forked from awendt/pyrelacs
Merge branch 'jgrewe-uistuff'
This commit is contained in:
commit
5dadf1bd7c
5
.gitignore
vendored
5
.gitignore
vendored
@ -161,3 +161,8 @@ cython_debug/
|
||||
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
|
||||
#.idea/
|
||||
|
||||
# ignore created data files
|
||||
*.nix
|
||||
|
||||
# ignore reource.py as it is created by pyside6-rcc resources.qrc -o resources.py
|
||||
resources.py
|
||||
@ -16,11 +16,12 @@ classifiers = [
|
||||
"Intended Audience :: End Users/Desktop",
|
||||
]
|
||||
include = [
|
||||
{ path = "pyproject.toml" }
|
||||
{ path = "pyproject.toml" },
|
||||
"pyrelacs/resources.py"
|
||||
]
|
||||
|
||||
[tool.poetry.dependencies]
|
||||
python = "^3.12"
|
||||
python = "^3.10"
|
||||
uldaq = "^1.2.3"
|
||||
typer = "^0.12.5"
|
||||
matplotlib = "^3.9.2"
|
||||
|
||||
0
pyrelacs/__init__.py
Normal file
0
pyrelacs/__init__.py
Normal file
186
pyrelacs/app.py
186
pyrelacs/app.py
@ -1,193 +1,21 @@
|
||||
import pathlib
|
||||
from PyQt6.QtGui import QAction
|
||||
import sys
|
||||
|
||||
from PyQt6.QtCore import QSize, QThreadPool, QSettings
|
||||
from PyQt6.QtWidgets import (
|
||||
QApplication,
|
||||
QGridLayout,
|
||||
QPushButton,
|
||||
QToolBar,
|
||||
QWidget,
|
||||
QMainWindow,
|
||||
QPlainTextEdit,
|
||||
)
|
||||
import pyqtgraph as pg
|
||||
import uldaq
|
||||
from IPython import embed
|
||||
from scipy.signal import welch, find_peaks
|
||||
import numpy as np
|
||||
import nixio as nix
|
||||
|
||||
from pyrelacs.util.logging import config_logging
|
||||
import pyrelacs.info as info
|
||||
from pyrelacs.worker import Worker
|
||||
from pyrelacs.repros.repros import Repro
|
||||
from PyQt6.QtCore import QSettings
|
||||
from PyQt6.QtWidgets import QApplication
|
||||
|
||||
from . import info
|
||||
from .ui.mainwindow import PyRelacs
|
||||
from .util.logging import config_logging
|
||||
log = config_logging()
|
||||
|
||||
|
||||
class PyRelacs(QMainWindow):
|
||||
def __init__(self):
|
||||
super().__init__()
|
||||
self.setWindowTitle("PyRelacs")
|
||||
self.beat_plot = pg.PlotWidget()
|
||||
self.power_plot = pg.PlotWidget()
|
||||
|
||||
self.threadpool = QThreadPool()
|
||||
self.repros = Repro()
|
||||
|
||||
self.daq_connect_button = QPushButton("Connect Daq")
|
||||
self.daq_connect_button.setCheckable(True)
|
||||
self.daq_connect_button.clicked.connect(self.connect_dac)
|
||||
|
||||
self.daq_disconnect_button = QPushButton("Disconnect Daq")
|
||||
self.daq_disconnect_button.setCheckable(True)
|
||||
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)
|
||||
|
||||
layout = QGridLayout()
|
||||
layout.addWidget(self.plot_calibration_button, 0, 0)
|
||||
layout.addWidget(self.daq_disconnect_button, 0, 1)
|
||||
layout.addWidget(self.beat_plot, 2, 0, 1, 2)
|
||||
layout.addWidget(self.power_plot, 3, 0, 1, 2)
|
||||
|
||||
self.toolbar = QToolBar("Repros")
|
||||
self.addToolBar(self.toolbar)
|
||||
self.repros_to_toolbar()
|
||||
|
||||
# self.setFixedSize(QSize(400, 300))
|
||||
widget = QWidget()
|
||||
widget.setLayout(layout)
|
||||
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]
|
||||
colors = ["red", "green", "blue", "black", "yellow"]
|
||||
for i, (stim, fish) in enumerate(
|
||||
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(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)
|
||||
# self.power_plot.plot(f[peaks], powerspec_sq[peaks], pen=None, symbol="x")
|
||||
|
||||
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)
|
||||
|
||||
def disconnect_dac(self):
|
||||
try:
|
||||
log.debug(f"{self.daq_device}")
|
||||
self.daq_device.disconnect()
|
||||
self.daq_device.release()
|
||||
log.debug(f"{self.daq_device}")
|
||||
self.daq_disconnect_button.setDisabled(True)
|
||||
self.daq_connect_button.setEnabled(True)
|
||||
except AttributeError:
|
||||
log.debug("DAQ was not connected")
|
||||
|
||||
def repros_to_toolbar(self):
|
||||
repro_names, file_names = self.repros.names_of_repros()
|
||||
for rep, fn in zip(repro_names, file_names):
|
||||
individual_repro_button = QAction(rep, self)
|
||||
individual_repro_button.setStatusTip("Button")
|
||||
individual_repro_button.triggered.connect(
|
||||
lambda checked, n=rep, f=fn: self.run_repro(n, f)
|
||||
)
|
||||
self.toolbar.addAction(individual_repro_button)
|
||||
|
||||
def run_repro(self, n, fn):
|
||||
log.debug(f"Running repro {n} in the file {fn}")
|
||||
worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
|
||||
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 print_output(self, s):
|
||||
print(s)
|
||||
|
||||
def thread_complete(self):
|
||||
print("THREAD COMPLETE!")
|
||||
|
||||
def progress_fn(self, n):
|
||||
print("%d%% done" % n)
|
||||
|
||||
from . import resources
|
||||
|
||||
def main():
|
||||
app = QApplication(sys.argv)
|
||||
app.setApplicationName(info.NAME)
|
||||
app.setApplicationVersion(str(info.VERSION))
|
||||
app.setOrganizationDomain(info.ORGANIZATION)
|
||||
# app.setAttribute(Qt.ApplicationAttribute.AA_DontShowIconsInMenus, False)
|
||||
|
||||
# read window settings
|
||||
settings = QSettings(info.ORGANIZATION, info.NAME)
|
||||
|
||||
0
pyrelacs/devices/__init__.py
Normal file
0
pyrelacs/devices/__init__.py
Normal file
738
pyrelacs/icons/connect.png
Normal file
738
pyrelacs/icons/connect.png
Normal file
@ -0,0 +1,738 @@
|
||||
<!DOCTYPE html>
|
||||
<html lang="en-US" data-theme="gitea-auto">
|
||||
<head>
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||||
<title>PylonRecorder/connect.png at master - PylonRecorder - Neuroetho git repository</title>
|
||||
<link rel="manifest" href="data:application/json;base64,eyJuYW1lIjoiTmV1cm9ldGhvIGdpdCByZXBvc2l0b3J5Iiwic2hvcnRfbmFtZSI6Ik5ldXJvZXRobyBnaXQgcmVwb3NpdG9yeSIsInN0YXJ0X3VybCI6Imh0dHBzOi8vd2hhbGUuYW0yOC51bmktdHVlYmluZ2VuLmRlL2dpdC8iLCJpY29ucyI6W3sic3JjIjoiaHR0cHM6Ly93aGFsZS5hbTI4LnVuaS10dWViaW5nZW4uZGUvZ2l0L2Fzc2V0cy9pbWcvbG9nby5wbmciLCJ0eXBlIjoiaW1hZ2UvcG5nIiwic2l6ZXMiOiI1MTJ4NTEyIn0seyJzcmMiOiJodHRwczovL3doYWxlLmFtMjgudW5pLXR1ZWJpbmdlbi5kZS9naXQvYXNzZXRzL2ltZy9sb2dvLnN2ZyIsInR5cGUiOiJpbWFnZS9zdmcreG1sIiwic2l6ZXMiOiI1MTJ4NTEyIn1dfQ==">
|
||||
<meta name="author" content="jgrewe">
|
||||
<meta name="description" content="PylonRecorder">
|
||||
<meta name="keywords" content="go,git,self-hosted,gitea">
|
||||
<meta name="referrer" content="no-referrer">
|
||||
|
||||
|
||||
<link rel="alternate" type="application/atom+xml" title="" href="/git/jgrewe/PylonRecorder.atom">
|
||||
<link rel="alternate" type="application/rss+xml" title="" href="/git/jgrewe/PylonRecorder.rss">
|
||||
|
||||
<link rel="icon" href="/git/assets/img/favicon.svg" type="image/svg+xml">
|
||||
<link rel="alternate icon" href="/git/assets/img/favicon.png" type="image/png">
|
||||
|
||||
<script>
|
||||
|
||||
window.addEventListener('error', function(e) {window._globalHandlerErrors=window._globalHandlerErrors||[]; window._globalHandlerErrors.push(e);});
|
||||
window.addEventListener('unhandledrejection', function(e) {window._globalHandlerErrors=window._globalHandlerErrors||[]; window._globalHandlerErrors.push(e);});
|
||||
window.config = {
|
||||
appUrl: 'https:\/\/whale.am28.uni-tuebingen.de\/git\/',
|
||||
appSubUrl: '\/git',
|
||||
assetVersionEncoded: encodeURIComponent('1.22.2'),
|
||||
assetUrlPrefix: '\/git\/assets',
|
||||
runModeIsProd: true ,
|
||||
customEmojis: {"codeberg":":codeberg:","git":":git:","gitea":":gitea:","github":":github:","gitlab":":gitlab:","gogs":":gogs:"},
|
||||
csrfToken: 'k817i33JP6vJFK5Nn4-CQBvnlBM6MTcyNzUxNDY3NTMzOTUzMzQ5MA',
|
||||
pageData: {},
|
||||
notificationSettings: {"EventSourceUpdateTime":10000,"MaxTimeout":60000,"MinTimeout":10000,"TimeoutStep":10000},
|
||||
enableTimeTracking: true ,
|
||||
|
||||
mermaidMaxSourceCharacters: 5000 ,
|
||||
|
||||
i18n: {
|
||||
copy_success: "Copied!",
|
||||
copy_error: "Copy failed",
|
||||
error_occurred: "An error occurred",
|
||||
network_error: "Network error",
|
||||
remove_label_str: "Remove item \"%s\"",
|
||||
modal_confirm: "Confirm",
|
||||
modal_cancel: "Cancel",
|
||||
more_items: "More items",
|
||||
},
|
||||
};
|
||||
|
||||
window.config.pageData = window.config.pageData || {};
|
||||
</script>
|
||||
<script src="/git/assets/js/webcomponents.js?v=1.22.2"></script>
|
||||
|
||||
<noscript>
|
||||
<style>
|
||||
.dropdown:hover > .menu { display: block; }
|
||||
.ui.secondary.menu .dropdown.item > .menu { margin-top: 0; }
|
||||
</style>
|
||||
</noscript>
|
||||
|
||||
|
||||
<meta property="og:title" content="PylonRecorder/connect.png at master">
|
||||
<meta property="og:url" content="https://whale.am28.uni-tuebingen.de/git//git/jgrewe/PylonRecorder/src/branch/master/images/connect.png">
|
||||
|
||||
|
||||
<meta property="og:type" content="object">
|
||||
|
||||
<meta property="og:image" content="https://whale.am28.uni-tuebingen.de/git/avatar/cdb337811e4b37c58146ccbdc0ecbfd5">
|
||||
|
||||
|
||||
<meta property="og:site_name" content="Neuroetho git repository">
|
||||
|
||||
<link rel="stylesheet" href="/git/assets/css/index.css?v=1.22.2">
|
||||
<link rel="stylesheet" href="/git/assets/css/theme-gitea-auto.css?v=1.22.2">
|
||||
|
||||
|
||||
</head>
|
||||
<body hx-headers='{"x-csrf-token": "k817i33JP6vJFK5Nn4-CQBvnlBM6MTcyNzUxNDY3NTMzOTUzMzQ5MA"}' hx-swap="outerHTML" hx-ext="morph" hx-push-url="false">
|
||||
|
||||
|
||||
<div class="full height">
|
||||
<noscript>This website requires JavaScript.</noscript>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<nav id="navbar" aria-label="Navigation Bar">
|
||||
<div class="navbar-left">
|
||||
|
||||
<a class="item" id="navbar-logo" href="/git/" aria-label="Dashboard">
|
||||
<img width="30" height="30" src="/git/assets/img/logo.svg" alt="Logo" aria-hidden="true">
|
||||
</a>
|
||||
|
||||
|
||||
<div class="ui secondary menu item navbar-mobile-right only-mobile">
|
||||
|
||||
|
||||
<a id="mobile-notifications-icon" class="item tw-w-auto tw-p-2" href="/git/notifications" data-tooltip-content="Notifications" aria-label="Notifications">
|
||||
<div class="tw-relative">
|
||||
<svg viewBox="0 0 16 16" class="svg octicon-bell" aria-hidden="true" width="16" height="16"><path d="M8 16a2 2 0 0 0 1.985-1.75c.017-.137-.097-.25-.235-.25h-3.5c-.138 0-.252.113-.235.25A2 2 0 0 0 8 16M3 5a5 5 0 0 1 10 0v2.947q0 .076.042.139l1.703 2.555A1.519 1.519 0 0 1 13.482 13H2.518a1.516 1.516 0 0 1-1.263-2.36l1.703-2.554A.26.26 0 0 0 3 7.947Zm5-3.5A3.5 3.5 0 0 0 4.5 5v2.947c0 .346-.102.683-.294.97l-1.703 2.556-.003.01.001.006q0 .003.004.006l.006.004.007.001h10.964l.007-.001.006-.004.004-.006.001-.007-.003-.01-1.703-2.554a1.75 1.75 0 0 1-.294-.97V5A3.5 3.5 0 0 0 8 1.5"/></svg>
|
||||
<span class="notification_count tw-hidden">0</span>
|
||||
</div>
|
||||
</a>
|
||||
|
||||
<button class="item tw-w-auto ui icon mini button tw-p-2 tw-m-0" id="navbar-expand-toggle" aria-label="Navigation Menu"><svg viewBox="0 0 16 16" class="svg octicon-three-bars" aria-hidden="true" width="16" height="16"><path d="M1 2.75A.75.75 0 0 1 1.75 2h12.5a.75.75 0 0 1 0 1.5H1.75A.75.75 0 0 1 1 2.75m0 5A.75.75 0 0 1 1.75 7h12.5a.75.75 0 0 1 0 1.5H1.75A.75.75 0 0 1 1 7.75M1.75 12h12.5a.75.75 0 0 1 0 1.5H1.75a.75.75 0 0 1 0-1.5"/></svg></button>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
<a class="item" href="/git/issues">Issues</a>
|
||||
|
||||
|
||||
<a class="item" href="/git/pulls">Pull Requests</a>
|
||||
|
||||
|
||||
|
||||
<a class="item" href="/git/milestones">Milestones</a>
|
||||
|
||||
|
||||
<a class="item" href="/git/explore/repos">Explore</a>
|
||||
|
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|
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|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<div class="navbar-right">
|
||||
|
||||
|
||||
|
||||
<a class="item not-mobile tw-mx-0" href="/git/notifications" data-tooltip-content="Notifications" aria-label="Notifications">
|
||||
<div class="tw-relative">
|
||||
<svg viewBox="0 0 16 16" class="svg octicon-bell" aria-hidden="true" width="16" height="16"><path d="M8 16a2 2 0 0 0 1.985-1.75c.017-.137-.097-.25-.235-.25h-3.5c-.138 0-.252.113-.235.25A2 2 0 0 0 8 16M3 5a5 5 0 0 1 10 0v2.947q0 .076.042.139l1.703 2.555A1.519 1.519 0 0 1 13.482 13H2.518a1.516 1.516 0 0 1-1.263-2.36l1.703-2.554A.26.26 0 0 0 3 7.947Zm5-3.5A3.5 3.5 0 0 0 4.5 5v2.947c0 .346-.102.683-.294.97l-1.703 2.556-.003.01.001.006q0 .003.004.006l.006.004.007.001h10.964l.007-.001.006-.004.004-.006.001-.007-.003-.01-1.703-2.554a1.75 1.75 0 0 1-.294-.97V5A3.5 3.5 0 0 0 8 1.5"/></svg>
|
||||
<span class="notification_count tw-hidden">0</span>
|
||||
</div>
|
||||
</a>
|
||||
|
||||
<div class="ui dropdown jump item tw-mx-0 tw-pr-2" data-tooltip-content="Create…">
|
||||
<span class="text">
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<a class="muted author-wrapper" title="Jan Grewe" href="/git/jgrewe"><strong>Jan Grewe</strong></a>
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<a class="muted author-wrapper" title="Jan Grewe" href="/git/jgrewe"><strong>Jan Grewe</strong></a>
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|
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<div class="file-header-right file-actions tw-flex tw-items-center tw-flex-wrap">
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<a class="ui mini basic button" href="/git/jgrewe/PylonRecorder/raw/branch/master/images/stop.png">Raw</a>
|
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|
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<a class="ui mini basic button" href="/git/jgrewe/PylonRecorder/src/commit/767f8b7e42f5ebba76f81c5009da496877abbdc9/images/stop.png">Permalink</a>
|
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<a class="ui mini basic button" href="/git/jgrewe/PylonRecorder/commits/branch/master/images/stop.png">History</a>
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</div>
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<a download href="/git/jgrewe/PylonRecorder/raw/branch/master/images/stop.png"><span class="btn-octicon" data-tooltip-content="Download file"><svg viewBox="0 0 16 16" class="svg octicon-download" aria-hidden="true" width="16" height="16"><path d="M2.75 14A1.75 1.75 0 0 1 1 12.25v-2.5a.75.75 0 0 1 1.5 0v2.5c0 .138.112.25.25.25h10.5a.25.25 0 0 0 .25-.25v-2.5a.75.75 0 0 1 1.5 0v2.5A1.75 1.75 0 0 1 13.25 14Z"/><path d="M7.25 7.689V2a.75.75 0 0 1 1.5 0v5.689l1.97-1.969a.749.749 0 1 1 1.06 1.06l-3.25 3.25a.75.75 0 0 1-1.06 0L4.22 6.78a.749.749 0 1 1 1.06-1.06z"/></svg></span></a>
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<a id="copy-content" class="btn-octicon " data-link="/git/jgrewe/PylonRecorder/raw/branch/master/images/stop.png" data-tooltip-content="Copy content"><svg viewBox="0 0 16 16" class="svg octicon-copy" aria-hidden="true" width="14" height="14"><path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"/><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"/></svg></a>
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<a class="btn-octicon" href="/git/jgrewe/PylonRecorder/rss/branch/master/images/stop.png" data-tooltip-content="RSS Feed">
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</a>
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<a href="/git/jgrewe/PylonRecorder/_delete/master/images/stop.png"><span class="btn-octicon btn-octicon-danger" data-tooltip-content="Delete File"><svg viewBox="0 0 16 16" class="svg octicon-trash" aria-hidden="true" width="16" height="16"><path d="M11 1.75V3h2.25a.75.75 0 0 1 0 1.5H2.75a.75.75 0 0 1 0-1.5H5V1.75C5 .784 5.784 0 6.75 0h2.5C10.216 0 11 .784 11 1.75M4.496 6.675l.66 6.6a.25.25 0 0 0 .249.225h5.19a.25.25 0 0 0 .249-.225l.66-6.6a.75.75 0 0 1 1.492.149l-.66 6.6A1.75 1.75 0 0 1 10.595 15h-5.19a1.75 1.75 0 0 1-1.741-1.575l-.66-6.6a.75.75 0 1 1 1.492-.15M6.5 1.75V3h3V1.75a.25.25 0 0 0-.25-.25h-2.5a.25.25 0 0 0-.25.25"/></svg></span></a>
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</div>
|
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</h4>
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<div class="ui bottom attached table unstackable segment">
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<div class="file-view">
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<div class="view-raw">
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<img src="/git/jgrewe/PylonRecorder/raw/branch/master/images/stop.png">
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|
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</div>
|
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|
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</div>
|
||||
</div>
|
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</div>
|
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|
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|
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</div>
|
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</div>
|
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</div>
|
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|
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|
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|
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<footer class="page-footer" role="group" aria-label="Footer">
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<div class="left-links" role="contentinfo" aria-label="About Software">
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<a target="_blank" rel="noopener noreferrer" href="https://about.gitea.com">Powered by Gitea</a>
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Version:
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<a href="/git/admin/config">1.22.2</a>
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Page: <strong>64ms</strong>
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Template: <strong>5ms</strong>
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</div>
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<div class="right-links" role="group" aria-label="Links">
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<div class="ui dropdown upward language">
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<span class="flex-text-inline"><svg viewBox="0 0 16 16" class="svg octicon-globe" aria-hidden="true" width="14" height="14"><path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0M5.78 8.75a9.64 9.64 0 0 0 1.363 4.177q.383.64.857 1.215c.245-.296.551-.705.857-1.215A9.64 9.64 0 0 0 10.22 8.75Zm4.44-1.5a9.64 9.64 0 0 0-1.363-4.177c-.307-.51-.612-.919-.857-1.215a10 10 0 0 0-.857 1.215A9.64 9.64 0 0 0 5.78 7.25Zm-5.944 1.5H1.543a6.51 6.51 0 0 0 4.666 5.5q-.184-.271-.352-.552c-.715-1.192-1.437-2.874-1.581-4.948m-2.733-1.5h2.733c.144-2.074.866-3.756 1.58-4.948q.18-.295.353-.552a6.51 6.51 0 0 0-4.666 5.5m10.181 1.5c-.144 2.074-.866 3.756-1.58 4.948q-.18.296-.353.552a6.51 6.51 0 0 0 4.666-5.5Zm2.733-1.5a6.51 6.51 0 0 0-4.666-5.5q.184.272.353.552c.714 1.192 1.436 2.874 1.58 4.948Z"/></svg> English</span>
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<script src="/git/assets/js/index.js?v=1.22.2" onerror="alert('Failed to load asset files from ' + this.src + '. Please make sure the asset files can be accessed.')"></script>
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</body>
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</html>
|
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|
||||
@ -3,6 +3,7 @@ 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()
|
||||
|
||||
@ -1,15 +1,16 @@
|
||||
import sys
|
||||
import importlib.util
|
||||
import ast
|
||||
import pathlib
|
||||
from typing import Tuple
|
||||
|
||||
from IPython import embed
|
||||
import nixio as nix
|
||||
from pyrelacs.util.logging import config_logging
|
||||
import importlib.util
|
||||
|
||||
from pyrelacs.util.logging import config_logging
|
||||
log = config_logging()
|
||||
|
||||
from IPython import embed
|
||||
|
||||
class Repro:
|
||||
"""
|
||||
|
||||
9
pyrelacs/resources.qrc
Normal file
9
pyrelacs/resources.qrc
Normal file
@ -0,0 +1,9 @@
|
||||
<!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>
|
||||
</qresource>
|
||||
</RCC>
|
||||
0
pyrelacs/ui/__init__.py
Normal file
0
pyrelacs/ui/__init__.py
Normal file
57
pyrelacs/ui/about.py
Normal file
57
pyrelacs/ui/about.py
Normal file
@ -0,0 +1,57 @@
|
||||
import pathlib
|
||||
|
||||
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()
|
||||
_root = pathlib.Path(__file__).parent.parent
|
||||
pixmap = QPixmap(str(pathlib.Path.joinpath(_root, "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)
|
||||
270
pyrelacs/ui/mainwindow.py
Normal file
270
pyrelacs/ui/mainwindow.py
Normal file
@ -0,0 +1,270 @@
|
||||
from PyQt6.QtGui import QAction, QIcon, QKeySequence
|
||||
from PyQt6.QtCore import Qt, QSize, QThreadPool
|
||||
from PyQt6.QtWidgets import (
|
||||
QGridLayout,
|
||||
QPushButton,
|
||||
QToolBar,
|
||||
QWidget,
|
||||
QMainWindow,
|
||||
QPlainTextEdit,
|
||||
QMenuBar,
|
||||
QStatusBar
|
||||
)
|
||||
import uldaq
|
||||
import numpy as np
|
||||
import nixio as nix
|
||||
import pyqtgraph as pg
|
||||
|
||||
from pathlib import Path as path
|
||||
from scipy.signal import welch, find_peaks
|
||||
|
||||
from ..worker import Worker
|
||||
from ..repros.repros import Repro
|
||||
from ..util.logging import config_logging
|
||||
from .about import AboutDialog
|
||||
log = config_logging()
|
||||
_root = path(__file__).parent.parent
|
||||
|
||||
from IPython import embed
|
||||
|
||||
class PyRelacs(QMainWindow):
|
||||
def __init__(self):
|
||||
super().__init__()
|
||||
# self.setToolButtonStyle(Qt.ToolButtonStyle.ToolButtonTextBesideIcon) # Ensure icons are displayed with text
|
||||
self.setWindowTitle("PyRelacs")
|
||||
self.beat_plot = pg.PlotWidget()
|
||||
self.power_plot = pg.PlotWidget()
|
||||
|
||||
self.threadpool = QThreadPool()
|
||||
self.repros = Repro()
|
||||
|
||||
self.text = QPlainTextEdit()
|
||||
self.text.setReadOnly(True)
|
||||
|
||||
self.setMenuBar(QMenuBar(self))
|
||||
self.setStatusBar(QStatusBar(self))
|
||||
self.create_actions()
|
||||
self.create_buttons()
|
||||
self.create_toolbars()
|
||||
|
||||
layout = QGridLayout()
|
||||
layout.addWidget(self.plot_calibration_button, 0, 0)
|
||||
layout.addWidget(self.daq_disconnect_button, 0, 1)
|
||||
layout.addWidget(self.beat_plot, 2, 0, 1, 2)
|
||||
layout.addWidget(self.power_plot, 3, 0, 1, 2)
|
||||
|
||||
self.toolbar = QToolBar("Repros")
|
||||
self.addToolBar(self.toolbar)
|
||||
self.repros_to_toolbar()
|
||||
|
||||
# self.setFixedSize(QSize(400, 300))
|
||||
widget = QWidget()
|
||||
widget.setLayout(layout)
|
||||
self.setCentralWidget(widget)
|
||||
|
||||
filename = path.joinpath(path.cwd(), "data.nix")
|
||||
self.nix_file = nix.File.open(
|
||||
str(filename), nix.FileMode.Overwrite
|
||||
)
|
||||
|
||||
def create_actions(self):
|
||||
self._rlx_exitaction = QAction(QIcon(str(path.joinpath(_root, "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(str(path.joinpath(_root, "icons/connect.png"))), "Connect DAQ", self)
|
||||
self._daq_connectaction.setStatusTip("Connect to daq device")
|
||||
# self._daq_connectaction.setShortcut(QKeySequence("Alt+d"))
|
||||
self._daq_connectaction.triggered.connect(self.connect_dac)
|
||||
|
||||
self._daq_disconnectaction = QAction(QIcon(str(path.joinpath(_root, "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.disconnect_dac)
|
||||
|
||||
self._daq_calibaction = QAction(QIcon(str(path.joinpath(_root, "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.plot_calibration)
|
||||
self.create_menu()
|
||||
|
||||
def create_menu(self):
|
||||
menu = self.menuBar()
|
||||
file_menu = menu.addMenu("&File")
|
||||
file_menu.addAction(self._rlx_exitaction)
|
||||
file_menu.addAction(self._rlx_aboutaction)
|
||||
|
||||
device_menu = menu.addMenu("&DAQ")
|
||||
device_menu.addAction(self._daq_connectaction)
|
||||
device_menu.addAction(self._daq_disconnectaction)
|
||||
device_menu.addSeparator()
|
||||
device_menu.addAction(self._daq_calibaction)
|
||||
|
||||
help_menu = menu.addMenu("&Help")
|
||||
help_menu.addSeparator()
|
||||
# help_menu.addAction(self._help_action)
|
||||
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")
|
||||
daq_toolbar.addAction(self._daq_connectaction)
|
||||
daq_toolbar.addAction(self._daq_disconnectaction)
|
||||
daq_toolbar.addAction(self._daq_calibaction)
|
||||
self.addToolBar(Qt.ToolBarArea.TopToolBarArea, daq_toolbar)
|
||||
|
||||
repro_toolbar = QToolBar("Repros")
|
||||
repro_names, file_names = self.repros.names_of_repros()
|
||||
for rep, fn in zip(repro_names, file_names):
|
||||
repro_action = QAction(rep, self)
|
||||
repro_action.setStatusTip(rep)
|
||||
repro_action.triggered.connect(
|
||||
lambda checked, n=rep, f=fn: self.run_repro(n, f)
|
||||
)
|
||||
repro_toolbar.addAction(repro_action)
|
||||
self.addToolBar(Qt.ToolBarArea.TopToolBarArea, repro_toolbar)
|
||||
|
||||
def create_buttons(self):
|
||||
self.daq_connect_button = QPushButton("Connect Daq")
|
||||
self.daq_connect_button.setCheckable(True)
|
||||
self.daq_connect_button.clicked.connect(self.connect_dac)
|
||||
|
||||
self.daq_disconnect_button = QPushButton("Disconnect Daq")
|
||||
self.daq_disconnect_button.setCheckable(True)
|
||||
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)
|
||||
|
||||
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]
|
||||
colors = ["red", "green", "blue", "black", "yellow"]
|
||||
for i, (stim, fish) in enumerate(
|
||||
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(colors[i])
|
||||
self.beat_plot.plot(
|
||||
np.arange(0, len(beat)) / 40_000.0,
|
||||
beat_squared,
|
||||
pen=pen,
|
||||
# name=stim.name,
|
||||
)
|
||||
self.power_plot.plot(f_sq, powerspec_sq, pen=pen)
|
||||
self.power_plot.plot(f[peaks], powerspec_sq[peaks], pen=None, symbol="x")
|
||||
|
||||
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")
|
||||
self.on_exit()
|
||||
self.daq_connect_button.setDisabled(True)
|
||||
|
||||
def disconnect_dac(self):
|
||||
try:
|
||||
log.debug(f"{self.daq_device}")
|
||||
self.daq_device.disconnect()
|
||||
self.daq_device.release()
|
||||
log.debug(f"{self.daq_device}")
|
||||
self.daq_disconnect_button.setDisabled(True)
|
||||
self.daq_connect_button.setEnabled(True)
|
||||
except AttributeError:
|
||||
log.debug("DAQ was not connected")
|
||||
|
||||
def repros_to_toolbar(self):
|
||||
repro_names, file_names = self.repros.names_of_repros()
|
||||
for rep, fn in zip(repro_names, file_names):
|
||||
individual_repro_button = QAction(rep, self)
|
||||
individual_repro_button.setStatusTip("Button")
|
||||
individual_repro_button.triggered.connect(
|
||||
lambda checked, n=rep, f=fn: self.run_repro(n, f)
|
||||
)
|
||||
self.toolbar.addAction(individual_repro_button)
|
||||
|
||||
def run_repro(self, n, fn):
|
||||
self.text.appendPlainText(f"started Repro {n}, {fn}")
|
||||
worker = Worker(self.repros.run_repro, self.nix_file, n, fn)
|
||||
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 on_exit(self):
|
||||
print("exit button!")
|
||||
self.close()
|
||||
|
||||
def on_about(self, e):
|
||||
about = AboutDialog(self)
|
||||
about.show()
|
||||
|
||||
def print_output(self, s):
|
||||
print(s)
|
||||
|
||||
def thread_complete(self):
|
||||
print("THREAD COMPLETE!")
|
||||
|
||||
def progress_fn(self, n):
|
||||
print("%d%% done" % n)
|
||||
0
pyrelacs/util/__init__.py
Normal file
0
pyrelacs/util/__init__.py
Normal file
Loading…
Reference in New Issue
Block a user