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Thijs Hekman 2023-12-19 11:24:04 +01:00
commit e5c40c6af3
113 changed files with 469 additions and 433 deletions

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@ -1,90 +0,0 @@
kind: pipeline
type: docker
name: archlinux
clone:
depth: 50
steps:
- name: archlinux_build
image: archlinux_build:latest
pull: if-not-exists
volumes:
- name: archlinux_ccache
path: /root/.ccache
commands:
# The following command is not required, we included this in the docker
# image of archlinux_build
# - pacman -S --noconfirm ccache openblas fftw pulseaudio pybind11
- git submodule update --init --recursive
- cmake .
# More than two makes ascee2 irresponsive for now
- make -j2
- name: archlinux_test
image: archlinux_build:latest
pull: if-not-exists
commands:
- scripts/test.sh
volumes:
- name: archlinux_ccache
host:
path: /tmp/archlinux_ccache
---
kind: pipeline
type: docker
name: ubuntu
clone:
depth: 3
volumes:
- name: archlinux_ccache
path: /root/.ccache
steps:
- name: ubuntu_build
image: ubuntu_build:latest
pull: if-not-exists
volumes:
- name: ubuntu_ccache
path: /root/.ccache
environment:
commands:
# The following commands are not required, we included this in the docker
# image of ubuntu_builud
- scripts/build_ubuntu.sh
- name: ubuntu_test
image: ubuntu_build:latest
pull: if-not-exists
commands:
- scripts/test.sh
volumes:
- name: ubuntu_ccache
host:
path: /tmp/ubuntu_ccache
---
kind: pipeline
type: docker
name: documentation_build
clone:
depth: 3
steps:
- name: build_docker_master
image: plugins/docker
settings:
repo: ascee/lasp_ascee_nl
tags: latest
username:
from_secret: docker_username
password:
from_secret: docker_password
when:
branch: master

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@ -0,0 +1,51 @@
name: Building, testing and releasing LASP if it has a tag
on:
- push
jobs:
Build-Test-Ubuntu:
runs-on: ubuntu-latest
container:
image: ascee/ubuntu_build:latest
volumes:
- lasp_dist:/dist
steps:
- name: Checkout
uses: actions/checkout@v4
with:
submodules: true
- name: Build and test
run: |
pip install build pytest
python3 -m build
pip install dist/lasp*.whl
pytest
- name: Copy dist files to /dist dir
run:
cp -v dist/* /dist
Release-Ubuntu:
runs-on: ubuntu-latest
container:
volumes:
- lasp_dist:/dist
needs: Build-Test-Ubuntu
if: startsWith(gitea.ref, 'refs/tags/v')
steps:
- name: Checkout
uses: actions/checkout@v4
- name: setup go
uses: https://github.com/actions/setup-go@v4
with:
go-version: '1.18'
- name: Release
uses: https://gitea.com/actions/release-action@main
working-directory: "/"
with:
files: |-
../../../../../dist/**
api_key: '${{secrets.RELEASE_TOKEN}}'

11
.gitignore vendored
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@ -6,23 +6,18 @@
.ninja*
build.ninja
dist
src/lasp.egg-info
test/.ipynb_checkpoints
src/lasp/lasp_config.h
_deps
compile_commands.json
CMakeFiles
CMakeCache.txt
cmake_install.cmake
Makefile
build
__pycache__
cython_debug
doc
.ropeproject
.ipynb_checkpoints
.spyproject
.cache
_skbuild
acme_log.log
testenv
.venv
.py-build-cmake_cache
cpp_src/lasp_config.h

18
.pre-commit-config.yaml Normal file
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@ -0,0 +1,18 @@
---
repos:
- repo: https://github.com/commitizen-tools/commitizen
rev: 3.5.3
hooks:
- id: commitizen
- id: commitizen-branch
stages: [push]
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v2.3.0
hooks:
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/psf/black
rev: 22.10.0
hooks:
- id: black

7
CHANGELOG.md Normal file
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@ -0,0 +1,7 @@
## v1.0.1 (2023-07-19)
### Fix
- Added patch number to semver in pyproject.toml
## v1.0.0 (2023-07-19)

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@ -1,7 +1,6 @@
cmake_minimum_required (VERSION 3.16)
project(LASP LANGUAGES C CXX VERSION 1.0)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED)
@ -121,7 +120,7 @@ include(portaudio)
include(uldaq)
#
add_definitions(-Dgsl_CONFIG_DEFAULTS_VERSION=1)
add_subdirectory(src/lasp)
add_subdirectory(cpp_src)
if(LASP_BUILD_CPP_TESTS)
add_subdirectory(test)
endif()

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@ -1,8 +1,5 @@
# Library for Acoustic Signal Processing
- Master branch: [![Build Status](https://drone.ascee.nl/api/badges/ASCEE/lasp/status.svg?ref=refs/heads/master)](https://drone.ascee.nl/ASCEE/lasp)
- Develop branch: [![Build Status](https://drone.ascee.nl/api/badges/ASCEE/lasp/status.svg?ref=refs/heads/develop)](https://drone.ascee.nl/ASCEE/lasp)
Welcome to LASP: Library for Acoustic Signal Processing. LASP is a C++ library
with a Python interface which is supposed to acquire and process (multi) sensor data in real time on a PC and output results.
@ -46,41 +43,48 @@ in a sister repository [lasp-doc](https://code.ascee.nl/ascee/lasp-doc).
If you have any question(s), please feel free to contact us: [email](info@ascee.nl).
# Installation - Linux (Debian-based)
# Installation - Linux (Ubuntu-based)
## Dependencies
## From wheel (recommended for non-developers)
One-liner:
### Prerequisites
- `$ sudo apt install python3-pybind11 libopenblas-dev python3-pip python3-scipy libusb-1.0-0-dev libpulse-dev cmake-curses-gui python3-h5py python3-dataclasses-json python3-matplotlib python3-appdirs`
Run the following on the command line to install all prerequisites on
Debian-based Linux:
- `sudo apt install python3-pip libfftw3-3 libopenblas-base libusb-1.0-0
libpulse0`
### Download and install LASP
Go to: [LASP releases](https://code.ascee.nl/ASCEE/lasp/releases/latest/) and
download the latest `.whl`. Then run:
- `pip install lasp-*-linux_x86_64.whl`
## From source (Ubuntu-based)
### Prerequisites
Run the following one-liner:
- `sudo apt install -y git python3 python3-virtualenv python3-venv libopenblas-dev python3-pip libfftw3-dev libusb-1.0-0-dev libpulse-dev python3-build`
If building RtAudio with the ALSA backend, you will also require the following packages:
- libclalsadrv-dev
- `sudo apt install libclalsadrv-dev`
If building RtAudio with the Jack Audio Connection Kit (JACK) backend, you will also require the following packages:
- libjack-jackd2-dev
- `sudo apt install libjack-jackd2-dev`
## Download & build
### Download & build
- `$ git clone --recursive https://code.ascee.nl/ASCEE/lasp.git`
- `$ cd lasp`
- `pip install -e .`
For a release build:
- `$ cmake .`
or optionally for a custom build:
- `$ ccmake .`
Configure and run:
- `$ make -j`
# Installation - (x86_64) Windows (with WinPython), build with MSYS2
# Installation - (x86_64) Windows (with WinPython), build with MSYS2 (NOT YET UPDATED!!)
## Prerequisites
@ -113,7 +117,11 @@ Configure and run:
# Documentation
In directory:
## Online
[Online LASP documentation](https://lasp.ascee.nl/).
## In directory
`$ sudo apt install doxygen graphviz`
`$ pip install doxypypy`
@ -126,21 +134,7 @@ This will build the documentation. It can be read by:
`$ <YOUR-BROWSER> doc/html/index.html`
Or via docker:
`$ docker build -t lasp_ascee_nl:latest .`
## Install
For an editable install (while developing):
- `$ pip3 install --prefix=$HOME/.local -e .`
To install locally, for a fixed version:
- `$ pip3 install --prefix=$HOME/.local`
## Usage
# Usage
- See examples directories for IPython notebooks.
- Please refer to the [documentation](https://lasp.ascee.nl/) for features.

53
cpp_src/CMakeLists.txt Normal file
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@ -0,0 +1,53 @@
# src/lasp/CMakeLists.txt
# Armadillo, don't build the wrapper lib, but instead directly link to
# openblas.
add_definitions(-DARMA_DONT_USE_WRAPPER)
configure_file(lasp_config.h.in lasp_config.h)
include_directories(${CMAKE_CURRENT_BINARY_DIR})
include_directories(SYSTEM
${PROJECT_SOURCE_DIR}/third_party/armadillo-code/include)
include_directories(${PROJECT_SOURCE_DIR}/third_party/DebugTrace-cpp/include)
include_directories(${PROJECT_SOURCE_DIR}/third_party/gsl-lite/include)
include_directories(${PROJECT_SOURCE_DIR}/third_party/tomlplusplus/include)
include_directories(${PROJECT_SOURCE_DIR}/third_party/thread-pool)
if(LASP_HAS_RTAUDIO)
include_directories(${PROJECT_SOURCE_DIR}/third_party/rtaudio)
endif()
if(LASP_HAS_ULDAQ)
include_directories(${PROJECT_SOURCE_DIR}/third_party/uldaq/src)
endif()
add_subdirectory(device)
add_subdirectory(dsp)
pybind11_add_module(lasp_cpp MODULE lasp_cpp.cpp
pybind11/lasp_deviceinfo.cpp
pybind11/lasp_daqconfig.cpp
pybind11//lasp_dsp_pybind.cpp
pybind11/lasp_streammgr.cpp
pybind11/lasp_daq.cpp
pybind11/lasp_deviceinfo.cpp
pybind11/lasp_pyindatahandler.cpp
pybind11/lasp_siggen.cpp
)
target_link_libraries(lasp_cpp PRIVATE lasp_device_lib lasp_dsp_lib
${OpenMP_CXX_LIBRARIES} ${LASP_FFT_LIBS} ${TARGET_OS_LINKLIBS})
# Install the Python module
install(TARGETS lasp_cpp
EXCLUDE_FROM_ALL
COMPONENT python_modules
DESTINATION ${PY_BUILD_CMAKE_MODULE_NAME})
# Install the debug file for the Python module (Windows only)
if (WIN32)
install(FILES $<TARGET_PDB_FILE:_add_module>
EXCLUDE_FROM_ALL
COMPONENT python_modules
DESTINATION ${PY_BUILD_CMAKE_MODULE_NAME}
OPTIONAL)
endif()

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@ -9,9 +9,6 @@
#ifndef LASP_CONFIG_H
#define LASP_CONFIG_H
const int LASP_VERSION_MAJOR = @CMAKE_PROJECT_VERSION_MAJOR@;
const int LASP_VERSION_MINOR = @CMAKE_PROJECT_VERSION_MINOR@;
/* Debug flag */
#cmakedefine01 LASP_DEBUG

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@ -52,12 +52,5 @@ PYBIND11_MODULE(lasp_cpp, m) {
init_datahandler(m);
init_siggen(m);
// We store the version number of the code via CMake, and create an
// attribute in the C++ code.
m.attr("__version__") = std::to_string(LASP_VERSION_MAJOR) + "." +
std::to_string(LASP_VERSION_MINOR);
m.attr("LASP_VERSION_MAJOR") = LASP_VERSION_MAJOR;
m.attr("LASP_VERSION_MINOR") = LASP_VERSION_MINOR;
}
/** @} */

55
pyproject.toml Normal file
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@ -0,0 +1,55 @@
[project]
name = "lasp"
readme = "README.md"
requires-python = ">=3.10"
description = "Library for Acoustic Signal Processing"
license = { "file" = "LICENSE" }
authors = [{ "name" = "J.A. de Jong", "email" = "j.a.dejong@ascee.nl" }]
version = "1.0.1"
keywords = ["DSP", "DAQ", "Signal processing"]
classifiers = [
"Development Status :: 3 - Alpha",
"Topic :: Software Development :: Libraries :: Python Modules",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Topic :: Scientific/Engineering",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Operating System :: POSIX :: Linux",
"Operating System :: Microsoft :: Windows",
]
urls = { "Documentation" = "https://lasp.ascee.nl" }
dependencies = ["scipy", "numpy", "matplotlib>=3.7.2", "appdirs",
"dataclasses_json", "h5py"]
[build-system] # How pip and other frontends should build this project
requires = ["py-build-cmake~=0.1.8", "pybind11" ]
build-backend = "py_build_cmake.build"
[tool.py-build-cmake.module] # Where to find the Python module to package
directory = "python_src"
[tool.py-build-cmake.sdist] # What to include in source distributions
include = ["CMakeLists.txt", "cmake", "cpp_src", "python_src", "img", "scripts",
"third_party"]
[tool.py-build-cmake.cmake] # How to build the CMake project
build_type = "Release"
source_path = "."
build_args = ["-j12"]
install_components = ["python_modules"]
[tool.py-build-cmake.editable]
# This might not work properly on Windows. Comment this out when testing on
# Windows.
mode = "symlink"
[tool.commitizen]
name = "cz_conventional_commits"
tag_format = "v$version"
version_scheme = "semver"
version_provider = "pep621"
update_changelog_on_bump = true

View File

@ -2,10 +2,11 @@
LASP: Library for Acoustic Signal Processing
"""
from .lasp_cpp import *
import lasp.lasp_cpp
from .lasp_version import __version__
from .lasp_common import *
__version__ = lasp_cpp.__version__
from .lasp_cpp import *
# from .lasp_imptube import * # TwoMicImpedanceTube
from .lasp_measurement import * # Measurement, scaleBlockSens
@ -14,6 +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

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@ -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

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@ -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,
def fromtxt(
fn,
skiprows,
samplerate,
sensitivity,
mfn=None,
timestamp=None,
delimiter='\t',
firstcoltime=True):
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]),
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')
compression="gzip",
)
ad[0] = dat
return Measurement(mfn)
@staticmethod
def fromnpy(data,
def fromnpy(
data,
samplerate,
sensitivity,
mfn,
timestamp=None,
qtys: List[SIQtys] = None,
channelNames: List[str] = None,
force=False) -> Measurement:
force=False,
) -> Measurement:
"""
Converts a numpy array to a LASP Measurement file, opens the
associated Measurement object and returns it. The measurement file will
@ -802,57 +818,60 @@ class Measurement:
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")
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'] = [qty.toInt() for qty in qtys]
# 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]),
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')
compression="gzip",
)
ad[0] = data
return Measurement(mfn)
@ -865,9 +884,11 @@ 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:
@ -878,16 +899,19 @@ 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),
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')
compression="gzip",
)
ad[0] = data
return Measurement(newfn)

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

View File

@ -0,0 +1,6 @@
import importlib.metadata
__version__ = importlib.metadata.version(__package__ or __name__)
LASP_VERSION_MAJOR, LASP_VERSION_MINOR, LASP_VERSION_PATCH = [
int(a) for a in __version__.split(".")
]

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