cellmap_flow.dashboard.services.launch
Start the models picked on the Models tab, and show each in the viewer.
update_run_models(): stop and forget the models no longer picked, start the ones newly picked, each in its own thread. A finetune job’s server is the Finetune tab’s to stop, never this one’s.run_model()/run_hf_model()/run_bioimage_model()/run_cellpose_model(): start one catalog, Hugging Face, BioImage Model Zoo or Cellpose model’s inference server (start_hosts, which records the job) and add its layer, the one Submit would give it. Each is served from its type’sdefault_env, when the type sets one (serving.launch.server_argv_for): a zoo model from pixi’sbioimageioenvironment, a Cellpose one fromcellpose4.
Attributes
Functions
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Run a Hugging Face model by repo ID. |
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Run a model given as its config (an entry the Models tab's Add built), |
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A zoo model's job, layer and config name, from the key it is loaded |
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Run a BioImage Model Zoo model: |
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A Cellpose model's job, layer and config name: "cpsam_v2" serving all |
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Run a Cellpose model: |
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The models running, or on their way: the session's jobs and the |
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Kill |
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Run |
Module Contents
- cellmap_flow.dashboard.services.launch.logger
- cellmap_flow.dashboard.services.launch.run_model(model_path, name, st_data)
- cellmap_flow.dashboard.services.launch.run_hf_model(repo, name, st_data)
Run a Hugging Face model by repo ID.
- cellmap_flow.dashboard.services.launch.run_model_config(model_config, st_data)
Run a model given as its config (an entry the Models tab’s Add built), in its environment, as Submit runs the catalog’s.
- cellmap_flow.dashboard.services.launch.bioimage_job_name(key: str) str
A zoo model’s job, layer and config name, from the key it is loaded by: “affable-shark” is affable_shark. A DOI’s slash and dots go too.
- cellmap_flow.dashboard.services.launch.run_bioimage_model(params, st_data)
Run a BioImage Model Zoo model:
paramsare its BioModelConfig arguments, name included (bioimage_catalog.bioimage_entry).
- cellmap_flow.dashboard.services.launch.CELLPOSE_MODELS
- cellmap_flow.dashboard.services.launch.cellpose_job_name(model: str, output: str) str
A Cellpose model’s job, layer and config name: “cpsam_v2” serving all its channels (flows, the default) is cellpose_sam_v2, its probability alone cellpose_sam_v2_probability and its masks cellpose_sam_v2_masks.
The output is in the name, so one model’s outputs can run side by side (the probability to look at, the masks to proofread), each its own job and layer; the default output keeps the plain name. The voxel size and the slice linking are not: changing them restarts that job instead (
update_run_models), rather than leaving the old one running beside.
- cellmap_flow.dashboard.services.launch.run_cellpose_model(params, st_data)
Run a Cellpose model:
paramsare its CellposeModelConfig arguments, name included (_cellpose_params).
- cellmap_flow.dashboard.services.launch.running_names() set
The models running, or on their way: the session’s jobs and the launches not finished yet.
- cellmap_flow.dashboard.services.launch.kill_n_remove_from_neuroglancer(jobs, s)
Kill
jobsand drop their layers from the viewer states.
- cellmap_flow.dashboard.services.launch.update_run_models(names: List[str], hf_repos: List[str] = None, bioimage_models: List[dict] = None, cellpose_models: List[dict] = None)
Run
names(catalog models),hf_repos,bioimage_models({“id”, “voxel_size”} each) andcellpose_models({“model”, “voxel_size”, “output”, “stitch_threshold”} each), and stop every other model. A ValueError, before anything changes, when a zoo model needs a voxel size or a Cellpose model’s settings are missing or wrong.