fixed_paths.py

#  ------------------------------------------------------------------------------------------
#  Copyright (c) Microsoft Corporation. All rights reserved.
#  Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
#  ------------------------------------------------------------------------------------------
import logging
import os
import sys
from pathlib import Path
from typing import Optional

from InnerEye.Common.type_annotations import PathOrString


def repository_root_directory(path: Optional[PathOrString] = None) -> Path:
    """
    Gets the full path to the root directory that holds the present repository.
    :param path: if provided, a relative path to append to the absolute path to the repository root.
    :return: The full path to the repository's root directory, with symlinks resolved if any.
    """
    current = Path(__file__)
    root = current.parent.parent.parent
    if path:
        return root / path
    else:
        return root


def repository_parent_directory(path: Optional[PathOrString] = None) -> Path:
    """
    Gets the full path to the parent directory that holds the present repository.
    :param path: if provided, a relative path to append to the absolute path to the repository root.
    :return: The full path to the repository's root directory, with symlinks resolved if any.
    """
    root = repository_root_directory().parent
    if path:
        return root / path
    else:
        return root


INNEREYE_PACKAGE_NAME = "InnerEye"
# Child paths to include in a registered model that live outside InnerEye/.
ENVIRONMENT_YAML_FILE_NAME = "environment.yml"
PIP_REQUIREMENTS_FILE_NAME = "requirements.txt"

DEFAULT_AML_UPLOAD_DIR = "outputs"
DEFAULT_RESULT_IMAGE_NAME = "segmentation.nii.gz"
# Default filename if scoring produces a zipped DICOM-RT file.
DEFAULT_RESULT_ZIP_DICOM_NAME = "segmentation.dcm.zip"

DEFAULT_LOGS_DIR_NAME = "logs"

DEFAULT_MODEL_SUMMARIES_DIR_PATH = Path(DEFAULT_LOGS_DIR_NAME) / "model_summaries"

ML_RELATIVE_SOURCE_PATH = os.path.join("ML")
ML_RELATIVE_RUNNER_PATH = os.path.join(ML_RELATIVE_SOURCE_PATH, "runner.py")
ML_FULL_SOURCE_FOLDER_PATH = str(repository_root_directory() / ML_RELATIVE_SOURCE_PATH)

VISUALIZATION_NOTEBOOK_PATH = os.path.join("ML", "visualizers", "gradcam_visualization.ipynb")

# A file that contains secrets. This is expected to live in the root folder of the repository or project.
PROJECT_SECRETS_FILE = "InnerEyeTestVariables.txt"
# A file with additional settings that should not be added to source control.
# This file is expected to live in the root folder of the repository or project.
PRIVATE_SETTINGS_FILE = "InnerEyePrivateSettings.yml"

# Names of secrets stored as environment variables or in the PROJECT_SECRETS_FILE:
# Secret for the Service Principal
SERVICE_PRINCIPAL_KEY = "APPLICATION_KEY"

INNEREYE_PACKAGE_ROOT = repository_root_directory(INNEREYE_PACKAGE_NAME)
SETTINGS_YAML_FILE_NAME = "settings.yml"
SETTINGS_YAML_FILE = INNEREYE_PACKAGE_ROOT / SETTINGS_YAML_FILE_NAME

MODEL_INFERENCE_JSON_FILE_NAME = 'model_inference_config.json'

# The names of files at the repository root that are required for running the inference pipeline.
SCORE_SCRIPT = "score.py"
SCRIPTS_AT_ROOT = [SCORE_SCRIPT]
RUN_SCORING_SCRIPT = f"{INNEREYE_PACKAGE_NAME}/Scripts/download_model_and_run_scoring.py"

# Constants needed for the score.py script
DEFAULT_DATA_FOLDER = "data"
DEFAULT_TEST_IMAGE_NAME = "test.nii.gz"
DEFAULT_TEST_ZIP_NAME = "test.zip"

# The property in the model registry that holds the name of the Python environment
PYTHON_ENVIRONMENT_NAME = "python_environment_name"


def get_environment_yaml_file() -> Path:
    """
    Returns the path where the environment.yml file is located. This can be inside of the InnerEye package, or in
    the repository root when working with the code as a submodule.
    The function throws an exception if the file is not found at either of the two possible locations.
    :return: The full path to the environment files.
    """
    # The environment file is copied into the package folder in setup.py.
    env = INNEREYE_PACKAGE_ROOT / ENVIRONMENT_YAML_FILE_NAME
    if not env.exists():
        env = repository_root_directory(ENVIRONMENT_YAML_FILE_NAME)
        if not env.exists():
            raise ValueError(f"File {ENVIRONMENT_YAML_FILE_NAME} was not found not found in the package folder "
                             f"{INNEREYE_PACKAGE_ROOT}, and not in the repository root {repository_root_directory()}.")
    return env


def add_submodules_to_path() -> None:
    """
    This function adds all submodules that the code uses to sys.path and to the environment variables. This is
    necessary to make the code work without any further changes when switching from/to using hi-ml as a package
    or as a submodule for development.
    It also adds the InnerEye root folder to sys.path. The latter is necessary to make AzureML and Pytorch Lightning
    work together: When spawning additional processes for DDP, the working directory is not correctly picked
    up in sys.path.
    """
    innereye_root = repository_root_directory()
    folders_to_add = [(innereye_root, "InnerEye")]
    for (folder, subfolder_that_must_exist) in folders_to_add:
        if (folder / subfolder_that_must_exist).is_dir():
            folder_str = str(folder)
            if folder_str not in sys.path:
                logging.debug(f"Adding folder {folder} to sys.path")
                sys.path.insert(0, folder_str)
            else:
                logging.debug(f"Not adding folder {folder} because it is already in sys.path")
        else:
            logging.debug(f"Not adding folder {folder} because it does not have subfolder {subfolder_that_must_exist}")