Manage atlas versions in a separate widget

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

@@ -21,7 +21,7 @@
     NapariAtlasRepresentation,
 )
 from brainrender_napari.utils.brainglobe_logo import header_widget
-from brainrender_napari.widgets.atlas_table_view import AtlasTableView
+from brainrender_napari.widgets.atlas_viewer_view import AtlasViewerView
 from brainrender_napari.widgets.structure_view import StructureView
 
 
@@ -40,10 +40,12 @@ 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_table_view = AtlasTableView(parent=self)
+        self.atlas_table_view = AtlasViewerView(parent=self)
 
         self.show_structure_names = QCheckBox()
         self.show_structure_names.setChecked(False)
@@ -79,9 +81,6 @@ def __init__(self, napari_viewer: Viewer):
         self.layout().addWidget(self.structure_tree_group)
 
         # connect atlas view widget signals
-        self.atlas_table_view.download_atlas_confirmed.connect(
-            self._on_download_atlas_confirmed
-        )
         self.atlas_table_view.add_atlas_requested.connect(
             self._on_add_atlas_requested
         )
@@ -102,11 +101,6 @@ def __init__(self, napari_viewer: Viewer):
             self._on_add_structure_requested
         )
 
-    def _on_download_atlas_confirmed(self, atlas_name):
-        """Ensure structure view is displayed if new atlas downloaded."""
-        show_structure_names = self.show_structure_names.isChecked()
-        self.structure_view.refresh(atlas_name, show_structure_names)
-
     def _on_add_structure_requested(self, structure_name: str):
         """Add given structure as napari atlas representation"""
         selected_atlas = BrainGlobeAtlas(

brainrender_napari/data_models/atlas_table_model.py

@@ -0,0 +1,96 @@
+from bg_atlasapi.list_atlases import (
+    get_all_atlases_lastversions,
+    get_atlases_lastversions,
+    get_downloaded_atlases,
+    get_local_atlas_version,
+)
+from qtpy.QtCore import QAbstractTableModel, QModelIndex, Qt
+
+from brainrender_napari.utils.load_user_data import (
+    read_atlas_metadata_from_file,
+)
+
+
+class AtlasTableModel(QAbstractTableModel):
+    """A table data model for atlases."""
+
+    def __init__(self):
+        super().__init__()
+        self.refresh_data()
+
+    def refresh_data(self) -> None:
+        """Refresh model data by calling atlas API"""
+        all_atlases = get_all_atlases_lastversions()
+        data = []
+        for name, latest_version in all_atlases.items():
+            if name in get_atlases_lastversions().keys():
+                data.append(
+                    [
+                        name,
+                        self._format_name(name),
+                        get_local_atlas_version(name),
+                        latest_version,
+                    ]
+                )
+            else:
+                data.append(
+                    [name, self._format_name(name), "n/a", latest_version]
+                )
+
+        self._data = data
+
+    def _format_name(self, name: str) -> str:
+        formatted_name = name.split("_")
+        formatted_name[0] = formatted_name[0].capitalize()
+        formatted_name[-1] = f"({formatted_name[-1].split('um')[0]} \u03BCm)"
+        return " ".join([formatted for formatted in formatted_name])
+
+    def data(self, index: QModelIndex, role=Qt.DisplayRole):
+        if role == Qt.DisplayRole:
+            return self._data[index.row()][index.column()]
+        if role == Qt.ToolTipRole:
+            hovered_atlas_name = self._data[index.row()][0]
+            return AtlasTableModel._get_tooltip_text(hovered_atlas_name)
+
+    def rowCount(self, index: QModelIndex = QModelIndex()):
+        return len(self._data)
+
+    def columnCount(self, index: QModelIndex = QModelIndex()):
+        return len(self._data[0])
+
+    def headerData(
+        self, section: int, orientation: Qt.Orientation, role: Qt.ItemDataRole
+    ):
+        """Customises the horizontal header data of model,
+        and raises an error if an unexpected column is found."""
+        if role == Qt.DisplayRole and orientation == Qt.Orientation.Horizontal:
+            if section == 0:
+                return "Raw name"
+            elif section == 1:
+                return "Atlas"
+            elif section == 2:
+                return "Local version"
+            elif section == 3:
+                return "Latest version"
+            else:
+                raise ValueError("Unexpected horizontal header value.")
+        else:
+            return super().headerData(section, orientation, role)
+
+    @classmethod
+    def _get_tooltip_text(cls, atlas_name: str):
+        """Returns the atlas metadata as a formatted string,
+        as well as instructions on how to interact with the atlas."""
+        if atlas_name in get_downloaded_atlases():
+            metadata = read_atlas_metadata_from_file(atlas_name)
+            metadata_as_string = ""
+            for key, value in metadata.items():
+                metadata_as_string += f"{key}:\t{value}\n"
+
+            tooltip_text = f"{atlas_name} (double-click to add to viewer)\
+            \n{metadata_as_string}"
+        elif atlas_name in get_all_atlases_lastversions().keys():
+            tooltip_text = f"{atlas_name} (double-click to download)"
+        else:
+            raise ValueError("Tooltip text called with invalid atlas name.")
+        return tooltip_text

brainrender_napari/data_models/structure_tree_model.py

@@ -0,0 +1,144 @@
+from typing import Dict, List
+
+from bg_atlasapi.structure_tree_util import get_structures_tree
+from qtpy.QtCore import QAbstractItemModel, QModelIndex, Qt
+from qtpy.QtGui import QStandardItem
+
+
+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()

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