Add cvat_labels_file conf parameter to support CSV label definitions with attributes (#1824)

* Added read_labels_from_file and changed init_datastore to parse CSV labels with JSON attributes passed via cvat_labels_file

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix: corrected issues from previous PR submission related to imports

Signed-off-by: Muhammad Bilal <bilalcodehub>

* Fix: corrected issues from previous PR submission

Signed-off-by: Muhammad Bilal <[email protected]>

* Fix: Add setuptools>=61 for Windows build compatibility with girder-client

Signed-off-by: bilalcodehub <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix: upgrade setuptools early in CI to avoid girder-client error on Windows

Signed-off-by: bilalcodehub <[email protected]>

* Fix: resolve mypy type error in endoscopy main.py

Signed-off-by: bilalcodehub <[email protected]>

---------

Signed-off-by: Muhammad Bilal <bilalcodehub>
Signed-off-by: Muhammad Bilal <[email protected]>
Signed-off-by: bilalcodehub <[email protected]>
Co-authored-by: bilalcodehub <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.github/workflows/pythonapp.yml

@@ -45,7 +45,7 @@ jobs:
           rm -rf /opt/hostedtoolcache
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip wheel
+          python -m pip install --upgrade pip setuptools wheel
           pip install -r requirements.txt
 
   build:

requirements.txt

@@ -29,6 +29,8 @@ pydicom-seg==0.4.1
 pynetdicom==2.0.2
 pynrrd==1.0.0
 numpymaxflow==0.0.7
+setuptools>=61
+setuptools-scm<8.0.0
 girder-client==3.2.3
 ninja==1.11.1.1
 einops==0.7.0

sample-apps/endoscopy/main.py

@@ -9,10 +9,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import csv
+import json
 import logging
 import os
 from datetime import timedelta
-from typing import Dict
+from typing import Dict, List, Union
 
 import lib.configs
 import numpy as np
@@ -96,9 +98,64 @@ def __init__(self, app_dir, studies, conf):
         )
         self.downloading = False
 
+    def read_labels_from_file(self, file_path: str) -> List[Dict[str, Union[str, int, list]]]:
+        labels = []
+
+        try:
+            with open(file_path) as csvfile:
+                reader = csv.DictReader(csvfile)
+
+                for row in reader:
+                    # Check for required fields
+                    if "name" in row and "id" in row and "color" in row:
+                        attributes = []
+                        # Process the attributes if they exist and are not empty
+                        if "attributes" in row and row["attributes"].strip():
+                            try:
+                                attributes = json.loads(row["attributes"].strip())
+                            except json.JSONDecodeError as e:
+                                logger.warning(f"Could not parse attributes JSON for row {row}: {e}")
+
+                        entry = {
+                            "name": row["name"],
+                            "id": int(row["id"]),
+                            "color": row["color"],
+                            "type": "any",
+                            "attributes": attributes,
+                        }
+                        labels.append(entry)
+                    else:
+                        logger.warning(f"Skipping row due to missing fields: {row}")
+
+                logger.info(f"Loaded {len(labels)} labels from {file_path}")
+        except FileNotFoundError:
+            logger.error(f"Label file {file_path} not found!")
+        except Exception as e:
+            logger.error(f"Error reading label file {file_path}: {e}")
+
+        return labels
+
     def init_datastore(self) -> Datastore:
         if settings.MONAI_LABEL_DATASTORE_URL and settings.MONAI_LABEL_DATASTORE.lower() == "cvat":
             logger.info(f"Using CVAT: {self.studies}")
+
+            labels: List[Dict[str, Union[str, int, list]]] = []
+
+            # If cvat_labels_file is specified and not null, read labels from that file
+            cvat_labels_file = self.conf.get("cvat_labels_file")
+            if cvat_labels_file:
+                try:
+                    labels = self.read_labels_from_file(cvat_labels_file)
+                except Exception as e:
+                    logger.error(f"Error reading CVAT labels file {cvat_labels_file}: {e}")
+            else:
+                label_str = self.conf.get("cvat_labels")
+                if label_str:
+                    try:
+                        labels = json.loads(label_str)
+                    except Exception as e:
+                        logger.error(f"Error parsing cvat_labels config: {e}")
+
             return CVATDatastore(
                 datastore_path=self.studies,
                 api_url=settings.MONAI_LABEL_DATASTORE_URL,
@@ -107,7 +164,7 @@ def init_datastore(self) -> Datastore:
                 project=self.conf.get("cvat_project", "MONAILabel"),
                 task_prefix=self.conf.get("cvat_task_prefix", "ActiveLearning_Iteration"),
                 image_quality=int(self.conf.get("cvat_image_quality", "70")),
-                labels=self.conf.get("cvat_labels"),
+                labels=labels,
                 normalize_label=strtobool(self.conf.get("cvat_normalize_label", "true")),
                 segment_size=int(self.conf.get("cvat_segment_size", "1")),
                 extensions=settings.MONAI_LABEL_DATASTORE_FILE_EXT,