libertem-dectris 0.2.13

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LiberTEM-dectris-rs

This is a Python package for efficiently receiving data from DECTRIS detectors with the zeromq interface. The low-level, high-frequency operations are performed in a background thread implemented in rust, and multiple frames are batched together for further processing in Python.

It is built for LiberTEM-live, but can also be used stand-alone.

Usage

import numpy as np
import libertem_dectris
from libertem_live.detectors.dectris.DEigerClient import DEigerClient

# trigger acquisition via the REST API, needs `libertem-live`
nimages = 256 * 256
ec = DEigerClient('localhost', 8910)  # hostname and port of the DCU REST API
ec.setDetectorConfig('ntrigger', 1)
ec.setDetectorConfig('nimages', 1)
ec.setDetectorConfig('trigger_mode', 'exte')
ec.setDetectorConfig('ntrigger', nimages)
result = ec.sendDetectorCommand('arm')
sequence_id = result['sequence id'] 

conn = libertem_dectris.DectrisConnection(
    uri="tcp://localhost:9999",
    handle_path="/tmp/dectris_shm",
    frame_stack_size=32,
    num_slots=2000,
    bytes_per_frame=512*512,
    huge=False,
)

# as we have armed the detector above, we know the sequence number
# that we should expect:
# (in other cases, can also call
# `conn.start_passive` and `conn.wait_for_arm` to passively wait for
# the detector to be armed)
conn.start(sequence_id)

# any other process can use a `CamClient` to use data
# stored in the SHM:
cam_client = libertem_dectris.CamClient(conn.get_socket_path())

try:
    while True:
        # get at most `max_size` frames as a stack
        # (might get less at the end of the acquisition)
        stack_handle = conn.get_next_stack(max_size=32)

        # if the receiver is idle, stack_handle will be None here:
        if stack_handle is None:
            break

        # the expected shape and data type:
        frame_shape = tuple(reversed(stack_handle.get_shape()))
        dtype = np.dtype(stack_handle.get_pixel_type()).newbyteorder(
            stack_handle.get_endianess()
        )

        # pre-allocate some memory for the pixel data:
        # (would be pulled out of the loop in real code)
        buf = np.zeros((len(stack_handle),) + frame_shape, dtype=dtype)

        # decompress into the pre-allocated buffer
        cam_client.decompress_frame_stack(stack_handle, out=buf)

        # free up the shared memory slot for this frame stack:
        cam_client.done(stack_handle)

        # we can still use the decompressed data:
        buf.sum()
finally:
    conn.close()  # clean up background thread etc.
    cam_client.close()

Changelog

v0.2.13

• Updated dependencies and improved error handling

v0.2.12

• Refactored and unified interface - allows for more code sharing between crates
• Some robustness changes around adding timeout parameters for many top-level operations

v0.2.11

• Re-release for CI changes

v0.2.10

• Add functionality to generate mock data for sending via the simulator
• Add missing numpy dependency
• Make debug output a bit more reliable

v0.2.9

• Add more debug and trace output

v0.2.7

• Log more details in DectrisConnection.log_shm_stats and change log level to INFO
• Increase timeout for sending headers and frames

v0.2.4 - v0.2.6

• Updated examples and CI configuration

v0.2.3

• Add env_logger: set environment variable LIBERTEM_DECTRIS_LOG_LEVEL to e.g. 'INFO' to enable logging
• Improved error handling: raise an exception instead of panicing on serialization errors
• Ignore messages with mismatching series ID
• Add explicit checks for the correct header_detail levels
• Move code into monorepo

v0.2.2

• Vendor bitshuffle and add Frame.decompress_into method, PR #10

v0.2.1

• Catch frame ID mismatch, PR #9

v0.2.0

• Added libertem_dectris.headers submodule that exports header classes
• Added ways to create libertem_dectris.Frame and libertem_dectris.FrameStack objects from Python, mostly useful for testing
• Added binding to random port for the simulator
• Properly parametrize with zmq endpoint URI
• Fix many clippy complaints

v0.1.0

Initial release!

Development

This package is using pyo3 with maturin to create the Python bindings. First, make sure maturin is installed in your Python environment:

(venv) $ pip install maturin

Then, after each change to the rust code, run maturin develop -r to build and install a new version of the wheel.

As we vendor bitshuffle, make sure to clone with git clone --recursive ..., or manually take care of initializing and updating submodules.

Release

• update changelog above
• bump version in Cargo.toml if not already bumped, and push
• create a release from the GitHub UI, creating a new tag vX.Y.Z
• done!