From 789d6e244025cf57249406b60264e27a959307e3 Mon Sep 17 00:00:00 2001 From: Francisco Hernandez Vivanco <49014169+fhernandezvivanco@users.noreply.github.com> Date: Fri, 5 Jul 2024 16:31:15 +1000 Subject: [PATCH] Load arbitrary number of datafiles from a master file (#6) * add option to specify number of datafiles loaded * bump version * raise HTTPException when datafiles cannot be loaded * update get_master_file return schema --- .pre-commit-config.yaml | 10 +- .../routes/ansto_endpoints/load_hdf5_files.py | 34 +- ansto_simplon_api/schemas/ansto_endpoints.py | 9 + ansto_simplon_api/simulate_zmq_stream.py | 218 ++---------- poetry.lock | 316 +++++++++--------- pyproject.toml | 6 +- 6 files changed, 234 insertions(+), 359 deletions(-) create mode 100644 ansto_simplon_api/schemas/ansto_endpoints.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2a7345e..2722889 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ default_language_version: python: python3.11 repos: - repo: https://github.com/myint/autoflake - rev: v2.2.1 + rev: v2.3.1 hooks: - id: autoflake name: Autoflake @@ -14,13 +14,13 @@ repos: - --remove-duplicate-keys - --remove-unused-variables - repo: https://github.com/psf/black - rev: 23.7.0 + rev: 24.4.2 hooks: - id: black name: Black language_version: python3.11 - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.6.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -36,7 +36,7 @@ repos: args: ["--fix=lf"] - id: requirements-txt-fixer - repo: https://github.com/PyCQA/isort - rev: 5.12.0 + rev: 5.13.2 hooks: - id: isort name: Import Sort @@ -44,7 +44,7 @@ repos: - --settings=. exclude: /__init__\.py$ - repo: https://github.com/PyCQA/flake8 - rev: 6.1.0 + rev: 7.1.0 hooks: - id: flake8 name: Flake8 diff --git a/ansto_simplon_api/routes/ansto_endpoints/load_hdf5_files.py b/ansto_simplon_api/routes/ansto_endpoints/load_hdf5_files.py index c2f1477..749f27f 100644 --- a/ansto_simplon_api/routes/ansto_endpoints/load_hdf5_files.py +++ b/ansto_simplon_api/routes/ansto_endpoints/load_hdf5_files.py @@ -1,14 +1,40 @@ from fastapi import APIRouter +from fastapi.exceptions import HTTPException +from starlette import status -from ...schemas.configuration import SimplonRequestStr +from ...schemas.ansto_endpoints import LoadHDF5File from ...simulate_zmq_stream import zmq_stream router = APIRouter(prefix="/ansto_endpoints", tags=["ANSTO Endpoints"]) -@router.put("/load_hdf5_master_file") -async def set_user_data(hdf5_file_path: SimplonRequestStr): - zmq_stream.hdf5_file_path = hdf5_file_path.value +@router.put("/hdf5_master_file") +async def set_master_file(hdf5_model: LoadHDF5File): + try: + zmq_stream.create_list_of_compressed_frames( + hdf5_file_path=hdf5_model.hdf5_file_path, + compression=hdf5_model.compression, + number_of_datafiles=hdf5_model.number_of_datafiles, + ) + except IndexError: + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail="The number of datafiles specified exceed the number of datafiles available " + "in the master file. Reduce number_of_datafiles", + ) + except Exception as e: + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e) + ) zmq_stream.frame_id = 0 zmq_stream.image_number = 0 return {"value": zmq_stream.hdf5_file_path} + + +@router.get("/hdf5_master_file") +async def get_master_file() -> LoadHDF5File: + return LoadHDF5File( + hdf5_file_path=zmq_stream.hdf5_file_path, + number_of_datafiles=zmq_stream.number_of_data_files, + compression=zmq_stream.compression, + ) diff --git a/ansto_simplon_api/schemas/ansto_endpoints.py b/ansto_simplon_api/schemas/ansto_endpoints.py new file mode 100644 index 0000000..04d2dd8 --- /dev/null +++ b/ansto_simplon_api/schemas/ansto_endpoints.py @@ -0,0 +1,9 @@ +from typing import Literal + +from pydantic import BaseModel, Field + + +class LoadHDF5File(BaseModel): + hdf5_file_path: str = Field(examples=["/path/to/master_file"]) + number_of_datafiles: int | None = Field(default=None, examples=[1]) + compression: Literal["bslz4", "none"] = Field(default="bslz4", examples=["bslz4"]) diff --git a/ansto_simplon_api/simulate_zmq_stream.py b/ansto_simplon_api/simulate_zmq_stream.py index ff16a9b..9028ae3 100644 --- a/ansto_simplon_api/simulate_zmq_stream.py +++ b/ansto_simplon_api/simulate_zmq_stream.py @@ -5,7 +5,6 @@ from copy import deepcopy from datetime import datetime, timezone from os import environ -from typing import Any import bitshuffle import cbor2 @@ -72,7 +71,8 @@ def __init__( self.socket = self.context.socket(zmq.PUSH) self.socket.bind(self.address) - self._sequence_id = 0 + self.frames = None + self.sequence_id = 0 self.frame_id = 0 @@ -82,6 +82,9 @@ def __init__( self.series_unique_id = None self.frames = None self.hdf5_file_path = hdf5_file_path + self.create_list_of_compressed_frames( + self.hdf5_file_path, self.compression, self.number_of_data_files + ) logging.info(f"ZMQ Address: {self.address}") logging.info(f"Hdf5 file path: {self.hdf5_file_path}") @@ -90,7 +93,10 @@ def __init__( logging.info(f"Number of data files: {self.number_of_data_files}") def create_list_of_compressed_frames( - self, hdf5_file_path: str, compression: str + self, + hdf5_file_path: str, + compression: str, + number_of_datafiles: int | None = None, ) -> list[dict]: """ Creates a list of compressed frames from a hdf5 file @@ -102,6 +108,9 @@ def create_list_of_compressed_frames( compression : str Compression type. Accepted compression types are lz4 and bslz4. Default value is bslz4 + number_of_datafiles: int | None = None + The number of datafiles loaded in memory. If number_of_datafiles=None, + we load all datafiles specified in the master file Raises ------ @@ -114,24 +123,26 @@ def create_list_of_compressed_frames( A list containing a dictionary of compressed frames, and frame metadata """ + self.hdf5_file_path = hdf5_file_path + self.compression = compression + self.number_of_data_files = number_of_datafiles - hdf5_file = h5py.File(hdf5_file_path) - keys = list(hdf5_file["entry"]["data"].keys()) + with h5py.File(hdf5_file_path) as hdf5_file: + keys = list(hdf5_file["entry"]["data"].keys()) - datafile_list: list[npt.NDArray] = [ - np.array(hdf5_file["entry"]["data"][keys[i]]) - for i in range(self.number_of_data_files) - ] + if number_of_datafiles is None: + self.number_of_data_files = len(keys) - # Would make more sense in the __init__ section - # but then we'd need to read the file twice - self.start_message, self.image_message, self.end_message = Parse( - hdf5_file - ).header() + datafile_list: list[npt.NDArray] = [ + np.array(hdf5_file["entry"]["data"][keys[i]]) + for i in range(self.number_of_data_files) + ] - # Delete the hdf5_file, we got what we needed - hdf5_file.close() - del hdf5_file + # Would make more sense in the __init__ section + # but then we'd need to read the file twice + self.start_message, self.image_message, self.end_message = Parse( + hdf5_file + ).header() number_of_frames_per_data_file = [ datafile.shape[0] for datafile in datafile_list @@ -175,7 +186,7 @@ def create_list_of_compressed_frames( logging.info(f"Number of unique frames: {len(frame_list)}") del datafile_list - return frame_list + self.frames = frame_list def create_image_cbor_object( self, @@ -338,177 +349,6 @@ def start_stream(self) -> None: self.stream_frames(self.frames) self.stream_end_message() - @property - def sequence_id(self) -> int: - """ - Gets the sequence_id - - Returns - ------- - self._sequence_id: int - The sequence_id - """ - return self._sequence_id - - @sequence_id.setter - def sequence_id(self, value: int) -> None: - """ - Sets the sequence_id - - Returns - ------- - None - """ - self._sequence_id = value - - @property - def image_number(self) -> int: - """ - Gets the image_number - - Returns - ------- - self._image_number: int - The image_number - """ - return self._image_number - - @image_number.setter - def image_number(self, value: int) -> None: - """ - Sets the image_number - - Returns - ------- - None - """ - self._image_number = value - - @property - def number_of_frames_per_trigger(self) -> None: - """ - Sets the number of frames per trigger - - Returns - ------- - None - """ - return self._number_of_frames_per_trigger - - @number_of_frames_per_trigger.setter - def number_of_frames_per_trigger(self, value: int) -> None: - """ - Sets the image_number - - Parameters - ---------- - value : int - The number of frames per trigger - - Returns - ------- - None - """ - self._number_of_frames_per_trigger = value - logging.info(f"nimages set to: {value}") - - @property - def user_data(self) -> Any: - """ - Gets the user data - - Returns - ------- - self._user_data : Any - The user data - """ - return self._user_data - - @user_data.setter - def user_data(self, value: Any) -> None: - """ - Sets the user data - - Parameters - ---------- - value : Any - New value - - Returns - ------- - None - """ - self._user_data = value - - @property - def compression(self) -> str: - """ - Gets the compression type - - Returns - ------- - self._user_data : Any - The user data - """ - return self._compression - - @compression.setter - def compression(self, value: str) -> None: - """ - Sets the compression type - - Parameters - ---------- - value : str - New value - - Returns - ------- - None - """ - allowed_compressions = ["bslz4", "none"] - if value.lower() in allowed_compressions: - self._compression = value - try: - self.frames = self.create_list_of_compressed_frames( - self.hdf5_file_path, self.compression - ) - except AttributeError: - pass - else: - raise ValueError( - "Allowed compressions are bslz4 and none only" f"not {value}" - ) - - @property - def hdf5_file_path(self) -> str: - """ - Gets the hdf5_file_path - - Returns - ------- - self._hdf5_file_path : str - The hdf5 file name - """ - return self._hdf5_file_path - - @hdf5_file_path.setter - def hdf5_file_path(self, value: str) -> None: - """ - Sets the hdf5 file name and loads frames from the HDF5 file into memory - - Parameters - ---------- - value : str - The hdf5 filename - """ - logging.info("Loading dataset...") - self._hdf5_file_path = value - self.frames = self.create_list_of_compressed_frames( - self._hdf5_file_path, self.compression - ) - logging.info("Dataset loaded") - ZMQ_ADDRESS = environ.get("ZMQ_ADDRESS", "tcp://*:5555") try: diff --git a/poetry.lock b/poetry.lock index 909e898..0a4f246 100644 --- a/poetry.lock +++ b/poetry.lock @@ -147,13 +147,13 @@ test = ["coverage (>=7)", "hypothesis", "pytest"] [[package]] name = "certifi" -version = "2024.2.2" +version = "2024.6.2" 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