Merge pull request #31 from Ipuch/multiframerate

- multiple colors for xp markers
- nan avoided to compute the location of the floor
- little offset to avoid mesh flickering between force plates and floor
- fix: dependencies
- first notebook example

environment.yml

@@ -4,7 +4,7 @@ channels:
 - default
 dependencies:
 - ezc3d
-- rerun-sdkrerun-sdk=0.16.1
+- rerun-sdk=0.16.1
 - numpy
 - biorbd>=1.10.5
 - trimesh

examples/c3d/running_gait.ipynb

@@ -0,0 +1,55 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "aabbe278-4fdb-43ac-b880-4fea8dd0b057",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pyorerun as prr\n",
+    "import rerun as rr\n",
+    "\n",
+    "prr.c3d(\n",
+    "    \"Running_0002.c3d\",\n",
+    "    show_floor=True,\n",
+    "    show_force_plates=True,\n",
+    "    show_forces=True,\n",
+    "    down_sampled_forces=True,\n",
+    "    video=(\"Running_0002_Oqus_6_15004.avi\", \"Running_0002_Oqus_9_15003.avi\"),\n",
+    "    notebook=True,\n",
+    ")\n",
+    "rr.notebook_show(width=1200, height=600)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a80e92a4-89d4-4d02-b69a-07e22651838b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyorerun/multi_frame_rate_phase_rerun.py

@@ -73,13 +73,15 @@ def cumulative_frames_in_merged_t_span(self) -> list[list[int]]:
         frame_t_span_idx = self.frame_t_span_idx
         return [calculate_cumulative_frames(p, frame_t_span_idx) for p in range(self.nb_phases)]
 
-    def rerun(self, name: str = "animation_phase", init: bool = True, clear_last_node: bool = False) -> None:
+    def rerun(
+        self, name: str = "animation_phase", init: bool = True, clear_last_node: bool = False, notebook: bool = False
+    ) -> None:
         if self.nb_phases == 1:
-            self.phase_reruns[0].rerun(name, init, clear_last_node)
+            self.phase_reruns[0].rerun(name, init, clear_last_node, notebook)
             return
 
         if init:
-            rr.init(f"{name}_{0}", spawn=True)
+            rr.init(f"{name}_{0}", spawn=True if not notebook else False)
 
         for phase_rerun in self.phase_reruns:
             frame = 0

pyorerun/phase_rerun.py

@@ -190,9 +190,11 @@ def add_video(self, name, video_array: np.ndarray) -> None:
 
         self.xp_data.add_data(Video(name=f"{self.name}/{name}", video_array=video_array))
 
-    def rerun(self, name: str = "animation_phase", init: bool = True, clear_last_node: bool = False) -> None:
+    def rerun(
+        self, name: str = "animation_phase", init: bool = True, clear_last_node: bool = False, notebook: bool = False
+    ) -> None:
         if init:
-            rr.init(f"{name}_{self.phase}", spawn=True)
+            rr.init(f"{name}_{self.phase}", spawn=True if not notebook else False)
 
         frame = 0
         rr.set_time_seconds("stable_time", self.t_span[frame])

pyorerun/rrc3d.py

@@ -20,6 +20,7 @@ def rrc3d(
     video: str | tuple[str, ...] = None,
     video_crop_mode: str = "from_c3d",
     marker_trajectories: bool = False,
+    notebook: bool = False,
 ) -> None:
     """
     Display a c3d file in rerun.
@@ -44,6 +45,8 @@ def rrc3d(
         The mode to crop the video. If 'from_c3d', the video will be cropped to the same time span as the c3d file.
     marker_trajectories: bool
         If True, show the marker trajectories.
+    notebook: bool
+        If True, display the animation in the notebook.
     """
 
     # Load a c3d file
@@ -90,7 +93,7 @@ def rrc3d(
 
     if show_floor:
         square_width = max_xy_coordinate_span_by_markers(pyomarkers)
-        phase_rerun.add_floor(square_width, height_offset=lowest_corner)
+        phase_rerun.add_floor(square_width, height_offset=lowest_corner - 0.0005)
 
     if video is not None:
         for i, vid in enumerate(video if isinstance(video, tuple) else [video]):
@@ -108,7 +111,7 @@ def rrc3d(
             phase_reruns[-1].add_video(vid_name, vid)
 
     multi_phase_rerun = MultiFrameRatePhaseRerun(phase_reruns)
-    multi_phase_rerun.rerun(filename)
+    multi_phase_rerun.rerun(filename, notebook=notebook)
 
     if marker_trajectories:
         # todo: find a better way to display curves but hacky way ok for now
@@ -119,10 +122,10 @@ def rrc3d(
 
 def max_xy_coordinate_span_by_markers(pyomarkers: PyoMarkers) -> float:
     """Return the max span of the x and y coordinates of the markers."""
-    min_pyomarkers = np.min(np.min(pyomarkers.to_numpy(), axis=2), axis=1)
-    max_pyomarkers = np.max(np.max(pyomarkers.to_numpy(), axis=2), axis=1)
-    x_absolute_max = np.max(np.abs([min_pyomarkers[0], max_pyomarkers[0]]))
-    y_absolute_max = np.max(np.abs([min_pyomarkers[1], max_pyomarkers[1]]))
+    min_pyomarkers = np.nanmin(np.nanmin(pyomarkers.to_numpy(), axis=2), axis=1)
+    max_pyomarkers = np.nanmax(np.nanmax(pyomarkers.to_numpy(), axis=2), axis=1)
+    x_absolute_max = np.nanmax(np.abs([min_pyomarkers[0], max_pyomarkers[0]]))
+    y_absolute_max = np.nanmax(np.abs([min_pyomarkers[1], max_pyomarkers[1]]))
 
     return np.max([x_absolute_max, y_absolute_max])
 

pyorerun/xp_components/markers.py

@@ -7,16 +7,30 @@
 
 
 class MarkersXp(Markers, ExperimentalData):
+
+    _counter = 0  # counter for each instance of the class to change the color of the markers
+    _MARKERS_COLORS = [
+        np.array([255, 255, 255]),
+        np.array([245, 66, 53]),
+        np.array([232, 30, 99]),
+        np.array([33, 149, 245]),
+        np.array([76, 176, 79]),
+        np.array([103, 56, 182]),
+    ]
+
     def __init__(self, name, markers: PyoMarkers):
+
         self.name = name + "/markers"
         self.markers = markers
         self.markers_numpy = markers.to_numpy()
         self.markers_properties = MarkerProperties(
             markers_names=markers.channel.values.tolist(),
             radius=0.01,
-            color=np.array([255, 255, 255]),
+            color=MarkersXp._MARKERS_COLORS[MarkersXp._counter],
         )
 
+        MarkersXp._counter = (MarkersXp._counter + 1) % len(MarkersXp._MARKERS_COLORS)
+
     @property
     def nb_markers(self):
         return len(self.markers_names)

pyproject.toml

@@ -22,7 +22,7 @@ classifiers = [
 dependencies = [
 #    "ezc3d", # Not yet available on pypi, use `conda install -c conda-forge ezc3d`
     "numpy",
-    "rerun-sdk=0.16.1",
+    "rerun-sdk==0.16.1",
     "trimesh",
     "pyomeca",
     "tk",