
-            schema = get_schema()
-            json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
-            yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
-            schemas.layout.display = 'block'
-            transform_checkbox.layout.display = 'block'
-            self.update_warp(transform_checkbox.value)
-
-        def convert_coordinate(map_coord):
-            y, x = map_coord
-            if self._ts is not None:
-                y = self._ts.sizeY - y   # type: ignore[attr-defined]
-            return [int(x), int(y)]
+    def update_warp_schemas(self):
+        yaml_schema = self._warp_widgets.get('yaml')
+        json_schema = self._warp_widgets.get('json')
+        schema_accordion = self._warp_widgets.get('accordion')
+        transform_checkbox = self._warp_widgets.get('transform')
+        help_text = self._warp_widgets.get('help_text')
+        if (
+            self._ts is None or
+            yaml_schema is None or
+            json_schema is None or
+            schema_accordion is None or
+            transform_checkbox is None or
+            help_text is None
+        ):
+            return
+        schema = self.get_warp_schema()
+        yaml.Dumper.ignore_aliases = lambda self, data: True
+        yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
+        json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
+        schema_accordion.layout.display = 'block'
+        transform_checkbox.layout.display = 'block'
+        help_text.value = (
+            'Reference the schemas below to use this warp with '
+            'the MultiFileTileSource (either as YAML or JSON).'
+        )
+        self.update_warp(transform_checkbox.value)
+
+    def add_warp_editor(self):
+        from ipyleaflet import DivIcon, Marker
+        from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
+
+        self.warp_editor_validate_source()
+        markers = {'src': [], 'dst': []}
+        marker_style = (
+            'border-radius: 50%; position: relative;'
+            'height: 16px; width: 16px; top: -8px; left: -8px;'
+            'text-align: center; font-size: 11px;'
+        )
+        help_text = Label('To begin editing a warp, click on the image to place reference points.')
+        transform_checkbox = Checkbox(description='Show Transformed', value=True)
+        transform_checkbox.layout.display = 'none'
+        transform_checkbox.observe(self.toggle_warp_transform, names=['value'])
+        yaml_schema = HTML('yaml')
+        json_schema = HTML('json')
+        copy_yaml_button = Button(description='Copy YAML', icon='fa-copy')
+        copy_json_button = Button(description='Copy JSON', icon='fa-copy')
+        copy_yaml_button.on_click(self.copy_warp_schema)
+        copy_json_button.on_click(self.copy_warp_schema)
+        yaml_box = VBox(children=[copy_yaml_button, yaml_schema])
+        json_box = VBox(children=[copy_json_button, json_schema])
+        schema_accordion = Accordion(children=[yaml_box, json_box], titles=('YAML', 'JSON'))
+        schema_accordion.layout.display = 'none'
+        schema_copy_output = Output()
+        schema_copy_output.layout.display = 'none'
+        self._warp_widgets = dict(
+            help_text=help_text,
+            transform=transform_checkbox,
+            yaml=yaml_schema,
+            json=json_schema,
+            accordion=schema_accordion,
+            copy_output=schema_copy_output,
+        )
 
         def create_reference_point_pair(coord):
-            converted = convert_coordinate(coord)
+            converted = self.convert_warp_coordinate(coord)
             index = len(self.warp_points['src'])
             self.warp_points['src'].append(converted)
             self.warp_points['dst'].append(converted)
@@ -516,34 +546,28 @@ def remove_reference_point_pair(marker):
                     m.title = f'{group_name} {i}'
                     html = re.sub(r'>\d+<', f'>{i}<', m.icon.html)
                     m.icon = DivIcon(html=html, icon_size=[0, 0])
-            update_schemas()
+            self.update_warp_schemas()
 
         def handle_drag(event):
             new = [round(v) for v in event.get('new')]
             marker_title = event.get('owner').title
             group_name = marker_title[:3]
             index = int(marker_title[3:])
-            self.warp_points[group_name][index] = convert_coordinate(new)
-            update_schemas()
+            self.warp_points[group_name][index] = self.convert_warp_coordinate(new)
+            self.update_warp_schemas()
 
         def handle_interaction(**kwargs):
             if kwargs.get('type') == 'click':
                 create_reference_point_pair(kwargs.get('coordinates'))
-                update_schemas()
+                self.update_warp_schemas()
                 help_text.value = (
                     'After placing reference points, you can drag them to define the warp. '
                     'You may also double-click any point to remove the point pair.'
                 )
 
-        def toggle_transform(event):
-            self.update_warp(event.get('new'))
-
-        transform_checkbox.observe(toggle_transform, names=['value'])
-        copy_yaml_button.on_click(copy_schema)
-        copy_json_button.on_click(copy_schema)
         if self._map is not None:
             self._map.on_interaction(handle_interaction)
-        return VBox(children)
+        return VBox([transform_checkbox, help_text, schema_accordion, schema_copy_output])
 
     def add_region_indicator(self):
         from ipyleaflet import GeomanDrawControl, Popup

From d9d9d36461d51c8553f80b05d52ad5e5c14578d8 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 29 Jul 2025 14:28:26 -0400
Subject: [PATCH 17/29] Fix `Function definition does not bind loop variable`

---
 large_image/tilesource/jupyter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index a01e17d5a..829b39c63 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -528,7 +528,7 @@ def create_reference_point_pair(coord):
                     icon=icon,
                     title=f'{group_name} {index}',
                 )
-                marker.on_dblclick(lambda **e: remove_reference_point_pair(marker))
+                marker.on_dblclick(lambda m=marker, **e: remove_reference_point_pair(m))
                 marker.observe(handle_drag, 'location')
                 markers[group_name].append(marker)
                 if self._map is not None:

From 4e44d4f663f12fe75fca0164b7f0ff3a246220e4 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 29 Jul 2025 14:47:19 -0400
Subject: [PATCH 18/29] Fix typing

---
 large_image/tilesource/jupyter.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 829b39c63..ff391abf7 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -411,6 +411,8 @@ def warp_editor_validate_source(self):
             raise TileSourceError(msg)
 
     def get_warp_schema(self):
+        if self._ts is None:
+            return
         return dict(sources=[
             dict(
                 path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
@@ -464,9 +466,10 @@ def update_warp_schemas(self):
         ):
             return
         schema = self.get_warp_schema()
-        yaml.Dumper.ignore_aliases = lambda self, data: True
-        yaml_schema.value = f'<pre>{yaml.dump(schema)}</pre>'
-        json_schema.value = f'<pre>{json.dumps(schema, indent=4)}</pre>'
+        json_content = json.dumps(schema, indent=4)
+        yaml_content = yaml.dump(json.loads(json_content))  # convert from json to avoid aliases
+        yaml_schema.value = f'<pre>{yaml_content}</pre>'
+        json_schema.value = f'<pre>{json_content}</pre>'
         schema_accordion.layout.display = 'block'
         transform_checkbox.layout.display = 'block'
         help_text.value = (
@@ -480,7 +483,7 @@ def add_warp_editor(self):
         from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
 
         self.warp_editor_validate_source()
-        markers = {'src': [], 'dst': []}
+        markers: dict = {'src': [], 'dst': []}
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'

From 6dd96f8c6322820e88b481c6cacadb16c383edef Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Fri, 1 Aug 2025 14:41:18 -0400
Subject: [PATCH 19/29] Explicitly return None

---
 large_image/tilesource/jupyter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index ff391abf7..9d09e7f12 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -412,7 +412,7 @@ def warp_editor_validate_source(self):
 
     def get_warp_schema(self):
         if self._ts is None:
-            return
+            return None
         return dict(sources=[
             dict(
                 path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]

From 4639160b61119cbd755601cbb0afcea44307f2f2 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Fri, 1 Aug 2025 17:18:52 -0400
Subject: [PATCH 20/29] When transform enabled, make src points invisible and
 compute their positions with inverse transform

---
 large_image/tilesource/jupyter.py | 86 ++++++++++++++++++++++++-------
 1 file changed, 67 insertions(+), 19 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 9d09e7f12..701047e1c 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -38,6 +38,22 @@
 ipyvuePresent = importlib.util.find_spec('ipyvue') is not None
 aiohttpPresent = importlib.util.find_spec('aiohttp') is not None
 
+skimage_transform = None
+
+
+def _lazyImportSkimageTransform():
+    """
+    Import the skimage.transform module. This is only needed when `editWarp=True` is used.
+    """
+    global skimage_transform
+
+    if skimage_transform is None:
+        try:
+            import skimage.transform as skimage_transform
+        except ImportError:
+            msg = 'scikit-image transform module not found.'
+            raise TileSourceError(msg)
+
 
 class IPyLeafletMixin:
     """Mixin class to support interactive visualization in JupyterLab.
@@ -208,6 +224,7 @@ def __init__(
         if self._edit_warp:
             self.warp_points: dict[str, list[Optional[list[int]]]] = dict(src=[], dst=[])
             self._warp_widgets: dict = dict()
+            self._warp_markers: dict = {'src': [], 'dst': []}
         if (not url or not metadata) and gc and (id or resource):
             fileId = None
             if id is None:
@@ -410,6 +427,41 @@ def warp_editor_validate_source(self):
             msg = 'Warp editor mode not allowed; source file does not exist.'
             raise TileSourceError(msg)
 
+    def convert_coordinate_map_to_warp(self, map_coord):
+        y, x = map_coord
+        if self._ts is not None:
+            y = self._ts.sizeY - y   # type: ignore[attr-defined]
+        return [int(x), int(y)]
+
+    def convert_coordinate_warp_to_map(self, warp_coord):
+        x, y = warp_coord
+        if self._ts is not None:
+            y = self._ts.sizeY - y   # type: ignore[attr-defined]
+        return [int(y), int(x)]
+
+    def toggle_warp_transform(self, event):
+        self.update_warp(event.get('new'))
+
+    def inverse_warp(self, coord):
+        warp_src = self.warp_points['src']
+        warp_dst = self.warp_points['dst']
+        if len(warp_src) == 0:
+            return coord
+        if len(warp_src) == 1:
+            inverse_coord = [
+                v + warp_src[0][i] - warp_dst[0][i]
+                for i, v in enumerate(coord)
+            ]
+            return inverse_coord
+        _lazyImportSkimageTransform()
+        if len(warp_src) <= 3:
+            transformer = skimage_transform.AffineTransform()
+        else:
+            transformer = skimage_transform.ThinPlateSplineTransform()
+        transformer.estimate(np.array(warp_dst), np.array(warp_src))
+        inverse_coord = transformer([coord])[0]
+        return [int(v) for v in inverse_coord]
+
     def get_warp_schema(self):
         if self._ts is None:
             return None
@@ -420,15 +472,6 @@ def get_warp_schema(self):
             ),
         ])
 
-    def convert_warp_coordinate(self, map_coord):
-        y, x = map_coord
-        if self._ts is not None:
-            y = self._ts.sizeY - y   # type: ignore[attr-defined]
-        return [int(x), int(y)]
-
-    def toggle_warp_transform(self, event):
-        self.update_warp(event.get('new'))
-
     def copy_warp_schema(self, button):
         from IPython.display import Javascript
 
@@ -483,7 +526,6 @@ def add_warp_editor(self):
         from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
 
         self.warp_editor_validate_source()
-        markers: dict = {'src': [], 'dst': []}
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
@@ -515,10 +557,13 @@ def add_warp_editor(self):
         )
 
         def create_reference_point_pair(coord):
-            converted = self.convert_warp_coordinate(coord)
+            converted = self.convert_coordinate_map_to_warp(coord)
+            locations = dict(src=converted, dst=converted)
+            if transform_checkbox.value:
+                locations['src'] = self.inverse_warp(locations['src'])
             index = len(self.warp_points['src'])
-            self.warp_points['src'].append(converted)
-            self.warp_points['dst'].append(converted)
+            self.warp_points['src'].append(locations['src'])
+            self.warp_points['dst'].append(locations['dst'])
 
             for group_name, color in [
                 ('src', '#ff6a5e'), ('dst', '#19a7ff'),
@@ -526,14 +571,15 @@ def create_reference_point_pair(coord):
                 html = f'<div style="background-color: {color}; {marker_style}">{index}</div>'
                 icon = DivIcon(html=html, icon_size=[0, 0])
                 marker = Marker(
-                    location=coord,
+                    location=self.convert_coordinate_warp_to_map(locations[group_name]),
                     draggable=True,
                     icon=icon,
                     title=f'{group_name} {index}',
+                    visible=(group_name == 'dst' or not transform_checkbox.value),
                 )
                 marker.on_dblclick(lambda m=marker, **e: remove_reference_point_pair(m))
                 marker.observe(handle_drag, 'location')
-                markers[group_name].append(marker)
+                self._warp_markers[group_name].append(marker)
                 if self._map is not None:
                     self._map.add(marker)
 
@@ -542,10 +588,10 @@ def remove_reference_point_pair(marker):
             for group_name in ['src', 'dst']:
                 del self.warp_points[group_name][index]
                 if self._map is not None:
-                    self._map.remove(markers[group_name][index])
-                del markers[group_name][index]
+                    self._map.remove(self._warp_markers[group_name][index])
+                del self._warp_markers[group_name][index]
                 # reset indices of remaining markers
-                for i, m in enumerate(markers[group_name]):
+                for i, m in enumerate(self._warp_markers[group_name]):
                     m.title = f'{group_name} {i}'
                     html = re.sub(r'>\d+<', f'>{i}<', m.icon.html)
                     m.icon = DivIcon(html=html, icon_size=[0, 0])
@@ -556,7 +602,7 @@ def handle_drag(event):
             marker_title = event.get('owner').title
             group_name = marker_title[:3]
             index = int(marker_title[3:])
-            self.warp_points[group_name][index] = self.convert_warp_coordinate(new)
+            self.warp_points[group_name][index] = self.convert_coordinate_map_to_warp(new)
             self.update_warp_schemas()
 
         def handle_interaction(**kwargs):
@@ -713,6 +759,8 @@ def from_map(self, coordinate: Union[list[float], tuple[float, float]]) -> tuple
         return x, self._metadata['sizeY'] - y
 
     def update_warp(self, show_warp):
+        for marker in self._warp_markers['src']:
+            marker.visible = not show_warp
         current_frame = self.frame_selector.currentFrame if self.frame_selector is not None else 0
         if show_warp and len(self.warp_points['src']):
             self.update_layer_query(frame=current_frame, style=dict(warp=self.warp_points))

From 97396fc4fa26aca7fb611db883a251df3cab615a Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 5 Aug 2025 11:44:29 -0400
Subject: [PATCH 21/29] Update warp during drag, not just after release

---
 large_image/tilesource/jupyter.py | 34 +++++++++++++++++++++----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 701047e1c..cc746e1ab 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -225,6 +225,7 @@ def __init__(
             self.warp_points: dict[str, list[Optional[list[int]]]] = dict(src=[], dst=[])
             self._warp_widgets: dict = dict()
             self._warp_markers: dict = {'src': [], 'dst': []}
+            self._dragging_marker_id: Optional[str] = None
         if (not url or not metadata) and gc and (id or resource):
             fileId = None
             if id is None:
@@ -521,6 +522,20 @@ def update_warp_schemas(self):
         )
         self.update_warp(transform_checkbox.value)
 
+    def start_drag(self, marker):
+        self._dragging_marker_id = marker.title
+
+    def handle_drag(self, coords):
+        if self._dragging_marker_id is not None:
+            marker_title = self._dragging_marker_id
+            group_name = marker_title[:3]
+            index = int(marker_title[3:])
+            self.warp_points[group_name][index] = self.convert_coordinate_map_to_warp(coords)
+            self.update_warp_schemas()
+
+    def end_drag(self):
+        self._dragging_marker_id = None
+
     def add_warp_editor(self):
         from ipyleaflet import DivIcon, Marker
         from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
@@ -578,7 +593,8 @@ def create_reference_point_pair(coord):
                     visible=(group_name == 'dst' or not transform_checkbox.value),
                 )
                 marker.on_dblclick(lambda m=marker, **e: remove_reference_point_pair(m))
-                marker.observe(handle_drag, 'location')
+                marker.on_mousedown(lambda m=marker, **e: self.start_drag(m))
+                marker.on_mouseup(lambda **e: self.end_drag())
                 self._warp_markers[group_name].append(marker)
                 if self._map is not None:
                     self._map.add(marker)
@@ -597,22 +613,18 @@ def remove_reference_point_pair(marker):
                     m.icon = DivIcon(html=html, icon_size=[0, 0])
             self.update_warp_schemas()
 
-        def handle_drag(event):
-            new = [round(v) for v in event.get('new')]
-            marker_title = event.get('owner').title
-            group_name = marker_title[:3]
-            index = int(marker_title[3:])
-            self.warp_points[group_name][index] = self.convert_coordinate_map_to_warp(new)
-            self.update_warp_schemas()
-
         def handle_interaction(**kwargs):
-            if kwargs.get('type') == 'click':
-                create_reference_point_pair(kwargs.get('coordinates'))
+            event_type = kwargs.get('type')
+            coords = [round(v) for v in kwargs.get('coordinates')]
+            if event_type == 'click':
+                create_reference_point_pair(coords)
                 self.update_warp_schemas()
                 help_text.value = (
                     'After placing reference points, you can drag them to define the warp. '
                     'You may also double-click any point to remove the point pair.'
                 )
+            elif event_type == 'mousemove':
+                self.handle_drag(coords)
 
         if self._map is not None:
             self._map.on_interaction(handle_interaction)

From 965393928284045204577a5798706bf1743a41ed Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 5 Aug 2025 12:13:15 -0400
Subject: [PATCH 22/29] Fix typing

---
 large_image/tilesource/jupyter.py | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index cc746e1ab..1ed0df9d6 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -449,19 +449,21 @@ def inverse_warp(self, coord):
         if len(warp_src) == 0:
             return coord
         if len(warp_src) == 1:
-            inverse_coord = [
-                v + warp_src[0][i] - warp_dst[0][i]
-                for i, v in enumerate(coord)
-            ]
-            return inverse_coord
+            if warp_src[0] is not None and warp_dst[0] is not None:
+                inverse_coord = [
+                    v + warp_src[0][i] - warp_dst[0][i]
+                    for i, v in enumerate(coord)
+                ]
+                return inverse_coord
         _lazyImportSkimageTransform()
-        if len(warp_src) <= 3:
-            transformer = skimage_transform.AffineTransform()
-        else:
-            transformer = skimage_transform.ThinPlateSplineTransform()
-        transformer.estimate(np.array(warp_dst), np.array(warp_src))
-        inverse_coord = transformer([coord])[0]
-        return [int(v) for v in inverse_coord]
+        if skimage_transform is not None:
+            if len(warp_src) <= 3:
+                transformer = skimage_transform.AffineTransform()
+            else:
+                transformer = skimage_transform.ThinPlateSplineTransform()
+            transformer.estimate(np.array(warp_dst), np.array(warp_src))
+            inverse_coord = transformer([coord])[0]
+            return [int(v) for v in inverse_coord]
 
     def get_warp_schema(self):
         if self._ts is None:
@@ -615,7 +617,7 @@ def remove_reference_point_pair(marker):
 
         def handle_interaction(**kwargs):
             event_type = kwargs.get('type')
-            coords = [round(v) for v in kwargs.get('coordinates')]
+            coords = [round(v) for v in kwargs.get('coordinates', [])]
             if event_type == 'click':
                 create_reference_point_pair(coords)
                 self.update_warp_schemas()

From 1662f60f80830ea369119c1832c379803f1da554 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Tue, 5 Aug 2025 17:11:51 -0400
Subject: [PATCH 23/29] Fix schema copying: ensure newline characters are
 copied

---
 large_image/tilesource/jupyter.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 1ed0df9d6..31f9b93c1 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -468,12 +468,16 @@ def inverse_warp(self, coord):
     def get_warp_schema(self):
         if self._ts is None:
             return None
-        return dict(sources=[
+        schema = dict(sources=[
             dict(
                 path=str(self._ts.largeImagePath),  # type: ignore[attr-defined]
                 z=0, position=dict(x=0, y=0, warp=self.warp_points),
             ),
         ])
+        json_content = json.dumps(schema, indent=4)
+        # convert from json to avoid aliases
+        yaml_content = yaml.dump(json.loads(json_content))
+        return (json_content, yaml_content)
 
     def copy_warp_schema(self, button):
         from IPython.display import Javascript
@@ -481,15 +485,16 @@ def copy_warp_schema(self, button):
         schema_copy_output = self._warp_widgets.get('copy_output')
         if schema_copy_output is not None:
             content = ''
-            schema = self.get_warp_schema()
+            json_content, yaml_content = self.get_warp_schema()
             desc = button.description
             if 'YAML' in desc:
-                content = yaml.dump(schema)
+                content = yaml_content
             elif 'JSON' in desc:
-                content = json.dumps(schema)
-            copy_js = Javascript(f"navigator.clipboard.writeText('{re.escape(content)}')")
+                content = json_content
+            content = content.replace('\n', '\\n')
+            command = f"navigator.clipboard.writeText(unescape('{content}'))"
             schema_copy_output.clear_output()
-            schema_copy_output.append_display_data(copy_js)
+            schema_copy_output.append_display_data(Javascript(command))
             button.description = 'Copied!'
             button.icon = 'fa-check'
             time.sleep(2)
@@ -511,9 +516,7 @@ def update_warp_schemas(self):
             help_text is None
         ):
             return
-        schema = self.get_warp_schema()
-        json_content = json.dumps(schema, indent=4)
-        yaml_content = yaml.dump(json.loads(json_content))  # convert from json to avoid aliases
+        json_content, yaml_content = self.get_warp_schema()
         yaml_schema.value = f'<pre>{yaml_content}</pre>'
         json_schema.value = f'<pre>{json_content}</pre>'
         schema_accordion.layout.display = 'block'

From c8f9d7bff45f7f7b076a36fd4667efc9fee5aa56 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 6 Aug 2025 09:36:50 -0400
Subject: [PATCH 24/29] Use `SimilarityTransform` for colinear points

---
 large_image/tilesource/jupyter.py             | 28 +++++++++++++------
 .../large_image_source_multi/__init__.py      | 10 +++++++
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 31f9b93c1..83fa521c1 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -444,25 +444,35 @@ def toggle_warp_transform(self, event):
         self.update_warp(event.get('new'))
 
     def inverse_warp(self, coord):
-        warp_src = self.warp_points['src']
-        warp_dst = self.warp_points['dst']
-        if len(warp_src) == 0:
+        _lazyImportSkimageTransform()
+
+        warp_src = np.array(self.warp_points['src'])
+        warp_dst = np.array(self.warp_points['dst'])
+        n_points = warp_src.shape[0]
+        inverse_coord = None
+        if n_points == 0:
             return coord
-        if len(warp_src) == 1:
+        if n_points == 1:
             if warp_src[0] is not None and warp_dst[0] is not None:
                 inverse_coord = [
                     v + warp_src[0][i] - warp_dst[0][i]
                     for i, v in enumerate(coord)
                 ]
-                return inverse_coord
-        _lazyImportSkimageTransform()
-        if skimage_transform is not None:
-            if len(warp_src) <= 3:
+        elif skimage_transform is not None:
+            srcsvd = np.linalg.svd(warp_src - warp_src.mean(axis=0), compute_uv=False)
+            dstsvd = np.linalg.svd(warp_dst - warp_dst.mean(axis=0), compute_uv=False)
+            useSimilarity = n_points < 3 or min(
+                srcsvd[1] / (srcsvd[0] or 1), dstsvd[1] / (dstsvd[0] or 1)) < 1e-3
+
+            if useSimilarity:
+                transformer = skimage_transform.SimilarityTransform()
+            elif n_points <= 3:
                 transformer = skimage_transform.AffineTransform()
             else:
                 transformer = skimage_transform.ThinPlateSplineTransform()
-            transformer.estimate(np.array(warp_dst), np.array(warp_src))
+            transformer.estimate(warp_dst, warp_src)
             inverse_coord = transformer([coord])[0]
+        if inverse_coord is not None:
             return [int(v) for v in inverse_coord]
 
     def get_warp_schema(self):
diff --git a/sources/multi/large_image_source_multi/__init__.py b/sources/multi/large_image_source_multi/__init__.py
index 1ed2c5321..15c49f485 100644
--- a/sources/multi/large_image_source_multi/__init__.py
+++ b/sources/multi/large_image_source_multi/__init__.py
@@ -685,11 +685,21 @@ def _getWarp(self, warp, m):
         warp_dst = np.array(warp_dst or []).astype(float)
         warp_src = warp_src[:min(warp_src.shape[0], warp_dst.shape[0]), :]
         warp_dst = warp_dst[:warp_src.shape[0], :]
+
+        srcsvd = np.linalg.svd(warp_src - warp_src.mean(axis=0), compute_uv=False)
+        dstsvd = np.linalg.svd(warp_dst - warp_dst.mean(axis=0), compute_uv=False)
+        useSimilarity = warp_src.shape[0] < 3 or min(
+            srcsvd[1] / (srcsvd[0] or 1), dstsvd[1] / (dstsvd[0] or 1)) < 1e-3
+
         if warp_src.shape[0] < 1:
             pass
         elif warp_src.shape[0] == 1:
             m[0][2] += warp_dst[0][0] - warp_src[0][0]
             m[1][2] += warp_dst[0][1] - warp_src[0][1]
+        elif useSimilarity:
+            transformer = skimage_transform.SimilarityTransform()
+            transformer.estimate(warp_src, warp_dst)
+            m = transformer.params
         elif warp_src.shape[0] <= 3:
             transformer = skimage_transform.AffineTransform()
             transformer.estimate(warp_src, warp_dst)

From dbc13689134334337f4e74adc5d5d3e20762f60a Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 6 Aug 2025 10:22:00 -0400
Subject: [PATCH 25/29] Add basic tests for `editWarp` mode and `reference`
 mode

---
 test/test_jupyter.py | 74 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/test/test_jupyter.py b/test/test_jupyter.py
index 0c42a5f0b..10ec30bd5 100644
--- a/test/test_jupyter.py
+++ b/test/test_jupyter.py
@@ -164,3 +164,77 @@ def testJupyterIpyleafletMapGeospatialRegion():
     for callback in m._interaction_callbacks.callbacks:
         callback(type='click', coordinates=[lat, lon])
     assert source._map.info_label.value == ''.join([f'<div>{e}</div>' for e in expected])
+
+
+def testJupyterReferenceLayer():
+    testDir = os.path.dirname(os.path.realpath(__file__))
+    imagePath1 = os.path.join(testDir, 'test_files', 'rgb_geotiff.tiff')
+    imagePath2 = os.path.join(testDir, 'test_files', 'rgba_geotiff.tiff')
+    source1 = large_image.open(imagePath1, projection='EPSG:3857', noCache=True)
+    source2 = large_image.open(imagePath2, projection='EPSG:3857', noCache=True, reference=source1)
+    display = source2._map.make_map(
+        source2.metadata, source2.as_leaflet_layer(), source2.getCenter(srs='EPSG:4326'),
+    )
+    assert len(display.children) == 2
+    [slider, leafletMap] = display.children
+    assert slider.description == 'Reference Opacity'
+    for path in [imagePath1, imagePath2]:
+        assert any(path in layer.url for layer in leafletMap.layers)
+
+
+def initEditWarp():
+    testDir = os.path.dirname(os.path.realpath(__file__))
+    imagePath = os.path.join(testDir, 'test_files', 'rgb_geotiff.tiff')
+    source = large_image.open(imagePath, projection='EPSG:3857', noCache=True, editWarp=True)
+    display = source._map.make_map(
+        source.metadata, source.as_leaflet_layer(), source.getCenter(srs='EPSG:4326'),
+    )
+    return source._map, display
+
+
+def testJupyterEditWarp():
+    _, display = initEditWarp()
+    assert len(display.children) == 2
+    vbox = display.children[1]
+    assert len(vbox.children) == 4
+    assert vbox.children[0].description == 'Show Transformed'
+    assert vbox.children[0].layout.display == 'none'
+    assert vbox.children[1].value == (
+        'To begin editing a warp, click on the image to place reference points.'
+    )
+    assert vbox.children[2].titles == ('YAML', 'JSON')
+    assert vbox.children[3].layout.display == 'none'
+
+
+def testJupyterEditWarpConvertCoords():
+    sourceMap, _ = initEditWarp()
+    assert sourceMap.convert_coordinate_map_to_warp([10, 12]) == [12, 65526]
+    assert sourceMap.convert_coordinate_warp_to_map([12, 65526]) == [10, 12]
+
+
+def testJupyterEditWarpInverseWarp():
+    sourceMap, _ = initEditWarp()
+    # inverse from single ref point
+    sourceMap.warp_points = dict(
+        src=[[10, 10]],
+        dst=[[15, 15]],
+    )
+    assert sourceMap.inverse_warp([5, 5]) == [0, 0]
+    # inverse from two ref points
+    sourceMap.warp_points = dict(
+        src=[[10, 10], [5, 5]],
+        dst=[[15, 15], [3, 4]],
+    )
+    assert sourceMap.inverse_warp([2, 4]) == [4, 4]
+    # inverse from three ref points
+    sourceMap.warp_points = dict(
+        src=[[10, 10], [5, 5], [2, 4]],
+        dst=[[15, 15], [3, 4], [3, 6]],
+    )
+    assert sourceMap.inverse_warp([6, 9]) == [2, 5]
+    # inverse from four ref points
+    sourceMap.warp_points = dict(
+        src=[[10, 10], [5, 5], [2, 4], [6, 9]],
+        dst=[[15, 15], [3, 4], [3, 6], [3, 5]],
+    )
+    assert sourceMap.inverse_warp([8, 8]) == [7, 6]

From e46ca2df79d7470f681fd6073d3f2bebc129132c Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 6 Aug 2025 11:31:57 -0400
Subject: [PATCH 26/29] Move more functions outside of `add_warp_editor`
 function context

---
 large_image/tilesource/jupyter.py | 97 ++++++++++++++++---------------
 1 file changed, 51 insertions(+), 46 deletions(-)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index 83fa521c1..bed196bff 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -551,16 +551,63 @@ def handle_drag(self, coords):
     def end_drag(self):
         self._dragging_marker_id = None
 
-    def add_warp_editor(self):
+    def create_warp_reference_point_pair(self, coord):
         from ipyleaflet import DivIcon, Marker
-        from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
 
-        self.warp_editor_validate_source()
         marker_style = (
             'border-radius: 50%; position: relative;'
             'height: 16px; width: 16px; top: -8px; left: -8px;'
             'text-align: center; font-size: 11px;'
         )
+        converted = self.convert_coordinate_map_to_warp(coord)
+        locations = dict(src=converted, dst=converted)
+        transform_checkbox = self._warp_widgets.get('transform')
+        transform_enabled = transform_checkbox.value if transform_checkbox is not None else True
+        if transform_enabled:
+            locations['src'] = self.inverse_warp(locations['src'])
+        index = len(self.warp_points['src'])
+        self.warp_points['src'].append(locations['src'])
+        self.warp_points['dst'].append(locations['dst'])
+
+        for group_name, color in [
+            ('src', '#ff6a5e'), ('dst', '#19a7ff'),
+        ]:
+            html = f'<div style="background-color: {color}; {marker_style}">{index}</div>'
+            icon = DivIcon(html=html, icon_size=[0, 0])
+            marker = Marker(
+                location=self.convert_coordinate_warp_to_map(locations[group_name]),
+                draggable=True,
+                icon=icon,
+                title=f'{group_name} {index}',
+                visible=(group_name == 'dst' or not transform_enabled),
+            )
+            marker.on_dblclick(lambda m=marker, **e: self.remove_warp_reference_point_pair(m))
+            marker.on_mousedown(lambda m=marker, **e: self.start_drag(m))
+            marker.on_mouseup(lambda **e: self.end_drag())
+            self._warp_markers[group_name].append(marker)
+            if self._map is not None:
+                self._map.add(marker)
+
+    def remove_warp_reference_point_pair(self, marker):
+        from ipyleaflet import DivIcon
+
+        index = int(marker.title[3:])
+        for group_name in ['src', 'dst']:
+            del self.warp_points[group_name][index]
+            if self._map is not None:
+                self._map.remove(self._warp_markers[group_name][index])
+            del self._warp_markers[group_name][index]
+            # reset indices of remaining markers
+            for i, m in enumerate(self._warp_markers[group_name]):
+                m.title = f'{group_name} {i}'
+                html = re.sub(r'>\d+<', f'>{i}<', m.icon.html)
+                m.icon = DivIcon(html=html, icon_size=[0, 0])
+        self.update_warp_schemas()
+
+    def add_warp_editor(self):
+        from ipywidgets import HTML, Accordion, Button, Checkbox, Label, Output, VBox
+
+        self.warp_editor_validate_source()
         help_text = Label('To begin editing a warp, click on the image to place reference points.')
         transform_checkbox = Checkbox(description='Show Transformed', value=True)
         transform_checkbox.layout.display = 'none'
@@ -586,53 +633,11 @@ def add_warp_editor(self):
             copy_output=schema_copy_output,
         )
 
-        def create_reference_point_pair(coord):
-            converted = self.convert_coordinate_map_to_warp(coord)
-            locations = dict(src=converted, dst=converted)
-            if transform_checkbox.value:
-                locations['src'] = self.inverse_warp(locations['src'])
-            index = len(self.warp_points['src'])
-            self.warp_points['src'].append(locations['src'])
-            self.warp_points['dst'].append(locations['dst'])
-
-            for group_name, color in [
-                ('src', '#ff6a5e'), ('dst', '#19a7ff'),
-            ]:
-                html = f'<div style="background-color: {color}; {marker_style}">{index}</div>'
-                icon = DivIcon(html=html, icon_size=[0, 0])
-                marker = Marker(
-                    location=self.convert_coordinate_warp_to_map(locations[group_name]),
-                    draggable=True,
-                    icon=icon,
-                    title=f'{group_name} {index}',
-                    visible=(group_name == 'dst' or not transform_checkbox.value),
-                )
-                marker.on_dblclick(lambda m=marker, **e: remove_reference_point_pair(m))
-                marker.on_mousedown(lambda m=marker, **e: self.start_drag(m))
-                marker.on_mouseup(lambda **e: self.end_drag())
-                self._warp_markers[group_name].append(marker)
-                if self._map is not None:
-                    self._map.add(marker)
-
-        def remove_reference_point_pair(marker):
-            index = int(marker.title[3:])
-            for group_name in ['src', 'dst']:
-                del self.warp_points[group_name][index]
-                if self._map is not None:
-                    self._map.remove(self._warp_markers[group_name][index])
-                del self._warp_markers[group_name][index]
-                # reset indices of remaining markers
-                for i, m in enumerate(self._warp_markers[group_name]):
-                    m.title = f'{group_name} {i}'
-                    html = re.sub(r'>\d+<', f'>{i}<', m.icon.html)
-                    m.icon = DivIcon(html=html, icon_size=[0, 0])
-            self.update_warp_schemas()
-
         def handle_interaction(**kwargs):
             event_type = kwargs.get('type')
             coords = [round(v) for v in kwargs.get('coordinates', [])]
             if event_type == 'click':
-                create_reference_point_pair(coords)
+                self.create_warp_reference_point_pair(coords)
                 self.update_warp_schemas()
                 help_text.value = (
                     'After placing reference points, you can drag them to define the warp. '

From 13f9fdcca114c3454b573d56fc7bd5ce2730f583 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 6 Aug 2025 11:58:13 -0400
Subject: [PATCH 27/29] Add more tests for better coverage

---
 test/test_jupyter.py | 49 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/test/test_jupyter.py b/test/test_jupyter.py
index 10ec30bd5..3ad87b0a1 100644
--- a/test/test_jupyter.py
+++ b/test/test_jupyter.py
@@ -1,9 +1,11 @@
 import asyncio
+import json
 import os
 from urllib.parse import parse_qs, urlparse
 
 import aiohttp
 import pytest
+import yaml
 
 import large_image
 
@@ -212,6 +214,53 @@ def testJupyterEditWarpConvertCoords():
     assert sourceMap.convert_coordinate_warp_to_map([12, 65526]) == [10, 12]
 
 
+def testJupyterEditWarpCreateAndDeletePointPairs():
+    sourceMap, _ = initEditWarp()
+    sourceMap.create_warp_reference_point_pair([10, 10])
+    assert len(sourceMap._warp_markers['src']) == 1
+    assert len(sourceMap._warp_markers['dst']) == 1
+    marker = sourceMap._warp_markers['src'][0]
+    assert marker.location == [10, 10]
+    sourceMap.remove_warp_reference_point_pair(marker)
+    assert len(sourceMap._warp_markers['src']) == 0
+    assert len(sourceMap._warp_markers['dst']) == 0
+
+
+def testJupyterEditWarpSchemas():
+    sourceMap, display = initEditWarp()
+    warp = dict(
+        src=[[10, 10]],
+        dst=[[15, 15]],
+    )
+    expected = dict(sources=[
+        dict(
+            path=str(sourceMap._ts.largeImagePath),
+            z=0, position=dict(x=0, y=0, warp=warp),
+        ),
+    ])
+    sourceMap.warp_points = warp
+    sourceMap.update_warp_schemas()
+    json_schema = sourceMap._warp_widgets.get('json')
+    assert json_schema.value == f'<pre>{json.dumps(expected, indent=4)}</pre>'
+    yaml_schema = sourceMap._warp_widgets.get('yaml')
+    assert yaml_schema.value == f'<pre>{yaml.dump(expected)}</pre>'
+
+    assert len(display.children) == 2
+    vbox = display.children[1]
+    assert len(vbox.children) == 4
+    copy_output = vbox.children[3]
+    accordion = vbox.children[2]
+    yaml_section = accordion.children[0]
+    copy_yaml_button = yaml_section.children[0]
+    sourceMap.copy_warp_schema(copy_yaml_button)
+    assert len(copy_output.outputs) == 1
+    output = copy_output.outputs[0]
+    assert output['data']['application/javascript'] == (
+        "navigator.clipboard.writeText(unescape('%s'))"
+        % yaml.dump(expected).replace('\n', '\\n')
+    )
+
+
 def testJupyterEditWarpInverseWarp():
     sourceMap, _ = initEditWarp()
     # inverse from single ref point

From 6f4a41fbc37e33ccba9f58e7e93d2f10c6b2aa0e Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 6 Aug 2025 12:41:47 -0400
Subject: [PATCH 28/29] Protect against zero-length array in `svd`

---
 sources/multi/large_image_source_multi/__init__.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/sources/multi/large_image_source_multi/__init__.py b/sources/multi/large_image_source_multi/__init__.py
index 15c49f485..d19208ea6 100644
--- a/sources/multi/large_image_source_multi/__init__.py
+++ b/sources/multi/large_image_source_multi/__init__.py
@@ -686,10 +686,12 @@ def _getWarp(self, warp, m):
         warp_src = warp_src[:min(warp_src.shape[0], warp_dst.shape[0]), :]
         warp_dst = warp_dst[:warp_src.shape[0], :]
 
-        srcsvd = np.linalg.svd(warp_src - warp_src.mean(axis=0), compute_uv=False)
-        dstsvd = np.linalg.svd(warp_dst - warp_dst.mean(axis=0), compute_uv=False)
-        useSimilarity = warp_src.shape[0] < 3 or min(
-            srcsvd[1] / (srcsvd[0] or 1), dstsvd[1] / (dstsvd[0] or 1)) < 1e-3
+        useSimilarity = False
+        if len(warp_src) > 0 and len(warp_dst) > 0:
+            srcsvd = np.linalg.svd(warp_src - warp_src.mean(axis=0), compute_uv=False)
+            dstsvd = np.linalg.svd(warp_dst - warp_dst.mean(axis=0), compute_uv=False)
+            useSimilarity = warp_src.shape[0] < 3 or min(
+                srcsvd[1] / (srcsvd[0] or 1), dstsvd[1] / (dstsvd[0] or 1)) < 1e-3
 
         if warp_src.shape[0] < 1:
             pass

From d211f2d65cfc7d168a4580211baecc129317d2c0 Mon Sep 17 00:00:00 2001
From: Anne Haley <anne.haley@kitware.com>
Date: Wed, 27 Aug 2025 14:15:08 -0400
Subject: [PATCH 29/29] For multiframe images, apply warp when switching frames

---
 large_image/tilesource/jupyter.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/large_image/tilesource/jupyter.py b/large_image/tilesource/jupyter.py
index bed196bff..870903fb8 100644
--- a/large_image/tilesource/jupyter.py
+++ b/large_image/tilesource/jupyter.py
@@ -800,6 +800,15 @@ def update_warp(self, show_warp):
             self.update_layer_query(frame=current_frame, style=dict())
 
     def update_frame(self, frame, style, **kwargs):
+        if self._edit_warp:
+            transform_checkbox = self._warp_widgets.get('transform')
+            if (
+                transform_checkbox is not None and
+                transform_checkbox.value and
+                self.warp_points is not None and
+                len(self.warp_points['src'])
+            ):
+                style['warp'] = self.warp_points
         self.update_layer_query(frame=frame, style=style)
 
     def update_layer_query(self, frame, style, **kwargs):