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.gitignore vendored
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@ -161,8 +161,3 @@ cython_debug/
# option (not recommended) you can uncomment the following to ignore the entire idea folder. # option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/ #.idea/
# ignore created data files
*.nix
# ignore reource.py as it is created by pyside6-rcc resources.qrc -o resources.py
resources.py

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README.md
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@ -5,13 +5,9 @@ Relaxed ELectrophysiology Acquisition, Control, and Stimulation in python
Implementing [relacs](https://github.com/relacs/relacs) with MCC USB 1608GX-2AO / 1808X devices ([multifunction-usb-daq-devices](https://digilent.com/shop/mcc-daq/data-acquisition/low-cost-daq/)) Implementing [relacs](https://github.com/relacs/relacs) with MCC USB 1608GX-2AO / 1808X devices ([multifunction-usb-daq-devices](https://digilent.com/shop/mcc-daq/data-acquisition/low-cost-daq/))
# Installation # Installation
You have to install the MCC library (follow the installing instructions for [linux/macOS](https://github.com/mccdaq/uldaq) or [windows](https://github.com/mccdaq/mcculw)). You have to install the MCC library (follow the installing instructions for [linux](https://github.com/mccdaq/uldaq) or [windows](https://github.com/mccdaq/mcculw)).
For MacOs if you run into problems with the libusb library if installed with homebrew, there is an issue thread on the uldaq repository. After successful installing, you can use clone the reposity and install it with
[https://github.com/mccdaq/uldaq/issues/44](https://github.com/mccdaq/uldaq/issues/44)
After successful installing, you can use clone the repository and install it with
```sh ```sh
pip install -e . pip install -e .

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poetry.lock generated
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@ -1,23 +1,5 @@
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{file = "scipy-1.14.1.tar.gz", hash = "sha256:5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417"},
]
[package.dependencies]
numpy = ">=1.23.5,<2.3"
[package.extras]
dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.13.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<=7.3.7)", "sphinx-design (>=0.4.0)"]
test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
[[package]] [[package]]
name = "shellingham" name = "shellingham"
version = "1.5.4" version = "1.5.4"
@ -1169,50 +727,16 @@ files = [
] ]
[[package]] [[package]]
name = "stack-data" name = "tomli"
version = "0.6.3" version = "2.0.1"
description = "Extract data from python stack frames and tracebacks for informative displays" description = "A lil' TOML parser"
optional = false
python-versions = "*"
files = [
{file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
{file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
]
[package.dependencies]
asttokens = ">=2.1.0"
executing = ">=1.2.0"
pure-eval = "*"
[package.extras]
tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
[[package]]
name = "tomlkit"
version = "0.13.2"
description = "Style preserving TOML library"
optional = false optional = false
python-versions = ">=3.8" python-versions = ">=3.7"
files = [
{file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
{file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"},
]
[[package]]
name = "traitlets"
version = "5.14.3"
description = "Traitlets Python configuration system"
optional = false
python-versions = ">=3.8"
files = [ files = [
{file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
] ]
[package.extras]
docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
[[package]] [[package]]
name = "typer" name = "typer"
version = "0.12.5" version = "0.12.5"
@ -1252,18 +776,7 @@ files = [
{file = "uldaq-1.2.3.tar.gz", hash = "sha256:2d405ead334bb4e37c20b72d8ec498f0e372b08f1d3323f622abe0581ac28b98"}, {file = "uldaq-1.2.3.tar.gz", hash = "sha256:2d405ead334bb4e37c20b72d8ec498f0e372b08f1d3323f622abe0581ac28b98"},
] ]
[[package]]
name = "wcwidth"
version = "0.2.13"
description = "Measures the displayed width of unicode strings in a terminal"
optional = false
python-versions = "*"
files = [
{file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
{file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
]
[metadata] [metadata]
lock-version = "2.0" lock-version = "2.0"
python-versions = ">=3.11, <3.13" python-versions = "^3.12"
content-hash = "31433ed1dc0cc83dd7e781546dad5b8f068d59eaf692b4d3c12e07c604b1a6dd" content-hash = "6b680c385942c0a2c0eef934f3fb37fdc3d2e1dc058a7f2d891d4f2f0607d9c6"

36
pyproject.toml
View File

@ -1,48 +1,20 @@
[project]
organization = "de.uni-tuebingen.neuroetho"
copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
[tool.poetry] [tool.poetry]
name = "pyrelacs" name = "pyrelacs"
version = "0.1.0" version = "0.1.0"
description = "Relaxed ELectrophysiology Acquisition, Control, and Stimulation in python" description = "Relaxed ELectrophysiology Acquisition, Control, and Stimulation in python"
authors = ["wendtalexander <wendtalexander@protonmail.com>"] authors = ["wendtalexander <wendtalexander@protonmail.com>"]
repository = "https://whale.am28.uni-tuebingen.de/git/awendt/pyrelacs"
readme = "README.md" readme = "README.md"
license = "MIT"
classifiers = [
"Topic :: Scientific/Engineering",
"Intended Audience :: Science/Research",
"Intended Audience :: End Users/Desktop",
]
include = [
{ path = "pyproject.toml" },
"pyrelacs/resources.py"
]
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = ">=3.11, <3.13" python = "^3.12"
uldaq = "^1.2.3" uldaq = "^1.2.3"
typer = "^0.12.5" typer = "^0.12.5"
matplotlib = "^3.9.2" matplotlib = "^3.9.2"
numpy = "^1.9" numpy = "^2.1.1"
pyqt6 = "^6.7.1" pyqt6 = "^6.7.1"
tomlkit = "^0.13.2" tomli = "^2.0.1"
scipy = "^1.14.1"
nixio = "^1.5.3"
pyqtgraph = "^0.13.7"
pytest = "^8.3.3"
pglive = "^0.7.6"
pyyaml = "^6.0.2"
dacite = "^1.8.1"
quantities = "^0.16.0"
[tool.poetry.scripts]
pyrelacs = "pyrelacs.app:main"
[tool.poetry.group.dev.dependencies]
ipython = "^8.27.0"
[build-system] [build-system]
requires = ["poetry-core>=1.0.0"] requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api" build-backend = "poetry.core.masonry.api"

0
pyrelacs/__init__.py
View File

174
pyrelacs/app.py
View File

@ -1,52 +1,144 @@
from PyQt6.QtGui import QAction
import sys import sys
import pathlib
import ctypes
from PyQt6.QtCore import QSettings from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt
from PyQt6.QtWidgets import QApplication from PyQt6.QtWidgets import (
QApplication,
QGridLayout,
QPushButton,
QToolBar,
QWidget,
QMainWindow,
QPlainTextEdit,
)
import tomli
import uldaq
from IPython import embed from IPython import embed
import numpy as np
from pyrelacs import info from pyrelacs.util.logging import config_logging
from pyrelacs.config.config_loader import load_config
from pyrelacs.ui.mainwindow import PyRelacs
from pyrelacs import ( log = config_logging()
resources,
) # best created with pyside6-rcc resources.qrc -o resources.py (rcc produces an error...)
def main(): class PyRelacs(QMainWindow):
app = QApplication(sys.argv) def __init__(self):
app.setApplicationName(info.NAME) super().__init__()
app.setApplicationVersion(str(info.VERSION)) self.setWindowTitle("PyRelacs")
app.setOrganizationDomain(info.ORGANIZATION) self.setMinimumSize(1000, 1000)
# app.setAttribute(Qt.ApplicationAttribute.AA_DontShowIconsInMenus, False)
self.threadpool = QThreadPool()
# read window settings # for starting a Qprocess
settings = QSettings(info.ORGANIZATION, info.NAME) self.p = None
width = int(settings.value("app/width", 1024))
height = int(settings.value("app/height", 768)) self.daq_connect_button = QPushButton("Connect Daq")
x = int(settings.value("app/pos_x", 100)) self.daq_connect_button.setCheckable(True)
y = int(settings.value("app/pos_y", 100)) self.daq_connect_button.clicked.connect(self.connect_dac)
# load the config self.daq_disconnect_button = QPushButton("Disconnect Daq")
self.daq_disconnect_button.setCheckable(True)
config = load_config() self.daq_disconnect_button.clicked.connect(self.disconnect_dac)
# start the app
window = PyRelacs(config) self.text = QPlainTextEdit()
window.setMinimumWidth(200) self.text.setReadOnly(True)
window.setMinimumHeight(200)
window.resize(width, height) layout = QGridLayout()
window.move(x, y) layout.addWidget(self.daq_connect_button, 0, 0)
window.show() layout.addWidget(self.daq_disconnect_button, 0, 1)
exit_code = app.exec() layout.addWidget(self.text, 2, 0, 1, 2)
self.toolbar = QToolBar("Repros")
self.addToolBar(self.toolbar)
self.repro()
self.setFixedSize(QSize(400, 300))
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
def connect_dac(self):
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
try:
self.daq_device = uldaq.DaqDevice(devices[0])
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
self.daq_device.connect()
log.debug("Connected")
except IndexError:
log.debug("DAQ is not connected, closing")
QApplication.quit()
self.daq_connect_button.setDisabled(True)
# store window position and size def disconnect_dac(self):
pos = window.pos() try:
settings.setValue("app/width", window.width()) log.debug(f"{self.daq_device}")
settings.setValue("app/height", window.height()) self.daq_device.disconnect()
settings.setValue("app/pos_x", pos.x()) self.daq_device.release()
settings.setValue("app/pos_y", pos.y()) log.debug(f"{self.daq_device}")
sys.exit(exit_code) self.daq_disconnect_button.setDisabled(True)
self.daq_connect_button.setEnabled(True)
except AttributeError:
log.debug("DAQ was not connected")
def repro(self):
repos_path = pathlib.Path(__file__).parent / "repros"
repos_names = list(repos_path.glob("*.py"))
# exclude the repos.py file
repos_names = [
f.with_suffix("").name for f in repos_names if not f.name == "repos.py"
]
for rep in repos_names:
individual_repro_button = QAction(rep, self)
individual_repro_button.setStatusTip("Button")
individual_repro_button.triggered.connect(
lambda checked, n=rep: self.run_repro(n)
)
self.toolbar.addAction(individual_repro_button)
def message(self, s):
self.text.appendPlainText(s)
def run_repro(self, name_of_repo):
if self.p is None:
self.message(f"Executing process {name_of_repo}")
self.p = QProcess()
self.p.setWorkingDirectory(str(pathlib.Path(__file__).parent / "repros/"))
# log.debug(pathlib.Path(__file__).parent / "repos")
self.p.readyReadStandardOutput.connect(self.handle_stdout)
self.p.readyReadStandardError.connect(self.handle_stderr)
self.p.stateChanged.connect(self.handle_state)
self.p.finished.connect(self.process_finished)
self.p.start("python3", [f"{name_of_repo}" + ".py"])
def handle_stderr(self):
if self.p is not None:
data = self.p.readAllStandardError()
stderr = bytes(data).decode("utf8")
self.message(stderr)
def handle_stdout(self):
if self.p is not None:
data = self.p.readAllStandardOutput()
stdout = bytes(data).decode("utf8")
self.message(stdout)
def handle_state(self, state):
states = {
QProcess.ProcessState.NotRunning: "Not running",
QProcess.ProcessState.Starting: "Starting",
QProcess.ProcessState.Running: "Running",
}
state_name = states[state]
self.message(f"State changed: {state_name}")
def process_finished(self):
self.text.appendPlainText("Process finished")
self.p = None
if __name__ == "__main__": if __name__ == "__main__":
main() app = QApplication(sys.argv)
window = PyRelacs()
window.show()
app.exec()

76
pyrelacs/config.yaml
View File

@ -1,76 +0,0 @@
settings:
# If true daq should be used, else starts without daq
daq: False
# class names of the repros to run
repros: [Calibration, Sinus]
path: ~/projects/pyrelacs/test/
metadata:
SetupName : Setup1
Maintainer : Your name
Creator : Whoever
SetupLocation : virtual
Lab : XYZ-Lab
Institute : Your institute
University : Your university
Address : Your institute's address
pyrelacs:
data:
input:
inputsamplerate : 20
# Unit is rescaled to Hz
inputsamplerateunit : kHz
# BufferSize
inputtracecapacity : 600
# Unit is rescaled to s
inputtracecapacityunit : s
inputunipolar : false
inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ]
inputtracescale : [ 100, 1, 10, 1 ]
inputtraceunit : [ mV, mV, mV, mV ]
inputtracedevice : [ ai-1, ai-1, ai-1, ai-1 ]
inputtracechannel : [ 0, 2, 4, 6 ]
inputtracereference : [ ground, ground, ground, ground ]
inputtracemaxvalue : [ 100, 2, 2, 10 ]
inputtracecenter : [ true, false, false, false ]
output:
outputtraceid : [ GlobalEField, GlobalEFieldAM, LocalEField, I ]
outputtracedevice : [ ao-1, ao-1, ao-1, ao-1 ]
outputtracechannel : [ 0, 1, 2, 3 ]
outputtracescale : [ 1, 1, 1, 1 ]
outputtraceunit : [ V, V, V, V ]
outputtracemaxrate : [ 40, 40, 40, 40]
outputtracemaxrateunit : [kHz, kHz, kHz, kHz]
outputtracemodality : [ electric, electric, electric, current ]
sinus:
inputsamplerate : 20
inputsamplerateunit : kHz
# BufferSize
inputtracecapacity : 600
inputtracecapacityunit : s
outputtraceid : [ Sinus ]
outputtracedevice : [ ao-0 ]
outputtracechannel : [ 0 ]
outputtracescale : [ 1 ]
outputtraceunit : [ V ]
outputtracemaxrate : [ 40 ]
outputtracemaxrateunit : [kHz]
outputtracemodality : [ electric ]
devices:
DAQFlexCore:
analogoutputpins : [0, 1]
analoginputpinshigh : [0, 1, 2, 3,4,5,6,7]
analoginputpinslow : [1,2]
digitalpins : [0,1,2,3]
CS3310DIO:
ident : attdev-1
strobepin : 6
datainpin : 5
dataoutpin : -1
cspin : 4
mutepin : 7
zcenpin : -1

132
pyrelacs/config/config_loader.py
View File

@ -1,132 +0,0 @@
from typing import TypedDict, Union
from dataclasses import dataclass
import pathlib
import dacite
import yaml
from dacite import from_dict
from IPython import embed
from pyrelacs.util.logging import config_logging
log = config_logging()
@dataclass
class ValueUnit:
value: int
unit: str
@dataclass
class Settings:
daq: bool
repros: list[str]
path: str
@dataclass
class Metadata:
SetupName: str
Maintainer: str
Creator: str
SetupLocation: str
Lab: str
Institute: str
University: str
Address: str
@dataclass
class Input:
inputsamplerate: int
inputsamplerateunit: str
# BufferSize
inputtracecapacity: int
inputtracecapacityunit: str
inputunipolar: bool
inputtraceid: list[str]
inputtracescale: list[int]
inputtraceunit: list[str]
inputtracedevice: list[str]
inputtracechannel: list[int]
inputtracereference: list[str]
inputtracemaxvalue: list[int]
inputtracecenter: list[bool]
@dataclass
class Output:
outputtraceid: list[str]
outputtracedevice: list[str]
outputtracechannel: list[int]
outputtracescale: list[int]
outputtraceunit: list[str]
outputtracemaxrate: list[int]
outputtracemaxrateunit: list[str]
outputtracemodality: list[str]
@dataclass
class Data:
input: Input
output: Output
@dataclass
class Sinus:
inputsamplerate: int
inputsamplerateunit: str
# BufferSize
inputtracecapacity: int
inputtracecapacityunit: str
outputtraceid: list[str]
outputtracedevice: list[str]
outputtracechannel: list[int]
outputtracescale: list[int]
outputtraceunit: list[str]
outputtracemaxrate: list[int]
outputtracemaxrateunit: list[str]
outputtracemodality: list[str]
@dataclass
class PyRelacs:
data: Data
sinus: Sinus
@dataclass
class Config:
settings: Settings
metadata: Metadata
pyrelacs: PyRelacs
def load_config():
pyrelacs_config_path = pathlib.Path(__file__).parent.parent / "config.yaml"
log.debug(pyrelacs_config_path)
if not pyrelacs_config_path.is_file():
log.error("Config File was not found")
with open(pyrelacs_config_path, "r") as config_file:
try:
data = yaml.full_load(config_file)
try:
config = from_dict(data_class=Config, data=data)
return config
except dacite.DaciteError as e:
log.error(f"Invalid Config, {e}")
except yaml.YAMLError as e:
raise yaml.YAMLError(f"Error parsing YAML file: {e}")
if __name__ == "__main__":
pyrelacs_config_path = pathlib.Path(__file__).parent.parent / "config.yaml"
log.debug(pyrelacs_config_path)
if not pyrelacs_config_path.is_file():
log.error("Config File was not found")
with open(pyrelacs_config_path, "r") as config_file:
data = yaml.full_load(config_file)
embed()
exit()

81
pyrelacs/dataio/buffer.py
View File

@ -1,81 +0,0 @@
import time
import faulthandler
from collections import deque
from pyqtgraph import transformToArray
import uldaq
import numpy as np
from IPython import embed
import matplotlib.pyplot as plt
from pyrelacs.util.logging import config_logging
log = config_logging()
faulthandler.enable()
class DataBuffer:
def __init__(self, channels, samples):
self.channels = channels
self.samples = samples
def read_analog_continously(
self,
device: uldaq.DaqDevice,
samplerate: float = 40_000.0,
):
data_array = []
max_len_buffer = self.channels * self.samples
self.buffer = deque(maxlen=max_len_buffer)
samples_per_channel = 40_000
self.device = device
self.ai_device = self.device.get_ai_device()
data_analog_input = uldaq.create_float_buffer(
self.channels, samples_per_channel
)
er = self.ai_device.a_in_scan(
0,
1,
uldaq.AiInputMode.SINGLE_ENDED,
uldaq.Range.BIP10VOLTS,
samples_per_channel,
samplerate,
uldaq.ScanOption.CONTINUOUS,
uldaq.AInScanFlag.DEFAULT,
data=data_analog_input,
)
daq_status = uldaq.ScanStatus.IDLE
while daq_status == uldaq.ScanStatus.IDLE:
daq_status = self.ai_device.get_scan_status()[0]
prev_count = 0
prev_index = 0
while daq_status != uldaq.ScanStatus.IDLE:
daq_status, transfer_status = self.ai_device.get_scan_status()
# The index into the data buffer immediately following the last sample transferred.
curren_index = transfer_status.current_index
# total samples since start of the scan
total_samples = transfer_status.current_total_count
# The number of samples per channel transferred since the scan started
channel_samples = transfer_status.current_scan_count
self.ai_device.scan_stop()
if __name__ == "__main__":
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
try:
daq_device = uldaq.DaqDevice(devices[0])
except uldaq.ul_exception.ULException as e:
log.error("Did not found daq devices, please connect one")
raise e
daq_device.connect()
buf = DataBuffer(channels=2, samples=100_000)
buf.read_analog_continously(daq_device)

192
pyrelacs/dataio/circbuffer.py
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@ -1,192 +0,0 @@
from typing import Tuple
import numpy as np
from IPython import embed
from pyqtgraph.Qt.QtCore import QMutex
class CircBuffer:
def __init__(
self,
size: int,
channels: int = 1,
samplerate: float = 40_000.0,
mutex: QMutex = QMutex(),
):
self.__size = size
self.__channels = channels
self.__samplereate = samplerate
self.__buffer = np.zeros(
(channels, size), dtype=np.double
) # or dtype of your choice
self.__time = np.zeros((channels, size), dtype=np.double)
self.__index = [0 for i in range(channels)]
self.__is_full = [False for i in range(channels)]
self.__totalcount = [0 for i in range(channels)]
self.__overflows = [0 for i in range(channels)]
self.mutex = mutex
@property
def size(self):
return self.__size
@property
def samplerate(self):
return self.__samplereate
@property
def channel_count(self):
return self.__channels
def totalcount(self, channel: int = 0):
return self.__totalcount[channel]
def is_full(self, channel: int = 0):
return self.__is_full[channel]
def write_index(self, channel: int = 0):
return self.__index[channel]
def append(self, item, channel: int = 0):
self.mutex.lock()
self.__buffer[channel, self.write_index(channel)] = item
self.__index[channel] = (self.write_index(channel) + 1) % self.__size
self.__totalcount[channel] += 1
self.__time[channel, self.write_index(channel)] = (
self.__time[channel, self.write_index(channel) - 1] + 1 / self.__samplereate
)
if self.__index[channel] == 0:
self.__is_full[channel] = True
self.__overflows[channel] += 1
self.mutex.unlock()
def get_all(self, channel: int = 0):
"""
Return all valid values from the specified channel
"""
if self.__is_full[channel]:
return np.concatenate(
(
self.__buffer[channel, self.__index[channel] :],
self.__buffer[channel, : self.__index[channel]],
)
)
else:
return self.__buffer[channel, : self.__index[channel]]
def has_value(self, index, channel):
if index <= 0 and self.is_full(channel):
return True
elif index < 0 and not self.is_full(channel):
return False
if index >= self.size:
return False
# test if the ring buffer is at the start but
# and the index is greater than the write index
if index > self.write_index(channel) and self.is_full(channel):
return True
elif index >= self.write_index(channel) and not self.is_full(channel):
raise IndexError("Index has no value, not written")
if index == self.write_index(channel) and self.__totalcount[channel] == 0:
return False
return True
def valid_range(self, channel: int = 0) -> Tuple[int, int]:
"""
Return the start index and the extend that are valid within the buffer
Parameters
----------
channel : int
channel of the buffer
Returns
-------
Tuple[int, int]
start, extend of the valid range
"""
start = 0
extend = 0
if self.__totalcount[channel] == 0:
return start, extend
if not self.is_full(channel):
extend = self.__totalcount[channel]
else:
extend = self.size
return start, extend
def get(self, index: int = -1, channel: int = 0) -> Tuple[np.double, float]:
# easy case first, we can spare the effort of further checking
if index >= 0 and index <= self.write_index(channel):
if self.has_value(index, channel):
return (self.__buffer[channel, index], self.__time[channel, index])
else:
raise IndexError(
f"Invalid index {index} on ring buffer for channel{channel}"
)
if index < 0:
index = self.write_index() - 1
if self.has_value(index, channel):
return (self.__buffer[channel, index], self.__time[channel, index])
else:
raise IndexError(
f"Invalid index {index} on ring buffer for channel{channel}"
)
def read(self, start, extend=1, channel=0):
"""Reads a numpy array from buffer"""
if extend < 0:
raise IndexError(f"Invalid extend ({extend}) for channel {channel}")
if not self.is_full(channel):
if start < 0:
raise IndexError(f"Invalid start ({start}) for channel {channel}")
else:
if start < 0:
start = start + self.size
if extend == 1:
return np.array(self.get(start, channel))
vs, vc = self.valid_range(channel)
if start > self.__totalcount[channel]:
raise IndexError(
f"Invalid start index {start} is invalid with totalcount {self.__totalcount[channel]} for channel{channel}"
)
if start > self.size:
raise IndexError(
f"Invalid start index {start} for buffer with size {self.size}"
)
if extend > vc:
extend = vc
if (start + extend) > self.__totalcount[channel]:
raise IndexError(
f" Invalid range, extended over the totalcount of the buffer {self.__totalcount[channel]}"
)
if (start + extend) < self.size:
return (
self.__time[channel, start : start + extend],
self.__buffer[channel, start : start + extend],
)
else:
return (
np.concatenate(
(
self.__time[channel, start:],
self.__time[channel, : extend - self.size + start],
)
),
np.concatenate(
(
self.__buffer[channel, start:],
self.__buffer[channel, : extend - self.size + start],
)
),
)

175
pyrelacs/dataio/daq_producer.py
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@ -1,175 +0,0 @@
import time
import faulthandler
import uldaq
import numpy as np
from IPython import embed
import matplotlib.pyplot as plt
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.util.logging import config_logging
log = config_logging()
faulthandler.enable()
class DaqProducer:
def __init__(
self, buffer: CircBuffer, device: uldaq.DaqDevice, channels: list[int]
):
self.buffer = buffer
self.device = device
self.ai_device = self.device.get_ai_device()
self.channels = channels
self.stop = False
def read_analog_continously(
self,
*args,
**kwargs,
):
log.debug("starting acquisition")
if self.channels[0] == self.channels[1]:
channel_range = np.arange(1)
else:
channel_range = np.arange(self.channels[0], self.channels[1] + 1)
assert channel_range.size == self.buffer.channel_count, ValueError(
f"Missmatch in channel count,\n daq_channel: "
f"{channel_range.size}\n buffer_channel: {self.buffer.channel_count}"
)
# let the buffer for the daq device hold 5 seconds of data
daq_buffer_size = int(self.buffer.samplerate * 5)
data_in = uldaq.create_float_buffer(channel_range.size, daq_buffer_size)
log.debug(f"Buffersize for daq {len(data_in)}")
log.debug(f"Buffersize {self.buffer.size}")
er = self.ai_device.a_in_scan(
self.channels[0],
self.channels[1],
uldaq.AiInputMode.SINGLE_ENDED,
uldaq.Range.BIP10VOLTS,
daq_buffer_size,
self.buffer.samplerate,
uldaq.ScanOption.CONTINUOUS,
uldaq.AInScanFlag.DEFAULT,
data=data_in,
)
chunk_size = int(daq_buffer_size / 10)
wrote_chunk = False
start_time = time.time()
daq_status = uldaq.ScanStatus.IDLE
while daq_status == uldaq.ScanStatus.IDLE:
daq_status = self.ai_device.get_scan_status()[0]
while daq_status != uldaq.ScanStatus.IDLE:
prev_count = 0
prev_index = 0
while not self.stop:
daq_status, transfer_status = self.ai_device.get_scan_status()
# The index into the data buffer immediately following the last sample transferred.
current_index = transfer_status.current_index
# total samples since start of the scan
total_samples = transfer_status.current_total_count
# The number of samples per channel transferred since the scan started
channel_samples = transfer_status.current_scan_count
new_data_count = total_samples - prev_count
# check if counts if new data is bigger than the buffer
# if that happends stop the acquisition
if new_data_count > len(data_in):
self.ai_device.scan_stop()
log.error("A Buffer overrun occurred")
break
if new_data_count > chunk_size:
wrote_chunk = True
# index wraps around the buffer
if prev_index + chunk_size > len(data_in) - 1:
log.debug("Chunk wraps around buffersize")
first_chunk = len(data_in) - prev_index
[
self.buffer.append(data_in[prev_index + i])
for i in range(first_chunk)
]
second_chunk = chunk_size - first_chunk
[
self.buffer.append(data_in[i])
for i in range(second_chunk)
]
else:
log.debug("Writing chunk to buffer")
[
self.buffer.append(data_in[prev_index + i])
for i in range(chunk_size)
]
self.buffer.append(data_in[current_index])
if total_samples - prev_count > len(data_in):
self.ai_device.scan_stop()
log.error("A Buffer overrun occurred")
break
else:
wrote_chunk = False
if wrote_chunk:
prev_count += chunk_size
prev_index += chunk_size
prev_index %= daq_buffer_size
self.ai_device.scan_stop()
daq_status, transfer_status = self.ai_device.get_scan_status()
current_index = transfer_status.current_index
log.debug(daq_status)
log.debug(transfer_status.current_index)
log.debug(transfer_status.current_total_count)
log.debug(transfer_status.current_scan_count)
log.debug(self.buffer.totalcount())
log.debug("Appending last chunk")
if prev_index + chunk_size > len(data_in) - 1:
log.debug("Chunk wraps around buffersize")
first_chunk = len(data_in) - prev_index
[
self.buffer.append(data_in[prev_index + i])
for i in range(first_chunk)
]
second_chunk = chunk_size - first_chunk
[self.buffer.append(data_in[i]) for i in range(second_chunk)]
else:
log.debug("Writing chunk to buffer")
[
self.buffer.append(data_in[prev_index + i])
for i in range(chunk_size)
]
self.buffer.append(data_in[current_index])
log.info("stopping")
break
break
return "Done. "
def stop_aquisition(self):
self.stop = True
# if __name__ == "__main__":
# devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
# log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
# try:
# daq_device = uldaq.DaqDevice(devices[0])
# except uldaq.ul_exception.ULException as e:
# log.error("Did not found daq devices, please connect one")
# raise e
# daq_device.connect()
#
# buf = CircBuffer(size=1_000_000, samplerate=100)
# producer = DaqProducer(buf, daq_device, [1, 1])
# producer.read_analog_continously()

72
pyrelacs/dataio/nix_writer.py
View File

@ -1,72 +0,0 @@
import time
from IPython import embed
from PyQt6.QtCore import QMutex
import nixio
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.util.logging import config_logging
log = config_logging()
class NixWriter:
def __init__(self, buffer: CircBuffer) -> None:
self.buffer = buffer
def write_nix(
self,
data_array: nixio.DataArray,
mutex: QMutex,
channel: int = 0,
chunk_size=1000,
*args,
**kwargs,
):
index = 0
log.debug("Starting the writing")
self.write = True
while self.write:
total_count = self.buffer.totalcount(channel=channel)
if total_count - index >= chunk_size:
mutex.lock()
log.debug(index)
try:
_, data = self.buffer.read(
index, extend=chunk_size, channel=channel
)
if index == 0:
data_array.write_direct(data)
else:
data_array.append(data)
index += chunk_size
except IndexError as e:
time.sleep(0.001)
log.debug(f"{e}")
mutex.unlock()
else:
time.sleep(0.001)
continue
total_count = self.buffer.totalcount(channel=channel)
try:
mutex.lock()
_, data = self.buffer.read(
index, extend=total_count - index, channel=channel
)
data_array.append(data)
mutex.unlock()
index += total_count - index
except IndexError as e:
log.error(f"Could not read the last samples, {e}")
log.debug("Stoppint the writing")
log.debug(f"Samples written {index}")
def _write_header(self):
self.nix_file = nixio.File.open(path="data.nix", mode=nixio.FileMode.Overwrite)
self.block = self.nix_file.create_block("recording", "testfile")
self.data_array = self.block.create_data_array(
"Analog1", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
)
def stop_writing(self):
self.write = False

50
pyrelacs/dataio/sin_producer.py
View File

@ -1,50 +0,0 @@
import time
import numpy as np
from IPython import embed
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.util.logging import config_logging
log = config_logging()
class SinProducer:
def __init__(
self,
buffer: CircBuffer,
) -> None:
self.buffer = buffer
self.stop = False
def produce_sin(
self,
*args,
**kwargs,
) -> None:
AMPLITUDE = 2
FREQUENCY = 10
self.stop = False
log.debug("producing Sin")
start_time = time.time()
t = 0
while not self.stop:
s = AMPLITUDE * np.sin(2 * np.pi * FREQUENCY * t)
self.buffer.append(s)
t += 1 / self.buffer.samplerate
time.sleep(1 / self.buffer.samplerate)
end_time = time.time()
log.debug(f"duration sinus {end_time-start_time}")
log.debug(f"Stimulation time {t}")
log.debug(f"Total samples produced {self.buffer.totalcount()}")
def stop_request(self):
self.stop = True
if __name__ == "__main__":
buf = CircBuffer(1_000_000, 1, samplerate=10_000)
pro_sin = SinProducer(buf)
pro_sin.produce_sin()

0
pyrelacs/devices/__init__.py
View File

431
pyrelacs/devices/mccdaq.py
View File

@ -1,431 +0,0 @@
from ctypes import Array, c_double
import time
from typing import Union
from IPython import embed
import numpy.typing as npt
import uldaq
import numpy as np
from pyrelacs.util.logging import config_logging
log = config_logging()
class MccDaq:
"""
Represents the Digital/Analog Converter from Meassuring Computing.
provides methods for writing and reading the Analog / Digital input and output.
Connects to the DAC device.
Attributes
----------
daq_device : uldaq.DaqDevice
DaqDevice for handling connecting, releasing and disconnecting
ai_device : uldaq.AiDevice
The Analog input Device
ao_device :
Analog output Device
dio_device :
Digital Input Output
"""
def __init__(self) -> None:
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
try:
self.daq_device = uldaq.DaqDevice(devices[0])
except uldaq.ul_exception.ULException as e:
log.error("Did not found daq devices, please connect one")
raise e
try:
self.daq_device.connect()
except uldaq.ul_exception.ULException:
self.disconnect_daq()
self.connect_dac()
self.ai_device = self.daq_device.get_ai_device()
self.ao_device = self.daq_device.get_ao_device()
self.dio_device = self.daq_device.get_dio_device()
log.debug("Connected to MccDaq")
log.debug("Activating the Attenuator")
self.activate_attenuator()
def connect_dac(self):
"""
Connecting to the DAQ device
"""
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
if len(devices) == 0:
log.error("Did not found daq devices, please connect one")
exit(1)
self.daq_device = uldaq.DaqDevice(devices[0])
self.daq_device.connect()
self.ai_device = self.daq_device.get_ai_device()
self.ao_device = self.daq_device.get_ao_device()
self.dio_device = self.daq_device.get_dio_device()
log.debug("Connected")
def read_analog(
self,
channels: list[int],
duration: int,
samplerate: float,
AiInputMode: uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED,
Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
) -> Array[c_double]:
"""
Reading the analog input of the DAC device
Creates a c_double Array for storing the acquired data
Parameters
----------
channels : list[int]
channels to read from, provide only two int's in a list (ex [0, 1] or [0, 4])
for sampling from the range(channel0, channel4)
duration : int
duration of sampling period
samplerate : float
samplerate for the duration of sampling
AiInputMode : uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED
Contains attributes indicating A/D channel input modes.
Compares to Ground
Range : uldaq.Range = uldaq.Range.BIP10VOLTS
Range of the output
ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
Specific Flags for acuiring the input
AInScanFlag : uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT
Scaling of the data
Returns
-------
Array[c_double]
"""
assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
if channels[0] != channels[1]:
buffer_len_channels = 2
else:
buffer_len_channels = 1
buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
data_analog_input = uldaq.create_float_buffer(buffer_len_channels, buffer_len)
er = self.ai_device.a_in_scan(
channels[0],
channels[1],
AiInputMode,
Range,
buffer_len,
samplerate,
ScanOption,
AInScanFlag,
data=data_analog_input,
)
return data_analog_input
def write_analog(
self,
data: Union[list, npt.NDArray],
channels: list[int],
samplerate: float,
Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
) -> Array[c_double]:
"""
Writes data to the DAC device.
Creates a c_double Array for writing the data
Parameters
----------
data : Union[list, npt.NDArray]
data which should be written to the DAC
channels : list[int]
channels to read from, provide only two int's in a list (ex [0, 1])
for sampling from the range(channel0, channel1)
DAC USB 1608GX-2AO has only 2 output channels
samplerate : float
samplerate for the duration of sampling
Range : uldaq.Range = uldaq.Range.BIP10VOLTS
Range of the output
ScanOption : uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO
Specific Flags for acuiring the input
AOutScanFlag : uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT
For Scaling the data
Returns
-------
Array[c_double]
"""
assert len(channels) == 2, log.error("You can only provide two channels [0, 1]")
buffer = c_double * len(data)
data_analog_output = buffer(*data)
log.debug(f"Created C_double data {data_analog_output}")
try:
err = self.ao_device.a_out_scan(
channels[0],
channels[1],
Range,
int(len(data)),
samplerate,
ScanOption,
AOutScanFlag,
data_analog_output,
)
except Exception as e:
print(f"{e}")
self.set_analog_to_zero()
self.disconnect_daq()
return data_analog_output
def set_analog_to_zero(self, channels: list[int] = [0, 1]) -> None:
"""
Sets all analog outputs to zero
Parameters
----------
channels : list[int]
channels to read from, provide only two int's in a list (ex [0, 1])
for sampling from the range(channel0, channel1)
DAC USB 1608GX-2AO has only 2 output channels
"""
try:
err = self.ao_device.a_out_list(
channels[0],
channels[1],
[
uldaq.Range.BIP10VOLTS,
uldaq.Range.BIP10VOLTS,
],
uldaq.AOutListFlag.DEFAULT,
[0, 0],
)
except Exception as er:
log.error(f"{er}")
log.error("disconnection dac")
# self.disconnect_daq()
def digital_trigger(self, ch: int = 0) -> None:
"""
Writes a 1 to a specified digital channel, if the channel is already on 1 switches it to
0 and after Nano second it writes a 1 to the specified digital channel
Parameters
----------
ch : int
Channel to trigger
"""
data = self.read_bit(channel=ch)
if data:
self.write_bit(channel=ch, bit=0)
time.time_ns()
self.write_bit(channel=ch, bit=1)
else:
self.write_bit(channel=ch, bit=1)
def write_bit(self, channel: int = 0, bit: int = 1) -> None:
"""
Writes a 0 / 1 to a specified digitial channel
Parameters
----------
channel : int
Digital channel to write
bit : int
0 / 1 for writing to the digital channel
"""
self.dio_device.d_config_bit(
uldaq.DigitalPortType.AUXPORT, channel, uldaq.DigitalDirection.OUTPUT
)
self.dio_device.d_bit_out(
uldaq.DigitalPortType.AUXPORT, bit_number=channel, data=bit
)
def read_bit(self, channel: int = 0) -> int:
"""
Reads a 0 / 1 from the specified digital channel
Parameters
----------
channel : int
Digital channel to read from
Returns
-------
bit : int
0 or 1 from the digital channel
"""
bit = self.dio_device.d_bit_in(uldaq.DigitalPortType.AUXPORT, channel)
return bit
def disconnect_daq(self):
log.debug("Disconnecting DAQ")
self.deactivate_attenuator()
self.daq_device.disconnect()
self.daq_device.release()
def check_attenuator(self) -> None:
"""
For checking the attenuator in the DAC device that was implemented to attenuate the
analog signal to mV.
Writes to Channel 0 of the analog output with different attenuation levels
0, 0, -2, -5, -10, -20, -50 dB and the second 0 has a software mute
"""
SAMPLERATE = 40_000.0
DURATION = 5
AMPLITUDE = 1
SINFREQ = 1
t = np.arange(0, DURATION, 1 / SAMPLERATE)
data = AMPLITUDE * np.sin(2 * np.pi * SINFREQ * t)
# data_channels = np.concatenate((data, data))
db_values = [0, 0, -2, -5, -10, -20, -50]
for i, db_value in enumerate(db_values):
log.info(f"Attenuating the Channels, with {db_value}")
if i == 1:
log.info("Muting the Channels")
self.set_attenuation_level(
db_value, db_value, mute_channel1=True, mute_channel2=True
)
else:
self.set_attenuation_level(db_value, db_value)
_ = self.write_analog(
data,
[0, 0],
SAMPLERATE,
ScanOption=uldaq.ScanOption.EXTTRIGGER,
Range=uldaq.Range.BIP10VOLTS,
)
self.digital_trigger()
try:
self.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
self.write_bit(channel=0, bit=0)
self.set_analog_to_zero()
except uldaq.ul_exception.ULException:
log.debug("Operation timed out")
self.write_bit(channel=0, bit=0)
self.disconnect_daq()
self.connect_dac()
self.set_analog_to_zero()
finally:
self.write_bit(channel=0, bit=0)
self.disconnect_daq()
self.connect_dac()
self.set_analog_to_zero()
log.info("Sleeping for 1 second, before next attenuation")
time.sleep(1)
def set_attenuation_level(
self,
db_channel1: float = 5.0,
db_channel2: float = 5.0,
mute_channel1: bool = False,
mute_channel2: bool = False,
):
"""
Setting the attenuation level of the chip that is connected to the DAQ
The attenuation level is set by writing to the connected digital output pin 5
where the strobepin 6 is signaling the when the bit was send.
The cspin is set from 1 to 0 for the start and 0 to 1 for signaling the end
of the data write process.
The mute pin should be set to 1 for the device to be working.
More information in the AttCS3310.pdf in the doc
ident : attdev-1
strobepin : 6
datainpin : 5
dataoutpin: -1
cspin : 4
mutepin : 7
zcenpin : -1
Parameters
----------
db_channel1 : float
dB Attenuation level for the first channel
db_channel2 : float
dB Attenuation level for the second channel
mute_channel1 : bool
Software mute for the first channel
mute_channel2 : bool
Software mute for the second channel
"""
self.activate_attenuator()
hardware_possible_db = np.arange(-95.5, 32.0, 0.5)
byte_number = np.arange(1, 256)
byte_number_db1 = byte_number[hardware_possible_db == db_channel1][0]
binary_db1 = np.binary_repr(byte_number_db1, width=8)
byte_number_db2 = byte_number[hardware_possible_db == db_channel2][0]
binary_db2 = np.binary_repr(byte_number_db2, width=8)
if mute_channel1:
log.info("Muting channel one")
binary_db1 = "00000000"
if mute_channel2:
log.info("Muting channel one")
binary_db2 = "00000000"
channels_db = binary_db2 + binary_db1
self.write_bit(channel=4, bit=0)
for b in channels_db:
self.write_bit(channel=5, bit=int(b))
time.time_ns()
self.write_bit(channel=6, bit=1)
time.time_ns()
self.write_bit(channel=6, bit=0)
time.time_ns()
self.write_bit(channel=4, bit=1)
def activate_attenuator(self):
"""
Activation of the attenuator, where the cspin and mute pin is set to 1,
and the datapin and strobpin to 0
"""
for ch, b in zip([4, 5, 6, 7], [1, 0, 0, 1]):
self.write_bit(channel=ch, bit=b)
def deactivate_attenuator(self):
"""
Writes a 0 to the mute pin, which is deactivating the attenuator
"""
# mute should be enabled for starting calibration
self.write_bit(channel=7, bit=0)

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import tomllib
import pathlib
def load_project_settings(project_root):
# Read the pyproject.toml file
pyproject_path = pathlib.Path.joinpath(project_root, "pyproject.toml")
with open(pyproject_path, "rb") as f:
pyproject_content = tomllib.load(f)
info_dict = {
"name": pyproject_content["tool"]["poetry"]["name"],
"version": pyproject_content["tool"]["poetry"]["version"],
"description": pyproject_content["tool"]["poetry"]["description"],
"authors": pyproject_content["tool"]["poetry"]["authors"],
"readme": pyproject_content["tool"]["poetry"]["authors"],
"licence": pyproject_content["tool"]["poetry"]["license"],
"organization": pyproject_content["project"]["organization"],
"classifiers": pyproject_content["tool"]["poetry"]["classifiers"],
"copyright": pyproject_content["project"]["copyright"],
"repository": pyproject_content["tool"]["poetry"]["repository"],
}
return info_dict
_root = pathlib.Path(__file__).parent.parent
_infodict = load_project_settings(_root)
NAME = _infodict["name"]
VERSION = _infodict["version"]
AUTHORS = _infodict["authors"]
COPYRIGHT = _infodict["copyright"]
HOMEPAGE = _infodict["repository"]
CLASSIFIERS = _infodict["classifiers"]
DESCRIPTION = _infodict["description"]
ORGANIZATION = _infodict["organization"]

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pyrelacs/repros/__init__.py
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import ctypes
import uldaq
from IPython import embed
from pyrelacs.repros.repos import Repos
from pyrelacs.util.logging import config_logging
import numpy as np
import matplotlib.pyplot as plt
log = config_logging()
class Calibration(Repos):
def __init__(self) -> None:
super().__init__()
def run_calibration(self):
# Stimulus
time = np.arange(0, DURATION, 1 / SAMPLERATE)
data = AMPLITUDE * np.sin(2 * np.pi * SINFREQ * time)
# sending stimulus
stim, ao_device = self.send_analog_dac(
data, [0, 0], SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
)
read_data = self.read_analog_daq(
[0, 1], DURATION, SAMPLERATE, ScanOption=uldaq.ScanOption.EXTTRIGGER
)
self.digital_trigger()
ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 11)
self.digital_trigger(data=0)
self.disconnect_dac()
embed()
exit()
if __name__ == "__main__":
SAMPLERATE = 40_000.0
DURATION = 5
AMPLITUDE = 3
SINFREQ = 1
daq_input = Calibration()
daq_input.run_calibration()

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pyrelacs/repros/calibration/calibration.py
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import faulthandler
import time
import nixio as nix
import uldaq
from IPython import embed
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import welch, find_peaks
import pyqtgraph as pg
from pyrelacs.devices.mccdaq import MccDaq
from pyrelacs.util.logging import config_logging
log = config_logging()
# for more information on seg faults
faulthandler.enable()
class Calibration:
def __init__(self, config, mccdaq: MccDaq) -> None:
self.config = config
self.mccdaq = mccdaq
self.SAMPLERATE = 40_000.0
self.DURATION = 5
self.AMPLITUDE = 1
self.SINFREQ = 750
@staticmethod
def run(*args, **kwargs):
nix_block = args[0]
figure = args[1]
mccdaq = args[2]
config = args[3]
calb = Calibration(config, mccdaq)
calb.check_beat(nix_block)
calb.plot(figure, nix_block)
return "finished"
def check_amplitude(self):
db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
colors = ["red", "green", "blue", "black", "yellow"]
self.mccdaq.set_attenuation_level(db_channel1=0.0, db_channel2=0.0)
# write to ananlog 1
t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
fig, ax = plt.subplots()
for i, db_value in enumerate(db_values):
self.mccdaq.set_attenuation_level(
db_channel1=db_value, db_channel2=db_value
)
log.debug(f"{db_value}")
stim = self.mccdaq.write_analog(
data,
[0, 0],
self.SAMPLERATE,
ScanOption=uldaq.ScanOption.EXTTRIGGER,
)
data_channel_one = self.mccdaq.read_analog(
[0, 0],
self.DURATION,
self.SAMPLERATE,
ScanOption=uldaq.ScanOption.EXTTRIGGER,
)
time.sleep(1)
log.debug("Starting the Scan")
self.mccdaq.digital_trigger()
try:
self.mccdaq.ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 15)
log.debug("Scan finished")
self.mccdaq.write_bit(channel=0, bit=0)
time.sleep(1)
self.mccdaq.set_analog_to_zero()
except uldaq.ul_exception.ULException:
log.debug("Operation timed out")
# reset the diggital trigger
self.mccdaq.write_bit(channel=0, bit=0)
time.sleep(1)
self.mccdaq.set_analog_to_zero()
# self.mccdaq.disconnect_daq()
if i == 0:
ax.plot(t, stim, label=f"Input_{db_value}", color=colors[i])
ax.plot(t, data_channel_one, label=f"Reaout {db_value}", color=colors[i])
ax.legend()
plt.show()
# self.mccdaq.disconnect_daq()
def check_beat(self, nix_block: nix.Block):
self.mccdaq.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
# data = np.concatenate((data, data))
db_values = [0.0, -5.0, -8.5, -10.0]
colors = ["red", "blue", "black", "green"]
colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
# fig, axes = plt.subplots(2, 2, sharex="col")
for i, db_value in enumerate(db_values):
self.mccdaq.set_attenuation_level(db_channel1=db_value)
stim = self.mccdaq.write_analog(
data,
[0, 0],
self.SAMPLERATE,
ScanOption=uldaq.ScanOption.EXTTRIGGER,
)
readout = self.mccdaq.read_analog(
[0, 1],
self.DURATION,
self.SAMPLERATE,
ScanOption=uldaq.ScanOption.EXTTRIGGER,
)
self.mccdaq.digital_trigger()
log.info(self.mccdaq.ao_device)
ai_status = uldaq.ScanStatus.RUNNING
ao_status = uldaq.ScanStatus.RUNNING
log.debug(
f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
)
while (ai_status != uldaq.ScanStatus.IDLE) and (
ao_status != uldaq.ScanStatus.IDLE
):
# log.debug("Scanning")
time.time_ns()
ai_status = self.mccdaq.ai_device.get_scan_status()[0]
ao_status = self.mccdaq.ao_device.get_scan_status()[0]
self.mccdaq.write_bit(channel=0, bit=0)
log.debug(
f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
)
channel1 = np.array(readout[::2])
channel2 = np.array(readout[1::2])
stim_data = nix_block.create_data_array(
f"stimulus_{db_value}",
"nix.regular_sampled",
shape=data.shape,
data=channel1,
label="Voltage",
unit="V",
)
stim_data.append_sampled_dimension(
self.SAMPLERATE,
label="time",
unit="s",
)
fish_data = nix_block.create_data_array(
f"fish_{db_value}",
"Array",
shape=data.shape,
data=channel2,
label="Voltage",
unit="V",
)
fish_data.append_sampled_dimension(
self.SAMPLERATE,
label="time",
unit="s",
)
time.time_ns()
self.mccdaq.set_analog_to_zero()
def plot(self, figure, block):
self.figure = figure
self.figure.setBackground("w")
self.beat_plot = self.figure.addPlot(row=0, col=0)
self.power_plot = self.figure.addPlot(row=1, col=0)
self.beat_plot.addLegend()
self.power_plot.addLegend()
# self.power_plot.setLogMode(x=False, y=True)
colors = ["red", "green", "blue", "black", "yellow"]
for i, (stim, fish) in enumerate(
zip(list(block.data_arrays)[::2], list(block.data_arrays)[1::2])
):
f_stim, stim_power = welch(
stim[:],
fs=40_000.0,
window="flattop",
nperseg=100_000,
)
stim_power = decibel(stim_power)
stim_max_power_index = np.argmax(stim_power)
freq_stim = f_stim[stim_max_power_index]
f_fish, fish_power = welch(
fish[:],
fs=40_000.0,
window="flattop",
nperseg=100_000,
)
fish_power = decibel(fish_power)
fish_max_power_index = np.argmax(fish_power)
freq_fish = f_fish[fish_max_power_index]
beat_frequency = np.abs(freq_fish - freq_stim)
beat = stim[:] + fish[:]
beat_squared = beat**2
f, powerspec = welch(
beat_squared,
window="flattop",
fs=40_000.0,
nperseg=100_000,
)
powerspec = decibel(powerspec)
padding = 20
integration_window = powerspec[
(f > beat_frequency - padding) & (f < beat_frequency + padding)
]
peaks = find_peaks(powerspec, prominence=40)[0]
pen = pg.mkPen(colors[i])
self.beat_plot.plot(
np.arange(0, len(beat)) / 40_000.0,
beat,
pen=pen,
name=stim.name,
)
self.power_plot.plot(f, powerspec, pen=pen, name=stim.name)
self.power_plot.plot(f[peaks], powerspec[peaks], pen=None, symbol="x")
def decibel(power, ref_power=1.0, min_power=1e-20):
"""Transform power to decibel relative to ref_power.
\\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\]
Power values smaller than `min_power` are set to `-np.inf`.
Parameters
----------
power: float or array
Power values, for example from a power spectrum or spectrogram.
ref_power: float or None or 'peak'
Reference power for computing decibel.
If set to `None` or 'peak', the maximum power is used.
min_power: float
Power values smaller than `min_power` are set to `-np.inf`.
Returns
-------
decibel_psd: array
Power values in decibel relative to `ref_power`.
"""
if np.isscalar(power):
tmp_power = np.array([power])
decibel_psd = np.array([power])
else:
tmp_power = power
decibel_psd = power.copy()
if ref_power is None or ref_power == "peak":
ref_power = np.max(decibel_psd)
decibel_psd[tmp_power <= min_power] = float("-inf")
decibel_psd[tmp_power > min_power] = 10.0 * np.log10(
decibel_psd[tmp_power > min_power] / ref_power
)
if np.isscalar(power):
return decibel_psd[0]
else:
return decibel_psd

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pyrelacs/repros/calibration/config.yaml
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import ctypes
import uldaq
from IPython import embed
import matplotlib.pyplot as plt
import numpy as np
from pyrelacs.util.logging import config_logging
log = config_logging()
class ReadWrite:
def __init__(self) -> None:
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
self.daq_device = uldaq.DaqDevice(devices[0])
self.daq_device.connect()
log.debug("Connected")
# self.daq_device.enable_event(
# uldaq.DaqEventType.ON_DATA_AVAILABLE,
# 1,
# self.read_write,
# (uldaq.DaqEventType.ON_DATA_AVAILABLE, 1, 1),
# )
def read_write(self) -> None:
# event_type = callback_args.event_type
# event_data = callback_args.event_data
# user_data = callback_args.user_data
FS = 30_000.0
DURATION = 10
FREQUENCY = 100
time = np.arange(0, DURATION, 1 / FS)
data = 2 * np.sin(2 * np.pi * FREQUENCY * time)
buffer = ctypes.c_double * len(time)
data_c = buffer(*data)
buf = uldaq.create_float_buffer(1, len(time))
# Get the Ananlog In device and Analog Info
ai_device = self.daq_device.get_ai_device()
ai_info = ai_device.get_info()
# Get the Analog Out device
ao_device = self.daq_device.get_ao_device()
ao_info = ao_device.get_info()
er_ao = ao_device.a_out_scan(
0,
0,
uldaq.Range.BIP10VOLTS,
int(len(data)),
30_000.0,
uldaq.ScanOption.DEFAULTIO,
uldaq.AOutScanFlag.DEFAULT,
data_c,
)
er_ai = ai_device.a_in_scan(
1,
1,
uldaq.AiInputMode.SINGLE_ENDED,
uldaq.Range.BIP10VOLTS,
len(time),
FS,
uldaq.ScanOption.DEFAULTIO,
uldaq.AInScanFlag.DEFAULT,
data=buf,
)
ai_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, timeout=-1)
log.debug("Scanning")
self.daq_device.disconnect()
self.daq_device.release()
plt.plot(buf)
plt.plot(data_c)
plt.show()
if __name__ == "__main__":
daq_input = ReadWrite()
daq_input.read_write()

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import uldaq
import matplotlib.pyplot as plt
from pyrelacs.util.logging import config_logging
from .repos import Repos
log = config_logging()
class ReadData(Repos):
def __init__(self) -> None:
super().__init__()
def analog_in(self) -> None:
# Get the Ananlog In device and Analog Info
data = self.read_analog_daq(
[0, 0],
10,
3000.0,
)
plt.plot(data)
plt.show()
self.disconnect_dac()
if __name__ == "__main__":
daq_input = ReadData()
daq_input.analog_in()

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pyrelacs/repros/output.py Normal file
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import ctypes
import uldaq
from IPython import embed
from pyrelacs.repros.repos import Repos
from pyrelacs.util.logging import config_logging
import numpy as np
import matplotlib.pyplot as plt
log = config_logging()
class Output_daq(Repos):
def __init__(self) -> None:
super().__init__()
# devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
# self.daq_device = uldaq.DaqDevice(devices[0])
# self.daq_device.connect()
def write_daq(self):
log.debug("running repro")
time = np.arange(0, 10, 1 / 30_000.0)
data = 2 * np.sin(2 * np.pi * 1 * time)
self.send_analog_dac(
data, [0, 0], 30_000, ScanOption=uldaq.ScanOption.EXTTRIGGER
)
def trigger(self):
self.digital_trigger(1)
self.daq_device.disconnect()
self.daq_device.release()
if __name__ == "__main__":
daq_input = Output_daq()
daq_input.write_daq()
# daq_input.trigger()

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from ctypes import Array, c_double
from typing import Union
from IPython import embed
import numpy.typing as npt
import uldaq
import numpy as np
from pyrelacs.util.logging import config_logging
log = config_logging()
class Repos:
def __init__(self) -> None:
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
log.debug(f"Found daq devices {len(devices)}, connecting to the first one")
if len(devices) == 0:
log.error("Did not found daq devices, please connect one")
exit(1)
self.daq_device = uldaq.DaqDevice(devices[0])
self.daq_device.connect()
log.debug("Connected")
def read_analog_daq(
self,
channels: list[int],
duration: int,
samplerate: float,
AiInputMode: uldaq.AiInputMode = uldaq.AiInputMode.SINGLE_ENDED,
Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
AInScanFlag: uldaq.AInScanFlag = uldaq.AInScanFlag.DEFAULT,
) -> Array[c_double]:
if channels[0] == channels[1]:
channel_len = 1
else:
channel_len = len(channels)
assert len(channels) == 2, log.error("Please provide a list with two ints")
ai_device = self.daq_device.get_ai_device()
buffer_len = np.shape(np.arange(0, duration, 1 / samplerate))[0]
data_analog_input = uldaq.create_float_buffer(channel_len, buffer_len)
er = ai_device.a_in_scan(
channels[0],
channels[1],
AiInputMode,
Range,
buffer_len,
samplerate,
ScanOption,
AInScanFlag,
data=data_analog_input,
)
# ai_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, timeout=-1)
return data_analog_input
def send_analog_dac(
self,
data: Union[list, npt.NDArray],
channels: list[int],
samplerate: float,
Range: uldaq.Range = uldaq.Range.BIP10VOLTS,
ScanOption: uldaq.ScanOption = uldaq.ScanOption.DEFAULTIO,
AOutScanFlag: uldaq.AOutScanFlag = uldaq.AOutScanFlag.DEFAULT,
):
"""
Parameters
----------
data : Union[list, npt.NDArray]
channels : list[int]
duration : int
samplerate : float
AiInputMode : uldaq.AiInputMode
Range : uldaq.Range
ScanOption : uldaq.ScanOption
AInScanFlag : uldaq.AOutScanFlag
Returns
-------
Array[c_double]
ao_device
"""
buffer = c_double * len(data)
data_analog_output = buffer(*data)
log.debug(f"Created C_double data {data_analog_output}")
ao_device = self.daq_device.get_ao_device()
ao_info = ao_device.get_info()
err = ao_device.a_out_scan(
channels[0],
channels[1],
Range,
int(len(data)),
samplerate,
ScanOption,
AOutScanFlag,
data_analog_output,
)
log.info(f"The actual scan rate was {err}")
# ao_device.scan_wait(uldaq.WaitType.WAIT_UNTIL_DONE, 11)
return data_analog_output, ao_device
def digital_trigger(self, portn: int = 0, data: int = 1) -> None:
log.info(f"{self.daq_device}")
dio_device = self.daq_device.get_dio_device()
dio_device.d_config_bit(
uldaq.DigitalPortType.AUXPORT, portn, uldaq.DigitalDirection.OUTPUT
)
dio_device.d_bit_out(uldaq.DigitalPortType.AUXPORT, bit_number=portn, data=data)
def disconnect_dac(self):
self.daq_device.disconnect()
self.daq_device.release()
def clean_up():
pass
def run_repo(self) -> None:
pass
def stop_repo(self) -> None:
pass
def reload_repo(self) -> None:
pass

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import sys
import ast
import pathlib
from typing import Tuple
from IPython import embed
import nixio as nix
import importlib.util
from pyrelacs.util.logging import config_logging
log = config_logging()
class Repro:
"""
Repro Class that searches in the repro folder for classes instances and executes the
the run function in the searched class
"""
def __init__(self) -> None:
pass
def run_repro(self, name: str, file: pathlib.Path, *args, **kwargs) -> None:
spec = importlib.util.spec_from_file_location("rep", file)
if not spec:
log.error("Could not load the file")
else:
module = importlib.util.module_from_spec(spec)
if not module:
log.error("Could not load the module of the repro")
else:
sys.modules[name] = module
if spec.loader is not None:
spec.loader.exec_module(module)
else:
log.error(f"{spec.loader} is None")
if hasattr(module, name):
rep_class = getattr(module, name)
rep_class.run(*args, **kwargs)
else:
raise AttributeError(f"{file.name} has no {name} class")
def names_of_repros(self, include_repros: list[str]) -> Tuple[list, list]:
"""
Searches for class names in the repro folder in all python files
Parameters
----------
include_repros : list[str]
List of repros to include in the pyrelacs instance
Returns
-------
Tuple[list, list]
list of class names
list of file names from the class names
"""
file_path_cur = pathlib.Path(__file__).parent
python_files = list(file_path_cur.glob("**/*.py"))
exclude_files = ["repros.py", "__init__.py"]
python_files = [f for f in python_files if f.name not in exclude_files]
repro_names = []
file_names = []
for python_file in python_files:
with open(python_file, "r") as file:
file_content = file.read()
tree = ast.parse(file_content)
class_name = [
node.name
for node in ast.walk(tree)
if isinstance(node, ast.ClassDef)
]
repro_names.extend(class_name)
file_names.append(python_file)
file.close()
repro_names = [r for r in repro_names if r in include_repros]
file_names = [f for r, f in zip(repro_names, file_names) if r in include_repros]
return repro_names, file_names

17
pyrelacs/repros/sinus/sinus.py
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@ -1,17 +0,0 @@
import nixio
from pyrelacs.util.logging import config_logging
log = config_logging()
class Sinus:
def __init__(self) -> None:
pass
@staticmethod
def run(config, mccdaq, nix_block: nixio.Block, figure) -> None:
log.debug(config)
log.debug(mccdaq)
log.debug(nix_block)
log.debug(figure)

10
pyrelacs/resources.qrc
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@ -1,10 +0,0 @@
<!DOCTYPE RCC><RCC version="1.0">
<qresource>
<file>icons/exit.png</file>
<file>icons/connect.png</file>
<file>icons/disconnect.png</file>
<file>icons/record.png</file>
<file>icons/stop.png</file>
<file>icons/relacstuxheader.png</file>
</qresource>
</RCC>

0
pyrelacs/ui/__init__.py
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54
pyrelacs/ui/about.py
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@ -1,54 +0,0 @@
from PyQt6.QtGui import QPixmap
from PyQt6.QtWidgets import QDialog, QDialogButtonBox, QLabel, QVBoxLayout, QWidget
from PyQt6.QtCore import Qt
class AboutDialog(QDialog):
def __init__(self, parent=None) -> None:
super().__init__(parent=parent)
self.setModal(True)
about = About(self)
self.setLayout(QVBoxLayout())
self.layout().addWidget(about)
bbox = QDialogButtonBox(QDialogButtonBox.StandardButton.Ok)
bbox.accepted.connect(self.accept)
self.layout().addWidget(bbox)
class About(QWidget):
def __init__(self, parent=None) -> None:
super().__init__(parent=parent)
self.setLayout(QVBoxLayout())
heading = QLabel("pyRelacs")
font = heading.font()
font.setPointSize(18)
font.setBold(True)
heading.setFont(font)
heading.setAlignment(Qt.AlignmentFlag.AlignCenter)
subheading = QLabel("relacsed electrophysiological recordings")
subheading.setAlignment(Qt.AlignmentFlag.AlignCenter)
nix_link = QLabel("https://github.com/relacs")
nix_link.setOpenExternalLinks(True)
nix_link.setAlignment(Qt.AlignmentFlag.AlignCenter)
rtd_link = QLabel("https://relacs.net")
rtd_link.setOpenExternalLinks(True)
rtd_link.setAlignment(Qt.AlignmentFlag.AlignCenter)
iconlabel = QLabel()
pixmap = QPixmap(":/icons/relacstuxheader.png")
s = pixmap.size()
new_height = int(s.height() * 300/s.width())
pixmap = pixmap.scaled(300, new_height, Qt.AspectRatioMode.KeepAspectRatio, Qt.TransformationMode.FastTransformation)
iconlabel.setPixmap(pixmap)
iconlabel.setMaximumWidth(300)
iconlabel.setAlignment(Qt.AlignmentFlag.AlignCenter)
iconlabel.setScaledContents(True)
self.layout().addWidget(heading)
self.layout().addWidget(subheading)
self.layout().addWidget(iconlabel)
self.layout().addWidget(nix_link)
self.layout().addWidget(rtd_link)

391
pyrelacs/ui/mainwindow.py
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@ -1,391 +0,0 @@
import time
from pathlib import Path as path
from datetime import datetime
from dataclasses import asdict
from PyQt6.QtGui import QAction, QIcon, QKeySequence
from PyQt6.QtCore import Qt, QSize, QThreadPool, QMutex
from PyQt6.QtWidgets import (
QGridLayout,
QPushButton,
QTabWidget,
QToolBar,
QVBoxLayout,
QWidget,
QMainWindow,
QPlainTextEdit,
QMenuBar,
QStatusBar,
)
import nixio
import pyqtgraph as pg
import quantities as pq
from pyrelacs.devices.mccdaq import MccDaq
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.dataio.daq_producer import DaqProducer
from pyrelacs.dataio.nix_writer import NixWriter
from pyrelacs.dataio.sin_producer import SinProducer
from pyrelacs.worker import Worker
from pyrelacs.repros.repros import Repro
from pyrelacs.ui.about import AboutDialog
from pyrelacs.ui.plots.calibration import CalibrationPlot
from pyrelacs.ui.plots.continously import Continously
from pyrelacs.util.logging import config_logging
log = config_logging()
_root = path(__file__).parent.parent
from IPython import embed
class PyRelacs(QMainWindow):
def __init__(self, config):
super().__init__()
# loaded config
self.config = config
if self.config.settings.daq:
start = time.time()
self.mccdaq = MccDaq()
end = time.time()
log.debug(f"Connection to DAQ took {end - start}")
else:
self.mccdaq = None
self.repros = Repro()
self.setToolButtonStyle(
Qt.ToolButtonStyle.ToolButtonTextBesideIcon
) # Ensure icons are displayed with text
self.setWindowTitle("PyRelacs")
self.create_nix_file(f"{_root}/test.nix", self.config.metadata)
self.mutex = QMutex()
self.figure = pg.GraphicsLayoutWidget()
self.threadpool = QThreadPool()
self.text = QPlainTextEdit()
self.text.setReadOnly(True)
self.setMenuBar(QMenuBar(self))
self.setStatusBar(QStatusBar(self))
self.create_actions()
self.create_toolbars()
self.repro_tabs = QTabWidget()
self.create_repros_tabs()
layout = QGridLayout()
layout.addWidget(self.figure, 0, 0, 2, 2)
layout.addWidget(self.repro_tabs, 2, 0, 2, 2)
layout.addWidget(self.text, 4, 0, 1, 1)
widget = QWidget()
widget.setLayout(layout)
self.setCentralWidget(widget)
SAMPLERATE = pq.Quantity(
self.config.pyrelacs.data.input.inputsamplerate,
self.config.pyrelacs.data.input.inputsamplerateunit,
).rescale("Hz")
INPUTTRACECAPACITY = pq.Quantity(
self.config.pyrelacs.data.input.inputtracecapacity,
self.config.pyrelacs.data.input.inputtracecapacityunit,
).rescale("s")
start = time.time()
BUFFERSIZE = (SAMPLERATE * INPUTTRACECAPACITY).simplified
end = time.time()
log.debug(f"Buffer allocation took {end - start}")
self.buffer = CircBuffer(
size=int(BUFFERSIZE.base),
samplerate=float(SAMPLERATE.base),
mutex=self.mutex,
)
self.continously_plot = Continously(self.figure, self.buffer)
# self.continously_plot.plot()
if self.mccdaq:
log.debug("Creating Daq Generator")
self.daq_producer = DaqProducer(self.buffer, self.mccdaq.daq_device, [1, 1])
log.debug("Creating Sinus Generator")
self.sinus_producer = SinProducer(self.buffer)
self.nix_writer = NixWriter(self.buffer)
def create_actions(self):
self._rlx_exitaction = QAction(QIcon(":/icons/exit.png"), "Exit", self)
self._rlx_exitaction.setStatusTip("Close relacs")
self._rlx_exitaction.setShortcut(QKeySequence("Alt+q"))
self._rlx_exitaction.triggered.connect(self.on_exit)
self._rlx_aboutaction = QAction("about")
self._rlx_aboutaction.setStatusTip("Show about dialog")
self._rlx_aboutaction.setEnabled(True)
self._rlx_aboutaction.triggered.connect(self.on_about)
self._daq_connectaction = QAction(
QIcon(":icons/connect.png"), "Connect DAQ", self
)
if self.mccdaq:
self._daq_connectaction.setStatusTip("Connect to daq device")
# self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
self._daq_connectaction.triggered.connect(self.mccdaq.connect_dac)
self._daq_disconnectaction = QAction(
QIcon(":/icons/disconnect.png"), "Disconnect DAQ", self
)
self._daq_disconnectaction.setStatusTip("Disconnect the DAQ device")
# self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
self._daq_disconnectaction.triggered.connect(self.mccdaq.disconnect_daq)
# self._daq_calibaction = QAction(
# QIcon(":/icons/calibration.png"), "Plot calibration", self
# )
# self._daq_calibaction.setStatusTip("Calibrate the attenuator device")
# # self._daq_calibaction.setShortcut(QKeySequence("Alt+d"))
# self._daq_calibaction.triggered.connect(self.calibration_plot.plot)
self._run_action = QAction(QIcon(":/icons/record.png"), "RunDAQ", self)
self._run_action.triggered.connect(self.run_daq)
self._run_sinus_action = QAction(QIcon(":/icons/record.png"), "Sinus", self)
self._run_sinus_action.triggered.connect(self.run_sinus)
self._stop_recording = QAction(QIcon(":/icons/stop.png"), "Stop", self)
self._stop_recording.triggered.connect(self.stop_recording)
self._recenter_plot = QAction("Recenter", self)
self._recenter_plot.triggered.connect(self.recenter_continously_plot)
self._recenter_plot.setShortcut(QKeySequence("Alt+r"))
self._record = QAction(QIcon(":/icons/record.png"), "Record", self)
self._record.triggered.connect(self.record)
self.create_menu()
def create_menu(self):
menu = self.menuBar()
if menu is not None:
file_menu = menu.addMenu("&File")
device_menu = menu.addMenu("&DAQ")
help_menu = menu.addMenu("&Help")
if file_menu is not None:
file_menu.addAction(self._rlx_exitaction)
file_menu.addAction(self._rlx_aboutaction)
if device_menu is not None:
if self.config.settings.daq:
device_menu.addAction(self._daq_connectaction)
device_menu.addAction(self._daq_disconnectaction)
device_menu.addSeparator()
# device_menu.addAction(self._daq_calibaction)
device_menu.addAction(self._run_action)
if help_menu is not None:
help_menu.addSeparator()
# help_menu.addAction(self._help_action)
else:
log.error("could not create file menu and device menu")
self.on_exit()
self.setMenuBar(menu)
def create_toolbars(self):
rlx_toolbar = QToolBar("Relacs")
rlx_toolbar.addAction(self._rlx_exitaction)
rlx_toolbar.setIconSize(QSize(24, 24))
self.addToolBar(Qt.ToolBarArea.TopToolBarArea, rlx_toolbar)
daq_toolbar = QToolBar("DAQ")
if self.config.settings.daq:
daq_toolbar.addAction(self._daq_connectaction)
daq_toolbar.addAction(self._daq_disconnectaction)
# daq_toolbar.addAction(self._daq_calibaction)
daq_toolbar.addAction(self._run_action)
daq_toolbar.addAction(self._run_sinus_action)
daq_toolbar.addAction(self._stop_recording)
daq_toolbar.addAction(self._recenter_plot)
daq_toolbar.addSeparator()
daq_toolbar.addAction(self._record)
self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
def create_repros_tabs(self):
repro_names, file_names = self.repros.names_of_repros(
include_repros=self.config.settings.repros
)
nix_blocks = {
rep: self.nix_file.create_block(f"{rep}", "Data Repro")
for rep in repro_names
}
figures_repros = {rep: pg.GraphicsLayoutWidget() for rep in repro_names}
for rep, fn in zip(repro_names, file_names):
tab = QWidget()
tab_layout = QGridLayout()
run_repro_button = QPushButton(f"Run {rep}")
run_repro_button.setCheckable(True)
run_repro_button.clicked.connect(
lambda checked, n=rep, f=fn: self.run_repro(
n,
f,
nix_blocks,
figures_repros,
self.mccdaq,
self.config,
)
)
tab_layout.addWidget(run_repro_button, 0, 0, 1, 0)
tab_layout.addWidget(figures_repros[rep], 1, 0, 1, 1)
tab.setLayout(tab_layout)
self.repro_tabs.addTab(tab, f"{rep}")
def run_repro(
self,
name_of_repro: str,
file_of_repro: str,
nix_block,
figures,
*args,
):
self.text.appendPlainText(f"started Repro {name_of_repro}, {file_of_repro}")
nix_block_repro = nix_block[name_of_repro]
figure_repro = figures[name_of_repro]
worker = Worker(
self.repros.run_repro,
name_of_repro,
file_of_repro,
nix_block_repro,
figure_repro,
*args[-2:],
)
worker.signals.result.connect(self.print_output)
worker.signals.finished.connect(self.thread_complete)
worker.signals.progress.connect(self.progress_fn)
self.threadpool.start(worker)
def create_nix_file(self, file_path, metadata):
self.nix_file = nixio.File.open(
path=f"{file_path}", mode=nixio.FileMode.Overwrite
)
self.block = self.nix_file.create_block("recording", "testfile")
self.section = self.nix_file.create_section("metadata", "config.yaml")
for key, value in asdict(metadata).items():
self.section[key] = value
self.data_array_analog1 = self.block.create_data_array(
"Analog1", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
)
self.data_array_analog2 = self.block.create_data_array(
"Analog2", "ndarray", shape=(1000,), dtype=nixio.DataType.Double
)
def recenter_continously_plot(self):
self.continously_plot.refresh()
def plot_continously(self):
plot_con = Worker(self.continously_plot.plot)
plot_con.signals.result.connect(self.print_output)
plot_con.signals.finished.connect(self.thread_complete)
plot_con.signals.progress.connect(self.progress_fn)
self.threadpool.start(plot_con)
def run_daq(self):
read_daq = Worker(self.daq_producer.read_analog_continously)
read_daq.signals.result.connect(self.print_output)
read_daq.signals.finished.connect(self.thread_complete)
read_daq.signals.progress.connect(self.progress_fn)
self.threadpool.start(read_daq)
self.continously_plot.plot()
def run_sinus(self):
sinus_pro = Worker(self.sinus_producer.produce_sin)
sinus_pro.signals.result.connect(self.print_output)
sinus_pro.signals.finished.connect(self.thread_complete)
sinus_pro.signals.progress.connect(self.progress_fn)
self.threadpool.start(sinus_pro)
self.continously_plot.plot()
def record(self):
self.create_nix_file("test.nix", self.config.metadata)
log.debug("Created nix file")
nix_writer = Worker(
self.nix_writer.write_nix,
data_array=self.data_array_analog1,
mutex=self.mutex,
channel=0,
chunk_size=1000,
)
nix_writer.signals.result.connect(self.print_output)
nix_writer.signals.finished.connect(self.thread_complete)
nix_writer.signals.progress.connect(self.progress_fn)
self.threadpool.start(nix_writer)
nix_writer2 = Worker(
self.nix_writer.write_nix,
data_array=self.data_array_analog2,
mutex=self.mutex,
channel=0,
chunk_size=1000,
)
nix_writer2.signals.result.connect(self.print_output)
nix_writer2.signals.finished.connect(self.thread_complete)
nix_writer2.signals.progress.connect(self.progress_fn)
self.threadpool.start(nix_writer2)
def stop_recording(self):
self.add_to_textfield("Stopping the recording")
self.continously_plot.stop_plotting()
self.nix_writer.stop_writing()
log.debug("Stopping acquisiton")
try:
self.sinus_producer.stop_request()
log.debug("Stopping Sinus")
except AttributeError:
log.debug("Did not generate Sinus")
if hasattr(PyRelacs, "daq_device"):
log.debug("Stopping DAQ")
self.daq_producer.stop_aquisition()
def add_to_textfield(self, s: str):
self.text.appendPlainText(s)
def on_exit(self):
log.info("exit button!")
self.stop_recording()
self.add_to_textfield("exiting")
if self.mccdaq:
self.mccdaq.disconnect_daq()
log.info("closing GUI")
self.close()
def on_about(self, e):
about = AboutDialog(self)
about.show()
def print_output(self, s):
log.info(s)
self.add_to_textfield(s)
def thread_complete(self):
log.info("Thread complete!")
self.add_to_textfield("Thread complete!")
def progress_fn(self, n):
print("%d%% done" % n)

113
pyrelacs/ui/plots/calibration.py
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@ -1,113 +0,0 @@
from IPython import embed
import pyqtgraph as pg
import numpy as np
from scipy.signal import welch, find_peaks
from scipy.integrate import romb
class CalibrationPlot:
def __init__(self, figure: pg.GraphicsLayoutWidget, nix_file):
self.figure = figure
self.nix_file = nix_file
def plot(self):
self.figure.setBackground("w")
self.beat_plot = self.figure.addPlot(row=0, col=0)
self.power_plot = self.figure.addPlot(row=1, col=0)
self.beat_plot.addLegend()
self.power_plot.addLegend()
# self.power_plot.setLogMode(x=False, y=True)
block = self.nix_file.blocks[0]
colors = ["red", "green", "blue", "black", "yellow"]
for i, (stim, fish) in enumerate(
zip(list(block.data_arrays)[::2], list(block.data_arrays)[1::2])
):
f_stim, stim_power = welch(
stim[:],
fs=40_000.0,
window="flattop",
nperseg=100_000,
)
stim_power = self.decibel(stim_power)
stim_max_power_index = np.argmax(stim_power)
freq_stim = f_stim[stim_max_power_index]
f_fish, fish_power = welch(
fish[:],
fs=40_000.0,
window="flattop",
nperseg=100_000,
)
fish_power = self.decibel(fish_power)
fish_max_power_index = np.argmax(fish_power)
freq_fish = f_fish[fish_max_power_index]
beat_frequency = np.abs(freq_fish - freq_stim)
beat = stim[:] + fish[:]
beat_squared = beat**2
f, powerspec = welch(
beat_squared,
window="flattop",
fs=40_000.0,
nperseg=100_000,
)
powerspec = self.decibel(powerspec)
padding = 20
integration_window = powerspec[
(f > beat_frequency - padding) & (f < beat_frequency + padding)
]
peaks = find_peaks(powerspec, prominence=40)[0]
pen = pg.mkPen(colors[i])
self.beat_plot.plot(
np.arange(0, len(beat)) / 40_000.0,
beat,
pen=pen,
name=stim.name,
)
self.power_plot.plot(f, powerspec, pen=pen, name=stim.name)
self.power_plot.plot(f[peaks], powerspec[peaks], pen=None, symbol="x")
def decibel(self, power, ref_power=1.0, min_power=1e-20):
"""Transform power to decibel relative to ref_power.
\\[ decibel = 10 \\cdot \\log_{10}(power/ref\\_power) \\]
Power values smaller than `min_power` are set to `-np.inf`.
Parameters
----------
power: float or array
Power values, for example from a power spectrum or spectrogram.
ref_power: float or None or 'peak'
Reference power for computing decibel.
If set to `None` or 'peak', the maximum power is used.
min_power: float
Power values smaller than `min_power` are set to `-np.inf`.
Returns
-------
decibel_psd: array
Power values in decibel relative to `ref_power`.
"""
if np.isscalar(power):
tmp_power = np.array([power])
decibel_psd = np.array([power])
else:
tmp_power = power
decibel_psd = power.copy()
if ref_power is None or ref_power == "peak":
ref_power = np.max(decibel_psd)
decibel_psd[tmp_power <= min_power] = float("-inf")
decibel_psd[tmp_power > min_power] = 10.0 * np.log10(
decibel_psd[tmp_power > min_power] / ref_power
)
if np.isscalar(power):
return decibel_psd[0]
else:
return decibel_psd

88
pyrelacs/ui/plots/continously.py
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@ -1,88 +0,0 @@
import time
import pyqtgraph as pg
from IPython import embed
import numpy as np
from pyqtgraph.Qt.QtCore import QTimer
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.util.logging import config_logging
log = config_logging()
class Continously:
def __init__(self, figure: pg.GraphicsLayoutWidget, buffer: CircBuffer):
self.figure = figure
self.buffer = buffer
self.last_plotted_index = 0
self.timer = QTimer()
def plot(self, *args, **kwargs):
self.figure.setBackground("w")
prev_plot = self.figure.getItem(row=0, col=0)
if prev_plot:
self.figure.removeItem(prev_plot)
self.continous_ax = self.figure.addPlot(row=0, col=0)
pen = pg.mkPen("red")
self.time = np.zeros(self.buffer.size)
self.data = np.empty(self.buffer.size)
self.line = self.continous_ax.plot(
self.time,
self.data,
pen=pen,
# symbol="o",
)
# self.plot_index = 0
self.CHUNK_PLOT = int(self.buffer.samplerate / 6)
self.PLOT_HISTORY = 500_000 # The amount of data you want to keep on screen
self.timer.setInterval(150)
self.timer.timeout.connect(self.update_plot)
self.timer.start()
def update_plot(self):
current_index = self.buffer.write_index()
total_count = self.buffer.totalcount()
start_time = time.time()
if total_count - self.last_plotted_index >= self.CHUNK_PLOT:
try:
times, items = self.buffer.read(
self.last_plotted_index,
extend=self.CHUNK_PLOT,
)
self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
self.line.setData(
self.time,
self.data,
)
self.last_plotted_index += self.CHUNK_PLOT
except IndexError:
log.error("Could not acces the data from the buffer for plotting")
end_time = time.time()
log.debug(f"total time for plotting {end_time - start_time}")
else:
pass
def stop_plotting(self):
self.timer.stop()
if self.last_plotted_index > 0:
total_count = self.buffer.totalcount()
times, items = self.buffer.read(
self.last_plotted_index,
extend=total_count - self.last_plotted_index,
)
self.time = np.concatenate((self.time, times))[-self.PLOT_HISTORY :]
self.data = np.concatenate((self.data, items))[-self.PLOT_HISTORY :]
self.line.setData(
self.time,
self.data,
)
self.last_plotted_index += total_count - self.last_plotted_index
def refresh(self):
self.continous_ax.enableAutoRange()

0
pyrelacs/util/__init__.py
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75
pyrelacs/worker.py
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@ -1,75 +0,0 @@
import sys
import traceback
from PyQt6.QtCore import QRunnable, pyqtSlot, QObject, pyqtSignal
class WorkerSignals(QObject):
"""
Defines the signals available from a running worker thread.
Supported signals are:
finished
No data
error
tuple (exctype, value, traceback.format_exc() )
result
object data returned from processing, anything
progress
int indicating % progress
"""
finished = pyqtSignal()
error = pyqtSignal(tuple)
result = pyqtSignal(object)
progress = pyqtSignal(int)
class Worker(QRunnable):
"""
Worker thread
Inherits from QRunnable to handler worker thread setup, signals and wrap-up.
:param callback: The function callback to run on this worker thread. Supplied args and
kwargs will be passed through to the runner.
:type callback: function
:param args: Arguments to pass to the callback function
:param kwargs: Keywords to pass to the callback function
"""
def __init__(self, fn, *args, **kwargs):
super(Worker, self).__init__()
# Store constructor arguments (re-used for processing)
self.fn = fn
self.args = args
self.kwargs = kwargs
self.signals = WorkerSignals()
# Add the callback to our kwargs
self.kwargs["progress_callback"] = self.signals.progress
@pyqtSlot()
def run(self):
"""
Initialise the runner function with passed args, kwargs.
"""
# Retrieve args/kwargs here; and fire processing using them
try:
result = self.fn(*self.args, **self.kwargs)
except:
traceback.print_exc()
exctype, value = sys.exc_info()[:2]
self.signals.error.emit((exctype, value, traceback.format_exc()))
else:
self.signals.result.emit(result) # Return the result of the processing
finally:
self.signals.finished.emit() # Done

98
test/test_buffer.py
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@ -1,98 +0,0 @@
import pytest
import numpy as np
from IPython import embed
from pyrelacs.dataio.circbuffer import CircBuffer
def test_init():
buff = CircBuffer(1000, 2)
assert buff.size == 1000
assert buff.channel_count == 2
def test_hasvalue():
buff = CircBuffer(1000, 2)
assert buff.has_value(0, 0) == False
assert buff.has_value(-1, 0) == False
buff.append(10, 0)
assert buff.write_index(0) == 1
assert buff.write_index(1) == 0
assert buff.has_value(0, 0) == True
assert buff.has_value(0, 1) == False
buff.append(10, 1)
assert buff.write_index(1) == 1
assert buff.has_value(0, 1) == True
for i in range(1100):
buff.append(i, 0)
buff.append(i, 1)
assert buff.write_index(0) == buff.write_index(1)
assert buff.has_value(0, 0) == True
assert buff.has_value(0, 1) == True
assert buff.has_value(buff.write_index(0), 0) == True
assert buff.has_value(buff.write_index(1), 1) == True
def test_validrange():
buff = CircBuffer(1000, 2)
# without any values the range is (0, 0)
assert buff.valid_range() == (0, 0)
buff.append(0, 0)
assert buff.valid_range() == (0, 1)
for i in range(100):
buff.append(i, 0)
assert buff.valid_range() == (0, 101)
for i in range(1000):
buff.append(i, 0)
assert buff.valid_range() == (0, 1000)
def test_get():
buff = CircBuffer(1000, 2)
# with no items written to the buffer
with pytest.raises(IndexError):
item = buff.get(index=-1)
buff.append(10, 0)
item = buff.get(index=-1)
assert item == 10
# Check if index is not written jet
with pytest.raises(IndexError):
item = buff.get(index=10)
for i in range(1000):
buff.append(i, 0)
item = buff.get(index=-1)
# the first item should be 999.0 because of we append a value in the earlier test
assert item == 999.0
with pytest.raises(IndexError):
item = buff.get(10001)
def test_read():
pass
def test_write():
buff = CircBuffer(1000, 2)
samplecount = 1000
if __name__ == "__main__":
test_get()