Merge pull request #10 from FrancisCrickInstitute/staging

Re-org Schema for Napari v0.4.19 upgrade
FrancisCrickInstitute · Feb 12, 2024 · 572c698 · 572c698
2 parents 4007cb3 + aecebe7
commit 572c698
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diff --git a/aiod_registry/__init__.py b/aiod_registry/__init__.py
@@ -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
diff --git a/aiod_registry/manifests/mitonet.json b/aiod_registry/manifests/mitonet.json
@@ -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"
     }

diff --git a/aiod_registry/manifests/sam_test.json → aiod_registry/manifests/sam.json b/aiod_registry/manifests/sam_test.json → aiod_registry/manifests/sam.json
@@ -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": ""
     }

diff --git a/aiod_registry/manifests/unet_seai.json b/aiod_registry/manifests/unet_seai.json
@@ -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"
         }
-      ]
+      }
     }
-  ]
+  }
 }