datamint 2.3.0__py3-none-any.whl → 2.3.2__py3-none-any.whl

datamint/api/client.py

@@ -1,6 +1,9 @@
 from typing import Optional
 from .base_api import ApiConfig
-from .endpoints import ProjectsApi, ResourcesApi, AnnotationsApi, ChannelsApi, UsersApi, DatasetsInfoApi, ModelsApi
+from .endpoints import (ProjectsApi, ResourcesApi, AnnotationsApi,
+                        ChannelsApi, UsersApi, DatasetsInfoApi, ModelsApi,
+                        AnnotationSetsApi
+                        )
 import datamint.configs
 from datamint.exceptions import DatamintException
 
@@ -17,7 +20,8 @@ class Api:
         'channels': ChannelsApi,
         'users': UsersApi,
         'datasets': DatasetsInfoApi,
-        'models': ModelsApi
+        'models': ModelsApi,
+        'annotationsets': AnnotationSetsApi,
     }
 
     def __init__(self,
@@ -97,3 +101,7 @@ class Api:
     @property
     def models(self) -> ModelsApi:
         return self._get_endpoint('models')
+
+    @property
+    def annotationsets(self) -> AnnotationSetsApi:
+        return self._get_endpoint('annotationsets')

datamint/api/endpoints/__init__.py

@@ -7,6 +7,7 @@ from .resources_api import ResourcesApi
 from .users_api import UsersApi
 from .datasetsinfo_api import DatasetsInfoApi
 from .models_api import ModelsApi
+from .annotationsets_api import AnnotationSetsApi
 
 __all__ = [
     'AnnotationsApi',
@@ -16,4 +17,5 @@ __all__ = [
     'UsersApi',
     'DatasetsInfoApi',
     'ModelsApi',
+    'AnnotationSetsApi',
 ]

datamint/api/endpoints/annotations_api.py

@@ -6,6 +6,7 @@ from ..entity_base_api import ApiConfig, CreatableEntityApi, DeletableEntityApi
 from .models_api import ModelsApi
 from datamint.entities.annotation import Annotation
 from datamint.entities.resource import Resource
+from datamint.entities.project import Project
 from datamint.apihandler.dto.annotation_dto import AnnotationType, CreateAnnotationDto, LineGeometry, BoxGeometry, CoordinateSystem, Geometry
 import numpy as np
 import os
@@ -997,3 +998,33 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                            ) -> None:
         """Alias for :py:meth:`download_multiple_files`"""
         return self.download_multiple_files(annotations, save_paths)
+
+    def patch(self,
+              annotation: str | Annotation,
+              identifier: str) -> None:
+        """
+        Update the project assignment for an annotation.
+
+        Args:
+            annotation: The annotation unique id or Annotation instance.
+            identifier: The new identifier/label for the annotation.
+
+        Raises:
+            DatamintException: If the update fails.
+        """
+        annotation_id = self._entid(annotation)
+
+        payload = {'identifier': identifier}
+        # remove None values
+        payload = {k: v for k, v in payload.items() if v is not None}
+        if len(payload) == 0:
+            _LOGGER.info("No fields to update for annotation patch.")
+            return
+
+        resp = self._make_request('PATCH',
+                                  f'{self.endpoint_base}/{annotation_id}',
+                                  json=payload)
+
+        respdata = resp.json()
+        if isinstance(respdata, dict) and 'error' in respdata:
+            raise DatamintException(respdata['error'])

datamint/api/endpoints/annotationsets_api.py

@@ -0,0 +1,11 @@
+from datamint.api.base_api import BaseApi
+import logging
+
+_LOGGER = logging.getLogger(__name__)
+
+
+class AnnotationSetsApi(BaseApi):
+    def get_segmentation_group(self, annotation_set_id: str) -> dict:
+        """Get the segmentation group for a given annotation set ID."""
+        endpoint = f"/annotationsets/{annotation_set_id}/segmentation-group"
+        return self._make_request("GET", endpoint).json()

datamint/dataset/base_dataset.py

@@ -11,7 +11,6 @@ from torch.utils.data import DataLoader
 import torch
 from torch import Tensor
 from datamint.exceptions import DatamintException
-from medimgkit.dicom_utils import is_dicom
 from medimgkit.readers import read_array_normalized
 from medimgkit.format_detection import guess_extension, guess_typez
 from medimgkit.nifti_utils import NIFTI_MIMES, get_nifti_shape
@@ -306,6 +305,15 @@ class DatamintBaseDataset:
         """Setup label sets and mappings."""
         self.frame_lsets, self.frame_lcodes = self._get_labels_set(framed=True)
         self.image_lsets, self.image_lcodes = self._get_labels_set(framed=False)
+        worklist_id = self.get_info()['worklist_id']
+        groups: dict[str, dict] = self.api.annotationsets.get_segmentation_group(worklist_id)['groups']
+        # order by 'index' key
+        max_index = max([g['index'] for g in groups.values()])
+        self.seglabel_list : list[str] = ['UNKNOWN'] * max_index  # 1-based
+        for segname, g in groups.items():
+            self.seglabel_list[g['index'] - 1] = segname
+
+        self.seglabel2code = {label: idx + 1 for idx, label in enumerate(self.seglabel_list)}
 
     def _filter_items(self, images_metainfo: list[dict]) -> list[dict]:
         """Filter items that have annotations."""
@@ -357,9 +365,7 @@ class DatamintBaseDataset:
     @property
     def segmentation_labels_set(self) -> list[str]:
         """Returns the set of segmentation labels in the dataset."""
-        a = set(self.frame_lsets['segmentation'])
-        b = set(self.image_lsets['segmentation'])
-        return list(a.union(b))
+        return self.seglabel_list
 
     def _get_annotations_internal(
         self,
@@ -463,8 +469,8 @@ class DatamintBaseDataset:
             label_anns = self.get_annotations(i, type='label', scope=scope)
             multilabel_set.update(ann.name for ann in label_anns)
 
-            seg_anns = self.get_annotations(i, type='segmentation', scope=scope)
-            segmentation_labels.update(ann.name for ann in seg_anns)
+            # seg_anns = self.get_annotations(i, type='segmentation', scope=scope)
+            # segmentation_labels.update(ann.name for ann in seg_anns)
 
             cat_anns = self.get_annotations(i, type='category', scope=scope)
             multiclass_set.update((ann.name, ann.value) for ann in cat_anns)
@@ -472,17 +478,17 @@ class DatamintBaseDataset:
         # Sort and create mappings
         multilabel_list = sorted(multilabel_set)
         multiclass_list = sorted(multiclass_set)
-        segmentation_list = sorted(segmentation_labels)
+        # segmentation_list = sorted(segmentation_labels)
 
         sets = {
             'multilabel': multilabel_list,
-            'segmentation': segmentation_list,
+            # 'segmentation': segmentation_list,
             'multiclass': multiclass_list
         }
 
         codes_map = {
             'multilabel': {label: idx for idx, label in enumerate(multilabel_list)},
-            'segmentation': {label: idx + 1 for idx, label in enumerate(segmentation_list)},
+            # 'segmentation': {label: idx + 1 for idx, label in enumerate(segmentation_list)},
             'multiclass': {label: idx for idx, label in enumerate(multiclass_list)}
         }
 

datamint/dataset/dataset.py

@@ -191,7 +191,7 @@ class DatamintDataset(DatamintBaseDataset):
             author_labels = seg_labels[author]
 
             if frame_index is not None and ann.scope == 'frame':
-                seg_code = self.frame_lcodes['segmentation'][ann.name]
+                seg_code = self.seglabel2code[ann.name]
                 if author_segs[frame_index] is None:
                     author_segs[frame_index] = []
                     author_labels[frame_index] = []
@@ -199,7 +199,7 @@ class DatamintDataset(DatamintBaseDataset):
                 author_segs[frame_index].append(s)
                 author_labels[frame_index].append(seg_code)
             elif frame_index is None and ann.scope == 'image':
-                seg_code = self.image_lcodes['segmentation'][ann.name]
+                seg_code = self.seglabel2code[ann.name]
                 # apply to all frames
                 for i in range(nframes):
                     if author_segs[i] is None:

datamint/entities/project.py

@@ -3,6 +3,7 @@
 from datetime import datetime
 import logging
 from .base_entity import BaseEntity, MISSING_FIELD
+from typing import Any
 
 logger = logging.getLogger(__name__)
 
@@ -43,9 +44,10 @@ class Project(BaseEntity):
     resource_count: int
     annotated_resource_count: int
     description: str | None
-    ai_model_id: str | None
     viewable_ai_segs: list | None
     editable_ai_segs: list | None
+    registered_model: Any | None = MISSING_FIELD
+    ai_model_id: str | None = MISSING_FIELD
     closed_resources_count: int = MISSING_FIELD
     resources_to_annotate_count: int = MISSING_FIELD
     most_recent_experiment: str | None = MISSING_FIELD  # ISO timestamp string

{datamint-2.3.0.dist-info → datamint-2.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datamint
-Version: 2.3.0
+Version: 2.3.2
 Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3

{datamint-2.3.0.dist-info → datamint-2.3.2.dist-info}/RECORD

@@ -1,10 +1,11 @@
 datamint/__init__.py,sha256=ucsnxrYClh6pdy7psRJXWam_9rjAQB4NXzvy7xLovmo,824
 datamint/api/__init__.py,sha256=7QYkmDBXbKh8-zchV7k6Lpolaw6h-IK6ezfXROIWh2A,43
 datamint/api/base_api.py,sha256=Iu9oJEZ8YlIF5xcbH_M0Lkb7t9ZDNFLzjJp9bPDHW1c,16628
-datamint/api/client.py,sha256=qL6kW1lUma98LieDEkhRdJAGRcsEFlaBSg2oQ3ZePYY,3466
+datamint/api/client.py,sha256=WfcCpvH3tl0nQ9SgRdQG0qy8A7tD_2dytRxQUln3G9Y,3724
 datamint/api/dto/__init__.py,sha256=KOSNl1axDDE5eBt68MmsgkyE0Ds_1DDzWUg73iyoWvc,281
-datamint/api/endpoints/__init__.py,sha256=uN2EYxSL6T5O5poVmQs8CQpyy3_MZzHfNyniORcvKUc,454
-datamint/api/endpoints/annotations_api.py,sha256=Uyx-gnh5f-Di7MU_doQheYlSOkqjf7hlFnmaruvWQN4,47098
+datamint/api/endpoints/__init__.py,sha256=wi4liAb5-wOohwyzKUD6TxHGeZmUPaZerFUGa2IUju4,529
+datamint/api/endpoints/annotations_api.py,sha256=jhaWkLd01zKw-lVQYhBX288o9Ew2lQ-jmRP-0fz2fx0,48185
+datamint/api/endpoints/annotationsets_api.py,sha256=NIsPIjGGptiUBxHft-EhOMRG-DsQAthheVqd7ph0id4,409
 datamint/api/endpoints/channels_api.py,sha256=oQqxSw9DJzAqtVQI7-tc1llTdnsm-URx8jwtXNXnhio,867
 datamint/api/endpoints/datasetsinfo_api.py,sha256=WdzrUzK63w9gvAP6U--P65FbD-3X-jm9TPCcYnRNjas,597
 datamint/api/endpoints/models_api.py,sha256=tbVuajc-mCsIp5AKSCoq3uQRDWgKnJaIA6tf_ck8-XY,1502
@@ -25,14 +26,14 @@ datamint/client_cmd_tools/datamint_upload.py,sha256=rZEqBRZZDBFSlwMvIg_DbipqgBtQ
 datamint/configs.py,sha256=Bdp6NydYwyCJ2dk19_gf_o3M2ZyQOmMHpLi8wEWNHUk,1426
 datamint/dataset/__init__.py,sha256=4PlUKSvVhdfQvvuq8jQXrkdqnot-iTTizM3aM1vgSwg,47
 datamint/dataset/annotation.py,sha256=qN1IMjdfLD2ceQ6va3l76jOXA8Vb_c-eBk1oWQu6hW0,7994
-datamint/dataset/base_dataset.py,sha256=Za41Qf76nm3GmY7iA9mba_FGzzwF3gxqAwu4eY0_5b4,49479
-datamint/dataset/dataset.py,sha256=Oj_Xr6MaCdO2Nq16fFE345qoKMWaTzKk6M1G6ajSXMo,28959
+datamint/dataset/base_dataset.py,sha256=pJXU_nY9_D67E7G3cjnVnwdzjNNJgOhMt-i687oHgtw,49869
+datamint/dataset/dataset.py,sha256=c0887PcI6fEWG3FjM3gz_EYb9maH8v4ormZhm7vf4gE,28929
 datamint/entities/__init__.py,sha256=tbHE7rZb0R9Hm-Dc8VWEq3PlRl7BYOzffumrV0ZdsMs,444
 datamint/entities/annotation.py,sha256=ochAEh_JqxAe_FyYTNUfPT47KiIAG7CkBTim52bu7M8,6636
 datamint/entities/base_entity.py,sha256=DniakCgJ-gV7Hz8VKQA_dRYTp4DU5rcjLBVOuD1aZuA,1902
 datamint/entities/channel.py,sha256=9fl22eSx_ng98NosfQGs18cdaRdbeC3wXL61KhSg4Zo,1601
 datamint/entities/datasetinfo.py,sha256=O73Aq0tLflQomFzseful8a_cXqKdO9w2yP0p3zBcA-s,489
-datamint/entities/project.py,sha256=cK03qfVBVUTFJF0IZQCGfjX-ivzDytySakKoVbjfnz0,2588
+datamint/entities/project.py,sha256=FNweb1Q0ZQkWfbyijoV-UyqUXthzookdcyO-ophAl0U,2676
 datamint/entities/resource.py,sha256=7YCVihswd-bH-2AH4aMPIddt5ejwRqRFQAszI_sTWaU,4882
 datamint/entities/user.py,sha256=MREHDOsV9NOBEbXqiQ2ww6DmetN07CELId-ZQVpZCb8,620
 datamint/examples/__init__.py,sha256=zcYnd5nLVme9GCTPYH-1JpGo8xXK2WEYvhzcy_2alZc,39
@@ -45,7 +46,7 @@ datamint/logging.yaml,sha256=tOMxtc2UmwlIMTK6ljtnBwTco1PNrPeq3mx2iMuSbiw,482
 datamint/utils/logging_utils.py,sha256=9pRoaPrWu2jOdDCiAoUsjEdP5ZwaealWL3hjUqFvx9g,4022
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-2.3.0.dist-info/METADATA,sha256=lV7qLnGCc1NA5yShMM-oTLkoy5FAKWwGd9rNgeu6K_M,4203
-datamint-2.3.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-datamint-2.3.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-2.3.0.dist-info/RECORD,,
+datamint-2.3.2.dist-info/METADATA,sha256=wybrUAOXVw_v1HzHAamP9uGMO7mAemu87lmDf7-0mbE,4203
+datamint-2.3.2.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+datamint-2.3.2.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-2.3.2.dist-info/RECORD,,