lightning-pose-app 1.8.1a17__tar.gz → 1.8.1a19__tar.gz

{lightning_pose_app-1.8.1a17 → lightning_pose_app-1.8.1a19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lightning-pose-app
-Version: 1.8.1a17
+Version: 1.8.1a19
 Summary: 
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3

{lightning_pose_app-1.8.1a17 → lightning_pose_app-1.8.1a19}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "lightning-pose-app"
-version = "1.8.1a17"
+version = "1.8.1a19"
 requires-python = ">=3.10"
 dependencies = [
     "aiofiles~=24.1.0",

{lightning_pose_app-1.8.1a17 → lightning_pose_app-1.8.1a19}/src/litpose_app/routes/labeler/bundle_adjust.py

@@ -57,9 +57,8 @@ def bundle_adjust(
     return BundleAdjustResponse.model_validate(result)
 
 
-
 def _bundle_adjust_impl(
-    request: BundleAdjustRequest, project_info: ProjectInfo, config: Config
+        request: BundleAdjustRequest, project_info: ProjectInfo, config: Config
 ):
     camera_group_toml_path = find_calibration_file(
         request.sessionKey, project_info, config
@@ -76,7 +75,7 @@ def _bundle_adjust_impl(
         parts = framePath.split("/")
         if len(parts) < 3:
             return False
-        sessionViewNameWithDots = parts[-2] # e.g. 05272019_fly1_0_R1C24_Cam-A_rot-ccw-0.06_sec
+        sessionViewNameWithDots = parts[-2]  # e.g. 05272019_fly1_0_R1C24_Cam-A_rot-ccw-0.06_sec
 
         def processPart(sessionViewName):
             """Mirrors frame.model.ts get autolabelSessionKey()"""
@@ -142,20 +141,36 @@ def _bundle_adjust_impl(
     for view in views:
         df = dfs_by_view[view]
         dfs_by_view[view] = df.loc[df.index.to_series().apply(is_of_current_session)]
+        if len(dfs_by_view[view]) == 0:
+            raise RuntimeError(
+                f"Insufficient frames found after filtering for session {request.sessionKey}. Possible error in session extraction logic.")
 
-    # Normalize columns: x, y alternating.
+    # Remove rows with NaN coordinates
+    # Get indices of rows with NaN coordinates in any view
+    nan_indices = set()
     for view in views:
         df = dfs_by_view[view]
+        picked_columns = [c for c in df.columns if c[2] in ("x", "y")]
+        nan_indices.update(df.loc[:, picked_columns].dropna().index.symmetric_difference(df.index))
 
+    # Drop those indices from all views
+    for view in views:
+        dfs_by_view[view] = dfs_by_view[view].drop(nan_indices)
+        if len(dfs_by_view[view]) == 0:
+            raise RuntimeError(
+                f"Insufficient frames found after dropping NaN rows for session {request.sessionKey}.")
+    # Normalize columns: x, y alternating.
+    for view in views:
+        df = dfs_by_view[view]
         picked_columns = [c for c in df.columns if c[2] in ("x", "y")]
         assert len(picked_columns) % 2 == 0
         assert (
-            picked_columns[::2][0][2] == "x"
-            and len(set(list(map(lambda t: t[2], picked_columns[::2])))) == 1
+                picked_columns[::2][0][2] == "x"
+                and len(set(map(lambda t: t[2], picked_columns[::2]))) == 1
         )
         assert (
-            picked_columns[1::2][0][2] == "y"
-            and len(set(list(map(lambda t: t[2], picked_columns[1::2])))) == 1
+                picked_columns[1::2][0][2] == "y"
+                and len(set(map(lambda t: t[2], picked_columns[1::2]))) == 1
         )
         dfs_by_view[view] = df.loc[:, picked_columns]
 
@@ -179,9 +194,9 @@ def _bundle_adjust_impl(
 
     if target_path.exists():
         backup_path = (
-            project_info.data_dir
-            / config.CALIBRATION_BACKUPS_DIRNAME
-            / target_path.with_suffix(f".{time.time_ns()}.toml").name
+                project_info.data_dir
+                / config.CALIBRATION_BACKUPS_DIRNAME
+                / target_path.with_suffix(f".{time.time_ns()}.toml").name
         )
         backup_path.parent.mkdir(parents=True, exist_ok=True)
         os.rename(target_path, backup_path)

lightning_pose_app-1.8.1a19/src/litpose_app/routes/labeler/test_bundle_adjust.ipynb

@@ -0,0 +1,212 @@
+{
+ "cells": [
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-10-21T18:12:15.867772Z",
+     "start_time": "2025-10-21T18:12:12.121614Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from litpose_app.deps import project_info\n",
+    "from litpose_app.routes.rglob import rglob, RGlobRequest\n",
+    "from multiview_autolabel import *\n",
+    "from bundle_adjust import *\n",
+    "warm_up_anipose()"
+   ],
+   "id": "426cdcedf0207a92",
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-10-21T18:24:57.793056Z",
+     "start_time": "2025-10-21T18:24:57.786487Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "import numpy as np\n",
+    "# Assuming Camera and CameraGroup are in a file named 'cameras.py'\n",
+    "from aniposelib.cameras import CameraGroup, Camera\n",
+    "\n",
+    "\n",
+    "def demonstrate_triangulate():\n",
+    "    # --- 1. Create dummy Camera objects ---\n",
+    "    # For demonstration, we'll create two cameras with simple parameters.\n",
+    "    # In a real scenario, these would come from calibration.\n",
+    "\n",
+    "    # Camera 1 parameters\n",
+    "    camera_matrix_1 = np.array([[1000, 0, 640],\n",
+    "                                [0, 1000, 480],\n",
+    "                                [0, 0, 1]], dtype=np.float64)\n",
+    "    dist_coeffs_1 = np.array([0, 0, 0, 0, 0], dtype=np.float64)  # No distortion for simplicity\n",
+    "    rvec_1 = np.array([[0.], [0.], [0.]], dtype=np.float64)  # No rotation\n",
+    "    tvec_1 = np.array([[0.], [0.], [0.]], dtype=np.float64)  # Origin at world origin\n",
+    "    cam1 = Camera(name='cam1',\n",
+    "                  matrix=camera_matrix_1,\n",
+    "                  dist=dist_coeffs_1,\n",
+    "                  rvec=rvec_1,\n",
+    "                  tvec=tvec_1,\n",
+    "                  size=(1280, 960))  # Image width, height\n",
+    "\n",
+    "    # Camera 2 parameters - shifted and slightly rotated relative to Camera 1\n",
+    "    camera_matrix_2 = np.array([[1050, 0, 650],\n",
+    "                                [0, 1050, 470],\n",
+    "                                [0, 0, 1]], dtype=np.float64)\n",
+    "    dist_coeffs_2 = np.array([0.01, -0.02, 0, 0, 0], dtype=np.float64)  # Some distortion\n",
+    "    rvec_2 = np.array([[0.05], [-0.1], [0.03]], dtype=np.float64)  # Small rotation\n",
+    "    tvec_2 = np.array([[0.5], [0.1], [-0.2]], dtype=np.float64)  # Translated from origin\n",
+    "    cam2 = Camera(name='cam2',\n",
+    "                  matrix=camera_matrix_2,\n",
+    "                  dist=dist_coeffs_2,\n",
+    "                  rvec=rvec_2,\n",
+    "                  tvec=tvec_2,\n",
+    "                  size=(1280, 960))\n",
+    "\n",
+    "    print(\"Cameras initialized.\")\n",
+    "    print(f\"Camera 1 name: {cam1.get_name()}\")\n",
+    "    print(f\"Camera 2 name: {cam2.get_name()}\")\n",
+    "\n",
+    "    # --- 2. Create a CameraGroup ---\n",
+    "    camera_group = CameraGroup(cameras=[cam1, cam2])\n",
+    "    print(\"\\nCameraGroup created with 2 cameras.\")\n",
+    "\n",
+    "    # --- 3. Define a sample 3D point (world coordinates) ---\n",
+    "    # We will try to triangulate this point\n",
+    "    true_3d_point = np.array([[1.0, 2.0, 5.0]], dtype=np.float64)  # Shape (1, 3)\n",
+    "\n",
+    "    print(f\"\\nTrue 3D point in world coordinates: {true_3d_point}\")\n",
+    "\n",
+    "    # --- 4. Project the 3D point onto each camera to get 2D observations ---\n",
+    "    # The 'project' method of CameraGroup expects points for each camera.\n",
+    "    # The output of Camera.project is (N, 2) for N points.\n",
+    "    points_2d_cam1 = cam1.project(true_3d_point)\n",
+    "    points_2d_cam2 = cam2.project(true_3d_point)\n",
+    "\n",
+    "    # Reshape the points to match expected format (num_cameras, num_points, 2)\n",
+    "    points_2d_cam1 = points_2d_cam1.reshape(1, 2)\n",
+    "    points_2d_cam2 = points_2d_cam2.reshape(1, 2)\n",
+    "\n",
+    "    # TEST NAN\n",
+    "    #points_2d_cam1[0, 0] = np.nan\n",
+    "\n",
+    "    points_for_triangulation = np.stack([points_2d_cam1, points_2d_cam2])\n",
+    "\n",
+    "    print(f\"\\nProjected 2D point for Camera 1:\\n{points_2d_cam1}\")\n",
+    "    print(f\"Projected 2D point for Camera 2:\\n{points_2d_cam2}\")\n",
+    "    print(f\"Shape of points for triangulation: {points_for_triangulation.shape}\")\n",
+    "\n",
+    "    # --- 5. Use CameraGroup.triangulate to reconstruct the 3D point ---\n",
+    "    # We'll set undistort=True because cam2 has distortion coefficients.\n",
+    "    # The triangulate method returns a numpy array of shape (num_points, 3).\n",
+    "    triangulated_points = camera_group.triangulate(points_for_triangulation, undistort=True)\n",
+    "\n",
+    "    print(f\"\\nTriangulated 3D points:\\n{triangulated_points}\")\n",
+    "\n",
+    "    # Compare the triangulated point with the original 3D point\n",
+    "    if triangulated_points.shape[0] > 0:\n",
+    "        reconstructed_point = triangulated_points[0]\n",
+    "        error = np.linalg.norm(reconstructed_point - true_3d_point[0])\n",
+    "        print(f\"\\nOriginal 3D point: {true_3d_point[0]}\")\n",
+    "        print(f\"Reconstructed 3D point: {reconstructed_point}\")\n",
+    "        print(f\"Reconstruction error (L2 norm): {error:.6f}\")\n"
+   ],
+   "id": "d57c636c870d94d4",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Cameras initialized.\n",
+      "Camera 1 name: cam1\n",
+      "Camera 2 name: cam2\n",
+      "\n",
+      "CameraGroup created with 2 cameras.\n",
+      "\n",
+      "True 3D point in world coordinates: [[1. 2. 5.]]\n",
+      "\n",
+      "Projected 2D point for Camera 1:\n",
+      "[[ nan 880.]]\n",
+      "Projected 2D point for Camera 2:\n",
+      "[[847.82290042 865.22061803]]\n",
+      "Shape of points for triangulation: (2, 1, 2)\n",
+      "\n",
+      "Triangulated 3D points:\n",
+      "[[nan nan nan]]\n",
+      "\n",
+      "Original 3D point: [1. 2. 5.]\n",
+      "Reconstructed 3D point: [nan nan nan]\n",
+      "Reconstruction error (L2 norm): nan\n"
+     ]
+    }
+   ],
+   "execution_count": 10
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-10-21T18:12:16.051120Z",
+     "start_time": "2025-10-21T18:12:15.877447Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "\n",
+    "from collections import defaultdict\n",
+    "from pathlib import Path\n",
+    "\n",
+    "request = BundleAdjustRequest(sessionKey='05272019_fly1_0_R1C24__rot-ccw-0.06_sec')\n",
+    "\n",
+    "from litpose_app import deps\n",
+    "config = deps.config()\n",
+    "project_info = deps.project_info(config)\n",
+    "\n",
+    "bundle_adjust(request, project_info, config)\n",
+    "\n",
+    "\n"
+   ],
+   "id": "37a1ad52fe6211ac",
+   "outputs": [
+    {
+     "ename": "ValidationError",
+     "evalue": "1 validation error for BundleAdjustRequest\nmvlabelfile\n  Field required [type=missing, input_value={'sessionKey': '05272019_...1C24__rot-ccw-0.06_sec'}, input_type=dict]\n    For further information visit https://errors.pydantic.dev/2.11/v/missing",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[31m---------------------------------------------------------------------------\u001B[39m",
+      "\u001B[31mValidationError\u001B[39m                           Traceback (most recent call last)",
+      "\u001B[36mCell\u001B[39m\u001B[36m \u001B[39m\u001B[32mIn[3]\u001B[39m\u001B[32m, line 4\u001B[39m\n\u001B[32m      1\u001B[39m \u001B[38;5;28;01mfrom\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[34;01mcollections\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;28;01mimport\u001B[39;00m defaultdict\n\u001B[32m      2\u001B[39m \u001B[38;5;28;01mfrom\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[34;01mpathlib\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;28;01mimport\u001B[39;00m Path\n\u001B[32m----> \u001B[39m\u001B[32m4\u001B[39m request = \u001B[43mBundleAdjustRequest\u001B[49m\u001B[43m(\u001B[49m\u001B[43msessionKey\u001B[49m\u001B[43m=\u001B[49m\u001B[33;43m'\u001B[39;49m\u001B[33;43m05272019_fly1_0_R1C24__rot-ccw-0.06_sec\u001B[39;49m\u001B[33;43m'\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[32m      6\u001B[39m \u001B[38;5;28;01mfrom\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[34;01mlitpose_app\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;28;01mimport\u001B[39;00m deps\n\u001B[32m      7\u001B[39m config = deps.config()\n",
+      "\u001B[36mFile \u001B[39m\u001B[32m~/miniforge3/envs/lpv/lib/python3.12/site-packages/pydantic/main.py:253\u001B[39m, in \u001B[36mBaseModel.__init__\u001B[39m\u001B[34m(self, **data)\u001B[39m\n\u001B[32m    251\u001B[39m \u001B[38;5;66;03m# `__tracebackhide__` tells pytest and some other tools to omit this function from tracebacks\u001B[39;00m\n\u001B[32m    252\u001B[39m __tracebackhide__ = \u001B[38;5;28;01mTrue\u001B[39;00m\n\u001B[32m--> \u001B[39m\u001B[32m253\u001B[39m validated_self = \u001B[38;5;28;43mself\u001B[39;49m\u001B[43m.\u001B[49m\u001B[43m__pydantic_validator__\u001B[49m\u001B[43m.\u001B[49m\u001B[43mvalidate_python\u001B[49m\u001B[43m(\u001B[49m\u001B[43mdata\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mself_instance\u001B[49m\u001B[43m=\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[32m    254\u001B[39m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m \u001B[38;5;129;01mis\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m validated_self:\n\u001B[32m    255\u001B[39m     warnings.warn(\n\u001B[32m    256\u001B[39m         \u001B[33m'\u001B[39m\u001B[33mA custom validator is returning a value other than `self`.\u001B[39m\u001B[38;5;130;01m\\n\u001B[39;00m\u001B[33m'\u001B[39m\n\u001B[32m    257\u001B[39m         \u001B[33m\"\u001B[39m\u001B[33mReturning anything other than `self` from a top level model validator isn\u001B[39m\u001B[33m'\u001B[39m\u001B[33mt supported when validating via `__init__`.\u001B[39m\u001B[38;5;130;01m\\n\u001B[39;00m\u001B[33m\"\u001B[39m\n\u001B[32m    258\u001B[39m         \u001B[33m'\u001B[39m\u001B[33mSee the `model_validator` docs (https://docs.pydantic.dev/latest/concepts/validators/#model-validators) for more details.\u001B[39m\u001B[33m'\u001B[39m,\n\u001B[32m    259\u001B[39m         stacklevel=\u001B[32m2\u001B[39m,\n\u001B[32m    260\u001B[39m     )\n",
+      "\u001B[31mValidationError\u001B[39m: 1 validation error for BundleAdjustRequest\nmvlabelfile\n  Field required [type=missing, input_value={'sessionKey': '05272019_...1C24__rot-ccw-0.06_sec'}, input_type=dict]\n    For further information visit https://errors.pydantic.dev/2.11/v/missing"
+     ]
+    }
+   ],
+   "execution_count": 3
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

lightning_pose_app-1.8.1a17/src/litpose_app/routes/labeler/test_bundle_adjust.ipynb

@@ -1,113 +0,0 @@
-{
- "cells": [
-  {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-04T22:29:30.548302Z",
-     "start_time": "2025-09-04T22:29:28.207273Z"
-    }
-   },
-   "cell_type": "code",
-   "source": [
-    "import numpy as np\n",
-    "\n",
-    "from litpose_app.deps import project_info\n",
-    "from litpose_app.routes.rglob import rglob, RGlobRequest\n",
-    "from multiview_autolabel import *\n",
-    "from bundle_adjust import *\n",
-    "warm_up_anipose()"
-   ],
-   "id": "426cdcedf0207a92",
-   "outputs": [],
-   "execution_count": 1
-  },
-  {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-04T22:29:36.203750Z",
-     "start_time": "2025-09-04T22:29:30.552170Z"
-    }
-   },
-   "cell_type": "code",
-   "source": [
-    "\n",
-    "from collections import defaultdict\n",
-    "from pathlib import Path\n",
-    "\n",
-    "request = BundleAdjustRequest(sessionKey='05272019_fly1_0_R1C24__rot-ccw-0.06_sec')\n",
-    "\n",
-    "from litpose_app import deps\n",
-    "config = deps.config()\n",
-    "project_info = deps.project_info(config)\n",
-    "\n",
-    "bundle_adjust(request, project_info, config)\n",
-    "\n",
-    "\n"
-   ],
-   "id": "37a1ad52fe6211ac",
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Skipping /home/ksikka/work/LightningPoseData/fly-anipose/calibrations.csv because no view name was present.\n",
-      "Skipping /home/ksikka/work/LightningPoseData/fly-anipose/calibrations_new.csv because no view name was present.\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-A_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-B_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-C_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-D_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-E_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-F_new.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-A.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-B.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-C.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-D.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-E.csv\n",
-      "/home/ksikka/work/LightningPoseData/fly-anipose/CollectedData_Cam-F.csv\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2025-09-04 18:29:31,194 - INFO - finding looplift candidates\n",
-      "2025-09-04 18:29:32,323 - INFO - finding looplift candidates\n",
-      "2025-09-04 18:29:32,493 - INFO - finding looplift candidates\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'ok'"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "execution_count": 2
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
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