Merge pull request #276 from murthylab/develop

Develop

environment.yml

@@ -5,8 +5,6 @@ dependencies:
 - attrs
 - jsonpickle=1.2
 - networkx
-- cudatoolkit=10.0.*
-- cudnn
 - tensorflow-gpu=2.0
 - scikit-learn
 - h5py

sleap/config/shortcuts.yaml

@@ -26,6 +26,7 @@ prev video: QKeySequence.Back
 save as: QKeySequence.SaveAs
 save: Ctrl+S
 select next: '`'
+select to frame: Ctrl+Shift+J
 show edges: Ctrl+Shift+Tab
 show labels: Ctrl+Tab
 show trails: 

sleap/config/training_editor.yaml

@@ -3,7 +3,7 @@ model:
 - name: output_type
   label: Training For
   type: list
-  options: confmaps,topdown,pafs,centroids
+  options: confmaps,topdown_confidence_maps,pafs,centroids
   default: confmaps
 
 - name: arch # backbone_name

sleap/gui/app.py

@@ -280,6 +280,9 @@ def add_submenu_choices(menu, title, options, key):
 
         fileMenu.addSeparator()
         add_menu_item(fileMenu, "add videos", "Add Videos...", self.commands.addVideo)
+        add_menu_item(
+            fileMenu, "replace videos", "Replace Videos...", self.commands.replaceVideo
+        )
 
         fileMenu.addSeparator()
         add_menu_item(fileMenu, "save", "Save", self.commands.saveProject)
@@ -343,6 +346,9 @@ def prev_vid():
         goMenu.addSeparator()
 
         add_menu_item(goMenu, "goto frame", "Go to Frame...", self.commands.gotoFrame)
+        add_menu_item(
+            goMenu, "select to frame", "Select to Frame...", self.commands.selectToFrame
+        )
 
         ### View Menu ###
 
@@ -1010,25 +1016,38 @@ def updateStatusMessage(self, message: Optional[str] = None):
         current_video = self.state["video"]
         frame_idx = self.state["frame_idx"] or 0
 
+        spacer = "        "
+
         if message is None:
-            message = f"Frame: {frame_idx+1}/{len(current_video)}"
+            message = f"Frame: {frame_idx+1:,}/{len(current_video):,}"
             if self.player.seekbar.hasSelection():
                 start, end = self.state["frame_range"]
-                message += f" (selection: {start}-{end})"
+                message += f" (selection: {start+1:,}-{end+1:,})"
 
             if len(self.labels.videos) > 1:
                 message += f" of video {self.labels.videos.index(current_video)}"
 
-            message += f"    Labeled Frames: "
+            message += f"{spacer}Labeled Frames: "
             if current_video is not None:
                 message += (
                     f"{len(self.labels.get_video_user_labeled_frames(current_video))}"
                 )
+
                 if len(self.labels.videos) > 1:
                     message += " in video, "
             if len(self.labels.videos) > 1:
                 message += f"{len(self.labels.user_labeled_frames)} in project"
 
+            if current_video is not None:
+                pred_frame_count = len(
+                    self.labels.get_video_predicted_frames(current_video)
+                )
+                if pred_frame_count:
+                    message += f"{spacer}Predicted Frames: {pred_frame_count:,}"
+                    message += (
+                        f" ({pred_frame_count/current_video.num_frames*100:.2f}%)"
+                    )
+
         self.statusBar().showMessage(message)
 
     def loadProjectFile(self, filename: Optional[str] = None):

sleap/gui/commands.py

@@ -249,6 +249,10 @@ def gotoFrame(self):
         """Shows gui to go to frame by number."""
         self.execute(GoFrameGui)
 
+    def selectToFrame(self):
+        """Shows gui to go to frame by number."""
+        self.execute(SelectToFrameGui)
+
     def gotoVideoAndFrame(self, video: Video, frame_idx: int):
         """Activates video and goes to frame."""
         NavCommand.go_to(self, frame_idx, video)
@@ -259,6 +263,10 @@ def addVideo(self):
         """Shows gui for adding videos to project."""
         self.execute(AddVideo)
 
+    def replaceVideo(self):
+        """Shows gui for replacing videos to project."""
+        self.execute(ReplaceVideo)
+
     def removeVideo(self):
         """Removes selected video from project."""
         self.execute(RemoveVideo)
@@ -846,6 +854,29 @@ def ask(cls, context: "CommandContext", params: dict) -> bool:
         return okay
 
 
+class SelectToFrameGui(NavCommand):
+    @classmethod
+    def do_action(cls, context: "CommandContext", params: dict):
+        context.app.player.setSeekbarSelection(
+            params["from_frame_idx"], params["to_frame_idx"]
+        )
+
+    @classmethod
+    def ask(cls, context: "CommandContext", params: dict) -> bool:
+        frame_number, okay = QtWidgets.QInputDialog.getInt(
+            context.app,
+            "Select To Frame...",
+            "Frame Number:",
+            context.state["frame_idx"] + 1,
+            1,
+            context.state["video"].frames,
+        )
+        params["from_frame_idx"] = context.state["frame_idx"]
+        params["to_frame_idx"] = frame_number - 1
+
+        return okay
+
+
 # Editing Commands
 
 
@@ -882,6 +913,33 @@ def ask(context: CommandContext, params: dict) -> bool:
         return len(params["import_list"]) > 0
 
 
+class ReplaceVideo(EditCommand):
+    topics = [UpdateTopic.video]
+
+    @staticmethod
+    def do_action(context: CommandContext, params: dict):
+        new_paths = params["new_video_paths"]
+
+        for video, new_path in zip(context.labels.videos, new_paths):
+            if new_path != video.backend.filename:
+                video.backend.filename = new_path
+                video.backend.reset()
+
+    @staticmethod
+    def ask(context: CommandContext, params: dict) -> bool:
+        """Shows gui for replacing videos in project."""
+        paths = [video.backend.filename for video in context.labels.videos]
+
+        okay = MissingFilesDialog(filenames=paths, replace=True).exec_()
+
+        if not okay:
+            return False
+
+        params["new_video_paths"] = paths
+
+        return True
+
+
 class RemoveVideo(EditCommand):
     topics = [UpdateTopic.video]
 

sleap/gui/inference.py

@@ -363,6 +363,9 @@ def _get_current_training_jobs(self) -> Dict[ModelOutputType, TrainingJob]:
             # Use already trained model if desired
             if form_data.get(f"_use_trained_{str(model_type)}", default_use_trained):
                 job.use_trained_model = True
+            elif model_type == ModelOutputType.TOPDOWN_CONFIDENCE_MAP:
+                if form_data.get(f"_use_trained_confmaps", default_use_trained):
+                    job.use_trained_model = True
 
             # Clear parameters that shouldn't be copied
             job.val_set_filename = None

sleap/gui/missingfiles.py

@@ -14,7 +14,12 @@
 
 class MissingFilesDialog(QtWidgets.QDialog):
     def __init__(
-        self, filenames: List[str], missing: List[bool] = None, *args, **kwargs
+        self,
+        filenames: List[str],
+        missing: List[bool] = None,
+        replace: bool = False,
+        *args,
+        **kwargs,
     ):
         """
         Creates dialog window for finding missing files.
@@ -42,10 +47,13 @@ def __init__(
 
         layout = QtWidgets.QVBoxLayout()
 
-        info_text = (
-            f"{missing_count} file(s) which could not be found. "
-            "Please double-click on a file to locate it..."
-        )
+        if replace:
+            info_text = "Double-click on a file to replace it..."
+        else:
+            info_text = (
+                f"{missing_count} file(s) which could not be found. "
+                "Please double-click on a file to locate it..."
+            )
         info_label = QtWidgets.QLabel(info_text)
         layout.addWidget(info_label)
 

sleap/gui/overlays/tracks.py

@@ -9,10 +9,12 @@
 import attr
 import itertools
 
-from typing import List
+from typing import Iterable, List
 
 from PySide2 import QtCore, QtGui
 
+MAX_NODES_IN_TRAIL = 30
+
 
 @attr.s(auto_attribs=True)
 class TrackTrailOverlay:
@@ -37,42 +39,48 @@ class TrackTrailOverlay:
     trail_length: int = 10
     show: bool = False
 
-    def get_track_trails(self, frame_selection, track: Track):
+    def get_track_trails(self, frame_selection: Iterable["LabeledFrame"]):
         """Get data needed to draw track trail.
 
         Args:
-            frame_selection: an interable with the :class:`LabeledFrame`
+            frame_selection: an iterable with the :class:`LabeledFrame`
                 objects to include in trail.
-            track: the :class:`Track` for which to get trail
 
         Returns:
-            list of lists of (x, y) tuples
+            Dictionary keyed by track, value is list of lists of (x, y) tuples
                 i.e., for every node in instance, we get a list of positions
         """
 
-        all_trails = [[] for _ in range(len(self.labels.nodes))]
+        all_track_trails = dict()
+
+        nodes = self.labels.nodes
+        if len(nodes) > MAX_NODES_IN_TRAIL:
+            nodes = nodes[:MAX_NODES_IN_TRAIL]
 
         for frame in frame_selection:
-            frame_idx = frame.frame_idx
 
-            inst_on_track = [instance for instance in frame if instance.track == track]
-            if inst_on_track:
-                # just use the first instance from this track in this frame
-                inst = inst_on_track[0]
-                # loop through all nodes
-                for node_i, node in enumerate(self.labels.nodes):
+            for inst in frame:
+                if inst.track is not None:
+                    if inst.track not in all_track_trails:
+                        all_track_trails[inst.track] = [[] for _ in range(len(nodes))]
+
+                    # loop through all nodes
+                    for node_i, node in enumerate(nodes):
+
+                        if node in inst.nodes and inst[node].visible:
+                            point = (inst[node].x, inst[node].y)
 
-                    if node in inst.nodes and inst[node].visible:
-                        point = (inst[node].x, inst[node].y)
-                    elif len(all_trails[node_i]):
-                        point = all_trails[node_i][-1]
-                    else:
-                        point = None
+                        # Add last location of node so that we can easily
+                        # calculate trail length (since we adjust opacity).
+                        elif len(all_track_trails[inst.track][node_i]):
+                            point = all_track_trails[inst.track][node_i][-1]
+                        else:
+                            point = None
 
-                    if point is not None:
-                        all_trails[node_i].append(point)
+                        if point is not None:
+                            all_track_trails[inst.track][node_i].append(point)
 
-        return all_trails
+        return all_track_trails
 
     def get_frame_selection(self, video: Video, frame_idx: int):
         """
@@ -116,17 +124,14 @@ def add_to_scene(self, video: Video, frame_idx: int):
             video: current video
             frame_idx: index of the frame to which the trail is attached
         """
-        if not self.show:
+        if not self.show or self.trail_length == 0:
             return
 
         frame_selection = self.get_frame_selection(video, frame_idx)
-        tracks_in_frame = self.get_tracks_in_frame(
-            video, frame_idx, include_trails=True
-        )
 
-        for track in tracks_in_frame:
+        all_track_trails = self.get_track_trails(frame_selection)
 
-            trails = self.get_track_trails(frame_selection, track)
+        for track, trails in all_track_trails.items():
 
             color = QtGui.QColor(*self.player.color_manager.get_track_color(track))
             pen = QtGui.QPen()