various minor bugfixes

.gitignore

@@ -3,6 +3,9 @@
 # ignore compiled C objects
 *.so
 
+# vim swap files
+*.swp
+
 # ignore temp files produced during analysis
 Sound Files/Noise examples/Noise_10s/*.xlsx
 Sound Files/Noise examples/Noise_10s/*.data

Dialogs.py

@@ -5,23 +5,10 @@
 # Since most of them just get user selections, they are mostly just a mess of UI things
 import sys,os
 
-try:
-    from PyQt4.QtCore import *
-    pyqt4 = True
-except ImportError as e:
-    pyqt4 = False
-
-if pyqt4:
-    from PyQt4.QtCore import *
-    from PyQt4.QtGui import *
-    #import PyQt4.phonon as phonon
-else:
-    from PyQt5.QtGui import *
-    from PyQt5.QtWidgets import *
-    from PyQt5.QtCore import *
-
-#from PyQt4.QtCore import *
-#from PyQt4.QtGui import *
+from PyQt5.QtGui import *
+from PyQt5.QtWidgets import *
+from PyQt5.QtCore import *
+
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtCore, QtGui
 import pyqtgraph.functions as fn
@@ -247,7 +234,7 @@ def __init__(self, maxv, parent=None):
         self.algs = QComboBox()
         #self.algs.addItems(["Amplitude","Energy Curve","Harma","Median Clipping","Wavelets"])
         self.algs.addItems(["Default","Median Clipping","Fundamental Frequency","FIR","Wavelets","Harma","Power","Cross-Correlation"])
-        self.algs.currentIndexChanged[QString].connect(self.changeBoxes)
+        self.algs.currentIndexChanged[str].connect(self.changeBoxes)
         self.prevAlg = "Default"
         self.undo = QPushButton("Undo")
         self.resLabel = QLabel("Output Resolution (secs)")
@@ -526,7 +513,7 @@ def __init__(self, parent=None,DOC=True,sampleRate=None):
             self.algs.addItems(["Wavelets", "Bandpass", "Butterworth Bandpass", "Median Filter"])
         else:
             self.algs.addItems(["Wavelets", "Bandpass", "Butterworth Bandpass"])
-        self.algs.currentIndexChanged[QString].connect(self.changeBoxes)
+        self.algs.currentIndexChanged[str].connect(self.changeBoxes)
         self.prevAlg = "Wavelets"
 
         # Wavelet: Depth of tree, threshold type, threshold multiplier, wavelet
@@ -856,7 +843,6 @@ def __init__(self, sg, audiodata, sampleRate, label, lut, colourStart, colourEnd
         self.tbox = QLineEdit(self)
         self.tbox.setMaximumWidth(150)
         self.tbox.returnPressed.connect(self.birdTextEntered)
-        #self.connect(self.tbox, SIGNAL('textChanged(QString*)'), self.birdTextEntered)
         self.tbox.setEnabled(False)
 
         #self.close = QPushButton("Done")
@@ -921,24 +907,23 @@ def __init__(self, sg, audiodata, sampleRate, label, lut, colourStart, colourEnd
 
     def playSeg(self):  #This is not the right place though
         import wavio
-        import platform
-        if platform.system() == 'Darwin':
-            filename = 'temp.wav'
-        else:
-            import tempfile
-            f = tempfile.NamedTemporaryFile(mode='w+t', delete=False)
-            filename = f.name
-        self.audiodata = self.audiodata.astype('int16')
-        wavio.write(filename,self.audiodata,self.sampleRate,scale='dtype-limits',sampwidth=2)
-        import PyQt4.phonon as phonon
-        # Create a media object
-        media_obj = phonon.Phonon.MediaObject(self)
-        audio_output = phonon.Phonon.AudioOutput(phonon.Phonon.MusicCategory, self)
-        phonon.Phonon.createPath(media_obj, audio_output)
-        media_obj.setTickInterval(20)
-        media_obj.setCurrentSource(phonon.Phonon.MediaSource(filename))
-        media_obj.seek(0)
-        media_obj.play()
+        # import platform
+        # if platform.system() == 'Darwin':
+        #     filename = 'temp.wav'
+        # else:
+        #     import tempfile
+        #     f = tempfile.NamedTemporaryFile(mode='w+t', delete=False)
+        #     filename = f.name
+        # self.audiodata = self.audiodata.astype('int16')
+        # wavio.write(filename,self.audiodata,self.sampleRate,scale='dtype-limits',sampwidth=2)
+        # # Create a media object
+        # media_obj = phonon.Phonon.MediaObject(self)
+        # audio_output = phonon.Phonon.AudioOutput(phonon.Phonon.MusicCategory, self)
+        # phonon.Phonon.createPath(media_obj, audio_output)
+        # media_obj.setTickInterval(20)
+        # media_obj.setCurrentSource(phonon.Phonon.MediaSource(filename))
+        # media_obj.seek(0)
+        # media_obj.play()
 
     def setImage(self, sg, audiodata, sampleRate, label):
 

SupportClasses.py

@@ -3,20 +3,10 @@
 
 # Support classes for the AviaNZ program
 # Mostly subclassed from pyqtgraph
-try:
-    from PyQt4.QtCore import *
-    pyqt4 = True
-except ImportError as e:
-    pyqt4 = False
-
-if pyqt4:
-    from PyQt4.QtCore import *
-    from PyQt4.QtGui import *
-else:
 #     from PyQt5.QtGui import QIcon, QPixmap
-    from PyQt5.QtWidgets import QAbstractButton
-    from PyQt5.QtCore import QTime, QFile, QIODevice, QBuffer, QByteArray
-    from PyQt5.QtMultimedia import QAudio, QAudioOutput, QAudioFormat
+from PyQt5.QtWidgets import QAbstractButton
+from PyQt5.QtCore import QTime, QFile, QIODevice, QBuffer, QByteArray
+from PyQt5.QtMultimedia import QAudio, QAudioOutput, QAudioFormat
 
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtCore, QtGui
@@ -692,10 +682,11 @@ class TimeAxisHour(pg.AxisItem):
     def __init__(self, *args, **kwargs):
         super(TimeAxisHour, self).__init__(*args, **kwargs)
         self.offset = 0
+        self.setLabel('Time', units='hh:mm:ss')
 
     def tickStrings(self, values, scale, spacing):
         # Overwrite the axis tick code
-        return [QTime().addSecs(value+self.offset).toString('hh:mm:ss') for value in values]
+        return [QTime(0,0,0).addSecs(value+self.offset).toString('hh:mm:ss') for value in values]
 
     def setOffset(self,offset):
         self.offset = offset
@@ -707,10 +698,11 @@ class TimeAxisMin(pg.AxisItem):
     def __init__(self, *args, **kwargs):
         super(TimeAxisMin, self).__init__(*args, **kwargs)
         self.offset = 0
+        self.setLabel('Time', units='mm:ss')
 
     def tickStrings(self, values, scale, spacing):
         # Overwrite the axis tick code
-        return [QTime().addSecs(value+self.offset).toString('mm:ss') for value in values]
+        return [QTime(0,0,0).addSecs(value+self.offset).toString('mm:ss') for value in values]
 
     def setOffset(self,offset):
         self.offset = offset
@@ -879,6 +871,7 @@ def endListener(self):
             self.stop()
 
     def pressedPlay(self):
+        sleep(0.1)
         # save starting position in bytes
         self.startpos = self.soundFile.pos()
         self.start(self.soundFile)
@@ -923,8 +916,7 @@ def seekToMs(self, ms):
     def applyVolSlider(self, value):
         # passes UI volume nonlinearly
         # value = QAudio.convertVolume(value / 100, QAudio.LogarithmicVolumeScale, QAudio.LinearVolumeScale)
-        value = (math.exp(value/100)-1)/(math.exp(1)-1)
-        print("setting volume to nonl %s" % value)
+        value = (math.exp(value/50)-1)/(math.exp(2)-1)
         self.setVolume(value)
 
 class FlowLayout(QtGui.QLayout):

WaveletFunctions.py

@@ -67,15 +67,14 @@ def ConvertWaveletNodeName(self,i):
         """ Convert from an integer to the 'ad' representations of the wavelet packets
         The root is 0 (''), the next level are 1 and 2 ('a' and 'd'), the next 3, 4, 5, 6 ('aa','ad','da','dd) and so on
         """
-        import string
         level = int(np.floor(np.log2(i + 1)))
         first = 2 ** level - 1
         if i == 0:
             b = ''
         else:
-            b = np.binary_repr(i - first, width=int(level))
-            b = string.replace(b, '0', 'a', maxreplace=-1)
-            b = string.replace(b, '1', 'd', maxreplace=-1)
+            b = np.binary_repr(int(i) - first, width=int(level))
+            b = b.replace('0', 'a')
+            b = b.replace('1', 'd')
         return b
 
     def BestTree(self,wp,threshold,costfn='threshold'):
@@ -165,11 +164,12 @@ def reconstructWPT(self,new_wp,wavelet,listleaves):
         while level > 0:
             first = 2 ** level - 1
             while working[0] >= first:
-                # Note this is Python2!
-                # And also that it assumes that the whole list is backwards
-                parent = (working[0] - 1) / 2
+                # Note that it assumes that the whole list is backwards
+                parent = (working[0] - 1) // 2
                 p = self.ConvertWaveletNodeName(parent)
+
                 new_wp[p].data = pywt.idwt(new_wp[self.ConvertWaveletNodeName(working[1])].data,new_wp[self.ConvertWaveletNodeName(working[0])].data, wavelet)[:len(new_wp[p].data)]
+
                 # Delete these two nodes from working
                 working = np.delete(working, 1)
                 working = np.delete(working, 0)
@@ -225,23 +225,12 @@ def waveletDenoise(self,data=None,thresholdType='soft',threshold=4.5,maxLevel=5,
         # pywavelet makes the whole tree. So if you don't give it blanks from places where you don't want the values in
         # the original tree, it copies the details from wp even though it wasn't asked for them.
         # Reconstruction with the zeros is different to not reconstructing.
-        # print("Checkpoint 2, %.5f" % (time.time() - opstartingtime)) 
-        # new_wp = pywt.WaveletPacket(data=np.zeros(len(wp.data)), wavelet=wp.wavelet, mode='zero', maxlevel=wp.maxlevel)
-
-        # for level in range(wp.maxlevel + 1):
-        #      print(level)
-        #      numpoints = len(wp.get_level(level, 'natural')[0].data)
-        #      print(numpoints)
-        #      for n in new_wp.get_level(level, 'natural'):
-        #          n.data = np.zeros(numpoints)
 
         # Copy thresholded versions of the leaves into the new wpt
         new_wp = ce.ThresholdNodes(self, wp, bestleaves, threshold, thresholdType)
 
         # Reconstruct the internal nodes and the data
-        # print("Checkpoint 3, %.5f" % (time.time() - opstartingtime))
         new_wp = self.reconstructWPT(new_wp,wp.wavelet,bestleaves)
-        # print("Checkpoint 4, %.5f" % (time.time() - opstartingtime))
 
         return new_wp[''].data
 

ext/ce_denoise.pyx

@@ -100,6 +100,6 @@ def ThresholdNodes(self, oldtree, bestleaves, threshold, type):
 			else:
 				ce_thresnode(<double*> np.PyArray_DATA(oldtree[ind].data), <double*> np.PyArray_DATA(newtree[ind].data), length, threshold, 's')
 		else:
-			newtree[ind] = np.zeros(len(oldtree[ind].data))
+			newtree[ind].data = np.zeros(len(oldtree[ind].data))
 
 	return newtree

requirements.txt

@@ -25,7 +25,6 @@ scikit_learn==0.19.2
 # sudo apt install python3-pyqt5.qtmultimedia
 ## sudo apt install python-qt4
 ## sudo apt install libgstreamer1.0-dev - not sure??
-## sudo apt install python-qt4-phonon
 ## pip uninstall joblib; pip install -Iv joblib=0.11.0
 # pip install git+https://github.com/pyqtgraph/pyqtgraph