def pdf(x, a, b, mu = 0, sigma = 1):
""" Probablity density function of the truncated normal distribution
on the interval [a, b].
Args:
x: a value between a and b to calculate its pdf.
a: the left boundary of the truncated normal distribution.
b: the right boundary of the truncated normal distribution.
mu: the mean value.
sigma: the standard derivation.
Returns:
The probablity density at point x
Raises:
ValueError: the error is raised the value of x, a, and b are invalid.
"""
if a >= b:
raise ValueError("The interval's left boundary is larger than \
the right boundary ")
if x < a or x > b:
raise ValueError("The query position is outside of the interval")
if a == np.inf:
raise ValueError("The interval's left boundary can not be np.inf")
if b == -np.inf:
raise ValueError("The interval's right boundary can not be -np.inf")
x = (x - mu) / sigma
a = (a - mu) / sigma
b = (b - mu) / sigma
if a * b <= 0:
area = special.ndtr(b) - special.ndtr(a)
p = 1 / np.sqrt(2*np.pi) * np.exp(-0.5*x**2) / area
return p
else:
x = -np.abs(x)
if a > 0:
low = -np.abs(b)
up = -np.abs(a)
else:
low = -np.abs(a)
up = -np.abs(b)
low_log_area = special.log_ndtr(low)
up_log_area = special.log_ndtr(up)
low_log_area += 0.5 * up**2
up_log_area += 0.5 * up**2
area = np.exp(up_log_area) - np.exp(low_log_area)
p = 1 / np.sqrt(2*np.pi) * np.exp(-0.5*(x**2 - up**2)) / area
return p
def _compute_rdp_with_order(sample_rate, noise_stddev, order):
"""
Compute rdp for each order.
Args:
sample_rate (float): Sampling probability.
noise_stddev (float): Noise multiplier.
order: The order used for computing rdp.
Returns:
float, rdp value.
"""
if float(order).is_integer():
log_integrate = -np.inf
for k in range(order + 1):
term_k = (np.log(special.binom(order, k)) +
k * np.log(sample_rate) +
(order - k) * np.log(1 - sample_rate)
) + (k * k - k) / (2 * (noise_stddev**2))
log_integrate = _log_add(log_integrate, term_k)
return float(log_integrate) / (order - 1)
log_part_0, log_part_1 = -np.inf, -np.inf
k = 0
z0 = noise_stddev**2 * np.log(1 / sample_rate - 1) + 1 / 2
while True:
bi_coef = special.binom(order, k)
log_coef = np.log(abs(bi_coef))
j = order - k
term_k_part_0 = log_coef + k * np.log(sample_rate) + j * np.log(
1 - sample_rate) + (k * k -
k) / (2 *
(noise_stddev**2)) + special.log_ndtr(
(z0 - k) / noise_stddev)
term_k_part_1 = log_coef + j * np.log(sample_rate) + k * np.log(
1 - sample_rate) + (j * j -
j) / (2 *
(noise_stddev**2)) + special.log_ndtr(
(j - z0) / noise_stddev)
if bi_coef > 0:
log_part_0 = _log_add(log_part_0, term_k_part_0)
log_part_1 = _log_add(log_part_1, term_k_part_1)
else:
log_part_0 = _log_subtract(log_part_0, term_k_part_0)
log_part_1 = _log_subtract(log_part_1, term_k_part_1)
k += 1
if np.max([term_k_part_0, term_k_part_1]) < -30:
break
return _log_add(log_part_0, log_part_1) / (order - 1)
def _log_erfc(x: float) -> float:
r"""Computes :math:`log(erfc(x))` with high accuracy for large ``x``.
Helper function used in computation of :math:`log(A_\alpha)`
for a fractional alpha.
"""
return math.log(2) + special.log_ndtr(-x * 2**0.5)
def logq(t, tau, sigma):
"""
Logarithm of exponential pdf with scale tau convoluted with a normal with
scale sigma without the 1/tau factor.
"""
return -t / tau + 1 / 2 * (sigma / tau)**2 + special.log_ndtr(t / sigma -
sigma / tau)
def test_log_ndtr_values_gt31(self):
x = np.array([31.6, 32.8, 34.9, 37.1])
expected = [
-1.846036234858162e-219, -2.9440539964066835e-236,
-3.71721649450857e-267, -1.4047119663106221e-301
]
y = sc.log_ndtr(x)
assert_allclose(y, expected, rtol=3e-13)
def tobit_neg_log_likelihood_der(xs, ys, params):
x_left, x_mid, x_right = xs
y_left, y_mid, y_right = ys
b = params[:-1]
# s = math.exp(params[-1]) # in censReg, not using chain rule as below; they optimize in terms of log(s)
s = params[-1]
beta_jac = np.zeros(len(b))
sigma_jac = 0
if y_left is not None:
left_stats = (y_left - np.dot(x_left, b)) / s
l_pdf = scipy.stats.norm.logpdf(left_stats)
l_cdf = log_ndtr(left_stats)
left_frac = np.exp(l_pdf - l_cdf)
beta_left = np.dot(left_frac, x_left / s)
beta_jac -= beta_left
left_sigma = np.dot(left_frac, left_stats)
sigma_jac -= left_sigma
if y_right is not None:
right_stats = (np.dot(x_right, b) - y_right) / s
r_pdf = scipy.stats.norm.logpdf(right_stats)
r_cdf = log_ndtr(right_stats)
right_frac = np.exp(r_pdf - r_cdf)
beta_right = np.dot(right_frac, x_right / s)
beta_jac += beta_right
right_sigma = np.dot(right_frac, right_stats)
sigma_jac -= right_sigma
if y_mid is not None:
mid_stats = (y_mid - np.dot(x_mid, b)) / s
beta_mid = np.dot(mid_stats, x_mid / s)
beta_jac += beta_mid
mid_sigma = (np.square(mid_stats) - 1).sum()
sigma_jac += mid_sigma
combo_jac = np.append(
beta_jac, sigma_jac /
s) # by chain rule, since the expression above is dloglik/dlogsigma
return -combo_jac
def test_log_ndtr_values_16_31(self):
x = np.array([16.15, 20.3, 21.4, 26.2, 30.9])
expected = [
-5.678084565148492e-59, -6.429244467698346e-92,
-6.680402412553295e-102, -1.328698078458869e-151,
-5.972288641838264e-210
]
y = sc.log_ndtr(x)
assert_allclose(y, expected, rtol=2e-13)
def tobit_neg_log_likelihood_der(xs, ys, params):
x_left, x_mid, x_right = xs
y_left, y_mid, y_right = ys
b = params[:-1]
# s = math.exp(params[-1]) # in censReg, not using chain rule as below; they optimize in terms of log(s)
s = params[-1]
beta_jac = np.zeros(len(b))
sigma_jac = 0
if y_left is not None:
left_stats = (y_left - np.dot(x_left, b)) / s
l_pdf = scipy.stats.norm.logpdf(left_stats)
l_cdf = log_ndtr(left_stats)
left_frac = np.exp(l_pdf - l_cdf)
beta_left = np.dot(left_frac, x_left / s)
beta_jac -= beta_left
left_sigma = np.dot(left_frac, left_stats)
sigma_jac -= left_sigma
if y_right is not None:
right_stats = (np.dot(x_right, b) - y_right) / s
r_pdf = scipy.stats.norm.logpdf(right_stats)
r_cdf = log_ndtr(right_stats)
right_frac = np.exp(r_pdf - r_cdf)
beta_right = np.dot(right_frac, x_right / s)
beta_jac += beta_right
right_sigma = np.dot(right_frac, right_stats)
sigma_jac -= right_sigma
if y_mid is not None:
mid_stats = (y_mid - np.dot(x_mid, b)) / s
beta_mid = np.dot(mid_stats, x_mid / s)
beta_jac += beta_mid
mid_sigma = (np.square(mid_stats) - 1).sum()
sigma_jac += mid_sigma
combo_jac = np.append(beta_jac, sigma_jac / s) # by chain rule, since the expression above is dloglik/dlogsigma
return -combo_jac
def test_log_ndtr_values_8_16(self):
x = np.array([8.001, 8.06, 8.15, 8.5, 10, 12, 14, 16])
expected = [
-6.170639424817055e-16, -3.814722443652823e-16,
-1.819621363526629e-16, -9.479534822203318e-18,
-7.619853024160525e-24, -1.776482112077679e-33,
-7.7935368191928e-45, -6.388754400538087e-58
]
y = sc.log_ndtr(x)
assert_allclose(y, expected, rtol=5e-14)
def test_log_ndtr_moderate_le8(self):
x = np.array([-0.75, -0.25, 0, 0.5, 1.5, 2.5, 3, 4, 5, 7, 8])
expected = np.array([
-1.4844482299196562, -0.9130617648111351, -0.6931471805599453,
-0.3689464152886564, -0.06914345561223398, -0.006229025485860002,
-0.0013508099647481938, -3.167174337748927e-05,
-2.866516129637636e-07, -1.279812543886654e-12,
-6.220960574271786e-16
])
y = sc.log_ndtr(x)
assert_allclose(y, expected, rtol=1e-14)
def _log_erfc(x):
"""Compute log(erfc(x)) with high accuracy for large x."""
try:
return math.log(2) + special.log_ndtr(-x * 2**.5)
except NameError:
# If log_ndtr is not available, approximate as follows:
r = special.erfc(x)
if r == 0.0:
return (-math.log(math.pi) / 2 - math.log(x) - x**2 - .5 * x**-2 +
.625 * x**-4 - 37. / 24. * x**-6 + 353. / 64. * x**-8)
else:
return math.log(r)
def _log_erfc(x):
try:
return math.log(2) + special.log_ndtr(-x * 2**.5)
except NameError:
# If log_ndtr is not available, approximate as follows:
r = special.erfc(x)
if r == 0.0:
# Using the Laurent series at infinity for the tail of the erfc function:
# erfc(x) ~ exp(-x^2-.5/x^2+.625/x^4)/(x*pi^.5)
# To verify in Mathematica:
# Series[Log[Erfc[x]] + Log[x] + Log[Pi]/2 + x^2, {x, Infinity, 6}]
return (-math.log(math.pi) / 2 - math.log(x) - x**2 - .5 * x**-2 +
.625 * x**-4 - 37. / 24. * x**-6 + 353. / 64. * x**-8)
else:
return math.log(r)
def _test_grid_log(self, dtype, grid_spec, error_spec):
with self.test_session():
grid = _make_grid(dtype, grid_spec)
actual = sm.log_ndtr(grid).eval()
# Basic tests.
self.assertTrue(np.isfinite(actual).all())
# On the grid, -inf < log_cdf(x) < 0. In this case, we should be able
# to use a huge grid because we have used tricks to escape numerical
# difficulties.
self.assertTrue((actual < 0).all())
_check_strictly_increasing(actual)
# Versus scipy.
expected = special.log_ndtr(grid)
# Scipy prematurely goes to zero at some places that we don't. So don't
# include these in the comparison.
self.assertAllClose(expected.astype(np.float64)[expected < 0],
actual.astype(np.float64)[expected < 0],
rtol=error_spec.rtol, atol=error_spec.atol)
def _test_grid_log(self, dtype, grid_spec, error_spec):
with self.test_session():
grid = _make_grid(dtype, grid_spec)
actual = sm.log_ndtr(grid).eval()
# Basic tests.
self.assertTrue(np.isfinite(actual).all())
# On the grid, -inf < log_cdf(x) < 0. In this case, we should be able
# to use a huge grid because we have used tricks to escape numerical
# difficulties.
self.assertTrue((actual < 0).all())
_check_strictly_increasing(actual)
# Versus scipy.
expected = special.log_ndtr(grid)
# Scipy prematurely goes to zero at some places that we don't. So don't
# include these in the comparison.
self.assertAllClose(expected.astype(np.float64)[expected < 0],
actual.astype(np.float64)[expected < 0],
rtol=error_spec.rtol,
atol=error_spec.atol)
def _logcdf(x): #if x > 0: return math.log1p(-math.exp(TrueSkill.logcdf(-x))) return log_ndtr(x)
def main():
pass # For compatibility between running under Spyder and the CLI
#%% load data
fname = os.path.join(caiman_datadir(), 'example_movies', 'demoMovie.tif')
Y = cm.load(fname).astype(np.float32) #
# used as a background image
Cn = cm.local_correlations(Y.transpose(1, 2, 0))
#%% set up some parameters
# frame rate (Hz)
fr = 10
# approximate length of transient event in seconds
decay_time = 0.5
# expected half size of neurons
gSig = [6, 6]
# order of AR indicator dynamics
p = 1
# minimum SNR for accepting new components
min_SNR = 3.5
# correlation threshold for new component inclusion
rval_thr = 0.90
# number of background components
gnb = 3
# set up some additional supporting parameters needed for the algorithm (these are default values but change according to dataset characteristics)
# number of shapes to be updated each time (put this to a finite small value to increase speed)
max_comp_update_shape = np.inf
# maximum number of expected components used for memory pre-allocation (exaggerate here)
expected_comps = 50
# number of timesteps to consider when testing new neuron candidates
N_samples = np.ceil(fr * decay_time)
# exceptionality threshold
thresh_fitness_raw = log_ndtr(-min_SNR) * N_samples
# total length of file
T1 = Y.shape[0]
# set up CNMF initialization parameters
# merging threshold, max correlation allowed
merge_thresh = 0.8
# number of frames for initialization (presumably from the first file)
initbatch = 400
# size of patch
patch_size = 32
# amount of overlap between patches
stride = 3
# max number of components in each patch
K = 4
#%% obtain initial batch file used for initialization
# memory map file (not needed)
fname_new = Y[:initbatch].save(os.path.join(caiman_datadir(),
'example_movies', 'demo.mmap'),
order='C')
Yr, dims, T = cm.load_memmap(fname_new)
images = np.reshape(Yr.T, [T] + list(dims), order='F')
Cn_init = cm.local_correlations(np.reshape(Yr, dims + (T, ), order='F'))
#%% RUN (offline) CNMF algorithm on the initial batch
pl.close('all')
cnm_init = cnmf.CNMF(2,
k=K,
gSig=gSig,
merge_thresh=merge_thresh,
fr=fr,
p=p,
rf=patch_size // 2,
stride=stride,
skip_refinement=False,
normalize_init=False,
options_local_NMF=None,
minibatch_shape=100,
minibatch_suff_stat=5,
update_num_comps=True,
rval_thr=rval_thr,
thresh_fitness_delta=-50,
gnb=gnb,
decay_time=decay_time,
thresh_fitness_raw=thresh_fitness_raw,
batch_update_suff_stat=False,
max_comp_update_shape=max_comp_update_shape,
expected_comps=expected_comps,
dview=None,
min_SNR=min_SNR)
cnm_init = cnm_init.fit(images)
print(('Number of components:' + str(cnm_init.estimates.A.shape[-1])))
pl.figure()
crd = plot_contours(cnm_init.estimates.A.tocsc(), Cn_init, thr=0.9)
#%% run (online) OnACID algorithm
cnm = deepcopy(cnm_init)
cnm.params.data['dims'] = (60, 80)
cnm._prepare_object(np.asarray(Yr), T1)
t = initbatch
Y_ = cm.load(fname)[initbatch:].astype(np.float32)
for frame_count, frame in enumerate(Y_):
cnm.fit_next(t, frame.copy().reshape(-1, order='F'))
t += 1
#%% extract the results
C, f = cnm.estimates.C_on[gnb:cnm.M], cnm.estimates.C_on[:gnb]
A, b = cnm.estimates.Ab[:, gnb:cnm.M], cnm.estimates.Ab[:, :gnb]
print(('Number of components:' + str(A.shape[-1])))
#%% pass through the CNN classifier with a low threshold (keeps clearer neuron shapes and excludes processes)
use_CNN = True
if use_CNN:
# threshold for CNN classifier
thresh_cnn = 0.1
from caiman.components_evaluation import evaluate_components_CNN
predictions, final_crops = evaluate_components_CNN(
A,
dims,
gSig,
model_name=os.path.join(caiman_datadir(), 'model', 'cnn_model'))
A_exclude, C_exclude = A[:, predictions[:, 1] < thresh_cnn], C[
predictions[:, 1] < thresh_cnn]
A, C = A[:,
predictions[:,
1] >= thresh_cnn], C[predictions[:,
1] >= thresh_cnn]
noisyC = cnm.estimates.noisyC[gnb:cnm.M]
YrA = noisyC[predictions[:, 1] >= thresh_cnn] - C
else:
YrA = cnm.estimates.noisyC[gnb:cnm.M] - C
#%% plot results
pl.figure()
crd = cm.utils.visualization.plot_contours(A, Cn, thr=0.9)
view_patches_bar(Yr, A, C, b, f, dims[0], dims[1], YrA, img=Cn)
def log_p_exp_gauss(t, tau, sigma):
"""
(Logarithm of) exponential pdf with scale tau convoluted with a normal with
scale sigma.
"""
return -np.log(tau) - t/tau + 1/2 * (sigma / tau) ** 2 + special.log_ndtr(t / sigma - sigma / tau)
#%% set up some parameters
fr = 10 # frame rate (Hz)
decay_time = 0.5 # approximate length of transient event in seconds
gSig = [6,6] # expected half size of neurons
p = 1 # order of AR indicator dynamics
min_SNR = 3.5 # minimum SNR for accepting new components
rval_thr = 0.90 # correlation threshold for new component inclusion
gnb = 3 # number of background components
# set up some additional supporting parameters needed for the algorithm (these are default values but change according to dataset characteristics)
max_comp_update_shape = np.inf # number of shapes to be updated each time (put this to a finite small value to increase speed)
expected_comps = 250 # maximum number of expected components used for memory pre-allocation (exaggerate here)
N_samples = np.ceil(fr*decay_time) # number of timesteps to consider when testing new neuron candidates
thresh_fitness_raw = log_ndtr(-min_SNR)*N_samples # exceptionality threshold
T1 = Y.shape[0] # total length of file
# set up CNMF initialization parameters
merge_thresh = 0.8 # merging threshold, max correlation allowed
initbatch = 20000 # number of frames for initialization (presumably from the first file)
patch_size = 32 # size of patch
stride = 3 # amount of overlap between patches
K = 4 # max number of components in each patch
#********************************************************************************************************************************
#********************************************************************************************************************************
#********************************************************************************************************************************
#%% obtain initial batch file used for initialization
min_SNR = 3.5 # correlation threshold for new component inclusion rval_thr = 0.90 # number of background components gnb = 3 # set up some additional supporting parameters needed for the algorithm (these are default values but change according to dataset characteristics) # number of shapes to be updated each time (put this to a finite small value to increase speed) max_comp_update_shape = np.inf # maximum number of expected components used for memory pre-allocation (exaggerate here) expected_comps = 50 # number of timesteps to consider when testing new neuron candidates N_samples = np.ceil(fr * decay_time) # exceptionality threshold thresh_fitness_raw = log_ndtr(-min_SNR) * N_samples # total length of file T1 = Y.shape[0] # set up CNMF initialization parameters # merging threshold, max correlation allowed merge_thresh = 0.8 # number of frames for initialization (presumably from the first file) initbatch = 400 # size of patch patch_size = 32 # amount of overlap between patches stride = 3 # max number of components in each patch K = 4
def _log_ndtr_cpu(x, dtype):
from scipy import special
return special.log_ndtr(x).astype(dtype)
def log_ndtr_ndtri_exp(y):
return log_ndtr(ndtri_exp(y))
def normcdfln(x): # pragma: no cover
return special.log_ndtr(x)
def _logcdf(x):
#if x > 0: return math.log1p(-math.exp(TrueSkill.logcdf(-x)))
return log_ndtr(x)
def Caiman_online(root):
for k, ele in enumerate(root.winfo_children()):
if k > 0: ele.destroy()
#print '...text************'
root.minsize(width=1000, height=600)
root.data = emptyObject()
#root.data_folder root.data.root_dir = '/media/cat/4TB/in_vivo/rafa/alejandro/G2M5/20170511/000/'
root.data.file_name = ''
#root.caiman_folder = np.loadtxt('caiman_folder_location.txt',dtype=str)
#******** Filename Selector
def button0():
print("...selecting file...")
root.data.file_name = tkFileDialog.askopenfilename(
initialdir=root.data_folder,
defaultextension=".tif",
filetypes=(("tif", "*.tif"), ("npy", "*.npy"), ("All Files",
"*.*")))
print(root.data.file_name)
root.data_folder = os.path.split(root.data.file_name)[0]
np.savetxt('data_folder_location.txt', [root.data_folder], fmt="%s")
e.delete(0, END)
e.insert(0, root.data.file_name)
root.title(os.path.split(root.data.file_name)[1])
b0 = Button(root, text="Filename:", anchor="w",
command=button0) #Label(root, text="Filename: ").grid(row=0)
b0.place(x=0, y=0)
e = Entry(root, justify='left') #text entry for the filename
e.delete(0, END)
e.insert(0, root.data.file_name)
e.place(x=110, y=4, width=600)
x_offset = 0
y_offset = 30
l00 = Label(root, text='_' * 200)
l00.place(x=x_offset, y=y_offset, height=30, width=1000)
#******** CNMF Parameters ******************
#
x_offset = 0
y_offset = 55
l0 = Label(root,
text='CNMF Initialization Parameters',
fg="red",
justify='left')
l0.place(x=x_offset, y=y_offset, height=30, width=190)
#Param 1
x_offset = 10
y_offset = +80
l1 = Label(root, text='Merge Threshold')
l1.place(x=x_offset, y=y_offset, height=30, width=100)
e1 = Entry(root, justify='left', width=4) #text entry for the filename
e1.delete(0, END)
e1.insert(0, 0.8)
e1.place(x=x_offset + 103, y=y_offset + 5)
x_offset += 140
##Param 2
#l2 = Label(root, text='Autoregress order')
#l2.place(x=x_offset,y=y_offset, height=30,width=130)
#e2 = Entry(root, justify='left', width=3) #text entry for the filename
#e2.delete(0, END)
#e2.insert(0, 1)
#e2.place(x=x_offset+120,y=y_offset+5)
#x_offset+=150
#Param 3
l3 = Label(root, text='Initial Batch')
l3.place(x=x_offset, y=y_offset, height=30, width=100)
e3 = Entry(root, justify='left', width=5) #text entry for the filename
e3.delete(0, END)
e3.insert(0, 20000)
e3.place(x=x_offset + 88, y=y_offset + 5)
x_offset += 145
#Param 4
l4 = Label(root, text='patch_size')
l4.place(x=x_offset, y=y_offset, height=30, width=100)
e4 = Entry(root, justify='left', width=3) #text entry for the filename
e4.delete(0, END)
e4.insert(0, 32)
e4.place(x=x_offset + 85, y=y_offset + 5)
x_offset += 160
#Param 5
l5 = Label(root, text='stride')
l5.place(x=x_offset, y=y_offset, height=30, width=40)
e5 = Entry(root, justify='left', width=3) #text entry for the filename
e5.delete(0, END)
e5.insert(0, 3)
e5.place(x=x_offset + 38, y=y_offset + 5)
x_offset += 100
#Param 6
l6 = Label(root, text='K')
l6.place(x=x_offset, y=y_offset, height=30, width=15)
e6 = Entry(root, justify='left', width=3) #text entry for the filename
e6.delete(0, END)
e6.insert(0, 4)
e6.place(x=x_offset + 15, y=y_offset + 5)
#***************************************************
#Recording Defaults
#NEW LINE
x_offset = 0
y_offset += 50
print(x_offset, y_offset)
l_1 = Label(root, text='Recording Defaults', fg="blue", justify='left')
l_1.place(x=x_offset, y=y_offset, height=30, width=120)
y_offset += 25
#Param 2
l7 = Label(root, text='frame_rate (hz)')
l7.place(x=x_offset, y=y_offset, height=30, width=110)
x_offset += 105
e7 = Entry(root, justify='left', width=4) #text entry for the filename
e7.delete(0, END)
e7.insert(0, 10)
e7.place(x=x_offset, y=y_offset + 5)
#Param 3
x_offset += 30
l8 = Label(root, text='decay_time (s)')
l8.place(x=x_offset, y=y_offset, height=30, width=110)
x_offset += 100
e8 = Entry(root, justify='left', width=4) #text entry for the filename
e8.delete(0, END)
e8.insert(0, 0.5)
e8.place(x=x_offset, y=y_offset + 5)
#Param 3
x_offset += 50
l9 = Label(root, text='neuron (pixels)')
l9.place(x=x_offset, y=y_offset, height=30, width=100)
x_offset += 100
e9 = Entry(root, justify='left', width=4) #text entry for the filename
e9.delete(0, END)
e9.insert(0, '6, 6')
e9.place(x=x_offset, y=y_offset + 5)
#Param 3
x_offset += 40
l10 = Label(root, text='order AR dynamics')
l10.place(x=x_offset, y=y_offset, height=30, width=145)
x_offset += 135
e10 = Entry(root, justify='left', width=3) #text entry for the filename
e10.delete(0, END)
e10.insert(0, 1)
e10.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 40
l11 = Label(root, text='min_SNR')
l11.place(x=x_offset, y=y_offset, height=30, width=65)
x_offset += 62
e11 = Entry(root, justify='left', width=4) #text entry for the filename
e11.delete(0, END)
e11.insert(0, 3.5)
e11.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 40
l12 = Label(root, text='rval_thr')
l12.place(x=x_offset, y=y_offset, height=30, width=65)
x_offset += 60
e12 = Entry(root, justify='left', width=4) #text entry for the filename
e12.delete(0, END)
e12.insert(0, 0.90)
e12.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 40
l13 = Label(root, text='# bkgr comp')
l13.place(x=x_offset, y=y_offset, height=30, width=105)
x_offset += 95
e13 = Entry(root, justify='left', width=4) #text entry for the filename
e13.delete(0, END)
e13.insert(0, 3)
e13.place(x=x_offset, y=y_offset + 5)
#***************************************************
#Temporary Initalization Defaults
#NEW LINE
x_offset = 0
y_offset += 50
print(x_offset, y_offset)
l_1 = Label(root,
text='Initialization Defaults',
fg="green",
justify='left')
l_1.place(x=x_offset, y=y_offset, height=30, width=140)
y_offset += 30
#Param
x_offset = 0
x_width = 120
l14 = Label(root, text='# updated shapes')
l14.place(x=x_offset, y=y_offset, height=30, width=x_width)
x_offset += x_width
e14 = Entry(root, justify='left', width=4) #text entry for the filename
e14.delete(0, END)
e14.insert(0, 'inf')
e14.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 45
x_width = 125
l15 = Label(root, text='# expected shapes')
l15.place(x=x_offset, y=y_offset, height=30, width=x_width)
x_offset += x_width
e15 = Entry(root, justify='left', width=4) #text entry for the filename
e15.delete(0, END)
e15.insert(0, 2000)
e15.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 45
x_width = 80
l16 = Label(root, text='# timesteps')
l16.place(x=x_offset, y=y_offset, height=30, width=x_width)
x_offset += x_width
e16 = Entry(root, justify='left', width=4) #text entry for the filename
e16.delete(0, END)
N_samples = np.ceil(float(e7.get()) * float(e8.get()))
e16.insert(0, N_samples)
e16.place(x=x_offset, y=y_offset + 5)
#Param
from scipy.special import log_ndtr
x_offset += 45
x_width = 140
l17 = Label(root, text='exceptionality thresh')
l17.place(x=x_offset, y=y_offset, height=30, width=x_width)
x_offset += x_width
e17 = Entry(root, justify='left', width=5) #text entry for the filename
e17.delete(0, END)
e17.insert(0, log_ndtr(-float(e11.get())) * N_samples)
e17.place(x=x_offset, y=y_offset + 5)
#Param
x_offset += 55
x_width = 105
l18 = Label(root, text='total len of file')
l18.place(x=x_offset, y=y_offset, height=30, width=x_width)
x_offset += x_width
e18 = Entry(root, justify='left', width=5) #text entry for the filename
e18.delete(0, END)
e18.insert(0, 'all')
e18.place(x=x_offset, y=y_offset + 5)
y_offset += 30
x_offset = 0
l000 = Label(root, text='_' * 200)
l000.place(x=x_offset, y=y_offset, height=30, width=1000)
#********** COMMAND LINE OUTPUT BOX **********
tkinter_window = False #Redirect command line outputs to text box in tkinter;
if tkinter_window:
t = Text(root, wrap='word', height=20, width=100)
t.place(x=10, y=250, in_=root)
#********* DEMO_ONACID BUTTON **********************
def button1(l):
l.config(foreground='red')
root.update()
#Save existing config file
np.savez(str(root.data.file_name)[:-4]+"_runtime_params", \
merge_thr=e1.get(), #merge threshold
initibatch = e3.get(), #Initial batch
patch_size=e4.get(), #patch size
stride=e5.get(), #stride
K=e6.get(), #K
frame_rate=e7.get(), #frame_rate
decay_time=e8.get(), #decay_time
neuron_size=e9.get(), #neuron size pixesl
AR_dynamics=e10.get(), #AR dynamics order
min_SNR=e11.get(), #min_SNR
rval_threshold = e12.get(), # rval_threshold
no_bkgr_components=e13.get(), # #bkground componenets
no_updated_shapes=e14.get(), # #udpated shapes
no_expected_shapes=e15.get(), # #expected shapes
no_timesteps=e16.get(), # #timesteps
exceptionality_threshold=e17.get(), # exceptionatliy threshold
total_len_file=e18.get(), # total len of file
caiman_location = str(root.caiman_folder)
)
print(type(str(root.caiman_folder)))
print(type(root.caiman_folder))
if tkinter_window:
import io, subprocess
#proc = subprocess.Popen(["python", "-u", "/home/cat/code/CaImAn/demo_OnACID.py", root.data.file_name], stdout=subprocess.PIPE)
proc = subprocess.Popen([
"python", "-u",
str(root.caiman_folder) + "/demo_OnACID_2.py",
root.data.file_name
],
stdout=subprocess.PIPE)
while True:
line = proc.stdout.readline()
if line != '':
t.insert(END, '%s\n' % line.rstrip())
t.see(END)
t.update_idletasks()
sys.stdout.flush()
else:
break
else:
print("python -u ")
print(root.caiman_folder)
#p = os.system("python -u "+str(root.caiman_folder)+"/demo_OnACID_2.py "+root.data.file_name)
print("python -u " + str(root.caiman_folder) +
"/demo_OnACID_2.py " + str(root.data.file_name))
p = os.system("python -u " + str(root.caiman_folder) +
"/demo_OnACID_2.py " + str(root.data.file_name))
l = Label(root, textvariable='green', fg='red')
b1 = Button(root,
text="demo_OnACID",
foreground='blue',
command=lambda: button1(l))
b1.place(x=0, y=y_offset + 50, in_=root)
def _log_erfc(x):
"""Compute log(erfc(x)) with high accuracy for large x."""
return math.log(2) + special.log_ndtr(-x * 2**0.5)