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+{"slug":"autobio-insert-centrifuge-5430-i00-privileged--uc5stsz","task":"autobio-insert-centrifuge-5430-i00-privileged","bench":"autobio","mode":"privileged","run":"codex-gpt6_luna-xhigh","agent":"codex","model":"gpt-6-luna","effort":"xhigh","state":"success","success":1,"reward":{"success":1,"replay_success":1,"deterministic":1,"instance_ok":1,"progress":1.0,"n_actions":9442,"sim_steps":9442,"task_failure":0,"grader_error":0,"video_rendered":1,"agent_sessions":48,"agent_resets":0,"agent_sim_steps":231567,"agent_records":0,"agent_replays":4,"agent_cost_self_reported":1},"wall_s":2396,"tokens":{"in":11239698,"cached":10557784,"out":156087,"usd":0.27},"task_text":"# AutoBio · insert_centrifuge_5430 — frozen instance\n\nYou control a **UR5e** arm (6 joints) with a Robotiq 2F-85 gripper, fixed to the bench, in AutoBio's simulated biology laboratory (MuJoCo 3.3.0), via Python, through joint\nposition targets.\n**Task:** Load a second 1.5 mL tube into the centrifuge's rotor, into the slot diametrically opposite the tube that is already in it (slot 8 of 30, `s.task.slot_id`; the tube in the rotor is in slot 23). The tube to load stands in the plate on the bench. Success at the first control step where the tube's body is within 5 mm of its seated position in that slot (`s.task.final_tar_tubepose`) and its height is between 0.955 and 0.961 m.\n\nOn the bench: a centrifuge (an Eppendorf 5430 model) with its lid open and a 30-slot rotor holding one 1.5 mL tube, and a well plate with a second 1.5 mL tube standing in it.\n\nAutoBio's own success test is `s.task.check()`: class `InsertCentrifuge5430` in `/opt/AutoBio/autobio/load_centrifuge_5430.py`.\nRobot Coding Bench evaluates it after every control step: the first step at which it holds ends the episode in success (AutoBio's own rule for this task; its time limit is lifted).\n\nThis is a *fixed scene instance*: the start pose, the objects and the goal never change between resets. You may reset and\nretry as many times as you want. Your deliverable is **one replayable trajectory**, not a general policy.\n\n## Deliverable\nWrite the final trajectory to `/app/output/trajectory.npz` with `Session.save_trajectory(...)` (below). It is replayed\nopen-loop from the same initial state in two fresh processes and scored 1 if both episodes end in success in the same\nstate, else 0. Also leave the script that produced it at `/app/output/gen.py`.\n\nYour time budget is 3600 s of wall clock. Save a trajectory as soon as you have one that works, improve it while\ntime remains, and do not stop early.\n\n## Tooling (already installed; run `python` from any directory)\n```python\nfrom rcb_autobio import Session\ns = Session(instance=\"/app/instance.json\") # a few seconds\ns.reset() # back to the frozen initial state (unlimited)\ns.state() # privileged view: qpos, qvel, ctrl, the targets in effect, tool poses, gripper openings, score\ns.task, s.model, s.data # AutoBio's task object (its scene helpers and check()), MuJoCo model / data: read them freely\ns.actuators() # the 7 controlled actuators in action order: name, unit, range, kp, kv, force range\ns.command() # the targets in effect (after reset: the ones that hold the initial pose)\ns.step(a) # one control step (2 ms) with 7 targets; s.step(a, n=25) holds them 25 steps; False once the episode is over\ns.status() # {'success', 'done', 'reason', 'score', 'steps', 'state_sha', 'instance_ok', ...}\ns.record_start(); ...; actions = s.record_stop() # (T, 7) targets, one row per control step executed\ns.replay(actions) # resets, replays open-loop until the episode ends or the rows do, returns status -> self-check\ns.save_trajectory(actions, \"/app/output/trajectory.npz\")\ns.tcp_poses() # tool frames (`tcp`): x y z + wxyz quaternion, world frame\ns.fk(q); s.ik({frame: pose}) # kinematics of the arm joints (s.kinematic_joints()), no physics, no collision check\ns.render_frame(\"table_cam_front\") # RGB uint8 (480, 640, 3); cameras: table_cam_front, table_cam_left, wrist_cam; s.render_depth(cam): metres\ns.render_video(actions, \"/app/output/check.mp4\", cameras=[\"table_cam_front\"])\ns.close() # release the renderer when you are done with a Session\n```\nThere are no ready-made motions: AutoBio's scripted experts are not in this image. Its other code is, under\n`/opt/AutoBio/autobio` (importable once a Session exists): the scene helpers `s.task` is built from, its inverse\nkinematics (`kinematics.py`) and its path timing (`topp.py`).\n\nCLI equivalent of the grader:\n`python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repeat 2`\n\n## Conventions\n- Action: 7 position targets per control step, in this order: `shoulder_pan`, `shoulder_lift`, `elbow`, `wrist_1`, `wrist_2`, `wrist_3`, `2f85_fingers_actuator` (the Robotiq gripper: 0 open .. 255 closed). Arm joints are in rad. Each entry is the target of a PD position drive (stiffness, damping and force limit per entry: `s.actuators()`); a target outside the entry's range is clipped to it.\n- One control step is one physics step, 2 ms: a row is executed for exactly one step, so a motion lasting 1 s is 500\n rows (repeat a row to hold a target). Your wall-clock time is the budget (the reference replays at about\n 600 control steps/s here); the one technical cap is 600000 rows per trajectory (1200 s of simulated\n time). A MuJoCo physics warning (an unstable simulation) ends the episode as a failure.\n- World frame: z up, metres; poses are x y z + wxyz quaternion; angles in rad.\n- Only the rows are replayed: anything else you change in `s.model` or `s.data` is lost in the grader's fresh process.\n","step_times":"recorded","sim_total":{"submit":0,"reset":0},"replay":"autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/replay.mp4","replay_last":"autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/replay_last.jpg","steps":[{"id":6,"t":0.0,"say":"I’ll inspect the task’s success condition and the frozen scene, then build and replay a trajectory against the same check the grader uses. I’ll save the first successful trajectory before tuning it further.","calls":[{"kind":"shell","label":"ls -la /app && sed -n '1,260p' /opt/AutoBio/autobio/load_centrifuge_5430.py","code":"ls -la /app && sed -n '1,260p' /opt/AutoBio/autobio/load_centrifuge_5430.py"}],"out":{"text":"total 16\ndrwxr-xr-x 1 root root 4096 Oct 10 08:43 .\ndrwxr-xr-x 1 root root 4096 Oct 10 08:45 ..\n-rw-rw-r-- 1 root root 3730 Oct 10 08:43 instance.json\ndrwxr-xr-x 2 root root 4096 Oct 10 08:38 output\nimport mujoco\nmujoco.mj_loadPluginLibrary('./libmjlab.so.3.3.0')\nimport numpy as np\nimport math\nfrom kinematics import IK, Pose, slerp, mul_pose, neg_pose\nfrom topp import Topp\nfrom task import Task, Expert, Manager, SCENE_ROOT\nfrom instrument import Centrifuge_Eppendorf_5430\n\ndef set_gravcomp(body: mujoco.MjsBody):\n body.gravcomp = 1\n for child in body.bodies:\n set_gravcomp(child)\n\nclass GridSlot:\n\n def __init__(self, model: mujoco.MjModel, prefix: str):\n self.model = model\n self.prefix = prefix\n self.grids = dict()\n for i in range(self.model.nsite):\n site_name = mujoco.mj_id2name(self.model, mujoco.mjtObj.mjOBJ_SITE, i)\n if not site_name.startswith(prefix):\n continue\n parts = site_name.split('-')\n slot_type = parts[1]\n if slot_type not in self.grids:\n info = dict()\n info['origin'] = i\n user = self.model.site_user[i]\n info['rows'] = user[1]\n info['row_gap'] = user[2]\n info['cols'] = user[3]\n info['col_gap'] = user[4]\n info['height'] = user[5]\n self.grids[slot_type] = info\n else:\n print(f\"Duplicate grid slot ty\n… (6,999 characters left out) …\nat\n self.tube.set_pose(self.data, Pose(tubepos, quat))\n self.tube2.set_pose(self.data, self.instrument.get_tube_pose(self.data, (slot_id + 15) % 30, 'proximal'))\n mujoco.mj_kinematics(self.model, self.data)\n\n self.slot_id = slot_id\n self.tar_tubepose = self.instrument.get_tube_pose(self.data, self.slot_id, 'distal')\n self.final_tar_tubepose = self.instrument.get_tube_pose(self.data, self.slot_id, 'proximal')\n\n self.task_info = {\n 'prefix': 'Insert a second centrifuge tube into the slot that is symmetrically opposite to the currently placed tube',\n 'state_indices': self.arm.state_indices,\n 'action_indices': self.arm.action_indices,\n 'camera_mapping': {\n 'image': 'table_cam_front',\n 'wrist_image': '/ur:wrist_cam'\n },\n 'seed': seed,\n }\n\n return self.task_info\n\n def check(self):\n tube_height = self.tube.get_body_pose(self.data).pos\n tube_pos_2 = [self.tube.get_body_pose(self.data).pos[0], self.tube.get_body_pose(self.data).pos[1], self.tube.get_body_pose(self.data).pos[2]]\n site_pos = [self.final_tar_tubepose.pos[0], self.final_tar_tubepose.pos[1], self.final_tar_tubepose.pos[2]]\n squared_distance_site = sum((p1 - p2) ** 2 for p1, p2 in zip(tube_pos_2, site_pos))\n distance_site = math.sqrt(squared_distance_site)\n return 0.955 < tube_height[2] < 0.961 and distance_site < 0.005\n\n\n\n","exit":[],"pics":[]},"tok":{"in":10581,"cached":null,"out":201,"think":83,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":7,"t":3.5,"say":"","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, json\ns=Session(instance='/app/instance.json')\nprint('status',s.status())\nprint('state',s.state())\nprint('slot',s.task.slot_id)\nprint('final',s.task.final_tar_tubepose.pos,s.task.final_tar_tubepose.quat)\nprint('tar',s.task.tar_tubepose.pos,s.task.tar_tubepose.quat)\nprint('tube',s.task.tube.get_pose(s.data).pos,s.task.tube.get_pose(s.data).quat)\nprint('tube body',s.task.tube.get_body_pose(s.data).pos)\nprint('other',s.task.tube2.get_pose(s.data).pos)\nprint('tcp',s.tcp_poses())\nprint('act',s.actuators())\nprint('command',s.command())\nprint('joints',s.task.arm.jnt_span, s.data.qpos[list(s.task.arm.jnt_span)])\nprint('body obj',s.model.body('1/centrifuge_1-5ml_screw_body').id)\nprint('task check',s.task.check())\nimg=s.render_frame('table_cam_front')\nfrom PIL import Image\nImage.fromarray(img).save('/app/output/start.png')\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":13715,"cached":10578,"out":400,"think":59,"usd":0.0007},"sim":{"submit":0,"reset":0}},{"id":8,"t":10.8,"say":"","calls":[{"kind":"shell","label":"find /opt/AutoBio/autobio -maxdepth 2 -type f | sort | head -100","code":"find /opt/AutoBio/autobio -maxdepth 2 -type f | sort | head -100"},{"kind":"robot","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np\nfrom PIL import Image\ns=Session(instance='/app/instance.json')\nfor c in ['table_cam_front','table_cam_left','wrist_cam']:\n try: Image.fromarray(s.render_frame(c)).save('/app/output/'+c+'.png')\n except Exception as e: print(c,e)\nprint('tube geoms')\nfor gid in range(s.model.ngeom):\n b=s.model.geom_bodyid[gid]\n if b in [s.task.tube.body_id,s.task.tube.cap_id]:\n print(gid, s.model.geom(gid).name, s.model.geom_size[gid],s.model.geom_pos[gid],s.model.geom_quat[gid], 'body',b)\nprint('site id',s.task.arm.site_id)\nprint('tcp',s.tcp_poses())\ns.close()\nPY"}],"out":{"text":"/opt/AutoBio/autobio/README.md\n/opt/AutoBio/autobio/aloha_analytical_ik.py\n/opt/AutoBio/autobio/collision_mesh.py\n/opt/AutoBio/autobio/evaluate.py\n/opt/AutoBio/autobio/evaluate_openpi.py\n/opt/AutoBio/autobio/evaluate_rdt.py\n/opt/AutoBio/autobio/evaluator.py\n/opt/AutoBio/autobio/grasp/__init__.py\n/opt/AutoBio/autobio/grasp/body.py\n/opt/AutoBio/autobio/grasp/equality.py\n/opt/AutoBio/autobio/grasp/geom.py\n/opt/AutoBio/autobio/grasp/hierarchy.py\n/opt/AutoBio/autobio/grasp/joint.py\n/opt/AutoBio/autobio/grasp/quat.py\n/opt/AutoBio/autobio/grasp/site.py\n/opt/AutoBio/autobio/grasp/symbolic.py\n/opt/AutoBio/autobio/grasp/transform.py\n/opt/AutoBio/autobio/instrument.py\n/opt/AutoBio/autobio/kinematics.py\n/opt/AutoBio/autobio/libmjlab.so.3.3.0\n/opt/AutoBio/autobio/liquid.py\n/opt/AutoBio/autobio/load_centrifuge_5430.py\n/opt/AutoBio/autobio/mani_centrifuge_5430.py\n/opt/AutoBio/autobio/mani_centrifuge_5910.py\n/opt/AutoBio/autobio/mani_centrifuge_mini.py\n/opt/AutoBio/autobio/mani_pipette.py\n/opt/AutoBio/autobio/mani_thermal_cycler.py\n/opt/AutoBio/autobio/mani_thermal_mixer.py\n/opt/AutoBio/autobio/mani_vortex_mixer.py\n/opt/AutoBio/autobio/meshplane.so\n/opt/AutoBio/autobio/pickup_centrifuge_tube.py\n/opt/AutoBio/autobio/render.bash\n/opt/AutoBio/autobio/render.py\n/opt/AutoBio/autobio/render_blender.py\n/opt/AutoBio/autobio/render_blender_driver.py\n/opt/AutoBio/autobio/render_liquid.py\n/opt/AutoBio/autobio/render_ui.py\n/opt/AutoBio/autobio/render_video.bash\n/opt/AutoBio/autobio/screw_loosen.py\n/opt/AutoBio/autobio/screw_tighten.py\n/opt/AutoBio/autobio/serialize.py\n/opt/AutoBio/autobio/simulation.py\n/opt/AutoBio/autobio/task.py\n/opt/AutoBio/autobio/thermal_mixer_ui.py\n/opt/AutoBio/autobio/topp.py\n/opt/AutoBio/autobio/transfer_centrifuge_tube.py\n/opt/AutoBio/autobio/validate.py\n","exit":[],"pics":[]},"tok":{"in":15889,"cached":13712,"out":478,"think":167,"usd":0.0006},"sim":{"submit":0,"reset":0}},{"id":9,"t":18.1,"say":"","calls":[{"kind":"shell","label":"sed -n '1,300p' /opt/AutoBio/autobio/pickup_centrifuge_tube.py && sed -n '1,280p' /opt/AutoBio/autobio/transfe","code":"sed -n '1,300p' /opt/AutoBio/autobio/pickup_centrifuge_tube.py && sed -n '1,280p' /opt/AutoBio/autobio/transfer_centrifuge_tube.py && sed -n '1,300p' /opt/AutoBio/autobio/mani_centrifuge_5430.py"}],"out":{"text":"import numpy as np\nimport mujoco\nmujoco.mj_loadPluginLibrary('./libmjlab.so.3.3.0')\n\nfrom kinematics import AlohaAnalyticalIK, Pose, slerp\nfrom topp import Topp\nfrom task import Task, Expert, Manager, SCENE_ROOT\n\ndef set_gravcomp(body: mujoco.MjsBody):\n body.gravcomp = 1\n for child in body.bodies:\n set_gravcomp(child)\n\nclass GridSlot:\n\n def __init__(self, model: mujoco.MjModel, prefix: str):\n self.model = model\n self.prefix = prefix\n self.grids = dict()\n for i in range(self.model.nsite):\n site_name = mujoco.mj_id2name(self.model, mujoco.mjtObj.mjOBJ_SITE, i)\n if not site_name.startswith(prefix):\n continue\n parts = site_name.split('-')\n slot_type = parts[1]\n if slot_type not in self.grids:\n info = dict()\n info['origin'] = i\n user = self.model.site_user[i]\n info['rows'] = user[1]\n info['row_gap'] = user[2]\n info['cols'] = user[3]\n info['col_gap'] = user[4]\n info['height'] = user[5]\n self.grids[slot_type] = info\n else:\n print(f\"Duplicate grid slot type '{slot_type}' found in '{site_name}'\")\n\n if len(self.grids) == 0:\n raise ValueError(f\"No grid slots found with prefix '{prefix}'\")\n\n def get_position(self, data: mujoco.MjData, row: int, col: int, slot_type: str='default', hei: int=0) -> np\n… (18,073 characters left out) …\ne ValueError(f\"Unknown location: {loc}\")\n\n\nclass Centrifuge5430Manipulate(Task):\n default_scene = SCENE_ROOT / \"mani_centrifuge_5430.xml\"\n default_task = \"centrifuge_5430_close_lid\"\n\n time_limit = 15.0\n early_stop = True\n\n @classmethod\n def prepare(cls, spec: mujoco.MjSpec) -> mujoco.MjSpec:\n body = spec.body('/ur:world')\n set_gravcomp(body)\n return spec\n\n def __init__(self, spec: mujoco.MjSpec):\n self.instrument = Centrifuge_5430('/centrifuge_eppendorf_5430:')\n manager = Manager.from_spec(spec, [self.instrument])\n super().__init__(manager)\n self.arm = UR5eArm(self.model, '/ur:')\n\n def reset(self, seed: int | None = None):\n super().reset(seed=seed)\n self.manager.reset(keyframe=0)\n\n # Randomize the arm joint position\n perturbation = self.arm.qpos_perturb()\n self.data.qpos[self.arm.jnt_span] += perturbation\n self.data.ctrl[self.arm.act_span] += perturbation\n\n self.task_info = {\n 'prefix': 'close the lid of the centrifuge eppendorf 5430',\n 'state_indices': self.arm.state_indices,\n 'action_indices': self.arm.action_indices,\n 'camera_mapping': {\n 'image': 'table_cam_left',\n 'wrist_image': '/ur:wrist_cam'\n },\n 'seed': seed,\n }\n\n return self.task_info\n\n def check(self):\n # Add any task-specific completion checks if needed\n return True\n\n\n\n","exit":[],"pics":[]},"tok":{"in":17519,"cached":15886,"out":178,"think":56,"usd":0.0005},"sim":{"submit":0,"reset":0}},{"id":10,"t":20.2,"say":"","calls":[{"kind":"shell","label":"rg -n 'class Expert|def act|tar_tubepose|final_tar' /opt/AutoBio/autobio/load_centrifuge_5430.py /opt/AutoBio/","code":"rg -n 'class Expert|def act|tar_tubepose|final_tar' /opt/AutoBio/autobio/load_centrifuge_5430.py /opt/AutoBio/autobio /opt/tools/rcb_autobio.py | head -150"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":23675,"cached":17516,"out":115,"think":17,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":11,"t":24.9,"say":"","calls":[{"kind":"look","label":"table_cam_front.png","code":"/app/output/table_cam_front.png"}],"out":{"text":"","exit":[],"pics":["autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s011_0.jpg"]},"tok":{"in":24148,"cached":23672,"out":478,"think":442,"usd":0.0005},"sim":{"submit":0,"reset":0}},{"id":12,"t":27.8,"say":"","calls":[{"kind":"look","label":"table_cam_left.png","code":"/app/output/table_cam_left.png"}],"out":{"text":"","exit":[],"pics":["autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s012_0.jpg"]},"tok":{"in":25009,"cached":24145,"out":83,"think":47,"usd":0.0004},"sim":{"submit":0,"reset":0}},{"id":13,"t":30.4,"say":"","calls":[{"kind":"shell","label":"print(open('/app/instance.json').read())","code":"sed -n '1,320p' /opt/AutoBio/autobio/kinematics.py && python - <<'PY'\nimport json\nprint(open('/app/instance.json').read())\nPY"}],"out":{"text":"from dataclasses import dataclass\nimport numpy as np\nfrom grasp.hierarchy import build_hierarchy\nfrom grasp.quat import quatapply, quatinv, quatcompose\nimport mujoco\nimport jax\njax.config.update('jax_enable_x64', True)\njax.config.update('jax_platforms', 'cpu')\nimport jax.numpy as jnp\nfrom scipy.optimize import minimize\n\n@dataclass\nclass Pose:\n pos: np.ndarray\n quat: np.ndarray\n\ndef mul_pose(p1: Pose, p2: Pose) -> Pose:\n res_pos, res_quat = np.zeros(3), np.zeros(4)\n mujoco.mju_mulPose(\n res_pos, res_quat,\n p1.pos, p1.quat,\n p2.pos, p2.quat\n )\n return Pose(res_pos, res_quat)\n\ndef neg_pose(p: Pose) -> Pose:\n res_pos, res_quat = np.zeros(3), np.zeros(4)\n mujoco.mju_negPose(res_pos, res_quat, p.pos, p.quat)\n return Pose(res_pos, res_quat)\n\ndef slerp(q0: np.ndarray, q1: np.ndarray, amount=0.5):\n \"\"\"Spherical Linear Interpolation between quaternions.\n Implemented as described in https://en.wikipedia.org/wiki/Slerp\n\n Find a valid quaternion rotation at a specified distance along the\n minor arc of a great circle passing through any two existing quaternion\n endpoints lying on the unit radius hypersphere.\n\n This is a class method and is called as a method of the class itself rather than on a particular instance.\n\n Params:\n q0: first endpoint rotation as a Quaternion object\n q1: second endpoint rotation as a Quaternion object\n amount: interpolation parameter between 0 and 1. This describes the linea\n… (9,035 characters left out) …\n28.0\n ]\n },\n {\n \"index\": 6,\n \"name\": \"2f85_fingers_actuator\",\n \"mujoco_name\": \"/ur:2f85:fingers_actuator\",\n \"kind\": \"gripper\",\n \"unit\": \"0 (open) .. 255 (closed)\",\n \"drives\": \"/ur:2f85:split\",\n \"arm\": \"arm\",\n \"range\": [\n 0.0,\n 255.0\n ],\n \"kp\": 0.3137255,\n \"kv\": 10.0,\n \"force_range\": [\n -5.0,\n 5.0\n ]\n }\n ],\n \"arms\": [\n {\n \"key\": \"arm\",\n \"kind\": \"ur5e\",\n \"tcp\": \"tcp\",\n \"joints\": [\n \"shoulder_pan\",\n \"shoulder_lift\",\n \"elbow\",\n \"wrist_1\",\n \"wrist_2\",\n \"wrist_3\"\n ]\n }\n ],\n \"robot_joints\": [\n \"shoulder_pan\",\n \"shoulder_lift\",\n \"elbow\",\n \"wrist_1\",\n \"wrist_2\",\n \"wrist_3\",\n \"2f85_right_driver_joint\",\n \"2f85_right_coupler_joint\",\n \"2f85_right_spring_link_joint\",\n \"2f85_right_follower_joint\",\n \"2f85_left_driver_joint\",\n \"2f85_left_coupler_joint\",\n \"2f85_left_spring_link_joint\",\n \"2f85_left_follower_joint\"\n ],\n \"cameras\": [\n \"table_cam_front\",\n \"table_cam_left\",\n \"wrist_cam\"\n ],\n \"default_cameras\": [\n \"table_cam_front\",\n \"wrist_cam\"\n ],\n \"initial_command\": [\n -0.48858645812997803,\n -1.6019468502837966,\n 1.6423891235245514,\n -1.4777237828511123,\n -1.5213745212856111,\n -1.61704731708292,\n 0.0\n ],\n \"initial_score\": 0.0,\n \"reference_rows\": 4582,\n \"expert_rows\": 5164,\n \"steps_per_s\": 600,\n \"idle_score_10s\": 0.0,\n \"reference_steps\": 4582,\n \"reference_sha\": \"6e3d76ae346a08d6\",\n \"reference_score\": 1.0,\n \"reference_source\": \"AutoBio's scripted expert (load_centrifuge_5430.py @ 0850421), seed 0\"\n}\n\n","exit":[],"pics":[]},"tok":{"in":25476,"cached":25006,"out":111,"think":25,"usd":0.0004},"sim":{"submit":0,"reset":0}},{"id":14,"t":36.2,"say":"","calls":[{"kind":"shell","label":"rg -n '2f85:pinch|fingers_actuator|centrifuge_1-5ml_screw_body|rack-0|well' /opt/AutoBio/autobio/scenes /opt/A","code":"rg -n '2f85:pinch|fingers_actuator|centrifuge_1-5ml_screw_body|rack-0|well' /opt/AutoBio/autobio/scenes /opt/AutoBio/autobio 2>/dev/null | head -100"}],"out":{"text":"/opt/AutoBio/autobio/mani_pipette.py:30: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/mani_pipette.py:31: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n/opt/AutoBio/autobio/transfer_centrifuge_tube.py:60: self.site_name = f'{prefix}2f85:pinch' \n/opt/AutoBio/autobio/transfer_centrifuge_tube.py:66: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id \n/opt/AutoBio/autobio/mani_thermal_cycler.py:23: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/mani_thermal_cycler.py:28: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n/opt/AutoBio/autobio/load_centrifuge_5430.py:61: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/load_centrifuge_5430.py:66: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n/opt/AutoBio/autobio/load_centrifuge_5430.py:108: body = model.body(f'{body_prefix}centrifuge_1-5ml_screw_body')\n/opt/AutoBio/autobio/mani_centrifuge_5430.py:25: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/mani_centrifuge_5430.py:30: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n/opt/AutoBio/autobio/mani_thermal_mixer.py:73: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/mani_thermal_mixer.py:78: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n/opt/AutoBio/autobio/mani_thermal_mixer.py:154: s\n… (5,717 characters left out) …\nt/AutoBio/autobio/model/scene/gallery.xml:86: \n/opt/AutoBio/autobio/model/scene/gallery.xml:96: \n/opt/AutoBio/autobio/model/scene/gallery.xml:100: \n/opt/AutoBio/autobio/model/scene/lab.xml:25: \n/opt/AutoBio/autobio/model/scene/mani_thermal_mixer.xml:16: \n/opt/AutoBio/autobio/model/scene/mani_thermal_mixer.xml:43: \n/opt/AutoBio/autobio/model/scene/mani_thermal_mixer.xml:51: \n/opt/AutoBio/autobio/model/scene/mani_thermal_mixer.xml:52: \n/opt/AutoBio/autobio/assets/container/pcr_plate_96well_vis.obj:1:o pcr_plate_96_well\n/opt/AutoBio/autobio/mani_centrifuge_mini.py:24: self.site_name = f'{prefix}2f85:pinch'\n/opt/AutoBio/autobio/mani_centrifuge_mini.py:29: self.gripper_id = model.actuator(f'{prefix}2f85:fingers_actuator').id\n","exit":[],"pics":[]},"tok":{"in":29312,"cached":25473,"out":656,"think":555,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":15,"t":39.9,"say":"","calls":[{"kind":"shell","label":"sed -n '1,150p' /opt/AutoBio/autobio/model/scene/insert_centrifuge_5430.xml && sed -n '1,100p' /opt/AutoBio/au","code":"sed -n '1,150p' /opt/AutoBio/autobio/model/scene/insert_centrifuge_5430.xml && sed -n '1,100p' /opt/AutoBio/autobio/model/object/centrifuge_1-5ml_screw.xml && sed -n '1,230p' /opt/AutoBio/autobio/model/robot/2f85.xml && sed -n '1,220p' /opt/AutoBio/autobio/model/object/centrifuge_plate_60well.gen.xml"}],"out":{"text":"\n\n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n","exit":[],"pics":[]},"tok":{"in":33011,"cached":29309,"out":187,"think":29,"usd":0.0008},"sim":{"submit":0,"reset":0}},{"id":16,"t":49.3,"say":"","calls":[{"kind":"shell","label":"rg -n 'def ik|def fk|def record_start|def replay|def step' /opt/tools/rcb_autobio.py | head -50 && sed -n '300","code":"rg -n 'def ik|def fk|def record_start|def replay|def step' /opt/tools/rcb_autobio.py | head -50 && sed -n '300,520p' /opt/tools/rcb_autobio.py"}],"out":{"text":"226: def step(self, a, n: int = 1) -> bool:\n270: def record_start(self) -> None:\n285: def replay(self, actions, video: str | None = None, cameras=None, fps: int = 25) -> dict:\n481: def fk(self, q, links=None) -> dict:\n491: def ik(self, targets: dict, seed=None, tol_pos_m: float = 1e-3, tol_rot_rad: float = 1e-2, max_iters: int = 300) -> dict:\n if video:\n frames.append(np.hstack([self.render_frame(c) for c in cams]))\n out[\"video\"] = _write_video(video, frames, fps)\n self._rec = rec\n _log({\"ev\": \"replay\", \"rows\": int(len(A)), \"success\": out[\"success\"]})\n return out\n\n def save_trajectory(self, actions, path: str, meta: dict | None = None) -> None:\n A = self._rows(actions)\n if len(A) > MAX_STEPS:\n raise ValueError(f\"a trajectory has at most {MAX_STEPS} rows ({MAX_STEPS * CONTROL_DT:g} s of simulated time), got {len(A)}\")\n os.makedirs(os.path.dirname(os.path.abspath(path)), exist_ok=True)\n np.savez_compressed(path, actions=A, task=self.family, meta=json.dumps(meta or {}))\n\n def render_video(self, actions, path: str, cameras=None, fps: int = 25) -> dict:\n return self.replay(actions, video=path, cameras=cameras, fps=fps)\n\n # ------------------------------------------------------------------------------------------- hashes\n def _model_sha(self) -> str:\n mj = self._mj\n buf = np.zeros(mj.mj_sizeModel(self.model), dtype=np.uint8)\n mj.mj_saveMode\n… (8,526 characters left out) …\n qz]}, world frame):\n damped least squares on each arm's 6 joints within their ranges, no collision checking. `tol_rot_rad` >= 3.1\n ignores orientation. Returns {\"ok\", \"q\", \"error\": {frame: (pos_m, rot_rad)}}; q covers every arm (an arm\n without a target keeps its seed).\"\"\"\n mj, m = self._mj, self.model\n qadr = np.concatenate([a.qadr for a in self.arms])\n q = np.array(seed if seed is not None else self.data.qpos[qadr], dtype=np.float64).reshape(-1)\n if q.shape[0] != len(qadr):\n raise ValueError(f\"seed is {len(qadr)} joint positions\")\n errors, off = {}, 0\n jacp, jacr = np.zeros((3, m.nv)), np.zeros((3, m.nv))\n for a in self.arms:\n sl = slice(off, off + len(a.qadr))\n off += len(a.qadr)\n if a.tcp not in targets:\n continue\n tgt = np.asarray(targets[a.tcp], dtype=np.float64)\n sid = m.site(a.site).id\n lo = np.array([m.jnt_range[j, 0] if m.jnt_limited[j] else -np.inf for j in a.joint_ids])\n hi = np.array([m.jnt_range[j, 1] if m.jnt_limited[j] else np.inf for j in a.joint_ids])\n use_rot = tol_rot_rad < 3.1\n\n def err(qa):\n qq = q.copy()\n qq[sl] = qa\n self._fk0(qq)\n e_p = tgt[:3] - self._k0.site_xpos[sid]\n cur, neg, dq3 = np.zeros(4), np.zeros(4), np.zeros(4)\n mj.mju_mat2Quat(cur, self._k0.site_xmat[sid])\n","exit":[],"pics":[]},"tok":{"in":40437,"cached":33008,"out":529,"think":435,"usd":0.0015},"sim":{"submit":0,"reset":0}},{"id":17,"t":66.8,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np\ns=Session(instance='/app/instance.json')\nq=np.array(s.command()[:6]); p=s.tcp_poses()['tcp']\nimport mujoco\nM=np.zeros((3,3)); mujoco.mju_quat2Mat(M,np.array(p[3:])); print('axes',M)\nfor qt in [np.array([0.,1,0,0]),np.array([0.,0,1,0]),np.array([0.7071,0.7071,0,0])]:\n p0=[0.3244,.4873,.90,*qt]\n out=s.ik({'tcp':p0},seed=q,tol_pos_m=1e-4,tol_rot_rad=1e-2)\n print('target',qt,'ok',out['ok'],'q',out['q'],'err',out['error'])\n if out['ok']:\n print('fk',s.fk(out['q'])['tcp'])\ns.close()\nPY"}],"out":{"text":"Traceback (most recent call last):\n File \"\", line 6, in \nTypeError: mju_quat2Mat(): incompatible function arguments. The following argument types are supported:\n 1. (res: numpy.ndarray[numpy.float64[9, 1], flags.writeable], quat: numpy.ndarray[numpy.float64[4, 1]]) -> None\n\nInvoked with: array([[0., 0., 0.],\n [0., 0., 0.],\n [0., 0., 0.]]), array([-0.05780267, 0.2204217 , 0.97280999, 0.04139876])\n","exit":[],"pics":[]},"tok":{"in":44195,"cached":40434,"out":2113,"think":1837,"usd":0.0019},"sim":{"submit":0,"reset":0}},{"id":18,"t":72.6,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco\ns=Session(instance='/app/instance.json')\nq=np.array(s.command()[:6]); p=s.tcp_poses()['tcp']\nM=np.zeros(9); mujoco.mju_quat2Mat(M,np.array(p[3:])); print('axes',M.reshape(3,3))\nfor qt in [np.array([0.,1,0,0]),np.array([0.,0,1,0]),np.array([0.70710678,0.70710678,0,0])]:\n p0=[0.3244,.4873,.90,*qt]\n out=s.ik({'tcp':p0},seed=q,tol_pos_m=1e-4,tol_rot_rad=1e-2)\n print('target',qt,'ok',out['ok'],'q',out['q'],'err',out['error'])\n if out['ok']:\n print('fk',s.fk(out['q'])['tcp'])\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":46483,"cached":44192,"out":293,"think":12,"usd":0.0009},"sim":{"submit":0,"reset":0}},{"id":19,"t":92.8,"say":"The frozen instance matches slot 8, and the task check is based on the tube body’s base position (within 5 mm) and z height—not its orientation. I’m testing a physical grasp at the cap and will carry the tube with its slot orientation so it can seat cleanly.","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco\ns=Session(instance='/app/instance.json')\nq0=np.asarray(s.command()[:6]); qcur=q0.copy()\nopen0=np.array([*q0,0.])\nqdown=np.array([0.,1.,0.,0.])\ndef go(p, grip, dur=.6):\n global qcur\n ik=s.ik({'tcp':[*p[:3],*p[3:]]},seed=qcur,tol_pos_m=2e-5,tol_rot_rad=2e-3)\n print('ik',ik['ok'],ik['error'], np.round(ik['q'],3))\n q1=np.asarray(ik['q']); N=int(dur/.002)\n for i in range(1,N+1):\n t=i/N; t=t*t*(3-2*t)\n a=np.r_[qcur*(1-t)+q1*t,grip]\n if not s.step(a): break\n qcur=q1\n print('tcp',s.tcp_poses()['tcp'][:3], 'tube',s.task.tube.get_body_pose(s.data).pos,'open',s.gripper_openings(),'status',s.status()['success'],'steps',s.steps)\n\ngo([.3244,.4873,.96,*qdown],0,.8)\ngo([.3244,.4873,.866,*qdown],0,.8)\ngo([.3244,.4873,.866,*qdown],220,.8)\n# print contacts tube-related\nfor ci in range(s.data.ncon):\n c=s.data.contact[ci]\n n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_GEOM,c.geom1); n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_GEOM,c.geom2)\n if (c.geom1>=2103 or c.geom2>=2103) or ('pad' in str(n1) or 'pad' in str(n2)):\n print('contact',n1,n2,c.dist)\n# test lift to z 1.02\n\ngo([.3244,.4873,1.02,*qdown],220,1.)\nprint('final tube',s.task.tube.get_pose(s.data).pos,s.task.tube.get_pose(s.data).quat, 'check',s.task.check())\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":47410,"cached":46480,"out":2901,"think":2247,"usd":0.002},"sim":{"submit":0,"reset":0}},{"id":20,"t":129.0,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport mujoco, numpy as np\ns=Session(instance='/app/instance.json')\nfor b in range(s.model.nbody):\n name=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b) or ''\n if 'centrifuge_eppendorf_5430' in name:\n print('body',b,name,'pos',s.data.xpos[b], 'quat',s.data.xquat[b], 'parent',s.model.body_parentid[b])\nfor i in range(s.model.nsite):\n name=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_SITE,i) or ''\n if 'slot' in name.lower() or 'rotor' in name.lower() or 'lid' in name.lower():\n print('site',i,name, s.data.site_xpos[i])\n# only names and xyz for instrument geoms (bodies descendant) approximate\nfor g in range(s.model.ngeom):\n b=s.model.geom_bodyid[g]; name=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b) or ''\n if 'centrifuge_eppendorf_5430' in name:\n gn=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_GEOM,g)\n print('geom',g,gn,'body',name,'world',s.data.geom_xpos[g], 'size',s.model.geom_size[g][:3])\ns.close()\nPY"}],"out":{"text":"Warning: truncated output (original token count: 15028)\nTotal output lines: 455\n\nWarning: truncated output (original token count: 69010)\nTotal output lines: 2040\n\nbody 3 centrifuge_eppendorf_5430 pos [0. 0. 0.824] quat [0.70710678 0. 0. 0.70710678] parent 1\nbody 4 /centrifuge_eppendorf_5430:world pos [0. 0. 0.824] quat [0.70710678 0. 0. 0.70710678] parent 3\nbody 5 /centrifuge_eppendorf_5430:body pos [0. 0. 0.8503094] quat [0.70710678 0. 0. 0.70710678] parent 4\nbody 6 /centrifuge_eppendorf_5430:lid pos [-0.21119162 0. 1.0282937 ] quat [ 0.70506788 -0.05365901 -0.05365901 0.70506788] parent 5\nbody 7 /centrifuge_eppendorf_5430:rotor pos [-0.05516829 -0.03123857 0.8503094 ] quat [-0.96372479 0. 0. 0.26689799] parent 5\nsite 2 /centrifuge_eppendorf_5430:lid [-0.25050584 0. 1.37872671]\nsite 3 /centrifuge_eppendorf_5430:slot00 [-0.07496159 -0.06423293 0.9777394 ]\nsite 4 /centrifuge_eppendorf_5430:slot01 [-0.06076477 -0.07084079 0.9777394 ]\nsite 5 /centrifuge_eppendorf_5430:slot02 [-0.04550434 -0.07435256 0.9777394 ]\nsite 6 /centrifuge_eppendorf_5430:slot03 [-0.02984724 -0.07461478 0.9777394 ]\nsite 7 /centrifuge_eppendorf_5430:slot04 [-0.01447777 -0.07161597 0.9777394 ]\nsite 8 /centrifuge_eppendorf_5430:slot05 [-6.76486266e-05 -6.54871956e-02 9.77739400e-01]\nsite 9 /centrifuge_eppendorf_5430:slot06 [ 0.01275333 -0.05649632 0.9777394 ]\nsite 10 /centrifuge_eppendorf_\n… (37,108 characters left out) …\n13 None body /centrifuge_eppendorf_5430:rotor world [-0.1006663 -0.06861922 0.9542256 ] size [0.00050516 0.00183727 0.00298092]\ngeom 2014 None body /centrifuge_eppendorf_5430:rotor world [-0.10712504 -0.07103213 0.96386153] size [0.00140053 0.00148182 0.0031789 ]\ngeom 2015 None body /centrifuge_eppendorf_5430:rotor world [-0.10765831 -0.07023636 0.95543672] size [0.00095081 0.00352319 0.00618764]\ngeom 2016 None body /centrifuge_eppendorf_5430:rotor world [-0.1000097 -0.07817861 0.95655074] size [0.00256572 0.00572424 0.00644035]\ngeom 2017 None body /centrifuge_eppendorf_5430:rotor world [-0.10012945 -0.06662419 0.95448304] size [0.00155845 0.00214359 0.00372703]\ngeom 2018 None body /centrifuge_eppendorf_5430:rotor world [-0.10915663 -0.06823784 0.95573027] size [0.00250808 0.00392284 0.00673094]\ngeom 2019 None body /centrifuge_eppendorf_5430:rotor world [-0.09801359 -0.06825465 0.95446754] size [0.00201018 0.00261791 0.00388492]\ngeom 2020 None body /centrifuge_eppendorf_5430:rotor world [-0.09671271 -0.07507307 0.95658756] size [0.0014553 0.00243123 0.004378 ]\ngeom 2021 None body /centrifuge_eppendorf_5430:rotor world [-0.1088107 -0.06728636 0.96044122] size [0.0021815 0.00252952 0.00518185]\ngeom 2022 None body /centrifuge_eppendorf_5430:rotor world [-0.10804193 -0.07042593 0.95995353] size [0.00063473 0.00146113 0.00361708]\ngeom 2023 None body /centrifuge_eppendorf_5430:rotor world [-0.10809438 -0.07052337 0.96154326] size [0.00060386 0.00072826 0.0021266 ]\n","exit":[],"pics":[]},"tok":{"in":53979,"cached":47407,"out":3936,"think":3544,"usd":0.0033},"sim":{"submit":0,"reset":0}},{"id":21,"t":149.6,"say":"","calls":[{"kind":"robot","label":"writes test_insert.py","code":"cat > /tmp/test_insert.py <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco, math\ns=Session(instance='/app/instance.json')\n# pose helpers\ndef mul(a,b):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\ndef inv(a):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\ndef pose_body():\n p=s.task.tube.get_body_pose(s.data);return np.r_[p.pos,p.quat]\ndef pose_tcp():return np.array(s.tcp_poses()['tcp'])\ndef interp_pose(a,b,t):\n p=a[:3]*(1-t)+b[:3]*t\n q=np.zeros(4);mujoco.mju_slerp(q,a[3:],b[3:],t)\n return np.r_[p,q]\nqcmd=np.array(s.command()[:6]); grip=0\nNtot=0\ndef move_tool(target, gripper=None, duration=.6, label='tool'):\n global qcmd,grip,Ntot\n if gripper is None:gripper=grip\n ik=s.ik({'tcp':target.tolist()},seed=qcmd,tol_pos_m=1e-4,tol_rot_rad=2e-3)\n if not ik['ok']:\n raise RuntimeError((label,ik))\n q1=np.array(ik['q']);q0=qcmd.copy();N=max(2,int(duration/.002))\n for i in range(1,N+1):\n t=i/N;t=t*t*(3-2*t)\n s.step(np.r_[q0*(1-t)+q1*t,gripper]);Ntot+=1\n if s.status()['done']:break\n qcmd=q1;grip=gripper\n print(label,'tcp',np.round(pose_tcp()[:3],4),'tube',np.round(pose_body()[:3],4), 'qerr',ik['error'],'opening',s.gripper_openings()['gripper'],'steps',s.steps,'success',s.status()['success'])\n return not s.status()['done']\ndef move_object(target, rel, duration=.45,label='object'):\n tcp=mul(target,inv(rel))\n return move_tool(tcp, None, duration,label)\ndef interp_obj_path(a,b,rel,n=5,duration=.3,label='path'):\n for i in range(1,n+1):\n target=interp_pose(a,b,i/n)\n if not move_object(target,rel,duration,f'{label}{i}/{n}'):\n return False\n return True\nqdown=np.array([0.,1.,0.,0.])\n# preposition and descend\nmove_tool(np.r_[.3244,.4873,.96,qdown],0,.8,'pregrasp')\nmove_tool(np.r_[.3244,.4873,.866,qdown],0,.7,'grasp')\n# close while stationary\nmove_tool(pose_tcp(),220,.7,'close')\n# settle while holding\n# step same command for 0.2 seconds\nfor i in range(100):\n s.step(np.r_[qcmd,220]);Ntot+=1\n if s.status()['done']:break\nprint('after hold', 'tube',pose_body(),'tcp',pose_tcp(), 'success',s.status()['success'])\nrel=mul(inv(pose_tcp()),pose_body())\nprint('relative tool->tube',rel)\n# lift high, keep actual orientation\ncur=pose_body().copy(); high=cur.copy(); high[2]=1.06\nmove_object(high,rel,.8,'lift')\ncur=pose_body().copy()\n# horizontal path 7 steps\nend=cur.copy(); end[:2]=s.task.final_tar_tubepose.pos[:2];end[2]=1.06\nif interp_obj_path(cur,end,rel,n=7,duration=.32,label='transfer'):\n cur=pose_body().copy(); print('at target xy high',cur)\n # rotate at high, desired q\n finalq=s.task.final_tar_tubepose.quat.copy()\n rot=end.copy();rot[3:]=finalq\n # use interpolation from actual pose after transport\n interp_obj_path(cur,rot,rel,n=6,duration=.3,label='rotate')\n cur=pose_body().copy(); print('rotated',cur,'target',s.task.final_tar_tubepose.pos,s.task.final_tar_tubepose.quat)\n # lower into slot in 6 steps\n target=np.r_[s.task.final_tar_tubepose.pos,finalq]\n interp_obj_path(cur,target,rel,n=10,duration=.3,label='lower')\nprint('DONE status',s.status())\nprint('body',pose_body(),'target',s.task.final_tar_tubepose.pos, 'check',s.task.check())\nfrom PIL import Image\nfor cam in ['table_cam_front','table_cam_left']:\n Image.fromarray(s.render_frame(cam)).save('/app/output/test_'+cam+'.png')\ns.close()\nPY\npython /tmp/test_insert.py"}],"out":{"text":"pregrasp tcp [0.3265 0.4866 0.9629] tube [0.3244 0.4873 0.825 ] qerr {'tcp': (5.008554839516932e-08, 8.869793319857996e-07)} opening 0.08393112276849862 steps 400 success False\ngrasp tcp [0.3243 0.4873 0.8676] tube [0.3244 0.4873 0.8249] qerr {'tcp': (8.993626572238482e-06, 1.1923973699072114e-06)} opening 0.0839306374363776 steps 749 success False\nclose tcp [0.3243 0.4873 0.8675] tube [0.3243 0.4874 0.8258] qerr {'tcp': (5.5948544758225034e-05, 1.248371801871881e-05)} opening 0.013188517802505979 steps 1098 success False\nafter hold tube [ 3.24306123e-01 4.87457312e-01 8.25831056e-01 9.99997545e-01\n 2.12642290e-03 5.84315927e-04 -2.15903648e-04] tcp [ 3.24299197e-01 4.87288133e-01 8.67504034e-01 -4.63356314e-04\n 9.99999460e-01 -9.83107477e-05 -9.24713765e-04] success False\nrelative tool->tube [ 8.39684182e-05 -1.30568349e-04 4.16730335e-02 1.66320878e-03\n -9.99998552e-01 -1.15897439e-04 3.40286873e-04]\nlift tcp [0.3265 0.4863 1.0984] tube [0.3242 0.4876 1.0563] qerr {'tcp': (1.0282589985108747e-06, 1.330487886230037e-07)} opening 0.013343992678803152 steps 1598 success False\nTraceback (most recent call last):\n File \"/tmp/test_insert.py\", line 61, in \n if interp_obj_path(cur,end,rel,n=7,duration=.32,label='transfer'):\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/tmp/test_insert.py\", line 37, in interp_obj_path\n target=interp_pose(a,b,i/n)\n ^^^^^^^^^^^^^^^^^^^^\n File \"/tmp/test_insert.py\", line 14, in interp_pose\n q=np.zeros(4);mujoco.mju_slerp(q,a[3:],b[3:],t)\n ^^^^^^^^^^^^^^^^\nAttributeError: module 'mujoco' has no attribute 'mju_slerp'. Did you mean: 'mj_step'?\n","exit":[],"pics":[]},"tok":{"in":75607,"cached":53976,"out":2727,"think":1512,"usd":0.0046},"sim":{"submit":0,"reset":0}},{"id":22,"t":159.5,"say":"","calls":[{"kind":"shell","label":"sed -i 's/import numpy as np, mujoco, math/import numpy as np, mujoco, math\\nfrom kinematics import slerp/' /t","code":"sed -i 's/import numpy as np, mujoco, math/import numpy as np, mujoco, math\\nfrom kinematics import slerp/' /tmp/test_insert.py\nsed -i 's/q=np.zeros(4);mujoco.mju_slerp(q,a\\[3:\\],b\\[3:\\],t)/q=slerp(a[3:],b[3:],t)/' /tmp/test_insert.py\npython /tmp/test_insert.py"}],"out":{"text":"Traceback (most recent call last):\n File \"/tmp/test_insert.py\", line 3, in \n from kinematics import slerp\nModuleNotFoundError: No module named 'kinematics'\n","exit":[],"pics":[]},"tok":{"in":79071,"cached":75604,"out":336,"think":196,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":23,"t":170.6,"say":"","calls":[{"kind":"shell","label":"p='/tmp/test_insert.py'","code":"python - <<'PY'\np='/tmp/test_insert.py'\ns=open(p).read().replace('from kinematics import slerp\\n','')\ns=s.replace(\"def interp_pose(a,b,t):\\n p=a[:3]*(1-t)+b[:3]*t\\n q=slerp(a[3:],b[3:],t)\\n return np.r_[p,q]\",'''def quat_slerp(q0,q1,t):\n q0=q0.copy();q1=q1.copy(); dot=float(np.dot(q0,q1))\n if dot<0:q1=-q1;dot=-dot\n if dot>0.9995:\n q=q0+t*(q1-q0);return q/np.linalg.norm(q)\n th=np.arccos(np.clip(dot,-1,1));return (np.sin((1-t)*th)*q0+np.sin(t*th)*q1)/np.sin(th)\ndef interp_pose(a,b,t):\n p=a[:3]*(1-t)+b[:3]*t\n q=quat_slerp(a[3:],b[3:],t)\n return np.r_[p,q]''')\nopen(p,'w').write(s)\nPY\npython /tmp/test_insert.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":79476,"cached":79068,"out":404,"think":92,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":24,"t":225.3,"say":"","calls":[{"kind":"shell","label":"p='/tmp/test_insert.py'","code":"python - <<'PY'\np='/tmp/test_insert.py'\ns=open(p).read()\na=s.index(\"# lift high, keep actual orientation\")\nb=s.index(\"print('DONE status'\",a)\nnew='''# lift high, keep actual orientation\ncur=pose_body().copy(); high=cur.copy(); high[2]=1.06\nmove_object(high,rel,.8,'lift')\n# Work in the centrifuge slot axis: the distal body pose is final + 35 mm along tube z.\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\naxis=np.zeros(3);mujoco.mju_quat2Mat(np.zeros(9),final[3:])\nR=np.zeros(9);mujoco.mju_quat2Mat(R,final[3:]);axis=R.reshape(3,3)[:,2]\nprint('slot axis',axis,'distal',s.task.tar_tubepose.pos,'final',final[:3])\napproach=final.copy();approach[:3]=final[:3]+0.16*axis\nprint('approach pose',approach)\n# Translate across the bench while high, still holding current orientation.\ncur=pose_body().copy(); end=cur.copy();end[:3]=approach[:3]\ninterp_obj_path(cur,end,rel,n=9,duration=.28,label='transfer')\n# Rotate at high over the open rotor, then measure the held transform again.\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy(); rot=cur.copy();rot[3:]=final[3:]\ninterp_obj_path(cur,rot,rel,n=8,duration=.28,label='rotate')\n# Correct residual pose error from contact and gripper compliance at the approach height.\nrel=mul(inv(pose_tcp()),pose_body())\nmove_object(approach,rel,.5,'align_approach')\nrel=mul(inv(pose_tcp()),pose_body())\nprint('before insert actual',pose_body(),'target approach',approach,'rel',rel)\n# Insert along slot axis in 20 mm increments. Re-estimate the grasp transform each time.\nfor i,d in enumerate(np.linspace(.14,0.,8),1):\n target=final.copy();target[:3]=final[:3]+d*axis\n rel=mul(inv(pose_tcp()),pose_body())\n if not move_object(target,rel,.35,f'insert{i}/8'):\n break\n print(' target d',d,'err',np.linalg.norm(pose_body().pos if hasattr(pose_body(),'pos') else pose_body()[:3]-target[:3]))\n'''\ns=s[:a]+new+s[b:]\n# fix accidental precedence weird print line replace simpler\ns=s.replace(\"print(' target d',d,'err',np.linalg.norm(pose_body().pos if hasattr(pose_body(),'pos') else pose_body()[:3]-target[:3]))\",\"print(' target d',d,'err',np.linalg.norm(pose_body()[:3]-target[:3]))\")\nopen('/tmp/test_insert2.py','w').write(s)\nPY\npython /tmp/test_insert2.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":82806,"cached":79473,"out":6436,"think":5681,"usd":0.0044},"sim":{"submit":0,"reset":0}},{"id":25,"t":251.2,"say":"","calls":[{"kind":"robot","label":"# run prefix of test_insert2, change grip max and stop after rotate","code":"python - <<'PY'\n# run prefix of test_insert2, change grip max and stop after rotate\np=open('/tmp/test_insert2.py').read()\np=p.replace(\"220,.7,'close'\", \"255,.8,'close'\").replace('s.step(np.r_[qcmd,220])','s.step(np.r_[qcmd,255])')\na=p.index(\"# Work in the centrifuge slot axis\")\nb=p.index(\"# Correct residual pose error\",a)\np=p[:a]+'''# Rotate at the current high pose\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\nrel=mul(inv(pose_tcp()),pose_body())\nprint('before rot',pose_body(),'rel',rel)\ncur=pose_body().copy();rot=cur.copy();rot[3:]=final[3:]\ninterp_obj_path(cur,rot,rel,n=8,duration=.28,label='rotate')\nprint('after rot actual',pose_body(),'tcp',pose_tcp())\n'''+p[b:]\np=p.replace(\"print('DONE status'\", \"print('DONE status'\")\nopen('/tmp/test_grip255.py','w').write(p)\nPY\npython /tmp/test_grip255.py"}],"out":{"text":"pregrasp tcp [0.3265 0.4866 0.9629] tube [0.3244 0.4873 0.825 ] qerr {'tcp': (5.008554839516932e-08, 8.869793319857996e-07)} opening 0.08393112276849862 steps 400 success False\ngrasp tcp [0.3243 0.4873 0.8676] tube [0.3244 0.4873 0.8249] qerr {'tcp': (8.993626572238482e-06, 1.1923973699072114e-06)} opening 0.0839306374363776 steps 749 success False\nclose tcp [0.3243 0.4873 0.8675] tube [0.3243 0.4874 0.8255] qerr {'tcp': (5.5948544758225034e-05, 1.248371801871881e-05)} opening 0.012340040039304823 steps 1149 success False\nafter hold tube [ 3.24297820e-01 4.87447996e-01 8.25484505e-01 9.99998322e-01\n 1.60361390e-03 8.75364000e-04 -1.38263401e-04] tcp [ 3.24299048e-01 4.87288183e-01 8.67504012e-01 -4.63521111e-04\n 9.99999460e-01 -9.83443458e-05 -9.25052273e-04] success False\nrelative tool->tube [ 7.64843811e-05 -1.20866180e-04 4.20195674e-02 1.14013452e-03\n -9.99999348e-01 -3.88414687e-05 4.95935748e-05]\nlift tcp [0.3265 0.4863 1.0987] tube [0.3259 0.4865 1.0564] qerr {'tcp': (1.0778891888025218e-06, 1.3560360470413536e-07)} opening 0.012350553672084923 steps 1649 success False\nbefore rot [ 0.32589665 0.4864731 1.05635915 0.9997341 0.00197695 0.00967422\n -0.02083825] rel [-6.64082742e-04 -1.94982870e-04 4.23369885e-02 2.48887634e-03\n -9.99720198e-01 -2.09231105e-02 -1.07496486e-02]\nrotate1/8 tcp [0.3219 0.4877 1.0991] tube [0.326 0.4868 1.0572] qerr {'tcp': (5.3088119788596876e-06, 1.7893849074547254e-06)} opening 0.012340382187554226 steps 1789 success Fal\n… (165 characters left out) …\n1929 success False\nrotate3/8 tcp [0.3133 0.4906 1.0968] tube [0.3262 0.4866 1.0569] qerr {'tcp': (7.339319252350135e-06, 1.4673359474236967e-06)} opening 0.012332321930924924 steps 2069 success False\nrotate4/8 tcp [0.3092 0.4923 1.095 ] tube [0.3262 0.4866 1.0569] qerr {'tcp': (7.226711249953794e-06, 1.049723855332355e-06)} opening 0.012340150482452059 steps 2209 success False\nrotate5/8 tcp [0.3054 0.4942 1.0928] tube [0.3261 0.4866 1.0568] qerr {'tcp': (7.30041777795653e-06, 2.3177110161651803e-06)} opening 0.012345500607409104 steps 2349 success False\nrotate6/8 tcp [0.3019 0.4961 1.09 ] tube [0.3261 0.4866 1.0568] qerr {'tcp': (4.4615196957994394e-05, 1.5513207182029757e-05)} opening 0.012351146106500475 steps 2489 success False\nrotate7/8 tcp [0.2989 0.4982 1.0869] tube [0.3261 0.4866 1.0568] qerr {'tcp': (3.419400083092689e-05, 9.564851540778193e-06)} opening 0.01240819557767096 steps 2629 success False\nrotate8/8 tcp [0.2964 0.5002 1.0833] tube [0.3262 0.4866 1.0567] qerr {'tcp': (3.473316017941754e-05, 1.048739542593864e-05)} opening 0.012367053429331087 steps 2769 success False\nafter rot actual [ 0.32620672 0.48658403 1.0567059 0.88294715 -0.08513043 -0.41240179\n -0.20756179] tcp [ 0.29644525 0.50024016 1.083262 0.10388283 0.8859154 -0.17428579\n 0.41711716]\nTraceback (most recent call last):\n File \"/tmp/test_grip255.py\", line 73, in \n move_object(approach,rel,.5,'align_approach')\n ^^^^^^^^\nNameError: name 'approach' is not defined\n","exit":[],"pics":[]},"tok":{"in":92719,"cached":82803,"out":1645,"think":1322,"usd":0.0029},"sim":{"submit":0,"reset":0}},{"id":26,"t":266.0,"say":"","calls":[{"kind":"shell","label":"sed -e \"s/220,.7,'close'/255,.8,'close'/\" -e 's/np.r_\\[qcmd,220\\]/np.r_[qcmd,255]/' /tmp/test_insert2.py > /tm","code":"sed -e \"s/220,.7,'close'/255,.8,'close'/\" -e 's/np.r_\\[qcmd,220\\]/np.r_[qcmd,255]/' /tmp/test_insert2.py > /tmp/test_insert255.py\npython /tmp/test_insert255.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":95895,"cached":92716,"out":743,"think":638,"usd":0.0017},"sim":{"submit":0,"reset":0}},{"id":27,"t":308.5,"say":"","calls":[{"kind":"shell","label":"p='/tmp/test_insert255.py'","code":"python - <<'PY'\np='/tmp/test_insert255.py'\ns=open(p).read()\na=s.index(\"# Work in the centrifuge slot axis\")\nb=s.index(\"# Correct residual pose error\",a)\nnew='''# Compute the slot axis and approach point.\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\nR=np.zeros(9);mujoco.mju_quat2Mat(R,final[3:]);axis=R.reshape(3,3)[:,2]\napproach=final.copy();approach[:3]=final[:3]+0.16*axis\nprint('slot axis',axis,'approach',approach)\n# Rotate while still over the plate, well clear of the centrifuge.\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy();rot=cur.copy();rot[3:]=final[3:]\ninterp_obj_path(cur,rot,rel,n=8,duration=.28,label='rotate_above_plate')\nrel=mul(inv(pose_tcp()),pose_body())\n# Carry the correctly oriented tube high to a point along the slot axis.\ncur=pose_body().copy();end=cur.copy();end[:3]=approach[:3];end[3:]=final[3:]\ninterp_obj_path(cur,end,rel,n=9,duration=.32,label='transfer_final_orient')\n'''\ns=s[:a]+new+s[b:]\nopen('/tmp/test_insert_rotate_first.py','w').write(s)\nPY\npython /tmp/test_insert_rotate_first.py"}],"out":{"text":"pregrasp tcp [0.3265 0.4866 0.9629] tube [0.3244 0.4873 0.825 ] qerr {'tcp': (5.008554839516932e-08, 8.869793319857996e-07)} opening 0.08393112276849862 steps 400 success False\ngrasp tcp [0.3243 0.4873 0.8676] tube [0.3244 0.4873 0.8249] qerr {'tcp': (8.993626572238482e-06, 1.1923973699072114e-06)} opening 0.0839306374363776 steps 749 success False\nclose tcp [0.3243 0.4873 0.8675] tube [0.3243 0.4874 0.8255] qerr {'tcp': (5.5948544758225034e-05, 1.248371801871881e-05)} opening 0.012340040039304823 steps 1149 success False\nafter hold tube [ 3.24297820e-01 4.87447996e-01 8.25484505e-01 9.99998322e-01\n 1.60361390e-03 8.75364000e-04 -1.38263401e-04] tcp [ 3.24299048e-01 4.87288183e-01 8.67504012e-01 -4.63521111e-04\n 9.99999460e-01 -9.83443458e-05 -9.25052273e-04] success False\nrelative tool->tube [ 7.64843811e-05 -1.20866180e-04 4.20195674e-02 1.14013452e-03\n -9.99999348e-01 -3.88414687e-05 4.95935748e-05]\nlift tcp [0.3265 0.4863 1.0987] tube [0.3259 0.4865 1.0564] qerr {'tcp': (1.0778891888025218e-06, 1.3560360470413536e-07)} opening 0.012350553672084923 steps 1649 success False\nslot axis [-0.69895275 0.32532616 0.63688927] approach [-0.05938338 0.01068445 1.06053501 0.88330389 -0.09207651 -0.41602558\n -0.19549649]\nrotate_above_plate1/8 tcp [0.3219 0.4877 1.0991] tube [0.326 0.4868 1.0572] qerr {'tcp': (5.3088119788596876e-06, 1.7893849074547254e-06)} opening 0.012340382187554226 steps 1789 success False\nrotate_above_plate2/8 tcp [0.3176 0.489 1.0981] tube [0.3\n… (676 characters left out) …\n0607409104 steps 2349 success False\nrotate_above_plate6/8 tcp [0.3019 0.4961 1.09 ] tube [0.3261 0.4866 1.0568] qerr {'tcp': (4.4615196957994394e-05, 1.5513207182029757e-05)} opening 0.012351146106500475 steps 2489 success False\nrotate_above_plate7/8 tcp [0.2989 0.4982 1.0869] tube [0.3261 0.4866 1.0568] qerr {'tcp': (3.419400083092689e-05, 9.564851540778193e-06)} opening 0.01240819557767096 steps 2629 success False\nrotate_above_plate8/8 tcp [0.2964 0.5002 1.0833] tube [0.3262 0.4866 1.0567] qerr {'tcp': (3.473316017941754e-05, 1.048739542593864e-05)} opening 0.012367053429331087 steps 2769 success False\nTraceback (most recent call last):\n File \"/tmp/test_insert_rotate_first.py\", line 76, in \n interp_obj_path(cur,end,rel,n=9,duration=.32,label='transfer_final_orient')\n File \"/tmp/test_insert_rotate_first.py\", line 44, in interp_obj_path\n if not move_object(target,rel,duration,f'{label}{i}/{n}'):\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/tmp/test_insert_rotate_first.py\", line 40, in move_object\n return move_tool(tcp, None, duration,label)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/tmp/test_insert_rotate_first.py\", line 29, in move_tool\n raise RuntimeError((label,ik))\nRuntimeError: ('transfer_final_orient1/9', {'ok': False, 'q': [-1.151100841709482, -3.1013378682842987, 2.643173938048321, -1.8638741716932816, -1.0492362562704334, 1.019726619360206], 'error': {'tcp': (0.05132381403151252, 0.011383087526254927)}})\n","exit":[],"pics":[]},"tok":{"in":100116,"cached":95892,"out":4039,"think":3642,"usd":0.0035},"sim":{"submit":0,"reset":0}},{"id":28,"t":328.7,"say":"","calls":[{"kind":"shell","label":"sed -n '480,570p' /opt/tools/rcb_autobio.py && sed -n '1,160p' /opt/AutoBio/autobio/topp.py","code":"sed -n '480,570p' /opt/tools/rcb_autobio.py && sed -n '1,160p' /opt/AutoBio/autobio/topp.py"}],"out":{"text":"\n def fk(self, q, links=None) -> dict:\n \"\"\"Tool frames and camera-mount links (world frame; x y z + wxyz quaternion) for arm joint positions `q` (see\n kinematic_joints()); every other joint as at the start. Stateless: the simulation is not touched.\"\"\"\n self._fk0(q)\n names = list(links or (self.tcp_frames() + list(self._links())))\n return {n: self._link_pose(self._k0, n) for n in names}\n\n def tcp_frames(self) -> list:\n return [a.tcp for a in self.arms]\n\n def ik(self, targets: dict, seed=None, tol_pos_m: float = 1e-3, tol_rot_rad: float = 1e-2, max_iters: int = 300) -> dict:\n \"\"\"Arm joint positions that put tool frames at `targets` ({frame: [x, y, z, qw, qx, qy, qz]}, world frame):\n damped least squares on each arm's 6 joints within their ranges, no collision checking. `tol_rot_rad` >= 3.1\n ignores orientation. Returns {\"ok\", \"q\", \"error\": {frame: (pos_m, rot_rad)}}; q covers every arm (an arm\n without a target keeps its seed).\"\"\"\n mj, m = self._mj, self.model\n qadr = np.concatenate([a.qadr for a in self.arms])\n q = np.array(seed if seed is not None else self.data.qpos[qadr], dtype=np.float64).reshape(-1)\n if q.shape[0] != len(qadr):\n raise ValueError(f\"seed is {len(qadr)} joint positions\")\n errors, off = {}, 0\n jacp, jacr = np.zeros((3, m.nv)), np.zeros((3, m.nv))\n for a in self.arms:\n sl = slice(off, off + len(a.qadr))\n \n… (2,891 characters left out) …\n, \"unit\": j[\"unit\"], \"position_limits\": j[\"range\"],\n \"velocity_limit\": None, \"effort_limit\": (a[\"force_range\"][1] if a and a[\"force_range\"] else None),\n \"group\": f\"{j['arm']}:{j['group']}\",\n \"note\": f\"driven by the action entry `{a['name']}`\" if a else \"not driven by an action entry\",\n })\nfrom typing import Callable, List\nfrom dataclasses import dataclass\nimport numpy as np\nimport toppra as ta\nfrom kinematics import Pose\n\nclass Topp:\n # re-parameterize trajectory using TOPP-RA\n\n def __init__(self, dof: int, qc_vel: float, qc_acc: float, ik: Callable):\n self.dof = dof\n self.qc_vel = [(-qc_vel, qc_vel)] * self.dof\n self.qc_vel = ta.constraint.JointVelocityConstraint(np.array(self.qc_vel))\n self.qc_acc = [(-qc_acc, qc_acc)] * self.dof\n self.qc_acc = ta.constraint.JointAccelerationConstraint(np.array(self.qc_acc))\n self.ik: Callable = ik\n \n def jnt_traj(self, pose_path: List[Pose],):\n assert self.ik is not None, \"IK solver not set\"\n ss = np.linspace(0, 1, len(pose_path))\n jnts = [self.ik(pose.pos, pose.quat) for pose in pose_path]\n path = ta.SplineInterpolator(ss, jnts)\n instance = ta.algorithm.TOPPRA([self.qc_vel, self.qc_acc], path)\n return instance.compute_trajectory(0, 0)\n\n @staticmethod\n def query(traj: ta.interpolator.AbstractGeometricPath, t: float):\n t = np.clip(t, 0, traj.duration)\n return traj.eval(t)","exit":[],"pics":[]},"tok":{"in":105766,"cached":100113,"out":1363,"think":1283,"usd":0.0024},"sim":{"submit":0,"reset":0}},{"id":29,"t":348.1,"say":"","calls":[{"kind":"shell","label":"p='/tmp/test_insert_rotate_first.py'","code":"python - <<'PY'\np='/tmp/test_insert_rotate_first.py'\ns=open(p).read()\na=s.index(\"# Compute the slot axis and approach point.\")\nb=s.index(\"# Correct residual pose error\",a)\nnew='''# Compute the slot axis and target transforms.\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\nR=np.zeros(9);mujoco.mju_quat2Mat(R,final[3:]);axis=R.reshape(3,3)[:,2]\nhighgoal=final.copy();highgoal[:3]=final[:3];highgoal[2]=1.06\napproach=final.copy();approach[:3]=final[:3]+0.10*axis\nprint('slot axis',axis,'highgoal',highgoal,'approach',approach)\n# Transfer upright to a point high above the target, then align the tube to the rotor.\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy();end=cur.copy();end[:3]=highgoal[:3]\ninterp_obj_path(cur,end,rel,n=8,duration=.32,label='transfer_above_rotor')\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy();rot=cur.copy();rot[3:]=final[3:]\ninterp_obj_path(cur,rot,rel,n=8,duration=.28,label='rotate_above_rotor')\n# Correct residual pose error at height, using the latest measured grasp transform.\nrel=mul(inv(pose_tcp()),pose_body())\nmove_object(highgoal,rel,.5,'align_high')\nrel=mul(inv(pose_tcp()),pose_body())\n# Move outward along the tube axis to clear the rotor, then insert along that same slot axis.\nmove_object(approach,rel,.6,'approach_axis')\n'''\ns=s[:a]+new+s[b:]\n# avoid second align_approach duplicate is okay but target approach now; it will run after rel update\nopen('/tmp/test_insert_finalpath.py','w').write(s)\nPY\npython /tmp/test_insert_finalpath.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":108841,"cached":105763,"out":2838,"think":2314,"usd":0.0029},"sim":{"submit":0,"reset":0}},{"id":30,"t":388.9,"say":"The grasp is stable during lifting and transport. Insertion is currently stopping against geometry above the rotor, so I’m tracing the tube’s contacts and correcting the approach path before saving a candidate replay.","calls":[{"kind":"robot","label":"p='/tmp/test_insert_finalpath.py'","code":"python - <<'PY'\np='/tmp/test_insert_finalpath.py'\ns=open(p).read()\ns=s.replace(\"print(label,'tcp',np.round(pose_tcp()[:3],4),'tube',np.round(pose_body()[:3],4), 'qerr'\", \"print(label,'tcp',np.round(pose_tcp()[:3],4),'tube',np.round(pose_body()[:3],4),'tq',np.round(pose_body()[3:],3), 'qerr'\")\nneedle=\"print('before insert actual',pose_body(),'target approach',approach,'rel',rel)\"\ninsert='''print('before insert actual',pose_body(),'target approach',approach,'rel',rel)\n# summarize contacts touching either part of the tube\nids=set([s.task.tube.body_id,s.task.tube.cap_id])\nseen={}\nfor ci in range(s.data.ncon):\n c=s.data.contact[ci]; b1=int(s.model.geom_bodyid[c.geom1]);b2=int(s.model.geom_bodyid[c.geom2])\n if b1 in ids or b2 in ids:\n n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1);n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2)\n seen[(n1,n2)]=min(seen.get((n1,n2),1),float(c.dist))\nprint('tube contacts',seen)\nfrom PIL import Image\nImage.fromarray(s.render_frame('table_cam_left')).save('/app/output/at_approach.png')\n'''\ns=s.replace(needle,insert)\n# truncate after contact before insertion loop\nmarker=\"# Insert along slot axis in 20 mm increments. Re-estimate the grasp transform each time.\"\ns=s[:s.index(marker)]+\"print('ENDTEST',s.status())\\ns.close()\\n\"\nopen('/tmp/contacts.py','w').write(s)\nPY\npython /tmp/contacts.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":115324,"cached":108838,"out":3794,"think":3262,"usd":0.0038},"sim":{"submit":0,"reset":0}},{"id":31,"t":433.3,"say":"","calls":[{"kind":"shell","label":"rg -n 'slot|replicate|tube|rotor' /opt/AutoBio/autobio/model/instrument/centrifuge_eppendorf_5430.xml | head -","code":"rg -n 'slot|replicate|tube|rotor' /opt/AutoBio/autobio/model/instrument/centrifuge_eppendorf_5430.xml | head -100 && sed -n '1,180p' /opt/AutoBio/autobio/model/instrument/centrifuge_eppendorf_5430.xml"}],"out":{"text":"35: \n36: \n37: \n38: \n39: \n40: \n41: \n42: \n43: \n44: \n45: \n46: \n47: \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n","exit":[],"pics":[]},"tok":{"in":122322,"cached":115321,"out":3884,"think":3772,"usd":0.004},"sim":{"submit":0,"reset":0}},{"id":32,"t":456.9,"say":"","calls":[{"kind":"shell","label":"p='/tmp/test_insert_rotate_first.py'","code":"python - <<'PY'\np='/tmp/test_insert_rotate_first.py'\ns=open(p).read()\na=s.index(\"# Compute the slot axis and approach point.\")\nb=s.index(\"print('DONE status'\",a)\nnew='''# Use the distal tube pose as the opening alignment, then slide back along the slot axis.\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\ntar=np.r_[s.task.tar_tubepose.pos.copy(),s.task.tar_tubepose.quat.copy()]\nhigh=tar.copy();high[2]+=0.08\nprint('distal',tar,'final',final,'high',high)\n# Carry upright to directly above the slot, well above the housing.\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy();end=cur.copy();end[:3]=high[:3]\ninterp_obj_path(cur,end,rel,n=8,duration=.32,label='transfer_over_slot')\n# Rotate to the slot direction while still high.\nrel=mul(inv(pose_tcp()),pose_body())\ncur=pose_body().copy();rot=cur.copy();rot[3:]=final[3:]\ninterp_obj_path(cur,rot,rel,n=8,duration=.28,label='orient_over_slot')\n# Align body at a point above the distal end.\nrel=mul(inv(pose_tcp()),pose_body())\nmove_object(high,rel,.5,'align_high')\n# Descend vertically to the distal pose; update the grasp transform at each small step.\ncur=pose_body().copy()\nfor i,z in enumerate(np.linspace(high[2]-0.01,tar[2],8),1):\n t=tar.copy();t[2]=z\n rel=mul(inv(pose_tcp()),pose_body())\n if not move_object(t,rel,.3,f'descend{i}/8'):break\n# Slide the tube from distal to proximal along the rotor slot axis.\nfor i,u in enumerate(np.linspace(0.2,1.0,8),1):\n t=interp_pose(tar,final,u)\n rel=mul(inv(pose_tcp()),pose_body())\n if not move_object(t,rel,.3,f'seat{i}/8'):break\n'''\ns=s[:a]+new+s[b:]\nopen('/tmp/test_insert_distal.py','w').write(s)\nPY\npython /tmp/test_insert_distal.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":135351,"cached":122319,"out":3463,"think":2875,"usd":0.0046},"sim":{"submit":0,"reset":0}},{"id":33,"t":488.9,"say":"","calls":[{"kind":"look","label":"at_approach.png","code":"/app/output/at_approach.png"}],"out":{"text":"","exit":[],"pics":["autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s033_0.jpg"]},"tok":{"in":142658,"cached":135348,"out":1699,"think":1661,"usd":0.0031},"sim":{"submit":0,"reset":0}},{"id":34,"t":526.8,"say":"","calls":[{"kind":"robot","label":"writes servo_test.py","code":"cat > /tmp/servo_test.py <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco\n\ndef mul(a,b):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\ndef inv(a):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\ndef quat_slerp(q0,q1,t):\n q0=np.asarray(q0).copy();q1=np.asarray(q1).copy();dot=float(np.dot(q0,q1))\n if dot<0:q1=-q1;dot=-dot\n if dot>0.9995:\n q=q0+t*(q1-q0);return q/np.linalg.norm(q)\n th=np.arccos(np.clip(dot,-1,1));return (np.sin((1-t)*th)*q0+np.sin(t*th)*q1)/np.sin(th)\ndef interp(a,b,t):return np.r_[a[:3]*(1-t)+b[:3]*t,quat_slerp(a[3:],b[3:],t)]\ndef smooth(t):return t*t*(3-2*t)\n\ns=Session(instance='/app/instance.json')\nactions=[]\nqcmd=np.array(s.command()[:6]);grip=0\n\ndef body():\n p=s.task.tube.get_body_pose(s.data);return np.r_[p.pos,p.quat]\ndef tcp():return np.asarray(s.tcp_poses()['tcp'])\ndef armq():return s.data.qpos[list(s.task.arm.jnt_span)].copy()\ndef row(a):\n global actions\n actions.append(np.asarray(a,dtype=np.float64).copy())\n return s.step(actions[-1])\ndef move_tool(target, g, duration, label):\n global qcmd,grip\n ik=s.ik({'tcp':np.asarray(target).tolist()},seed=qcmd,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=600)\n if not ik['ok']: raise RuntimeError((label,ik))\n q1=np.asarray(ik['q']); q0=qcmd.copy(); N=max(2,round(duration/.002))\n for i in range(1,N+1):\n t=smooth(i/N)\n if not row(np.r_[q0*(1-t)+q1*t,g]): return False\n qcmd=q1;grip=g\n print(label,'body',np.round(body()[:3],4),'tcp',np.round(tcp()[:3],4),'grip',s.gripper_openings()['gripper'],'steps',s.steps)\n return True\n\ndef move_obj_servo(dest,duration,label,chunk=5):\n start=body().copy(); N=max(chunk,round(duration/.002)); print('servo begin',label,'from',np.round(start[:3],4),'to',np.round(dest[:3],4),'N',N)\n for k in range(0,N,chunk):\n take=min(chunk,N-k); t=smooth((k+take)/N); desired=interp(start,dest,t)\n rel=mul(inv(tcp()),body())\n target=mul(desired,inv(rel))\n ik=s.ik({'tcp':target.tolist()},seed=armq(),tol_pos_m=1e-4,tol_rot_rad=2e-3,max_iters=600)\n if not ik['ok']:\n print('IK fail',label,k,ik['error'], 'target',target)\n raise RuntimeError((label,k,ik))\n a=np.r_[np.asarray(ik['q']),255.]\n for j in range(take):\n if not row(a):\n print('done early',s.status());return False\n if (k//chunk)%max(1,int(.1*N/chunk))==0:\n p=body(); err=np.linalg.norm(p[:3]-desired[:3]);\n print(' ',label,k,'err',round(err,4),'p',np.round(p[:3],4),'q',np.round(p[3:],3))\n p=body(); print('servo end',label,'body',np.round(p[:3],5),'qerr',np.linalg.norm(p[3:]-dest[3:]),'poserr',np.linalg.norm(p[:3]-dest[:3]),'steps',s.steps)\n return True\n\nqdown=np.array([0.,1.,0.,0.])\nmove_tool([.3244,.4873,.96,*qdown],0,.8,'pre')\nmove_tool([.3244,.4873,.866,*qdown],0,.7,'grasp')\nmove_tool(tcp(),255,.8,'close')\nfor i in range(100):\n if not row(np.r_[qcmd,255.]):break\nprint('postclose',body(),tcp())\ncur=body().copy();cur[2]=1.06\nrel=mul(inv(tcp()),body()); tgoal=mul(cur,inv(rel))\nmove_tool(tgoal,255,1.0,'lift')\n# Transfer upright to high directly above the distal slot.\nfinal=np.r_[s.task.final_tar_tubepose.pos.copy(),s.task.final_tar_tubepose.quat.copy()]\ntar=np.r_[s.task.tar_tubepose.pos.copy(),s.task.tar_tubepose.quat.copy()]\nhigh=tar.copy(); high[2]=1.06; high[3:]=np.array([1.,0,0,0])\ncur=body().copy(); dst=high.copy();dst[3:]=cur[3:]\nmove_obj_servo(dst,2.0,'transfer',chunk=5)\n# Rotate at the distal target xy, high above the rotor.\nrot=high.copy();rot[3:]=final[3:]\nmove_obj_servo(rot,1.2,'rotate',chunk=5)\n# Hold / correct to exact pose after the rotation.\nmove_obj_servo(rot,.5,'rot_hold',chunk=5)\n# Lower vertically over the distal reference, then seat along its axis.\nmove_obj_servo(tar,1.6,'descend',chunk=5)\nmove_obj_servo(final,1.0,'seat',chunk=5)\nprint('FINAL',s.status(),body(),'target',final,'check',s.task.check(),'rows',len(actions))\nfrom PIL import Image\nfor cam in ['table_cam_front','table_cam_left']:\n Image.fromarray(s.render_frame(cam)).save('/app/output/servo_'+cam+'.png')\ns.close()\nPY\npython /tmp/servo_test.py"}],"out":{"text":"pre body [0.3244 0.4873 0.825 ] tcp [0.3265 0.4866 0.9629] grip 0.08393112276849862 steps 400\ngrasp body [0.3244 0.4873 0.8249] tcp [0.3243 0.4873 0.8676] grip 0.08393064738715776 steps 750\nclose body [0.3243 0.4874 0.8255] tcp [0.3243 0.4873 0.8675] grip 0.012340046727909112 steps 1150\npostclose [ 3.24292783e-01 4.87452856e-01 8.25524834e-01 9.99998159e-01\n 1.70347566e-03 8.80270297e-04 -7.66279119e-05] [ 3.24292398e-01 4.87285327e-01 8.67549900e-01 -4.64702147e-04\n 9.99999459e-01 -9.78718651e-05 -9.25929001e-04]\nlift body [0.3251 0.4868 1.0576] tcp [0.3257 0.4867 1.0999] grip 0.012362331820640796 steps 1750\nservo begin transfer from [0.3251 0.4868 1.0576] to [ 0.028 -0.03 1.06 ] N 1000\n transfer 0 err 0.0006 p [0.3254 0.4868 1.0582] q [ 1. 0.001 0.009 -0.022]\n transfer 100 err 0.0062 p [0.3187 0.4765 1.0577] q [ 0.995 0.002 0.009 -0.103]\n transfer 200 err 0.0122 p [0.299 0.4411 1.058 ] q [ 0.995 0.002 0.009 -0.103]\n transfer 300 err 0.0161 p [0.2674 0.3857 1.0583] q [ 0.989 0. 0.01 -0.15 ]\n transfer 400 err 0.0188 p [0.2283 0.3172 1.0587] q [ 0.976 -0. 0.01 -0.216]\n transfer 500 err 0.0199 p [0.1849 0.2414 1.059 ] q [ 0.966 -0.001 0.01 -0.258]\n transfer 600 err 0.0198 p [0.1409 0.165 1.0602] q [ 0.964 0.001 0.003 -0.267]\n transfer 700 err 0.0167 p [0.0989 0.0927 1.0596] q [ 0.969 -0.003 0.011 -0.246]\n transfer 800 err 0.013 p [0.064 0.0326 1.0597] q [ 0.978 -0.001 0.011 -0.209]\n transfer 900 err 0.0078 p [ 0.0391 -0.01 1.0\n… (2,059 characters left out) …\n.004 p [ 0.0281 -0.027 1.0629] q [ 0.868 0.039 -0.35 -0.35 ]\nservo end rot_hold body [ 0.04383 -0.02756 1.06787] qerr 0.2602232495586178 poserr 0.017857387319163247 steps 3600\nservo begin descend from [ 0.0438 -0.0276 1.0679] to [ 0.028 -0.03 0.9809] N 800\n descend 0 err 0.0048 p [ 0.0411 -0.0257 1.0644] q [ 0.89 -0.038 -0.414 -0.185]\n descend 80 err 0.002 p [ 0.0442 -0.0261 1.0661] q [ 0.861 0.011 -0.427 -0.277]\n descend 160 err 0.0027 p [ 0.0431 -0.0263 1.0603] q [ 0.851 0.018 -0.429 -0.301]\n descend 240 err 0.0033 p [ 0.0414 -0.0266 1.0511] q [ 0.861 0.002 -0.427 -0.278]\n descend 320 err 0.0038 p [ 0.0393 -0.0269 1.0397] q [ 0.869 -0.018 -0.425 -0.254]\n descend 400 err 0.005 p [ 0.0373 -0.0274 1.0281] q [ 0.877 -0.036 -0.423 -0.226]\n descend 480 err 0.0157 p [ 0.0408 -0.0153 1.0107] q [ 0.91 -0.051 -0.385 0.146]\nIK fail descend 525 {'tcp': (0.0029174685516584697, 0.00029751528964716556)} target [ 0.07813051 -0.07929864 0.95024876 0.12169782 -0.16977916 -0.32477053\n -0.92243633]\nTraceback (most recent call last):\n File \"/tmp/servo_test.py\", line 83, in \n move_obj_servo(tar,1.6,'descend',chunk=5)\n File \"/tmp/servo_test.py\", line 50, in move_obj_servo\n raise RuntimeError((label,k,ik))\nRuntimeError: ('descend', 525, {'ok': False, 'q': [-1.7283503684467425, 0.19191322777090472, -1.711909570616789e-08, 0.6380009248132303, -1.4394255303255352, -2.6707047340543375], 'error': {'tcp': (0.0029174685516584697, 0.00029751528964716556)}})\n","exit":[],"pics":[]},"tok":{"in":144741,"cached":142655,"out":6051,"think":4493,"usd":0.0047},"sim":{"submit":0,"reset":0}},{"id":35,"t":555.8,"say":"## AutoBio insertion checkpoint\n\n### Progress\n\n- The frozen instance loads correctly: `slot_id == 8`, with the existing tube in slot 23.\n- The task check uses the tube body’s base position only: distance under 5 mm from `final_tar_tubepose`, with z between 0.955 and 0.961 m. Orientation is not checked.\n- No successful trajectory has been found or saved yet. `/app/output/trajectory.npz` and `/app/output/gen.py` still need to be produced.\n- The user authorized repeated resets and retries; the 3600 s budget remains ample.\n\n### Key poses and grasp\n\n- Source tube base: approximately `[0.3244, 0.4873, 0.8245]`, identity quaternion.\n- Grasp pose that worked: TCP at `[0.3244, 0.4873, 0.866]`, quaternion `[0, 1, 0, 0]`.\n- Opening the gripper to 0 and closing to 255 works. The tube lifts reliably; raising the TCP to about z=1.10 brings the tube base to about z=1.056.\n- At 255, gripper opening is about 12.3 mm. The grasp is adequate for lifting and upright transport, but the tube slips when rotated or pushed during insertion.\n- Final target body pose: position `[0.05244906, -0.04136773, 0.95863272]`, quaternion `[0.88330389, -0.09207651, -0.41602558, -0.19549649]`.\n- Distal target body pose: `[0.02798571, -0.02998132, 0.98092385]`, same quaternion. The slot axis is `[-0.69895275, 0.32532616, 0.63688927]`; the two target positions differ by 35 mm along that axis.\n\n### What has been tried\n\nSeveral scripts in `/tmp` contain experiments; the most recent is `/tmp/servo_test.py`. Generated images are in `/app/output/`, including `at_approach.png`.\n\n- Upright lift and transport to above the rotor work.\n- Rotating the tube while gripping can work temporarily, but the cap grasp slips under longer rotations and insertion forces.\n- Approaching along the slot axis from far above led to positional drift or blockage.\n- Approaching the distal target vertically, then moving to the final target, also drifted during orientation and descent.\n- The latest feedback attempt recomputed the TCP target every 5 physics steps. It became unstable around the rotor: the tube orientation drifted, and IK failed during descent with about 2.9 mm position error. This likely needs larger update intervals and continuity from the previous IK command; seeding from live joint state allowed branch changes near singularities.\n\n### Next steps\n\n1. Improve feedback trajectory generation: try 20–25 physics steps per IK update and seed each IK solve from the previous commanded joint target.\n2. Keep the successful pickup and upright transfer. Experiment with a slower, better constrained orientation change and insertion from the distal pose.\n3. Monitor tube pose, gripper contacts, and rotor angle during insertion to distinguish tube slip from rotor or instrument contact.\n4. Once `s.task.check()` succeeds, immediately save with `Session.save_trajectory(...)`, then replay twice with the provided CLI. Leave the generating script at `/app/output/gen.py`.","calls":[],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":149306,"cached":null,"out":2331,"think":1600,"usd":0.0198},"sim":{"submit":0,"reset":0}},{"id":36,"t":557.8,"say":"I’ll continue from the pickup and pose experiments, first checking the existing scripts and current task geometry, then I’ll iterate until a saved trajectory passes the replay check.","calls":[{"kind":"shell","label":"ls -la /app/output && ls -la /tmp/*servo* /tmp/*traj* 2>/dev/null","code":"ls -la /app/output && ls -la /tmp/*servo* /tmp/*traj* 2>/dev/null"}],"out":{"text":"total 488\ndrwxr-xr-x 1 root root 4096 Oct 10 08:52 .\ndrwxr-xr-x 1 root root 4096 Oct 10 08:43 ..\n-rw-r--r-- 1 root root 65659 Oct 10 08:52 at_approach.png\n-rw-r--r-- 1 root root 2814 Oct 10 08:54 rcb_session_log.jsonl\n-rw-r--r-- 1 root root 65739 Oct 10 08:45 start.png\n-rw-r--r-- 1 root root 65739 Oct 10 08:45 table_cam_front.png\n-rw-r--r-- 1 root root 58296 Oct 10 08:45 table_cam_left.png\n-rw-r--r-- 1 root root 65130 Oct 10 08:53 test_table_cam_front.png\n-rw-r--r-- 1 root root 64923 Oct 10 08:53 test_table_cam_left.png\n-rw-r--r-- 1 root root 78830 Oct 10 08:45 wrist_cam.png\n-rw-r--r-- 1 root root 3976 Oct 10 08:54 /tmp/servo_test.py\n","exit":[],"pics":[]},"tok":{"in":11387,"cached":10578,"out":212,"think":107,"usd":0.0003},"sim":{"submit":0,"reset":0}},{"id":37,"t":560.3,"say":"","calls":[{"kind":"shell","label":"cat /tmp/servo_test.py","code":"cat /tmp/servo_test.py"},{"kind":"shell","label":"cat /app/output/rcb_session_log.jsonl","code":"cat /app/output/rcb_session_log.jsonl"},{"kind":"shell","label":"sed -n '1,280p' /opt/AutoBio/autobio/load_centrifuge_5430.py","code":"sed -n '1,280p' /opt/AutoBio/autobio/load_centrifuge_5430.py"},{"kind":"shell","label":"rg -n \"centrifuge|final_tar_tubepose|slot_id|class Insert\" /opt/AutoBio/autobio","code":"rg -n \"centrifuge|final_tar_tubepose|slot_id|class Insert\" /opt/AutoBio/autobio"}],"out":{"text":"Warning: truncated output (original token count: 10674)\nTotal output lines: 4\n\n{\"i\":0,\"status\":\"fulfilled\",\"value\":{\"chunk_id\":\"cf706b\",\"wall_time_seconds\":0.000003432,\"exit_code\":0,\"original_token_count\":994,\"output\":\"from rcb_autobio import Session\\nimport numpy as np, mujoco\\n\\ndef mul(a,b):\\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\\ndef inv(a):\\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\\ndef quat_slerp(q0,q1,t):\\n q0=np.asarray(q0).copy();q1=np.asarray(q1).copy();dot=float(np.dot(q0,q1))\\n if dot<0:q1=-q1;dot=-dot\\n if dot>0.9995:\\n q=q0+t*(q1-q0);return q/np.linalg.norm(q)\\n th=np.arccos(np.clip(dot,-1,1));return (np.sin((1-t)*th)*q0+np.sin(t*th)*q1)/np.sin(th)\\ndef interp(a,b,t):return np.r_[a[:3]*(1-t)+b[:3]*t,quat_slerp(a[3:],b[3:],t)]\\ndef smooth(t):return t*t*(3-2*t)\\n\\ns=Session(instance='/app/instance.json')\\nactions=[]\\nqcmd=np.array(s.command()[:6]);grip=0\\n\\ndef body():\\n p=s.task.tube.get_body_pose(s.data);return np.r_[p.pos,p.quat]\\ndef tcp():return np.asarray(s.tcp_poses()['tcp'])\\ndef armq():return s.data.qpos[list(s.task.arm.jnt_span)].copy()\\ndef row(a):\\n global actions\\n actions.append(np.asarray(a,dtype=np.float64).copy())\\n return s.step(actions[-1])\\ndef move_tool(target, g, duration, label):\\n global qcmd,grip\\n ik=s.ik({'tcp':np.asarray(target).tolist()},seed=qcmd,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=600)\\n if not ik['ok']: raise RuntimeError((label\n… (37,105 characters left out) …\nge_mini.py:125: default_scene = SCENE_ROOT / \\\"mani_centrifuge_mini.xml\\\"\\n/opt/AutoBio/autobio/mani_centrifuge_mini.py:126: default_task = \\\"centrifuge_mini_close_lid\\\"\\n/opt/AutoBio/autobio/mani_centrifuge_mini.py:138: self.instrument = Centrifuge_mini('/centrifuge_tiangen_tgear_mini:')\\n/opt/AutoBio/autobio/mani_centrifuge_mini.py:153: 'prefix': 'close the lid of the centrifuge mini',\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:78: self.cap_id = model.body(f'{cap_prefix}centrifuge_15ml_cap').id\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:79: self.cap_jnt_adr = model.joint(f'centrifuge_15ml_cap').qposadr.item()\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:80: self.body_id = model.body(f'{body_prefix}centrifuge_15ml_body').id\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:81: self.body_jnt_adr = model.joint(f'centrifuge_15ml_body').qposadr.item()\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:120: cs = ContainerSystem(\\\"1/centrifuge_15ml_body-visual\\\")\\n/opt/AutoBio/autobio/mani_vortex_mixer.py:150: 'prefix': 'dual-Aloha arms mixing the centrifuge tube on the vortex mixer: one operates test tube, the other operates the vortex mixer',\\n/opt/AutoBio/autobio/collision_mesh.py:28:def centrifuge_rack(length, width, height, d_small, d_big, space, row: int, column: int):\\n/opt/AutoBio/autobio/collision_mesh.py:61:def centrifuge_plate(length, width, height, d, margin_l, margin_w, space_l, space_w, row: int, column: int):\\n\"}}","exit":[],"pics":[]},"tok":{"in":11900,"cached":11384,"out":226,"think":25,"usd":0.0003},"sim":{"submit":0,"reset":0}},{"id":38,"t":564.8,"say":"","calls":[{"kind":"shell","label":"python /tmp/servo_test.py > /tmp/servo_test.log 2>&1","code":"python /tmp/servo_test.py > /tmp/servo_test.log 2>&1"}],"out":{"text":"","exit":[1],"pics":[]},"tok":{"in":25775,"cached":11897,"out":514,"think":455,"usd":0.0021},"sim":{"submit":0,"reset":0}},{"id":39,"t":578.1,"say":"","calls":[{"kind":"shell","label":"tail -100 /tmp/servo_test.log","code":"tail -100 /tmp/servo_test.log"}],"out":{"text":"pre body [0.3244 0.4873 0.825 ] tcp [0.3265 0.4866 0.9629] grip 0.08393112276849862 steps 400\ngrasp body [0.3244 0.4873 0.8249] tcp [0.3243 0.4873 0.8676] grip 0.08393064738715776 steps 750\nclose body [0.3243 0.4874 0.8255] tcp [0.3243 0.4873 0.8675] grip 0.012340046727909112 steps 1150\npostclose [ 3.24292783e-01 4.87452856e-01 8.25524834e-01 9.99998159e-01\n 1.70347566e-03 8.80270297e-04 -7.66279119e-05] [ 3.24292398e-01 4.87285327e-01 8.67549900e-01 -4.64702147e-04\n 9.99999459e-01 -9.78718651e-05 -9.25929001e-04]\nlift body [0.3251 0.4868 1.0576] tcp [0.3257 0.4867 1.0999] grip 0.012362331820640796 steps 1750\nservo begin transfer from [0.3251 0.4868 1.0576] to [ 0.028 -0.03 1.06 ] N 1000\n transfer 0 err 0.0006 p [0.3254 0.4868 1.0582] q [ 1. 0.001 0.009 -0.022]\n transfer 100 err 0.0062 p [0.3187 0.4765 1.0577] q [ 0.995 0.002 0.009 -0.103]\n transfer 200 err 0.0122 p [0.299 0.4411 1.058 ] q [ 0.995 0.002 0.009 -0.103]\n transfer 300 err 0.0161 p [0.2674 0.3857 1.0583] q [ 0.989 0. 0.01 -0.15 ]\n transfer 400 err 0.0188 p [0.2283 0.3172 1.0587] q [ 0.976 -0. 0.01 -0.216]\n transfer 500 err 0.0199 p [0.1849 0.2414 1.059 ] q [ 0.966 -0.001 0.01 -0.258]\n transfer 600 err 0.0198 p [0.1409 0.165 1.0602] q [ 0.964 0.001 0.003 -0.267]\n transfer 700 err 0.0167 p [0.0989 0.0927 1.0596] q [ 0.969 -0.003 0.011 -0.246]\n transfer 800 err 0.013 p [0.064 0.0326 1.0597] q [ 0.978 -0.001 0.011 -0.209]\n transfer 900 err 0.0078 p [ 0.0391 -0.01 1.0\n… (2,059 characters left out) …\n.004 p [ 0.0281 -0.027 1.0629] q [ 0.868 0.039 -0.35 -0.35 ]\nservo end rot_hold body [ 0.04383 -0.02756 1.06787] qerr 0.2602232495586178 poserr 0.017857387319163247 steps 3600\nservo begin descend from [ 0.0438 -0.0276 1.0679] to [ 0.028 -0.03 0.9809] N 800\n descend 0 err 0.0048 p [ 0.0411 -0.0257 1.0644] q [ 0.89 -0.038 -0.414 -0.185]\n descend 80 err 0.002 p [ 0.0442 -0.0261 1.0661] q [ 0.861 0.011 -0.427 -0.277]\n descend 160 err 0.0027 p [ 0.0431 -0.0263 1.0603] q [ 0.851 0.018 -0.429 -0.301]\n descend 240 err 0.0033 p [ 0.0414 -0.0266 1.0511] q [ 0.861 0.002 -0.427 -0.278]\n descend 320 err 0.0038 p [ 0.0393 -0.0269 1.0397] q [ 0.869 -0.018 -0.425 -0.254]\n descend 400 err 0.005 p [ 0.0373 -0.0274 1.0281] q [ 0.877 -0.036 -0.423 -0.226]\n descend 480 err 0.0157 p [ 0.0408 -0.0153 1.0107] q [ 0.91 -0.051 -0.385 0.146]\nIK fail descend 525 {'tcp': (0.0029174685516584697, 0.00029751528964716556)} target [ 0.07813051 -0.07929864 0.95024876 0.12169782 -0.16977916 -0.32477053\n -0.92243633]\nTraceback (most recent call last):\n File \"/tmp/servo_test.py\", line 83, in \n move_obj_servo(tar,1.6,'descend',chunk=5)\n File \"/tmp/servo_test.py\", line 50, in move_obj_servo\n raise RuntimeError((label,k,ik))\nRuntimeError: ('descend', 525, {'ok': False, 'q': [-1.7283503684467425, 0.19191322777090472, -1.711909570616789e-08, 0.6380009248132303, -1.4394255303255352, -2.6707047340543375], 'error': {'tcp': (0.0029174685516584697, 0.00029751528964716556)}})\n","exit":[],"pics":[]},"tok":{"in":26347,"cached":25772,"out":56,"think":7,"usd":0.0004},"sim":{"submit":0,"reset":0}},{"id":40,"t":586.1,"say":"","calls":[{"kind":"shell","label":"rg -n \"class Centrifuge_Eppendorf_5430|class Centrifuge_5430|num_slots|slot_sites\" /opt/AutoBio/autobio/instru","code":"rg -n \"class Centrifuge_Eppendorf_5430|class Centrifuge_5430|num_slots|slot_sites\" /opt/AutoBio/autobio/instrument.py /opt/AutoBio/autobio -g'*.py'"},{"kind":"shell","label":"sed -n '1,240p' /opt/AutoBio/autobio/instrument.py","code":"sed -n '1,240p' /opt/AutoBio/autobio/instrument.py"},{"kind":"shell","label":"rg --files /opt/AutoBio/autobio/model | rg '5430|rotor' | head -50","code":"rg --files /opt/AutoBio/autobio/model | rg '5430|rotor' | head -50"},{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np\ns=Session(instance='/app/instance.json')\nprint('act',s.actuators())\nprint('state',s.state())\nprint('final',s.task.final_tar_tubepose)\nprint('distal',s.task.tar_tubepose)\nprint('tcp',s.tcp_poses())\nprint('tube',s.task.tube.get_body_pose(s.data))\nprint('rotor qpos',s.data.qpos[s.task.instrument.rotor_qposadr])\nprint('slot pose',s.task.instrument.get_slot_pose(s.data,8))\nprint('slot axis',s.task.instrument.get_slot_pose(s.data,8).quat)\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":29135,"cached":26344,"out":1119,"think":721,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":41,"t":593.9,"say":"","calls":[{"kind":"shell","label":"sed -n '1,280p' /opt/AutoBio/autobio/model/instrument/centrifuge_eppendorf_5430.xml && sed -n '1,120p' /opt/Au","code":"sed -n '1,280p' /opt/AutoBio/autobio/model/instrument/centrifuge_eppendorf_5430.xml && sed -n '1,120p' /opt/AutoBio/autobio/model/scene/insert_centrifuge_5430.xml"}],"out":{"text":"\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n","exit":[],"pics":[]},"tok":{"in":66398,"cached":63020,"out":707,"think":575,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":50,"t":786.3,"say":"The upright descent contacted the rotor and pushed the tube aside. I’ve mapped the slot’s insertion axis; the tube only needs that axis aligned, so I’ll try a rotation with no extra spin about the tube and enter along the slot axis.","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":70728,"cached":66395,"out":4482,"think":3924,"usd":0.0034},"sim":{"submit":0,"reset":0}},{"id":51,"t":791.0,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen3.log 2>&1","code":"python /app/output/gen.py > /tmp/gen3.log 2>&1"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":75234,"cached":70725,"out":198,"think":141,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":52,"t":823.5,"say":"","calls":[{"kind":"shell","label":"tail -85 /tmp/gen3.log && ls -lh /app/output/trajectory.npz 2>/dev/null","code":"tail -85 /tmp/gen3.log && ls -lh /app/output/trajectory.npz 2>/dev/null"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":75489,"cached":75231,"out":70,"think":6,"usd":0.0008},"sim":{"submit":0,"reset":0}},{"id":53,"t":839.4,"say":"","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np\ns=Session(instance='/app/instance.json')\na=[]; q=np.array(s.command()[:6]);\ndef row(x):\n a.append(np.r_[x, g]); return s.step(a[-1])\ndef mv(pos,gnew,sec):\n global q,g\n g=gnew\n ik=s.ik({'tcp':pos},seed=q,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800);print('ik',ik)\n q1=np.array(ik['q']);n=round(sec/.002);q0=q.copy()\n for i in range(1,n+1):\n t=i/n;t=t*t*(3-2*t);row(q0*(1-t)+q1*t)\n q=q1\n return np.array(s.tcp_poses()['tcp'])\ng=0;src=np.array([.3244,.4873,.8245]);qd=[0,1,0,0]\nprint('start',s.task.tube.get_body_pose(s.data))\nprint('pre',mv([src[0],src[1],.91,*qd],0,.8))\nprint('at',mv([src[0],src[1],.849,*qd],0,.5))\nprint('close',mv(list(s.tcp_poses()['tcp']),255,.8),'opening',s.gripper_openings())\nfor _ in range(100):row(q)\nprint('closed body',s.task.tube.get_body_pose(s.data),'open',s.gripper_openings())\nprint('lift',mv([src[0],src[1],.97,*qd],255,1.0),'opening',s.gripper_openings())\nprint('after lift',s.task.tube.get_body_pose(s.data),'open',s.gripper_openings())\nprint('status',s.status())\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":78554,"cached":75486,"out":2063,"think":1589,"usd":0.0022},"sim":{"submit":0,"reset":0}},{"id":54,"t":867.8,"say":"","calls":[{"kind":"look","label":"start.png","code":"/app/output/start.png"}],"out":{"text":"","exit":[],"pics":["autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s054_0.jpg"]},"tok":{"in":81616,"cached":78551,"out":3018,"think":2981,"usd":0.0027},"sim":{"submit":0,"reset":0}},{"id":55,"t":887.8,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":85018,"cached":81613,"out":2851,"think":2321,"usd":0.0027},"sim":{"submit":0,"reset":0}},{"id":56,"t":893.1,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen4.log 2>&1","code":"python /app/output/gen.py > /tmp/gen4.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":87893,"cached":85015,"out":82,"think":25,"usd":0.0013},"sim":{"submit":0,"reset":0}},{"id":57,"t":929.1,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:31063,chars:\"\",yield_time_ms:30000,max_output_tokens:1000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":88031,"cached":87890,"out":61,"think":13,"usd":0.0009},"sim":{"submit":0,"reset":0}},{"id":58,"t":931.8,"say":"","calls":[{"kind":"shell","label":"tail -30 /tmp/gen4.log && ls -lh /app/output/at_hover.png /app/output/after_orient.png 2>/dev/null","code":"tail -30 /tmp/gen4.log && ls -lh /app/output/at_hover.png /app/output/after_orient.png 2>/dev/null"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":88148,"cached":88028,"out":81,"think":9,"usd":0.0009},"sim":{"submit":0,"reset":0}},{"id":59,"t":935.6,"say":"","calls":[{"kind":"look","label":"at_hover.png","code":"/app/output/at_hover.png"},{"kind":"look","label":"after_orient.png","code":"/app/output/after_orient.png"}],"out":{"text":"","exit":[],"pics":["autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s059_0.jpg","autobio-insert-centrifuge-5430-i00-privileged--uc5stsz/s059_1.jpg"]},"tok":{"in":96575,"cached":88145,"out":84,"think":9,"usd":0.002},"sim":{"submit":0,"reset":0}},{"id":60,"t":970.8,"say":"","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json'); q=np.array(s.command()[:6]); rows=0","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco, collections\ns=Session(instance='/app/instance.json'); q=np.array(s.command()[:6]); rows=0\ndef body():\n p=s.task.tube.get_body_pose(s.data);return np.r_[p.pos,p.quat]\ndef tcp():return np.array(s.tcp_poses()['tcp'])\ndef mm(a,b):\n p=np.zeros(3);z=np.zeros(4);mujoco.mju_mulPose(p,z,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,z]\ndef inv(a):\n p=np.zeros(3);z=np.zeros(4);mujoco.mju_negPose(p,z,a[:3],a[3:]);return np.r_[p,z]\ndef step(a):\n global rows;rows+=1;return s.step(a)\ndef move(target,g,n):\n global q\n ik=s.ik({'tcp':target},seed=q,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800); assert ik['ok'],ik\n q1=np.array(ik['q']);q0=q.copy()\n for i in range(1,n+1):\n t=i/n;t=t*t*(3-2*t)\n if not step(np.r_[q0*(1-t)+q1*t,g]):return False\n q=q1;return True\ndef pos(goal,dur,chunk=10):\n start=body()[:3].copy();N=round(dur/.002)\n for k in range(0,N,chunk):\n take=min(chunk,N-k);t=(k+take)/N;t=t*t*(3-2*t);p=start*(1-t)+goal*t\n B=body();T=tcp();rel=mm(inv(T),B);w=mm(np.r_[p,B[3:]],inv(rel));ik=s.ik({'tcp':w.tolist()},seed=q,tol_pos_m=5e-5,tol_rot_rad=2e-3,max_iters=800);assert ik['ok'],ik\n q[:]=ik['q'];\n for j in range(take):\n if not step(np.r_[q,255.]):return False\n return True\nsrc=body();qd=[0,1,0,0]\nmove([src[0],src[1],.96,*qd],0,400);move([src[0],src[1],.866,*qd],0,350);move(tcp(),255,400)\nfor _ in range(100):step(np.r_[q,255.])\npos([src[0],src[1],1.105],2.)\nfor p in ([.27,.35,1.105],[.18,.20,1.105],[.10,.055,1.105]):pos(p,2.5)\n# approximate hover final from slot axis\nfin=s.task.final_tar_tubepose.pos.copy();dis=s.task.tar_tubepose.pos.copy();axis=(dis-fin)/np.linalg.norm(dis-fin);hover=np.r_[fin[:2]+.16*axis[:2],1.105]\npos(hover,2.5)\nprint('rows',rows,'body',body(),'tcp',tcp(),'q',q)\nct=collections.Counter()\nfor i in range(s.data.ncon):\n c=s.data.contact[i];g1,g2=c.geom1,c.geom2;b1=int(s.model.geom_bodyid[g1]);b2=int(s.model.geom_bodyid[g2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1);n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2)\n if (n1 and n1.startswith('/ur')) or (n2 and n2.startswith('/ur')):ct[(n1,n2)]+=1\nprint('robot contacts',ct)\nprint('some all',collections.Counter([(mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,int(s.model.geom_bodyid[s.data.contact[i].geom1])),mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,int(s.model.geom_bodyid[s.data.contact[i].geom2]))) for i in range(s.data.ncon)]).most_common(20))\ns.close()\nPY"}],"out":{"text":"Traceback (most recent call last):\n File \"\", line 33, in \n File \"\", line 24, in pos\nTypeError: can't multiply sequence by non-int of type 'float'\n","exit":[],"pics":[]},"tok":{"in":97404,"cached":96572,"out":5387,"think":4368,"usd":0.0038},"sim":{"submit":0,"reset":0}},{"id":61,"t":983.4,"say":"","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json'); q=np.array(s.command()[:6]); rows=0","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco, collections\ns=Session(instance='/app/instance.json'); q=np.array(s.command()[:6]); rows=0\ndef body():\n p=s.task.tube.get_body_pose(s.data);return np.r_[p.pos,p.quat]\ndef tcp():return np.array(s.tcp_poses()['tcp'])\ndef mm(a,b):\n p=np.zeros(3);z=np.zeros(4);mujoco.mju_mulPose(p,z,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,z]\ndef inv(a):\n p=np.zeros(3);z=np.zeros(4);mujoco.mju_negPose(p,z,a[:3],a[3:]);return np.r_[p,z]\ndef step(a):\n global rows;rows+=1;return s.step(a)\ndef move(target,g,n):\n global q\n ik=s.ik({'tcp':target},seed=q,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800); assert ik['ok'],ik\n q1=np.array(ik['q']);q0=q.copy()\n for i in range(1,n+1):\n t=i/n;t=t*t*(3-2*t)\n if not step(np.r_[q0*(1-t)+q1*t,g]):return False\n q=q1;return True\ndef pos(goal,dur,chunk=10):\n global q\n start=body()[:3].copy();goal=np.array(goal,dtype=float);N=round(dur/.002)\n for k in range(0,N,chunk):\n take=min(chunk,N-k);t=(k+take)/N;t=t*t*(3-2*t);p=start*(1-t)+goal*t\n B=body();T=tcp();rel=mm(inv(T),B);w=mm(np.r_[p,B[3:]],inv(rel));ik=s.ik({'tcp':w.tolist()},seed=q,tol_pos_m=5e-5,tol_rot_rad=2e-3,max_iters=800);assert ik['ok'],ik\n q[:]=ik['q'];\n for j in range(take):\n if not step(np.r_[q,255.]):return False\n return True\nsrc=body();qd=[0,1,0,0]\nmove([src[0],src[1],.96,*qd],0,400);move([src[0],src[1],.866,*qd],0,350);move(tcp(),255,400)\nfor _ in range(100):step(np.r_[q,255.])\npos([src[0],src[1],1.105],2.)\nfor p in ([.27,.35,1.105],[.18,.20,1.105],[.10,.055,1.105]):pos(p,2.5)\nfin=s.task.final_tar_tubepose.pos.copy();dis=s.task.tar_tubepose.pos.copy();axis=(dis-fin)/np.linalg.norm(dis-fin);hover=np.r_[fin[:2]+.16*axis[:2],1.105]\npos(hover,2.5)\nprint('rows',rows,'body',body(),'tcp',tcp(),'q',q)\nct=collections.Counter()\nfor i in range(s.data.ncon):\n c=s.data.contact[i];g1,g2=c.geom1,c.geom2;b1=int(s.model.geom_bodyid[g1]);b2=int(s.model.geom_bodyid[g2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1);n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2)\n if (n1 and n1.startswith('/ur')) or (n2 and n2.startswith('/ur')):ct[(n1,n2)]+=1\nprint('robot contacts',ct)\nctall=collections.Counter()\nfor i in range(s.data.ncon):\n c=s.data.contact[i];b1=int(s.model.geom_bodyid[c.geom1]);b2=int(s.model.geom_bodyid[c.geom2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1);n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2);ctall[(n1,n2)]+=1\nprint('all contacts',ctall.most_common(30))\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":102861,"cached":97401,"out":1129,"think":76,"usd":0.0022},"sim":{"submit":0,"reset":0}},{"id":62,"t":1016.9,"say":"","calls":[{"kind":"robot","label":"s=Session(instance='/app/instance.json');q=np.array(s.command()[:6])","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np,mujoco\ns=Session(instance='/app/instance.json');q=np.array(s.command()[:6])\ndef mm(a,b):\n p=np.zeros(3);r=np.zeros(4);mujoco.mju_mulPose(p,r,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,r]\ndef iv(a):\n p=np.zeros(3);r=np.zeros(4);mujoco.mju_negPose(p,r,a[:3],a[3:]);return np.r_[p,r]\ndef body():\n x=s.task.tube.get_body_pose(s.data);return np.r_[x.pos,x.quat]\ndef tcp():return np.asarray(s.tcp_poses()['tcp'])\ndef row(x):return s.step(x)\ndef mt(pos,g,sec):\n global q\n ik=s.ik({'tcp':pos},seed=q,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800);q1=np.array(ik['q']);q0=q.copy();n=round(sec/.002)\n for i in range(1,n+1):\n t=i/n;t=t*t*(3-2*t);row(np.r_[q0*(1-t)+q1*t,g])\n q=q1\nsrc=body();qd=[0,1,0,0]\nmt([src[0],src[1],.96,*qd],0,.8);mt([src[0],src[1],.866,*qd],0,.7);mt(tcp(),255,.8)\nfor _ in range(100):row(np.r_[q,255.])\ndef ps(goal,sec):\n global q\n start=body()[:3].copy();goal=np.asarray(goal);n=round(sec/.002);chunk=10\n for k in range(0,n,chunk):\n take=min(chunk,n-k);t=(k+take)/n;t=t*t*(3-2*t);p=start*(1-t)+goal*t;B=body();T=tcp();rel=mm(iv(T),B);w=mm(np.r_[p,B[3:]],iv(rel));ik=s.ik({'tcp':w.tolist()},seed=q,tol_pos_m=5e-5,tol_rot_rad=2e-3,max_iters=800);q[:]=ik['q']\n for _ in range(take):row(np.r_[q,255.])\nps([src[0],src[1],1.105],2.)\nfor p in ([.27,.35,1.105],[.18,.20,1.105],[.1,.055,1.105]):ps(p,2.5)\nfin=s.task.final_tar_tubepose.pos.copy();axis=(s.task.tar_tubepose.pos-fin);axis/=np.linalg.norm(axis);hover=np.r_[fin[:2]+.16*axis[:2],1.105];ps(hover,2.5)\nprint('at hover qpos',s.data.qpos[s.task.arm.jnt_span],'cmd',q)\nprint('body',body(),'tcp',tcp())\nc=axis[2];cross=np.cross([0,0,1],axis);qa=np.r_[np.sqrt((1+c)/2),cross/np.sqrt(2*(1+c))];g=np.r_[hover,qa];rel=mm(iv(tcp()),body());tg=mm(g,iv(rel))\nprint('axis',axis,'qalign',qa,'goalbody',g,'rel',rel,'tg',tg)\nik=s.ik({'tcp':tg.tolist()},seed=q,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800);print('ik',ik)\nprint('fk',s.fk(ik['q']))\nprint('tcp delta current to goal',tg-tcp())\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":104325,"cached":102858,"out":2447,"think":1535,"usd":0.0024},"sim":{"submit":0,"reset":0}},{"id":63,"t":1054.0,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco, collections\ns=Session(instance='/app/instance.json')\narmspan=list(s.task.arm.jnt_span); tube=s.task.tube\nqreset=s.data.qpos.copy();src=tube.get_body_pose(s.data);source=np.r_[src.pos,src.quat]; qdown=np.array([0,1,0,0.])\ntcp_pre=np.r_[source[:2],.866,qdown]\nik0=s.ik({'tcp':tcp_pre.tolist()},seed=s.command()[:6],tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800)\ns.data.qpos[armspan]=ik0['q'];mujoco.mj_forward(s.model,s.data)\ntcp=np.array(s.tcp_poses()['tcp']);b=tube.get_body_pose(s.data);body=np.r_[b.pos,b.quat]\ndef mm(a,b):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\ndef iv(a):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\nrel=mm(iv(tcp),body);print('grasp q',ik0['q'],'tcp',tcp,'body',body,'rel',rel)\nfin=s.task.final_tar_tubepose.pos.copy();axis=(s.task.tar_tubepose.pos-fin);axis/=np.linalg.norm(axis);entry=fin+.16*axis;hover=np.r_[entry[:2],1.105]\nc=axis[2];cross=np.cross([0,0,1.],axis);qa=np.r_[np.sqrt((1+c)/2),cross/np.sqrt(2*(1+c))]\n# initial upright target IK to create seed at hover\nbup=np.r_[hover,[1.,0,0,0]]; tcpup=mm(bup,iv(rel));ikup=s.ik({'tcp':tcpup.tolist()},seed=ik0['q'],tol_pos_m=1e-5,tol_rot_rad=1e-3,max_iters=1000);print('up',ikup)\nseed=np.array(ikup['q']);qpos0=s.data.qpos.copy();\nrotor=s.model.body('centrifuge_eppendorf_5430:rotor').id if False else None\nfor deg in range(0,360,15):\n phi=np.deg2rad(deg); qz=np.array([np.cos(phi/2),0,0,np.sin(phi/2)])\n qb=np.zeros(4);mujoco.mju_mulQuat(qb,qa,qz)\n bg=np.r_[hover,qb];tg=mm(bg,iv(rel));ik=s.ik({'tcp':tg.tolist()},seed=seed,tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=1000)\n if not ik['ok']:\n print(deg,'IKFAIL',ik['error']);continue\n s.data.qpos[:]=qpos0;s.data.qpos[armspan]=ik['q'];s.data.qpos[tube.pos_span]=bg[:3];s.data.qpos[tube.quat_span]=bg[3:];mujoco.mj_forward(s.model,s.data)\n ct=collections.Counter(); contacts=[]\n for i in range(s.data.ncon):\n ctc=s.data.contact[i]; g1,g2=ctc.geom1,ctc.geom2;b1=int(s.model.geom_bodyid[g1]);b2=int(s.model.geom_bodyid[g2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1) or str(b1);n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2) or str(b2)\n if n1.startswith('/ur:') or n2.startswith('/ur:'):\n ct[(n1,n2)]+=1\n print(deg,'q',np.round(ik['q'],2),'dq',round(np.linalg.norm(np.array(ik['q'])-seed),2),'urcontacts',sum(ct.values()),'pairs',ct.most_common(4))\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":107511,"cached":104322,"out":2879,"think":1863,"usd":0.0029},"sim":{"submit":0,"reset":0}},{"id":64,"t":1064.1,"say":"","calls":[{"kind":"shell","label":"sed -n '1,300p' /opt/AutoBio/autobio/kinematics.py","code":"sed -n '1,300p' /opt/AutoBio/autobio/kinematics.py"}],"out":{"text":"from dataclasses import dataclass\nimport numpy as np\nfrom grasp.hierarchy import build_hierarchy\nfrom grasp.quat import quatapply, quatinv, quatcompose\nimport mujoco\nimport jax\njax.config.update('jax_enable_x64', True)\njax.config.update('jax_platforms', 'cpu')\nimport jax.numpy as jnp\nfrom scipy.optimize import minimize\n\n@dataclass\nclass Pose:\n pos: np.ndarray\n quat: np.ndarray\n\ndef mul_pose(p1: Pose, p2: Pose) -> Pose:\n res_pos, res_quat = np.zeros(3), np.zeros(4)\n mujoco.mju_mulPose(\n res_pos, res_quat,\n p1.pos, p1.quat,\n p2.pos, p2.quat\n )\n return Pose(res_pos, res_quat)\n\ndef neg_pose(p: Pose) -> Pose:\n res_pos, res_quat = np.zeros(3), np.zeros(4)\n mujoco.mju_negPose(res_pos, res_quat, p.pos, p.quat)\n return Pose(res_pos, res_quat)\n\ndef slerp(q0: np.ndarray, q1: np.ndarray, amount=0.5):\n \"\"\"Spherical Linear Interpolation between quaternions.\n Implemented as described in https://en.wikipedia.org/wiki/Slerp\n\n Find a valid quaternion rotation at a specified distance along the\n minor arc of a great circle passing through any two existing quaternion\n endpoints lying on the unit radius hypersphere.\n\n This is a class method and is called as a method of the class itself rather than on a particular instance.\n\n Params:\n q0: first endpoint rotation as a Quaternion object\n q1: second endpoint rotation as a Quaternion object\n amount: interpolation parameter between 0 and 1. This describes the linea\n… (5,304 characters left out) …\nImplementedError:\n raise ValueError(format_error(\"Edge case detected\"))\n\n if solutions is None or len(solutions) == 0:\n raise ValueError(format_error(\"No valid IK solutions found\"))\n\n # Solution selection\n dists = np.linalg.norm(solutions - self.initial_qpos, axis=1)\n solution = solutions[np.argmin(dists)]\n\n if solution[4] == 0.0:\n print(format_error(\"Gimbal lock detected\"))\n\n self.initial_qpos = solution\n return solution\n\n\nclass FK:\n # General forward kinematics\n def __init__(self, dof: int, model, data, root: str, site: str):\n self.dof = dof\n self.model = model\n root = mujoco.mj_name2id(model, mujoco.mjtObj.mjOBJ_BODY, root)\n base = model.body_parentid[root]\n hierarchy = build_hierarchy(model, root)\n self.hierarchy = hierarchy\n site = hierarchy.site_name2id[site]\n self.site = site\n self.basepose = Pose(\n pos=data.xpos[base],\n quat=data.xquat[base]\n )\n \n def forward(self, qpos: np.ndarray) -> Pose:\n assert len(qpos) == self.dof\n _, _, site_poses = self.hierarchy.resolve_pose(qpos)\n site_pose = site_poses[self.site]\n res_pos = np.zeros(3)\n res_quat = np.zeros(4)\n mujoco.mju_mulPose(\n res_pos, res_quat,\n self.basepose.pos, self.basepose.quat,\n site_pose.pos, site_pose.quat\n )\n return Pose(res_pos, res_quat)","exit":[],"pics":[]},"tok":{"in":114158,"cached":107508,"out":726,"think":664,"usd":0.0023},"sim":{"submit":0,"reset":0}},{"id":65,"t":1074.8,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json');rng=np.random.default_rng(4)","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np, mujoco, collections\ns=Session(instance='/app/instance.json');rng=np.random.default_rng(4)\nsp=list(s.task.arm.jnt_span); tube=s.task.tube;qsave=s.data.qpos.copy();src=tube.get_body_pose(s.data);p0=np.r_[src.pos,src.quat];\n# grasp relationship from kinematic grasp pose\nqd=[0,1,0,0];ig=s.ik({'tcp':[src.pos[0],src.pos[1],.866,*qd]},seed=s.command()[:6],tol_pos_m=1e-5,tol_rot_rad=1e-3,max_iters=1000)\ns.data.qpos[sp]=ig['q'];mujoco.mj_forward(s.model,s.data);tcp=np.asarray(s.tcp_poses()['tcp']);b=tube.get_body_pose(s.data);body=np.r_[b.pos,b.quat]\ndef mm(a,b):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\ndef iv(a):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\nrel=mm(iv(tcp),body);fin=s.task.final_tar_tubepose.pos.copy();ax=s.task.tar_tubepose.pos-fin;ax/=np.linalg.norm(ax);entry=fin+.16*ax;pos=np.r_[entry[:2],1.105];cc=ax[2];cross=np.cross([0,0,1.],ax);qa=np.r_[np.sqrt((1+cc)/2),cross/np.sqrt(2*(1+cc))];bg=np.r_[pos,qa];tg=mm(bg,iv(rel));\n# Generate seeds: other known q; random bounded candidates; perturbations from solutions\nranges=s.model.jnt_range[:6]\nseeds=[np.array(s.command()[:6]),np.array(ig['q']),np.array([-2.45,-1.61,1.8,-1.27,-.8,-1.08]),np.array([-2.45,-1.61,-1.8,1.27,.8,2.06]),np.array([1.,-1.,1.,-1.,-1.5,0.])]\nfor center in list(seeds):\n for _ in range(4):seeds.append(np.clip(center+rng.normal(0,1.8,6),ranges[:,0]+.001,ranges[:,1]-.001))\nsolutions=[]\nfor j,seed in enumerate(seeds):\n ik=s.ik({'tcp':tg.tolist()},seed=seed,tol_pos_m=3e-5,tol_rot_rad=2e-3,max_iters=1000)\n if not ik['ok']:continue\n q=np.array(ik['q']);\n # save current but set robot and first tube target pose\n s.data.qpos[:]=qsave;s.data.qpos[sp]=q;s.data.qpos[tube.pos_span]=bg[:3];s.data.qpos[tube.quat_span]=bg[3:];mujoco.mj_forward(s.model,s.data)\n ct=collections.Counter()\n for i in range(s.data.ncon):\n c=s.data.contact[i];b1=int(s.model.geom_bodyid[c.geom1]);b2=int(s.model.geom_bodyid[c.geom2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1) or '';n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2) or ''\n if n1.startswith('/ur:') and 'centrifuge_eppendorf' in n2:ct[(n1,n2)]+=1\n if n2.startswith('/ur:') and 'centrifuge_eppendorf' in n1:ct[(n2,n1)]+=1\n score=sum(ct.values());key=tuple(np.round(q,2))\n if not any(x[0]==key for x in solutions): solutions.append((key,score,ct,j,np.linalg.norm(q-np.array(s.command()[:6]))))\nprint('goal tcp',tg,'seed count',len(seeds),'solutions',len(solutions))\nfor x in sorted(solutions,key=lambda x:(x[1],x[4]))[:30]:print(x)\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":117082,"cached":114155,"out":1486,"think":436,"usd":0.0023},"sim":{"submit":0,"reset":0}},{"id":66,"t":1111.3,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json'); sp=list(s.task.arm.jnt_span);tb=s.task.tube;qbase=s.data.qpos.copy()","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np,mujoco,collections\ns=Session(instance='/app/instance.json'); sp=list(s.task.arm.jnt_span);tb=s.task.tube;qbase=s.data.qpos.copy();src=tb.get_body_pose(s.data);qd=[0,1,0,0];ig=s.ik({'tcp':[src.pos[0],src.pos[1],.866,*qd]},seed=s.command()[:6],tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=800);s.data.qpos[sp]=ig['q'];mujoco.mj_forward(s.model,s.data);tcp=np.asarray(s.tcp_poses()['tcp']);b=tb.get_body_pose(s.data);bp=np.r_[b.pos,b.quat]\ndef mm(a,b):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_mulPose(p,q,a[:3],a[3:],b[:3],b[3:]);return np.r_[p,q]\ndef iv(a):\n p=np.zeros(3);q=np.zeros(4);mujoco.mju_negPose(p,q,a[:3],a[3:]);return np.r_[p,q]\nrel=mm(iv(tcp),bp);fin=s.task.final_tar_tubepose.pos.copy();ax=s.task.tar_tubepose.pos-fin;ax/=np.linalg.norm(ax);c=ax[2];cr=np.cross([0,0,1.],ax);qa=np.r_[np.sqrt((1+c)/2),cr/np.sqrt(2*(1+c))];seed=np.array(ig['q']);\nfor d in [.3,.25,.2,.16,.12,.10,.08,.06,.04,.02,0]:\n pos=fin+d*ax;bg=np.r_[pos,qa];tg=mm(bg,iv(rel));ik=s.ik({'tcp':tg.tolist()},seed=seed,tol_pos_m=2e-5,tol_rot_rad=1e-3,max_iters=1200)\n if not ik['ok']:print('d',d,'IKFAIL',ik['error']);continue\n seed=np.array(ik['q']);s.data.qpos[:]=qbase;s.data.qpos[sp]=seed;s.data.qpos[tb.pos_span]=pos;s.data.qpos[tb.quat_span]=qa;mujoco.mj_forward(s.model,s.data)\n hits=[]\n for i in range(s.data.ncon):\n ct=s.data.contact[i];b1=int(s.model.geom_bodyid[ct.geom1]);b2=int(s.model.geom_bodyid[ct.geom2]);n1=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b1) or '';n2=mujoco.mj_id2name(s.model,mujoco.mjtObj.mjOBJ_BODY,b2) or ''\n if (n1.startswith('/ur:') and 'centrifuge_eppendorf' in n2) or (n2.startswith('/ur:') and 'centrifuge_eppendorf' in n1): hits.append((n1,n2,ct.dist))\n print('d',round(d,3),'pos',np.round(pos,3),'q',np.round(seed,2),'hits',len(hits),'minDist',round(min([h[2] for h in hits],default=0),5),'pairs',collections.Counter((h[0],h[1]) for h in hits).most_common(3))\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":121015,"cached":117079,"out":5063,"think":4247,"usd":0.0042},"sim":{"submit":0,"reset":0}},{"id":67,"t":1130.7,"say":"","calls":[{"kind":"shell","label":"rg -n \"pinch|left_pad|right_pad\" /opt/AutoBio/autobio/model/robot/ur5e_gripper.xml /opt/AutoBio/autobio/model/","code":"rg -n \"pinch|left_pad|right_pad\" /opt/AutoBio/autobio/model/robot/ur5e_gripper.xml /opt/AutoBio/autobio/model/robot/2f85.xml"}],"out":{"text":"/opt/AutoBio/autobio/model/robot/2f85.xml:67: \n/opt/AutoBio/autobio/model/robot/2f85.xml:97: \n/opt/AutoBio/autobio/model/robot/2f85.xml:98: \n/opt/AutoBio/autobio/model/robot/2f85.xml:99: \n/opt/AutoBio/autobio/model/robot/2f85.xml:138: \n/opt/AutoBio/autobio/model/robot/2f85.xml:139: \n/opt/AutoBio/autobio/model/robot/2f85.xml:140: \n","exit":[],"pics":[]},"tok":{"in":127492,"cached":121012,"out":1953,"think":1866,"usd":0.003},"sim":{"submit":0,"reset":0}},{"id":68,"t":1134.3,"say":"","calls":[{"kind":"shell","label":"sed -n '45,160p' /opt/AutoBio/autobio/model/robot/2f85.xml && sed -n '120,260p' /opt/AutoBio/autobio/model/rob","code":"sed -n '45,160p' /opt/AutoBio/autobio/model/robot/2f85.xml && sed -n '120,260p' /opt/AutoBio/autobio/model/robot/ur5e_gripper.xml"}],"out":{"text":" \n \n \n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n18: \n20: \n26: \n\n\n \n\n \n\n \n \n \n \n\n \n \n \n\n \n \n \n \n \n \n\n \n \n \n \n \n\n \n\n","exit":[],"pics":[]},"tok":{"in":86759,"cached":85753,"out":782,"think":637,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":111,"t":1756.5,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":88387,"cached":86756,"out":4726,"think":4375,"usd":0.0034},"sim":{"submit":0,"reset":0}},{"id":112,"t":1765.0,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":93137,"cached":88384,"out":1068,"think":866,"usd":0.002},"sim":{"submit":0,"reset":0}},{"id":113,"t":1771.9,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":94229,"cached":93134,"out":360,"think":240,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":114,"t":1782.0,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":94613,"cached":94226,"out":292,"think":161,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":115,"t":1802.8,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen10.log 2>&1","code":"python /app/output/gen.py > /tmp/gen10.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":94929,"cached":94610,"out":66,"think":9,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":116,"t":1814.5,"say":"","calls":[{"kind":"shell","label":"tail -20 /tmp/gen10.log","code":"tail -20 /tmp/gen10.log"}],"out":{"text":"Traceback (most recent call last):\n File \"/app/output/gen.py\", line 252, in \n run()\n File \"/app/output/gen.py\", line 193, in run\n if not move_tcp(pre, 0, 0.8, 'pregrasp'):\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/app/output/gen.py\", line 65, in move_tcp\n raise RuntimeError((label, 'IK', ik))\nRuntimeError: ('pregrasp', 'IK', {'ok': False, 'q': [0.05701929756723972, 1.232578326057919, 2.3048532446743856e-09, -1.578565975724072, -3.08764330580775, -1.9162624817780425], 'error': {'tcp': (0.08074091676949811, 0.01932981454769894)}})\n","exit":[],"pics":[]},"tok":{"in":95052,"cached":94926,"out":55,"think":7,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":117,"t":1842.0,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nimport numpy as np, mujoco\nfrom rcb_autobio import Session\ns=Session(instance='/app/instance.json')\nqside=np.array([2**-.5,0,-2**-.5,0]); qt=np.array([2**-.5,0,0,2**-.5]); out=np.zeros(4); mujoco.mju_mulQuat(out,qt,qside); q=out\nv=np.zeros(3);mujoco.mju_rotVecQuat(v,[0,0,1],q)\nsrc=s.task.tube.get_body_pose(s.data).pos.copy()\nprint('src',src,'q',q,'approach',v,'tcp default',s.tcp_poses()['tcp'])\nfor label,p in [('sidepre',src+np.array([0,0,.042])+0.08*v),('sidegrasp',src+np.array([0,0,.042])),('above',src+np.array([0,0,.28])),('highside',src+np.array([0,0,.20])),('preclose',src+np.array([0,0,.042])+0.04*v)]:\n pose=np.r_[p,q]\n ik=s.ik({'tcp':pose.tolist()},seed=s.command()[:6],tol_pos_m=2e-5,tol_rot_rad=2e-3,max_iters=1000)\n print(label,p,ik)\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":95333,"cached":95049,"out":1236,"think":881,"usd":0.0016},"sim":{"submit":0,"reset":0}},{"id":118,"t":1855.0,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":97316,"cached":95330,"out":506,"think":385,"usd":0.0015},"sim":{"submit":0,"reset":0}},{"id":119,"t":1872.8,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen11.log 2>&1","code":"python /app/output/gen.py > /tmp/gen11.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":97846,"cached":97313,"out":82,"think":25,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":120,"t":1889.0,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:2672,chars:\"\",yield_time_ms:10000,max_output_tokens:1000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":97986,"cached":97843,"out":60,"think":12,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":121,"t":1912.0,"say":"","calls":[{"kind":"shell","label":"rg -n \"RESULT|SAVED|CONTACTS|pregrasp|grasp |picked|pose IK failure|seat .*err|end seat\" /tmp/gen11.log | tail","code":"rg -n \"RESULT|SAVED|CONTACTS|pregrasp|grasp |picked|pose IK failure|seat .*err|end seat\" /tmp/gen11.log | tail -35 && ls -l /app/output/trajectory.npz 2>/dev/null"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":98102,"cached":97983,"out":104,"think":7,"usd":0.001},"sim":{"submit":0,"reset":0}},{"id":122,"t":1935.8,"say":"The 90° grasp roll flips the tube while approaching, so I’ve discarded that variant. The end contacts are consistent with the gripper pads blocking the last part of insertion; I’m keeping the stable side orientation and moving the pinch point up to the cap center to give the gripper more clearance.","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":98906,"cached":98099,"out":2111,"think":1694,"usd":0.0021},"sim":{"submit":0,"reset":0}},{"id":123,"t":1941.9,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen12.log 2>&1","code":"python /app/output/gen.py > /tmp/gen12.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":101041,"cached":98903,"out":65,"think":8,"usd":0.0013},"sim":{"submit":0,"reset":0}},{"id":124,"t":1963.4,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:93793,chars:\"\",yield_time_ms:10000,max_output_tokens:1000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":101165,"cached":101038,"out":58,"think":10,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":125,"t":1980.6,"say":"","calls":[{"kind":"shell","label":"rg -n \"RESULT|SAVED|CONTACTS|pregrasp|grasp |picked|pose IK failure|end seat|seat [0-9]\" /tmp/gen12.log | tail","code":"rg -n \"RESULT|SAVED|CONTACTS|pregrasp|grasp |picked|pose IK failure|end seat|seat [0-9]\" /tmp/gen12.log | tail -35 && ls -l /app/output/trajectory.npz 2>/dev/null"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":101279,"cached":101162,"out":107,"think":7,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":126,"t":2003.7,"say":"The higher pinch point cleared the final contact enough for success. The trajectory has been saved at the first successful control step; I’m now checking that both fresh-process replays succeed in the same state.","calls":[{"kind":"shell","label":"python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repe","code":"python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repeat 2"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":102494,"cached":101276,"out":356,"think":236,"usd":0.0013},"sim":{"submit":0,"reset":0}},{"id":127,"t":2025.6,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:96763,chars:\"\",yield_time_ms:10000,max_output_tokens:3000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"{\"family\": \"insert_centrifuge_5430\", \"rule\": \"first\", \"success\": true, \"done\": true, \"reason\": \"success\", \"score\": 1.0, \"steps\": 11689, \"sim_time_s\": 23.378, \"resets\": 1, \"state_sha\": \"637c0dd8aad427e4\", \"instance_ok\": true, \"model_sha\": \"a45ad43e4c568577\", \"init_sha\": \"843c5cc8cbffee91\"}\n","exit":[],"pics":[]},"tok":{"in":102906,"cached":102491,"out":967,"think":919,"usd":0.0016},"sim":{"submit":0,"reset":0}},{"id":128,"t":2038.2,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:96763,chars:\"\",yield_time_ms:10000,max_output_tokens:3000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":104049,"cached":102903,"out":105,"think":57,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":129,"t":2057.5,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:96763,chars:\"\",yield_time_ms:10000,max_output_tokens:3000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"{\"family\": \"insert_centrifuge_5430\", \"rule\": \"first\", \"success\": true, \"done\": true, \"reason\": \"success\", \"score\": 1.0, \"steps\": 11689, \"sim_time_s\": 23.378, \"resets\": 2, \"state_sha\": \"637c0dd8aad427e4\", \"instance_ok\": true, \"model_sha\": \"a45ad43e4c568577\", \"init_sha\": \"843c5cc8cbffee91\"}\n{\"deterministic\": true}\n","exit":[0],"pics":[]},"tok":{"in":104210,"cached":104046,"out":127,"think":79,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":130,"t":2086.5,"say":"","calls":[{"kind":"shell","label":"p='/app/output/gen.py'","code":"cp /app/output/trajectory.npz /tmp/trajectory-good.npz && cp /app/output/gen.py /tmp/gen-good.py && python - <<'PY'\np='/app/output/gen.py'\ns=open(p).read()\ns=s.replace(\"0.8, 'pregrasp'\", \"0.6, 'pregrasp'\")\ns=s.replace(\"0.7, 'grasp'\", \"0.5, 'grasp'\")\ns=s.replace(\"255, 0.8, 'close'\", \"255, 0.6, 'close'\")\ns=s.replace(\"servo_body_position(lift, 2.0\", \"servo_body_position(lift, 1.5\")\ns=s.replace(\"servo_body_pose(orient_source, 4.0\", \"servo_body_pose(orient_source, 3.0\")\ns=s.replace(\"f'transfer{i}', 2.5\", \"f'transfer{i}', 2.0\")\ns=s.replace(\"servo_body_pose(entry_pose, 2.0\", \"servo_body_pose(entry_pose, 1.6\")\nopen(p,'w').write(s)\nPY\nrg -n \"move_tcp\\(|servo_body_position\\(lift|orient_source|transfer{i}|entry_pose|seat_pose\" /app/output/gen.py | tail -20"}],"out":{"text":"rg: regex parse error:\n (?:move_tcp\\(|servo_body_position\\(lift|orient_source|transfer{i}|entry_pose|seat_pose)\n ^\nerror: repetition quantifier expects a valid decimal\n","exit":[],"pics":[]},"tok":{"in":104519,"cached":104207,"out":1327,"think":1000,"usd":0.0017},"sim":{"submit":0,"reset":0}},{"id":131,"t":2098.6,"say":"","calls":[{"kind":"shell","label":"sed -n '185,255p' /app/output/gen.py && ls -l /tmp/trajectory-good.npz /tmp/gen-good.py","code":"sed -n '185,255p' /app/output/gen.py && ls -l /tmp/trajectory-good.npz /tmp/gen-good.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":105912,"cached":104516,"out":90,"think":20,"usd":0.0013},"sim":{"submit":0,"reset":0}},{"id":132,"t":2121.0,"say":"","calls":[{"kind":"edit","label":"a file","code":"patch));\n"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":106872,"cached":105909,"out":238,"think":142,"usd":0.0013},"sim":{"submit":0,"reset":0}},{"id":133,"t":2135.6,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen13.log 2>&1","code":"python /app/output/gen.py > /tmp/gen13.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":107134,"cached":106869,"out":92,"think":35,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":134,"t":2157.7,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:4946,chars:\"\",yield_time_ms:10000,max_output_tokens:1000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":107284,"cached":107131,"out":55,"think":7,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":135,"t":2180.1,"say":"","calls":[{"kind":"shell","label":"rg -n \"RESULT|SAVED|CONTACTS|IK failure|exception|seat .*err|end seat|steps\" /tmp/gen13.log | tail -25 && tail","code":"rg -n \"RESULT|SAVED|CONTACTS|IK failure|exception|seat .*err|end seat|steps\" /tmp/gen13.log | tail -25 && tail -15 /tmp/gen13.log && stat -c '%n %s %y' /app/output/trajectory.npz /tmp/trajectory-good.npz"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":107396,"cached":107281,"out":121,"think":12,"usd":0.0011},"sim":{"submit":0,"reset":0}},{"id":136,"t":2202.2,"say":"","calls":[{"kind":"shell","label":"python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repe","code":"python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repeat 2"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":109882,"cached":107393,"out":267,"think":194,"usd":0.0015},"sim":{"submit":0,"reset":0}},{"id":137,"t":2218.1,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:46635,chars:\"\",yield_time_ms:10000,max_output_tokens:3000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"{\"family\": \"insert_centrifuge_5430\", \"rule\": \"first\", \"success\": true, \"done\": true, \"reason\": \"success\", \"score\": 1.0, \"steps\": 9442, \"sim_time_s\": 18.884, \"resets\": 1, \"state_sha\": \"1825a2ce72ec4cd5\", \"instance_ok\": true, \"model_sha\": \"a45ad43e4c568577\", \"init_sha\": \"843c5cc8cbffee91\"}\n","exit":[],"pics":[]},"tok":{"in":110206,"cached":109879,"out":91,"think":43,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":138,"t":2238.2,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:46635,chars:\"\",yield_time_ms:10000,max_output_tokens:3000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"{\"family\": \"insert_centrifuge_5430\", \"rule\": \"first\", \"success\": true, \"done\": true, \"reason\": \"success\", \"score\": 1.0, \"steps\": 9442, \"sim_time_s\": 18.884, \"resets\": 2, \"state_sha\": \"1825a2ce72ec4cd5\", \"instance_ok\": true, \"model_sha\": \"a45ad43e4c568577\", \"init_sha\": \"843c5cc8cbffee91\"}\n{\"deterministic\": true}\n","exit":[0],"pics":[]},"tok":{"in":110474,"cached":110203,"out":62,"think":14,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":139,"t":2269.1,"say":"Both replays of the shorter trajectory reached the same success state. I’m making one more conservative timing pass while keeping this validated version backed up, then I’ll retain whichever version passes the same two replay checks.","calls":[{"kind":"shell","label":"p='/app/output/gen.py'","code":"cp /app/output/trajectory.npz /tmp/trajectory-good-short.npz && cp /app/output/gen.py /tmp/gen-good-short.py && python - <<'PY'\np='/app/output/gen.py'\ns=open(p).read()\ns=s.replace(\"0.6, 'pregrasp'\", \"0.4, 'pregrasp'\")\ns=s.replace(\"0.5, 'grasp'\", \"0.4, 'grasp'\")\ns=s.replace(\"255, 0.6, 'close'\", \"255, 0.5, 'close'\")\ns=s.replace(\"servo_body_position(lift, 1.5\", \"servo_body_position(lift, 1.2\")\ns=s.replace(\"servo_body_pose(orient_source, 3.0\", \"servo_body_pose(orient_source, 2.4\")\ns=s.replace(\"p, 2.0, f'transfer{i}'\", \"p, 1.5, f'transfer{i}'\")\ns=s.replace(\"servo_body_pose(entry_pose, 1.6\", \"servo_body_pose(entry_pose, 1.3\")\nopen(p,'w').write(s)\nPY\nsed -n '188,238p' /app/output/gen.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":110719,"cached":110471,"out":1246,"think":884,"usd":0.0018},"sim":{"submit":0,"reset":0}},{"id":140,"t":2279.5,"say":"","calls":[{"kind":"shell","label":"python /app/output/gen.py > /tmp/gen14.log 2>&1","code":"python /app/output/gen.py > /tmp/gen14.log 2>&1"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":112701,"cached":110716,"out":64,"think":7,"usd":0.0014},"sim":{"submit":0,"reset":0}},{"id":141,"t":2304.4,"say":"","calls":[{"kind":"shell","label":"waits for the running program's output","code":"const r = await tools.write_stdin({session_id:18101,chars:\"\",yield_time_ms:10000,max_output_tokens:1000});\ntext(JSON.stringify(r));\n"}],"out":{"text":"","exit":[0],"pics":[]},"tok":{"in":112825,"cached":112698,"out":56,"think":8,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":142,"t":2325.6,"say":"","calls":[{"kind":"shell","label":"rg -n \"RESULT|SAVED|CONTACTS|IK failure|end seat|pregrasp body|picked|seat [0-9]\" /tmp/gen14.log | tail -30 &&","code":"rg -n \"RESULT|SAVED|CONTACTS|IK failure|end seat|pregrasp body|picked|seat [0-9]\" /tmp/gen14.log | tail -30 && tail -12 /tmp/gen14.log && stat -c '%n %s %y' /app/output/trajectory.npz /tmp/trajectory-good-short.npz"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":112938,"cached":112822,"out":126,"think":10,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":143,"t":2357.0,"say":"The more aggressive timing pass missed the success window at the final insertion, while the prior 18.9-second trajectory still remains saved and passed both replays. I’m restoring its matching generator and keeping that validated version as the deliverable.","calls":[{"kind":"shell","label":"cp /tmp/gen-good-short.py /app/output/gen.py && ls -l /app/output/gen.py /app/output/trajectory.npz && rg -n \"","code":"cp /tmp/gen-good-short.py /app/output/gen.py && ls -l /app/output/gen.py /app/output/trajectory.npz && rg -n \"pregrasp'|grasp'|close'|lift,|orient_source,|transfer\\{i\\}|entry_pose|seat_pose\" /app/output/gen.py"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":115085,"cached":112935,"out":1635,"think":1471,"usd":0.0022},"sim":{"submit":0,"reset":0}},{"id":144,"t":2363.2,"say":"","calls":[{"kind":"shell","label":"p='/app/output/trajectory.npz'","code":"cmp -s /app/output/gen.py /tmp/gen-good-short.py && echo generator_matches_validated && sha256sum /app/output/trajectory.npz /tmp/trajectory-good-short.npz && python - <<'PY'\nimport numpy as np\np='/app/output/trajectory.npz'\nd=np.load(p)\nprint('arrays', [(k,d[k].shape,d[k].dtype) for k in d.files])\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":117012,"cached":115082,"out":177,"think":46,"usd":0.0015},"sim":{"submit":0,"reset":0}},{"id":145,"t":2390.2,"say":"The final trajectory is saved at [trajectory.npz](/app/output/trajectory.npz), with its generator at [gen.py](/app/output/gen.py).\n\nThe two-process replay check passed both times: success, 9,442 steps, and matching state hash `1825a2ce72ec4cd5`. The saved trajectory is about 19% shorter than the first successful version.","calls":[],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":117345,"cached":117009,"out":253,"think":166,"usd":0.0013},"sim":{"submit":0,"reset":0}}]}
\ No newline at end of file
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index 0000000000000000000000000000000000000000..c7be932413cf5c73b7f801077da62ea9197b980e
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+++ b/runs/autobio-insert-i00-privileged--wmbfpc6.json
@@ -0,0 +1 @@
+{"slug":"autobio-insert-i00-privileged--wmbfpc6","task":"autobio-insert-i00-privileged","bench":"autobio","mode":"privileged","run":"codex-gpt6_luna-xhigh","agent":"codex","model":"gpt-6-luna","effort":"xhigh","state":"success","success":1,"reward":{"success":1,"replay_success":1,"deterministic":1,"instance_ok":1,"progress":1.0,"n_actions":6068,"sim_steps":6068,"task_failure":0,"grader_error":0,"video_rendered":1,"agent_sessions":35,"agent_resets":0,"agent_sim_steps":216026,"agent_records":14,"agent_replays":18,"agent_cost_self_reported":1},"wall_s":909,"tokens":{"in":2608171,"cached":2483968,"out":42675,"usd":0.06},"task_text":"# AutoBio · insert — frozen instance\n\nYou control a **UR5e** arm (6 joints) with a Robotiq 2F-85 gripper, fixed to the bench, in AutoBio's simulated biology laboratory (MuJoCo 3.3.0), via Python, through joint\nposition targets.\n**Task:** Move the 50 mL centrifuge tube from the rack it stands in to the other rack, into the slot at row 0, column 4 (AutoBio's indices: `s.task.rack2.get_position(s.data, 0, 4, '50ml')`). Success at the first control step where the tube's body is within 15 mm (horizontally) of that slot's centre and its height is between 0.829 and 0.831 m (standing in a slot it is at 0.830 m).\n\nOn the bench: two 10-slot tube racks (2 rows of 5 each) side by side, with one capped 50 mL tube standing in one of them.\n\nAutoBio's own success test is `s.task.check()`: class `Insert` in `/opt/AutoBio/autobio/transfer_centrifuge_tube.py`.\nRobot Coding Bench evaluates it after every control step: the first step at which it holds ends the episode in success (AutoBio's own rule for this task; its time limit is lifted).\n\nThis is a *fixed scene instance*: the start pose, the objects and the goal never change between resets. You may reset and\nretry as many times as you want. Your deliverable is **one replayable trajectory**, not a general policy.\n\n## Deliverable\nWrite the final trajectory to `/app/output/trajectory.npz` with `Session.save_trajectory(...)` (below). It is replayed\nopen-loop from the same initial state in two fresh processes and scored 1 if both episodes end in success in the same\nstate, else 0. Also leave the script that produced it at `/app/output/gen.py`.\n\nYour time budget is 3600 s of wall clock. Save a trajectory as soon as you have one that works, improve it while\ntime remains, and do not stop early.\n\n## Tooling (already installed; run `python` from any directory)\n```python\nfrom rcb_autobio import Session\ns = Session(instance=\"/app/instance.json\") # a few seconds\ns.reset() # back to the frozen initial state (unlimited)\ns.state() # privileged view: qpos, qvel, ctrl, the targets in effect, tool poses, gripper openings, score\ns.task, s.model, s.data # AutoBio's task object (its scene helpers and check()), MuJoCo model / data: read them freely\ns.actuators() # the 7 controlled actuators in action order: name, unit, range, kp, kv, force range\ns.command() # the targets in effect (after reset: the ones that hold the initial pose)\ns.step(a) # one control step (2 ms) with 7 targets; s.step(a, n=25) holds them 25 steps; False once the episode is over\ns.status() # {'success', 'done', 'reason', 'score', 'steps', 'state_sha', 'instance_ok', ...}\ns.record_start(); ...; actions = s.record_stop() # (T, 7) targets, one row per control step executed\ns.replay(actions) # resets, replays open-loop until the episode ends or the rows do, returns status -> self-check\ns.save_trajectory(actions, \"/app/output/trajectory.npz\")\ns.tcp_poses() # tool frames (`tcp`): x y z + wxyz quaternion, world frame\ns.fk(q); s.ik({frame: pose}) # kinematics of the arm joints (s.kinematic_joints()), no physics, no collision check\ns.render_frame(\"table_cam_front\") # RGB uint8 (480, 640, 3); cameras: table_cam_front, table_cam_left, wrist_cam; s.render_depth(cam): metres\ns.render_video(actions, \"/app/output/check.mp4\", cameras=[\"table_cam_front\"])\ns.close() # release the renderer when you are done with a Session\n```\nThere are no ready-made motions: AutoBio's scripted experts are not in this image. Its other code is, under\n`/opt/AutoBio/autobio` (importable once a Session exists): the scene helpers `s.task` is built from, its inverse\nkinematics (`kinematics.py`) and its path timing (`topp.py`).\n\nCLI equivalent of the grader:\n`python /opt/tools/rcb_autobio.py replay --instance /app/instance.json --traj /app/output/trajectory.npz --repeat 2`\n\n## Conventions\n- Action: 7 position targets per control step, in this order: `shoulder_pan`, `shoulder_lift`, `elbow`, `wrist_1`, `wrist_2`, `wrist_3`, `2f85_fingers_actuator` (the Robotiq gripper: 0 open .. 255 closed). Arm joints are in rad. Each entry is the target of a PD position drive (stiffness, damping and force limit per entry: `s.actuators()`); a target outside the entry's range is clipped to it.\n- One control step is one physics step, 2 ms: a row is executed for exactly one step, so a motion lasting 1 s is 500\n rows (repeat a row to hold a target). Your wall-clock time is the budget (the reference replays at about\n 1000 control steps/s here); the one technical cap is 600000 rows per trajectory (1200 s of simulated\n time). A MuJoCo physics warning (an unstable simulation) ends the episode as a failure.\n- World frame: z up, metres; poses are x y z + wxyz quaternion; angles in rad.\n- Only the rows are replayed: anything else you change in `s.model` or `s.data` is lost in the grader's fresh process.\n","step_times":"recorded","sim_total":{"submit":0,"reset":0},"replay":"autobio-insert-i00-privileged--wmbfpc6/replay.mp4","replay_last":"autobio-insert-i00-privileged--wmbfpc6/replay_last.jpg","steps":[{"id":6,"t":0.0,"say":"I’ll inspect the scene helpers, initial robot and tube poses, and the task’s success check, then build and replay a trajectory against the frozen instance.","calls":[{"kind":"shell","label":"ls -la /app && sed -n '1,260p' /opt/AutoBio/autobio/transfer_centrifuge_tube.py && sed -n '1,220p' /opt/AutoBi","code":"ls -la /app && sed -n '1,260p' /opt/AutoBio/autobio/transfer_centrifuge_tube.py && sed -n '1,220p' /opt/AutoBio/autobio/kinematics.py"}],"out":{"text":"total 16\ndrwxr-xr-x 1 root root 4096 Oct 10 08:43 .\ndrwxr-xr-x 1 root root 4096 Oct 10 08:45 ..\n-rw-rw-r-- 1 root root 3676 Oct 10 08:43 instance.json\ndrwxr-xr-x 2 root root 4096 Oct 10 08:41 output\nimport numpy as np\nimport mujoco\nmujoco.mj_loadPluginLibrary('./libmjlab.so.3.3.0')\n\nfrom kinematics import Pose, slerp, IK\nfrom topp import Topp\nfrom task import Task, Expert, Manager, SCENE_ROOT\n\ndef set_gravcomp(body: mujoco.MjsBody):\n body.gravcomp = 1\n for child in body.bodies:\n set_gravcomp(child)\n\nclass GridSlot:\n\n def __init__(self, model: mujoco.MjModel, prefix: str):\n self.model = model\n self.prefix = prefix\n self.grids = dict()\n for i in range(self.model.nsite):\n site_name = mujoco.mj_id2name(self.model, mujoco.mjtObj.mjOBJ_SITE, i)\n if not site_name.startswith(prefix):\n continue\n parts = site_name.split('-')\n slot_type = parts[1]\n if slot_type not in self.grids:\n info = dict()\n info['origin'] = i\n user = self.model.site_user[i]\n info['rows'] = user[1]\n info['row_gap'] = user[2]\n info['cols'] = user[3]\n info['col_gap'] = user[4]\n info['height'] = user[5]\n self.grids[slot_type] = info\n else:\n print(f\"Duplicate grid slot type '{slot_type}' found in '{site_name}'\")\n\n if len(self.grids) == 0:\n \n… (12,640 characters left out) …\nImplementedError:\n raise ValueError(format_error(\"Edge case detected\"))\n\n if solutions is None or len(solutions) == 0:\n raise ValueError(format_error(\"No valid IK solutions found\"))\n\n # Solution selection\n dists = np.linalg.norm(solutions - self.initial_qpos, axis=1)\n solution = solutions[np.argmin(dists)]\n\n if solution[4] == 0.0:\n print(format_error(\"Gimbal lock detected\"))\n\n self.initial_qpos = solution\n return solution\n\n\nclass FK:\n # General forward kinematics\n def __init__(self, dof: int, model, data, root: str, site: str):\n self.dof = dof\n self.model = model\n root = mujoco.mj_name2id(model, mujoco.mjtObj.mjOBJ_BODY, root)\n base = model.body_parentid[root]\n hierarchy = build_hierarchy(model, root)\n self.hierarchy = hierarchy\n site = hierarchy.site_name2id[site]\n self.site = site\n self.basepose = Pose(\n pos=data.xpos[base],\n quat=data.xquat[base]\n )\n \n def forward(self, qpos: np.ndarray) -> Pose:\n assert len(qpos) == self.dof\n _, _, site_poses = self.hierarchy.resolve_pose(qpos)\n site_pose = site_poses[self.site]\n res_pos = np.zeros(3)\n res_quat = np.zeros(4)\n mujoco.mju_mulPose(\n res_pos, res_quat,\n self.basepose.pos, self.basepose.quat,\n site_pose.pos, site_pose.quat\n )\n return Pose(res_pos, res_quat)","exit":[],"pics":[]},"tok":{"in":12353,"cached":1792,"out":207,"think":74,"usd":0.0012},"sim":{"submit":0,"reset":0}},{"id":7,"t":8.0,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\nimport numpy as np\ns=Session(instance='/app/instance.json')\nprint('status',s.status())\nprint('state',s.state())\nprint('act',s.actuators())\nprint('cmd',s.command())\nprint('task info',s.task.task_info)\nprint('tube',s.task.object.get_body_pose(s.data).pos,s.task.object.get_body_pose(s.data).quat)\nprint('target',s.task.tube_end_pos)\nprint('rack1 grid',s.task.rack1.grids)\nprint('rack2 grid',s.task.rack2.grids)\nfor r in range(2):\n for c in range(5):\n print('slot',r,c,'src',s.task.rack1.get_position(s.data,r,c,'50ml'),'dst',s.task.rack2.get_position(s.data,r,c,'50ml'))\nprint('tcp',s.tcp_poses())\nprint('qpos',s.data.qpos[:6])\ns.close()\nPY"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":16883,"cached":1792,"out":343,"think":61,"usd":0.0017},"sim":{"submit":0,"reset":0}},{"id":8,"t":16.9,"say":"","calls":[{"kind":"shell","label":"rg -n \"centrifuge_50ml|2f85:pinch|rack|site.*50ml|/dev/null | head -100"}],"out":{"text":"","exit":[],"pics":[]},"tok":{"in":19566,"cached":16128,"out":277,"think":88,"usd":0.0006},"sim":{"submit":0,"reset":0}},{"id":9,"t":19.6,"say":"","calls":[{"kind":"shell","label":"s=Session(instance='/app/instance.json')","code":"python - <<'PY'\nfrom rcb_autobio import Session\ns=Session(instance='/app/instance.json')\nfrom transfer_centrifuge_tube import SCENE_ROOT\nprint(SCENE_ROOT)\nimport rcb_autobio, inspect\nprint(rcb_autobio.__file__)\nprint(inspect.getsource(Session.step)); print(inspect.getsource(Session.ik)); print(inspect.getsource(Session.replay))\ns.close()\nPY\nfind /opt/AutoBio -name insert.xml -o -name task.py"}],"out":{"text":"/opt/AutoBio/autobio/model/scene\n/opt/tools/rcb_autobio.py\n def step(self, a, n: int = 1) -> bool:\n \"\"\"One control step (2 ms) with the position targets `a` (one per controlled actuator), or `n` steps holding\n them. Returns False once the episode is over (then nothing is executed until reset()).\"\"\"\n a = np.asarray(a, dtype=np.float64).reshape(-1)\n if a.shape[0] != self.n_act or not np.all(np.isfinite(a)):\n raise ValueError(f\"an action is {self.n_act} finite numbers, got shape {a.shape}\")\n if self.done:\n return False\n c = np.clip(a, self.lo, self.hi)\n for _ in range(int(n)):\n self.data.ctrl[self.act_idx] = c\n self.task.manager.step()\n self.steps += 1\n self.total_steps += 1\n if self._rec is not None:\n self._rec.append(c.copy())\n self._judge()\n if not self.done and self.steps >= MAX_STEPS: # rule `final` is judged here; rule `first` has not succeeded\n self.done, self.reason = True, \"max_control_steps\"\n if self.done:\n break\n return not self.done\n\n def ik(self, targets: dict, seed=None, tol_pos_m: float = 1e-3, tol_rot_rad: float = 1e-2, max_iters: int = 300) -> dict:\n \"\"\"Arm joint positions that put tool frames at `targets` ({frame: [x, y, z, qw, qx, qy, qz]}, world frame):\n damped least squares on each arm's 6 joints within their ranges, no collision \n… (2,833 characters left out) …\ntcp] = (float(np.linalg.norm(e_p)), float(np.linalg.norm(e_r)))\n ok = bool(errors) and all(\n p < tol_pos_m and (tol_rot_rad >= 3.1 or r < tol_rot_rad) for p, r in errors.values()\n )\n return {\"ok\": ok, \"q\": q.tolist(), \"error\": errors}\n\n def replay(self, actions, video: str | None = None, cameras=None, fps: int = 25) -> dict:\n \"\"\"Reset, then execute the rows open-loop, one per control step, until the episode ends or the rows do; returns\n status(). This is what the grader does (in two fresh processes).\"\"\"\n A = self._rows(actions)\n rec, self._rec = self._rec, None\n self._reset_task()\n # real time at `fps`, or a time lapse when that would be more than 1500 frames\n frames, every = [], max(int(round(1.0 / (fps * CONTROL_DT))), -(-len(A) // 1500), 1)\n cams = list(cameras or self.default_cameras()) if video else []\n for k, row in enumerate(A):\n if video and k % every == 0:\n frames.append(np.hstack([self.render_frame(c) for c in cams]))\n if not self.step(row):\n break\n out = self.status()\n if video:\n frames.append(np.hstack([self.render_frame(c) for c in cams]))\n out[\"video\"] = _write_video(video, frames, fps)\n self._rec = rec\n _log({\"ev\": \"replay\", \"rows\": int(len(A)), \"success\": out[\"success\"]})\n return out\n\n/opt/AutoBio/autobio/task.py\n/opt/AutoBio/autobio/model/scene/insert.xml\n","exit":[],"pics":[]},"tok":{"in":19936,"cached":19200,"out":178,"think":21,"usd":0.0004},"sim":{"submit":0,"reset":0}},{"id":10,"t":27.3,"say":"","calls":[{"kind":"shell","label":"rg -n \"centrifuge_50ml|2f85:pinch|name=\\\"[12]/|site.*50ml\" /opt/AutoBio/autobio/model/scene/insert.xml | head ","code":"rg -n \"centrifuge_50ml|2f85:pinch|name=\\\"[12]/|site.*50ml\" /opt/AutoBio/autobio/model/scene/insert.xml | head -100 && sed -n '1,180p' /opt/AutoBio/autobio/model/scene/insert.xml && rg -n \"def record_start|def record_stop|def save_trajectory|def reset|def _reset_task|def _judge\" /opt/tools/rcb_autobio.py"}],"out":{"text":"17: \n31: \n37: \n38: \n39: \n40: \n42: \n43: \n44: \n\n\n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n191: def _reset_task(self) -> None:\n207: def reset(self) -> None:\n214: def _judge(self) -> None:\n270: def record_start(self) -> None:\n273: def record_stop(self) -> np.ndarray:\n307: def save_trajectory(self, actions, path: str, meta: dict | None = None) -> None:\n","exit":[],"pics":[]},"tok":{"in":21767,"cached":19200,"out":213,"think":60,"usd":0.0006},"sim":{"submit":0,"reset":0}},{"id":11,"t":29.6,"say":"","calls":[{"kind":"shell","label":"sed -n '180,340p' /opt/tools/rcb_autobio.py && cat /opt/AutoBio/autobio/model/object/centrifuge_50ml_screw.xml","code":"sed -n '180,340p' /opt/tools/rcb_autobio.py && cat /opt/AutoBio/autobio/model/object/centrifuge_50ml_screw.xml && sed -n '1,220p' /opt/AutoBio/autobio/model/object/centrifuge_10slot.gen.xml && rg -n \"name=\\\"2f85:pinch|pinch|finger\" /opt/AutoBio/autobio/model/robot/ur5e_gripper.xml | head -80"}],"out":{"text":" self._copy_state(self._k0)\n self._cams = self._camera_names()\n self.model_sha = self._model_sha()\n self.init_sha = self.state_sha()\n self.instance_ok = bool(\n self.model_sha == self.instance.get(\"model_sha\") and self.init_sha == self.instance.get(\"init_sha\")\n )\n atexit.register(self.close)\n _log({\"ev\": \"session_start\", \"family\": self.family, \"instance_ok\": self.instance_ok})\n\n # ------------------------------------------------------------------------------------------- episode\n def _reset_task(self) -> None:\n rng = np.random.get_state() # AutoBio seeds numpy's global generator in reset(); the caller's stream is kept\n with _in_root():\n self.info = self.task.reset(seed=self.seed)\n np.random.set_state(rng)\n self.model, self.data = self.task.model, self.task.data\n self.act_idx = np.asarray(self.info[\"action_indices\"], dtype=int).ravel()\n self.resets += 1\n self.steps = 0\n self.done = False\n self.success = False\n self.reason = None\n self._view_key = None\n self._drop_extras() # the render helpers hold references into the task's state\n self.score = float(self.task.check())\n\n def reset(self) -> None:\n \"\"\"Back to the frozen initial state (AutoBio's reset with the instance's seed).\"\"\"\n self._reset_task()\n if self._rec is not None:\n self._rec = []\n _log({\"ev\": \"reset\"})\n\n\n… (13,693 characters left out) …\n/>\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n","exit":[],"pics":[]},"tok":{"in":23436,"cached":21248,"out":184,"think":31,"usd":0.0005},"sim":{"submit":0,"reset":0}},{"id":12,"t":32.8,"say":"","calls":[{"kind":"shell","label":"rg -n \"pinch|fingers_actuator|\n99: \n107: \n113: \n\n \n\n