sample-apps/vista2d installation instructions incomplete #1810
Description
Describe the bug
I understand how to fix the following bug, but am reporting it since the instructions here need to be updated.
After running the instructions:
> monailabel apps --download --name vista2d --output apps
> pip install -r ./apps/vista2d/requirements.txt
> monailabel start_server --app apps/vista2d --studies datasets --conf models vista2d --conf preload true --conf skip_trainers true
Withe the contents of apps/vista2d/requirements.txt being:
# Copyright (c) MONAI Consortium
# Licensed under the Apache License Version 2.0 (the License);
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing software
# distributed under the License is distributed on an AS IS BASIS
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
cellpose==3.0.8
natsort==8.4.0
roifile==2024.5.24
fastremap==1.15.0
I receive the following error, regarding missing dependencies:
Using PYTHONPATH=/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages:
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: app = /home/ngogober/MONAILabel/apps/vista2d
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: studies = /home/ngogober/MONAILabel/datasets
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: conf = [['models', 'vista2d'], ['preload', 'true'], ['skip_trainers', 'true']]
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: root_path =
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2025-01-30 19:24:13,982] [462579] [MainThread] [INFO] (__main__:296) -
Allow Origins: ['*']
[2025-01-30 19:24:14,591] [462579] [MainThread] [INFO] (uvicorn.error:83) - Started server process [462579]
[2025-01-30 19:24:14,591] [462579] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
App Init...
[2025-01-30 19:24:14,592] [462579] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: /home/ngogober/MONAILabel/apps/vista2d; studies: /home/ngogober/MONAILabel/datasets; conf: {'models': 'vista2d', 'preload': 'true', 'skip_trainers': 'true'}
[2025-01-30 19:24:14,648] [462579] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.VISTA2DApp'>
[2025-01-30 19:24:15,237] [462579] [MainThread] [INFO] (monailabel.utils.others.generic:304) - +++ Adding Bundle from Zoo: vista2d => /home/ngogober/MONAILabel/apps/vista2d/model/vista2d
2025-01-30 19:24:15,238 - INFO - --- input summary of monai.bundle.scripts.download ---
2025-01-30 19:24:15,238 - INFO - > name: 'vista2d'
2025-01-30 19:24:15,238 - INFO - > bundle_dir: '/home/ngogober/MONAILabel/apps/vista2d/model'
2025-01-30 19:24:15,238 - INFO - > source: 'monaihosting'
2025-01-30 19:24:15,238 - INFO - > repo: 'Project-MONAI/model-zoo/hosting_storage_v1'
2025-01-30 19:24:15,238 - INFO - > remove_prefix: 'monai_'
2025-01-30 19:24:15,238 - INFO - > progress: True
2025-01-30 19:24:15,238 - INFO - ---
vista2d_v0.3.0.zip: 652MB [00:20, 33.0MB/s]
2025-01-30 19:24:36,258 - INFO - Downloaded: /home/ngogober/MONAILabel/apps/vista2d/model/vista2d_v0.3.0.zip
2025-01-30 19:24:36,258 - INFO - Expected md5 is None, skip md5 check for file /home/ngogober/MONAILabel/apps/vista2d/model/vista2d_v0.3.0.zip.
2025-01-30 19:24:36,258 - INFO - Writing into directory: /home/ngogober/MONAILabel/apps/vista2d/model.
[2025-01-30 19:24:39,692] [462579] [MainThread] [INFO] (monailabel.utils.others.generic:364) - +++ Using Bundle Models: ['vista2d']
[2025-01-30 19:24:39,692] [462579] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: /home/ngogober/MONAILabel/datasets
[2025-01-30 19:24:39,694] [462579] [MainThread] [INFO] (monailabel.datastore.local:130) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2025-01-30 19:24:39,695] [462579] [MainThread] [INFO] (monailabel.datastore.local:577) - Invalidate count: 0
[2025-01-30 19:24:39,695] [462579] [MainThread] [INFO] (monailabel.datastore.local:151) - Start observing external modifications on datastore (AUTO RELOAD)
[2025-01-30 19:24:39,721] [462579] [MainThread] [ERROR] (uvicorn.error:121) - Traceback (most recent call last):
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/utils/module.py", line 243, in instantiate
return component(**kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/networks/nets/cell_sam_wrapper.py", line 59, in __init__
raise ValueError(
ValueError: SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/starlette/routing.py", line 693, in lifespan
async with self.lifespan_context(app) as maybe_state:
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/fastapi/routing.py", line 133, in merged_lifespan
async with original_context(app) as maybe_original_state:
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/contextlib.py", line 210, in __aenter__
return await anext(self.gen)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/monailabel/app.py", line 49, in lifespan
instance = app_instance()
^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/monailabel/interfaces/utils/app.py", line 50, in app_instance
app = c(app_dir=app_dir, studies=studies, conf=conf)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/apps/vista2d/main.py", line 48, in __init__
super().__init__(
File "/home/ngogober/MONAILabel/monailabel/interfaces/app.py", line 101, in __init__
self._infers = self.init_infers()
^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/apps/vista2d/main.py", line 64, in init_infers
i = VISTA2DInfer(b, self.conf, model_state_dict="state_dict")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/monailabel/tasks/infer/bundle.py", line 121, in __init__
network = self.bundle_config.get_parsed_content(self.const.key_network_def(), instantiate=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/bundle/config_parser.py", line 290, in get_parsed_content
return self.ref_resolver.get_resolved_content(id=id, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/bundle/reference_resolver.py", line 193, in get_resolved_content
return self._resolve_one_item(id=id, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/bundle/reference_resolver.py", line 171, in _resolve_one_item
self.resolved_content[id] = item.instantiate() if kwargs.get("instantiate", True) else item
^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/bundle/config_item.py", line 292, in instantiate
return instantiate(modname, mode, **args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ngogober/MONAILabel/.pixi/envs/default/lib/python3.12/site-packages/monai/utils/module.py", line 253, in instantiate
raise RuntimeError(
RuntimeError: Failed to instantiate component 'monai.networks.nets.cell_sam_wrapper.CellSamWrapper' with keywords: checkpoint
set '_mode_=debug' to enter the debugging mode.
[2025-01-30 19:24:39,722] [462579] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.