added tests and .gitignore file, performed spell-checking, changed __…

…curveFit from scipy.optimize() to numpy.polyfit(), disabled travis e-mail notification
nspi · Sep 4, 2016 · 2768f68 · 2768f68
1 parent fc35959
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.idea/
diff --git a/.travis.yml b/.travis.yml
@@ -15,4 +15,7 @@ install:
 python:
   - "2.7"
 
-script: "nosetests"
+script: "nosetests"
+
+notifications:
+  email: false
diff --git a/src/data/LOGFILE b/src/data/LOGFILE
@@ -140,3 +140,190 @@
 03.09.2016 01:10:12 gui_toolbarButtons DEBUG [<_MainThread(MainThread, started 139977439106880)>, <VideoThread(Thread-1, started 139976792540928)>, <GuiSignalProcessor(Thread-8, started 139976737269504)>, <GuiSignalPlotter(Thread-7, started 139976745662208)>]
 03.09.2016 01:10:12 gui_toolbarButtons INFO Program will halt now...
 03.09.2016 01:10:12 gui_signalProcessor INFO Reached end of signal processing thread
+04.09.2016 10:20:11 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 10:20:11 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 10:20:11 gui INFO Created status bar
+04.09.2016 10:20:11 gui INFO Created toolbar for ROI definition
+04.09.2016 10:20:11 gui INFO Created part of the GUI that shows video
+04.09.2016 10:20:12 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 10:20:12 gui INFO Created toolbar with buttons
+04.09.2016 10:20:12 gui INFO Main window was created
+04.09.2016 10:20:12 gui INFO Starting TkInter main loop
+04.09.2016 10:20:32 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 10:20:32 gui_toolbarButtons INFO Camera is started
+04.09.2016 10:20:32 video INFO Camera index was set because user pressed start button
+04.09.2016 10:20:32 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 10:20:32 video INFO User pressed start and wants to use the camera
+04.09.2016 10:20:32 video INFO The camera was initialized
+04.09.2016 10:20:32 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 10:20:37 settings INFO Parameter: 5 was changed
+04.09.2016 10:20:37 gui_toolbarROI INFO Viola-Jones algorithm was activated by the user
+04.09.2016 10:20:38 settings INFO Parameter: 5 was changed
+04.09.2016 10:20:38 gui_toolbarROI INFO Viola-Jones algorithm was disabled by the user
+04.09.2016 10:20:40 settings INFO Parameter: 5 was changed
+04.09.2016 10:20:40 gui_toolbarROI INFO Viola-Jones algorithm was activated by the user
+04.09.2016 10:20:44 settings INFO Parameter: 5 was changed
+04.09.2016 10:20:44 gui_toolbarROI INFO Viola-Jones algorithm was disabled by the user
+04.09.2016 13:45:21 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 13:45:21 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 13:45:21 gui INFO Created status bar
+04.09.2016 13:45:21 gui INFO Created toolbar for ROI definition
+04.09.2016 13:45:21 gui INFO Created part of the GUI that shows video
+04.09.2016 13:45:21 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 13:45:21 gui INFO Created toolbar with buttons
+04.09.2016 13:45:21 gui INFO Main window was created
+04.09.2016 13:45:21 gui INFO Starting TkInter main loop
+04.09.2016 13:45:26 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 13:45:26 gui_toolbarButtons INFO Camera is started
+04.09.2016 13:45:26 video INFO Camera index was set because user pressed start button
+04.09.2016 13:45:26 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 13:45:26 video INFO User pressed start and wants to use the camera
+04.09.2016 13:45:26 video INFO The camera was initialized
+04.09.2016 13:45:26 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 13:45:28 settings INFO Parameter: 5 was changed
+04.09.2016 13:45:28 gui_toolbarROI INFO Viola-Jones algorithm was activated by the user
+04.09.2016 13:45:31 settings INFO Parameter: 5 was changed
+04.09.2016 13:45:31 gui_toolbarROI INFO Viola-Jones algorithm was disabled by the user
+04.09.2016 13:46:08 settings INFO Parameter: 5 was changed
+04.09.2016 13:46:08 gui_toolbarROI INFO Viola-Jones algorithm was activated by the user
+04.09.2016 13:46:10 settings INFO Parameter: 5 was changed
+04.09.2016 13:46:10 gui_toolbarROI INFO Viola-Jones algorithm was disabled by the user
+04.09.2016 13:46:10 settings INFO Parameter: 5 was changed
+04.09.2016 13:46:10 gui_toolbarROI INFO Viola-Jones algorithm was activated by the user
+04.09.2016 13:46:12 settings INFO Parameter: 5 was changed
+04.09.2016 13:46:12 gui_toolbarROI INFO Viola-Jones algorithm was disabled by the user
+04.09.2016 13:46:24 gui_toolbarButtons INFO User pressed ''quit'' button - now halting threads
+04.09.2016 13:46:24 gui_toolbarButtons INFO Signal display thread was closed
+04.09.2016 13:46:24 gui_toolbarButtons INFO Camera capture thread was closed
+04.09.2016 13:46:24 gui_toolbarButtons INFO Tk mainloop() was halted
+04.09.2016 13:46:24 gui_toolbarButtons DEBUG [<_MainThread(MainThread, started 140495370209088)>, <VideoThread(Thread-1, started 140494723643136)>, <GuiSignalProcessor(Thread-8, started 140494668371712)>, <GuiSignalPlotter(Thread-7, started 140494676764416)>]
+04.09.2016 13:46:24 gui_toolbarButtons INFO Program will halt now...
+04.09.2016 13:46:24 video INFO The camera was released
+04.09.2016 13:46:24 gui_signalProcessor INFO Reached end of signal processing thread
+04.09.2016 13:54:00 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 13:54:00 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 13:54:00 gui INFO Created status bar
+04.09.2016 13:54:00 gui INFO Created toolbar for ROI definition
+04.09.2016 13:54:00 gui INFO Created part of the GUI that shows video
+04.09.2016 13:54:00 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 13:54:00 gui INFO Created toolbar with buttons
+04.09.2016 13:54:00 gui INFO Main window was created
+04.09.2016 13:54:00 gui INFO Starting TkInter main loop
+04.09.2016 13:54:02 gui_toolbarButtons INFO User pressed ''quit'' button - now halting threads
+04.09.2016 13:54:02 gui_toolbarButtons INFO Signal display thread was closed
+04.09.2016 13:54:02 gui_toolbarButtons INFO Camera capture thread was closed
+04.09.2016 13:54:02 gui_toolbarButtons INFO Tk mainloop() was halted
+04.09.2016 13:54:02 gui_toolbarButtons DEBUG [<_MainThread(MainThread, started 140633930327872)>, <VideoThread(Thread-1, started 140633283761920)>, <GuiSignalPlotter(Thread-7, started 140633236883200)>, <GuiSignalProcessor(Thread-8, started 140633228490496)>]
+04.09.2016 13:54:02 gui_toolbarButtons INFO Program will halt now...
+04.09.2016 13:54:02 gui_signalProcessor INFO Reached end of signal processing thread
+04.09.2016 14:54:04 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 14:54:04 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 14:54:04 gui INFO Created status bar
+04.09.2016 14:54:04 gui INFO Created toolbar for ROI definition
+04.09.2016 14:54:04 gui INFO Created part of the GUI that shows video
+04.09.2016 14:54:04 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 14:54:04 gui INFO Created toolbar with buttons
+04.09.2016 14:54:04 gui INFO Main window was created
+04.09.2016 14:54:04 gui INFO Starting TkInter main loop
+04.09.2016 14:54:21 gui_toolbarButtons INFO User has chosen valid directory with images
+04.09.2016 14:54:22 gui_toolbarButtons INFO Files have been loaded successfully.
+04.09.2016 14:54:23 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 14:54:23 gui_toolbarButtons INFO Camera is started
+04.09.2016 14:54:23 video INFO Camera index was set because user pressed start button
+04.09.2016 14:54:23 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 14:54:23 video INFO User pressed start and wants to use frames from hard disk
+04.09.2016 14:54:23 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 14:54:37 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 14:54:37 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 14:54:37 gui INFO Created status bar
+04.09.2016 14:54:37 gui INFO Created toolbar for ROI definition
+04.09.2016 14:54:38 gui INFO Created part of the GUI that shows video
+04.09.2016 14:54:38 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 14:54:38 gui INFO Created toolbar with buttons
+04.09.2016 14:54:38 gui INFO Main window was created
+04.09.2016 14:54:38 gui INFO Starting TkInter main loop
+04.09.2016 14:54:48 gui_toolbarButtons INFO User has chosen valid directory with images
+04.09.2016 14:54:48 gui_toolbarButtons INFO Files have been loaded successfully.
+04.09.2016 14:54:49 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 14:54:49 gui_toolbarButtons INFO Camera is started
+04.09.2016 14:54:49 video INFO Camera index was set because user pressed start button
+04.09.2016 14:54:49 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 14:54:49 video INFO User pressed start and wants to use frames from hard disk
+04.09.2016 14:54:49 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 14:55:20 settings WARNING Unexpected error when reading configuration. Trying again.
+04.09.2016 14:55:33 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 14:55:33 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 14:55:33 gui INFO Created status bar
+04.09.2016 14:55:33 gui INFO Created toolbar for ROI definition
+04.09.2016 14:55:33 gui INFO Created part of the GUI that shows video
+04.09.2016 14:55:33 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 14:55:33 gui INFO Created toolbar with buttons
+04.09.2016 14:55:33 gui INFO Main window was created
+04.09.2016 14:55:33 gui INFO Starting TkInter main loop
+04.09.2016 14:55:45 gui_toolbarButtons INFO User has chosen valid directory with images
+04.09.2016 14:55:46 gui_toolbarButtons INFO Files have been loaded successfully.
+04.09.2016 14:55:47 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 14:55:47 gui_toolbarButtons INFO Camera is started
+04.09.2016 14:55:47 video INFO Camera index was set because user pressed start button
+04.09.2016 14:55:47 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 14:55:47 video INFO User pressed start and wants to use frames from hard disk
+04.09.2016 14:55:47 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 14:56:11 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 14:56:11 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 14:56:11 gui INFO Created status bar
+04.09.2016 14:56:11 gui INFO Created toolbar for ROI definition
+04.09.2016 14:56:11 gui INFO Created part of the GUI that shows video
+04.09.2016 14:56:11 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 14:56:11 gui INFO Created toolbar with buttons
+04.09.2016 14:56:11 gui INFO Main window was created
+04.09.2016 14:56:11 gui INFO Starting TkInter main loop
+04.09.2016 14:56:23 gui_toolbarButtons INFO User has chosen valid directory with images
+04.09.2016 14:56:24 gui_toolbarButtons INFO Files have been loaded successfully.
+04.09.2016 14:56:24 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 14:56:24 gui_toolbarButtons INFO Camera is started
+04.09.2016 14:56:24 video INFO Camera index was set because user pressed start button
+04.09.2016 14:56:24 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 14:56:25 video INFO User pressed start and wants to use frames from hard disk
+04.09.2016 14:56:25 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 14:56:34 gui_toolbarROI WARNING Your ROI definition was inadequate (y_min < y_max). The values were corrected.
+04.09.2016 14:56:54 settings WARNING Unexpected error when reading configuration. Trying again.
+04.09.2016 14:59:20 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 14:59:20 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 14:59:20 gui INFO Created status bar
+04.09.2016 14:59:20 gui INFO Created toolbar for ROI definition
+04.09.2016 14:59:20 gui INFO Created part of the GUI that shows video
+04.09.2016 14:59:20 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 14:59:21 gui INFO Created toolbar with buttons
+04.09.2016 14:59:21 gui INFO Main window was created
+04.09.2016 14:59:21 gui INFO Starting TkInter main loop
+04.09.2016 14:59:31 gui_toolbarButtons INFO User has chosen valid directory with images
+04.09.2016 14:59:32 gui_toolbarButtons INFO Files have been loaded successfully.
+04.09.2016 14:59:32 gui_toolbarButtons INFO Start button has been pressed
+04.09.2016 14:59:32 gui_toolbarButtons INFO Camera is started
+04.09.2016 14:59:32 video INFO Camera index was set because user pressed start button
+04.09.2016 14:59:32 gui_toolbarButtons INFO Enabling event: eventCameraChosen 
+04.09.2016 14:59:32 video INFO User pressed start and wants to use frames from hard disk
+04.09.2016 14:59:32 gui_windowVideo INFO First frame from webcam was received and ROI was adjusted
+04.09.2016 15:00:07 gui_toolbarButtons INFO User pressed ''quit'' button - now halting threads
+04.09.2016 15:00:07 gui_toolbarButtons INFO Signal display thread was closed
+04.09.2016 15:00:07 gui_signalProcessor INFO Reached end of signal processing thread
+04.09.2016 15:00:07 gui_toolbarButtons INFO Camera capture thread was closed
+04.09.2016 15:00:07 gui_toolbarButtons INFO Tk mainloop() was halted
+04.09.2016 15:00:07 gui_toolbarButtons DEBUG [<_MainThread(MainThread, started 139901600790336)>, <VideoThread(Thread-1, started 139901092853504)>, <GuiSignalPlotter(Thread-7, started 139901045974784)>]
+04.09.2016 15:00:07 gui_toolbarButtons INFO Program will halt now...
+04.09.2016 15:01:11 video INFO Found 1 OpenCV-compatible cameras
+04.09.2016 15:01:11 gui INFO Link to thread that delivers video frames was stored in GUI thread
+04.09.2016 15:01:11 gui INFO Created status bar
+04.09.2016 15:01:11 gui INFO Created toolbar for ROI definition
+04.09.2016 15:01:11 gui INFO Created part of the GUI that shows video
+04.09.2016 15:01:12 gui INFO Created part of the GUI that shows the signal extracted from the video
+04.09.2016 15:01:12 gui INFO Created toolbar with buttons
+04.09.2016 15:01:12 gui INFO Main window was created
+04.09.2016 15:01:12 gui INFO Starting TkInter main loop
+04.09.2016 15:01:14 gui_toolbarButtons INFO User pressed ''quit'' button - now halting threads
+04.09.2016 15:01:14 gui_toolbarButtons INFO Signal display thread was closed
+04.09.2016 15:01:14 gui_toolbarButtons INFO Camera capture thread was closed
+04.09.2016 15:01:14 gui_toolbarButtons INFO Tk mainloop() was halted
+04.09.2016 15:01:14 gui_toolbarButtons DEBUG [<_MainThread(MainThread, started 139989756749632)>, <VideoThread(Thread-1, started 139989248812800)>, <GuiSignalPlotter(Thread-7, started 139989201934080)>, <GuiSignalProcessor(Thread-8, started 139989193541376)>]
+04.09.2016 15:01:14 gui_toolbarButtons INFO Program will halt now...
+04.09.2016 15:01:14 gui_signalProcessor INFO Reached end of signal processing thread
diff --git a/src/gui_signalPlotter.py b/src/gui_signalPlotter.py
@@ -102,7 +102,7 @@ def run(self):
                                 self.subplotInstanceBottom.plot(self.spectrumAxis, self.valuesOutput2)
                                 self.subplotInstanceBottom.plot(self.spectrumAxis[self.spectrumMax],
                                                                 self.valuesOutput2[self.spectrumMax], 'r*')
-                            # Otherwise, plot placehoder
+                            # Otherwise, plot placeholder
                             else:
                                 self.subplotInstanceBottom.plot(self.valuesOutput2)
 

diff --git a/src/gui_signalProcessor.py b/src/gui_signalProcessor.py
@@ -79,8 +79,7 @@ def __waitToAdjustFPS(self, startTime, endTime):
         if int(self.waitTime*1000) > 0:
             cv2.waitKey(int(self.waitTime * 1000))
         elif int(self.waitTime*1000) == 0:
-            cv2.waitKey(33) # cv2.waitKey(0) results in error
-
+            cv2.waitKey(33)  # cv2.waitKey(0) results in error
 
     def run(self):
         """The main functionality of the thread: The signal is obtained and plotted"""

diff --git a/src/gui_toolbarROI.py b/src/gui_toolbarROI.py
@@ -179,7 +179,7 @@ def getROI(self):
         return self.x_min, self.x_max, self.y_min, self.y_max
 
     def setROI(self, x_min, x_max, y_min, y_max):
-        """Sets ROI to new defintion"""
+        """Sets ROI to new definition"""
         self.x_min = x_min
         self.textbox_x1.delete(1.0, Tk.END)
         self.textbox_x1.insert(Tk.END, self.x_min)

diff --git a/src/settings.ini b/src/settings.ini
@@ -4,7 +4,7 @@ bool_use_webcam = 1.0
 # use which camera port?
 idx_camera = 1.0
 # use which algorithm?
-idx_algorithm = 0.0
+idx_algorithm = 1.0
 # show curves?
 bool_show_curves = 1.0
 # store frames on hard disk?

diff --git a/src/signal_processing.py b/src/signal_processing.py
@@ -4,8 +4,6 @@
 
 import numpy as np
 import datetime
-import scipy.optimize as sci
-import scipy.signal as sig
 
 
 class SignalProcessor:
@@ -20,7 +18,6 @@ def __init__(self):
         # Get time for filterWaveform() algorithm
         self.currTime = datetime.datetime.now()
 
-
     def filterWaveform(self, inputRawSignal, inputOutputSignal, inputParam1, inputParam2, inputParam3):
         """This function filters the video signal and thereby obtains a waveform more similar to pulse oximetry.
            This is a real-time implementation of the algorithm described in:
@@ -56,7 +53,7 @@ def filterWaveform(self, inputRawSignal, inputOutputSignal, inputParam1, inputPa
         valueM = self.__curveFit(valuesXdata, valuesNormDiffWindow)
 
         # Get output: Computed signal
-        OutputSignal = np.append(OutputSignal, valueM[1])
+        OutputSignal = np.append(OutputSignal, valueM[0])
 
         # Apply running max window
         valueRunningMax = np.amax(OutputSignal[-inputParam1:])
@@ -93,8 +90,8 @@ def computeHR(self, inputRawSignal, estimatedFPS):
         Proceedings of the 49th Annual Conference of the German Society for Biomedical Engineering, Luebeck, Germany,
         16.-18.09.2015.
 
-        Plese note that the different length of the input signal N and that a moving average filter as described in
-        section 2.4) of the referenec is not applied.
+        Please note that the different length of the input signal N and that a moving average filter as described in
+        section 2.4) of the reference is not applied.
         """
 
         # Get normalized signal
@@ -135,7 +132,7 @@ def computeHR(self, inputRawSignal, estimatedFPS):
         limitsBool = (hrMin < freqAxis) & (hrMax > freqAxis)
         limitsIdx = np.linspace(0, N - 1, N)
 
-        # Get indices of frequncies between hrMin and hrMax
+        # Get indices of frequencies between hrMin and hrMax
         limits = limitsIdx[limitsBool.nonzero()]
         limits = limits.astype(int)
 
@@ -151,7 +148,7 @@ def normalize(self, inputSignal):
 
         outputSignal = inputSignal
 
-        # Prohobit dividing by zero
+        # Prohibit dividing by zero
         if np.max(np.abs(outputSignal)) > 0:
             maxVal = np.max(np.abs(outputSignal))
             minVal = np.min(np.abs(outputSignal))
@@ -165,26 +162,17 @@ def __curveFit(self, inputSignal1, inputSignal2):
         """perform curve fitting and return slope value"""
 
         # Todo: Add gaussian weights
-
-        # Perform curve fit with weighted signal
-        m, ret = sci.curve_fit(self.__curveFitFunc, inputSignal1, inputSignal2)
+        m = np.polyfit(inputSignal1, inputSignal2, 1)
 
         return m
 
-
-    def __curveFitFunc(self, x, a, b):
-        """"linear curve fit function"""
-        return a * x + b
-
-
     def nextpow2(self, number):
         """Simple implementation of MATLAB nextpow2 """
         currValue = 2
         while currValue <= number:
             currValue = currValue * 2
         return currValue
 
-
     def computeZeroPaddingValues(self, number):
         """During zero padding, we want to fill zeros before and after signal.
         This function computes the number of zeros"""