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Re-org Schema for Napari v0.4.19 upgrade #10

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merged 9 commits into from
Feb 12, 2024
Merged

Re-org Schema for Napari v0.4.19 upgrade #10

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bd21de5
Abstract schema fields, embed task-level params, dictify, determine l…
sea-shunned Dec 7, 2023
dc50a9e
Update schemas to new dict-based structure
sea-shunned Dec 7, 2023
4d0d8dc
Make parameter name and underlying argument name clearer
sea-shunned Dec 8, 2023
7471980
The perils of replace all
sea-shunned Dec 8, 2023
785d670
Improve param value description and type handling
sea-shunned Dec 8, 2023
68024cb
Expand schema to include metadata
sea-shunned Dec 18, 2023
12902c1
Merge pull request #8 from FrancisCrickInstitute/schema_metadata
sea-shunned Dec 18, 2023
663f6a3
Produce JSON schema when run as main
sea-shunned Dec 18, 2023
aecebe7
Merge pull request #9 from FrancisCrickInstitute/create_schema
sea-shunned Dec 18, 2023
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2 changes: 1 addition & 1 deletion aiod_registry/__init__.py
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@@ -1,2 +1,2 @@
from aiod_registry.schema import ModelManifest
from aiod_registry.schema import ModelManifest, TASK_NAMES
from aiod_registry.utils import get_manifest_paths, load_manifests
57 changes: 37 additions & 20 deletions aiod_registry/manifests/mitonet.json
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@@ -1,69 +1,86 @@
{
"name": "Mitonet",
"versions": [
{
"name": "MitoNet v1",
"tasks": [
{
"task": "mito",
"metadata": {
"description": "MitoNet is a deep learning model for mitochondria segmentation in EM images.",
"authors": [
{
"name": "Ryan Conrad",
"affiliation": "Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA"
},
{
"name": "Kedar Narayan",
"affiliation": "Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA"
}
],
"pubs": [
{
"info": "Main paper that describes model & data",
"url": "https://doi.org/10.1016/j.cels.2022.12.006"
}
]
},
"versions": {
"MitoNet v1": {
"tasks": {
"mito": {
"location": "https://zenodo.org/record/6861565/files/MitoNet_v1.pth?download=1"
}
]
}
},
{
"name": "MitoNet Mini v1",
"tasks": [
{
"task": "mito",
"MitoNet Mini v1": {
"tasks": {
"mito": {
"location": "https://zenodo.org/record/6861565/files/MitoNet_v1_mini.pth?download=1"
}
]
}
}
],
},
"params": [
{
"name": "Plane",
"arg_name": "plane",
"value": ["XY", "XZ", "YZ", "All"],
"tooltip": "Whether to use all planes (XY, XZ, YZ) or a single plane"
},
{
"name": "Downsampling",
"arg_name": "downsampling",
"value": [1, 2, 4, 8, 16, 32, 64],
"tooltip": "Downsampling factor for the input image"
},
{
"name": "Segmentation threshold",
"short_name": "conf_threshold",
"arg_name": "conf_threshold",
"value": 0.5,
"tooltip": "Confidence threshold for the segmentation"
},
{
"name": "Center threshold",
"short_name": "center_threshold",
"arg_name": "center_threshold",
"value": 0.1,
"tooltip": "Confidence threshold for the center"
},
{
"name": "Minimum distance",
"short_name": "min_distance",
"arg_name": "min_distance",
"value": 3,
"tooltip": "Minimum distance between object centers"
},
{
"name": "Maximum objects",
"short_name": "max_objects",
"arg_name": "max_objects",
"value": 1000,
"tooltip": "Maximum number of objects to segment per class"
},
{
"name": "Semantic only",
"short_name": "semantic_only",
"arg_name": "semantic_only",
"value": false,
"tooltip": "Only run semantic segmentation for all classes"
},
{
"name": "Fine boundaries",
"short_name": "fine_boundaries",
"arg_name": "fine_boundaries",
"value": false,
"tooltip": "Finer boundaries between objects"
}
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102 changes: 49 additions & 53 deletions aiod_registry/manifests/sam_test.json → aiod_registry/manifests/sam.json
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@@ -1,122 +1,118 @@
{
"name": "Segment Anything",
"short_name": "sam",
"versions": [
{
"name": "default",
"tasks": [
{
"task": "everything",
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth",
"config_path": null
"metadata": {
"description": "Segment Anything is a vision foundation model with flexible prompting.",
"url": "https://segment-anything.com/",
"repo": "https://github.com/facebookresearch/segment-anything",
"pubs": [
{
"info": "Main paper that describes model & data",
"url": "https://arxiv.org/abs/2304.02643"
}
]
},
"versions": {
"default": {
"tasks": {
"everything": {
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth"
}
]
}
},
{
"name": "vit_h",
"tasks": [
{
"task": "everything",
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth",
"config_path": null
"vit_h": {
"tasks": {
"everything": {
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth"
}
]
}
},
{
"name": "vit_l",
"tasks": [
{
"task": "everything",
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_l_0b3195.pth",
"config_path": null
"vit_l": {
"tasks": {
"everything": {
"location": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_l_0b3195.pth"
}
]
}
},
{
"name": "vit_b",
"tasks": [
{
"task": "Mito",
"location":"https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth",
"config_path": null
"vit_b": {
"tasks": {
"everything": {
"location":"https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth"
}
]
}
},
{
"name": "MedSAM",
"tasks": [
{
"task": "everything",
"location": "https://syncandshare.desy.de/index.php/s/yLfdFbpfEGSHJWY/download/medsam_20230423_vit_b_0.0.1.pth",
"config_path": null
"MedSAM": {
"tasks": {
"everything": {
"location": "https://syncandshare.desy.de/index.php/s/yLfdFbpfEGSHJWY/download/medsam_20230423_vit_b_0.0.1.pth"
}
]
}
}
],
},
"params": [
{
"name": "Points per side",
"short_name": "points_per_side",
"arg_name": "points_per_side",
"value": 32,
"tooltip": ""
},
{
"name": "Points per batch",
"short_name": "points_per_batch",
"arg_name": "points_per_batch",
"value": 64,
"tooltip": ""
},
{
"name": "Pred IoU threshold",
"short_name": "pred_iou_thresh",
"arg_name": "pred_iou_thresh",
"value": 0.88,
"tooltip": ""
},
{
"name": "Stability score threshold",
"short_name": "stability_score_thresh",
"arg_name": "stability_score_thresh",
"value": 0.95,
"tooltip": ""
},
{
"name": "Stability score offset",
"short_name": "stability_score_offset",
"arg_name": "stability_score_offset",
"value": 1,
"tooltip": ""
},
{
"name": "Box nms_thresh",
"short_name": "box_nms_thresh",
"arg_name": "box_nms_thresh",
"value": 0.7,
"tooltip": ""
},
{
"name": "Crop N layers",
"short_name": "crop_n_layers",
"arg_name": "crop_n_layers",
"value": 0,
"tooltip": ""
},
{
"name": "Crop NMS thresh",
"short_name": "crop_nms_thresh",
"arg_name": "crop_nms_thresh",
"value": 0.7,
"tooltip": ""
},
{
"name": "Crop overlap ratio",
"short_name": "crop_overlap_ratio",
"arg_name": "crop_overlap_ratio",
"value": 0.34133,
"tooltip": ""
},
{
"name": "Crop B points downscale factor",
"short_name": "crop_n_points_downscale_factor",
"arg_name": "crop_n_points_downscale_factor",
"value": 0.5,
"tooltip": ""
},
{
"name": "Min mask region area",
"short_name": "min_mask_region_area",
"arg_name": "min_mask_region_area",
"value": 3,
"tooltip": ""
}
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34 changes: 16 additions & 18 deletions aiod_registry/manifests/unet_seai.json
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@@ -1,31 +1,29 @@
{
"name": "SEAI U-Net",
"short_name": "seai_unet",
"versions": [
{
"name": "U-Net",
"tasks": [
{
"task": "mito",
"location": "/nemo/stp/ddt/working/shandc/aiod_models/mito_5nm_intensity_augs_warp.best.969.pt",
"config_path": "/nemo/stp/ddt/working/shandc/aiod_models/mito_5nm_intensity_augs_warp.yml"
"metadata": {
"description": "SEAI U-Net developed on internal Crick EM data"
},
"versions": {
"U-Net": {
"tasks": {
"mito": {
"location": "/Users/shandc/Documents/ai_ondemand/mito_5nm_intensity_augs_warp.best.969.pt",
"config_path": "/Users/shandc/Documents/ai_ondemand/mito_5nm_intensity_augs_warp.yml"
}
]
}
},
{
"name": "Attention U-Net",
"tasks": [
{
"task": "mito",
"Attention U-Net": {
"tasks": {
"mito": {
"location": "/nemo/stp/ddt/working/shandc/aiod_models/Attention_HUNet_3e5_Adam_restart_12_16.best.1266.pt",
"config_path": "/nemo/stp/ddt/working/shandc/aiod_models/Attention_HUNet_3e5_Adam_restart_12_16.yml"
},
{
"task": "ne",
"ne": {
"location": "/nemo/stp/ddt/working/shandc/aiod_models/Attention_HUNet_NE.best.368.pt",
"config_path": "/nemo/stp/ddt/working/shandc/aiod_models/Attention_HUNet_NE.yml"
}
]
}
}
]
}
}
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