def plot_polar(phi, r, ax=None):
y_r = config['y_range']
y_th0 = config['y_thresholds'][0]
y_th1 = config['y_thresholds'][1]
y_target_norm = analysis.normalize(config['y_target'], y_r)
y_th0_norm = analysis.normalize(y_th0, y_r)
y_th1_norm = analysis.normalize(y_th1, y_r)
phi_target = np.arccos(y_target_norm)
phi_th0 = np.arccos(y_th0_norm)
phi_th1 = np.arccos(y_th1_norm)
if ax is None:
fig = plt.figure(figsize=(15, 15))
ax = fig.add_subplot(111, polar=True)
ax.set_thetamin(0)
ax.set_thetamax(180)
ax.set_xticks(np.pi / 180. * np.linspace(180, 0, 4, endpoint=False))
ax.fill_betweenx(r,
np.pi - phi_target,
np.pi - phi,
color=config['color_standard'],
alpha=0.2)
ax.plot([np.pi - phi_target, np.pi - phi_target], [0, 1],
dashes=(2, 3),
c=config['color_default'])
if y_th0:
phi_cold = np.where(phi > phi_th0, phi, phi_th0)
ax.fill_betweenx(r,
np.pi - phi_th0,
np.pi - phi_cold,
color=config['color_cold'],
alpha=0.2)
ax.plot([np.pi - phi_th0, np.pi - phi_th0], [0, 1],
dashes=(4, 4),
c=config['color_cold'])
if y_th1:
phi_warm = np.where(phi < phi_th1, phi, phi_th1)
ax.fill_betweenx(r,
np.pi - phi_th1,
np.pi - phi_warm,
color=config['color_warm'],
alpha=0.2)
ax.plot([np.pi - phi_th1, np.pi - phi_th1], [0, 1],
dashes=(4, 4),
c=config['color_warm'])
ax.plot(np.pi - phi, r, c=config['color_default'])
return ax
def analyze():
raw = request.get_data()
curve = raw_to_dataframe(raw)
curve = normalize(curve)
last_coin['curve'] = curve
last_coin['datetime'] = datetime.today().isoformat()
coin = classify_coin(curve)
last_coin['coin'] = coin
if last_coin['coin'] == -1:
last_coin['coin'] = 'unknown'
return 'ok'
# print(np.shape(test_V_arr_for_combo))
#==============================================================================================================
# Process Base and Mixture Data
#==============================================================================================================
# dim(trace_V_arr) = (3, 1000, 2300) which is (num base odors, num neurons in network, # timesteps after start=100ms)
# dim(X) = (6900, 1000) which is (num base odors*# timesteps after start=100ms, num neurons in network)
X = np.hstack(trace_V_arr).T
#normalize training (base odor) data
mini = np.min(
X) # lowest voltage of any neuron's voltages at any time for any odor
maxi = np.max(
X) # highest voltage of any neuron's voltages at any time for any odor
normalized_Training_Voltages = anal.normalize(
X, mini, maxi) # 0 if minimum value, 1 if maximum value.
point_Labels = np.hstack(label_arr)
# Train the SVM on base odors and labels
clf = anal.learnSVM(normalized_Training_Voltages, point_Labels)
for rowNum, aCombo in enumerate(baseNum):
# load, ignoring four of the outputs
_,_,_,test_V_arr_for_combo[rowNum],_,label_test_arr_for_combo[rowNum] \
= anal.load_data(te_prefix+'combo_'+str(rowNum)+"_", num_runs = number_Of_Mix_Runs)
test_data = test_V_arr_for_combo[rowNum] # mixed odor voltage
test_data = anal.normalize(
test_data, mini,
# run the simulation and save to disk
ex.createData(run_params_train, I_arr, states, net)
ex.mixtures2(run_params_test, I_arr[:num_odors_mix], states, net)
# load in the data from disk
spikes_t_arr, spikes_i_arr, I_arr, trace_V_arr, trace_t_arr, label_arr = anal.load_data(tr_prefix,
num_runs=num_odors_train)
spikes_t_test_arr, spikes_i_test_arr, I_test_arr, test_V_arr, test_t_arr, label_test_arr = anal.load_data(te_prefix,
num_runs=num_alpha * num_test)
X = np.hstack(trace_V_arr).T
# normalize training data
mini = np.min(X)
maxi = np.max(X)
X = anal.normalize(X, mini, maxi)
y = np.hstack(label_arr)
# train the SVM
clf = anal.learnSVM(X, y)
test_data = test_V_arr
test_data = anal.normalize(test_data, mini, maxi)
y_test = np.mean(label_test_arr, axis=1)
pred_arr = []
A_arr = []
for i in range(len(test_data)):
pred = clf.predict(test_data[i].T)
def count_vessels(probesizemicron, theta=[0]):
# algorithm pseudocode:
# normalize image slice
# rotate probe
# slice rotated image to generate line profiles
# low pass filter line profiles to remove noise
# find peaks of line profile (local maxima)
# discard peaks below empirical threshold
# count the number of peaks --> number of crossed vessels at location
# no need to adjust discard theshold with depth
# repeat above for all substacks in the whole imaging volume
# p.s. tested on 50um substacks
thresh = -0.6
# create sub-z tiff stack
subzstack = subz_from_3dtiff(tif3darray, 50)
print tif3darray.shape
print subzstack.shape
# make mask of probe cross-section
probesizepix = micron2pix(probesizemicron)
l = max(probesizepix)
k = np.zeros((l, l))
k[l / 2] = 1 # horizontal probe
damage2d = np.zeros(
(len(theta), ((subzstack.shape[1] - l) / downsample + 1),
((subzstack.shape[2] - l) / downsample + 1)))
lineprofiles = np.zeros((subzstack.shape[0], len(theta),
((subzstack.shape[1] - l) / downsample + 1),
((subzstack.shape[1] - l) / downsample + 1)),
dtype=object)
print damage2d.shape
for lnum, layer in enumerate(subzstack):
print 'layer ' + str(lnum + 1) + ' of ' + str(subzstack.shape[0])
layer = dsp.normalize(layer)
for i, t in enumerate(theta):
print('%s degrees' ', all translations...' % t)
rotated = misc.imrotate(k, t, interp='nearest')
# get rid of rotation artifacts
rotated[rotated < rotated.max()] = 0
rotated[rotated == rotated.max()] = 1
# for y in xrange(layer.shape[0]+l): # add step here...
ys = 0
for y in xrange(0, layer.shape[0] - l, downsample):
xs = 0
# for x in xrange(layer.shape[1]-l): # add step here...
for x in xrange(0, layer.shape[1] - l, downsample):
a = rotated * layer[y:y + l, x:x + l]
b = a.T[a.T.nonzero()]
# luminance est of collision
# profl = b
profl = dsp.smoothg(
b, 20) # smoothed profile for this location
# if b.mean() > .5:
c = profl > 1.5
damage2d[i, ys, xs] += np.diff(c).nonzero()[0][::2].size
profl[profl > 1.5] = 1.5
profl[profl < thresh] = thresh # discard small peaks
lineprofiles[lnum, i, ys, xs] = profl
# count peaks --> vessels
# damage2d[i,y,x] += sum(dsp.islocmax(profl))
damage2d[i, ys, xs] += argrelmax(profl, order=5)[0].size
# damage2d[i, ys, xs] += len(find_events(profl, thresh))
# damage2d[i, ys, xs] += len(find_peaks_cwt(b, np.arange(5, 20)))
xs += 1
ys += 1
return damage2d, lineprofiles, subzstack
def count_vessels(probesizemicron, theta = [0]):
# algorithm pseudocode:
# normalize image slice
# rotate probe
# slice rotated image to generate line profiles
# low pass filter line profiles to remove noise
# find peaks of line profile (local maxima)
# discard peaks below empirical threshold
# count the number of peaks --> number of crossed vessels at location
# no need to adjust discard theshold with depth
# repeat above for all substacks in the whole imaging volume
# p.s. tested on 50um substacks
thresh = -0.6
# create sub-z tiff stack
subzstack = subz_from_3dtiff(tif3darray, 50)
print tif3darray.shape
print subzstack.shape
# make mask of probe cross-section
probesizepix = micron2pix(probesizemicron)
l = max(probesizepix)
k = np.zeros((l,l))
k[l/2] = 1 # horizontal probe
damage2d = np.zeros((len(theta),
((subzstack.shape[1] - l) / downsample + 1),
((subzstack.shape[2] - l) / downsample + 1)))
lineprofiles = np.zeros((subzstack.shape[0], len(theta),
((subzstack.shape[1] - l) / downsample + 1),
((subzstack.shape[1] - l) / downsample + 1)), dtype=object)
print damage2d.shape
for lnum,layer in enumerate(subzstack):
print 'layer '+str(lnum+1)+' of '+str(subzstack.shape[0])
layer = dsp.normalize(layer)
for i, t in enumerate(theta):
print('%s degrees'', all translations...'%t)
rotated = misc.imrotate(k, t, interp='nearest')
# get rid of rotation artifacts
rotated[rotated < rotated.max()] = 0
rotated[rotated == rotated.max()] = 1
# for y in xrange(layer.shape[0]+l): # add step here...
ys = 0
for y in xrange(0, layer.shape[0]-l, downsample):
xs = 0
# for x in xrange(layer.shape[1]-l): # add step here...
for x in xrange(0, layer.shape[1]-l, downsample):
a=rotated*layer[y:y+l,x:x+l]
b=a.T[a.T.nonzero()]
# luminance est of collision
# profl = b
profl = dsp.smoothg(b,20) # smoothed profile for this location
# if b.mean() > .5:
c = profl > 1.5
damage2d[i,ys,xs] += np.diff(c).nonzero()[0][::2].size
profl[profl > 1.5] = 1.5
profl[profl < thresh] = thresh # discard small peaks
lineprofiles[lnum, i, ys, xs] = profl
# count peaks --> vessels
# damage2d[i,y,x] += sum(dsp.islocmax(profl))
damage2d[i,ys,xs] += argrelmax(profl, order=5)[0].size
# damage2d[i, ys, xs] += len(find_events(profl, thresh))
# damage2d[i, ys, xs] += len(find_peaks_cwt(b, np.arange(5, 20)))
xs += 1
ys += 1
return damage2d, lineprofiles, subzstack