Merge branch 'main' into feat-device-reader-constructors

Author: bruno-f-cruz

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.9, 3.11]
+        python-version: [3.9, 3.12]
       fail-fast: false
     steps:
       - name: Checkout

.gitignore

@@ -1,12 +1,23 @@
-# Environment files
-.vscode
-.venv
-
-# Python temp files
-__pycache__
-*.pyc
-*.egg-info
-dist
-
-# Data files
-/data
+# Byte-compiled / optimized / DLL files
+__pycache__/
+
+# Distribution / packaging
+dist/
+_version.py
+*.egg-info/
+*.egg
+
+# IDE
+.vscode/*
+
+# misc
+log*.txt
+scratch/
+scratch*.py
+
+# Test
+.coverage
+
+# Environment
+.venv/
+uv.lock

harp/__init__.py

@@ -1,6 +1,5 @@
-from harp.io import REFERENCE_EPOCH, MessageType, read
+from harp.io import REFERENCE_EPOCH, MessageType, read, to_buffer, to_file
 from harp.reader import create_reader
 from harp.schema import read_schema
 
-
-__all__ = ["REFERENCE_EPOCH", "MessageType", "read", "create_reader", "read_schema"]
+__all__ = ["REFERENCE_EPOCH", "MessageType", "read", "to_buffer", "to_file", "create_reader", "read_schema"]

harp/io.py

@@ -4,9 +4,12 @@
 from typing import Any, BinaryIO, Optional, Union
 
 import numpy as np
+import numpy.typing as npt
 import pandas as pd
 from pandas._typing import Axes
 
+from harp.typing import _BufferLike, _FileLike
+
 REFERENCE_EPOCH = datetime(1904, 1, 1)
 """The reference epoch for UTC harp time."""
 
@@ -21,8 +24,9 @@ class MessageType(IntEnum):
 
 
 _SECONDS_PER_TICK = 32e-6
+_PAYLOAD_TIMESTAMP_MASK = 0x10
 _messagetypes = [type.name for type in MessageType]
-_payloadtypes = {
+_dtypefrompayloadtype = {
     1: np.dtype(np.uint8),
     2: np.dtype(np.uint16),
     4: np.dtype(np.uint32),
@@ -33,33 +37,34 @@ class MessageType(IntEnum):
     136: np.dtype(np.int64),
     68: np.dtype(np.float32),
 }
+_payloadtypefromdtype = {v: k for k, v in _dtypefrompayloadtype.items()}
 
 
 def read(
-    file: Union[str, bytes, PathLike[Any], BinaryIO],
+    file_or_buf: Union[_FileLike, _BufferLike],
     address: Optional[int] = None,
     dtype: Optional[np.dtype] = None,
     length: Optional[int] = None,
     columns: Optional[Axes] = None,
     epoch: Optional[datetime] = None,
     keep_type: bool = False,
 ):
-    """Read single-register Harp data from the specified file.
+    """Read single-register Harp data from the specified file or buffer.
 
     Parameters
     ----------
-    file
-        Open file object or filename containing binary data from
+    file_or_buf
+        File path, open file object, or buffer containing binary data from
         a single device register.
     address
         Expected register address. If specified, the address of
-        the first message in the file is used for validation.
+        the first message is used for validation.
     dtype
         Expected data type of the register payload. If specified, the
-        payload type of the first message in the file is used for validation.
+        payload type of the first message is used for validation.
     length
         Expected number of elements in register payload. If specified, the
-        payload length of the first message in the file is used for validation.
+        payload length of the first message is used for validation.
     columns
         The optional column labels to use for the data values.
     epoch
@@ -72,9 +77,20 @@ def read(
     -------
         A pandas data frame containing message data, sorted by time.
     """
-    data = np.fromfile(file, dtype=np.uint8)
+    if isinstance(file_or_buf, (str, PathLike, BinaryIO)) or hasattr(file_or_buf, "readinto"):
+        # TODO: in the below we ignore the type as otherwise
+        # we have no way to runtime check _IOProtocol
+        data = np.fromfile(file_or_buf, dtype=np.uint8)  # type: ignore
+    else:
+        data = np.frombuffer(file_or_buf, dtype=np.uint8)
+
     if len(data) == 0:
-        return pd.DataFrame(columns=columns, index=pd.Index([], dtype=np.float64, name="Time"))
+        return pd.DataFrame(
+            columns=columns,
+            index=pd.DatetimeIndex([], name="Time")
+            if epoch
+            else pd.Index([], dtype=np.float64, name="Time"),
+        )
 
     if address is not None and address != data[2]:
         raise ValueError(f"expected address {address} but got {data[2]}")
@@ -84,20 +100,20 @@ def read(
     nrows = len(data) // stride
     payloadtype = data[4]
     payloadoffset = 5
-    if payloadtype & 0x10 != 0:
+    if payloadtype & _PAYLOAD_TIMESTAMP_MASK != 0:
         seconds = np.ndarray(nrows, dtype=np.uint32, buffer=data, offset=payloadoffset, strides=stride)
         payloadoffset += 4
         micros = np.ndarray(nrows, dtype=np.uint16, buffer=data, offset=payloadoffset, strides=stride)
         payloadoffset += 2
         time = micros * _SECONDS_PER_TICK + seconds
-        payloadtype = payloadtype & ~np.uint8(0x10)
+        payloadtype = payloadtype & ~np.uint8(_PAYLOAD_TIMESTAMP_MASK)
         if epoch is not None:
             time = epoch + pd.to_timedelta(time, "s")  # type: ignore
         index = pd.Series(time)
         index.name = "Time"
 
     payloadsize = stride - payloadoffset - 1
-    payloadtype = _payloadtypes[payloadtype]
+    payloadtype = _dtypefrompayloadtype[payloadtype]
     if dtype is not None and dtype != payloadtype:
         raise ValueError(f"expected payload type {dtype} but got {payloadtype}")
 
@@ -120,3 +136,139 @@ def read(
         msgtype = pd.Categorical.from_codes(msgtype, categories=_messagetypes)  # type: ignore
         result[MessageType.__name__] = msgtype
     return result
+
+
+def to_file(
+    data: pd.DataFrame,
+    file: _FileLike,
+    address: int,
+    dtype: Optional[np.dtype] = None,
+    length: Optional[int] = None,
+    port: Optional[int] = None,
+    epoch: Optional[datetime] = None,
+    message_type: Optional[MessageType] = None,
+):
+    """Write single-register Harp data to the specified file.
+
+    Parameters
+    ----------
+    data
+        Pandas data frame containing message payload.
+    file
+        File path, or open file object in which to store binary data from
+        a single device register.
+    address
+        Register address used to identify all formatted Harp messages.
+    dtype
+        Data type of the register payload. If specified, all data will
+        be converted before formatting the binary payload.
+    length
+        Expected number of elements in register payload. If specified, the
+        number of columns in the input data frame is validated.
+    port
+        Optional port value used for all formatted Harp messages.
+    epoch
+        Reference datetime at which time zero begins. If specified,
+        the input data frame must have a datetime index.
+    message_type
+        Optional message type used for all formatted Harp messages.
+        If not specified, data must contain a MessageType column.
+    """
+    buffer = to_buffer(data, address, dtype, port, length, epoch, message_type)
+    buffer.tofile(file)
+
+
+def to_buffer(
+    data: pd.DataFrame,
+    address: int,
+    dtype: Optional[np.dtype] = None,
+    length: Optional[int] = None,
+    port: Optional[int] = None,
+    epoch: Optional[datetime] = None,
+    message_type: Optional[MessageType] = None,
+) -> npt.NDArray[np.uint8]:
+    """Convert single-register Harp data to a flat binary buffer.
+
+    Parameters
+    ----------
+    data
+        Pandas data frame containing message payload.
+    address
+        Register address used to identify all formatted Harp messages.
+    dtype
+        Data type of the register payload. If specified, all data will
+        be converted before formatting the binary payload.
+    length
+        Expected number of elements in register payload. If specified, the
+        number of columns in the input data frame is validated.
+    port
+        Optional port value used for all formatted Harp messages.
+    epoch
+        Reference datetime at which time zero begins. If specified,
+        the input data frame must have a datetime index.
+    message_type
+        Optional message type used for all formatted Harp messages.
+        If not specified, data must contain a MessageType column.
+
+    Returns
+    -------
+        An array object containing message data formatted according
+        to the Harp binary protocol.
+    """
+    nrows = len(data)
+    if nrows == 0:
+        return np.empty(0, dtype=np.uint8)
+
+    if MessageType.__name__ in data.columns:
+        msgtype = data[MessageType.__name__].cat.codes
+        payload = data[data.columns.drop(MessageType.__name__)].values
+    elif message_type is not None:
+        msgtype = message_type
+        payload = data.values
+    else:
+        raise ValueError(f"message type must be specified either in the data or as argument")
+
+    time = data.index
+    is_timestamped = True
+    if epoch is not None:
+        if not isinstance(time, pd.DatetimeIndex):
+            raise ValueError(f"expected datetime index to encode with epoch but got {time.inferred_type}")
+        time = (time - epoch).total_seconds()
+    elif isinstance(time, pd.RangeIndex):
+        is_timestamped = False
+
+    if dtype is not None:
+        payload = payload.astype(dtype, copy=False)
+
+    ncols = payload.shape[1]
+    if length is not None and ncols != length:
+        raise ValueError(f"expected payload length {length} but got {ncols}")
+
+    if port is None:
+        port = 255
+
+    payloadtype = _payloadtypefromdtype[payload.dtype]
+    payloadlength = ncols * payload.dtype.itemsize
+    stride = payloadlength + 6
+    if is_timestamped:
+        payloadtype |= _PAYLOAD_TIMESTAMP_MASK
+        stride += 6
+
+    buffer = np.empty((nrows, stride), dtype=np.uint8)
+    buffer[:, 0] = msgtype
+    buffer[:, 1:5] = [stride - 2, address, port, payloadtype]
+
+    payloadoffset = 5
+    if is_timestamped:
+        seconds = time.astype(np.uint32)
+        micros = np.around(((time - seconds) / _SECONDS_PER_TICK).values).astype(np.uint16)
+        buffer[:, 5:9] = np.ndarray((nrows, 4), dtype=np.uint8, buffer=seconds.values)
+        buffer[:, 9:11] = np.ndarray((nrows, 2), dtype=np.uint8, buffer=micros)
+        payloadoffset += 6
+
+    payloadstop = payloadoffset + payloadlength
+    buffer[:, payloadoffset:payloadstop] = np.ndarray(
+        (nrows, payloadlength), dtype=np.uint8, buffer=np.ascontiguousarray(payload)
+    )
+    buffer[:, -1] = np.sum(buffer[:, 0:-1], axis=1, dtype=np.uint8)
+    return buffer.reshape(-1)