V0 migration model. Renaming - surgery required

src/spyglass/common/__init__.py

@@ -70,9 +70,9 @@
 from .prepopulate import populate_from_yaml, prepopulate_default
 
 from spyglass.linearization.v0 import (  # isort:skip
-    IntervalLinearizationSelection,
-    IntervalLinearizedPosition,
-    LinearizationParameters,
+    LinearizationParams,
+    LinearizedSelection,
+    LinearizedV0,
     TrackGraph,
 )
 
@@ -89,8 +89,6 @@
     "ElectrodeGroup",
     "FirFilterParameters",
     "Institution",
-    "IntervalLinearizationSelection",
-    "IntervalLinearizedPosition",
     "IntervalList",
     "IntervalPositionInfo",
     "IntervalPositionInfoSelection",
@@ -101,7 +99,9 @@
     "Lab",
     "LabMember",
     "LabTeam",
-    "LinearizationParameters",
+    "LinearizationParams",
+    "LinearizedV0",
+    "LinearizedSelection",
     "Nwbfile",
     "NwbfileKachery",
     "PositionInfoParameters",

src/spyglass/common/common_position.py

@@ -496,157 +496,6 @@ def _data_to_df(data, prefix="head_", add_frame_ind=False):
         return df
 
 
-# ------------------------------ Migrated Tables ------------------------------
-
-from spyglass.linearization.v0 import main as linV0  # noqa: E402
-
-(
-    LinearizationParameters,
-    TrackGraph,
-    IntervalLinearizationSelection,
-    IntervalLinearizedPosition,
-) = deprecated_factory(
-    [
-        ("LinearizationParameters", linV0.LinearizationParameters),
-        ("TrackGraph", linV0.TrackGraph),
-        (
-            "IntervalLinearizationSelection",
-            linV0.IntervalLinearizationSelection,
-        ),
-        (
-            "IntervalLinearizedPosition",
-            linV0.IntervalLinearizedPosition,
-        ),
-    ],
-    old_module=__name__,
-)
-
-
-class NodePicker:
-    """Interactive creation of track graph by looking at video frames."""
-
-    def __init__(
-        self, ax=None, video_filename=None, node_color="#1f78b4", node_size=100
-    ):
-        if ax is None:
-            ax = plt.gca()
-        self.ax = ax
-        self.canvas = ax.get_figure().canvas
-        self.cid = None
-        self._nodes = []
-        self.node_color = node_color
-        self._nodes_plot = ax.scatter(
-            [], [], zorder=5, s=node_size, color=node_color
-        )
-        self.edges = [[]]
-        self.video_filename = video_filename
-
-        if video_filename is not None:
-            self.video = cv2.VideoCapture(video_filename)
-            frame = self.get_video_frame()
-            ax.imshow(frame, picker=True)
-            ax.set_title(
-                "Left click to place node.\nRight click to remove node."
-                "\nShift+Left click to clear nodes."
-                "\nCntrl+Left click two nodes to place an edge"
-            )
-
-        self.connect()
-
-    @property
-    def node_positions(self):
-        return np.asarray(self._nodes)
-
-    def connect(self):
-        if self.cid is None:
-            self.cid = self.canvas.mpl_connect(
-                "button_press_event", self.click_event
-            )
-
-    def disconnect(self):
-        if self.cid is not None:
-            self.canvas.mpl_disconnect(self.cid)
-            self.cid = None
-
-    def click_event(self, event):
-        if not event.inaxes:
-            return
-        if (event.key not in ["control", "shift"]) & (
-            event.button == 1
-        ):  # left click
-            self._nodes.append((event.xdata, event.ydata))
-        if (event.key not in ["control", "shift"]) & (
-            event.button == 3
-        ):  # right click
-            self.remove_point((event.xdata, event.ydata))
-        if (event.key == "shift") & (event.button == 1):
-            self.clear()
-        if (event.key == "control") & (event.button == 1):
-            point = (event.xdata, event.ydata)
-            distance_to_nodes = np.linalg.norm(
-                self.node_positions - point, axis=1
-            )
-            closest_node_ind = np.argmin(distance_to_nodes)
-            if len(self.edges[-1]) < 2:
-                self.edges[-1].append(closest_node_ind)
-            else:
-                self.edges.append([closest_node_ind])
-
-        self.redraw()
-
-    def redraw(self):
-        # Draw Node Circles
-        if len(self.node_positions) > 0:
-            self._nodes_plot.set_offsets(self.node_positions)
-        else:
-            self._nodes_plot.set_offsets([])
-
-        # Draw Node Numbers
-        self.ax.texts = []
-        for ind, (x, y) in enumerate(self.node_positions):
-            self.ax.text(
-                x,
-                y,
-                ind,
-                zorder=6,
-                fontsize=12,
-                horizontalalignment="center",
-                verticalalignment="center",
-                clip_on=True,
-                bbox=None,
-                transform=self.ax.transData,
-            )
-        # Draw Edges
-        self.ax.lines = []  # clears the existing lines
-        for edge in self.edges:
-            if len(edge) > 1:
-                x1, y1 = self.node_positions[edge[0]]
-                x2, y2 = self.node_positions[edge[1]]
-                self.ax.plot(
-                    [x1, x2], [y1, y2], color=self.node_color, linewidth=2
-                )
-
-        self.canvas.draw_idle()
-
-    def remove_point(self, point):
-        if len(self._nodes) > 0:
-            distance_to_nodes = np.linalg.norm(
-                self.node_positions - point, axis=1
-            )
-            closest_node_ind = np.argmin(distance_to_nodes)
-            self._nodes.pop(closest_node_ind)
-
-    def clear(self):
-        self._nodes = []
-        self.edges = [[]]
-        self.redraw()
-
-    def get_video_frame(self):
-        is_grabbed, frame = self.video.read()
-        if is_grabbed:
-            return cv2.cvtColor(frame, cv2.COLOR_BGR2RGB)
-
-
 @schema
 class PositionVideo(dj.Computed):
     """Creates a video of the computed head position and orientation as well as
@@ -656,7 +505,6 @@ class PositionVideo(dj.Computed):
 
     definition = """
     -> IntervalPositionInfo
-    ---
     """
 
     def make(self, key):
@@ -887,6 +735,159 @@ def make_video(
         cv2.destroyAllWindows()
 
 
+# ------------------------------ Migrated Tables ------------------------------
+
+from spyglass.linearization.v0 import main as linV0  # noqa: E402
+
+(
+    LinearizationParameters,
+    TrackGraph,
+    IntervalLinearizationSelection,
+    IntervalLinearizedPosition,
+) = deprecated_factory(
+    [
+        ("LinearizationParameters", linV0.LinearizationParams),
+        ("TrackGraph", linV0.TrackGraph),
+        (
+            "IntervalLinearizationSelection",
+            linV0.LinearizedSelection,
+        ),
+        (
+            "IntervalLinearizedPosition",
+            linV0.LinearizedV0,
+        ),
+    ],
+    old_module=__name__,
+)
+
+# ------------------------ Helper classes and functions ------------------------
+
+
+class NodePicker:
+    """Interactive creation of track graph by looking at video frames."""
+
+    def __init__(
+        self, ax=None, video_filename=None, node_color="#1f78b4", node_size=100
+    ):
+        if ax is None:
+            ax = plt.gca()
+        self.ax = ax
+        self.canvas = ax.get_figure().canvas
+        self.cid = None
+        self._nodes = []
+        self.node_color = node_color
+        self._nodes_plot = ax.scatter(
+            [], [], zorder=5, s=node_size, color=node_color
+        )
+        self.edges = [[]]
+        self.video_filename = video_filename
+
+        if video_filename is not None:
+            self.video = cv2.VideoCapture(video_filename)
+            frame = self.get_video_frame()
+            ax.imshow(frame, picker=True)
+            ax.set_title(
+                "Left click to place node.\nRight click to remove node."
+                "\nShift+Left click to clear nodes."
+                "\nCntrl+Left click two nodes to place an edge"
+            )
+
+        self.connect()
+
+    @property
+    def node_positions(self):
+        return np.asarray(self._nodes)
+
+    def connect(self):
+        if self.cid is None:
+            self.cid = self.canvas.mpl_connect(
+                "button_press_event", self.click_event
+            )
+
+    def disconnect(self):
+        if self.cid is not None:
+            self.canvas.mpl_disconnect(self.cid)
+            self.cid = None
+
+    def click_event(self, event):
+        if not event.inaxes:
+            return
+        if (event.key not in ["control", "shift"]) & (
+            event.button == 1
+        ):  # left click
+            self._nodes.append((event.xdata, event.ydata))
+        if (event.key not in ["control", "shift"]) & (
+            event.button == 3
+        ):  # right click
+            self.remove_point((event.xdata, event.ydata))
+        if (event.key == "shift") & (event.button == 1):
+            self.clear()
+        if (event.key == "control") & (event.button == 1):
+            point = (event.xdata, event.ydata)
+            distance_to_nodes = np.linalg.norm(
+                self.node_positions - point, axis=1
+            )
+            closest_node_ind = np.argmin(distance_to_nodes)
+            if len(self.edges[-1]) < 2:
+                self.edges[-1].append(closest_node_ind)
+            else:
+                self.edges.append([closest_node_ind])
+
+        self.redraw()
+
+    def redraw(self):
+        # Draw Node Circles
+        if len(self.node_positions) > 0:
+            self._nodes_plot.set_offsets(self.node_positions)
+        else:
+            self._nodes_plot.set_offsets([])
+
+        # Draw Node Numbers
+        self.ax.texts = []
+        for ind, (x, y) in enumerate(self.node_positions):
+            self.ax.text(
+                x,
+                y,
+                ind,
+                zorder=6,
+                fontsize=12,
+                horizontalalignment="center",
+                verticalalignment="center",
+                clip_on=True,
+                bbox=None,
+                transform=self.ax.transData,
+            )
+        # Draw Edges
+        self.ax.lines = []  # clears the existing lines
+        for edge in self.edges:
+            if len(edge) > 1:
+                x1, y1 = self.node_positions[edge[0]]
+                x2, y2 = self.node_positions[edge[1]]
+                self.ax.plot(
+                    [x1, x2], [y1, y2], color=self.node_color, linewidth=2
+                )
+
+        self.canvas.draw_idle()
+
+    def remove_point(self, point):
+        if len(self._nodes) > 0:
+            distance_to_nodes = np.linalg.norm(
+                self.node_positions - point, axis=1
+            )
+            closest_node_ind = np.argmin(distance_to_nodes)
+            self._nodes.pop(closest_node_ind)
+
+    def clear(self):
+        self._nodes = []
+        self.edges = [[]]
+        self.redraw()
+
+    def get_video_frame(self):
+        is_grabbed, frame = self.video.read()
+        if is_grabbed:
+            return cv2.cvtColor(frame, cv2.COLOR_BGR2RGB)
+
+
 def _fix_col_names(spatial_df):
     """Renames columns in spatial dataframe according to previous norm
 

src/spyglass/linearization/merge.py

@@ -1,5 +1,6 @@
 import datajoint as dj
 
+from spyglass.linearization.v0.main import LinearizedV0  # noqa F401
 from spyglass.linearization.v1.main import LinearizedV1  # noqa F401
 
 from ..utils.dj_merge_tables import _Merge
@@ -15,6 +16,13 @@ class LinearizedOutput(_Merge):
     source: varchar(32)
     """
 
+    class LinearizedV0(dj.Part):  # noqa F811
+        definition = """
+        -> master
+        ---
+        -> LinearizedV0
+        """
+
     class LinearizedV1(dj.Part):  # noqa F811
         definition = """
         -> master

src/spyglass/linearization/v0/__init__.py

@@ -1,6 +1,13 @@
-from .main import (
-    IntervalLinearizationSelection,
-    IntervalLinearizedPosition,
-    LinearizationParameters,
+from spyglass.linearization.v0.main import (
+    LinearizationParams,
+    LinearizedSelection,
+    LinearizedV0,
     TrackGraph,
 )
+
+__all__ = [
+    "LinearizationParams",
+    "Linearized0",
+    "LinearizedSelection",
+    "TrackGraph",
+]