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4 Commits
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5c3c2c407a
| Author | SHA1 | Date | |
|---|---|---|---|
| 5c3c2c407a | |||
| 8ef8ac7506 | |||
| 7d3224f351 | |||
| a748385335 |
175
poetry.lock
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175
poetry.lock
generated
@ -189,6 +189,44 @@ ufo = ["fs (>=2.2.0,<3)"]
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unicode = ["unicodedata2 (>=15.1.0)"]
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unicode = ["unicodedata2 (>=15.1.0)"]
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[[package]]
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name = "h5py"
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version = "3.12.1"
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description = "Read and write HDF5 files from Python"
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{file = "numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:7349ab0fa0c429c82442a27a9673fc802ffdb7c7775fad780226cb234965e53c"},
|
||||||
{file = "numpy-2.1.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b9cd92c8f8e7b313b80e93cedc12c0112088541dcedd9197b5dee3738c1201"},
|
{file = "numpy-1.26.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:52b8b60467cd7dd1e9ed082188b4e6bb35aa5cdd01777621a1658910745b90be"},
|
||||||
{file = "numpy-2.1.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:afd9c680df4de71cd58582b51e88a61feed4abcc7530bcd3d48483f20fc76f2a"},
|
{file = "numpy-1.26.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d5241e0a80d808d70546c697135da2c613f30e28251ff8307eb72ba696945764"},
|
||||||
{file = "numpy-2.1.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:8661c94e3aad18e1ea17a11f60f843a4933ccaf1a25a7c6a9182af70610b2313"},
|
{file = "numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f870204a840a60da0b12273ef34f7051e98c3b5961b61b0c2c1be6dfd64fbcd3"},
|
||||||
{file = "numpy-2.1.1-cp312-cp312-win32.whl", hash = "sha256:950802d17a33c07cba7fd7c3dcfa7d64705509206be1606f196d179e539111ed"},
|
{file = "numpy-1.26.4-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:679b0076f67ecc0138fd2ede3a8fd196dddc2ad3254069bcb9faf9a79b1cebcd"},
|
||||||
{file = "numpy-2.1.1-cp312-cp312-win_amd64.whl", hash = "sha256:3fc5eabfc720db95d68e6646e88f8b399bfedd235994016351b1d9e062c4b270"},
|
{file = "numpy-1.26.4-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:47711010ad8555514b434df65f7d7b076bb8261df1ca9bb78f53d3b2db02e95c"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:046356b19d7ad1890c751b99acad5e82dc4a02232013bd9a9a712fddf8eb60f5"},
|
{file = "numpy-1.26.4-cp39-cp39-win32.whl", hash = "sha256:a354325ee03388678242a4d7ebcd08b5c727033fcff3b2f536aea978e15ee9e6"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:6e5a9cb2be39350ae6c8f79410744e80154df658d5bea06e06e0ac5bb75480d5"},
|
{file = "numpy-1.26.4-cp39-cp39-win_amd64.whl", hash = "sha256:3373d5d70a5fe74a2c1bb6d2cfd9609ecf686d47a2d7b1d37a8f3b6bf6003aea"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-macosx_14_0_arm64.whl", hash = "sha256:d4c57b68c8ef5e1ebf47238e99bf27657511ec3f071c465f6b1bccbef12d4136"},
|
{file = "numpy-1.26.4-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:afedb719a9dcfc7eaf2287b839d8198e06dcd4cb5d276a3df279231138e83d30"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-macosx_14_0_x86_64.whl", hash = "sha256:8ae0fd135e0b157365ac7cc31fff27f07a5572bdfc38f9c2d43b2aff416cc8b0"},
|
{file = "numpy-1.26.4-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:95a7476c59002f2f6c590b9b7b998306fba6a5aa646b1e22ddfeaf8f78c3a29c"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:981707f6b31b59c0c24bcda52e5605f9701cb46da4b86c2e8023656ad3e833cb"},
|
{file = "numpy-1.26.4-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:7e50d0a0cc3189f9cb0aeb3a6a6af18c16f59f004b866cd2be1c14b36134a4a0"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2ca4b53e1e0b279142113b8c5eb7d7a877e967c306edc34f3b58e9be12fda8df"},
|
{file = "numpy-1.26.4.tar.gz", hash = "sha256:2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010"},
|
||||||
{file = "numpy-2.1.1-cp313-cp313-musllinux_1_1_x86_64.whl", hash = "sha256:e097507396c0be4e547ff15b13dc3866f45f3680f789c1a1301b07dadd3fbc78"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:f7506387e191fe8cdb267f912469a3cccc538ab108471291636a96a54e599556"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313-win32.whl", hash = "sha256:251105b7c42abe40e3a689881e1793370cc9724ad50d64b30b358bbb3a97553b"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313-win_amd64.whl", hash = "sha256:f212d4f46b67ff604d11fff7cc62d36b3e8714edf68e44e9760e19be38c03eb0"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-macosx_10_13_x86_64.whl", hash = "sha256:920b0911bb2e4414c50e55bd658baeb78281a47feeb064ab40c2b66ecba85553"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-macosx_11_0_arm64.whl", hash = "sha256:bab7c09454460a487e631ffc0c42057e3d8f2a9ddccd1e60c7bb8ed774992480"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:cea427d1350f3fd0d2818ce7350095c1a2ee33e30961d2f0fef48576ddbbe90f"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-macosx_14_0_x86_64.whl", hash = "sha256:e30356d530528a42eeba51420ae8bf6c6c09559051887196599d96ee5f536468"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e8dfa9e94fc127c40979c3eacbae1e61fda4fe71d84869cc129e2721973231ef"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:910b47a6d0635ec1bd53b88f86120a52bf56dcc27b51f18c7b4a2e2224c29f0f"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-musllinux_1_1_x86_64.whl", hash = "sha256:13cc11c00000848702322af4de0147ced365c81d66053a67c2e962a485b3717c"},
|
|
||||||
{file = "numpy-2.1.1-cp313-cp313t-musllinux_1_2_aarch64.whl", hash = "sha256:53e27293b3a2b661c03f79aa51c3987492bd4641ef933e366e0f9f6c9bf257ec"},
|
|
||||||
{file = "numpy-2.1.1-pp310-pypy310_pp73-macosx_10_15_x86_64.whl", hash = "sha256:7be6a07520b88214ea85d8ac8b7d6d8a1839b0b5cb87412ac9f49fa934eb15d5"},
|
|
||||||
{file = "numpy-2.1.1-pp310-pypy310_pp73-macosx_14_0_x86_64.whl", hash = "sha256:52ac2e48f5ad847cd43c4755520a2317f3380213493b9d8a4c5e37f3b87df504"},
|
|
||||||
{file = "numpy-2.1.1-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:50a95ca3560a6058d6ea91d4629a83a897ee27c00630aed9d933dff191f170cd"},
|
|
||||||
{file = "numpy-2.1.1-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:99f4a9ee60eed1385a86e82288971a51e71df052ed0b2900ed30bc840c0f2e39"},
|
|
||||||
{file = "numpy-2.1.1.tar.gz", hash = "sha256:d0cf7d55b1051387807405b3898efafa862997b4cba8aa5dbe657be794afeafd"},
|
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
@ -672,6 +709,20 @@ files = [
|
|||||||
{file = "PyQt6_sip-13.8.0.tar.gz", hash = "sha256:2f74cf3d6d9cab5152bd9f49d570b2dfb87553ebb5c4919abfde27f5b9fd69d4"},
|
{file = "PyQt6_sip-13.8.0.tar.gz", hash = "sha256:2f74cf3d6d9cab5152bd9f49d570b2dfb87553ebb5c4919abfde27f5b9fd69d4"},
|
||||||
]
|
]
|
||||||
|
|
||||||
|
[[package]]
|
||||||
|
name = "pyqtgraph"
|
||||||
|
version = "0.13.7"
|
||||||
|
description = "Scientific Graphics and GUI Library for Python"
|
||||||
|
optional = false
|
||||||
|
python-versions = ">=3.9"
|
||||||
|
files = [
|
||||||
|
{file = "pyqtgraph-0.13.7-py3-none-any.whl", hash = "sha256:7754edbefb6c367fa0dfb176e2d0610da3ada20aa7a5318516c74af5fb72bf7a"},
|
||||||
|
{file = "pyqtgraph-0.13.7.tar.gz", hash = "sha256:64f84f1935c6996d0e09b1ee66fe478a7771e3ca6f3aaa05f00f6e068321d9e3"},
|
||||||
|
]
|
||||||
|
|
||||||
|
[package.dependencies]
|
||||||
|
numpy = ">=1.22.0"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "python-dateutil"
|
name = "python-dateutil"
|
||||||
version = "2.9.0.post0"
|
version = "2.9.0.post0"
|
||||||
@ -777,14 +828,14 @@ files = [
|
|||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "tomli"
|
name = "tomlkit"
|
||||||
version = "2.0.1"
|
version = "0.13.2"
|
||||||
description = "A lil' TOML parser"
|
description = "Style preserving TOML library"
|
||||||
optional = false
|
optional = false
|
||||||
python-versions = ">=3.7"
|
python-versions = ">=3.8"
|
||||||
files = [
|
files = [
|
||||||
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
|
{file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"},
|
||||||
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
|
{file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"},
|
||||||
]
|
]
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
@ -829,4 +880,4 @@ files = [
|
|||||||
[metadata]
|
[metadata]
|
||||||
lock-version = "2.0"
|
lock-version = "2.0"
|
||||||
python-versions = "^3.12"
|
python-versions = "^3.12"
|
||||||
content-hash = "477748fbc18bde095d13dea548108541c1b584242099398155787361b1dc31fe"
|
content-hash = "7321f58bda2e65a4a0674d43997ce31402e0fed876a77b37a1b86d83d569707a"
|
||||||
|
|||||||
@ -1,3 +1,7 @@
|
|||||||
|
[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"
|
||||||
@ -6,14 +10,11 @@ authors = ["wendtalexander <wendtalexander@protonmail.com>"]
|
|||||||
repository = "https://whale.am28.uni-tuebingen.de/git/awendt/pyrelacs"
|
repository = "https://whale.am28.uni-tuebingen.de/git/awendt/pyrelacs"
|
||||||
readme = "README.md"
|
readme = "README.md"
|
||||||
license = "MIT"
|
license = "MIT"
|
||||||
organization = "de.uni-tuebingen.neuroetho"
|
|
||||||
classifiers = [
|
classifiers = [
|
||||||
"Topic :: Scientific/Engineering",
|
"Topic :: Scientific/Engineering",
|
||||||
"Intended Audience :: Science/Research",
|
"Intended Audience :: Science/Research",
|
||||||
"Intended Audience :: End Users/Desktop",
|
"Intended Audience :: End Users/Desktop",
|
||||||
]
|
]
|
||||||
copyright = "(c) 2020, Neuroethology lab, Uni Tuebingen"
|
|
||||||
|
|
||||||
include = [
|
include = [
|
||||||
{ path = "pyproject.toml" }
|
{ path = "pyproject.toml" }
|
||||||
]
|
]
|
||||||
@ -23,15 +24,16 @@ 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 = "^2.1.1"
|
numpy = "^1.9"
|
||||||
pyqt6 = "^6.7.1"
|
pyqt6 = "^6.7.1"
|
||||||
tomli = "^2.0.1"
|
|
||||||
tomlkit = "^0.13.2"
|
tomlkit = "^0.13.2"
|
||||||
scipy = "^1.14.1"
|
scipy = "^1.14.1"
|
||||||
|
nixio = "^1.5.3"
|
||||||
|
pyqtgraph = "^0.13.7"
|
||||||
|
|
||||||
[tool.poetry.scripts]
|
[tool.poetry.scripts]
|
||||||
pyrelacs = "pyrelacs.app:main"
|
pyrelacs = "pyrelacs.app:main"
|
||||||
|
|
||||||
[build-system]
|
[build-system]
|
||||||
requires = ["poetry-core"]
|
requires = ["poetry-core>=1.0.0"]
|
||||||
build-backend = "poetry.core.masonry.api"
|
build-backend = "poetry.core.masonry.api"
|
||||||
|
|||||||
@ -1,8 +1,8 @@
|
|||||||
|
import pathlib
|
||||||
from PyQt6.QtGui import QAction
|
from PyQt6.QtGui import QAction
|
||||||
import sys
|
import sys
|
||||||
import pathlib
|
|
||||||
|
|
||||||
from PyQt6.QtCore import QProcess, QSize, QThreadPool, Qt, QSettings
|
from PyQt6.QtCore import QSize, QThreadPool, QSettings
|
||||||
from PyQt6.QtWidgets import (
|
from PyQt6.QtWidgets import (
|
||||||
QApplication,
|
QApplication,
|
||||||
QGridLayout,
|
QGridLayout,
|
||||||
@ -12,9 +12,12 @@ from PyQt6.QtWidgets import (
|
|||||||
QMainWindow,
|
QMainWindow,
|
||||||
QPlainTextEdit,
|
QPlainTextEdit,
|
||||||
)
|
)
|
||||||
|
import pyqtgraph as pg
|
||||||
import uldaq
|
import uldaq
|
||||||
from IPython import embed
|
from IPython import embed
|
||||||
|
from scipy.signal import welch, find_peaks
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
import nixio as nix
|
||||||
|
|
||||||
from pyrelacs.util.logging import config_logging
|
from pyrelacs.util.logging import config_logging
|
||||||
import pyrelacs.info as info
|
import pyrelacs.info as info
|
||||||
@ -29,6 +32,7 @@ class PyRelacs(QMainWindow):
|
|||||||
super().__init__()
|
super().__init__()
|
||||||
self.setWindowTitle("PyRelacs")
|
self.setWindowTitle("PyRelacs")
|
||||||
self.setMinimumSize(1000, 1000)
|
self.setMinimumSize(1000, 1000)
|
||||||
|
self.plot_graph = pg.PlotWidget()
|
||||||
|
|
||||||
self.threadpool = QThreadPool()
|
self.threadpool = QThreadPool()
|
||||||
self.repros = Repro()
|
self.repros = Repro()
|
||||||
@ -41,13 +45,18 @@ class PyRelacs(QMainWindow):
|
|||||||
self.daq_disconnect_button.setCheckable(True)
|
self.daq_disconnect_button.setCheckable(True)
|
||||||
self.daq_disconnect_button.clicked.connect(self.disconnect_dac)
|
self.daq_disconnect_button.clicked.connect(self.disconnect_dac)
|
||||||
|
|
||||||
|
self.plot_calibration_button = QPushButton("Plot Calibration")
|
||||||
|
self.plot_calibration_button.setCheckable(True)
|
||||||
|
self.plot_calibration_button.clicked.connect(self.plot_calibration)
|
||||||
|
|
||||||
self.text = QPlainTextEdit()
|
self.text = QPlainTextEdit()
|
||||||
self.text.setReadOnly(True)
|
self.text.setReadOnly(True)
|
||||||
|
|
||||||
layout = QGridLayout()
|
layout = QGridLayout()
|
||||||
layout.addWidget(self.daq_connect_button, 0, 0)
|
layout.addWidget(self.plot_calibration_button, 0, 0)
|
||||||
layout.addWidget(self.daq_disconnect_button, 0, 1)
|
layout.addWidget(self.daq_disconnect_button, 0, 1)
|
||||||
layout.addWidget(self.text, 2, 0, 1, 2)
|
layout.addWidget(self.text, 3, 0, 1, 2)
|
||||||
|
layout.addWidget(self.plot_graph, 2, 0, 1, 2)
|
||||||
|
|
||||||
self.toolbar = QToolBar("Repros")
|
self.toolbar = QToolBar("Repros")
|
||||||
self.addToolBar(self.toolbar)
|
self.addToolBar(self.toolbar)
|
||||||
@ -58,6 +67,67 @@ class PyRelacs(QMainWindow):
|
|||||||
widget.setLayout(layout)
|
widget.setLayout(layout)
|
||||||
self.setCentralWidget(widget)
|
self.setCentralWidget(widget)
|
||||||
|
|
||||||
|
self.nix_file = nix.File.open(
|
||||||
|
str(pathlib.Path(__file__).parent / "data"), nix.FileMode.ReadOnly
|
||||||
|
)
|
||||||
|
|
||||||
|
def plot_calibration(self):
|
||||||
|
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
|
||||||
|
|
||||||
|
block = self.nix_file.blocks[0]
|
||||||
|
for stim, fish in zip(
|
||||||
|
list(block.data_arrays)[::2], list(block.data_arrays)[1::2]
|
||||||
|
):
|
||||||
|
beat = stim[:] + fish[:]
|
||||||
|
beat_squared = beat**2
|
||||||
|
|
||||||
|
f, powerspec = welch(beat, fs=40_000.0)
|
||||||
|
powerspec = decibel(powerspec)
|
||||||
|
|
||||||
|
f_sq, powerspec_sq = welch(beat_squared, fs=40_000.0)
|
||||||
|
powerspec_sq = decibel(powerspec_sq)
|
||||||
|
peaks = find_peaks(powerspec_sq, prominence=20)[0]
|
||||||
|
pen = pg.mkPen()
|
||||||
|
self.plot_graph.plot(
|
||||||
|
np.arange(0, len(beat)) / 40_000.0, beat_squared, pen=pen
|
||||||
|
)
|
||||||
|
|
||||||
def connect_dac(self):
|
def connect_dac(self):
|
||||||
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
|
devices = uldaq.get_daq_device_inventory(uldaq.InterfaceType.USB)
|
||||||
try:
|
try:
|
||||||
@ -93,7 +163,7 @@ class PyRelacs(QMainWindow):
|
|||||||
|
|
||||||
def run_repro(self, n, fn):
|
def run_repro(self, n, fn):
|
||||||
self.text.appendPlainText(f"started Repro {n}, {fn}")
|
self.text.appendPlainText(f"started Repro {n}, {fn}")
|
||||||
worker = Worker(self.repros.run_repro, n, fn)
|
worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
|
||||||
worker.signals.result.connect(self.print_output)
|
worker.signals.result.connect(self.print_output)
|
||||||
worker.signals.finished.connect(self.thread_complete)
|
worker.signals.finished.connect(self.thread_complete)
|
||||||
worker.signals.progress.connect(self.progress_fn)
|
worker.signals.progress.connect(self.progress_fn)
|
||||||
@ -142,4 +212,3 @@ def main():
|
|||||||
|
|
||||||
if __name__ == "__main__":
|
if __name__ == "__main__":
|
||||||
main()
|
main()
|
||||||
|
|
||||||
|
|||||||
BIN
pyrelacs/data
Normal file
BIN
pyrelacs/data
Normal file
Binary file not shown.
@ -1,9 +1,10 @@
|
|||||||
import tomlkit
|
import tomlkit
|
||||||
import pathlib
|
import pathlib
|
||||||
|
|
||||||
|
|
||||||
def load_project_settings(project_root):
|
def load_project_settings(project_root):
|
||||||
# Read the pyproject.toml file
|
# Read the pyproject.toml file
|
||||||
with open(pathlib.Path.joinpath(project_root, 'pyproject.toml'), 'r') as f:
|
with open(pathlib.Path.joinpath(project_root, "pyproject.toml"), "r") as f:
|
||||||
pyproject_content = f.read()
|
pyproject_content = f.read()
|
||||||
|
|
||||||
# Parse the toml content
|
# Parse the toml content
|
||||||
@ -11,16 +12,16 @@ def load_project_settings(project_root):
|
|||||||
|
|
||||||
# Access project settings
|
# Access project settings
|
||||||
return {
|
return {
|
||||||
'name': pyproject['tool']['poetry']['name'],
|
"name": pyproject["tool"]["poetry"]["name"],
|
||||||
'version': pyproject['tool']['poetry']['version'],
|
"version": pyproject["tool"]["poetry"]["version"],
|
||||||
'description': pyproject['tool']['poetry']['description'],
|
"description": pyproject["tool"]["poetry"]["description"],
|
||||||
'authors': pyproject['tool']['poetry']['authors'],
|
"authors": pyproject["tool"]["poetry"]["authors"],
|
||||||
'readme': pyproject['tool']['poetry']['authors'],
|
"readme": pyproject["tool"]["poetry"]["authors"],
|
||||||
'licence': pyproject['tool']['poetry']['license'],
|
"licence": pyproject["tool"]["poetry"]["license"],
|
||||||
'organization': pyproject['tool']['poetry']['organization'],
|
"organization": pyproject["project"]["organization"],
|
||||||
'classifiers': pyproject['tool']['poetry']['classifiers'],
|
"classifiers": pyproject["tool"]["poetry"]["classifiers"],
|
||||||
'copyright': pyproject['tool']['poetry']['copyright'],
|
"copyright": pyproject["project"]["copyright"],
|
||||||
"repository": pyproject['tool']['poetry']['repository'],
|
"repository": pyproject["tool"]["poetry"]["repository"],
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -3,6 +3,7 @@ import sys
|
|||||||
import faulthandler
|
import faulthandler
|
||||||
import time
|
import time
|
||||||
|
|
||||||
|
import nixio as nix
|
||||||
import uldaq
|
import uldaq
|
||||||
from IPython import embed
|
from IPython import embed
|
||||||
import numpy as np
|
import numpy as np
|
||||||
@ -26,9 +27,9 @@ class Calibration(MccDac):
|
|||||||
self.SINFREQ = 750
|
self.SINFREQ = 750
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def run():
|
def run(nix_file: nix.File):
|
||||||
calb = Calibration()
|
calb = Calibration()
|
||||||
calb.check_beat()
|
calb.check_beat(nix_file)
|
||||||
|
|
||||||
def check_amplitude(self):
|
def check_amplitude(self):
|
||||||
db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
|
db_values = [0.0, -5.0, -10.0, -20.0, -50.0]
|
||||||
@ -84,7 +85,7 @@ class Calibration(MccDac):
|
|||||||
|
|
||||||
self.disconnect_dac()
|
self.disconnect_dac()
|
||||||
|
|
||||||
def check_beat(self):
|
def check_beat(self, nix_file: nix.File):
|
||||||
self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
|
self.set_attenuation_level(db_channel1=-10.0, db_channel2=0.0)
|
||||||
t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
|
t = np.arange(0, self.DURATION, 1 / self.SAMPLERATE)
|
||||||
data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
|
data = self.AMPLITUDE * np.sin(2 * np.pi * self.SINFREQ * t)
|
||||||
@ -92,7 +93,8 @@ class Calibration(MccDac):
|
|||||||
db_values = [0.0, -5.0, -8.5, -10.0]
|
db_values = [0.0, -5.0, -8.5, -10.0]
|
||||||
colors = ["red", "blue", "black", "green"]
|
colors = ["red", "blue", "black", "green"]
|
||||||
colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
|
colors_in = ["lightcoral", "lightblue", "grey", "lightgreen"]
|
||||||
fig, axes = plt.subplots(2, 2, sharex="col")
|
block = nix_file.create_block("Calibration", "data")
|
||||||
|
# fig, axes = plt.subplots(2, 2, sharex="col")
|
||||||
for i, db_value in enumerate(db_values):
|
for i, db_value in enumerate(db_values):
|
||||||
self.set_attenuation_level(db_channel1=db_value)
|
self.set_attenuation_level(db_channel1=db_value)
|
||||||
stim = self.write_analog(
|
stim = self.write_analog(
|
||||||
@ -127,8 +129,27 @@ class Calibration(MccDac):
|
|||||||
log.debug(
|
log.debug(
|
||||||
f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
|
f"Status Analog_output {ao_status}\n, Status Analog_input {ai_status}"
|
||||||
)
|
)
|
||||||
|
|
||||||
channel1 = np.array(readout[::2])
|
channel1 = np.array(readout[::2])
|
||||||
channel2 = np.array(readout[1::2])
|
channel2 = np.array(readout[1::2])
|
||||||
|
|
||||||
|
block.create_data_array(
|
||||||
|
f"stimulus_{db_value}",
|
||||||
|
"Array",
|
||||||
|
shape=data.shape,
|
||||||
|
data=channel1,
|
||||||
|
label="Voltage",
|
||||||
|
unit="V",
|
||||||
|
)
|
||||||
|
block.create_data_array(
|
||||||
|
f"fish_{db_value}",
|
||||||
|
"Array",
|
||||||
|
shape=data.shape,
|
||||||
|
data=channel2,
|
||||||
|
label="Voltage",
|
||||||
|
unit="V",
|
||||||
|
)
|
||||||
|
|
||||||
beat = channel1 + channel2
|
beat = channel1 + channel2
|
||||||
beat_square = beat**2
|
beat_square = beat**2
|
||||||
|
|
||||||
@ -145,69 +166,69 @@ class Calibration(MccDac):
|
|||||||
f_in, powerspec_in = welch(channel2, fs=self.SAMPLERATE)
|
f_in, powerspec_in = welch(channel2, fs=self.SAMPLERATE)
|
||||||
powerspec_in = decibel(powerspec_in)
|
powerspec_in = decibel(powerspec_in)
|
||||||
|
|
||||||
axes[0, 0].plot(
|
# axes[0, 0].plot(
|
||||||
t,
|
# t,
|
||||||
channel1,
|
# channel1,
|
||||||
label=f"{db_value} Readout Channel0",
|
# label=f"{db_value} Readout Channel0",
|
||||||
color=colors[i],
|
# color=colors[i],
|
||||||
)
|
# )
|
||||||
axes[0, 0].plot(
|
# axes[0, 0].plot(
|
||||||
t,
|
# t,
|
||||||
channel2,
|
# channel2,
|
||||||
label=f"{db_value} Readout Channel1",
|
# label=f"{db_value} Readout Channel1",
|
||||||
color=colors_in[i],
|
# color=colors_in[i],
|
||||||
)
|
# )
|
||||||
|
#
|
||||||
axes[0, 1].plot(
|
# axes[0, 1].plot(
|
||||||
f_stim,
|
# f_stim,
|
||||||
powerspec_stim,
|
# powerspec_stim,
|
||||||
label=f"{db_value} powerspec Channel0",
|
# label=f"{db_value} powerspec Channel0",
|
||||||
color=colors[i],
|
# color=colors[i],
|
||||||
)
|
# )
|
||||||
axes[0, 1].plot(
|
# axes[0, 1].plot(
|
||||||
f_in,
|
# f_in,
|
||||||
powerspec_in,
|
# powerspec_in,
|
||||||
label=f"{db_value} powerspec Channel2",
|
# label=f"{db_value} powerspec Channel2",
|
||||||
color=colors_in[i],
|
# color=colors_in[i],
|
||||||
)
|
# )
|
||||||
axes[0, 1].set_xlabel("Freq [HZ]")
|
# axes[0, 1].set_xlabel("Freq [HZ]")
|
||||||
axes[0, 1].set_ylabel("dB")
|
# axes[0, 1].set_ylabel("dB")
|
||||||
|
#
|
||||||
axes[1, 0].plot(
|
# axes[1, 0].plot(
|
||||||
t,
|
# t,
|
||||||
beat,
|
# beat,
|
||||||
label="Beat",
|
# label="Beat",
|
||||||
color=colors[i],
|
# color=colors[i],
|
||||||
)
|
# )
|
||||||
axes[1, 0].plot(
|
# axes[1, 0].plot(
|
||||||
t,
|
# t,
|
||||||
beat**2,
|
# beat**2,
|
||||||
label="Beat squared",
|
# label="Beat squared",
|
||||||
color=colors_in[i],
|
# color=colors_in[i],
|
||||||
)
|
# )
|
||||||
axes[1, 0].legend()
|
# axes[1, 0].legend()
|
||||||
|
#
|
||||||
axes[1, 1].plot(
|
# axes[1, 1].plot(
|
||||||
f,
|
# f,
|
||||||
powerspec,
|
# powerspec,
|
||||||
color=colors[i],
|
# color=colors[i],
|
||||||
)
|
# )
|
||||||
axes[1, 1].plot(
|
# axes[1, 1].plot(
|
||||||
f_sq,
|
# f_sq,
|
||||||
powerspec_sq,
|
# powerspec_sq,
|
||||||
color=colors_in[i],
|
# color=colors_in[i],
|
||||||
label=f"dB {db_value}, first peak {np.min(f_sq[peaks])}",
|
# label=f"dB {db_value}, first peak {np.min(f_sq[peaks])}",
|
||||||
)
|
# )
|
||||||
axes[1, 1].scatter(
|
# axes[1, 1].scatter(
|
||||||
f_sq[peaks],
|
# f_sq[peaks],
|
||||||
powerspec_sq[peaks],
|
# powerspec_sq[peaks],
|
||||||
color="maroon",
|
# color="maroon",
|
||||||
)
|
# )
|
||||||
axes[1, 1].set_xlabel("Freq [HZ]")
|
# axes[1, 1].set_xlabel("Freq [HZ]")
|
||||||
axes[1, 1].set_ylabel("dB")
|
# axes[1, 1].set_ylabel("dB")
|
||||||
axes[0, 0].legend()
|
# axes[0, 0].legend()
|
||||||
axes[1, 1].legend()
|
# axes[1, 1].legend()
|
||||||
plt.show()
|
# plt.show()
|
||||||
self.set_analog_to_zero()
|
self.set_analog_to_zero()
|
||||||
self.disconnect_dac()
|
self.disconnect_dac()
|
||||||
|
|
||||||
|
|||||||
@ -4,6 +4,7 @@ import ast
|
|||||||
import pathlib
|
import pathlib
|
||||||
|
|
||||||
from IPython import embed
|
from IPython import embed
|
||||||
|
import nixio as nix
|
||||||
from pyrelacs.util.logging import config_logging
|
from pyrelacs.util.logging import config_logging
|
||||||
|
|
||||||
log = config_logging()
|
log = config_logging()
|
||||||
@ -13,22 +14,24 @@ class Repro:
|
|||||||
def __init__(self) -> None:
|
def __init__(self) -> None:
|
||||||
pass
|
pass
|
||||||
|
|
||||||
def run_repro(self, name: str, file: pathlib.Path, *args, **kwargs) -> None:
|
def run_repro(
|
||||||
|
self, nix_file: nix.File, name: str, file: pathlib.Path, *args, **kwargs
|
||||||
|
) -> None:
|
||||||
spec = importlib.util.spec_from_file_location("rep", file)
|
spec = importlib.util.spec_from_file_location("rep", file)
|
||||||
if not spec:
|
if not spec:
|
||||||
log.error("Could not load the repro")
|
log.error("Could not load the file")
|
||||||
else:
|
else:
|
||||||
module = importlib.util.module_from_spec(spec)
|
module = importlib.util.module_from_spec(spec)
|
||||||
if not module:
|
if not module:
|
||||||
log.error("Could not load Class of the repro")
|
log.error("Could not load the module of the repro")
|
||||||
else:
|
else:
|
||||||
sys.modules[name] = module
|
sys.modules[name] = module
|
||||||
spec.loader.exec_module(module)
|
spec.loader.exec_module(module)
|
||||||
if hasattr(module, name):
|
if hasattr(module, name):
|
||||||
rep_class = getattr(module, name)
|
rep_class = getattr(module, name)
|
||||||
rep_class.run()
|
rep_class.run(nix_file)
|
||||||
else:
|
else:
|
||||||
raise AttributeError(f"{name} has no run function")
|
raise AttributeError(f"{file.name} has no {name} class")
|
||||||
|
|
||||||
def names_of_repros(self):
|
def names_of_repros(self):
|
||||||
file_path_cur = pathlib.Path(__file__).parent
|
file_path_cur = pathlib.Path(__file__).parent
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user