Add option to analysis export for exporting predictions for all frames including those with no predictions

sleap/gui/app.py

@@ -496,15 +496,42 @@ def add_submenu_choices(menu, title, options, key):
         add_menu_item(
             export_csv_menu,
             "export_csv_current",
-            "Current Video...",
+            "Current Video (only tracked frames)...",
             self.commands.exportCSVFile,
         )
         add_menu_item(
             export_csv_menu,
             "export_csv_all",
-            "All Videos...",
+            "All Videos (only tracked frames)...",
             lambda: self.commands.exportCSVFile(all_videos=True),
         )
+
+        fileMenu.addSeparator()
+        add_menu_item(
+            export_csv_menu,
+            "export_csv_current_all_frames",
+            "Current Video (all frames)...",
+            lambda: self.commands.exportCSVFile(all_frames=True),
+        )
+        add_menu_item(
+            export_csv_menu,
+            "export_csv_all_frames",
+            "All Videos (all frames)...",
+            lambda: self.commands.exportCSVFile(all_frames=True, all_videos=True),
+
+        export_csv_menu.addSeparator()
+        add_menu_item(
+            export_csv_menu,
+            "export_csv_current_all_frames",
+            "Current Video (all frames)...",
+            self.commands.exportCSVFile(all_frames=True),
+        )
+        add_menu_item(
+            export_csv_menu,
+            "export_csv_all_all_frames",
+            "All Videos (all frames)...",
+            lambda: self.commands.exportCSVFile(all_frames=True),
+        )
 
         add_menu_item(fileMenu, "export_nwb", "Export NWB...", self.commands.exportNWB)
 

sleap/gui/commands.py

@@ -326,13 +326,13 @@ def saveProjectAs(self):
         """Show gui to save project as a new file."""
         self.execute(SaveProjectAs)
 
-    def exportAnalysisFile(self, all_videos: bool = False):
+    def exportAnalysisFile(self, all_videos: bool = False, all_frames: bool = False):
         """Shows gui for exporting analysis h5 file."""
-        self.execute(ExportAnalysisFile, all_videos=all_videos, csv=False)
+        self.execute(ExportAnalysisFile, all_videos=all_videos, all_frames=all_frames, csv=False)
 
-    def exportCSVFile(self, all_videos: bool = False):
+    def exportCSVFile(self, all_videos: bool = False, all_frames: bool = False):
         """Shows gui for exporting analysis csv file."""
-        self.execute(ExportAnalysisFile, all_videos=all_videos, csv=True)
+        self.execute(ExportAnalysisFile, all_videos=all_videos, all_frames=all_frames, csv=True)
 
     def exportNWB(self):
         """Show gui for exporting nwb file."""
@@ -1142,13 +1142,24 @@ def do_action(cls, context: CommandContext, params: dict):
                 adaptor = NixAdaptor
             else:
                 adaptor = SleapAnalysisAdaptor
+
+        if params['all_frames']:
             adaptor.write(
                 filename=output_path,
+                all_frames=params.get('all_frames', False),
                 source_object=context.labels,
                 source_path=context.state["filename"],
                 video=video,
-            )
-
+                )
+        else:
+            adaptor.write(
+                filename=output_path,
+                all_frames=False,
+                source_object=context.labels,
+                source_path=context.state["filename"],
+                video=video,
+                )
+
     @staticmethod
     def ask(context: CommandContext, params: dict) -> bool:
         def ask_for_filename(default_name: str, csv: bool) -> str:

sleap/info/write_tracking_h5.py

@@ -348,14 +348,22 @@ def write_csv_file(output_path, data_dict):
             tracks.append(detection)
 
     tracks = pd.DataFrame(tracks)
-    tracks.to_csv(output_path, index=False)
+    all_frames = globals().get('all_frames', False)
+
+    if all_frames:
+        tracks = tracks.set_index('frame_idx')
+        tracks = tracks.reindex(range(0, len(data_dict['track_occupancy'])), fill_value=np.nan)
+        tracks = tracks.reset_index(drop=False)
+        tracks.to_csv(output_path, index=False)
+    else:
+        tracks.to_csv(output_path, index=False)
 
 
 def main(
     labels: Labels,
     output_path: str,
     labels_path: str = None,
-    all_frames: bool = True,
+    all_frames: bool = False,
     video: Video = None,
     csv: bool = False,
 ):

sleap/io/format/csv.py

@@ -45,6 +45,7 @@ def write(
         filename: str,
         source_object: Labels,
         source_path: str = None,
+        all_frames: bool: False,
         video: Video = None,
     ):
         """Writes csv file for :py:class:`Labels` `source_object`.
@@ -53,6 +54,8 @@ def write(
             filename: The filename for the output file.
             source_object: The :py:class:`Labels` from which to get data from.
             source_path: Path for the labels object
+            all_frames: A boolean flag to determine whether to include all frames
+                or only those with tracking data in the export.
             video: The :py:class:`Video` from which toget data from. If no `video` is
                 specified, then the first video in `source_object` videos list will be
                 used. If there are no :py:class:`Labeled Frame`s in the `video`, then no