ASCEE/lasp
ASCEE
/
lasp
4
1
Fork 0
Code Issues 4 Pull Requests Actions Releases 11 Activity

build(Removed-requirements,-they-are-in-pyproject.toml.-Added-lasp_version.py-that-will-obtain-version-from-metadata.): Black changed single quotes to double quotes. This commit should be tested now we have a patch number in the version

This commit is contained in:
Anne de Jong 2023-07-19 16:56:50 +02:00
parent 37048c54fa
commit d96c591183
6 changed files with 200 additions and 178 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
python_src/lasp/__init__.py
View File

@ -3,12 +3,10 @@ LASP: Library for Acoustic Signal Processing
"""
from .lasp_cpp import *
from ._version import __version__, __version_tuple__
LASP_VERSION_MAJOR = __version_tuple__[0]
LASP_VERSION_MINOR = __version_tuple__[1]
from .lasp_common import *
from .lasp_version import __version__
from .lasp_common import *
from .lasp_cpp import *
# from .lasp_imptube import * # TwoMicImpedanceTube
from .lasp_measurement import * # Measurement, scaleBlockSens
@ -17,6 +15,7 @@ from .lasp_slm import * # SLM, Dummy
from .lasp_record import * # RecordStatus, Recording
from .lasp_daqconfigs import *
from .lasp_measurementset import *
# from .lasp_siggen import * # SignalType, NoiseType, SiggenMessage, SiggenData, Siggen
# from .lasp_weighcal import * # WeighCal
# from .tools import * # SmoothingType, smoothSpectralData, SmoothingWidth

3
python_src/lasp/lasp_daqconfigs.py
View File

@ -1,5 +1,6 @@
# -*- coding: utf-8 -*-
from .lasp_cpp import DaqConfiguration, LASP_VERSION_MAJOR
from .lasp_cpp import DaqConfiguration
from .lasp_version import LASP_VERSION_MAJOR
"""!
Author: J.A. de Jong - ASCEE

342
python_src/lasp/lasp_measurement.py
View File

@ -1,6 +1,7 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from __future__ import annotations
"""!
Author: J.A. de Jong - ASCEE
@ -43,7 +44,7 @@ The video dataset can possibly be not present in the data.
"""
__all__ = ['Measurement', 'scaleBlockSens']
__all__ = ["Measurement", "scaleBlockSens"]
from contextlib import contextmanager
import h5py as h5
import numpy as np
@ -51,7 +52,8 @@ from .lasp_config import LASP_NUMPY_FLOAT_TYPE
from scipy.io import wavfile
import os, time, wave, logging
from .lasp_common import SIQtys, Qty, getFreq
from .lasp_cpp import Window, DaqChannel, LASP_VERSION_MAJOR, AvPowerSpectra
from .lasp_version import LASP_VERSION_MAJOR, LASP_VERSION_MINOR
from .lasp_cpp import Window, DaqChannel, AvPowerSpectra
from typing import List
from functools import lru_cache
@ -72,7 +74,7 @@ def getSampWidth(dtype):
elif dtype == np.float64:
return 8
else:
raise ValueError('Invalid data type: %s' % dtype)
raise ValueError("Invalid data type: %s" % dtype)
def scaleBlockSens(block, sens):
@ -87,9 +89,9 @@ def scaleBlockSens(block, sens):
assert sens.size == block.shape[1]
if np.issubdtype(block.dtype.type, np.integer):
sw = getSampWidth(block.dtype)
fac = 2**(8 * sw - 1) - 1
fac = 2 ** (8 * sw - 1) - 1
else:
fac = 1.
fac = 1.0
return block.astype(LASP_NUMPY_FLOAT_TYPE) / fac / sens[np.newaxis, :]
@ -107,7 +109,7 @@ class IterRawData:
"""
assert isinstance(channels, list)
fa = f['audio']
fa = f["audio"]
self.fa = fa
self.i = 0
@ -117,8 +119,8 @@ class IterRawData:
# nchannels = fa.shape[2]
self.channels = channels
self.istart = kwargs.pop('istart', 0)
self.istop = kwargs.pop('istop', blocksize*nblocks)
self.istart = kwargs.pop("istart", 0)
self.istop = kwargs.pop("istop", blocksize * nblocks)
self.firstblock = self.istart // blocksize
self.lastblock = self.istop // blocksize
@ -128,11 +130,11 @@ class IterRawData:
self.firstblock_start_offset = self.istart % blocksize
if self.istop < 0:
self.istop += blocksize*nblocks
self.istop += blocksize * nblocks
if self.istop <= self.istart:
raise ValueError('Stop index is smaller than start index')
raise ValueError("Stop index is smaller than start index")
if self.istop != blocksize*nblocks:
if self.istop != blocksize * nblocks:
self.lastblock_stop_offset = self.istop % blocksize
else:
self.lastblock_stop_offset = blocksize
@ -171,6 +173,7 @@ class IterData(IterRawData):
Iterate over blocks of data, scaled with sensitivity and integer scaling
between 0 and 1
"""
def __init__(self, fa, channels, sensitivity, **kwargs):
super().__init__(fa, channels, **kwargs)
self.sens = np.asarray(sensitivity)[self.channels]
@ -187,8 +190,8 @@ class Measurement:
def __init__(self, fn):
"""Initialize a Measurement object based on the filename."""
if '.h5' not in fn:
fn += '.h5'
if ".h5" not in fn:
fn += ".h5"
# Full filepath
self.fn = fn
@ -198,26 +201,26 @@ class Measurement:
# Open the h5 file in read-plus mode, to allow for changing the
# measurement comment.
with h5.File(fn, 'r') as f:
with h5.File(fn, "r") as f:
# Check for video data
try:
f['video']
f["video"]
self.has_video = True
except KeyError:
self.has_video = False
self.nblocks, self.blocksize, self.nchannels = f['audio'].shape
dtype = f['audio'].dtype
self.nblocks, self.blocksize, self.nchannels = f["audio"].shape
dtype = f["audio"].dtype
self.dtype = dtype
self.sampwidth = getSampWidth(dtype)
self.samplerate = f.attrs['samplerate']
self.N = (self.nblocks * self.blocksize)
self.samplerate = f.attrs["samplerate"]
self.N = self.nblocks * self.blocksize
self.T = self.N / self.samplerate
try:
self.version_major = f.attrs['LASP_VERSION_MAJOR']
self.version_minor = f.attrs['LASP_VERSION_MINOR']
self.version_major = f.attrs["LASP_VERSION_MAJOR"]
self.version_minor = f.attrs["LASP_VERSION_MINOR"]
except KeyError:
self.version_major = 0
self.version_minor = 1
@ -225,45 +228,47 @@ class Measurement:
# Due to a previous bug, the channel names were not stored
# consistently, i.e. as 'channel_names' and later camelcase.
try:
self._channelNames = f.attrs['channelNames']
self._channelNames = f.attrs["channelNames"]
except KeyError:
try:
self._channelNames = f.attrs['channel_names']
logging.info("Measurement file obtained which stores channel names with *old* attribute 'channel_names'")
self._channelNames = f.attrs["channel_names"]
logging.info(
"Measurement file obtained which stores channel names with *old* attribute 'channel_names'"
)
except KeyError:
# No channel names found in measurement file
logging.info('No channel name data found in measurement')
self._channelNames = [f'Unnamed {i}' for i in range(self.nchannels)]
logging.info("No channel name data found in measurement")
self._channelNames = [f"Unnamed {i}" for i in range(self.nchannels)]
# comment = read-write thing
if 'comment' in f.attrs:
self._comment = f.attrs['comment']
if "comment" in f.attrs:
self._comment = f.attrs["comment"]
else:
self._comment = ''
self._comment = ""
# Sensitivity
try:
sens = f.attrs['sensitivity']
self._sens = sens * \
np.ones(self.nchannels) if isinstance(
sens, float) else sens
sens = f.attrs["sensitivity"]
self._sens = (
sens * np.ones(self.nchannels) if isinstance(sens, float) else sens
)
except KeyError:
self._sens = np.ones(self.nchannels)
# The time is cached AND ALWAYS ASSUMED TO BE AN IMMUTABLE OBJECT.
# It is also cached. Changing the measurement timestamp should not
# be done.
self._time = f.attrs['time']
self._time = f.attrs["time"]
# Quantity stored as channel.
self._qtys = None
try:
qtys_enum_idx = f.attrs['qtys_enum_idx']
qtys_enum_idx = f.attrs["qtys_enum_idx"]
self._qtys = [SIQtys.fromInt(idx) for idx in qtys_enum_idx]
except KeyError:
try:
qtys_json = f.attrs['qtys']
qtys_json = f.attrs["qtys"]
# Load quantity data
self._qtys = [Qty.from_json(qty_json) for qty_json in qtys_json]
except KeyError:
@ -273,17 +278,19 @@ class Measurement:
if self._qtys is None:
self._qtys = [SIQtys.default() for i in range(self.nchannels)]
logging.debug(f'Physical quantity data not available in measurement file. Assuming {SIQtys.default}')
logging.debug(
f"Physical quantity data not available in measurement file. Assuming {SIQtys.default}"
)
def setAttribute(self, atrname, value):
"""
Set an attribute in the measurement file, and keep a local copy in
memory for efficient accessing.
"""
with self.file('r+') as f:
with self.file("r+") as f:
# Update comment attribute in the file
f.attrs[atrname] = value
setattr(self, '_' + atrname, value)
setattr(self, "_" + atrname, value)
@property
def name(self):
@ -297,14 +304,13 @@ class Measurement:
@channelNames.setter
def channelNames(self, newchnames):
if len(newchnames) != self.nchannels:
raise RuntimeError('Invalid length of new channel names')
self.setAttribute('channelNames', newchnames)
raise RuntimeError("Invalid length of new channel names")
self.setAttribute("channelNames", newchnames)
@property
def channelConfig(self):
chcfg = []
for chname, sens, qty in zip(self.channelNames, self.sensitivity,
self.qtys):
for chname, sens, qty in zip(self.channelNames, self.sensitivity, self.qtys):
ch = DaqChannel()
ch.enabled = True
ch.name = chname
@ -334,26 +340,26 @@ class Measurement:
@qtys.setter
def qtys(self, newqtys):
if not len(newqtys) == len(self._qtys):
raise ValueError('Invalid number of quantities')
raise ValueError("Invalid number of quantities")
qtys_int = [qty.toInt() for qty in newqtys]
# Use setAttribute here, but thos store the jsonified version as well,
# which we have to overwrite again with the deserialized ones. This is
# actually not a very nice way of coding.
with self.file('r+') as f:
with self.file("r+") as f:
# Update comment attribute in the file
f.attrs['qtys_enum_idx'] = qtys_int
f.attrs["qtys_enum_idx"] = qtys_int
self._qtys = newqtys
@contextmanager
def file(self, mode='r'):
def file(self, mode="r"):
"""Contextmanager which opens the storage file and yields the file.
Args:
mode: Opening mode for the file. Should either be 'r', or 'r+'
"""
if mode not in ('r', 'r+'):
raise ValueError('Invalid file opening mode.')
if mode not in ("r", "r+"):
raise ValueError("Invalid file opening mode.")
with h5.File(self.fn, mode) as f:
yield f
@ -373,9 +379,9 @@ class Measurement:
Args:
cmt: Comment text string to set
"""
with self.file('r+') as f:
with self.file("r+") as f:
# Update comment attribute in the file
f.attrs['comment'] = cmt
f.attrs["comment"] = cmt
self._comment = cmt
@property
@ -400,7 +406,7 @@ class Measurement:
"""
time_struct = time.localtime(self.time)
time_string = time.strftime('%Y-%m-%d %H:%M:%S', time_struct)
time_string = time.strftime("%Y-%m-%d %H:%M:%S", time_struct)
return time_string
def rms(self, channels=None, substract_average=False):
@ -415,8 +421,8 @@ class Measurement:
Returns:
1D array with rms values for each channel
"""
meansquare = 0. # Mean square of the signal, including its average
sum_ = 0. # Sumf of the values of the signal, used to compute average
meansquare = 0.0 # Mean square of the signal, including its average
sum_ = 0.0 # Sumf of the values of the signal, used to compute average
N = 0
with self.file() as f:
for block in self.iterData(channels):
@ -425,7 +431,7 @@ class Measurement:
N += Nblock
meansquare += np.sum(block**2, axis=0) / self.N
avg = sum_/N
avg = sum_ / N
# In fact, this is not the complete RMS, as in includes the DC
# If p = p_dc + p_osc, then rms(p_osc) = sqrt(ms(p)-ms(p_dc))
if substract_average:
@ -461,7 +467,7 @@ class Measurement:
return np.concatenate(rawdata, axis=0)
def iterData(self, channels, **kwargs):
sensitivity = kwargs.pop('sensitivity', self.sensitivity)
sensitivity = kwargs.pop("sensitivity", self.sensitivity)
if channels is None:
channels = list(range(self.nchannels))
with self.file() as f:
@ -496,9 +502,9 @@ class Measurement:
Cross-power-spectra. C[freq, ch_i, ch_j] = C_ij
"""
nfft = kwargs.pop('nfft', 2048)
window = kwargs.pop('windowType', Window.WindowType.Hann)
overlap = kwargs.pop('overlap', 50.0)
nfft = kwargs.pop("nfft", 2048)
window = kwargs.pop("windowType", Window.WindowType.Hann)
overlap = kwargs.pop("overlap", 50.0)
if channels is None:
channels = list(range(self.nchannels))
@ -527,35 +533,37 @@ class Measurement:
"""
# Create blocks of equal length N
Ntot = self.N
Nblocks = Ntot//N
Nblocks = Ntot // N
# TODO: This method graps the whole measurement file into memory. Can
# only be done with relatively small measurement files.
signal = self.data(channels)
# Estimate noise power in block
blocks = [signal[i*N:(i+1)*N] for i in range(Nblocks)]
blocks = [signal[i * N : (i + 1) * N] for i in range(Nblocks)]
if noiseCorrection:
# The difference between the measured signal in the previous block and
# the current block
en = [None] + [blocks[i] - blocks[i-1] for i in range(1,Nblocks)]
en = [None] + [blocks[i] - blocks[i - 1] for i in range(1, Nblocks)]
noise_est = [None] + [-np.average(en[i]*en[i+1]) for i in range(1,len(en)-1)]
noise_est = [None] + [
-np.average(en[i] * en[i + 1]) for i in range(1, len(en) - 1)
]
# Create weighting coefficients
sum_inverse_noise = sum([1/n for n in noise_est[1:]])
c_n = [1/(ni*sum_inverse_noise) for ni in noise_est[1:]]
sum_inverse_noise = sum([1 / n for n in noise_est[1:]])
c_n = [1 / (ni * sum_inverse_noise) for ni in noise_est[1:]]
else:
c_n = [1/(Nblocks-2)]*(Nblocks-2)
c_n = [1 / (Nblocks - 2)] * (Nblocks - 2)
assert np.isclose(sum(c_n), 1.0)
assert Nblocks-2 == len(c_n)
assert Nblocks - 2 == len(c_n)
# Average signal over blocks
avg = np.zeros((blocks[0].shape), dtype=float)
for n in range(0, Nblocks-2):
avg += c_n[n]*blocks[n+1]
for n in range(0, Nblocks - 2):
avg += c_n[n] * blocks[n + 1]
return avg
@ -578,7 +586,6 @@ class Measurement:
return freq, CS
@property
def sensitivity(self):
"""Sensitivity of the data in U^-1, from floating point data scaled
@ -607,9 +614,9 @@ class Measurement:
valid &= sens.shape[0] == self.nchannels
valid &= sens.dtype == float
if not valid:
raise ValueError('Invalid sensitivity value(s) given')
with self.file('r+') as f:
f.attrs['sensitivity'] = sens
raise ValueError("Invalid sensitivity value(s) given")
with self.file("r+") as f:
f.attrs["sensitivity"] = sens
self._sens = sens
def checkOverflow(self, channels):
@ -621,19 +628,17 @@ class Measurement:
for block in self.iterData(channels):
dtype = block.dtype
if dtype.kind == 'i':
if dtype.kind == "i":
# minvalue = np.iinfo(dtype).min
maxvalue = np.iinfo(dtype).max
if np.max(np.abs(block)) >= 0.9*maxvalue:
if np.max(np.abs(block)) >= 0.9 * maxvalue:
return True
else:
# Cannot check for floating point values.
return False
return False
def exportAsWave(self, fn=None, force=False, dtype=None,
normalize=False, **kwargs):
def exportAsWave(self, fn=None, force=False, dtype=None, normalize=False, **kwargs):
"""Export measurement file as wave. In case the measurement data is
stored as floats, the values are scaled to the proper integer (PCM)
data format.
@ -654,14 +659,16 @@ class Measurement:
fn = self.fn
fn = os.path.splitext(fn)[0]
if os.path.splitext(fn)[1] != '.wav':
fn += '.wav'
if os.path.splitext(fn)[1] != ".wav":
fn += ".wav"
if os.path.exists(fn) and not force:
raise RuntimeError(f'File already exists: {fn}')
raise RuntimeError(f"File already exists: {fn}")
if not np.isclose(self.samplerate%1,0):
raise RuntimeError(f'Sample rates should be approximately integer for exporting to Wave to work')
if not np.isclose(self.samplerate % 1, 0):
raise RuntimeError(
f"Sample rates should be approximately integer for exporting to Wave to work"
)
# TODO: With VERY large measurment files, this is not possible! Is this
# a theoretical case?
@ -673,20 +680,20 @@ class Measurement:
maxabs = np.max(np.abs(data))
data = data / maxabs # "data /= maxabs" fails if dtpyes differ
if dtype==None:
if dtype == None:
dtype = data.dtype # keep existing
logging.debug(f"dtype not passed as arg; using dtype = {dtype}")
# dtype conversion
if dtype=='int16':
if dtype == "int16":
newtype = np.int16
newsampwidth = 2
elif dtype=='int32':
elif dtype == "int32":
newtype = np.int32
newsampwidth = 4
elif dtype=='float32':
elif dtype == "float32":
newtype = np.float32
elif dtype=='float64':
elif dtype == "float64":
newtype = np.float64
else:
logging.debug(f"cannot handle this dtype {dtype}")
@ -697,22 +704,24 @@ class Measurement:
sensone = np.ones_like(self.sensitivity)
data = scaleBlockSens(data, sensone)
if dtype=='int16' or dtype=='int32':
if dtype == "int16" or dtype == "int32":
# Scale data to integer range and convert to integers
scalefac = 2**(8*newsampwidth-1)-1
data = (data*scalefac).astype(newtype)
scalefac = 2 ** (8 * newsampwidth - 1) - 1
data = (data * scalefac).astype(newtype)
wavfile.write(fn, int(self.samplerate), data.astype(newtype))
@staticmethod
def fromtxt(fn,
skiprows,
samplerate,
sensitivity,
mfn=None,
timestamp=None,
delimiter='\t',
firstcoltime=True):
def fromtxt(
fn,
skiprows,
samplerate,
sensitivity,
mfn=None,
timestamp=None,
delimiter="\t",
firstcoltime=True,
):
"""Converts a txt file to a LASP Measurement file, opens the associated
Measurement object and returns it. The measurement file will have the
same file name as the txt file, except with h5 extension.
@ -732,50 +741,57 @@ class Measurement:
sample time.
"""
if not os.path.exists(fn):
raise ValueError(f'File {fn} does not exist.')
raise ValueError(f"File {fn} does not exist.")
if timestamp is None:
timestamp = os.path.getmtime(fn)
if mfn is None:
mfn = os.path.splitext(fn)[0] + '.h5'
mfn = os.path.splitext(fn)[0] + ".h5"
else:
mfn = os.path.splitext(mfn)[0] + '.h5'
mfn = os.path.splitext(mfn)[0] + ".h5"
dat = np.loadtxt(fn, skiprows=skiprows, delimiter=delimiter)
if firstcoltime:
time = dat[:, 0]
if not np.isclose(time[1] - time[0], 1 / samplerate):
raise ValueError('Samplerate given does not agree with '
'samplerate in file')
raise ValueError(
"Samplerate given does not agree with " "samplerate in file"
)
# Chop off first column
dat = dat[:, 1:]
nchannels = dat.shape[1]
if nchannels != sensitivity.shape[0]:
raise ValueError(
f'Invalid sensitivity length given. Should be: {nchannels}')
f"Invalid sensitivity length given. Should be: {nchannels}"
)
with h5.File(mfn, 'w') as hf:
hf.attrs['samplerate'] = samplerate
hf.attrs['sensitivity'] = sensitivity
hf.attrs['time'] = timestamp
hf.attrs['blocksize'] = 1
hf.attrs['nchannels'] = nchannels
ad = hf.create_dataset('audio', (1, dat.shape[0], dat.shape[1]),
dtype=dat.dtype,
maxshape=(1, dat.shape[0], dat.shape[1]),
compression='gzip')
with h5.File(mfn, "w") as hf:
hf.attrs["samplerate"] = samplerate
hf.attrs["sensitivity"] = sensitivity
hf.attrs["time"] = timestamp
hf.attrs["blocksize"] = 1
hf.attrs["nchannels"] = nchannels
ad = hf.create_dataset(
"audio",
(1, dat.shape[0], dat.shape[1]),
dtype=dat.dtype,
maxshape=(1, dat.shape[0], dat.shape[1]),
compression="gzip",
)
ad[0] = dat
return Measurement(mfn)
@staticmethod
def fromnpy(data,
samplerate,
sensitivity,
mfn,
timestamp=None,
qtys: List[SIQtys] = None,
channelNames: List[str] = None,
force=False) -> Measurement:
def fromnpy(
data,
samplerate,
sensitivity,
mfn,
timestamp=None,
qtys: List[SIQtys] = None,
channelNames: List[str] = None,
force=False,
) -> Measurement:
"""
Converts a numpy array to a LASP Measurement file, opens the
associated Measurement object and returns it. The measurement file will
@ -784,76 +800,79 @@ class Measurement:
Args:
data: Numpy array, first column is sample, second is channel. Can
also be specified with a single column for single-channel data.
samplerate: Sampling frequency in [Hz]
sensitivity: 1D array of channel sensitivities in [U^-1], where U is
the recorded unit.
mfn: Filepath of the file where the data is stored.
timestamp: If given, a custom timestamp for the measurement
(integer containing seconds since epoch).
qtys: If a list of physical quantity data is given here
channelNames: Name of the channels
force: If True, overwrites existing files with specified `mfn`
name.
"""
if os.path.splitext(mfn)[1] != '.h5':
mfn += '.h5'
if os.path.splitext(mfn)[1] != ".h5":
mfn += ".h5"
if os.path.exists(mfn) and not force:
raise ValueError(f'File {mfn} already exist.')
raise ValueError(f"File {mfn} already exist.")
if timestamp is None:
timestamp = int(time.time())
if data.ndim != 2:
data = data[:, np.newaxis]
try:
len(sensitivity)
except:
raise ValueError('Sensitivity should be given as array-like data type')
raise ValueError("Sensitivity should be given as array-like data type")
sensitivity = np.asarray(sensitivity)
nchannels = data.shape[1]
if nchannels != sensitivity.shape[0]:
raise ValueError(
f'Invalid sensitivity length given. Should be: {nchannels}')
f"Invalid sensitivity length given. Should be: {nchannels}"
)
if channelNames is not None:
if len(channelNames) != nchannels:
raise RuntimeError("Illegal length of channelNames list given")
if qtys is None:
qtys = [SIQtys.AP]*nchannels
qtys = [SIQtys.AP] * nchannels
else:
if len(qtys) != nchannels:
raise RuntimeError("Illegal length of qtys list given")
qtyvals = [qty.value for qty in qtys]
with h5.File(mfn, 'w') as hf:
hf.attrs['samplerate'] = samplerate
hf.attrs['sensitivity'] = sensitivity
hf.attrs['time'] = timestamp
hf.attrs['blocksize'] = 1
hf.attrs['nchannels'] = nchannels
with h5.File(mfn, "w") as hf:
hf.attrs["samplerate"] = samplerate
hf.attrs["sensitivity"] = sensitivity
hf.attrs["time"] = timestamp
hf.attrs["blocksize"] = 1
hf.attrs["nchannels"] = nchannels
# Add physical quantity indices
hf.attrs['qtys_enum_idx'] = [qtyval.toInt() for qtyval in qtyvals]
hf.attrs["qtys_enum_idx"] = [qtyval.toInt() for qtyval in qtyvals]
# Add channel names in case given
if channelNames is not None:
hf.attrs['channelNames'] = channelNames
hf.attrs["channelNames"] = channelNames
ad = hf.create_dataset('audio', (1, data.shape[0], data.shape[1]),
dtype=data.dtype,
maxshape=(1, data.shape[0], data.shape[1]),
compression='gzip')
ad = hf.create_dataset(
"audio",
(1, data.shape[0], data.shape[1]),
dtype=data.dtype,
maxshape=(1, data.shape[0], data.shape[1]),
compression="gzip",
)
ad[0] = data
return Measurement(mfn)
@ -866,9 +885,11 @@ class Measurement:
base_fn = os.path.splitext(fn)[0]
if newfn is None:
newfn = base_fn + '.h5'
newfn = base_fn + ".h5"
if os.path.exists(newfn) and not force:
raise RuntimeError(f'Measurement file name {newfn} already exists in path, set "force" to true to overwrite')
raise RuntimeError(
f'Measurement file name {newfn} already exists in path, set "force" to true to overwrite'
)
samplerate, data = wavfile.read(fn)
if data.ndim == 2:
@ -879,16 +900,19 @@ class Measurement:
data = data[:, np.newaxis]
sensitivity = np.ones(nchannels)
with h5.File(newfn, 'w') as hf:
hf.attrs['samplerate'] = samplerate
hf.attrs['nchannels'] = nchannels
hf.attrs['time'] = timestamp
hf.attrs['blocksize'] = 1
hf.attrs['sensitivity'] = sensitivity
ad = hf.create_dataset('audio', (1, nframes, nchannels),
dtype=data.dtype,
maxshape=(1, nframes, nchannels),
compression='gzip')
with h5.File(newfn, "w") as hf:
hf.attrs["samplerate"] = samplerate
hf.attrs["nchannels"] = nchannels
hf.attrs["time"] = timestamp
hf.attrs["blocksize"] = 1
hf.attrs["sensitivity"] = sensitivity
ad = hf.create_dataset(
"audio",
(1, nframes, nchannels),
dtype=data.dtype,
maxshape=(1, nframes, nchannels),
compression="gzip",
)
ad[0] = data
return Measurement(newfn)

14
python_src/lasp/lasp_record.py
View File

@ -7,8 +7,8 @@ import dataclasses, logging, os, time, h5py, threading
import numpy as np
from .lasp_atomic import Atomic
from .lasp_cpp import (LASP_VERSION_MAJOR, LASP_VERSION_MINOR, InDataHandler,
StreamMgr)
from .lasp_cpp import InDataHandler, StreamMgr
from .lasp_version import LASP_VERSION_MAJOR, LASP_VERSION_MINOR
@dataclasses.dataclass
@ -84,10 +84,10 @@ class Recording:
try:
# Open the file
self.f = h5py.File(self.fn, "w", 'stdio')
self.f = h5py.File(self.fn, "w", "stdio")
self.f.flush()
except Exception as e:
logging.error(f'Error creating measurement file {e}')
logging.error(f"Error creating measurement file {e}")
raise
# This flag is used to delete the file on finish(), and can be used
@ -191,7 +191,7 @@ class Recording:
"""
if self.stop():
logging.debug('Stop flag set, early return in inCallback')
logging.debug("Stop flag set, early return in inCallback")
# Stop flag is raised. We do not add any data anymore.
return True
@ -225,12 +225,12 @@ class Recording:
with self.file_mtx:
self.f.flush()
# Remove indata handler, which also should remove callback function
# from StreamMgr. This, however does not have to happen
# from StreamMgr. This, however does not have to happen
# instantaneously. For which we have to implement extra mutex
# guards in this class
del self.indh
self.indh = None
# Remove handle to dataset otherwise the h5 file is not closed
# properly.
del self.ad

4
python_src/lasp/lasp_version.py Normal file
View File

@ -0,0 +1,4 @@
import importlib.metadata
__version__ = importlib.metadata.version(__package__ or __name__)
LASP_VERSION_MAJOR, LASP_VERSION_MINOR = [int(a) for a in __version__.split(".")]

6
requirements.txt
View File

@ -1,6 +0,0 @@
appdirs
dataclasses_json
scipy
matplotlib
h5py
pytest