BMDeep tutorial added

analysis/ann_groups_to_bq_table.py

@@ -0,0 +1,152 @@
+"""
+Script to query IDC for ANN objects referencing pathology whole-slide images, 
+download and parse them in parallel, extract annotation group info, and write results to BigQuery.
+
+Authentication:
+This script uses Google Application Default Credentials (ADC). The recommended way to authenticate is to run:
+    gcloud auth application-default login
+in your terminal before running this script. Ensure your account has access to BigQuery and Cloud Storage resources.
+"""
+import concurrent.futures
+from typing import List, Dict
+from google.cloud import bigquery
+from google.cloud import storage
+from google.api_core.exceptions import NotFound
+import highdicom as hd
+
+# CONFIGURATION
+PROJECT_ID = 'idc-pathomics-000'
+QUERY_TO_IDC = '''
+SELECT 
+    dcm_all.SOPInstanceUID,
+    dcm_all.SeriesInstanceUID, 
+    dcm_all.gcs_url
+FROM 
+    `bigquery-public-data.idc_current.dicom_all` AS dcm_all
+WHERE Modality = 'ANN'
+'''
+MAX_WORKERS = 8  
+BQ_DATASET = 'idc_pathology'
+BQ_TABLE = 'annotation_groups'
+BQ_TABLE_SCHEMA = [ 
+    bigquery.SchemaField('SOPInstanceUID', 'STRING'),
+    bigquery.SchemaField('SeriesInstanceUID', 'STRING'),
+    bigquery.SchemaField('annotated_property_category', 'RECORD', fields=[
+        bigquery.SchemaField('CodeValue', 'STRING'),
+        bigquery.SchemaField('CodeMeaning', 'STRING'),
+        bigquery.SchemaField('CodingSchemeDesignator', 'STRING'),
+    ]),
+    bigquery.SchemaField('annotated_property_type', 'RECORD', fields=[
+        bigquery.SchemaField('CodeValue', 'STRING'),
+        bigquery.SchemaField('CodeMeaning', 'STRING'),
+        bigquery.SchemaField('CodingSchemeDesignator', 'STRING'),
+    ]),
+    bigquery.SchemaField('num_annotations', 'INTEGER'),
+    bigquery.SchemaField('annotated_SeriesInstanceUID', 'STRING'),
+]
+
+
+def query_ann_files(client: bigquery.Client) -> List[Dict]:
+    query_job = client.query(QUERY_TO_IDC)
+    return [dict(row) for row in query_job]
+
+
+def process_ann_files(rows: List[Dict]) -> List[Dict]:
+    storage_client = storage.Client(project=PROJECT_ID)
+    results = []
+    with concurrent.futures.ThreadPoolExecutor(max_workers=MAX_WORKERS) as executor:
+        future_to_row = {
+            executor.submit(
+                parse_ann_blob,
+                storage_client,
+                row['gcs_url'],
+                row['SOPInstanceUID'],
+                row['SeriesInstanceUID']
+            ): row for row in rows
+        }
+        for future in concurrent.futures.as_completed(future_to_row):
+            row = future_to_row[future]
+            try:
+                ann_results = future.result()
+                results.extend(ann_results)
+            except Exception as e:
+                print(f'Error processing {row["gcs_url"]}: {e}')
+    return results
+
+
+def parse_ann_blob(storage_client: storage.Client, gcs_url: str, sop_instance_uid: str,series_instance_uid: str) -> List[Dict]:
+    # Parse bucket and blob name from GCS URL
+    parts = gcs_url[5:].split('/', 1)
+    bucket_name, blob_name = parts[0], parts[1]
+    bucket = storage_client.bucket(bucket_name)
+    blob = bucket.blob(blob_name)
+    results = []
+    with blob.open('rb') as file_obj:
+        ann = hd.ann.annread(file_obj)
+        for ann_group in ann.get_annotation_groups():
+            results.append({
+                'SOPInstanceUID': sop_instance_uid,
+                'SeriesInstanceUID': series_instance_uid,
+                'annotated_property_category': coded_concept_to_dict(ann_group.annotated_property_category),
+                'annotated_property_type': coded_concept_to_dict(ann_group.annotated_property_type),
+                'num_annotations': ann_group.number_of_annotations, 
+                'annotated_SeriesInstanceUID': ann.ReferencedSeriesSequence[0].SeriesInstanceUID
+            })
+    return results
+
+
+def coded_concept_to_dict(cc):
+    return {
+        'CodeValue': cc.value,
+        'CodeMeaning': cc.meaning,
+        'CodingSchemeDesignator': cc.scheme_designator
+    } if cc is not None else None
+
+
+def main():
+    bq_client = bigquery.Client(project=PROJECT_ID)
+    # Query ANN files
+    rows = query_ann_files(bq_client)
+    print(f'Found {len(rows)} ANN files to process.')
+    # Process ANN files in parallel
+    results = process_ann_files(rows)
+    print(f'Extracted annotation group info from {len(results)} groups.')
+    # Write to BigQuery
+    if results:
+        table_ref = bq_client.dataset(BQ_DATASET).table(BQ_TABLE)
+        # Always delete and recreate the table before inserting
+        try:
+            bq_client.delete_table(table_ref, not_found_ok=True)
+            print(f'Table {BQ_TABLE} deleted.')
+        except Exception as e:
+            print(f'Error deleting table: {e}')
+        table = bigquery.Table(table_ref, schema=BQ_TABLE_SCHEMA)
+        bq_client.create_table(table)
+        print(f'Table {BQ_TABLE} created.')
+        # Retry loop to ensure table is available before inserting
+        import time
+        found = False
+        for _ in range(10):
+            try:
+                bq_client.get_table(table_ref)
+                found = True
+                break
+            except NotFound:
+                time.sleep(2)
+        if not found:
+            print(f'Error: Table {BQ_TABLE} not found after creation. Saving results locally as ann_groups_results.json.')
+            import json
+            with open('ann_groups_results.json', 'w') as f:
+                json.dump(results, f, indent=2)
+            return
+        errors = bq_client.insert_rows_json(table_ref, results)
+        if errors:
+            print(f'BigQuery insert errors: {errors}')
+        else:
+            print('Results written to BigQuery.')
+    else:
+        print('No results to write.')
+
+
+if __name__ == '__main__':
+    main()