napari widgets to manage atlas versions

brainrender_napari/__init__.py

@@ -1,4 +1,4 @@
 __version__ = "0.0.1"
 
 
-__all__ = "BrainrenderWidget"
+__all__ = "BrainrenderWidget", "AtlasVersionManagerWidget"

brainrender_napari/atlas_version_manager_widget.py

@@ -0,0 +1,28 @@
+from qtpy.QtWidgets import QVBoxLayout, QWidget
+
+from brainrender_napari.utils.brainglobe_logo import header_widget
+from brainrender_napari.widgets.atlas_manager_view import AtlasManagerView
+
+
+class AtlasVersionManagerWidget(QWidget):
+    def __init__(self):
+        """Instantiates the version manager widget
+        and sets up coordinating connections"""
+        super().__init__()
+
+        self.setLayout(QVBoxLayout())
+        self.layout().addWidget(
+            header_widget(tutorial_file_name="update-atlas-napari.html")
+        )
+
+        # create widgets
+        self.atlas_manager_view = AtlasManagerView(parent=self)
+        self.layout().addWidget(self.atlas_manager_view)
+
+        self.atlas_manager_view.download_atlas_confirmed.connect(self._refresh)
+
+        self.atlas_manager_view.update_atlas_confirmed.connect(self._refresh)
+
+    def _refresh(self) -> None:
+        # refresh view once an atlas has been downloaded
+        self.atlas_manager_view = AtlasManagerView(parent=self)

brainrender_napari/brainrender_widget.py

@@ -38,7 +38,9 @@ def __init__(self, napari_viewer: Viewer):
 
         self._viewer = napari_viewer
         self.setLayout(QVBoxLayout())
-        self.layout().addWidget(header_widget())
+        self.layout().addWidget(
+            header_widget(tutorial_file_name="visualise-atlas-napari.html")
+        )
 
         # create widgets
         self.atlas_viewer_view = AtlasViewerView(parent=self)

brainrender_napari/napari.yaml

@@ -5,6 +5,11 @@ contributions:
     - id: brainrender-napari.make_brainrender_widget
       python_name: brainrender_napari.brainrender_widget:BrainrenderWidget
       title: Make Brainrender Napari
+    - id: brainrender-napari.make_atlas_version_manager_widget
+      python_name: brainrender_napari.atlas_version_manager_widget:AtlasVersionManagerWidget
+      title: Make Brainrender Napari
   widgets:
     - command: brainrender-napari.make_brainrender_widget
       display_name: Brainrender
+    - command: brainrender-napari.make_atlas_version_manager_widget
+      display_name: Atlas version manager

brainrender_napari/utils/brainglobe_logo.py

@@ -13,32 +13,31 @@
 <\h1>
 """
 
-_docs_links_html = """
-<h3>
-<p>Atlas visualisation</p>
-<p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-<p><a href="https://brainglobe.info/tutorials/visualise-atlas-napari.html" style="color:gray;">Tutorial</a></p>
-<p><a href="https://github.com/brainglobe/brainrender-napari" style="color:gray;">Source</a></p>
-<p><a href="https://doi.org/10.7554/eLife.65751" style="color:gray;">Citation</a></p>
-<p><small>For help, hover the cursor over the atlases/regions.</small>
-</h3>
-"""  # noqa: E501
-
-
-def _docs_links_widget():
-    docs_links_widget = QLabel(_docs_links_html)
+
+def _docs_links_widget(tutorial_file_name: str, parent: QWidget = None):
+    _docs_links_html = f"""
+    <h3>
+    <p>Atlas visualisation</p>
+    <p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
+    <p><a href="https://brainglobe.info/tutorials/{tutorial_file_name}" style="color:gray;">Tutorial</a></p>
+    <p><a href="https://github.com/brainglobe/brainrender-napari" style="color:gray;">Source</a></p>
+    <p><a href="https://doi.org/10.7554/eLife.65751" style="color:gray;">Citation</a></p>
+    <p><small>For help, hover the cursor over the atlases/regions.</small>
+    </h3>
+    """  # noqa: E501
+    docs_links_widget = QLabel(_docs_links_html, parent=parent)
     docs_links_widget.setOpenExternalLinks(True)
     return docs_links_widget
 
 
-def _logo_widget():
-    return QLabel(_logo_html)
+def _logo_widget(parent: QWidget = None):
+    return QLabel(_logo_html, parent=None)
 
 
-def header_widget(parent: QWidget = None):
+def header_widget(tutorial_file_name: str, parent: QWidget = None):
     box = QGroupBox(parent)
     box.setFlat(True)
     box.setLayout(QHBoxLayout())
-    box.layout().addWidget(_logo_widget())
-    box.layout().addWidget(_docs_links_widget())
+    box.layout().addWidget(_logo_widget(parent=box))
+    box.layout().addWidget(_docs_links_widget(tutorial_file_name, parent=box))
     return box

brainrender_napari/widgets/structure_view.py

@@ -2,158 +2,18 @@
 model and view classes for the structures that form part of an atlas.
 The view is only visible if the atlas is downloaded."""
 
-from typing import Dict, List
-
 from bg_atlasapi.list_atlases import get_downloaded_atlases
-from bg_atlasapi.structure_tree_util import get_structures_tree
-from qtpy.QtCore import QAbstractItemModel, QModelIndex, Qt, Signal
-from qtpy.QtGui import QStandardItem
+from qtpy.QtCore import QModelIndex, Signal
 from qtpy.QtWidgets import QTreeView, QWidget
 
+from brainrender_napari.data_models.structure_tree_model import (
+    StructureTreeModel,
+)
 from brainrender_napari.utils.load_user_data import (
     read_atlas_structures_from_file,
 )
 
 
-class StructureTreeItem(QStandardItem):
-    """A class to hold items in a tree model."""
-
-    def __init__(self, data, parent=None):
-        self.parent_item = parent
-        self.item_data = data
-        self.child_items = []
-
-    def appendChild(self, item):
-        self.child_items.append(item)
-
-    def child(self, row):
-        return self.child_items[row]
-
-    def childCount(self):
-        return len(self.child_items)
-
-    def columnCount(self):
-        return len(self.item_data)
-
-    def data(self, column):
-        try:
-            return self.item_data[column]
-        except IndexError:
-            return None
-
-    def parent(self):
-        return self.parent_item
-
-    def row(self):
-        if self.parent_item:
-            return self.parent_item.child_items.index(self)
-        return 0
-
-
-class StructureTreeModel(QAbstractItemModel):
-    """Implementation of a read-only QAbstractItemModel to hold
-    the structure tree information provided by the Atlas API in a Qt Model"""
-
-    def __init__(self, data: List, parent=None):
-        super().__init__()
-        self.root_item = StructureTreeItem(data=("acronym", "name", "id"))
-        self.build_structure_tree(data, self.root_item)
-
-    def build_structure_tree(self, structures: List, root: StructureTreeItem):
-        """Build the structure tree given a list of structures."""
-        tree = get_structures_tree(structures)
-        structure_id_dict = {}
-        for structure in structures:
-            structure_id_dict[structure["id"]] = structure
-
-        inserted_items: Dict[int, StructureTreeItem] = {}
-        for n_id in tree.expand_tree():  # sorts nodes by default,
-            # so parents will always be already in the QAbstractItemModel
-            # before their children
-            node = tree.get_node(n_id)
-            acronym = structure_id_dict[node.identifier]["acronym"]
-            name = structure_id_dict[node.identifier]["name"]
-            if (
-                len(structure_id_dict[node.identifier]["structure_id_path"])
-                == 1
-            ):
-                parent_item = root
-            else:
-                parent_id = tree.parent(node.identifier).identifier
-                parent_item = inserted_items[parent_id]
-
-            item = StructureTreeItem(
-                data=(acronym, name, node.identifier), parent=parent_item
-            )
-            parent_item.appendChild(item)
-            inserted_items[node.identifier] = item
-
-    def data(self, index: QModelIndex, role=Qt.DisplayRole):
-        """Provides read-only data for a given index if
-        intended for display, otherwise None."""
-        if not index.isValid():
-            return None
-
-        if role != Qt.DisplayRole:
-            return None
-
-        item = index.internalPointer()
-
-        return item.data(index.column())
-
-    def rowCount(self, parent: StructureTreeItem):
-        """Returns the number of rows(i.e. children) of an item"""
-        if parent.column() > 0:
-            return 0
-
-        if not parent.isValid():
-            parent_item = self.root_item
-        else:
-            parent_item = parent.internalPointer()
-
-        return parent_item.childCount()
-
-    def columnCount(self, parent: StructureTreeItem):
-        """The number of columns of an item."""
-        if parent.isValid():
-            return parent.internalPointer().columnCount()
-        else:
-            return self.root_item.columnCount()
-
-    def parent(self, index: QModelIndex):
-        """The first-column index of parent of the item
-        at a given index. Returns an empty index if the root,
-        or an invalid index, is passed.
-        """
-        if not index.isValid():
-            return QModelIndex()
-
-        child_item = index.internalPointer()
-        parent_item = child_item.parent()
-
-        if parent_item == self.root_item:
-            return QModelIndex()
-
-        return self.createIndex(parent_item.row(), 0, parent_item)
-
-    def index(self, row, column, parent=QModelIndex()):
-        """The index of the item at (row, column) with a given parent.
-        By default, the given parent is assumed to be the root."""
-        if not self.hasIndex(row, column, parent):
-            return QModelIndex()
-
-        if not parent.isValid():
-            parent_item = self.root_item
-        else:
-            parent_item = parent.internalPointer()
-
-        child_item = parent_item.child(row)
-        if child_item:
-            return self.createIndex(row, column, child_item)
-        else:
-            return QModelIndex()
-
-
 class StructureView(QTreeView):
     add_structure_requested = Signal(str)
 

tests/test_integration/test_atlas_version_manager_widget.py

@@ -0,0 +1,63 @@
+import pytest
+
+from brainrender_napari.atlas_version_manager_widget import (
+    AtlasVersionManagerWidget,
+)
+
+
+@pytest.fixture
+def atlas_version_manager_widget(qtbot) -> AtlasVersionManagerWidget:
+    """A fixture to provide a version manager widget.
+
+    Depends on qtbot so Qt event loop is started.
+    """
+    return AtlasVersionManagerWidget()
+
+
+def test_refresh_calls_view_constructor(atlas_version_manager_widget, mocker):
+    """Checks that refreshing the version manager widget
+    calls the view's constructor."""
+    atlas_manager_view_mock = mocker.patch(
+        "brainrender_napari.atlas_version_manager_widget.AtlasManagerView"
+    )
+    atlas_version_manager_widget._refresh()
+    atlas_manager_view_mock.assert_called_once_with(
+        parent=atlas_version_manager_widget
+    )
+
+
+def test_refresh_on_download(qtbot, mocker):
+    """Checks that when the view signals an atlas has been downloaded,
+    the version manager widget is refreshed."""
+    refresh_mock = mocker.patch(
+        "brainrender_napari.atlas_version_manager_widget.AtlasVersionManagerWidget._refresh"
+    )
+    # Don't use atlas_version_manager_widget fixture here,
+    # because otherwise mocking is ineffectual!
+    atlas_version_manager_widget = AtlasVersionManagerWidget()
+    with qtbot.waitSignal(
+        atlas_version_manager_widget.atlas_manager_view.download_atlas_confirmed
+    ):
+        atlas_version_manager_widget.atlas_manager_view.download_atlas_confirmed.emit(
+            "allen_mouse_100um"
+        )
+    refresh_mock.assert_called_once_with("allen_mouse_100um")
+
+
+def test_refresh_on_update(qtbot, mocker):
+    """Checks that when the view signals an atlas has been updated,
+    the version manager widget is updated."""
+    refresh_mock = mocker.patch(
+        "brainrender_napari.atlas_version_manager_widget"
+        ".AtlasVersionManagerWidget._refresh"
+    )
+    # Don't use atlas_version_manager_widget fixture here,
+    # because otherwise mocking is ineffectual!
+    atlas_version_manager_widget = AtlasVersionManagerWidget()
+    with qtbot.waitSignal(
+        atlas_version_manager_widget.atlas_manager_view.update_atlas_confirmed
+    ):
+        atlas_version_manager_widget.atlas_manager_view.update_atlas_confirmed.emit(
+            "allen_mouse_100um"
+        )
+    refresh_mock.assert_called_once_with("allen_mouse_100um")