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9 changed files with 193 additions and 143 deletions

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{file = "ipython-8.28.0.tar.gz", hash = "sha256:0d0d15ca1e01faeb868ef56bc7ee5a0de5bd66885735682e8a322ae289a13d1a"},
]
[package.dependencies]
colorama = {version = "*", markers = "sys_platform == \"win32\""}
decorator = "*"
exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
jedi = ">=0.16"
matplotlib-inline = "*"
pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
@ -904,16 +895,16 @@ PyQt6-sip = ">=13.8,<14"
[[package]]
name = "pyqt6-qt6"
version = "6.7.2"
version = "6.7.3"
description = "The subset of a Qt installation needed by PyQt6."
optional = false
python-versions = "*"
files = [
{file = "PyQt6_Qt6-6.7.2-py3-none-macosx_10_14_x86_64.whl", hash = "sha256:065415589219a2f364aba29d6a98920bb32810286301acbfa157e522d30369e3"},
{file = "PyQt6_Qt6-6.7.2-py3-none-macosx_11_0_arm64.whl", hash = "sha256:7f817efa86a0e8eda9152c85b73405463fbf3266299090f32bbb2266da540ead"},
{file = "PyQt6_Qt6-6.7.2-py3-none-manylinux_2_28_aarch64.whl", hash = "sha256:05f2c7d195d316d9e678a92ecac0252a24ed175bd2444cc6077441807d756580"},
{file = "PyQt6_Qt6-6.7.2-py3-none-manylinux_2_28_x86_64.whl", hash = "sha256:fc93945eaef4536d68bd53566535efcbe78a7c05c2a533790a8fd022bac8bfaa"},
{file = "PyQt6_Qt6-6.7.2-py3-none-win_amd64.whl", hash = "sha256:b2d7e5ddb1b9764cd60f1d730fa7bf7a1f0f61b2630967c81761d3d0a5a8a2e0"},
{file = "PyQt6_Qt6-6.7.3-py3-none-macosx_10_14_x86_64.whl", hash = "sha256:f517a93b6b1a814d4aa6587adc312e812ebaf4d70415bb15cfb44268c5ad3f5f"},
{file = "PyQt6_Qt6-6.7.3-py3-none-macosx_11_0_arm64.whl", hash = "sha256:8551732984fb36a5f4f3db51eafc4e8e6caf18617365830285306f2db17a94c2"},
{file = "PyQt6_Qt6-6.7.3-py3-none-manylinux_2_28_aarch64.whl", hash = "sha256:50c7482bcdcf2bb78af257fb10ed8b582f8daf91d829782393bc50ac5a0a900c"},
{file = "PyQt6_Qt6-6.7.3-py3-none-manylinux_2_28_x86_64.whl", hash = "sha256:cb525fdd393332de60887953029276a44de480fce1d785251ae639580f5e7246"},
{file = "PyQt6_Qt6-6.7.3-py3-none-win_amd64.whl", hash = "sha256:36ea0892b8caeb983af3f285f45fb8dfbb93cfd972439f4e01b7efb2868f6230"},
]
[[package]]
@ -973,11 +964,9 @@ files = [
[package.dependencies]
colorama = {version = "*", markers = "sys_platform == \"win32\""}
exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=1.5,<2"
tomli = {version = ">=1", markers = "python_version < \"3.11\""}
[package.extras]
dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
@ -998,13 +987,13 @@ six = ">=1.5"
[[package]]
name = "rich"
version = "13.8.1"
version = "13.9.2"
description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
optional = false
python-versions = ">=3.7.0"
python-versions = ">=3.8.0"
files = [
{file = "rich-13.8.1-py3-none-any.whl", hash = "sha256:1760a3c0848469b97b558fc61c85233e3dafb69c7a071b4d60c38099d3cd4c06"},
{file = "rich-13.8.1.tar.gz", hash = "sha256:8260cda28e3db6bf04d2d1ef4dbc03ba80a824c88b0e7668a0f23126a424844a"},
{file = "rich-13.9.2-py3-none-any.whl", hash = "sha256:8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1"},
{file = "rich-13.9.2.tar.gz", hash = "sha256:51a2c62057461aaf7152b4d611168f93a9fc73068f8ded2790f29fe2b5366d0c"},
]
[package.dependencies]
@ -1105,17 +1094,6 @@ pure-eval = "*"
[package.extras]
tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
[[package]]
name = "tomli"
version = "2.0.1"
description = "A lil' TOML parser"
optional = false
python-versions = ">=3.7"
files = [
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
[[package]]
name = "tomlkit"
version = "0.13.2"
@ -1194,5 +1172,5 @@ files = [
[metadata]
lock-version = "2.0"
python-versions = ">=3.10, <3.13"
content-hash = "e5e345e3e4d28ac0e7de7727be130454201be1949be08158e744cdc6089a3f66"
python-versions = ">=3.11, <3.13"
content-hash = "869348ffb24d0a55aee308a54cae333d5029c5aa52bc4082b720d766c63c2f9c"

View File

@ -21,7 +21,7 @@ include = [
]
[tool.poetry.dependencies]
python = ">=3.10, <3.13"
python = ">=3.11, <3.13"
uldaq = "^1.2.3"
typer = "^0.12.5"
matplotlib = "^3.9.2"

View File

@ -5,9 +5,6 @@ from PyQt6.QtWidgets import QApplication
from pyrelacs import info
from pyrelacs.ui.mainwindow import PyRelacs
from pyrelacs.util.logging import config_logging
log = config_logging()
from pyrelacs import (
resources,
@ -28,6 +25,7 @@ def main():
x = int(settings.value("app/pos_x", 100))
y = int(settings.value("app/pos_y", 100))
# load config
window = PyRelacs()
window.setMinimumWidth(200)
window.setMinimumHeight(200)

12
pyrelacs/config.yaml Normal file
View File

@ -0,0 +1,12 @@
Settings:
Repros: [Calibration]
Path: ~/projects/pyrelacs/test/
Metadata:
Lab: Neuroethology
PyRelacs:
Input:
Name: DAQ
Samplingrate: 40_000

View File

@ -8,9 +8,9 @@ class CircBuffer:
def __init__(
self,
size: int,
mutex: QMutex,
channels: int = 1,
samplerate: int = 40_000,
mutex: QMutex = QMutex(),
):
self.__size = size
self.__channels = channels
@ -123,7 +123,7 @@ class CircBuffer:
# 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[index])
return (self.__buffer[channel, index], self.__time[channel, index])
else:
raise IndexError(
f"Invalid index {index} on ring buffer for channel{channel}"
@ -132,7 +132,7 @@ class CircBuffer:
if index < 0:
index = self.write_index() - 1
if self.has_value(index, channel):
return (self.__buffer[channel, index], self.__time[index])
return (self.__buffer[channel, index], self.__time[channel, index])
else:
raise IndexError(
f"Invalid index {index} on ring buffer for channel{channel}"

View File

@ -0,0 +1,43 @@
from IPython import embed
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, *args, **kwargs):
self._write_header()
items = 0
chunk = 1000
log.debug("Starting the writing")
self.write = True
while self.write:
log.debug(items)
try:
data, _ = self.buffer.read(items, extend=chunk)
self.data_array.append(data)
except IndexError as e:
log.debug(f"{e}")
continue
items += chunk
log.debug("Stoppint the writing")
log.debug(f"Samples written {items}")
embed()
exit()
self.nix_file.close()
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

View File

@ -1,8 +1,5 @@
from math import sin
import time
from PyQt6.QtGui import QAction
import numpy as np
import matplotlib.pyplot as plt
from IPython import embed
from pyrelacs.dataio.circbuffer import CircBuffer
from pyrelacs.util.logging import config_logging
@ -42,6 +39,7 @@ class SinProducer:
log.debug(f"duration sinus {end_time-start_time}")
log.debug(f"Stimulation time {t}")
log.debug(f"{self.buffer.totalcount()}")
# data = self.buffer.get_all()
# log.debug(data.shape[0])
# log.debug(data.shape[0] / self.buffer.samplerate)

View File

@ -1,29 +1,26 @@
import tomlkit
import tomllib
import pathlib
def load_project_settings(project_root):
print(project_root)
# Read the pyproject.toml file
with open(pathlib.Path.joinpath(project_root, "pyproject.toml"), "r") as f:
pyproject_content = f.read()
pyproject_path = pathlib.Path.joinpath(project_root, "pyproject.toml")
with open(pyproject_path, "rb") as f:
pyproject_content = tomllib.load(f)
# Parse the toml content
pyproject = tomlkit.parse(pyproject_content)
# Access project settings
return {
"name": pyproject["tool"]["poetry"]["name"],
"version": pyproject["tool"]["poetry"]["version"],
"description": pyproject["tool"]["poetry"]["description"],
"authors": pyproject["tool"]["poetry"]["authors"],
"readme": pyproject["tool"]["poetry"]["authors"],
"licence": pyproject["tool"]["poetry"]["license"],
"organization": pyproject["project"]["organization"],
"classifiers": pyproject["tool"]["poetry"]["classifiers"],
"copyright": pyproject["project"]["copyright"],
"repository": pyproject["tool"]["poetry"]["repository"],
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

View File

@ -13,7 +13,6 @@ from PyQt6.QtWidgets import (
QStatusBar,
)
from pyqtgraph.Qt.QtCore import QThread
import uldaq
import nixio as nix
import pyqtgraph as pg
@ -21,6 +20,7 @@ import numpy as np
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
@ -51,13 +51,14 @@ class PyRelacs(QMainWindow):
self.figure = pg.GraphicsLayoutWidget()
filename = path.joinpath(path.cwd(), "data.nix")
if filename.exists():
self.nix_file = nix.File.open(str(filename), nix.FileMode.ReadOnly)
filename = path.joinpath(path.cwd(), "calibration.nix")
self.nix_file = nix.File.open(str(filename), nix.FileMode.Overwrite)
self.calibration_plot = CalibrationPlot(self.figure, self.nix_file)
# filename = path.joinpath(path.cwd(), "data.nix")
# if filename.exists():
# self.nix_file = nix.File.open(str(filename), nix.FileMode.ReadOnly)
# filename = path.joinpath(path.cwd(), "calibration.nix")
# self.nix_file = nix.File.open(str(filename), nix.FileMode.Overwrite)
#
# self.calibration_plot = CalibrationPlot(self.figure, self.nix_file)
# self.nix_file.close()
self.threadpool = QThreadPool()
self.repros = Repro()
@ -95,12 +96,14 @@ class PyRelacs(QMainWindow):
end = time.time()
log.debug(f"Connection to DAQ took {end - start}")
if hasattr(uldaq, "daq_device"):
if hasattr(PyRelacs, "daq_device"):
log.debug("Creating Daq Generator")
self.daq_producer = DaqProducer(self.buffer, self.daq_device, [1, 1])
else:
log.debug("Creating Sinus Generator")
self.sin_producer = SinProducer(self.buffer)
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)
@ -127,12 +130,12 @@ class PyRelacs(QMainWindow):
# self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
self._daq_disconnectaction.triggered.connect(self.disconnect_dac)
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._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"), "Run", self)
self._run_action.triggered.connect(self.run_daq)
@ -143,9 +146,12 @@ class PyRelacs(QMainWindow):
self._stop_recording = QAction(QIcon(":/icons/stop.png"), "Stop", self)
self._stop_recording.triggered.connect(self.stop_recording)
self._refresh = QAction("Recenter", self)
self._refresh.triggered.connect(self.recenter_continously_plot)
self._refresh.setShortcut(QKeySequence("Alt+r"))
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()
@ -164,7 +170,7 @@ class PyRelacs(QMainWindow):
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._daq_calibaction)
device_menu.addAction(self._run_action)
if help_menu is not None:
@ -185,11 +191,13 @@ class PyRelacs(QMainWindow):
daq_toolbar = QToolBar("DAQ")
daq_toolbar.addAction(self._daq_connectaction)
daq_toolbar.addAction(self._daq_disconnectaction)
daq_toolbar.addAction(self._daq_calibaction)
# 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._refresh)
daq_toolbar.addAction(self._recenter_plot)
daq_toolbar.addSeparator()
daq_toolbar.addAction(self._record)
self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
repro_toolbar = QToolBar("Repros")
@ -223,7 +231,7 @@ class PyRelacs(QMainWindow):
self.continously_plot.plot()
def run_sinus(self):
sinus_pro = Worker(self.sin_producer.produce_sin)
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)
@ -231,12 +239,27 @@ class PyRelacs(QMainWindow):
self.continously_plot.plot()
def record(self):
nix_writer = Worker(self.nix_writer.write_nix)
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)
def stop_recording(self):
self.add_to_textfield("Stopping the recording")
if hasattr(PyRelacs, "sin_producer"):
self.sin_producer.stop_request()
self.continously_plot.stop_plotting()
if hasattr(uldaq, "daq_device"):
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 connect_dac(self):
@ -247,8 +270,8 @@ class PyRelacs(QMainWindow):
self.daq_device.connect()
log.debug("connected")
except IndexError:
log.error("DAQ is not connected")
log.error("Please connect a DAQ device to the system")
log.info("DAQ is not connected")
log.info("Please connect a DAQ device to the system")
def disconnect_dac(self):
try:
@ -274,6 +297,7 @@ class PyRelacs(QMainWindow):
self.stop_recording()
self.add_to_textfield("exiting")
self.disconnect_dac()
log.info("closing GUI")
self.close()
def on_about(self, e):