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Name changes #13

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f340634
Change names in logproc for extracted variables
shivChitinous Jan 22, 2025
b83107a
Modify posAnalysis to reflect naming conventions, update how velociti…
shivChitinous Jan 22, 2025
0009fed
Modify how interpolation is done for savgol filtering
shivChitinous Jan 22, 2025
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65 changes: 49 additions & 16 deletions unityvr/analysis/posAnalysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,15 @@
##functions to process posDf dataframe

#obtain the position dataframe with derived quantities
def position(uvrDat, derive = True, rotate_by = None, filter_date = '2021-09-08', plot = False, plotsave=False, saveDir=None):
def position(uvrDat, derive = True, rotate_by = None, filter_date = '2021-09-08', plot = False, plotsave=False, saveDir=None, computeVel=False, **computeVelocitiesKwargs):
## input arguments
# set derive = True if you want to compute derived quantities (ds, s, dTh (change in angle), radangle (angle in radians(-pi,pi)))
# rotate_by: angle (degrees) by which to rotate the trajectory to ensure the bright part of the panorama is at 180 degree heading.
# filter_date: date of experiment after which right handed angle convention will not be forced when loading posDf; this is because
# converting from Unity's left handed angle convention to right handed convention was implemented after a certain
# date in the preproc.py file

posDf = uvrDat.posDf
posDf = uvrDat.posDf.copy() #NOT INPLACE

#angle correction
#this is required only for data that was preprocessed before the filter_date
Expand All @@ -33,20 +33,20 @@ def position(uvrDat, derive = True, rotate_by = None, filter_date = '2021-09-08'

#rotate
if rotate_by is not None:

#rotate the trajectory
posDf['x'], posDf['y'] = rotation_deg(posDf['x'],posDf['y'],rotate_by)
posDf['dx'], posDf['dy'] = rotation_deg(posDf['dx'],posDf['dy'],rotate_by)
posDf['dxattempt'], posDf['dyattempt'] = rotation_deg(posDf['dxattempt'],posDf['dyattempt'],rotate_by)

posDf['angle'] = (posDf['angle']+rotate_by)%360
uvrDat.metadata['rotated_by'] = (uvrDat.metadata['rotated_by']+rotate_by)%360 if ('rotated_by' in uvrDat.metadata) else (rotate_by%360)

#add dc2cm conversion factor
posDf.dc2cm = 10

if derive:
posDf['ds'] = np.sqrt(posDf['dx']**2+posDf['dy']**2)
posDf['s'] = np.cumsum(posDf['ds'])
posDf['dTh'] = (np.diff(posDf['angle'],prepend=posDf['angle'].iloc[0]) + 180)%360 - 180
posDf['radangle'] = ((posDf['angle']+180)%360-180)*np.pi/180
posDf = posDerive(posDf)
if computeVel:
posDf = computeVelocities(posDf,**computeVelocitiesKwargs)

if plot:
fig, ax = viz.plotTrajwithParameterandCondition(posDf, figsize=(10,5), parameter='angle')
Expand Down Expand Up @@ -119,17 +119,16 @@ def rotation_deg(x,y,theta):


# Add derrived quantities: Velocities
def computeVelocities(posDf, convf = 10, window=7, order=3):
#convf: conversion from dc (to cm if 10)
def computeVelocities(inDf, window=7, order=3):
posDf = inDf.copy()
#window and order for filter
from scipy.signal import savgol_filter

# add derrived parameter to positional dataframe
posDf['vT'] = np.hypot(np.gradient(posDf.x.values*convf), np.gradient(posDf.y.values*convf))*(1/posDf.dt)
posDf['vR'] = np.gradient(np.unwrap(posDf.angle.values))
posDf['vT'] = np.hypot(np.gradient(posDf.x.values), np.gradient(posDf.y.values))*(1/posDf.dt) #translational velocity in decimeter/second
posDf['vR'] = np.gradient(np.unwrap(posDf.angle.values)) #rotational velocity in degrees/second

posDf['vT_filt'] = savgol_filter(posDf.vT, window, order)
posDf['vR_filt'] = savgol_filter(posDf.vR, window, order)
posDf['vT_filt'] = savgolFilterInterpolated(posDf, 'vT', window, order) #savgol filtered velocities
posDf['vR_filt'] = savgolFilterInterpolated(posDf, 'vR', window, order)
return posDf

def getTimeDf(uvrDat, trialDir, posDf = None, imaging = False, rate = 9.5509):
Expand Down Expand Up @@ -159,4 +158,38 @@ def getTimeDf(uvrDat, trialDir, posDf = None, imaging = False, rate = 9.5509):
timeDf['count'] = np.arange(1,len(timeDf['time'])+1,1)
timeDf = carryAttrs(timeDf,posDf)

return timeDf
return timeDf

def posDerive(inDf):
posDf = inDf.copy() #NOT INPLACE
posDf['dx'] = np.diff(posDf['x'], prepend=0) #allocentric translation vector x component
posDf['dy'] = np.diff(posDf['y'], prepend=0) #allocentric translation vector y component
posDf['ds'] = np.sqrt(posDf['dx']**2+posDf['dy']**2) #magnitude of the translation vector
posDf['s'] = np.cumsum(posDf['ds']) #integrated pathlength from start
posDf['dTh'] = (np.diff(posDf['angle'],prepend=posDf['angle'].iloc[0]) + 180)%360 - 180
posDf['radangle'] = ((posDf['angle']+180)%360-180)*np.pi/180

#derive forward and side velocities: does not depend on rotation of trajectory and angle
if 'dx_ft' not in posDf:
xy = np.diff(posDf[['x', 'y']], axis=0)
rotation_mats = np.array([np.array([[np.cos(theta), -np.sin(theta)],
[np.sin(theta), np.cos(theta)]]).T for theta in np.deg2rad(posDf['angle'])[:-1]])
posDf['dx_ft'], posDf['dy_ft'] = np.vstack([[0,0],np.einsum('ijk,ik->ij', rotation_mats, xy)]).T #in egocentric frame, units: decimeters, #dx_ft is forward motion (forward is positive), dy_ft is side motion (rightward is positive)
return posDf

def savgolFilterInterpolated(posDf, value, window, order, timeStr = 'time', kind='linear'):
from scipy.signal import savgol_filter

df = posDf.copy()

#filtering with a savgol filter assumes that the data is evenly spaced
#interpolating the data to be evenly spaced
interpolated = sp.interpolate.interp1d(df[timeStr], df[value], kind=kind, bounds_error=False, fill_value='extrapolate')

equalTime = np.linspace(df[timeStr].min(),df[timeStr].max(),2*len(df[timeStr]))

filt = savgol_filter(interpolated(equalTime), window, order)

filtInterpolated = sp.interpolate.interp1d(equalTime, filt, kind='nearest', bounds_error=False, fill_value='extrapolate')

return filtInterpolated(df.time)
17 changes: 9 additions & 8 deletions unityvr/preproc/logproc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,9 @@
objDfCols = ['name','collider','px','py','pz','rx','ry','rz','sx','sy','sz']

posDfCols = ['frame','time','x','y','angle']
ftDfCols = ['frame','ficTracTReadMs','ficTracTWriteMs','dx','dy','dz']
ftDfCols = ['frame','ficTracTReadMs','ficTracTWriteMs','wx_ft','wy_ft','wz_ft']
dtDfCols = ['frame','time','dt']
tempDfCols = ['frame','time','temperature']
nidDfCols = ['frame','time','dt','pdsig','imgfsig']
texDfCols = ['frame','time','xtex','ytex']
vidDfCols = ['frame','time','img','duration']
Expand Down Expand Up @@ -266,10 +267,10 @@ def posDfFromLog(dat):
'x': match['worldPosition']['x'],
'y': match['worldPosition']['z'], #axes are named differently in Unity
'angle': (-match['worldRotationDegs']['y'])%360, #flip due to left handed convention in Unity
'dx':match['actualTranslation']['x'],
'dy':match['actualTranslation']['z'],
'dxattempt': match['attemptedTranslation']['x'],
'dyattempt': match['attemptedTranslation']['z']
'dx_ft':match['actualTranslation']['x'], #forward motion
'dy_ft':match['actualTranslation']['z'], #right sideslip
'dxattempt_ft': match['attemptedTranslation']['x'],
'dyattempt_ft': match['attemptedTranslation']['z']
}
entries[entry] = pd.Series(framedat).to_frame().T
print('correcting for Unity angle convention.')
Expand All @@ -288,9 +289,9 @@ def ftDfFromLog(dat):
framedat = {'frame': match['frame'],
'ficTracTReadMs': match['ficTracTimestampReadMs'],
'ficTracTWriteMs': match['ficTracTimestampWriteMs'],
'dx': match['ficTracDeltaRotationVectorLab']['x'],
'dy': match['ficTracDeltaRotationVectorLab']['y'],
'dz': match['ficTracDeltaRotationVectorLab']['z']}
'wx_ft': match['ficTracDeltaRotationVectorLab']['x'],
'wy_ft': match['ficTracDeltaRotationVectorLab']['y'],
'wz_ft': match['ficTracDeltaRotationVectorLab']['z']}
entries[entry] = pd.Series(framedat).to_frame().T

if len(entries) > 0:
Expand Down