diff --git a/README.md b/README.md index d975f08..7a68e2d 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ This project uses [uv](https://docs.astral.sh/uv/) to manage its dependencies. I Code formatting is done with [ruff](https://docs.astral.sh/ruff/), just use `ruff format src`. -## Running mr-t +## Running mr-t – normal mode If you have uv installed (see above) running the main program should be as easy as: @@ -29,6 +29,18 @@ Note that you have to install the dependencies mentioned in `pyproject.toml` bef There is a configurable `--frame-cache-limit` which, if you set it, will limit the number of frames held in memory to be no higher than this number. Meaning, the ZeroMQ messages will be held until the receiver picks them up. +## Running mr-t — simulation + +If you already have a finished image series stored in an HDF5 file, you can tell mr-t to read images from this file, instead of waiting for images via ZMQ. A sample command line looks like this: + +``` +uv run mr_t --input-h5-file ~/178_data-00000.nx5 --frame-cache-limit 5 --udp-host localhost --udp-port 9000 +``` + +Note that in addition to `--input-h5-file` we are passing `--frame-cache-limit 5`. This will read at most 5 frames from the HDF5 file and wait until the other side (the FPGA) has actually pulled images from this cache. If you don't do this, and the receiving end is too slow, you will eat up a lot of RAM with all the cached images. + +Currently only one HDF5 file is supported to be read, since the Dectris detectors write a `master` file which you can specify if you want to feed a whole image series. + ## How it works ### Main loop diff --git a/pyproject.toml b/pyproject.toml index 2464fde..5dce242 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,6 +7,7 @@ requires-python = ">=3.12" dependencies = [ "asyncudp==0.11.0", "culsans==0.7.1", + "h5py==3.14.0", "pyzmq==26.2.0", "structlog==24.4.0", "typed-argument-parser==1.10.1", diff --git a/src/mr_t/h5.py b/src/mr_t/h5.py index 9be7d49..4deff6d 100644 --- a/src/mr_t/h5.py +++ b/src/mr_t/h5.py @@ -1,22 +1,29 @@ -import culsans +import asyncio +from pathlib import Path +import h5py +from typing import AsyncIterator, Callable import structlog -from mr_t.eiger_stream1 import ZmqMessage +from mr_t.eiger_stream1 import ZmqHeader, ZmqImage, ZmqMessage, ZmqSeriesEnd parent_log = structlog.get_logger() -def h5_writer_process(queue: culsans.SyncQueue[int]) -> None: - parent_log.info("in writer process, starting main loop") - while True: - element = queue.get() # noqa: F841 - parent_log.info(f"got new element, queue size now: {queue.qsize()}") - parent_log.info("sleeping a bit") - # time.sleep(5) - queue.join() +async def receive_h5_messages( + input_file: Path, log: structlog.BoundLogger, cache_full: Callable[[], bool] +) -> AsyncIterator[ZmqMessage]: + log.info(f"begin reading frames from file {input_file}") - -async def write_to_h5(msg: ZmqMessage, q: culsans.AsyncQueue[ZmqMessage]) -> None: - parent_log.info("writing to h5") - await q.put(msg) - parent_log.info("writing to h5 DONE") + with h5py.File(input_file, "r") as f: + dataset = f["entry/data/data"] + assert isinstance(dataset, h5py.Dataset) + frame_count = len(dataset) + yield ZmqHeader( + series_id="1", config={"nimages": frame_count, "ntrigger": 1}, appendix=None + ) + for frame_number in range(0, frame_count): + if cache_full(): + await asyncio.sleep(0.5) + continue + yield ZmqImage(dataset[frame_number][:].tobytes()) + yield ZmqSeriesEnd() diff --git a/src/mr_t/server.py b/src/mr_t/server.py index 4365434..ff36aee 100644 --- a/src/mr_t/server.py +++ b/src/mr_t/server.py @@ -3,7 +3,16 @@ import struct import sys import logging -from typing import Any, AsyncIterable, AsyncIterator, Optional, TypeAlias, TypeVar +from typing import ( + Any, + AsyncIterable, + AsyncIterator, + Callable, + Optional, + TypeAlias, + TypeVar, +) +from pathlib import Path import asyncudp import structlog @@ -15,6 +24,7 @@ ZmqSeriesEnd, receive_zmq_messages, ) +from mr_t.h5 import receive_h5_messages parent_log = structlog.get_logger() @@ -22,7 +32,12 @@ class Arguments(Tap): udp_port: int udp_host: str - eiger_zmq_host_and_port: str + eiger_zmq_host_and_port: Optional[str] = ( # host:port of the Eiger ZMQ interface + None + ) + input_h5_file: Optional[ # hdf5 file to feed into Mr. T to mock the detector + Path + ] = None frame_cache_limit: Optional[ # Limit the number of incoming ZeroMQ images to this number (can prevent memory overruns) int ] = None @@ -191,13 +206,35 @@ class CurrentSeries: async def main_async() -> None: args = Arguments(underscores_to_dashes=True).parse_args() + if args.eiger_zmq_host_and_port is None and args.input_h5_file is None: + sys.stderr.write( + "invalid arguments: specify either an Eiger ZMQ host and port, or an H5 file to use" + ) + sys.exit(1) + if args.eiger_zmq_host_and_port is not None and args.input_h5_file is not None: + sys.stderr.write( + "invalid arguments: specify either an Eiger ZMQ host and port, or an H5 file to use, but not both!" + ) + sys.exit(2) + current_series: CurrentSeries | None = None - sender = receive_zmq_messages( - zmq_target=args.eiger_zmq_host_and_port, - log=parent_log.bind(system="eiger"), - cache_full=lambda: len(current_series.saved_frames) > args.frame_cache_limit + cache_full: Callable[[], 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