annofabcli 1.97.0__py3-none-any.whl → 1.99.0__py3-none-any.whl

annofabcli/annotation/remove_segmentation_overlap.py

@@ -0,0 +1,343 @@
+from __future__ import annotations
+
+import argparse
+import copy
+import logging
+import multiprocessing
+import sys
+import tempfile
+from collections.abc import Collection
+from pathlib import Path
+from typing import Any, Optional
+
+import annofabapi
+import numpy
+from annofabapi.pydantic_models.task_status import TaskStatus
+from annofabapi.segmentation import read_binary_image, write_binary_image
+from annofabapi.utils import can_put_annotation
+
+import annofabcli
+from annofabcli.common.cli import (
+    COMMAND_LINE_ERROR_STATUS_CODE,
+    PARALLELISM_CHOICES,
+    ArgumentParser,
+    CommandLine,
+    CommandLineWithConfirm,
+    build_annofabapi_resource_and_login,
+)
+from annofabcli.common.facade import AnnofabApiFacade
+
+logger = logging.getLogger(__name__)
+
+
+def remove_overlap_of_binary_image_array(
+    binary_image_array_by_annotation: dict[str, numpy.ndarray], annotation_id_list: list[str]
+) -> dict[str, numpy.ndarray]:
+    """
+    塗りつぶし画像の重なりを除去したbool配列をdictで返します。
+
+    Args:
+        binary_image_array_by_annotation: annotation_idをkeyとし、塗りつぶし画像のbool配列をvalueとするdict
+        annotation_id_list: 塗りつぶし画像のannotation_idのlist。背面から前面の順に格納されている
+
+    Returns:
+        重なりを除去した塗りつぶし画像のbool配列が格納されているdict。keyはannotation_id
+
+    """
+    assert set(binary_image_array_by_annotation.keys()) == set(annotation_id_list)
+
+    whole_2d_array = None  # 複数の塗りつぶしアノテーションを1枚に重ね合わせた状態。各要素はannotation_id
+
+    # 背面から塗りつぶしアノテーションのbool配列を重ねていく
+    for annotation_id in annotation_id_list:
+        input_binary_image_array = binary_image_array_by_annotation[annotation_id]
+        if whole_2d_array is None:
+            whole_2d_array = numpy.full(input_binary_image_array.shape, "", dtype=str)
+
+        whole_2d_array = numpy.where(input_binary_image_array, annotation_id, whole_2d_array)
+
+    output_binary_image_array_by_annotation = {}
+    for annotation_id in annotation_id_list:
+        output_binary_image_array: numpy.ndarray = whole_2d_array == annotation_id  # type: ignore[assignment]
+        output_binary_image_array_by_annotation[annotation_id] = output_binary_image_array
+
+    return output_binary_image_array_by_annotation
+
+
+class RemoveSegmentationOverlapMain(CommandLineWithConfirm):
+    def __init__(self, annofab_service: annofabapi.Resource, *, project_id: str, all_yes: bool, is_force: bool) -> None:
+        self.annofab_service = annofab_service
+        self.project_id = project_id
+        self.is_force = is_force
+        super().__init__(all_yes)
+
+    def remove_segmentation_overlap_and_save(self, details: list[dict[str, Any]], output_dir: Path) -> list[str]:
+        """
+        `getEditorAnnotation` APIで取得した`details`から、塗りつぶし画像の重なりの除去が必要な場合に、
+        重なりを除去した塗りつぶし画像を`output_dir`に出力します。
+        塗りつぶし画像のファイル名は`${annotation_id}.png`です。
+
+        Args:
+            details: `getEditorAnnotation` APIで取得した`details`
+            output_dir: 塗りつぶし画像の出力先のディレクトリ。
+
+        Returns:
+            重なりの除去が必要な塗りつぶし画像のannotation_idのlist
+        """
+        input_binary_image_array_by_annotation = {}
+        segmentation_annotation_id_list = []
+
+        for detail in details:
+            if detail["body"]["_type"] != "Outer":
+                continue
+
+            segmentation_response = self.annofab_service.wrapper.execute_http_get(detail["body"]["url"], stream=True)
+            segmentation_response.raw.decode_content = True
+            input_binary_image_array_by_annotation[detail["annotation_id"]] = read_binary_image(segmentation_response.raw)
+            segmentation_annotation_id_list.append(detail["annotation_id"])
+
+        # reversedを使っている理由:
+        # `details`には、前面から背面の順にアノテーションが格納されているため、
+        output_binary_image_array_by_annotation = remove_overlap_of_binary_image_array(
+            input_binary_image_array_by_annotation, list(reversed(segmentation_annotation_id_list))
+        )
+
+        updated_annotation_id_list = []
+        for annotation_id, output_binary_image_array in output_binary_image_array_by_annotation.items():
+            input_binary_image_array = input_binary_image_array_by_annotation[annotation_id]
+            if not numpy.array_equal(input_binary_image_array, output_binary_image_array):
+                output_file_path = output_dir / f"{annotation_id}.png"
+                write_binary_image(output_binary_image_array, output_file_path)
+                updated_annotation_id_list.append(annotation_id)
+
+        return updated_annotation_id_list
+
+    def update_segmentation_annotation(self, task_id: str, input_data_id: str, log_message_prefix: str = "") -> bool:
+        """
+        塗りつぶしアノテーションの重なりがあれば、`putAnnotation` APIを使用して重なりを除去します。
+
+        Args:
+            project_id: プロジェクトID
+            task_id: タスクID
+            annotation_id_list: 更新する塗りつぶし画像のannotation_idのlist
+        """
+        old_annotation, _ = self.annofab_service.api.get_editor_annotation(self.project_id, task_id, input_data_id, query_params={"v": "2"})
+        old_details = old_annotation["details"]
+        with tempfile.TemporaryDirectory() as temp_dir:
+            temp_dir_path = Path(temp_dir)
+            updated_annotation_id_list = self.remove_segmentation_overlap_and_save(old_details, temp_dir_path)
+            if len(updated_annotation_id_list) == 0:
+                logger.debug(
+                    f"{log_message_prefix}塗りつぶしアノテーションの重なりはなかったので、スキップします。 :: "
+                    f"task_id='{task_id}', input_data_id='{input_data_id}'"
+                )
+                return False
+
+            logger.debug(
+                f"{log_message_prefix}{len(updated_annotation_id_list)} 件の塗りつぶしアノテーションを更新します。 :: "
+                f"task_id='{task_id}', input_data_id='{input_data_id}', annotation_id_list={updated_annotation_id_list}"
+            )
+            new_details = []
+            for detail in old_details:
+                annotation_id = detail["annotation_id"]
+                new_detail = copy.deepcopy(detail)
+                new_detail["_type"] = "Update"
+                if annotation_id in updated_annotation_id_list:
+                    with (temp_dir_path / f"{annotation_id}.png").open("rb") as f:
+                        s3_path = self.annofab_service.wrapper.upload_data_to_s3(self.project_id, data=f, content_type="image/png")
+
+                    new_detail["body"]["path"] = s3_path
+
+                else:
+                    # 更新しない場合は、`body`をNoneにする
+                    new_detail["body"] = None
+
+                new_details.append(new_detail)
+
+        request_body = {
+            "project_id": self.project_id,
+            "task_id": task_id,
+            "input_data_id": input_data_id,
+            "details": new_details,
+            "format_version": "2.0.0",
+            "updated_datetime": old_annotation["updated_datetime"],
+        }
+        self.annofab_service.api.put_annotation(self.project_id, task_id, input_data_id, query_params={"v": "2"}, request_body=request_body)
+        logger.debug(
+            f"{log_message_prefix}{len(updated_annotation_id_list)} 件の塗りつぶしアノテーションを更新しました。 :: "
+            f"task_id='{task_id}', input_data_id='{input_data_id}'"
+        )
+        return True
+
+    def update_segmentation_annotation_for_task(self, task_id: str, *, task_index: Optional[int] = None) -> int:
+        """
+        1個のタスクに対して、塗りつぶしアノテーションの重なりを除去します。
+
+        Returns:
+            アノテーションを更新した入力データ数（フレーム数）
+        """
+        log_message_prefix = f"{task_index + 1} 件目 :: " if task_index is not None else ""
+
+        task = self.annofab_service.wrapper.get_task_or_none(project_id=self.project_id, task_id=task_id)
+        if task is None:
+            logger.warning(f"{log_message_prefix}task_id='{task_id}'であるタスクは存在しません。")
+            return 0
+
+        if task["status"] in {TaskStatus.WORKING.value, TaskStatus.COMPLETE.value}:
+            logger.debug(
+                f"{log_message_prefix}task_id='{task_id}'のタスクの状態は「作業中」または「完了」であるため、"
+                f"アノテーションの更新をスキップします。  :: status='{task['status']}'"
+            )
+            return 0
+
+        if not self.confirm_processing(f"task_id='{task_id}'の塗りつぶしアノテーションの重なりを除去しますか？"):
+            return 0
+
+        # 担当者割り当て変更チェック
+        changed_operator = False
+        original_operator_account_id = task["account_id"]
+        if not can_put_annotation(task, self.annofab_service.api.account_id):
+            if self.is_force:
+                logger.debug(f"{log_message_prefix}task_id='{task_id}' のタスクの担当者を自分自身に変更します。")
+                changed_operator = True
+                task = self.annofab_service.wrapper.change_task_operator(
+                    self.project_id,
+                    task_id,
+                    self.annofab_service.api.account_id,
+                    last_updated_datetime=task["updated_datetime"],
+                )
+            else:
+                logger.debug(
+                    f"{log_message_prefix}task_id='{task_id}' のタスクは、過去に誰かに割り当てられたタスクで、"
+                    f"現在の担当者が自分自身でないため、アノテーションの更新をスキップします。"
+                    f"担当者を自分自身に変更してアノテーションを更新する場合は、コマンドライン引数 '--force' を指定してください。"
+                )
+                return 0
+
+        success_input_data_count = 0
+        for input_data_id in task["input_data_id_list"]:
+            try:
+                result = self.update_segmentation_annotation(task_id, input_data_id, log_message_prefix=log_message_prefix)
+                if result:
+                    success_input_data_count += 1
+            except Exception:
+                logger.warning(
+                    f"{log_message_prefix}task_id='{task_id}', input_data_id='{input_data_id}'のアノテーションの更新に失敗しました。", exc_info=True
+                )
+                continue
+
+        # 担当者を元に戻す
+        if changed_operator:
+            logger.debug(
+                f"{log_message_prefix}task_id='{task_id}' のタスクの担当者を、元の担当者（account_id='{original_operator_account_id}'）に変更します。"
+            )
+            self.annofab_service.wrapper.change_task_operator(
+                self.project_id,
+                task_id,
+                original_operator_account_id,
+                last_updated_datetime=task["updated_datetime"],
+            )
+
+        return success_input_data_count
+
+    def update_segmentation_annotation_for_task_wrapper(self, tpl: tuple[int, str]) -> int:
+        try:
+            task_index, task_id = tpl
+            return self.update_segmentation_annotation_for_task(task_id, task_index=task_index)
+        except Exception:
+            logger.warning(f"task_id='{task_id}' のアノテーションの更新に失敗しました。", exc_info=True)
+            return 0
+
+    def main(
+        self,
+        task_ids: Collection[str],
+        parallelism: Optional[int] = None,
+    ) -> None:
+        logger.info(f"{len(task_ids)} 件のタスクの塗りつぶしアノテーションの重なりを除去します。")
+        success_input_data_count = 0
+        if parallelism is not None:
+            with multiprocessing.Pool(parallelism) as pool:
+                result_count_list = pool.map(self.update_segmentation_annotation_for_task_wrapper, enumerate(task_ids))
+                success_input_data_count = sum(result_count_list)
+
+        else:
+            for task_index, task_id in enumerate(task_ids):
+                try:
+                    result = self.update_segmentation_annotation_for_task(task_id, task_index=task_index)
+                    success_input_data_count += result
+                except Exception:
+                    logger.warning(f"task_id='{task_id}' のアノテーションの更新に失敗しました。", exc_info=True)
+                    continue
+
+        logger.info(f"{len(task_ids)} 件のタスクに含まれる入力データ {success_input_data_count} 件の塗りつぶしアノテーションを更新しました。")
+
+
+class RemoveSegmentationOverlap(CommandLine):
+    COMMON_MESSAGE = "annofabcli annotation remove_segmentation_overlap: error:"
+
+    def validate(self, args: argparse.Namespace) -> bool:
+        if args.parallelism is not None and not args.yes:
+            print(  # noqa: T201
+                f"{self.COMMON_MESSAGE} argument --parallelism: '--parallelism'を指定するときは、'--yes' を指定してください。",
+                file=sys.stderr,
+            )
+            return False
+
+        return True
+
+    def main(self) -> None:
+        args = self.args
+        if not self.validate(args):
+            sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
+
+        project_id = args.project_id
+        task_id_list = annofabcli.common.cli.get_list_from_args(args.task_id)
+
+        main_obj = RemoveSegmentationOverlapMain(
+            self.service,
+            project_id=project_id,
+            all_yes=self.all_yes,
+            is_force=args.force,
+        )
+
+        main_obj.main(task_id_list, parallelism=args.parallelism)
+
+
+def main(args: argparse.Namespace) -> None:
+    service = build_annofabapi_resource_and_login(args)
+    facade = AnnofabApiFacade(service)
+    RemoveSegmentationOverlap(service, facade, args).main()
+
+
+def parse_args(parser: argparse.ArgumentParser) -> None:
+    argument_parser = ArgumentParser(parser)
+    argument_parser.add_project_id()
+    argument_parser.add_task_id()
+
+    parser.add_argument(
+        "--force",
+        action="store_true",
+        help="過去に担当者を割り当てられていて、かつ現在の担当者が自分自身でない場合、タスクの担当者を一時的に自分自身に変更してからアノテーションをコピーします。",
+    )
+
+    parser.add_argument(
+        "--parallelism",
+        type=int,
+        choices=PARALLELISM_CHOICES,
+        help="並列度。指定しない場合は、逐次的に処理します。指定した場合は、``--yes`` も指定してください。",
+    )
+
+    parser.set_defaults(subcommand_func=main)
+
+
+def add_parser(subparsers: Optional[argparse._SubParsersAction] = None) -> argparse.ArgumentParser:
+    subcommand_name = "remove_segmentation_overlap"
+    subcommand_help = "塗りつぶしアノテーションの重なりを除去します。"
+    description = (
+        "塗りつぶしアノテーションの重なりを除去します。"
+        "Annofabでインスタンスセグメンテーションは重ねることができてしまいます。"
+        "この重なりをなくしたいときに有用です。"
+    )
+    parser = annofabcli.common.cli.add_parser(subparsers, subcommand_name, subcommand_help, description)
+    parse_args(parser)
+    return parser

annofabcli/annotation/subcommand_annotation.py

@@ -10,6 +10,8 @@ import annofabcli.annotation.dump_annotation
 import annofabcli.annotation.import_annotation
 import annofabcli.annotation.list_annotation
 import annofabcli.annotation.list_annotation_count
+import annofabcli.annotation.merge_segmentation
+import annofabcli.annotation.remove_segmentation_overlap
 import annofabcli.annotation.restore_annotation
 import annofabcli.common.cli
 
@@ -27,6 +29,8 @@ def parse_args(parser: argparse.ArgumentParser) -> None:
     annofabcli.annotation.import_annotation.add_parser(subparsers)
     annofabcli.annotation.list_annotation.add_parser(subparsers)
     annofabcli.annotation.list_annotation_count.add_parser(subparsers)
+    annofabcli.annotation.merge_segmentation.add_parser(subparsers)
+    annofabcli.annotation.remove_segmentation_overlap.add_parser(subparsers)
     annofabcli.annotation.restore_annotation.add_parser(subparsers)
 
 

annofabcli/annotation_specs/put_label_color.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import argparse
 import logging
+import sys
 from dataclasses import dataclass
 from typing import Any, Optional
 
@@ -10,6 +11,7 @@ import annofabapi
 import annofabcli
 import annofabcli.common.cli
 from annofabcli.common.cli import (
+    COMMAND_LINE_ERROR_STATUS_CODE,
     ArgumentParser,
     CommandLine,
     CommandLineWithConfirm,
@@ -100,6 +102,9 @@ class PutLabelColor(CommandLine):
         args = self.args
         label_color = get_json_from_args(args.json)
 
+        if not isinstance(label_color, dict):
+            print("annofabcli annotation_specs put_label_color: error: JSON形式が不正です。オブジェクトを指定してください。", file=sys.stderr)  # noqa: T201
+            sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
         main_obj = PuttingLabelColorMain(service=self.service, project_id=args.project_id, all_yes=args.yes)
         main_obj.main(label_color, comment=args.comment)
 

annofabcli/comment/delete_comment.py

@@ -225,6 +225,9 @@ class DeleteComment(CommandLine):
         super().validate_project(args.project_id, [ProjectMemberRole.ACCEPTER, ProjectMemberRole.OWNER])
 
         dict_comments = annofabcli.common.cli.get_json_from_args(args.json)
+        if not isinstance(dict_comments, dict):
+            print(f"{self.COMMON_MESSAGE} argument --json: JSON形式が不正です。オブジェクトを指定してください。", file=sys.stderr)  # noqa: T201
+            sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
         main_obj = DeleteCommentMain(self.service, project_id=args.project_id, all_yes=self.all_yes)
         main_obj.delete_comments_for_task_list(
             comment_ids_for_task_list=dict_comments,

annofabcli/comment/put_inspection_comment.py

@@ -44,6 +44,9 @@ class PutInspectionComment(CommandLine):
         super().validate_project(args.project_id, [ProjectMemberRole.ACCEPTER, ProjectMemberRole.OWNER])
 
         dict_comments = annofabcli.common.cli.get_json_from_args(args.json)
+        if not isinstance(dict_comments, dict):
+            print(f"{self.COMMON_MESSAGE} argument --json: JSON形式が不正です。オブジェクトを指定してください。", file=sys.stderr)  # noqa: T201
+            sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
         comments_for_task_list = convert_cli_comments(dict_comments, comment_type=CommentType.INSPECTION)
         main_obj = PutCommentMain(self.service, project_id=args.project_id, comment_type=CommentType.INSPECTION, all_yes=self.all_yes)
         main_obj.add_comments_for_task_list(

annofabcli/comment/put_onhold_comment.py

@@ -42,6 +42,9 @@ class PutInspectionComment(CommandLine):
         super().validate_project(args.project_id)
 
         dict_comments = annofabcli.common.cli.get_json_from_args(args.json)
+        if not isinstance(dict_comments, dict):
+            print(f"{self.COMMON_MESSAGE} argument --json: JSON形式が不正です。オブジェクトを指定してください。", file=sys.stderr)  # noqa: T201
+            sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
         comments_for_task_list = convert_cli_comments(
             dict_comments,
             comment_type=CommentType.ONHOLD,

annofabcli/input_data/change_input_data_name.py

@@ -177,7 +177,10 @@ class ChangeInputDataName(CommandLine):
             changed_input_data_list = create_changed_input_data_list_from_csv(args.csv)
 
         elif args.json is not None:
-            input_data_dict_list: list[dict[str, str]] = get_json_from_args(args.json)
+            input_data_dict_list = get_json_from_args(args.json)
+            if not isinstance(input_data_dict_list, list):
+                print("annofabcli input_data change_name: error: JSON形式が不正です。オブジェクトの配列を指定してください。", file=sys.stderr)  # noqa: T201
+                sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
             changed_input_data_list = create_changed_input_data_list_from_dict(input_data_dict_list)
         else:
             raise RuntimeError("'--csv'または'--json'のいずれかを指定してください。")

annofabcli/input_data/put_input_data.py

@@ -356,6 +356,10 @@ class PutInputData(CommandLine):
 
         elif args.json is not None:
             input_data_dict_list = get_json_from_args(args.json)
+            if not isinstance(input_data_dict_list, list):
+                print(f"{self.COMMON_MESSAGE} argument --json: JSON形式が不正です。オブジェクトの配列を指定してください。", file=sys.stderr)  # noqa: T201
+                sys.exit(COMMAND_LINE_ERROR_STATUS_CODE)
+
             input_data_list = self.get_input_data_list_from_dict(input_data_dict_list, allow_duplicated_input_data=args.allow_duplicated_input_data)
             self.put_input_data_list(project_id, input_data_list=input_data_list, overwrite=args.overwrite, parallelism=args.parallelism)