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DialogsTraining.py
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# This is part of the AviaNZ interface
# Holds most of the code for the various dialog boxes
# Version 2.0 18/11/19
# Authors: Stephen Marsland, Nirosha Priyadarshani, Julius Juodakis
# AviaNZ bioacoustic analysis program
# Copyright (C) 2017--2019
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Dialogs used for filter training / testing.
# These are relatively complicated wizards which also do file I/O
import os
import time
import platform
import copy
from shutil import copyfile
from PyQt5.QtGui import QIcon, QValidator, QAbstractItemView, QPixmap, QColor, QFileDialog, QScrollArea
from PyQt5.QtCore import QDir, Qt, QEvent, QSize
from PyQt5.QtWidgets import QLabel, QSlider, QPushButton, QListWidget, QListWidgetItem, QComboBox, QWizard, QWizardPage, QLineEdit, QTextEdit, QSizePolicy, QFormLayout, QVBoxLayout, QHBoxLayout, QCheckBox, QLayout, QApplication, QRadioButton, QGridLayout
import matplotlib.markers as mks
import matplotlib.pyplot as plt
import matplotlib.ticker as mtick
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import pyqtgraph as pg
import numpy as np
import colourMaps
import SupportClasses, SupportClasses_GUI
import SignalProc
import WaveletSegment
import Segment
import Clustering
import Training
class BuildRecAdvWizard(QWizard):
# page 1 - select training data
class WPageData(QWizardPage):
def __init__(self, config, parent=None):
super(BuildRecAdvWizard.WPageData, self).__init__(parent)
self.setTitle('Training data')
self.setSubTitle('To start training, you need labelled calls from your species as training data (see the manual). Select the folder where this data is located. Then select the species.')
self.setMinimumSize(600, 150)
self.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.adjustSize()
self.trainDirName = QLineEdit()
self.trainDirName.setReadOnly(True)
self.btnBrowse = QPushButton('Browse')
self.btnBrowse.clicked.connect(self.browseTrainData)
colourNone = QColor(config['ColourNone'][0], config['ColourNone'][1], config['ColourNone'][2], config['ColourNone'][3])
colourPossibleDark = QColor(config['ColourPossible'][0], config['ColourPossible'][1], config['ColourPossible'][2], 255)
colourNamed = QColor(config['ColourNamed'][0], config['ColourNamed'][1], config['ColourNamed'][2], config['ColourNamed'][3])
self.listFiles = SupportClasses_GUI.LightedFileList(colourNone, colourPossibleDark, colourNamed)
self.listFiles.setMinimumWidth(150)
self.listFiles.setMinimumHeight(225)
self.listFiles.setSelectionMode(QAbstractItemView.NoSelection)
selectSpLabel = QLabel("Choose the species for which you want to build the recogniser")
self.species = QComboBox() # fill during browse
self.species.addItems(['Choose species...'])
space = QLabel()
space.setFixedHeight(20)
# SampleRate parameter
self.fs = QSlider(Qt.Horizontal)
self.fs.setTickPosition(QSlider.TicksBelow)
self.fs.setTickInterval(2000)
self.fs.setRange(0, 32000)
self.fs.setValue(0)
self.fs.valueChanged.connect(self.fsChange)
self.fstext = QLabel('')
form1 = QFormLayout()
form1.addRow('', self.fstext)
form1.addRow('Preferred sampling rate (Hz)', self.fs)
# training page layout
layout1 = QHBoxLayout()
layout1.addWidget(self.trainDirName)
layout1.addWidget(self.btnBrowse)
layout = QVBoxLayout()
layout.addWidget(space)
layout.addLayout(layout1)
layout.addWidget(self.listFiles)
layout.addWidget(space)
layout.addWidget(selectSpLabel)
layout.addWidget(self.species)
layout.addLayout(form1)
layout.setAlignment(Qt.AlignVCenter)
self.setLayout(layout)
def browseTrainData(self):
trainDir = QFileDialog.getExistingDirectory(self, 'Choose folder for training')
self.trainDirName.setText(trainDir)
self.fillFileList(trainDir)
def fsChange(self, value):
value = value // 4000 * 4000
if value < 4000:
value = 4000
self.fstext.setText(str(value))
def fillFileList(self, dirName):
""" Generates the list of files for a file listbox. """
if not os.path.isdir(dirName):
print("Warning: directory doesn't exist")
return
self.listFiles.fill(dirName, fileName=None, readFmt=True, addWavNum=True, recursive=True)
# while reading the file, we also collected a list of species present there
spList = list(self.listFiles.spList)
# and sample rate info
fs = list(self.listFiles.fsList)
if len(fs)==0:
print("Warning: no suitable files found")
return
# might need better limits on selectable sample rate here
self.fs.setValue(int(np.min(fs)))
self.fs.setRange(4000, int(np.max(fs)))
self.fs.setSingleStep(4000)
self.fs.setTickInterval(4000)
spList.insert(0, 'Choose species...')
self.species.clear()
self.species.addItems(spList)
if len(spList)==2:
self.species.setCurrentIndex(1)
# page 2 - precluster
class WPagePrecluster(QWizardPage):
def __init__(self, parent=None):
super(BuildRecAdvWizard.WPagePrecluster, self).__init__(parent)
self.setTitle('Confirm data input')
self.setSubTitle('When ready, press \"Cluster\" to start clustering. The process may take a long time.')
self.setMinimumSize(250, 150)
self.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.adjustSize()
revtop = QLabel("The following parameters were set:")
self.params = QLabel("")
self.params.setStyleSheet("QLabel { color : #808080; }")
self.warnLabel = QLabel("")
self.warnLabel.setStyleSheet("QLabel { color : #800000; }")
layout2 = QVBoxLayout()
layout2.addWidget(revtop)
layout2.addWidget(self.params)
layout2.addWidget(self.warnLabel)
self.setLayout(layout2)
self.setButtonText(QWizard.NextButton, 'Cluster >')
def initializePage(self):
self.wizard().button(QWizard.NextButton).setDefault(False)
self.wizard().saveTestBtn.setVisible(False)
# parse some params
fs = int(self.field("fs"))//4000*4000
if fs not in [8000, 16000, 24000, 32000, 36000, 48000]:
self.warnLabel.setText("Warning: unusual sampling rate selected, make sure it is intended.")
else:
self.warnLabel.setText("")
self.params.setText("Species: %s\nTraining data: %s\nSampling rate: %d Hz\n" % (self.field("species"), self.field("trainDir"), fs))
# page 3 - calculate and adjust clusters
class WPageCluster(QWizardPage):
def __init__(self, config, parent=None):
super(BuildRecAdvWizard.WPageCluster, self).__init__(parent)
self.setTitle('Cluster similar looking calls')
self.setSubTitle('AviaNZ has tried to identify similar calls in your dataset. Please check the output, and move calls as appropriate.')
# start larger than minimumSize, but not bigger than the screen:
screenresol = QApplication.primaryScreen().availableSize()
self.manualSizeHint = QSize(min(800, 0.9*screenresol.width()), min(600, 0.9*screenresol.height()))
self.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding)
self.adjustSize()
instr = QLabel("To move one call, just drag it with the mouse. To move more, click on them so they are marked with a tick and drag any of them. To merge two types, select all of one group by clicking the empty box next to the name, and then drag any of them. You might also want to name each type of call.")
instr.setWordWrap(True)
self.sampleRate = 0
self.segments = []
self.clusters = {}
self.clustercentres = {}
self.duration = 0
self.feature = 'we'
self.picbuttons = []
self.cboxes = []
self.tboxes = []
self.nclasses = 0
self.config = config
self.segsChanged = False
self.hasCTannotations = True
self.lblSpecies = QLabel()
self.lblSpecies.setStyleSheet("QLabel { color : #808080; }")
# Volume control
self.volSlider = QSlider(Qt.Horizontal)
self.volSlider.valueChanged.connect(self.volSliderMoved)
self.volSlider.setRange(0, 100)
self.volSlider.setValue(50)
volIcon = QLabel()
volIcon.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
volIcon.setPixmap(QPixmap('img/volume.png').scaled(18, 18, transformMode=1))
# Brightness, and contrast sliders
labelBr = QLabel()
labelBr.setPixmap(QPixmap('img/brightstr24.png').scaled(18, 18, transformMode=1))
labelBr.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
self.brightnessSlider = QSlider(Qt.Horizontal)
self.brightnessSlider.setMinimum(0)
self.brightnessSlider.setMaximum(100)
self.brightnessSlider.setValue(20)
self.brightnessSlider.setTickInterval(1)
self.brightnessSlider.valueChanged.connect(self.setColourLevels)
labelCo = QLabel()
labelCo.setPixmap(QPixmap('img/contrstr24.png').scaled(18, 18, transformMode=1))
labelCo.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
self.contrastSlider = QSlider(Qt.Horizontal)
self.contrastSlider.setMinimum(0)
self.contrastSlider.setMaximum(100)
self.contrastSlider.setValue(20)
self.contrastSlider.setTickInterval(1)
self.contrastSlider.valueChanged.connect(self.setColourLevels)
self.btnCreateNewCluster = QPushButton('Create cluster')
self.btnCreateNewCluster.setFixedWidth(150)
self.btnCreateNewCluster.clicked.connect(self.createNewcluster)
self.btnDeleteSeg = QPushButton('Remove selected segment/s')
self.btnDeleteSeg.setFixedWidth(200)
self.btnDeleteSeg.clicked.connect(self.deleteSelectedSegs)
# page 3 layout
layout1 = QVBoxLayout()
layout1.addWidget(instr)
layout1.addWidget(self.lblSpecies)
hboxSpecContr = QHBoxLayout()
hboxSpecContr.addWidget(volIcon)
hboxSpecContr.addWidget(self.volSlider)
hboxSpecContr.addWidget(labelBr)
hboxSpecContr.addWidget(self.brightnessSlider)
hboxSpecContr.addWidget(labelCo)
hboxSpecContr.addWidget(self.contrastSlider)
hboxSpecContr.setContentsMargins(20, 0, 20, 10)
hboxSpecContr.setStretch(0, 1)
hboxSpecContr.setStretch(1, 3)
hboxSpecContr.setStretch(2, 1)
hboxSpecContr.setStretch(3, 3)
hboxSpecContr.setStretch(4, 1)
hboxSpecContr.setStretch(5, 3)
hboxSpecContr.addStretch(2)
hboxBtns2 = QHBoxLayout()
hboxBtns2.addWidget(self.btnCreateNewCluster)
hboxBtns2.addWidget(self.btnDeleteSeg)
hboxBtns2.setAlignment(Qt.AlignRight | Qt.AlignVCenter)
hboxBtns = QHBoxLayout()
hboxBtns.addLayout(hboxBtns2)
# top part
vboxTop = QVBoxLayout()
vboxTop.addLayout(hboxSpecContr)
vboxTop.addLayout(hboxBtns)
# set up the images
self.flowLayout = SupportClasses_GUI.Layout()
self.flowLayout.setMinimumSize(380, 247)
self.flowLayout.buttonDragged.connect(self.moveSelectedSegs)
self.flowLayout.layout.setSizeConstraint(QLayout.SetMinimumSize)
self.scrollArea = QScrollArea(self)
#self.scrollArea.setWidgetResizable(True)
self.scrollArea.setWidget(self.flowLayout)
self.scrollArea.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding)
# set overall layout of the dialog
self.vboxFull = QVBoxLayout()
self.vboxFull.addLayout(layout1)
self.vboxFull.addLayout(vboxTop)
self.vboxFull.addWidget(self.scrollArea)
self.setLayout(self.vboxFull)
def initializePage(self):
self.wizard().saveTestBtn.setVisible(False)
# parse field shared by all subfilters
fs = int(self.field("fs"))//4000*4000
self.wizard().speciesData = {"species": self.field("species"), "SampleRate": fs, "Filters": []}
with pg.BusyCursor():
print("Processing. Please wait...")
# Check if the annotations come with call type labels, if so skip auto clustering
self.CTannotations()
if self.hasCTannotations:
# self.segments: [parent_audio_file, [segment], class_label]
self.segments, self.nclasses, self.duration = self.getClustersGT()
self.setSubTitle('AviaNZ found call type annotations in your dataset. You can still make corrections by moving calls as appropriate.')
else:
# return format:
# self.segments: [parent_audio_file, [segment], [syllables], [features], class_label]
# fs: sampling freq
# self.nclasses: number of class_labels
# duration: median length of segments
self.cluster = Clustering.Clustering([], [], 5)
self.segments, _, self.nclasses, self.duration = self.cluster.cluster(self.field("trainDir"), self.field("species"), feature=self.feature)
# segments format: [[file1, seg1, [syl1, syl2], [features1, features2], predict], ...]
# self.segments, fs, self.nclasses, self.duration = self.cluster.cluster_by_dist(self.field("trainDir"),
# self.field("species"),
# feature=self.feature,
# max_clusters=5,
# single=True)
self.setSubTitle('AviaNZ has tried to identify similar calls in your dataset. Please check the output, and move calls as appropriate.')
# Create and show the buttons
self.clearButtons()
self.addButtons()
self.updateButtons()
print("buttons added")
self.segsChanged = True
self.completeChanged.emit()
def isComplete(self):
# empty cluster names?
if len(self.clusters)==0:
return False
# duplicate cluster names aren't updated:
for ID in range(self.nclasses):
if self.clusters[ID] != self.tboxes[ID].text():
return False
# no segments at all?
if len(self.segments)==0:
return False
# if all good, then check if we need to redo the pages.
# segsChanged should be updated by any user changes!
if self.segsChanged:
self.segsChanged = False
self.wizard().redoTrainPages()
return True
def validatePage(self):
self.updateAnnotations()
return True
def cleanupPage(self):
self.clusters = {}
def CTannotations(self):
""" Check if all the segments from target species has call type annotations"""
self.hasCTannotations = True
listOfDataFiles = QDir(self.field("trainDir")).entryList(['*.data'])
for file in listOfDataFiles:
# Read the annotation
segments = Segment.SegmentList()
segments.parseJSON(os.path.join(self.field("trainDir"), file))
SpSegs = segments.getSpecies(self.field("species"))
for segix in SpSegs:
seg = segments[segix]
for label in seg[4]:
if label["species"] == self.field("species") and "calltype" not in label:
self.hasCTannotations = False
break
def getClustersGT(self):
""" Get call type clusters from annotations
:returns
[parent_audio_file, [segment], [syllables], [features], class_label]
# fs: sampling freq
# self.nclasses: number of class_labels
# duration: median length of segments
call types
"""
ctTexts = []
CTsegments = []
duration = []
listOfDataFiles = QDir(self.field("trainDir")).entryList(['*.data'])
listOfWavFiles = QDir(self.field("trainDir")).entryList(['*.wav'])
for file in listOfDataFiles:
if file[:-5] in listOfWavFiles:
# Read the annotation
segments = Segment.SegmentList()
segments.parseJSON(os.path.join(self.field("trainDir"), file))
SpSegs = segments.getSpecies(self.field("species"))
for segix in SpSegs:
seg = segments[segix]
for label in seg[4]:
if label["species"] == self.field("species") and "calltype" in label:
if label["calltype"] not in ctTexts:
ctTexts.append(label["calltype"])
for i in range(len(ctTexts)):
self.clusters[i] = ctTexts[i]
for file in listOfDataFiles:
if file[:-5] in listOfWavFiles:
# Read the annotation
segments = Segment.SegmentList()
wavfile = os.path.join(self.field("trainDir"), file[:-5])
segments.parseJSON(os.path.join(self.field("trainDir"), file))
SpSegs = segments.getSpecies(self.field("species"))
for segix in SpSegs:
seg = segments[segix]
for label in seg[4]:
if label["species"] == self.field("species") and "calltype" in label:
CTsegments.append([wavfile, seg, list(self.clusters.keys())[list(self.clusters.values()).index(label["calltype"])]])
duration.append(seg[1]-seg[0])
return CTsegments, len(self.clusters), np.median(duration)
def backupDatafiles(self):
# Let's backup original data fiels before updating them
print("Backing up files ", self.field("trainDir"))
listOfDataFiles = QDir(self.field("trainDir")).entryList(['*.data'])
for file in listOfDataFiles:
source = self.field("trainDir") + '/' + file
destination = source[:-5] + ".backup"
if os.path.isfile(destination):
pass
else:
copyfile(source, destination)
def updateAnnotations(self):
""" Update annotation files. Assign call types suggested by clusters and remove any segment deleted in the
clustering. Keep a backup of the original .data."""
self.backupDatafiles()
print("Updating annotation files ", self.field("trainDir"))
listOfDataFiles = QDir(self.field("trainDir")).entryList(['*.data'])
for file in listOfDataFiles:
# Read the annotation
segments = Segment.SegmentList()
newsegments = Segment.SegmentList()
segments.parseJSON(os.path.join(self.field("trainDir"), file))
allSpSegs = np.arange(len(segments)).tolist()
newsegments.metadata = segments.metadata
for segix in allSpSegs:
seg = segments[segix]
if self.field("species") not in [fil["species"] for fil in seg[4]]:
newsegments.addSegment(seg) # leave non-target segments unchanged
else:
for seg2 in self.segments:
if seg2[1] == seg:
# find the index of target sp and update call type
seg[4][[fil["species"] for fil in seg[4]].index(self.field("species"))]["calltype"] = self.clusters[seg2[-1]]
newsegments.addSegment(seg)
newsegments.saveJSON(os.path.join(self.field("trainDir"), file))
def merge(self):
""" Listener for the merge button. Merge the rows (clusters) checked into one cluster.
"""
# Find which clusters/rows to merge
self.segsChanged = True
tomerge = []
i = 0
for cbox in self.cboxes:
if cbox.checkState() != 0:
tomerge.append(i)
i += 1
print('rows/clusters to merge are:', tomerge)
if len(tomerge) < 2:
return
# Generate new class labels
nclasses = self.nclasses - len(tomerge) + 1
max_label = nclasses - 1
labels = []
c = self.nclasses - 1
while c > -1:
if c in tomerge:
labels.append((c, 0))
else:
labels.append((c, max_label))
max_label -= 1
c -= 1
# print('[old, new] labels')
labels = dict(labels)
# print(labels)
keys = [i for i in range(self.nclasses) if i not in tomerge] # the old keys those didn't merge
# print('old keys left: ', keys)
# update clusters dictionary {ID: cluster_name}
clusters = {0: self.clusters[tomerge[0]]}
for i in keys:
clusters.update({labels[i]: self.clusters[i]})
print('before update: ', self.clusters)
self.clusters = clusters
print('after update: ', self.clusters)
self.nclasses = nclasses
# update the segments
for seg in self.segments:
seg[-1] = labels[seg[-1]]
# update the cluster combobox
#self.cmbUpdateSeg.clear()
#for x in self.clusters:
#self.cmbUpdateSeg.addItem(self.clusters[x])
# Clean and redraw
self.clearButtons()
self.updateButtons()
self.completeChanged.emit()
def moveSelectedSegs(self,dragPosy,source):
""" Listener for Apply button to move the selected segments to another cluster.
Change the cluster ID of those selected buttons and redraw all the clusters.
"""
# TODO: check: I think the dict is always in descending order down screen?
self.segsChanged = True
# The first line seemed neater, but the verticalSpacing() doesn't update when you rescale the window
#movetoID = dragPosy//(self.picbuttons[0].size().height()+self.flowLayout.layout.verticalSpacing())
movetoID = dragPosy//(self.flowLayout.layout.geometry().height()//self.nclasses)
# drags which start and end in the same cluster most likely were just long clicks:
for ix in range(len(self.picbuttons)):
if self.picbuttons[ix] == source:
if self.segments[ix][-1] == movetoID:
source.clicked.emit()
return
# Even if the button that was dragged isn't highlighted, make it so
source.mark = 'yellow'
for ix in range(len(self.picbuttons)):
if self.picbuttons[ix].mark == 'yellow':
self.segments[ix][-1] = movetoID
self.picbuttons[ix].mark = 'green'
# update self.clusters, delete clusters with no members
todelete = []
for ID, label in self.clusters.items():
empty = True
for seg in self.segments:
if seg[-1] == ID:
empty = False
break
if empty:
todelete.append(ID)
self.clearButtons()
# Generate new class labels
if len(todelete) > 0:
keys = [i for i in range(self.nclasses) if i not in todelete] # the old keys those didn't delete
# print('old keys left: ', keys)
nclasses = self.nclasses - len(todelete)
max_label = nclasses - 1
labels = []
c = self.nclasses - 1
while c > -1:
if c in keys:
labels.append((c, max_label))
max_label -= 1
c -= 1
# print('[old, new] labels')
labels = dict(labels)
print(labels)
# update clusters dictionary {ID: cluster_name}
clusters = {}
for i in keys:
clusters.update({labels[i]: self.clusters[i]})
print('before move: ', self.clusters)
self.clusters = clusters
print('after move: ', self.clusters)
# update the segments
for seg in self.segments:
seg[-1] = labels[seg[-1]]
self.nclasses = nclasses
# redraw the buttons
self.updateButtons()
self.updateClusterNames()
self.completeChanged.emit()
def createNewcluster(self):
""" Listener for Create cluster button to move the selected segments to a new cluster.
Change the cluster ID of those selected buttons and redraw all the clusters.
"""
self.segsChanged = True
# There should be at least one segment selected to proceed
proceed = False
for ix in range(len(self.picbuttons)):
if self.picbuttons[ix].mark == 'yellow':
proceed = True
break
if proceed:
# User to enter new cluster name
#newLabel, ok = QInputDialog.getText(self, 'Cluster name', 'Enter unique Cluster Name\t\t\t')
#if not ok:
#self.completeChanged.emit()
#return
names = [self.tboxes[ID].text() for ID in range(self.nclasses)]
nextNumber = 0
newLabel = 'Cluster_'+str(nextNumber)
names.append(newLabel)
while len(names) != len(set(names)):
del(names[-1])
nextNumber += 1
newLabel = 'Cluster_'+str(nextNumber)
names.append(newLabel)
# create new cluster ID, label
newID = len(self.clusters)
self.clusters[newID] = newLabel
self.nclasses += 1
print('after adding new cluster: ', self.clusters)
for ix in range(len(self.picbuttons)):
if self.picbuttons[ix].mark == 'yellow':
self.segments[ix][-1] = newID
self.picbuttons[ix].mark = 'green'
# Delete clusters with no members left and update self.clusters before adding the new cluster
todelete = []
for ID, label in self.clusters.items():
empty = True
for seg in self.segments:
if seg[-1] == ID:
empty = False
break
if empty:
todelete.append(ID)
# Generate new class labels
if len(todelete) > 0:
keys = [i for i in range(self.nclasses) if i not in todelete] # the old keys those didn't delete
# print('old keys left: ', keys)
nclasses = self.nclasses - len(todelete)
max_label = nclasses - 1
labels = []
c = self.nclasses - 1
while c > -1:
if c in keys:
labels.append((c, max_label))
max_label -= 1
c -= 1
# print('[old, new] labels')
labels = dict(labels)
print(labels)
# update clusters dictionary {ID: cluster_name}
clusters = {}
for i in keys:
clusters.update({labels[i]: self.clusters[i]})
print('before: ', self.clusters)
self.clusters = clusters
self.nclasses = nclasses
print('after: ', self.clusters)
# update the segments
for seg in self.segments:
seg[-1] = labels[seg[-1]]
# redraw the buttons
self.clearButtons()
self.updateButtons()
#self.cmbUpdateSeg.addItem(newLabel)
self.completeChanged.emit()
else:
msg = SupportClasses_GUI.MessagePopup("t", "Select", "Select calls to make the new cluster")
msg.exec_()
self.completeChanged.emit()
return
def deleteSelectedSegs(self):
""" Listener for Delete button to delete the selected segments completely.
"""
inds = []
for ix in range(len(self.picbuttons)):
if self.picbuttons[ix].mark == 'yellow':
inds.append(ix)
if len(inds)==0:
print("No segments selected")
return
self.segsChanged = True
for ix in reversed(inds):
del self.segments[ix]
del self.picbuttons[ix]
# update self.clusters, delete clusters with no members
todelete = []
for ID, label in self.clusters.items():
empty = True
for seg in self.segments:
if seg[-1] == ID:
empty = False
break
if empty:
todelete.append(ID)
self.clearButtons()
# Generate new class labels
if len(todelete) > 0:
keys = [i for i in range(self.nclasses) if i not in todelete] # the old keys those didn't delete
# print('old keys left: ', keys)
nclasses = self.nclasses - len(todelete)
max_label = nclasses - 1
labels = []
c = self.nclasses - 1
while c > -1:
if c in keys:
labels.append((c, max_label))
max_label -= 1
c -= 1
labels = dict(labels)
# print(labels)
# update clusters dictionary {ID: cluster_name}
clusters = {}
for i in keys:
clusters.update({labels[i]: self.clusters[i]})
print('before delete: ', self.clusters)
self.clusters = clusters
print('after delete: ', self.clusters)
# update the segments
for seg in self.segments:
seg[-1] = labels[seg[-1]]
self.nclasses = nclasses
# redraw the buttons
self.updateButtons()
self.completeChanged.emit()
def updateClusterNames(self):
# Check duplicate names
self.segsChanged = True
names = [self.tboxes[ID].text() for ID in range(self.nclasses)]
if len(names) != len(set(names)):
msg = SupportClasses_GUI.MessagePopup("w", "Name error", "Duplicate cluster names! \nTry again")
msg.exec_()
self.completeChanged.emit()
return
if "(Other)" in names:
msg = SupportClasses_GUI.MessagePopup("w", "Name error", "Name \"(Other)\" is reserved! \nTry again")
msg.exec_()
self.completeChanged.emit()
return
for ID in range(self.nclasses):
self.clusters[ID] = self.tboxes[ID].text()
self.completeChanged.emit()
print('updated clusters: ', self.clusters)
def addButtons(self):
""" Only makes the PicButtons and self.clusters dict
"""
self.picbuttons = []
if not self.hasCTannotations:
self.clusters = []
for i in range(self.nclasses):
self.clusters.append((i, 'Cluster_' + str(i)))
self.clusters = dict(self.clusters) # Dictionary of {ID: cluster_name}
# largest spec will be this wide
maxspecsize = max([seg[1][1]-seg[1][0] for seg in self.segments]) * self.field("fs") // 256
# Create the buttons for each segment
for seg in self.segments:
sp = SignalProc.SignalProc(512, 256)
sp.readWav(seg[0], seg[1][1]-seg[1][0], seg[1][0], silent=True)
# set increment to depend on Fs to have a constant scale of 256/tgt seconds/px of spec
incr = 256 * sp.sampleRate // self.field("fs")
sgRaw = sp.spectrogram(window='Hann', incr=incr, mean_normalise=True, onesided=True,
multitaper=False, need_even=False)
maxsg = np.min(sgRaw)
self.sg = np.abs(np.where(sgRaw == 0, 0.0, 10.0 * np.log10(sgRaw / maxsg)))
self.setColourMap()
# buffer the image to largest spec size, so that the resulting buttons would have equal scale
if self.sg.shape[0]<maxspecsize:
padlen = int(maxspecsize - self.sg.shape[0])//2
sg = np.pad(self.sg, ((padlen, padlen), (0,0)), 'constant', constant_values=np.quantile(self.sg, 0.1))
else:
sg = self.sg
newButton = SupportClasses_GUI.PicButton(1, np.fliplr(sg), sp.data, sp.audioFormat, seg[1][1]-seg[1][0], 0, seg[1][1], self.lut, self.colourStart, self.colourEnd, False, cluster=True)
self.picbuttons.append(newButton)
# (updateButtons will place them in layouts and show them)
def selectAll(self):
""" Tick all buttons in the row and vise versa"""
for ID in range(len(self.cboxes)):
if self.cboxes[ID].isChecked():
for ix in range(len(self.segments)):
if self.segments[ix][-1] == ID:
self.picbuttons[ix].mark = 'yellow'
self.picbuttons[ix].buttonClicked = True
self.picbuttons[ix].setChecked(True)
self.picbuttons[ix].repaint()
else:
for ix in range(len(self.segments)):
if self.segments[ix][-1] == ID:
self.picbuttons[ix].mark = 'green'
self.picbuttons[ix].buttonClicked = False
self.picbuttons[ix].setChecked(False)
self.picbuttons[ix].repaint()
def updateButtons(self):
""" Draw the existing buttons, and create check- and text-boxes.
Called when merging clusters or initializing the page. """
self.cboxes = [] # List of check boxes
self.tboxes = [] # Corresponding list of text boxes
for r in range(self.nclasses):
c = 0
# print('**', self.clusters[r])
tbox = QLineEdit(self.clusters[r])
tbox.setMinimumWidth(80)
tbox.setMaximumHeight(150)
tbox.setStyleSheet("border: none;")
tbox.setAlignment(Qt.AlignCenter)
tbox.textChanged.connect(self.updateClusterNames)
self.tboxes.append(tbox)
self.flowLayout.addWidget(self.tboxes[-1], r, c)
c += 1
cbox = QCheckBox("")
cbox.clicked.connect(self.selectAll)
self.cboxes.append(cbox)
self.flowLayout.addWidget(self.cboxes[-1], r, c)
c += 1
# Find the segments under this class and show them
for segix in range(len(self.segments)):
if self.segments[segix][-1] == r:
self.flowLayout.addWidget(self.picbuttons[segix], r, c)
c += 1
self.picbuttons[segix].show()
self.flowLayout.adjustSize()
self.flowLayout.update()
self.setColourLevels()
def clearButtons(self):
""" Remove existing buttons, call when merging clusters
"""
for ch in self.cboxes:
ch.hide()
for tbx in self.tboxes:
tbx.hide()
for btnum in reversed(range(self.flowLayout.layout.count())):
item = self.flowLayout.layout.itemAt(btnum)
if item is not None:
self.flowLayout.layout.removeItem(item)
r, c = self.flowLayout.items[item.widget()]
del self.flowLayout.items[item.widget()]
del self.flowLayout.rows[r][c]
item.widget().hide()
self.flowLayout.update()
def setColourLevels(self):
""" Listener for the brightness and contrast sliders being changed. Also called when spectrograms are loaded, etc.
Translates the brightness and contrast values into appropriate image levels.
"""
minsg = np.min(self.sg)
maxsg = np.max(self.sg)
brightness = self.brightnessSlider.value()
contrast = self.contrastSlider.value()
colourStart = (brightness / 100.0 * contrast / 100.0) * (maxsg - minsg) + minsg
colourEnd = (maxsg - minsg) * (1.0 - contrast / 100.0) + colourStart
for btn in self.picbuttons:
btn.stopPlayback()
btn.setImage(self.lut, colourStart, colourEnd, False)
btn.update()
def volSliderMoved(self, value):
# try/pass to avoid race situations when smth is not initialized
try:
for btn in self.picbuttons:
btn.media_obj.applyVolSlider(value)
except Exception:
pass
def setColourMap(self):
""" Listener for the menu item that chooses a colour map.
Loads them from the file as appropriate and sets the lookup table.
"""
cmap = self.config['cmap']
pos, colour, mode = colourMaps.colourMaps(cmap)
cmap = pg.ColorMap(pos, colour,mode)
self.lut = cmap.getLookupTable(0.0, 1.0, 256)
minsg = np.min(self.sg)
maxsg = np.max(self.sg)
self.colourStart = (self.config['brightness'] / 100.0 * self.config['contrast'] / 100.0) * (maxsg - minsg) + minsg
self.colourEnd = (maxsg - minsg) * (1.0 - self.config['contrast'] / 100.0) + self.colourStart
# page 4 - set params for training
class WPageParams(QWizardPage):
def __init__(self, cluster, segments, picbtn, parent=None):
super(BuildRecAdvWizard.WPageParams, self).__init__(parent)
self.setTitle("Training parameters: %s" % cluster)
self.setSubTitle("These fields were completed using the training data. Adjust if required.\nWhen ready, "
"press \"Train\". The process may take a long time.")
#self.setMinimumSize(350, 430)
self.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.MinimumExpanding)
self.adjustSize()
self.lblSpecies = QLabel("")
self.lblSpecies.setStyleSheet("QLabel { color : #808080; }")
self.numSegs = QLabel("")
self.numSegs.setStyleSheet("QLabel { color : #808080; }")
self.segments = segments
lblCluster = QLabel(cluster)
lblCluster.setStyleSheet("QLabel { color : #808080; }")
# small image of the cluster and other info
calldescr = QFormLayout()
calldescr.addRow('Species:', self.lblSpecies)
calldescr.addRow('Call type:', lblCluster)
calldescr.addRow('Number of segments:', self.numSegs)
imgCluster = QLabel()
imgCluster.setFixedHeight(100)
picimg = QPixmap.fromImage(picbtn.im1)
imgCluster.setPixmap(picimg.scaledToHeight(100))
# TimeRange parameters
form1_step4 = QFormLayout()
self.minlen = QLineEdit(self)
self.minlen.setText('')
form1_step4.addRow('Min call length (sec)', self.minlen)
self.maxlen = QLineEdit(self)
self.maxlen.setText('')
form1_step4.addRow('Max call length (sec)', self.maxlen)
self.avgslen = QLineEdit(self)
self.avgslen.setText('')
form1_step4.addRow('Avg syllable length (sec)', self.avgslen)
self.maxgap = QLineEdit(self)
self.maxgap.setText('')
form1_step4.addRow('Max gap between syllables (sec)', self.maxgap)
# FreqRange parameters
self.fLow = QSlider(Qt.Horizontal)
self.fLow.setTickPosition(QSlider.TicksBelow)
self.fLow.setTickInterval(2000)
self.fLow.setRange(0, 32000)
self.fLow.setSingleStep(100)
self.fLow.valueChanged.connect(self.fLowChange)
self.fLowtext = QLabel('')
form1_step4.addRow('', self.fLowtext)
form1_step4.addRow('Lower frq. limit (Hz)', self.fLow)
self.fHigh = QSlider(Qt.Horizontal)
self.fHigh.setTickPosition(QSlider.TicksBelow)
self.fHigh.setTickInterval(2000)
self.fHigh.setRange(0, 32000)
self.fHigh.setSingleStep(100)
self.fHigh.valueChanged.connect(self.fHighChange)
self.fHightext = QLabel('')
form1_step4.addRow('', self.fHightext)
form1_step4.addRow('Upper frq. limit (Hz)', self.fHigh)
### Step4 layout
hboxTop = QHBoxLayout()
hboxTop.addLayout(calldescr)
hboxTop.addSpacing(30)
hboxTop.addWidget(imgCluster)
layout_step4 = QVBoxLayout()
layout_step4.setSpacing(10)