Fex

include README.md

#!/usr/bin/env python

import os
import sys
from PyQt5.QtWidgets import QApplication

from mainwin import MainWin

def fpath(fname):
	for p in site.getsitepackages():
		if os.path.isfile(p + '/' + fname):
			return p + '/' + fname
	return None

if __name__ == '__main__':
	app = QApplication(sys.argv)
	win = MainWin()
	sys.exit(app.exec_())

import os
import sys
from PyQt5.QtWidgets import QApplication

from mainwin import MainWin
from config import Config

def fpath(fname):
	for p in site.getsitepackages():
		if os.path.isfile(p + '/' + fname):
			return p + '/' + fname
	return None

if __name__ == '__main__':
	app = QApplication(sys.argv)
	conf = Config()
	win = MainWin(conf)
	sys.exit(app.exec_())

import os
import site
from configparser import SafeConfigParser
from PyQt5.QtGui import QPalette
from PyQt5.QtWidgets import QWidget
from PyQt5.QtCore import Qt

class Container(object):
	pass

_files = [p + '/default.cfg' for p in site.getsitepackages()]
# TODO test for 'APPDATA' in environ on windows?
#    what's normally in the environment variables on win??
if 'XDG_CONFIG_HOME' in os.environ:
	_files.append(os.environ['XDG_CONFIG_HOME'] + '/fex/config.cfg')
elif 'HOME' in os.environ:
	_files.append(os.environ['HOME'] + '/.config/fex/config.cfg')
_files.append(os.getcwd() + '/fex.cfg')

class Config(object):
	def __init__(self):
		w = QWidget()
		self._parser = SafeConfigParser({
			'QPalette-Window': w.palette().color(QPalette.Window).name(),
			'QPalette-Background': w.palette().color(QPalette.Background).name(),
			'QPalette-WindowText': w.palette().color(QPalette.WindowText).name(),
			'QPalette-Foreground': w.palette().color(QPalette.Foreground).name(),
			'QPalette-Base': w.palette().color(QPalette.Base).name(),
			'QPalette-AlternateBase': w.palette().color(QPalette.AlternateBase).name(),
			'QPalette-ToolTipBase': w.palette().color(QPalette.ToolTipBase).name(),
			'QPalette-ToolTipText': w.palette().color(QPalette.ToolTipText).name(),
			'QPalette-Text': w.palette().color(QPalette.Text).name(),
			'QPalette-Button': w.palette().color(QPalette.Button).name(),
			'QPalette-ButtonText': w.palette().color(QPalette.ButtonText).name(),
			'QPalette-BrightText': w.palette().color(QPalette.BrightText).name(),
			'QToolButton-IconOnly': str(Qt.ToolButtonIconOnly),
			'QToolButton-TextOnly': str(Qt.ToolButtonTextOnly),
			'QToolButton-TextBesideIcon': str(Qt.ToolButtonTextBesideIcon),
			'QToolButton-TextUnderIcon': str(Qt.ToolButtonTextUnderIcon),
			'QToolButton-FollowStyle': str(Qt.ToolButtonFollowStyle)
			})
		f = self._parser.read(_files)

		self._spect = Container()
		self._spect.window = self._parser.getint('spectrogram','window')
		self._spect.overlap = self._parser.getint('spectrogram','overlap')
		self._spect.hipass = self._parser.getint('spectrogram','high-pass')
		self._spect.lopass = self._parser.getint('spectrogram','low-pass')
		self._spect.threshold = self._parser.getint('spectrogram','threshold')
		self._spect.winfunc = self._parser.get('spectrogram','window-function')
		self._spect.logfreq = self._parser.getboolean('spectrogram','log10-freq')
		self._spect.invert = self._parser.getboolean('spectrogram','invert-colors')
		self._spect.border = self._parser.get('spectrogram','border-color')
		self._spect.line = self._parser.get('spectrogram','line-color')
		self._spect.ratio = self._parser.getfloat('spectrogram','ratio')

		self._mainwin = Container()
		self._mainwin.menubar = self._parser.getboolean('main-window','menubar-visible')
		self._mainwin.macmenu = self._parser.getboolean('main-window','mac-native-menu')
		self._mainwin.toolbar = self._parser.getboolean('main-window','toolbar-visible')
		self._mainwin.toolbarposition = self._parser.get('main-window','toolbar-position')
		self._mainwin.toolbarstyle = self._parser.getint('main-window','toolbar-style')
		self._mainwin.statusbar = self._parser.getboolean('main-window','statusbar-visible')
		self._mainwin.theme = self._parser.get('main-window','theme-name')
		self._mainwin.maximized = self._parser.getboolean('main-window','start-maximized')

	def spectrogram(self):
		return self._spect

	def mainwin(self):
		return self._mainwin

# SPECTROGRAM
# window (int number of samples)
#    window length of fft in number of samples (powers of 2 are best)
# overlap (int number of samples)
#    overlap between adjacent windows
# window-function (string)
#    available functions: boxcar triang blackman hamming hann bartlett
#    flattop parzen bohman blackmanharris nuttall barthann
# high-pass / low-pass (int Hz)
#    signal outside this pseudo-bandpass filter are dropped from
#    analysis
# threshold (in dB)
#    signals more than threshold dB below the peak of the recording are
#    dropped
# log10-freq (bool)
#    whether frequency values should be log10 transformed prior to the
#    calculation of frequency excursion (see ...)
# invert-colors (bool)
#    display white-on-black spectrogram
# border-color, line-color (color)
#    colors of spectrogram window border and excursion line overlay see
#    "COLORS" below for options
# ration (float)
#    ... (name to change soon)
[spectrogram]
window = 256
overlap = 192
window-function = hamming
high-pass = 1250
low-pass = 10000
threshold = 14
log10-freq = false
invert-colors = false
border-color = dimgrey
line-color = royalblue
ratio = 8

# MAIN-WINDOW
# menu-visible, toolbar-visible, statusbar-visible (bool)
#   whether these ui elements should be displayed
# mac-native-menu (bool)
#   osx only: use osx-style integrated menu (not implemented yet)
# toolbar-position (?)
#   not implemented yet
# toolbar-style (int)
#   ...
# theme-name (str)
#   ...
[main-window]
menubar-visible = true
mac-native-menu = false
toolbar-visible = true
toolbar-position = top
statusbar-visible = true
toolbar-style = %(QToolButton-FollowStyle)s
theme-name = oxygen
start-maximized = false

# COLORS
# All colors are specified as a string as one of the following:
# 1) hex digits:
#   #RGB (each of R, G, and B is a single hex digit)
#   #RRGGBB
#   #AARRGGBB
#   #RRRGGGBBB
#   #RRRRGGGGBBBB
# 2) An svg color name
#   (see https://www.w3.org/TR/SVG/types.html#ColorKeywords)
# 3) A Qt Color role variable (see VARIABLES below)

# VARIABLES
# This file uses pythons ConfigParser string interpolation.  Any setting
# can include the value of another setting as "%(NAME)s".  The following
# variables are set to the Qt defaults prior to this file being parsed
# and can be used as desired:
#   QPalette-Window
#   QPalette-Background
#   QPalette-WindowText
#   QPalette-Foreground
#   QPalette-Base
#   QPalette-AlternateBase
#   QPalette-ToolTipBase
#   QPalette-ToolTipText
#   QPalette-Text
#   QPalette-Button
#   QPalette-ButtonText
#   QPalette-BrightText
#   QToolButton-IconOnly
#   QToolButton-TextOnly
#   QToolButton-TextBesideIcon
#   QToolButton-TextUnderIcon
#   QToolButton-FollowStyle

#from numpy import *
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *

from spectrogram import Spectrogram
import time

class MainWin(QMainWindow):
	def __init__(self, config):
		super().__init__()
		self.fnames = [ '/home/jmcclure/data/warb/batch4/4/4355.wav' ]
		self.conf = config.mainwin()
		self.spect_conf = config.spectrogram()
		self.init_actions()
		self.init_menubar()
		self.init_toolbar()
		self.init_statusbar()
		self.init_body(config.spectrogram())
		self.setGeometry(0, 0, 800, 600)
		self.setWindowTitle("Fex: Frequency Excursion Calculator")
		self.setWindowIcon(QIcon('web.png'))	# TODO
		if self.conf.maximized:
			self.setWindowState(Qt.WindowMaximized)
		self.show()
		QTimer.singleShot(20,self.next_spectrogram)

	# Todo handle drag & drop of sound files

	def update_status_fex(self, pex, tex):
		self.pex = pex
		self.tex = tex
		self.fex = pex / tex

	def update_status_text(self, x, y):
		self.status_text.setText("FEX: %.3f   %0.3fs %0.1fKHz" %(self.fex,x,y))

	def init_body(self, config):
		self.body = QWidget()
		self.body.setBackgroundRole(QPalette.AlternateBase)
		self.body.setAutoFillBackground(True)
		self.body.setContentsMargins(10,10,10,10)
		self.setCentralWidget(self.body)
		self.body.show()

	def next_spectrogram(self):
		if len(self.fnames) > 0:
			self.fname = self.fnames.pop(0)
		self.spect = Spectrogram(self.fname, self.body, self.spect_conf)
		self.spect.fexChanged.connect(self.update_status_fex)
		self.spect.mouseOver.connect(self.update_status_text)

	def init_actions(self):
		# https://specifications.freedesktop.org/icon-naming-spec/icon-naming-spec-latest.html
		QIcon.setThemeName(self.conf.theme)
		# TODO icons are left out until I've identified a decent set

		#self.aQuit = QAction(QIcon.fromTheme('application-exit'), '&Quit', self)
		self.aQuit = QAction('&Quit', self)
		self.aQuit.setShortcut('Ctrl+Q')
		self.aQuit.setStatusTip('Quit Fex')
		self.aQuit.triggered.connect(qApp.quit)

		self.aNormal = QAction('&Normal', self)
		self.aNormal.setShortcut('Ctrl+X')
		self.aNormal.setStatusTip('Set Normal Mode')
		self.aNormal.triggered.connect(lambda: self.spect.mode_normal())

		self.aCursor = QAction('Cursor', self)
		self.aCursor.setShortcut('Ctrl+C')
		self.aCursor.setStatusTip('Enable Cursor Tool')
		self.aCursor.triggered.connect(lambda: self.spect.mode_cursor())

		self.aErase = QAction('Erase', self)
		self.aErase.setShortcut('Ctrl+E')
		self.aErase.setStatusTip('Eraser Tool To Remove Noise')
		self.aErase.triggered.connect(lambda: self.spect.mode_erase())

		self.aZoom = QAction(QIcon.fromTheme('zoom-original'), '&Normal', self)
		self.aZoom.setShortcut('Ctrl+0')
		self.aZoom.setStatusTip('Fit Window')
		self.aZoom.triggered.connect(lambda: self.spect.mode_normal())

	def init_menubar(self):
		self.menubar = self.menuBar()
		self.menubar.setVisible(self.conf.menubar)
		fileMenu = self.menubar.addMenu('&File')
		fileMenu.addAction(self.aQuit)
		fileTools = self.menubar.addMenu('&Tools')
		fileTools.addAction(self.aNormal)
		fileTools.addAction(self.aCursor)
		fileTools.addAction(self.aErase)

	def init_toolbar(self):
		self.toolbar = self.addToolBar('ToolBar1')
		self.toolbar.setVisible(self.conf.toolbar)
		self.toolbar.setToolButtonStyle(self.conf.toolbarstyle)
		self.toolbar.addAction(self.aQuit)
		self.toolbar.addSeparator()
		self.toolbar.addAction(self.aNormal)
		self.toolbar.addAction(self.aCursor)
		self.toolbar.addAction(self.aErase)
		self.toolbar.addSeparator()
		self.toolbar.addAction(self.aZoom)

	def init_statusbar(self):
		self.statusbar = self.statusBar()
		self.status_text = QLabel()
		self.statusBar().addPermanentWidget(self.status_text)
		# TODO add song count a/b

import wave
from numpy import *
from scipy.signal import spectrogram
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *

class Spectrogram(QWidget):

	fexChanged = pyqtSignal(float, float)
	mouseOver = pyqtSignal(float, float)

	def __init__(self, fname, parent, config):
		super().__init__(parent)
		self.conf = config
		self.fname = fname
		self.setMouseTracking(True)
		self.setGeometry(parent.contentsRect())
		oldPos = QPoint()
		with wave.open(fname, 'rb') as song:
			channels, bs, samprate, nsamp, comp, compnam  = song.getparams()
			# TODO checks
			data = fromstring(song.readframes(nsamp), dtype=uint16)
		f, t, amp = spectrogram(data, samprate, config.winfunc, config.window,
				config.overlap, detrend=False, mode = 'psd',
				return_onesided=True)
		# pseudo-bandpass filter
		bot = argmax(f > config.hipass)
		top = argmin(f < config.lopass)
		f = f[bot:top]
		amp = amp[bot:top,:]

		thresh = amp.max() / 10**(config.threshold / 10.0)
		thresh = 255.0 - thresh * 255.0 / amp.max()
		config.threshold = thresh
		amp = 255.0 - amp * 255.0 / amp.max()
		print("Avg pts per time bin = %s" %(sum(amp < thresh) / len(t)))

		f /= 1000.0
		# create image
		# TODO only grab inside bandpass
		amp = flipud(amp)
		self.imgdata = array(amp, uint8)
		self.freq = flipud(f)
		self.time = t
		h, w = self.imgdata.shape

		self.image = QImage(self.imgdata.tobytes(), w, h, w, QImage.Format_Grayscale8)
		if self.conf.invert:
			self.image.invertPixels()
		self.fit()
		self.eraser = self.create_eraser(50, 150)
		self.cursorX = self.create_cursor(1, self.height() * 4)
		self.cursorY = self.create_cursor(self.width() * 4, 1)
		self.cursorX.hide()
		self.cursorY.hide()
		self.eraser.hide()
		self.show()

	def create_eraser(self, w, h):
		eraser = QWidget(self)
		eraser.setAttribute(Qt.WA_TransparentForMouseEvents)
		effect = QGraphicsOpacityEffect(eraser)
		effect.setOpacity(0.4)
		eraser.setGraphicsEffect(effect)
		eraser.setGeometry(0, 0, w, h)
		eraser.setAutoFillBackground(True)
		p = eraser.palette()
		p.setColor(eraser.backgroundRole(), Qt.yellow)
		eraser.setPalette(p)
		return eraser

	def mode_normal(self):
		self.unsetCursor()
		self.eraser.hide()
		self.cursorX.hide()
		self.cursorY.hide()

	def mode_cursor(self):
		self.setCursor(Qt.BlankCursor)
		self.eraser.hide()
		self.cursorX.show()
		self.cursorY.show()

	def mode_erase(self):
		self.setCursor(Qt.BlankCursor)
		self.cursorX.hide()
		self.cursorY.hide()
		self.eraser.show()

	def create_cursor(self, w, h):
		cursor = QWidget(self)
		cursor.setAttribute(Qt.WA_TransparentForMouseEvents)
		effect = QGraphicsOpacityEffect(cursor)
		effect.setOpacity(0.4)
		cursor.setGraphicsEffect(effect)
		cursor.setGeometry(0, 0, w, h)
		cursor.setAutoFillBackground(True)
		p = cursor.palette()
		p.setColor(cursor.backgroundRole(), Qt.red)
		cursor.setPalette(p)
		return cursor

	def paintEvent(self, e):
		qp = QPainter()
		qp.begin(self)
		qp.setRenderHint(QPainter.SmoothPixmapTransform)
		qp.drawImage(self.contentsRect(), self.image, self.image.rect())
		r = QRect(0, 0, self.width() - 1, self.height() - 1)
		qp.setPen(QColor(self.conf.border))
		qp.drawRect(r)
		path = QPainterPath()
		pfreq = 0.0
		ptime = 0.0
		pex = 0.0
		tex = 0.0
		qp.setPen(QColor(self.conf.line))
		for x, y in enumerate(argmin(self.imgdata, 0)):
			if self.imgdata[y,x] > self.conf.threshold:
				continue
			t = self.time[x]
			f = self.freq[y]	# TODO log10?
			if pfreq == 0.0:
				path.moveTo(x * self.sx, y * self.sy)
			else:
				path.lineTo(x * self.sx, y * self.sy)
				pex += sqrt((f - pfreq)**2 + (t - ptime)**2)
				tex += t - ptime
			ptime = t
			pfreq = f
		qp.drawPath(path)
		qp.end()
		self.fexChanged.emit(pex, tex)

	def fit(self):
		s = self.image.size()
		asp = s.width() / (s.height() * self.conf.ratio)
		if self.size().height() * asp > self.size().width():
			self.resize(self.width(), self.width() / asp)
		else:
			self.resize(self.height() * asp, self.height())

	def resizeEvent(self, e):
		self.sx = self.width() / self.image.width()
		self.sy = self.height() / self.image.height()

	def mousePressEvent(self, e):
		self.__pos = self.pos()
		self.__size = self.size()
		self.__epos = self.mapToParent(e.pos())
		if e.button() == Qt.MiddleButton:
			self.fit()

	def mouseMoveEvent(self, e):
		x = e.pos().x() - self.eraser.width() / 2.0
		y = e.pos().y() - self.eraser.height() / 2.0
		self.eraser.move(x, y)
		x = e.pos().x()
		y = e.pos().y()
		self.cursorX.move(x, 0)
		self.cursorY.move(0, y)
		s = self.imgdata.shape
		x = clip(int(s[1] * e.pos().x() / self.width()), 0, self.time.size)
		y = clip(int(s[0] * e.pos().y() / self.height()), 0, self.freq.size)
		self.mouseOver.emit(self.time[x], self.time[y])
		if e.buttons() and self.cursorX.isVisible():
			self.mouseCursorEvent(e)
		elif e.buttons() and self.eraser.isVisible():
			self.mouseEraseEvent(e)
		elif e.buttons():
			self.mouseNormalEvent(e)

	def mouseCursorEvent(self, e):
		pass

	def mouseEraseEvent(self, e):
		pass

	def mouseNormalEvent(self, e):
		if e.buttons() == Qt.LeftButton:
			diff = self.mapToParent(e.pos()) - self.__epos + self.__pos
			self.move(diff)
		elif e.buttons() == Qt.RightButton:
			diff = self.mapToParent(e.pos()) - self.__epos
			w = self.__size.width() + diff.x()
			h = self.__size.height() + diff.y()
			self.resize(w, h)

	def mouseReleaseEvent(self, e):
		self.cursorX.resize(1, self.height() * 4)
		self.cursorY.resize(self.width() * 4, 1)

from setuptools import setup

def readme():
	with open('README.md') as f:
		return f.read()

setup(name='fexqt',
	version='0.1a',
	description='Frequency Excursion Calculator',
	long_description=readme(),
	classifiers=[
		'Development Status :: 3 - Alpha',
		'License :: OSI Approved :: MIT License',
		'Intended Audience :: Science/Research',
		'Programming Language :: Python :: 3',
		'Topic :: Multimedia :: Sound/Audio :: Analysis',
		'Topic :: Scientific/Engineering :: Visualization'
	],
	url='http://jessemcclure.org',
	author='Jesse McClure',
	author_email='jmcclure@broadinstitute.org',
	license='MIT',
	packages=['fexqt'],
	install_requires=['PyQt5','scipy'],
	scripts=['bin/fex'],
	include_package_data=True,
	zip_safe=False)