def toRadialShape(im, s=1024, smooth=501): """ desc: Extracts the radial outline from an image. argumens: im: desc: An image with 0 for background and 1 for shape. type: ndarray keywords: s: desc: The length of the output arrays. type: int smooth: desc: Smoothing window for the radius or None for no smoothing. type: [int, NoneType] returns: desc: A tuple with an array of angles and an array of radii. type: tuple """ im = edgeDetect(im) cx = im.shape[0]/2 cy = im.shape[1]/2 x, y = np.where(im != 0) a = np.arctan2(y-cy, x-cx) r = np.sqrt((x-cx)**2+(y-cy)**2) a = np.concatenate( (a-2*np.pi, a, a+2*np.pi) ) r = np.concatenate( (r, r, r ) ) i = np.argsort(a) a = a[i] r = r[i] if smooth != None: r = tk.smooth(r, windowLen=smooth) f = interpolate.interp1d(a, r) ia = np.linspace(-np.pi, np.pi, s) ir = f(ia) return ia, ir
def __finishTrial__(self, trialDict):
"""
Perform some finalization after we we have parsed a trial
Arguments:
trialDict -- a trial dictionary
"""
nPhase = len(self.traceDict)
i = 1
if self.traceImg or self.tracePlot:
plt.clf()
plt.close()
plt.figure(figsize=(12,12))
plt.subplots_adjust(hspace=.5, wspace=.5)
for phase, trace in self.traceDict.iteritems():
a = np.array(trace, dtype=float)
if len(a) == 0:
continue
origA = a.copy()
if self.blinkReconstruct:
a[:,2] = TraceKit.blinkReconstruct(a[:,2])
if self.traceSmoothParams != None:
a[:,0] = TraceKit.smooth(a[:,0], **self.traceSmoothParams)
a[:,1] = TraceKit.smooth(a[:,1], **self.traceSmoothParams)
a[:,2] = TraceKit.smooth(a[:,2], **self.traceSmoothParams)
self.traceDict[phase] = a
path = os.path.join(self.traceFolder, '%s-%.5d-%s.npy' \
% (trialDict['file'], trialDict['trialId'], phase))
if not os.path.exists(self.traceFolder):
print('Creating traceFolder: %s' % self.traceFolder)
os.makedirs(self.traceFolder)
np.save(path, a)
trialDict['__trace_%s__' % phase] = path
if self.traceImg or self.tracePlot:
plt.subplot(nPhase, 3, i)
i += 1
plt.title('X(%s)' % phase)
plt.plot(a[:,0])
if self.traceSmoothParams != None:
plt.plot(origA[:,0])
plt.subplot(nPhase, 3, i)
i += 1
plt.title('Y(%s)' % phase)
plt.plot(a[:,1])
if self.traceSmoothParams != None:
plt.plot(origA[:,1])
plt.subplot(nPhase, 3, i)
i += 1
plt.title('Pupil(%s)' % phase)
plt.plot(a[:,2])
if self.traceSmoothParams != None or self.blinkReconstruct:
plt.plot(origA[:,2])
if self.traceImg or self.tracePlot:
plt.suptitle(path)
if self.traceImg:
path = os.path.join(self.traceFolder, 'png', '%s-%.5d-%s.png' \
% (trialDict['file'], trialDict['trialId'], phase))
if not os.path.exists(os.path.join(self.traceFolder, 'png')):
print('Creating traceImgFolder: %s' % os.path.join( \
self.traceFolder, 'png'))
if not os.path.exists(os.path.join(self.traceFolder, 'png')):
os.makedirs(os.path.join(self.traceFolder, 'png'))
plt.savefig(path)
if self.tracePlot:
plt.show()
