diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d5c80a5c..bb5fabb3 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,7 +20,7 @@ jobs: fail-fast: false matrix: os: ['ubuntu-latest', 'windows-latest', 'macos-14'] - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.11", "3.12", "3.13", "3.14"] exclude: - os: 'windows-latest' python-version: "3.13" diff --git a/mio/data/tubes/stream/stream-fpga.yaml b/mio/data/tubes/stream/stream-fpga.yaml new file mode 100644 index 00000000..b41705b0 --- /dev/null +++ b/mio/data/tubes/stream/stream-fpga.yaml @@ -0,0 +1,35 @@ +noob_id: stream-fpga +description: | + Source of fpga data for the stream device + +input: + config: + type: mio.devices.stream.StreamDevConfig + scope: tube + capture_binary: + type: pathlib.Path | None + scope: tube + +nodes: + fpga: + type: mio.devices.stream.nodes.iter_fpga + params: + config: input.config + split_buffers: + type: mio.devices.stream.nodes.SplitBuffers + params: + config: input.config + depends: + - chunk: fpga.chunk + + # binary i/o + write_binary: + type: mio.io.append_binary + depends: + - path: input.capture_binary + - data: fpga.chunk + + return: + type: return + depends: + - buffers: split_buffers.buffers diff --git a/mio/data/tubes/stream/stream-frame.yaml b/mio/data/tubes/stream/stream-frame.yaml new file mode 100644 index 00000000..2e0c57db --- /dev/null +++ b/mio/data/tubes/stream/stream-frame.yaml @@ -0,0 +1,11 @@ +noob_id: 1 +description: | + Frame assembly from buffers + +input: + config: + type: mio.devices.stream.StreamDevConfig + scope: tube + buffers: + type: list[bytes] + scope: process diff --git a/mio/data/tubes/stream/stream.yaml b/mio/data/tubes/stream/stream.yaml new file mode 100644 index 00000000..94424301 --- /dev/null +++ b/mio/data/tubes/stream/stream.yaml @@ -0,0 +1,23 @@ +noob_id: stream +description: | + Combined core streamdev pipeline (WIP) + +input: + config: + type: mio.devices.stream.StreamDevConfig + scope: tube + capture_binary: + type: pathlib.Path | None + scope: tube + +nodes: + fpga: + type: tube + params: + tube: stream-fpga + frame-assembly: + type: tube + params: + tube: stream-frame + depends: + - buffers: fpga.buffers diff --git a/mio/devices/base/headers.py b/mio/devices/base/headers.py index 2f56109b..91200a7e 100644 --- a/mio/devices/base/headers.py +++ b/mio/devices/base/headers.py @@ -1,18 +1,12 @@ """Base device headers""" -import sys from collections.abc import Sequence -from typing import Any, ClassVar +from typing import Any, ClassVar, Self import pandera.pandas as pa from mio.models import Container, Table -if sys.version_info <= (3, 11): - from typing_extensions import Self -else: - from typing import Self - class BufferHeader(Container): """ diff --git a/mio/devices/stream/config.py b/mio/devices/stream/config.py index 35d29703..60bcf87d 100644 --- a/mio/devices/stream/config.py +++ b/mio/devices/stream/config.py @@ -231,3 +231,10 @@ def buffer_npix(self) -> list[int]: ) quotient, remainder = divmod(px_per_frame, payload_bytes) return [payload_bytes] * int(quotient) + ([int(remainder)] if remainder else []) + + @property + def read_length(self) -> int: + """ + How many bytes to read from the FPGA per chunk, roughly the expected size of a buffer + """ + return int(max(self.buffer_npix) * self.pix_depth / 8 / 16) * 16 diff --git a/mio/devices/stream/headers.py b/mio/devices/stream/headers.py index ee3ee768..edbb4bb2 100644 --- a/mio/devices/stream/headers.py +++ b/mio/devices/stream/headers.py @@ -2,7 +2,6 @@ from __future__ import annotations -import sys import time from typing import TYPE_CHECKING, ClassVar @@ -19,10 +18,7 @@ if TYPE_CHECKING: from mio.devices.stream.config import StreamDevConfig -if sys.version_info < (3, 11): - from typing_extensions import Self -else: - from typing import Self +from typing import Self class ADCScaling(MiniscopeConfig): diff --git a/mio/devices/stream/nodes.py b/mio/devices/stream/nodes.py index b4b333cc..81e16ed2 100644 --- a/mio/devices/stream/nodes.py +++ b/mio/devices/stream/nodes.py @@ -9,11 +9,17 @@ import queue import time from collections.abc import Callable, Generator, Iterator +from functools import cached_property from pathlib import Path +from typing import Annotated as A from typing import Any, Union +from typing import Literal as L import numpy as np from bitstring import BitArray, Bits +from noob import Name, Node +from noob.event import MetaSignal +from pydantic import PrivateAttr from mio import init_logger from mio.devices.stream import StreamBufferHeader, StreamDevConfig @@ -33,6 +39,61 @@ pass # okDev stays None; error raised when actually trying to use FPGA +def iter_fpga(config: StreamDevConfig) -> Generator[A[bytes, Name("chunk")], None, None]: + """ + Iterate a raw binary stream from the FPGA in chunks + (not necessarily split into buffers) + """ + # set up fpga interfaces + dev = init_okdev(config.bitstream, config.read_length) + + while True: + yield next(dev) + + +class SplitBuffers(Node): + """ + Collect raw chunks from the FPGA, yield buffers + + The data are passed in fixed chunks. + Then we concatenate the chunks and try to look for {attr}`.SplitBuffers.preamble` in the data. + The data between every pair of {attr}`.SplitBuffers.preamble` + is considered to be a single buffer and yielded. + """ + + config: StreamDevConfig + _buffer: BitArray = PrivateAttr(default_factory=BitArray) + + @cached_property + def preamble(self) -> Bits: + """ + The preamble that indicates the start of a buffer. + + If ``config.reverse_header_bits`` is true, the preamble is bit-flipped + """ + pre = Bits(self.config.preamble) + if self.config.reverse_header_bits: + pre = pre[::-1] + return pre + + def process(self, chunk: bytes) -> A[list[bytes] | L[MetaSignal.NoEvent], Name("chunks")]: + """ + Append the chunk to the buffer, return any split buffers, if found. + """ + self._buffer += BitArray(chunk) + pos = list(self._buffer.findall(self.preamble)) + buffers = [self._buffer[start:stop].tobytes() for start, stop in zip(pos[:-1], pos[1:])] + if buffers: + self._buffer = self._buffer[pos[-1] :] + return buffers + else: + return MetaSignal.NoEvent + + def deinit(self) -> None: + """Clear the internal buffer""" + self._buffer = BitArray() + + def exact_iter(f: Callable, sentinel: Any) -> Generator[Any, None, None]: """ A version of :func:`iter` that compares with `is` rather than `==` diff --git a/mio/interfaces/mocks.py b/mio/interfaces/mocks.py index bebf3308..bd2f8dd6 100644 --- a/mio/interfaces/mocks.py +++ b/mio/interfaces/mocks.py @@ -10,13 +10,8 @@ # ruff: noqa: D102 import os -import sys from pathlib import Path - -if sys.version_info < (3, 11): - from typing_extensions import Self -else: - from typing import Self +from typing import Self from mio.exceptions import EndOfRecordingException diff --git a/mio/interfaces/opalkelly.py b/mio/interfaces/opalkelly.py index ffaee048..ed5a172f 100644 --- a/mio/interfaces/opalkelly.py +++ b/mio/interfaces/opalkelly.py @@ -2,12 +2,7 @@ Interfaces for OpalKelly (model number?) FPGAs """ -import sys - -if sys.version_info < (3, 11): - from typing_extensions import Self -else: - from typing import Self +from typing import Self from mio.exceptions import ( DeviceConfigurationError, diff --git a/mio/io/binary.py b/mio/io/binary.py new file mode 100644 index 00000000..7525085f --- /dev/null +++ b/mio/io/binary.py @@ -0,0 +1,12 @@ +"""Raw bytes i/o""" + +from pathlib import Path + + +def append_binary(path: Path | None, data: bytes) -> None: + """Just append some binary to a path!""" + if path is None: + # FIXME: Still working how we want enabling/disabling binary i/o to look like in streamdev + return + with open(path, "ab") as f: + f.write(data) diff --git a/mio/models/dataset.py b/mio/models/dataset.py index 012deffd..1caa345c 100644 --- a/mio/models/dataset.py +++ b/mio/models/dataset.py @@ -56,11 +56,10 @@ """ import re -import sys import warnings from pathlib import Path from typing import Annotated as A -from typing import Any, Literal, TypeAlias +from typing import Any, Literal, Self, TypeAlias, TypedDict import pandas as pd from numpydantic import NDArraySchema @@ -80,11 +79,6 @@ from mio.models.process import NoisePatchConfig from mio.utils import _format_ranges -if sys.version_info < (3, 11): - from typing_extensions import Self, TypedDict -else: - from typing import Self, TypedDict - VIDEO_EXTENSIONS = (".avi", ".mp4") RECORDING_TYPES = Literal["raw", "stitched"] DERIVATION_TYPES = Literal["stitched"] diff --git a/mio/models/devupdate.py b/mio/models/devupdate.py index b49af5ba..65d6f5bd 100644 --- a/mio/models/devupdate.py +++ b/mio/models/devupdate.py @@ -2,17 +2,12 @@ Models for device update commands. """ -import sys from enum import Enum +from typing import Self import serial.tools.list_ports from pydantic import BaseModel, field_validator, model_validator -if sys.version_info < (3, 11): - from typing_extensions import Self -else: - from typing import Self - class DeviceCommand(Enum): """Commands for device.""" diff --git a/mio/models/mixins.py b/mio/models/mixins.py index 0ca0cfe9..8abba422 100644 --- a/mio/models/mixins.py +++ b/mio/models/mixins.py @@ -5,7 +5,6 @@ import re import shutil -import sys from collections.abc import Iterator from importlib.metadata import version from itertools import chain @@ -14,6 +13,8 @@ Any, ClassVar, Literal, + NotRequired, + Self, TypedDict, TypeVar, overload, @@ -22,11 +23,6 @@ import yaml from pydantic import BaseModel, Field, ValidationError, field_validator -if sys.version_info < (3, 11): - from typing_extensions import NotRequired, Self -else: - from typing import NotRequired, Self - from mio.types import ConfigID, ConfigSource, PythonIdentifier, valid_config_id T = TypeVar("T") diff --git a/mio/models/models.py b/mio/models/models.py index 927a230a..ae27e2a6 100644 --- a/mio/models/models.py +++ b/mio/models/models.py @@ -2,20 +2,14 @@ Base and meta model classes. """ -import sys from pathlib import Path -from typing import Any, ClassVar +from typing import Any, ClassVar, Self import pandas as pd import pandera.pandas as pa from pandera.typing import DataFrame from pydantic import BaseModel -if sys.version_info < (3, 11): - from typing_extensions import Self -else: - from typing import Self - class MiniscopeIOModel(BaseModel): """ diff --git a/mio/process/frame_helper.py b/mio/process/frame_helper.py index 1dc095a5..964cc725 100644 --- a/mio/process/frame_helper.py +++ b/mio/process/frame_helper.py @@ -4,8 +4,8 @@ from __future__ import annotations -import sys from abc import abstractmethod +from typing import TypedDict import cv2 import numpy as np @@ -18,11 +18,6 @@ NoisePatchConfig, ) -if sys.version_info < (3, 11): - from typing_extensions import TypedDict -else: - from typing import TypedDict - logger = init_logger("frame_helper") diff --git a/mio/types.py b/mio/types.py index a05f6341..c662d71c 100644 --- a/mio/types.py +++ b/mio/types.py @@ -6,16 +6,14 @@ import sys from os import PathLike from pathlib import Path -from typing import Annotated, Any +from typing import Annotated, Any, TypeAlias from pydantic import AfterValidator, Field -if sys.version_info < (3, 10) or sys.version_info < (3, 13): - from typing import TypeAlias - +if sys.version_info < (3, 13): from typing_extensions import TypeIs else: - from typing import TypeAlias, TypeIs + from typing import TypeIs CONFIG_ID_PATTERN = r"[\w\-\/#]+" """ diff --git a/mio/utils.py b/mio/utils.py index 457ec51e..c944e785 100644 --- a/mio/utils.py +++ b/mio/utils.py @@ -83,3 +83,8 @@ def _format_ranges(indices: list[int] | set[int]) -> list[str]: ranges.append(f"{start}-{end}" if start != end else str(start)) return ranges + + +def add_noob_sources() -> list[Path]: + """Provide the tubes directory so that noob can find it!""" + return [Path(__file__).parent / "data" / "tubes"] diff --git a/pylock.toml b/pylock.toml index 12e93f17..603e4412 100644 --- a/pylock.toml +++ 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"==3.14.*" +requires_python = ">=3.14.0,<4.0" diff --git a/pyproject.toml b/pyproject.toml index f1e7443b..d5d4841b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ authors = [ license = {text = "AGPL-3.0"} dynamic = ["version"] -requires-python = "<4.0,>=3.10" +requires-python = "<4.0,>=3.11" dependencies = [ "opencv-python>=4.7.0.72; platform_system!='Darwin'", "opencv-python>=4.7.0.72,<4.13.0.90; platform_system=='Darwin'", # latest versions not built with ffmpeg support @@ -29,6 +29,7 @@ dependencies = [ 'scipy>=1.16.1; python_version>="3.14"', # first version with wheels for 3.14 "numpydantic>=1.8.1", "pandera>=0.31.1", + "noob>=1000.0.1", ] readme = "README.md" @@ -89,6 +90,9 @@ all = [ "mio[tests,docs,dev,ntp]" ] +[project.entry-points."noob.add_sources"] +tubes = "mio.utils:add_noob_sources" + [project.scripts] mio = "mio.cli.main:cli" @@ -105,8 +109,8 @@ format.composite = [ docs-prod = "python -m sphinx -M html ./docs ./docs/_build -W -E -a --keep-going" # lock twice until we drop 3.10 because of scipy dropping wheels for 3.10 lock.composite = [ - 'pdm lock --with :all --python="<3.14.*"', - 'pdm lock --with :all --python=">=3.14.*" --append' + 'pdm lock --with :all --python="<3.14"', + 'pdm lock --with :all --python=">=3.14" --append' ] [tool.pdm.build] @@ -145,7 +149,7 @@ omit = [ ] [tool.ruff] -target-version = "py310" +target-version = "py311" include = ["mio/**/*.py", "tests/**/*.py", "pyproject.toml"] exclude = ["docs", "mio/vendor", "noxfile.py"] line-length = 100 @@ -227,6 +231,6 @@ follow_imports = "silent" warn_unreachable = true [tool.black] -target-version = ['py310', 'py311', 'py312', 'py313'] +target-version = ['py311', 'py312', 'py313'] extend-exclude = 'mio/vendor/.*' line-length = 100 diff --git a/tests/test_process/test_frame_helper.py b/tests/test_process/test_frame_helper.py index 93e59906..665196bc 100644 --- a/tests/test_process/test_frame_helper.py +++ b/tests/test_process/test_frame_helper.py @@ -1,5 +1,5 @@ import sys -from enum import Enum +from enum import StrEnum from pprint import pformat import cv2 @@ -19,7 +19,7 @@ from typing import TypedDict -class GroundTruthCategory(str, Enum): +class GroundTruthCategory(StrEnum): check_pattern = "check_pattern" blacked_out = "blacked_out"