diff --git a/docker/luna_tutorial/vmount/notebooks/1_dataset-prep.ipynb b/docker/luna_tutorial/vmount/notebooks/1_dataset-prep.ipynb index 71cc6308..053d1d58 100644 --- a/docker/luna_tutorial/vmount/notebooks/1_dataset-prep.ipynb +++ b/docker/luna_tutorial/vmount/notebooks/1_dataset-prep.ipynb @@ -244,881 +244,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "/opt/conda/lib/python3.9/site-packages/distributed/node.py:182: UserWarning: Port 8787 is already in use.\n", - "Perhaps you already have a cluster running?\n", - "Hosting the HTTP server on port 41313 instead\n", - " warnings.warn(\n", - "[ ] | 0% Completed | 2.8s\u001b[32m2023-08-01 19:00:31.805\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 0.72s\u001b[0m\n", - "\u001b[32m2023-08-01 19:00:31.817\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 0.75s\u001b[0m\n", - "\u001b[32m2023-08-01 19:00:31.894\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 0.8s\u001b[0m\n", - "[ ] | 0% Completed | 3.4s\u001b[32m2023-08-01 19:00:32.506\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 1.42s\u001b[0m\n", - "[######################## ] | 60% Completed | 3.9s\u001b[32m2023-08-01 19:00:33.005\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 1.93s\u001b[0m\n", - "\u001b[32m2023-08-01 19:00:45.355\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.slide_etl\u001b[0m:\u001b[36mcli\u001b[0m:\u001b[36m93\u001b[0m - \u001b[1m id ... properties.aperio.Left\n", - "0 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 30.009504\n", - "1 01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 30.463894\n", - "2 01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 29.765535\n", - "3 01OV008-308ad404-7079-4ff8-8232-12ee2e ... 29.130108\n", - "4 01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 30.761105\n", + "\u001b[32m2023-08-03 01:50:46.648\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.slide_etl\u001b[0m:\u001b[36mcli\u001b[0m:\u001b[36m95\u001b[0m - \u001b[1m id ... properties.tiffslide.mpp-y\n", + "0 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.2501\n", + "1 01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 0.2501\n", + "2 01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 0.2501\n", + "3 01OV008-308ad404-7079-4ff8-8232-12ee2e ... 0.2501\n", + "4 01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 0.2501\n", "\n", "[5 rows x 70 columns]\u001b[0m\n", - "\u001b[32m2023-08-01 19:00:45.462\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.slide_etl\u001b[0m:\u001b[36mcli\u001b[0m:\u001b[36m105\u001b[0m - \u001b[1mWriting to parquet file\u001b[0m\n", - "\u001b[32m2023-08-01 19:00:45.508\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 45.04s\u001b[0m\n", - "2023-08-01 19:00:46,896 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,261 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,350 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,378 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2023-08-01 19:00:47,424 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,528 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,533 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,601 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,622 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,683 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,684 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2023-08-01 19:00:47,725 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,745 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,742 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,801 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,829 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,839 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,843 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,868 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,871 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,815 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2023-08-01 19:00:47,889 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,903 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,925 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,941 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,954 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:47,957 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2023-08-01 19:00:48,027 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:48,047 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:48,099 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:48,126 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n", - "2023-08-01 19:00:54,058 - distributed.nanny - WARNING - Worker process still alive after 3.199991149902344 seconds, killing\n", - "2023-08-01 19:00:54,059 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,060 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,061 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,061 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,062 - distributed.nanny - WARNING - Worker process still alive after 3.199999694824219 seconds, killing\n", - "2023-08-01 19:00:54,063 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing\n", - "2023-08-01 19:00:54,063 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,064 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,064 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing\n", - "2023-08-01 19:00:54,065 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,066 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,066 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,067 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,067 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,068 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing\n", - "2023-08-01 19:00:54,068 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,069 - distributed.nanny - WARNING - Worker process still alive after 3.199999389648438 seconds, killing\n", - "2023-08-01 19:00:54,070 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,071 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,072 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,073 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,073 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,074 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,074 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,075 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,076 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,077 - distributed.nanny - WARNING - Worker process still alive after 3.1999995422363288 seconds, killing\n", - "2023-08-01 19:00:54,078 - distributed.nanny - WARNING - Worker process still alive after 3.1999983215332035 seconds, killing\n", - "2023-08-01 19:00:54,080 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,081 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,082 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,083 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,084 - distributed.nanny - WARNING - Worker process still alive after 3.199998474121094 seconds, killing\n", - "2023-08-01 19:00:54,085 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,085 - distributed.nanny - WARNING - Worker process still alive after 3.1999989318847657 seconds, killing\n", - "2023-08-01 19:00:54,086 - distributed.nanny - WARNING - Worker process still alive after 3.1999958801269535 seconds, killing\n", - "2023-08-01 19:00:54,087 - distributed.nanny - WARNING - Worker process still alive after 3.199997711181641 seconds, killing\n", - "2023-08-01 19:00:54,088 - distributed.nanny - WARNING - Worker process still alive after 3.199998474121094 seconds, killing\n", - "2023-08-01 19:00:54,088 - distributed.nanny - WARNING - Worker process still alive after 3.1999992370605472 seconds, killing\n", - "2023-08-01 19:00:54,089 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,090 - distributed.nanny - WARNING - Worker process still alive after 3.199994201660157 seconds, killing\n", - "2023-08-01 19:00:54,090 - distributed.nanny - WARNING - Worker process still alive after 3.19999740600586 seconds, killing\n", - "2023-08-01 19:00:54,091 - distributed.nanny - WARNING - Worker process still alive after 3.1999990844726565 seconds, killing\n", - "2023-08-01 19:00:54,092 - distributed.nanny - WARNING - Worker process still alive after 3.1999975585937506 seconds, killing\n", - "2023-08-01 19:00:54,092 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,093 - distributed.nanny - WARNING - Worker process still alive after 3.1999990844726565 seconds, killing\n", - "2023-08-01 19:00:54,093 - distributed.nanny - WARNING - Worker process still alive after 3.1999978637695317 seconds, killing\n", - "2023-08-01 19:00:54,094 - distributed.nanny - WARNING - Worker process still alive after 3.1999986267089846 seconds, killing\n", - "2023-08-01 19:00:54,095 - distributed.nanny - WARNING - Worker process still alive after 3.1999987792968754 seconds, killing\n", - "2023-08-01 19:00:54,095 - distributed.nanny - WARNING - Worker process still alive after 3.1999978637695317 seconds, killing\n", - "2023-08-01 19:00:54,096 - distributed.nanny - WARNING - Worker process still alive after 3.199995727539063 seconds, killing\n", - "2023-08-01 19:00:54,096 - distributed.nanny - WARNING - Worker process still alive after 3.1999963378906253 seconds, killing\n", - "2023-08-01 19:00:54,097 - distributed.nanny - WARNING - Worker process still alive after 3.199995727539063 seconds, killing\n", - "2023-08-01 19:00:54,097 - distributed.nanny - WARNING - Worker process still alive after 3.1999966430664064 seconds, killing\n", - "2023-08-01 19:00:54,098 - distributed.nanny - WARNING - Worker process still alive after 3.19999740600586 seconds, killing\n", - "2023-08-01 19:00:54,099 - distributed.nanny - WARNING - Worker process still alive after 3.1999981689453127 seconds, killing\n", - "2023-08-01 19:00:54,099 - distributed.nanny - WARNING - Worker process still alive after 3.1999960327148442 seconds, killing\n", - "2023-08-01 19:00:54,099 - distributed.nanny - WARNING - Worker process still alive after 3.1999983215332035 seconds, killing\n", - "2023-08-01 19:00:54,100 - distributed.nanny - WARNING - Worker process still alive after 3.1999983215332035 seconds, killing\n", - "2023-08-01 19:00:54,101 - distributed.nanny - WARNING - Worker process still alive after 3.199996795654297 seconds, killing\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2023-08-01 19:00:54,102 - distributed.nanny - WARNING - Worker process still alive after 3.199996795654297 seconds, killing\r\n", - "2023-08-01 19:00:54,103 - distributed.nanny - WARNING - Worker process still alive after 3.1999868774414066 seconds, killing\r\n", - "2023-08-01 19:00:54,103 - distributed.nanny - WARNING - Worker process still alive after 3.1999980163574224 seconds, killing\r\n", - "2023-08-01 19:00:54,104 - distributed.nanny - WARNING - Worker process still alive after 3.1999981689453127 seconds, killing\r\n", - "2023-08-01 19:00:54,104 - distributed.nanny - WARNING - Worker process still alive after 3.199996795654297 seconds, killing\r\n", - "2023-08-01 19:00:54,105 - distributed.nanny - WARNING - Worker process still alive after 3.1999934387207034 seconds, killing\r\n", - "2023-08-01 19:00:54,105 - distributed.nanny - WARNING - Worker process still alive after 3.199996795654297 seconds, killing\r\n", - "2023-08-01 19:00:54,106 - distributed.nanny - WARNING - Worker process still alive after 3.1999971008300783 seconds, killing\r\n", - "2023-08-01 19:00:54,106 - distributed.nanny - WARNING - Worker process still alive after 3.1999980163574224 seconds, killing\r\n", - "2023-08-01 19:00:54,107 - distributed.nanny - WARNING - Worker process still alive after 3.1999951171875 seconds, killing\r\n", - "2023-08-01 19:00:54,107 - distributed.nanny - WARNING - Worker process still alive after 3.199994506835938 seconds, killing\r\n", - "2023-08-01 19:00:54,108 - distributed.nanny - WARNING - Worker process still alive after 3.199997711181641 seconds, killing\r\n", - "2023-08-01 19:00:54,108 - distributed.nanny - WARNING - Worker process still alive after 3.19999740600586 seconds, killing\r\n", - "2023-08-01 19:00:54,109 - distributed.nanny - WARNING - Worker process still alive after 3.1999975585937506 seconds, killing\r\n", - "2023-08-01 19:00:54,109 - distributed.nanny - WARNING - Worker process still alive after 3.199997711181641 seconds, killing\r\n", - "2023-08-01 19:00:54,110 - distributed.nanny - WARNING - Worker process still alive after 3.1999975585937506 seconds, killing\r\n", - "2023-08-01 19:00:54,110 - distributed.nanny - WARNING - Worker process still alive after 3.199994201660157 seconds, killing\r\n", - "2023-08-01 19:00:54,111 - distributed.nanny - WARNING - Worker process still alive after 3.1999969482421875 seconds, killing\r\n", - "2023-08-01 19:00:54,111 - distributed.nanny - WARNING - Worker process still alive after 3.1999958801269535 seconds, killing\r\n", - "2023-08-01 19:00:54,112 - distributed.nanny - WARNING - Worker process still alive after 3.1999986267089846 seconds, killing\r\n", - "2023-08-01 19:00:54,112 - distributed.nanny - WARNING - Worker process still alive after 3.199998474121094 seconds, killing\r\n" + "\u001b[32m2023-08-03 01:50:46.702\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.slide_etl\u001b[0m:\u001b[36mcli\u001b[0m:\u001b[36m107\u001b[0m - \u001b[1mWriting to parquet file\u001b[0m\n", + "\u001b[32m2023-08-03 01:50:46.726\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 4.82s\u001b[0m\n" ] } ], @@ -1157,9 +292,251 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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idproject_namecommentslide_sizeuuidurlchannel0_Rchannel0_Gchannel0_Bchannel1_R...properties.tiffslide.series-indexproperties.tiffslide.level[1].downsampleproperties.tiffslide.bounds-yproperties.aperio.Topproperties.tiffslide.level[3].tile-heightproperties.tiffslide.commentproperties.tiffslide.vendorproperties.aperio.Time Zoneproperties.aperio.OriginalHeightproperties.tiffslide.mpp-y
001OV002-bd8cdc70-3d46-40ae-99c4-90ef77PRO-12-123Example Ingestion Job237047223cd8c82fb-69d4-3ef2-8cb7-1eb0919c8d36file:///home/pollardw/vmount/PRO-12-123/data/t...0.6207220.6515000.4361790.344821...04.000000None19.529366256.0Aperio Image Library vFS90 01\\r\\n56000x54940 [...aperioGMT-05:00549400.2501
101OV002-ed65cf94-8bc6-492b-9149-adc16fPRO-12-123Example Ingestion Job240691747e60d567c-a5d6-3030-b890-49f454eeee6cfile:///home/pollardw/vmount/PRO-12-123/data/t...0.6286320.6136120.4778090.386583...04.000121None17.250914256.0Aperio Image Library vFS90 01\\r\\n53000x49887 [...aperioGMT-05:00498870.2501
201OV007-9b90eb78-2f50-4aeb-b010-d642f9PRO-12-123Example Ingestion Job26279633771a882f0-b708-3a57-b152-b5ddfffe84bafile:///home/pollardw/vmount/PRO-12-123/data/t...0.5718930.6598420.4873880.268574...04.000067None17.753954256.0Aperio Image Library vFS90 01\\r\\n114000x60210 ...aperioGMT-05:00602100.2501
301OV008-308ad404-7079-4ff8-8232-12ee2ePRO-12-123Example Ingestion Job20747941193604598-ede6-312b-b060-5375a9823e4bfile:///home/pollardw/vmount/PRO-12-123/data/t...0.5857550.6756880.4475890.343329...04.000000None18.320700NaNAperio Image Library vFS90 01\\r\\n55000x38728 [...aperioGMT-05:00387280.2501
401OV008-7579323e-2fae-43a9-b00f-a15c28PRO-12-123Example Ingestion Job215796305ae824866-e870-32b9-90d2-b261fe78ce94file:///home/pollardw/vmount/PRO-12-123/data/t...0.6182130.6661160.4172550.267862...04.000034None20.990768256.0Aperio Image Library vFS90 01\\r\\n44000x59309 [...aperioGMT-05:00593090.2501
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5 rows × 70 columns

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" + ], + "text/plain": [ + " id project_name comment \\\n", + "0 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 PRO-12-123 Example Ingestion Job \n", + "1 01OV002-ed65cf94-8bc6-492b-9149-adc16f PRO-12-123 Example Ingestion Job \n", + "2 01OV007-9b90eb78-2f50-4aeb-b010-d642f9 PRO-12-123 Example Ingestion Job \n", + "3 01OV008-308ad404-7079-4ff8-8232-12ee2e PRO-12-123 Example Ingestion Job \n", + "4 01OV008-7579323e-2fae-43a9-b00f-a15c28 PRO-12-123 Example Ingestion Job \n", + "\n", + " slide_size uuid \\\n", + "0 237047223 cd8c82fb-69d4-3ef2-8cb7-1eb0919c8d36 \n", + "1 240691747 e60d567c-a5d6-3030-b890-49f454eeee6c \n", + "2 262796337 71a882f0-b708-3a57-b152-b5ddfffe84ba \n", + "3 207479411 93604598-ede6-312b-b060-5375a9823e4b \n", + "4 215796305 ae824866-e870-32b9-90d2-b261fe78ce94 \n", + "\n", + " url channel0_R channel0_G \\\n", + "0 file:///home/pollardw/vmount/PRO-12-123/data/t... 0.620722 0.651500 \n", + "1 file:///home/pollardw/vmount/PRO-12-123/data/t... 0.628632 0.613612 \n", + "2 file:///home/pollardw/vmount/PRO-12-123/data/t... 0.571893 0.659842 \n", + "3 file:///home/pollardw/vmount/PRO-12-123/data/t... 0.585755 0.675688 \n", + "4 file:///home/pollardw/vmount/PRO-12-123/data/t... 0.618213 0.666116 \n", + "\n", + " channel0_B channel1_R ... properties.tiffslide.series-index \\\n", + "0 0.436179 0.344821 ... 0 \n", + "1 0.477809 0.386583 ... 0 \n", + "2 0.487388 0.268574 ... 0 \n", + "3 0.447589 0.343329 ... 0 \n", + "4 0.417255 0.267862 ... 0 \n", + "\n", + " properties.tiffslide.level[1].downsample properties.tiffslide.bounds-y \\\n", + "0 4.000000 None \n", + "1 4.000121 None \n", + "2 4.000067 None \n", + "3 4.000000 None \n", + "4 4.000034 None \n", + "\n", + " properties.aperio.Top properties.tiffslide.level[3].tile-height \\\n", + "0 19.529366 256.0 \n", + "1 17.250914 256.0 \n", + "2 17.753954 256.0 \n", + "3 18.320700 NaN \n", + "4 20.990768 256.0 \n", + "\n", + " properties.tiffslide.comment \\\n", + "0 Aperio Image Library vFS90 01\\r\\n56000x54940 [... \n", + "1 Aperio Image Library vFS90 01\\r\\n53000x49887 [... \n", + "2 Aperio Image Library vFS90 01\\r\\n114000x60210 ... \n", + "3 Aperio Image Library vFS90 01\\r\\n55000x38728 [... \n", + "4 Aperio Image Library vFS90 01\\r\\n44000x59309 [... \n", + "\n", + " properties.tiffslide.vendor properties.aperio.Time Zone \\\n", + "0 aperio GMT-05:00 \n", + "1 aperio GMT-05:00 \n", + "2 aperio GMT-05:00 \n", + "3 aperio GMT-05:00 \n", + "4 aperio GMT-05:00 \n", + "\n", + " properties.aperio.OriginalHeight properties.tiffslide.mpp-y \n", + "0 54940 0.2501 \n", + "1 49887 0.2501 \n", + "2 60210 0.2501 \n", + "3 38728 0.2501 \n", + "4 59309 0.2501 \n", + "\n", + "[5 rows x 70 columns]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "import os\n", "LUNA_HOME = os.environ[\"LUNA_HOME\"]\n", @@ -1201,11 +578,70 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": { "scrolled": false }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32m2023-08-03 01:51:01.237\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.dsa.dsa_api_handler\u001b[0m:\u001b[36msystem_check\u001b[0m:\u001b[36m447\u001b[0m - \u001b[1mSuccessfully connected to DSA\u001b[0m\n", + "\u001b[32m2023-08-03 01:51:01.263\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.pathology.dsa.dsa_api_handler\u001b[0m:\u001b[36mget_collection_uuid\u001b[0m:\u001b[36m32\u001b[0m - \u001b[34m\u001b[1mFound collections _accessLevel ... updated\n", + "_id ... \n", + "64c2d70a780496a4e184cb16 2 ... 2023-07-27T20:43:54.029000+00:00\n", + "\n", + "[1 rows x 9 columns]\u001b[0m\n", + "\u001b[32m2023-08-03 01:51:01.264\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.dsa.dsa_api_handler\u001b[0m:\u001b[36mget_collection_uuid\u001b[0m:\u001b[36m44\u001b[0m - \u001b[1mFound collection id=64c2d70a780496a4e184cb16 for collection=TCGA collection\u001b[0m\n", + "\u001b[32m2023-08-03 01:51:01.273\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.dsa.dsa_api_handler\u001b[0m:\u001b[36mget_slide_df\u001b[0m:\u001b[36m524\u001b[0m - \u001b[1mFound 5 slides!\u001b[0m\n", + "\u001b[32m2023-08-03 01:51:01.275\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.dsa_annotation_etl\u001b[0m:\u001b[36mdsa_annotation_etl\u001b[0m:\u001b[36m146\u001b[0m - \u001b[1mDashboard: http://192.168.176.4:8787/status\u001b[0m\n", + " _id ... annotation_name\n", + "slide_id ... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb18 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70c780496a4e184cb24 ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70e780496a4e184cb2e ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d710780496a4e184cb3a ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d711780496a4e184cb46 ... ov_regional\n", + "\n", + "[37 rows x 41 columns]\n", + "\u001b[32m2023-08-03 01:51:01.913\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.dsa_annotation_etl\u001b[0m:\u001b[36mdsa_annotation_etl\u001b[0m:\u001b[36m178\u001b[0m - 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"01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 01OV002-ed65cf94-8bc6-492b-9149-adc16f.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 01OV007-9b90eb78-2f50-4aeb-b010-d642f9.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 01OV008-308ad404-7079-4ff8-8232-12ee2e.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 01OV008-7579323e-2fae-43a9-b00f-a15c28.svs \n", + "\n", + " ... xmax ymin ymax \\\n", + "slide_id ... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 28661.0 40529.0 44372.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 33932.0 35713.0 39793.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 25542.0 18922.0 21735.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 30651.0 23202.0 26990.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 17365.0 26776.0 29672.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 23500.0 16457.0 19848.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... NaN NaN NaN \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 25783.0 4477.0 8874.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 19778.0 4925.0 8728.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 12487.0 28794.0 34122.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 17692.0 10030.0 16216.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... 15544.0 29416.0 33936.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f ... NaN NaN NaN \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 14698.0 38558.0 42478.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 90028.0 17627.0 20103.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 87377.0 27279.0 29663.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 97400.0 26598.0 28177.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 15718.0 14948.0 17225.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 13059.0 16566.0 18370.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... 7571.0 14199.0 15951.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 ... NaN NaN NaN \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 26787.0 7561.0 10402.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 21863.0 8532.0 11072.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 38687.0 18301.0 19409.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 38443.0 21701.0 23747.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 30451.0 14502.0 26079.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 16345.0 15568.0 16623.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... 24735.0 15599.0 17067.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e ... NaN NaN NaN \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 28755.0 19860.0 21427.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 15095.0 17451.0 19701.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 20765.0 13531.0 15375.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 17465.0 11547.0 13601.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 12733.0 26212.0 27987.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 22424.0 12780.0 13898.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... 21173.0 13423.0 14415.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 ... NaN NaN NaN \n", + "\n", + " bbox_area \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 13108473.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 9792000.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 5583805.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 14015600.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 11097472.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 6921031.0 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 NaN \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 24473702.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 19376285.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 11972016.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 37821204.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 14138560.0 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f NaN \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 30419200.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 5407584.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 3869232.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 2006909.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 4378671.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 1405316.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 2298624.0 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 NaN \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 3096690.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 2377440.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 620480.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 6187104.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 100279974.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 1446405.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 2058136.0 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e NaN \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 6387092.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 3636000.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 3444592.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 3037866.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 2254250.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 1357252.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 1126912.0 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 NaN \n", + "\n", + " x_coords \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [28211, 28328, 28587, 28630, 28655, 28661, 286... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [32252, 32252, 32220, 32164, 32140, 32108, 320... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [24180, 24136, 24063, 23980, 23874, 23813, 237... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [30133, 30073, 30005, 29951, 29904, 29857, 298... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [16525, 16597, 16701, 16781, 16845, 16901, 169... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [23389, 23435, 23463, 23481, 23500, 23500, 234... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [24143, 23829, 23663, 23611, 23532, 23436, 233... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [19647, 19691, 19735, 19778, 19778, 19770, 197... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [10388, 10374, 10334, 10294, 10253, 10240, 102... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [15745, 15904, 16062, 16235, 16351, 16452, 165... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [12928, 12872, 12808, 12776, 12728, 12704, 126... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [13850, 13762, 13682, 13626, 13570, 13490, 134... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [88952, 88912, 88848, 88792, 88752, 88704, 886... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [86674, 86674, 86668, 86633, 86621, 86598, 865... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [96999, 97030, 97061, 97098, 97141, 97178, 972... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [15605, 15605, 15605, 15616, 15627, 15632, 156... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [12688, 12721, 12764, 12791, 12817, 12844, 128... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [7039, 7015, 6963, 6859, 6739, 6679, 6639, 660... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [26095, 25925, 25819, 25786, 25754, 25721, 257... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [21846, 21863, 21863, 21846, 21822, 21806, 217... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [38411, 38419, 38439, 38459, 38469, 38481, 385... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [38390, 38362, 38326, 38229, 38197, 38145, 379... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [29241, 28934, 28506, 27955, 27741, 27557, 274... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [15784, 15840, 15909, 15949, 15973, 15993, 160... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [24707, 24700, 24634, 24544, 24508, 24485, 244... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [25997, 25965, 25932, 25876, 25856, 25836, 256... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [14583, 14511, 14384, 14256, 14074, 14026, 139... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [20485, 20513, 20549, 20577, 20601, 20621, 206... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [16776, 16766, 16756, 16730, 16704, 16678, 166... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [12443, 12462, 12494, 12514, 12542, 12599, 126... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [22006, 21967, 21911, 21859, 21826, 21821, 218... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [20741, 20725, 20677, 20621, 20577, 20561, 205... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "\n", + " y_coords \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [42225, 42546, 43126, 43261, 43379, 43607, 437... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [37097, 37001, 36897, 36745, 36713, 36689, 366... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [18972, 18978, 19017, 19078, 19161, 19217, 192... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [26411, 26465, 26506, 26532, 26553, 26566, 265... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [27088, 26992, 26896, 26840, 26816, 26808, 267... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 [18929, 19021, 19103, 19186, 19250, 19425, 194... \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [4477, 4477, 4503, 4521, 4556, 4591, 4608, 464... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [5125, 5370, 5605, 5876, 6076, 6190, 6268, 634... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [30395, 30328, 30207, 30059, 29938, 29830, 296... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [10073, 10059, 10030, 10030, 10073, 10117, 101... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f [29472, 29504, 29568, 29608, 29672, 29712, 298... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [41438, 41478, 41518, 41542, 41582, 41614, 416... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [17667, 17647, 17631, 17627, 17627, 17639, 176... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [27291, 27326, 27402, 27724, 27771, 27894, 279... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [26604, 26610, 26635, 26659, 26696, 26739, 268... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [16231, 16285, 16446, 16575, 16661, 16688, 167... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [16850, 16888, 16936, 16974, 17017, 17049, 171... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 [14211, 14211, 14231, 14275, 14335, 14371, 144... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [7561, 7569, 7634, 7683, 7740, 7813, 7862, 794... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [9151, 9224, 9273, 9371, 9452, 9501, 9542, 959... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [18675, 18637, 18573, 18533, 18519, 18507, 184... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [23685, 23701, 23712, 23735, 23739, 23747, 237... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [24267, 24536, 24804, 25071, 25190, 25309, 254... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [15684, 15673, 15662, 15658, 15651, 15647, 156... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e [16018, 15990, 15821, 15656, 15620, 15607, 155... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [19938, 19923, 19899, 19872, 19864, 19860, 198... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [17451, 17460, 17501, 17551, 17658, 17690, 177... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [14427, 14431, 14451, 14471, 14495, 14523, 145... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [11851, 11812, 11772, 11726, 11695, 11656, 116... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [26686, 26654, 26642, 26637, 26641, 26668, 267... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [13625, 13621, 13587, 13539, 13492, 13480, 134... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 [13671, 13651, 13615, 13579, 13555, 13539, 135... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "\n", + " slide_geojson \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 None \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f None \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 None \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e None \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 None \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "\n", + " collection_uuid \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 64c2d70a780496a4e184cb16 \n", + "\n", + " collection_name annotation_name \n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 TCGA collection ov_regional \n", + "\n", + "[37 rows x 41 columns]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "from pyarrow.parquet import read_table\n", "annotations_table = f\"{TABLE_DIR}/ANNOTATIONS/slide_annotation_dataset_TCGA collection_ov_regional.parquet\"\n", @@ -1244,9 +2291,92 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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slide_geojsonid
slide_id
01OV002-bd8cdc70-3d46-40ae-99c4-90ef77/home/pollardw/vmount/PRO-12-123/data/toy_data...NaN
01OV002-ed65cf94-8bc6-492b-9149-adc16f/home/pollardw/vmount/PRO-12-123/data/toy_data...NaN
01OV007-9b90eb78-2f50-4aeb-b010-d642f9/home/pollardw/vmount/PRO-12-123/data/toy_data...NaN
01OV008-308ad404-7079-4ff8-8232-12ee2e/home/pollardw/vmount/PRO-12-123/data/toy_data...NaN
01OV008-7579323e-2fae-43a9-b00f-a15c28/home/pollardw/vmount/PRO-12-123/data/toy_data...NaN
\n", + "
" + ], + "text/plain": [ + " slide_geojson \\\n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 /home/pollardw/vmount/PRO-12-123/data/toy_data... \n", + "\n", + " id \n", + "slide_id \n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 NaN \n", + "01OV002-ed65cf94-8bc6-492b-9149-adc16f NaN \n", + "01OV007-9b90eb78-2f50-4aeb-b010-d642f9 NaN \n", + "01OV008-308ad404-7079-4ff8-8232-12ee2e NaN \n", + "01OV008-7579323e-2fae-43a9-b00f-a15c28 NaN " + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "pd.read_parquet(annotations_table) \\\n", " .query(\"type=='geojson'\")[['slide_geojson']] \\\n", diff --git a/docker/luna_tutorial/vmount/notebooks/2_tiling-file.ipynb b/docker/luna_tutorial/vmount/notebooks/2_tiling-file.ipynb index 49aed304..e2301bbf 100755 --- a/docker/luna_tutorial/vmount/notebooks/2_tiling-file.ipynb +++ b/docker/luna_tutorial/vmount/notebooks/2_tiling-file.ipynb @@ -24,7 +24,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -40,17 +40,6 @@ "SLIDE = f\"{DATASET_DIR}/{SLIDE_ID}.svs\"" ] }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "# env DATASET_URL=file:///$LUNA_HOME/PRO-12-123/" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -62,43 +51,15 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "/opt/conda/lib/python3.9/site-packages/distributed/node.py:182: UserWarning: Port 8787 is already in use.\n", - "Perhaps you already have a cluster running?\n", - "Hosting the HTTP server on port 42858 instead\n", - " warnings.warn(\n", "saving to /home/pollardw/vmount/PRO-12-123/tiling/test/tiles/01OV002-bd8cdc70-3d46-40ae-99c4-90ef77.tiles.parquet\n", - "\u001b[32m2023-07-31 13:50:20.002\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 14.88s\u001b[0m\n", - "2023-07-31 13:50:20,018 - distributed.worker - ERROR - Failed to communicate with scheduler during heartbeat.\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 225, in read\n", - " frames_nbytes = await stream.read_bytes(fmt_size)\n", - "tornado.iostream.StreamClosedError: Stream is closed\n", - "\n", - "The above exception was the direct cause of the following exception:\n", - "\n", - "Traceback (most recent call last):\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/worker.py\", line 1215, in heartbeat\n", - " response = await retry_operation(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 400, in retry_operation\n", - " return await retry(\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/utils_comm.py\", line 385, in retry\n", - " return await coro()\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 1221, in send_recv_from_rpc\n", - " return await send_recv(comm=comm, op=key, **kwargs)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/core.py\", line 986, in send_recv\n", - " response = await comm.read(deserializers=deserializers)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 241, in read\n", - " convert_stream_closed_error(self, e)\n", - " File \"/opt/conda/lib/python3.9/site-packages/distributed/comm/tcp.py\", line 144, in convert_stream_closed_error\n", - " raise CommClosedError(f\"in {obj}: {exc}\") from exc\n", - "distributed.comm.core.CommClosedError: in : Stream is closed\n" + "\u001b[32m2023-08-03 02:29:40.526\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 9.95s\u001b[0m\n" ] } ], @@ -109,18 +70,57 @@ "--output-urlpath {TILING_DIR}/test/tiles" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# ! ls -1 {TILING_DIR}/test/tiles" - ] - }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32m2023-08-03 02:29:44.980\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m282\u001b[0m - \u001b[1mSlide dimensions (53760, 54840)\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:44.980\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m286\u001b[0m - \u001b[1mThumbnail scale factor: 20\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:47.116\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 2.14s\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:47.117\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m289\u001b[0m - \u001b[1mSample array size: (2742, 2688, 3)\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:47.123\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m292\u001b[0m - \u001b[1mSlide dimensions (53760, 54840)\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:47.124\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m296\u001b[0m - \u001b[1mThumbnail scale factor: 20\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:49.334\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mget_downscaled_thumbnail ran in 2.21s\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:49.334\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m299\u001b[0m - \u001b[1mSample array size: (2742, 2688, 3)\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:50.509\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m307\u001b[0m - \u001b[1mEnhancing image...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:51.597\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m319\u001b[0m - \u001b[1mHSV space conversion...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:53.011\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m329\u001b[0m - \u001b[1mCalculating max saturation...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:53.597\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m339\u001b[0m - \u001b[1mCalculate and filter shadow mask...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:54.267\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m347\u001b[0m - \u001b[1mFilter out shadow/dust/etc...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:55.782\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m359\u001b[0m - \u001b[1mCalculating otsu threshold...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:56.107\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m362\u001b[0m - \u001b[1mCalculating stain vectors...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:57.876\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m365\u001b[0m - \u001b[1mCalculating stain background thresholds...\u001b[0m\n", + "\u001b[32m2023-08-03 02:29:57.876\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m366\u001b[0m - \u001b[1mChannel 0\u001b[0m\n", + "\u001b[32m2023-08-03 02:30:00.109\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m372\u001b[0m - \u001b[1mChannel 1\u001b[0m\n", + "\u001b[32m2023-08-03 02:30:02.053\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m381\u001b[0m - \u001b[1mSaving otsu mask\u001b[0m\n", + "\u001b[32m2023-08-03 02:30:02.681\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m391\u001b[0m - \u001b[1mSaving stain thumbnail\u001b[0m\n", + "\u001b[32m2023-08-03 02:30:05.850\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m398\u001b[0m - \u001b[1mSaving stain masks\u001b[0m\n", + "\u001b[32m2023-08-03 02:30:06.770\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m421\u001b[0m - \u001b[1mStarting otsu thresholding, threshold=0.7305114077818627\u001b[0m\n", + "\u001b[32m2023-08-03 02:31:22.478\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m468\u001b[0m - \u001b[1mFiltering based on query: otsu_score > 0.1\u001b[0m\n", + "\u001b[32m2023-08-03 02:31:22.487\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.run_tissue_detection\u001b[0m:\u001b[36mdetect_tissue\u001b[0m:\u001b[36m471\u001b[0m - \u001b[1m address ... otsu_score\n", + "01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 292 x3_y81_z10 ... 0.12\n", + " 295 x3_y84_z10 ... 0.16\n", + " 296 x3_y85_z10 ... 0.32\n", + " 297 x3_y86_z10 ... 0.64\n", + " 298 x3_y87_z10 ... 0.43\n", + "... ... ... ...\n", + " 9816 x93_y65_z10 ... 0.32\n", + " 9817 x93_y66_z10 ... 0.34\n", + " 9818 x93_y67_z10 ... 0.58\n", + " 9819 x93_y68_z10 ... 0.68\n", + " 9820 x93_y69_z10 ... 0.33\n", + "\n", + "[5088 rows x 8 columns]\u001b[0m\n", + "saving to /home/pollardw/vmount/PRO-12-123/tiling/test/detect/01OV002-bd8cdc70-3d46-40ae-99c4-90ef77.tiles.parquet\n", + "\u001b[32m2023-08-03 02:31:22.559\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 97.81s\u001b[0m\n" + ] + } + ], "source": [ "!detect_tissue {SLIDE} \\\n", "{TILING_DIR}/test/tiles/01OV002-bd8cdc70-3d46-40ae-99c4-90ef77.tiles.parquet \\\n", @@ -131,56 +131,93 @@ }, { "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "!ls {TILING_DIR}/test/detect" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "!ls {DATASET_DIR}/table/ANNOTATIONS" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "!label_tiles --help" - ] - }, - { - "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32m2023-08-03 02:31:25.464\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.generate_tile_labels\u001b[0m:\u001b[36mgenerate_tile_labels\u001b[0m:\u001b[36m88\u001b[0m - \u001b[1mslide_id=01OV002-bd8cdc70-3d46-40ae-99c4-90ef77\u001b[0m\n", + "/home/pollardw/vmount/PRO-12-123/data/toy_data_set/table/ANNOTATIONS/01OV002-bd8cdc70-3d46-40ae-99c4-90ef77.annotation.geojson TCGA collection ov_regional\n", + "100%|█████████████████████████████████████| 5088/5088 [00:00<00:00, 6020.64it/s]\n", + "\u001b[32m2023-08-03 02:31:26.365\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.generate_tile_labels\u001b[0m:\u001b[36mgenerate_tile_labels\u001b[0m:\u001b[36m157\u001b[0m - \u001b[1m level_0 ... intersection_area\n", + "address ... \n", + "x26_y56_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.053094\n", + "x26_y57_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.341454\n", + "x27_y56_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.655530\n", + "x27_y57_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.898266\n", + "x28_y55_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.258913\n", + "... ... ... ...\n", + "x65_y72_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.419049\n", + "x65_y73_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.553953\n", + "x65_y74_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.102413\n", + "x66_y70_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.187448\n", + "x66_y71_z10 01OV002-bd8cdc70-3d46-40ae-99c4-90ef77 ... 0.062544\n", + "\n", + "[170 rows x 11 columns]\u001b[0m\n", + "\u001b[32m2023-08-03 02:31:26.395\u001b[0m | \u001b[34m\u001b[1mDEBUG \u001b[0m | \u001b[36mluna.common.utils\u001b[0m:\u001b[36mwrapper\u001b[0m:\u001b[36m146\u001b[0m - \u001b[34m\u001b[1mcli ran in 0.93s\u001b[0m\n" + ] + } + ], "source": [ "!label_tiles \\\n", "\"{DATASET_DIR}/table/ANNOTATIONS/slide_annotation_dataset_TCGA collection_ov_regional.parquet\" \\\n", - "\"{TILING_DIR}/test/detect/{SLIDE_ID}-filtered.tiles.parquet\" \\\n", + "\"{TILING_DIR}/test/detect/{SLIDE_ID}.tiles.parquet\" \\\n", "{SLIDE_ID} \\\n", "--output-urlpath \"{TILING_DIR}/test/label\"" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": { "scrolled": false }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32m2023-08-03 02:31:30.548\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mluna.pathology.cli.save_tiles\u001b[0m:\u001b[36msave_tiles\u001b[0m:\u001b[36m127\u001b[0m - \u001b[1mNow generating tiles with batch_size=200!\u001b[0m\n", + "Traceback (most recent call last): ] | 0% Completed | 0.4s\u001b[2K\n", + " File \"/opt/conda/bin/save_tiles\", line 8, in \n", + " sys.exit(fire_cli())\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 176, in fire_cli\n", + " fire.Fire(cli)\n", + " File \"/opt/conda/lib/python3.9/site-packages/fire/core.py\", line 141, in Fire\n", + " component_trace = _Fire(component, args, parsed_flag_args, context, name)\n", + " File \"/opt/conda/lib/python3.9/site-packages/fire/core.py\", line 475, in _Fire\n", + " component, remaining_args = _CallAndUpdateTrace(\n", + " File \"/opt/conda/lib/python3.9/site-packages/fire/core.py\", line 691, in _CallAndUpdateTrace\n", + " component = fn(*varargs, **kwargs)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/common/utils.py\", line 144, in wrapper\n", + " result = func(*args, **kwargs)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/common/utils.py\", line 65, in wrapper\n", + " result = func(*args, **kwargs)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 76, in cli\n", + " df = save_tiles(\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/common/utils.py\", line 126, in wrapper\n", + " result = func(**new_args_dict)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 128, in save_tiles\n", + " df = _save_tiles(df, slide_urlpath, output_urlpath, batch_size, storage_options, output_storage_options)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/common/utils.py\", line 126, in wrapper\n", + " result = func(**new_args_dict)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 168, in _save_tiles\n", + " for result in future.result():\n", + " File \"/opt/conda/lib/python3.9/site-packages/distributed/client.py\", line 284, in result\n", + " raise exc.with_traceback(tb)\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 153, in f_many\n", + " return [\n", + " File \"/opt/conda/lib/python3.9/site-packages/luna/pathology/cli/save_tiles.py\", line 155, in \n", + " x.address,\n", + "AttributeError: 'Tile' object has no attribute 'address'\n" + ] + } + ], "source": [ "!save_tiles {SLIDE} \\\n", - "{TILING_DIR}/test/label \\\n", + "{TILING_DIR}/test/label/{SLIDE_ID}.regional_label.tiles.parquet \\\n", "--num_cores 4 \\\n", "--batch_size 200 \\\n", "--dataset-id PRO_TILES \\\n", @@ -189,7 +226,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": { "scrolled": false }, @@ -222,11 +259,31 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": { "scrolled": true }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0\n" + ] + }, + { + "ename": "AttributeError", + "evalue": "'Series' object has no attribute 'slide_image'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[7], line 11\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m index, row \u001b[38;5;129;01min\u001b[39;00m df_slides\u001b[38;5;241m.\u001b[39miterrows():\n\u001b[1;32m 9\u001b[0m \u001b[38;5;28mprint\u001b[39m (index)\n\u001b[0;32m---> 11\u001b[0m pool\u001b[38;5;241m.\u001b[39msubmit(pipeline, index, \u001b[43mrow\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mslide_image\u001b[49m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m../PRO-12-123/data/toy_data_set/table/ANNOTATIONS\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "File \u001b[0;32m/opt/conda/lib/python3.9/site-packages/pandas/core/generic.py:5902\u001b[0m, in \u001b[0;36mNDFrame.__getattr__\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m 5895\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 5896\u001b[0m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_internal_names_set\n\u001b[1;32m 5897\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_metadata\n\u001b[1;32m 5898\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_accessors\n\u001b[1;32m 5899\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_info_axis\u001b[38;5;241m.\u001b[39m_can_hold_identifiers_and_holds_name(name)\n\u001b[1;32m 5900\u001b[0m ):\n\u001b[1;32m 5901\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m[name]\n\u001b[0;32m-> 5902\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mobject\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__getattribute__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mname\u001b[49m\u001b[43m)\u001b[49m\n", + "\u001b[0;31mAttributeError\u001b[0m: 'Series' object has no attribute 'slide_image'" + ] + } + ], "source": [ "from concurrent.futures import ThreadPoolExecutor\n", "import pandas as pd\n",