create script for each procedure

script/createfulltrace.py

@@ -0,0 +1,70 @@
+import os,sys
+sys.path.append('.')
+import modules.coordsi as csi
+import modules.wavacc as wav
+import numpy as np
+import pandas as pd
+import scipy as sp
+import csv
+
+def main(input):
+    if len(input) != 2:
+        print('Usage: python3 ./scripts/createkpi.py <parent path of interpolation csv>')
+        sys.exit(1)
+    root = input[1]
+    handledir = './handletrace/'
+    if not os.path.exists('./fulltrace'):
+        try:
+            os.makedirs('./fulltrace')
+        except Exception as e:
+            print(e)
+    listdir = os.listdir(root)
+    for index in listdir:
+        try:
+            filepath = os.path.join(root, index)
+            print(filepath)
+            filename = os.path.join(index)
+            original_wave=[]
+            with open(filepath, 'r') as f:
+                reader = csv.reader(f)
+                for row in reader:
+                    original_wave = row
+            for x in range(0, len(original_wave)):
+                original_wave[x] = float(original_wave[x])
+            stroke = []
+            threshold = 0.15
+            s_start = 0
+            s_end = 0
+            for i in range(1, len(original_wave)-1):
+               if original_wave[i] < -threshold and original_wave[i+1] > threshold:
+                   s_start = i
+               elif original_wave[i] > threshold and original_wave[i+1] < -threshold:
+                   if s_start != 0:
+                       s_end = i
+               if s_start != 0 and s_end != 0:
+                   stroke.append([s_start, s_end])
+                   s_start = 0
+                   s_end = 0
+            df = pd.read_csv(os.path.join('./handletrace/', filename))
+            df['status'] = 'idle'
+
+            for i in stroke:
+                #set df['status'] == 'in' when sroke[i][0] is same as index of df.
+                df.loc[i[0]:i[0], 'status'] = 'in'
+                ##set df['status'] == 'out' when sroke[i][1] is same as index of df.
+                df.loc[i[1]:i[1], 'status'] = 'out'
+                for frame in range(i[0]+1, i[1]):
+                    df.loc[frame:frame, 'status'] = 'suction'
+            df.to_csv(os.path.join('./fulltrace/', index), index=False)
+        except Exception as e:
+            print(e)
+            continue
+
+
+
+if __name__ == '__main__':
+    try:
+        main(sys.argv)
+    except Exception as e:
+        print(e)
+        sys.exit(1)

script/createhandletrace.py

@@ -1,33 +1,46 @@
 import os, sys
 import pandas as pd
-import numpy as np
-sys.path.append('..')
+sys.path.append('.')
 import modules.coordsi as csi
 import math
 import time
 
-# initialize root path
-root = './List_Data_Call/'
+def main(input):
+    if len(input) != 2:
+        print('Usage: python3 ./scripts/createhandletrace.py <parent path of surgery ID> ')
+        sys.exit(1)
+    root = input[1]
+    summary_1 = csi.summaryOriginCoord(root, camid=1)
 
-summary_1 = csi.summaryOriginCoord(root, camid=1)
+    if not os.path.exists('./handletrace'):
+        try:
+            os.makedirs('./handletrace')
+        except Exception as e:
+            print(e)
+    #make a loop for each index
+    for index, row in summary_1.iterrows():
+        timestamp = []
+        start_time = time.time()
+        df = csi.readCam(os.path.join(index,'cam1.csv'))
+        df = csi.convertToSI(df, 3.5, 1.5, 3.4)
+        df = csi.getVelocity(df)
+        df = csi.getAcceleration(df)
+        df = csi.getFullTrace(df,row['approx_total_frame'] )
+        df = csi.addValidDetection(df, 25.0)
+        try:
+            df.to_csv(os.path.join('./handletrace/', index[17:]+'.csv'), index=False)
+        #save spend time and index of summary_1 in timestamp list    
+            timestamp.append([index, time.time() - start_time])
+            print([index, time.time() - start_time])
+        except Exception as e:
+            print(e)
+            continue
+    #save timestamp list to csv file
+    pd.DataFrame(timestamp, columns=['index', 'time']).to_csv('./handletrace/timestamp.csv', index=False)
 
-#make a loop for each index
-for index, row in summary_1.iterrows():
-    timestamp = []
-    start_time = time.time()
-    df = csi.readCam(os.path.join(index,'cam1.csv'))
-    df = csi.convertToSI(df, 3.5, 1.5, 3.4)
-    df = csi.getVelocity(df)
-    df = csi.getAcceleration(df)
-    df = csi.getFullTrace(df,row['approx_total_frame'] )
-    df = csi.addValidDetection(df, 25.0)
+if __name__ == '__main__':
     try:
-        df.to_csv(os.path.join('./handletrace/', index[17:]+'.csv'), index=False)
-    #save spend time and index of summary_1 in timestamp list    
-        timestamp.append([index, time.time() - start_time])
-        print([index, time.time() - start_time])
+        main(sys.argv)
     except Exception as e:
         print(e)
-        continue
-#save timestamp list to csv file
-pd.DataFrame(timestamp, columns=['index', 'time']).to_csv('./handletrace/timestamp.csv', index=False)
+        sys.exit(1)

script/createinterpolation.py

@@ -0,0 +1,57 @@
+import os,sys
+sys.path.append('.')
+import modules.coordsi as csi
+import modules.wavacc as wav
+import numpy as np
+import pandas as pd
+import scipy as sp
+import csv
+
+def main(input):
+    if len(input) != 2:
+        print('Usage: python3 ./scripts/createinterpolation.py <path of handletrace dir> ')
+        sys.exit(1)
+    root = input[1]
+    if not os.path.exists('./interpolation'):
+        try:
+            os.makedirs('./interpolation')
+        except Exception as e:
+            print(e)
+    listdir = os.listdir(root)
+
+    for index in listdir:
+        try:
+            df = wav.openDataframe(os.path.join(root, index))
+            frame = list(df.index.values)
+            acc = pd.Series.tolist(df['acceleration'])
+            val = pd.Series.tolist(df['isValid'])
+            vel = pd.Series.tolist(df['velocity'])
+            merged = []
+            for i in range(0, len(val)):
+                merged.append([frame[i], val[i], acc[i]])
+            for i in range(0, len(merged)):
+                if merged[i][1] == 0 and merged[i][2] != 0:
+                    merged[i][2] = 0
+            valid_frame = []
+            vaild_dot = []
+            for i in range(0, len(merged)):
+                if merged[i][1] == 1:
+                    valid_frame.append(merged[i][0])
+                    vaild_dot.append(merged[i][2])
+            cubic_interpolation = sp.interpolate.interp1d(frame, acc, kind='cubic')
+            cubic_interpolation = cubic_interpolation(frame)            
+            with open(os.path.join('./interpolation', index), 'w') as f:
+                #save cubic interpolation only
+                writer = csv.writer(f)
+                writer.writerow(cubic_interpolation)
+        except Exception as e:
+            print(e)
+            continue
+
+
+if __name__ == '__main__':
+    try:
+        main(sys.argv)
+    except Exception as e:
+        print(e)
+        sys.exit(1)