update path of modules

modules/coordsi.py

@@ -0,0 +1,143 @@
+import os, sys
+import pandas as pd
+import numpy as np
+import sklearn as sk
+from sklearn import preprocessing
+import math
+'''
+coordsi.py is a module for convert coordinates to SI unit.
+
+Warning: This module convert coordinates with heuristic method.
+This moudle will be deprecated
+'''
+
+def readCam (filepath):
+    '''
+    Create a dataframe from cam*.csv file.
+    You must specify camera id. default is 1.
+    '''
+    try:
+        df = pd.read_csv(filepath, header=0, dtype={'x': np.float64, 'y': np.float64, 'z': np.float64, 'frame': np.int64})
+        return df
+    except Exception as e:
+        print(e)
+
+def summaryOriginCoord (root, camid=0):
+    '''
+    Show brief information of listed surgeon coordinate.
+    '''
+    d = root
+    try:
+        if camid == 1 or camid == 2 :
+            df = pd.DataFrame(columns=['approx_total_frame', 'x_min', 'x_max', 'y_min', 'y_max', 'z_min', 'z_max'])
+            subdirs = [x[0] for x in os.walk(d)]
+            for d in subdirs[1:]:
+                row = []
+                #get a list of files in directory
+                files = os.listdir(d)
+                count_svo = len([s for s in files if "_1.csv" in s])
+                filpath = os.path.join(d,'cam'+str(camid)+'.csv')
+                if os.path.isfile(filpath):
+                    arr = readCam(os.path.join(d,'cam'+str(camid)+'.csv'))
+                    row = [3600 *count_svo, arr['x'].min(), arr['x'].max(), arr['y'].min(), arr['y'].max(), arr['z'].min(), arr['z'].max()]
+                    df.loc[d] = row
+                else:
+                    print('Warning: '+filpath+' is not exist.')
+                    continue
+            return df
+        else:
+            print("Error: Camera ID must be 1 or 2. type camid=1 or camid=2 after dirpath")
+    except Exception as e:
+        print(e)
+
+    
+
+
+def convertToSI (origin, w, l, h):
+    '''
+    Waring: This function will be deprecated!
+    Convert coordinates to SI unit with w, l, h.
+    w, l, h are heuristic value. It will be changed after calibration and each surgeon room will geat unique value.
+    '''
+    try:
+        df = origin.copy()
+        #normailze dataframe[0] from -1 to 1
+        df['x'] = preprocessing.minmax_scale(df['x'], feature_range=(-(w/2), (w/2)), axis=0, copy=True)
+        #normailze dataframe[1] from -0.75 to 0.75
+        df['y'] = preprocessing.minmax_scale(df['y'], feature_range=(-(l/2), (l/2)), axis=0, copy=True)
+        #subtract dataframe[z] from int(4) and normailze from 0.93m to 1.8m (0 as floor)
+        df['z'] = h - df['z']
+        df['z'] = preprocessing.minmax_scale(df['z'], feature_range=(0.93,1.8), axis=0, copy=True)
+        #change column order x, y to y, x
+        df = df[['y', 'x', 'z', 'frame']]
+        #change column name y to X, x to Y
+        df = df.rename(columns={'y': 'x', 'x': 'y'})
+        return df
+    except Exception as e:
+        print(e)
+
+def getVelocity (dataframe):
+    try:
+        df  = dataframe
+        df['positionvectorvalue'] = (df['x']**2 + df['y']**2 + df['z']**2)
+        buffer1, buffer2 = df['positionvectorvalue'].copy(), df['positionvectorvalue'].copy()
+        buffer1, buffer2 = buffer1.to_frame(), buffer2.to_frame()
+        buffer1, buffer2 = list(buffer1.loc[:, 'positionvectorvalue']), list(buffer2.loc[:, 'positionvectorvalue'])
+        buffer3 = [0.0]
+        for x in range(0, len(buffer2)-1):
+            buffer3.append(buffer2[x])
+        buffer3  = np.array(buffer1) - np.array(buffer3)
+        for x in range(0, len(buffer3)):
+            buffer3[x] = math.sqrt(abs(buffer3[x]))
+        buffer3[0] = 0.0
+        df['velocity'] = buffer3
+        return df
+    except Exception as e:
+        print(e)
+
+def getAcceleration (dataframe):
+    try:
+        df = dataframe
+        buffer1, buffer2 = df['velocity'].copy(), df['velocity'].copy()
+        buffer1, buffer2 = buffer1.to_frame(), buffer2.to_frame()
+        buffer1, buffer2 = list(buffer1.loc[:, 'velocity']), list(buffer2.loc[:, 'velocity'])
+        buffer3 = [0.0]
+        for x in range(0, len(buffer2)-1):
+            buffer3.append(buffer2[x])
+        buffer3  = np.array(buffer1) - np.array(buffer3)
+        buffer3[1] = 0.0
+        df['acceleration'] = buffer3
+        return df
+    except Exception as e:
+        print(e)
+
+def getFullTrace (dataframe, approx_total_frame):
+    try:
+        df = dataframe
+        total_frame = int(approx_total_frame)
+        handletrace = pd.DataFrame(columns=['x', 'y', 'z', 'frame', 'positionvectorvalue', 'velocity', 'acceleration', 'isValid'])
+        handletrace = pd.concat([handletrace, pd.DataFrame(np.zeros((total_frame,8)), columns=['x', 'y', 'z', 'frame', 'positionvectorvalue','velocity', 'acceleration', 'isValid'])], axis=0)
+        for x in range(0, len(df)):
+            handletrace.loc[df.loc[x, 'frame']] = df.loc[x]
+        handletrace['isValid'] = handletrace['isValid'].fillna(0)
+        return handletrace
+    except Exception as e:
+        print(e)
+
+def addValidDetection (dataframe, threshold = 25.0):
+    '''
+    threshold value is suitable for only 1st surgeon room(Seoul 801).
+    We can make threshold in every surgeon room by using epipolar geometry.(but needs more cameras with different positions)
+    '''
+    try:
+        df = dataframe
+        top = threshold
+        bottom = -threshold
+        for x in range(0, len(df)):
+            if bottom < df['acceleration'][x] < top:
+                df['isValid'][x] = 1
+            else:
+                df['isValid'][x] = 0
+        return df
+    except Exception as e:
+        print(e)        

modules/wavacc.py

@@ -0,0 +1,34 @@
+import sys, os, math, time
+import numpy as np
+import pandas as pd
+'''
+wavacc.py for interpolate accelerometer data and extract feature as stroke.
+Denosing step is not implemented this module. See addValidDetection function in coordsi.py for denoising.
+'''
+def interpolation(df):
+    try:
+        #implement data here
+    except Exception as e:
+        print(e)
+        return df
+    
+def decomposition(df):
+    try:
+        #implemnet decompositino with wavelet transform here
+    except Exception as e:
+        print(e)
+        return df
+
+def getStroke(df):
+    try:
+        #implement get stroke here
+    except Exception as e:
+        print(e)
+        return df
+
+def mergeToDataFrame(df):
+    try:
+        #implement merge to dataframe here
+    except Exception as e:
+        print(e)
+        return df

script/createhandletrace.py

@@ -1,6 +1,7 @@
 import os, sys
 import pandas as pd
 import numpy as np
+sys.path.append('..')
 import modules.coordsi as csi
 import math
 import time

toysnippet/moduleimprot.ipynb

@@ -0,0 +1,44 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.append('..')\n",
+    "import modules.coordsi as csi"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.0"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

toysnippet/sandbox.ipynb

@@ -9,7 +9,8 @@
     "import os, sys\n",
     "import pandas as pd\n",
     "import numpy as np\n",
-    "import coordsi as csi\n",
+    "sys.path.append('../')\n",
+    "import modules.coordsi as csi\n",
     "import math\n",
     "import time"
    ]