combined sensor finder changes

README.md

@@ -27,7 +27,7 @@ Using a timespan of:  0.9 and a threshold of:  (9, 3.5) the placement: 	 ('Posit
 Placement Finder:
 To run only the Placement Finder for one file go to the placement_finder
 and run
-python3 placement_finder
+python3 placement_finder.py
 The result should be:
 For the metadata palcement:	 chest    	was the:  chest  	chosen
 For the metadata palcement:	 forearm    was the:  forearm  	chosen
@@ -38,7 +38,23 @@ For the metadata palcement:	 upperarm   was the:  upper arm chosen
 For the metadata palcement:	 waist    	was the:  waist  	chosen
 
 
-Sensor 
+Sensor Finder:
+To run only the Sensor Finder for one file go to the sensor_finder
+and run:
+python3 sensor_finder.py
+The result should be:
+For the wanted placement:  forearm the sensor with the metadata placement:  forearm was chosen.
+All available metadata placements were:  ['chest', 'forearm', 'head', 'shin', 'thigh', 'upperarm', 'waist']
+
+Combined Sensor Finder:
+To run only the Sensor Finder for one file go to the combined-sensor-finder
+and run:
+python3 combined-sensor-finder.py
+The result should be:
+For the wanted placement:  forearm the sensor with the metadata placement:  forearm was chosen.
+All available metadata placements were:  ['chest', 'forearm', 'head', 'shin', 'thigh', 'upperarm', 'waist']
+
+
 
 
 

Thesis-Code/combined-sensor-finder/combined-sensor-finder.py

@@ -3,7 +3,8 @@
 from placement_finder import *
 from sensor_finder import *
 
-def combined_sensor_finder(sensors, placement, position_key, acc_freq=0, gyr_freq=0):
+
+def combined_sensor_finder(sensors, placement, acc_freq=0, gyr_freq=0):
     """
     This function compares certain thresholds and compares sensors
     pairwise to decide which sensor belongs to a given placement.
@@ -21,7 +22,6 @@ def combined_sensor_finder(sensors, placement, position_key, acc_freq=0, gyr_fre
 
         placement: one placement as string
 
-        position_key: the key as string which can identify related accelerometer and gyroscope streams
     :return:
         The accelerometer and gyroscope stream which is most likely to belong to the given placement
     """
@@ -38,7 +38,7 @@ def combined_sensor_finder(sensors, placement, position_key, acc_freq=0, gyr_fre
             print("Are you sure these are correct sensors? ")
             freq = acc_freq
     else:
-        print("Needs to be implemented if frequencies are different for accelerometer and gyroscope \n \
+        print("Not yet implemented if frequencies are different for accelerometer and gyroscope \n \
                 The Accelerometer freq will be used ")
         freq = sensors[0][0].info.sample_rate
 
@@ -430,3 +430,87 @@ def combined_sensor_finder(sensors, placement, position_key, acc_freq=0, gyr_fre
     else:
         return "This placement is not in a subset of the used data set"
         
+def combination_linter(file, placement, bp_key=0):
+    """
+    This function checks for one given configuration
+    which sensor pair is most likely related to the wanted placement
+
+    :args:
+        file: the file path
+        placement: the wanted placement
+        bp_key: the key for the metadata to get the on-body placement (in the metadata) of a sensor.
+        If this key is not available choose another key to identify related accelerometers and gyroscopes.
+        The result will still be the chosen sensor pair however the printed results will not be usefull anymore.
+
+    :return:
+        accelerometer stream, gyroscope stream
+    """
+    a = read("a:", file=file)
+    s = read("s:", file=file)
+    # remove all sensors except accelerometer and gyroscope
+    a = get_acc_gyr(a)
+
+    # get the frequency
+    try:
+        freq1 = a[0].info.sample_rate
+        freq2 = a[1].info.sample_rate
+        if freq1 == freq2:
+            freq = freq1
+        else:
+            raise Exception("The frequency of sensor 0 and sensor 1 need to be the same")
+    except:
+        raise Exception("Either there are to few sensors available or sensor 0 and sensor 1 has no frequency or not the same frequency")
+
+    key = bp_key #"BODY_POSITION"
+    start, end = get_walking_sequences(s, freq)
+    sensors = get_acc_gyr(a)
+
+    # filter body parts which cannot be compared yet
+    bps = ["chest", "forearm", "wrist", "head", "thigh", "shin", "upperarm", "upper arm", "waist"]
+    s_help = []
+    for i in sensors:
+        if i.info.metadata[key].lower() in bps:
+            s_help.append(i)
+    sensors = s_help
+
+    minimum = min([len(stream) for stream in sensors])
+
+    sensors = [stream[start:end] for stream in sensors]
+    combi = list(paired_acc_gyr(sensors, key))
+    if not minimum > end:
+        if minimum < start:
+            i = 0
+            while i < len(combi):
+                if len(combi[i][0]) < start or len(combi[i][1]) < start:
+                    combi.pop(i)
+
+                    print("The matadata placement: ", combi[i][0].info.metadata[key], "needed to be discarded since ther was no walking sequence available")
+                    discarded_placement = combi[i][0].info.metadata[key]
+                else:
+                    i += 1
+            minimum = min([len(combi[i][0]) for i in range(len(combi))] + [len(combi[i][1]) for i in range(len(combi))])
+            if minimum < end:
+                end = minimum
+                print("So all sensors could be included in the decisiion process the end needed to be reset to: ", end)
+        elif minimum < end:
+            end = minimum
+            print("So all sensors could be included in the decisiion process the end needed to be reset to: ", end)
+        if start > end:
+            raise Exception("Somethings wrong with the walking data the start is after the end")
+
+    result = combined_sensor_finder(combi, placement, acc_freq=0, gyr_freq=0)
+    acc, gyr = result
+
+    print("For the wanted placement: ", placement, "the sensor with the metadata placement: ", acc.info.metadata[key], "was chosen.")
+    print("All available metadata placements were: ", [s[0].info.metadata[bp_key] for s in combi])
+    return result
+
+
+if __name__ == "__main__":
+    # set properties
+    file = "../Proband3.mkv"
+    placement = "forearm"
+    bp_key = "BODY_POSITION"
+
+    combination_linter(file, placement, bp_key)
+

Thesis-Code/combined-sensor-finder/placement_finder.py

@@ -5,6 +5,10 @@ placement different characteristics, which result in thresholds for different
 features. Depending on the actual values of these features the linter estimates
 the placement and 
 """
+from av.io import read
+import numpy as np
+from numpy import mean, sqrt, square, var, corrcoef, std, quantile, percentile
+from scipy.stats import skew, kurtosis
 
 def placement_decider(walking_acc, walking_gyro, freq=100, walking_mag=0):
     """

Thesis-Code/sensor_finder/sensor_finder.py

@@ -210,7 +210,7 @@ def n_placement_restriction(n, paired_sensors, restrictions):
             break
     return p_s
 
-def sensor_finder(sensors, placement, position_key):
+def sensor_finder(sensors, placement):
     """
     This function compares certain thresholds and compares sensors 
     pairwise to decide which sensor belongs to a given placement.
@@ -225,7 +225,6 @@ def sensor_finder(sensors, placement, position_key):
         
         placement: one placement as string
         
-        position_key: the key as string which can identify related accelerometer and gyroscope streams
     :return:
         The accelerometer and gyroscope stream which is most likely to belong to the given placement
     """
@@ -397,6 +396,19 @@ def sensor_finder(sensors, placement, position_key):
 
 
 def combination_linter(file, placement, bp_key):
+    """
+    This function checks for one given configuration
+    which sensor pair is most likely related to the wanted placement
+
+    :args:
+        file: the file path
+        placement: the wanted placement
+        bp_key: if available, the key for the metadata to get the on-body placement (in the metadata) of a sensor
+        
+    :return:
+        accelerometer stream, gyroscope stream
+    """
+
     a = read("a:", file=file)
     s = read("s:", file=file)
     # remove all sensors except accelerometer and gyroscope
@@ -449,7 +461,7 @@ def combination_linter(file, placement, bp_key):
         if start > end:
             raise Exception("Somethings wrong with the walking data the start is after the end")
 
-    result = sensor_finder(combi, placement, key)
+    result = sensor_finder(combi, placement)
     acc, gyr = result
 
     print("For the wanted placement: ", placement, "the sensor with the metadata placement: ", acc.info.metadata[key], "was chosen.")