Merge pull request #40 from harp-tech/write-buffer

Allow formatting data as binary protocol messages

Author: glopesdev

.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/io.py

@@ -24,8 +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),
@@ -36,6 +37,7 @@ class MessageType(IntEnum):
     136: np.dtype(np.int64),
     68: np.dtype(np.float32),
 }
+_payloadtypefromdtype = {v: k for k, v in _dtypefrompayloadtype.items()}
 
 
 def read(
@@ -140,20 +142,20 @@ def _fromraw(
     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}")
 
@@ -176,3 +178,127 @@ def _fromraw(
         msgtype = pd.Categorical.from_codes(msgtype, categories=_messagetypes)  # type: ignore
         result[MessageType.__name__] = msgtype
     return result
+
+
+def write(
+    file: Union[str, bytes, PathLike[Any], BinaryIO],
+    data: pd.DataFrame,
+    address: int,
+    dtype: Optional[np.dtype] = None,
+    port: Optional[int] = None,
+    epoch: Optional[datetime] = None,
+    message_type: Optional[MessageType] = None,
+):
+    """Write single-register Harp data to the specified file.
+
+    Parameters
+    ----------
+    file
+        Open file object or filename where to store binary data from
+        a single device register.
+    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.
+    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 = format(data, address, dtype, port, epoch, message_type)
+    buffer.tofile(file)
+
+
+def format(
+    data: pd.DataFrame,
+    address: int,
+    dtype: Optional[np.dtype] = None,
+    port: Optional[int] = None,
+    epoch: Optional[datetime] = None,
+    message_type: Optional[MessageType] = None,
+) -> npt.NDArray[np.uint8]:
+    """Format single-register Harp data as 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.
+    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.
+    """
+    if len(data) == 0:
+        return np.empty(0, dtype=np.uint8)
+
+    if "MessageType" in data.columns:
+        msgtype = data["MessageType"].cat.codes
+        payload = data[data.columns.drop("MessageType")].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)
+
+    if port is None:
+        port = 255
+
+    payloadtype = _payloadtypefromdtype[payload.dtype]
+    payloadlength = payload.shape[1] * payload.dtype.itemsize
+    stride = payloadlength + 6
+    if is_timestamped:
+        payloadtype |= _PAYLOAD_TIMESTAMP_MASK
+        stride += 6
+
+    nrows = len(data)
+    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)

harp/schema.py

@@ -8,6 +8,9 @@
 
 
 def _read_common_registers() -> Registers:
+    if __package__ is None:
+        raise ValueError("__package__ is None: unable to read common registers")
+
     file = resources.files(__package__) / "common.yml"
     with file.open("r") as fileIO:
         return parse_yaml_raw_as(Registers, fileIO.read())

tests/test_io.py

@@ -4,7 +4,7 @@
 import pytest
 from pytest import mark
 
-from harp.io import MessageType, parse, read
+from harp.io import MessageType, format, parse, read
 from tests.params import DataFileParam
 
 testdata = [
@@ -63,3 +63,26 @@ def test_read(dataFile: DataFileParam):
         if dataFile.expected_cols:
             for col in dataFile.expected_cols:
                 assert col in data.columns
+
+
+writedata = [
+    DataFileParam(path="data/device_0.bin", expected_rows=1, expected_address=0, keep_type=True),
+]
+
+
+@mark.parametrize("dataFile", writedata)
+def test_write(dataFile: DataFileParam):
+    if dataFile.expected_address is None:
+        raise AssertionError("expected address must be defined for all write tests")
+
+    buffer = np.fromfile(dataFile.path, np.uint8)
+    data = parse(
+        buffer,
+        address=dataFile.expected_address,
+        dtype=dataFile.expected_dtype,
+        length=dataFile.expected_length,
+        keep_type=dataFile.keep_type,
+    )
+    assert len(data) == dataFile.expected_rows
+    write_buffer = format(data, address=dataFile.expected_address)
+    assert np.array_equal(buffer, write_buffer)