def test_parrec2nii_sets_qform_sform_code1(*args):
# Check that set_sform(), set_qform() are called on the new header.
parrec2nii.verbose.switch = False
parrec2nii.io_orientation.return_value = [[0, 1],[1, 1],[2, 1]] # LAS+
nimg = Mock()
nhdr = MagicMock()
nimg.header = nhdr
parrec2nii.nifti1.Nifti1Image.return_value = nimg
pr_img = Mock()
pr_hdr = Mock()
pr_hdr.get_data_scaling.return_value = (npa([]), npa([]))
pr_hdr.get_bvals_bvecs.return_value = (None, None)
pr_hdr.get_affine.return_value = AN_OLD_AFFINE
pr_img.header = pr_hdr
parrec2nii.pr.load.return_value = pr_img
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
infile = 'nonexistent.PAR'
parrec2nii.proc_file(infile, opts)
nhdr.set_qform.assert_called_with(AN_OLD_AFFINE, code=1)
nhdr.set_sform.assert_called_with(AN_OLD_AFFINE, code=1)
def cuatro_cps(espacio,velocidad):
espacio=npa(espacio,dtype=np.float32)
velocidad = npa(velocidad,dtype=np.float32)
aceleracion = npa([0,0],dtype=np.float32)
pt = np.arange(0,time,h)
pe=[]
pv=[]
pa=[]
for t in pt:
x1=espacio[0]+d
x2=espacio[0]-d
x3=espacio[0]
y=espacio[1]
y2=y-b
aceleracion[0]=-x1/(x1**2+y**2)**(1.5)-x2/(x2**2+y**2)**(1.5)-x3/(x3**2+y2**2)**(1.5)
aceleracion[1]=-y/(x1**2+y**2)**(1.5)-y/(x2**2+y**2)**(1.5)-y2/(x3**2+y2**2)**(1.5)
velocidad+=(aceleracion*h)
espacio+=(velocidad*h)
if(abs(espacio[0])>xlim):break
if(abs(espacio[1])>ylim):break
if((x1**2+y**2)**0.5<=r):break
if((x2**2+y**2)**0.5<=r):break
if((x3**2+y2**2)**0.5<=r):break
pe.append(espacio.tolist())
pv.append(velocidad.tolist())
pa.append(aceleracion.tolist())
return npa(pe)
def get_evmax(xObs, yObs, domain, lenscale, sigvar=None, noisevar=None):
"""currently, nObs needs to be constant (i.e. xObs and yObs need to be
rectangular 2-tensors of shape (nExp x nObs) )"""
if not sigvar: sigvar=1.
if not noisevar: noisevar=1e-7 # default noiseless
assert len(xObs.shape) == 2, 'dim xObs must = 2 (nExp x nObs)'
assert len(domain.shape) == 1, 'dim domain must = 1'
nExp, nObs = xObs.shape # unpack
# get conditioned posteriors
print 'lenscale: ' + str(lenscale)
postmus = (conditioned_mu(domain, xObs[iexp], yObs[iexp],\
lenscale, sigvar, noisevar)
for iexp in xrange(nExp))
# get maxes of posteriors
imaxes = []
xmaxes = []
fmaxes = []
for postmu in postmus:
imax = postmu.argmax()
imaxes.append(imax)# nExp x 1
xmaxes.append(domain[imax]) # nExp x 1
fmaxes.append(postmu[imax]) # nExp x 1
# add experiment metadata for call to get_ranked_dists
imaxes = npa(imaxes)
fmaxes = npa(fmaxes)
lenscales = [lenscale] * nExp
iExps = arange(nExp)
return {'xmax': xmaxes,
'fmax': fmaxes,
'imax': imaxes,
'lenscale': lenscales,
'iExp': iExps}
def smooth(data, winwidth_in):
"""
Note: only 'gauss' smoothing employed
Original location: main/util/smooth.m
"""
if winwidth_in < 1:
return data
if not isinstance(data, np.ndarray):
data = npa(data)
if not len(data.shape) == 1:
raise ValueError('data is not a vector. Shape: ' + str(data.shape))
paddata = npa(np.hstack(
(data[0], data, data[-1]))) # pad to remove border errors
winwidth = int(np.floor(winwidth_in / 2) *
2) # force even winsize for odd window
window = norm.pdf(np.arange(0, winwidth + 1), winwidth / 2 + 1,
winwidth / 8)
window = window / np.sum(window) # normalize window
data_ext = np.hstack(
((np.zeros(winwidth // 2) + 1) * paddata[0], paddata,
(np.zeros(winwidth // 2) + 1) * paddata[-1]
)) # extend data to reduce convolution error at beginning and end
sdata_ext = convolve(data_ext, window) # convolute with window
sdata = sdata_ext[winwidth + 1:-winwidth - 1] # cut to data length
return sdata
def Esigmoid2prod(signs1, signs2, mu, cov):
r'''
Computes
E[(prod_i s_i s'_i): (x_i)_i ~ N(mu, cov)]
where
s_i = 1 if `signs1[i] == 0` or else sigmoid(`signs1[i]` * x_i)
s'_i = 1 if `signs2[i] == 0` or else sigmoid(`signs2[i]` * x_i)
sigmoid(x) = 0.5 (1 + erf(x))
sgn_i = `signs`[i]
Inputs:
signs1: a vector with entries from {-1, 0, 1}
signs2: a vector with entries from {-1, 0, 1}
'''
# the lazy way:
# duplicate cov to reduce to the case with no repeat variables.
signs1 = npa(signs1)
signs2 = npa(signs2)
mu = npa(mu)
cov = npa(cov)
n = cov.shape[0]
newcov = np.zeros([2 * n , 2 * n])
newcov[:n, :n] = newcov[:n, n:] = newcov[n:, :n] = newcov[n:, n:] = cov
newmu = np.concatenate([mu, mu], axis=0)
signs = np.concatenate([signs1, signs2], axis=0)
zero_idx = set(np.argwhere(signs==0).reshape(-1))
nonzero_idx = list(set(list(range(0, 2*n))) - zero_idx)
signs = signs[nonzero_idx]
newmu = newmu[nonzero_idx]
newcov = newcov[nonzero_idx, :][:, nonzero_idx]
return Esigmoidprod(signs, newmu, newcov)
def obj_func(self, cam):
fx, fy = x0_int[0], x0_int[1]
cx, cy = x0_int[2], x0_int[3]
distCoeffs = (0.0, 0.0, 0.0, 0.0, 0.0) ## hack no distortion
tvec = cam[0:3] # x,y,z
rvec = cam[3:6] # rodrigues
# project
#point2Ds_p = cv.project(point3Ds, cam)
cameraMatrix = np.array([[fx, 0, cx], [0, fy, cy], [0, 0, 1]])
point2Ds_p, jacobian = cv2.projectPoints(
npa(self.point3Ds, dtype=np.float), rvec, tvec, cameraMatrix,
distCoeffs)
#print point2Ds_p
point2Ds_pp = [list(p[0]) for p in point2Ds_p]
diff = npa(point2Ds_pp, dtype=np.float) - npa(self.point2Ds,
dtype=np.float)
diff = diff.flatten(1)
#import pdb;
#pdb.set_trace()
#print diff
res = np.linalg.norm(diff)
print res / len(self.point3Ds)
return diff
def import_data(raw_data, srate, downsample=1):
"""
Sets leda2 object to its appropriate values to allow analysis
Adapted from main/import/import_data.m
"""
if not isinstance(raw_data, np.ndarray):
raw_data = npa(raw_data, dtype='float64')
time_data = utils.genTimeVector(raw_data, srate)
conductance_data = npa(raw_data, dtype='float64')
if downsample > 1:
(time_data, conductance_data) = utils.downsamp(time_data,
conductance_data,
downsample, 'mean')
leda2.data.samplingrate = srate / downsample
leda2.data.time_data = time_data
leda2.data.conductance_data = conductance_data
leda2.data.conductance_error = np.sqrt(
np.mean(pow(np.diff(conductance_data), 2)) / 2)
leda2.data.N = len(conductance_data)
leda2.data.conductance_min = np.min(conductance_data)
leda2.data.conductance_max = np.max(conductance_data)
(leda2.data.conductance_smoothData,
leda2.data.conductance_smoothData_win) = utils.smooth_adapt(
conductance_data, srate, .00001)
analyse.trough2peak_analysis()
def cgd_get_gradient(x, error0, error_fcn, h):
"""
Original location: analyze/cg/cgd_get_gradient.m
"""
Npars = len(x)
gradient = np.zeros(Npars)
for i in range(Npars):
xc = npa(x)
xc[i] = xc[i] + h[i]
(error1, _0) = error_fcn(xc)
if error1 < error0:
gradient[i] = (error1 - error0)
else: # try opposite direction
xc = npa(x)
xc[i] = xc[i] - h[i]
(error1, _0) = error_fcn(xc)
if error1 < error0:
gradient[i] = -(error1 - error0)
else:
gradient[i] = 0
return gradient
def get_experimentError(dfs, lenscale):
pdb.set_trace()
# lenscale = dfs.LENSCALE.iat[0]
sigvar = dfs.SIGVAR.iat[0]
KDOMAIN = K_se(DOMAIN, DOMAIN, lenscale, sigvar)
out = dfs.groupby('itrial').apply(lambda df0:
get_trialError(npa(df0.xObs.iat[0]),
npa(df0.yObs.iat[0]),
df0.xDrill.iat[0],
df0.yDrill.iat[0],
DOMAIN,
KDOMAIN,
lenscale))
out = np.vstack(out.values)
xerr = out[:, 0]
yerr = out[:, 1]
xhat = out[:, 2]
yhat = out[:, 3]
return {'xerr': xerr,
'yerr': yerr,
'xhat': xhat,
'yhat': yhat}
def test_parrec2nii_sets_qform_sform_code1(*args):
# Check that set_sform(), set_qform() are called on the new header.
parrec2nii.verbose.switch = False
parrec2nii.io_orientation.return_value = [[0, 1], [1, 1], [2, 1]] # LAS+
nimg = Mock()
nhdr = MagicMock()
nimg.header = nhdr
parrec2nii.nifti1.Nifti1Image.return_value = nimg
pr_img = Mock()
pr_hdr = Mock()
pr_hdr.get_data_scaling.return_value = (npa([]), npa([]))
pr_hdr.get_bvals_bvecs.return_value = (None, None)
pr_hdr.get_affine.return_value = AN_OLD_AFFINE
pr_img.header = pr_hdr
parrec2nii.pr.load.return_value = pr_img
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
infile = 'nonexistent.PAR'
parrec2nii.proc_file(infile, opts)
nhdr.set_qform.assert_called_with(AN_OLD_AFFINE, code=1)
nhdr.set_sform.assert_called_with(AN_OLD_AFFINE, code=1)
def __init__(self, dt=0.1, map_size=(1, 1), minDist=0.1):
"""
You can add/locate attractors/repulsor and change initial state after the object instance creation:
env = ForceField()
# attractor: [x, y, force]
# force > 0: attraction, Force < 0: repulsion
env.attractors = npa([[0.70, 0.70, -0.02],
[0.60, 0.60, -0.02],
[0.78, 0.58, -0.02],
[0.20, 0.25, 0.04]])
# initial state x, y, vx, vy
env.initState = npa([25, 30, 0, 0])
:param dt: simulation time step
:param map_size: map size
:param minDist: virual miminal distance between agent and attractors
"""
self.dt = dt
self.map_size = map_size
self.minDist = minDist
self.attractors = npa([[0.70, 0.70, -0.02], [0.60, 0.60, -0.02],
[0.78, 0.58, -0.02], [0.20, 0.25, 0.04]])
self.initState = npa([0.25, 0.30, 0, 0]) # initial state x, y, vx, vy
self.state = self.initState
def topixel(a, offset):
c = npa(a)
b = npa(a)
for i in xrange(b.shape[0]):
b[i, 0] = (c[i, 0] - offset[0] - (-0.15)) * (1000.0 / (0.15 * 2))
b[i, 1] = (-(c[i, 1] - offset[1]) - (-0.15)) * (1000.0 / (0.15 * 2))
return b.astype(int).tolist()
def symRange(v, centre=0):
v -= centre
if np.abs(np.max(v)) > np.abs(np.min(v)):
lim = npa([-np.abs(np.max(v)), np.abs(np.max(v))])
else:
lim = npa([-np.abs(np.min(v)), np.abs(np.min(v))])
lim += centre
return lim
def m_step(data, mean1, covar1, mean2, covar2, probs):
new_mean1 = npa([0., 0.])
new_mean2 = npa([0., 0.])
for point, prob in zip(data, probs):
new_mean1 += prob[0] * point
new_mean2 += prob[1] * point
new_mean1 /= sum(p[0] for p in probs)
new_mean2 /= sum(p[1] for p in probs)
return new_mean1, new_mean2
def find_uniqueGrid(self, hist_xy, nBin=(21, 21)):
binx = np.linspace(0, self.map_size[0], nBin[0])
biny = np.linspace(0, self.map_size[1], nBin[1])
ix = np.digitize(hist_xy[:, 0], binx) - 1
iy = np.digitize(hist_xy[:, 1], biny) - 1
ixy = npa([ix, iy]).transpose()
ixy_unique = np.vstack({tuple(row) for row in ixy})
xy_unique = npa([binx[ixy_unique[:, 0]],
binx[ixy_unique[:, 1]]]).transpose()
return ixy_unique, xy_unique
def euler(espacio, velocidad, aceleracion, inicio=True):
pe = []
pv = []
pa = []
a = 1 if inicio else -1
for t in pt:
espacio += (velocidad * h * a)
velocidad += (aceleracion * h * a)
pe.append(espacio.tolist())
pv.append(velocidad.tolist())
pa.append(aceleracion.tolist())
return npa(pe), npa(pv), npa(pa)
def deconv_apply():
"""
Original location: Ledalab/analyze/deconvolution/sdeco.m>deconv_apply
"""
# Prepare target data for full resolution analysis
leda2.analysis0.target.tonicDriver = npa(
leda2.analysis0.target.poly.__call__(leda2.data.time_data))
leda2.analysis0.target.t = npa(leda2.data.time_data)
leda2.analysis0.target.d = npa(leda2.data.conductance_data)
leda2.analysis0.target.sr = leda2.data.samplingrate
sdeconv_analysis(leda2.analysis0.tau, 0)
leda2.analysis = leda2.analysis0 # remember we are copying by reference, look out for issues
# SCRs reconvolved from Driver-Peaks
t = leda2.data.time_data
driver = leda2.analysis.driver
(minL, maxL) = utils.get_peaks(driver)
minL = np.hstack((minL[:len(maxL)], len(t)))
# Impulse data
leda2.analysis.impulseOnset = t[minL[:-1]]
leda2.analysis.impulsePeakTime = t[maxL] # = effective peak-latency
leda2.analysis.impulseAmp = driver[maxL]
# SCR data
leda2.analysis.onset = leda2.analysis.impulsePeakTime
leda2.analysis.amp = np.zeros(len(maxL))
leda2.analysis.peakTime = np.zeros(len(maxL))
for iPeak in range(len(maxL)):
driver_segment = leda2.analysis.driver[minL[iPeak]:minL[
iPeak + 1]] # + 1 seems like a wrong idea...
sc_reconv = convolve(driver_segment, leda2.analysis.kernel)
leda2.analysis.amp[iPeak] = np.max(sc_reconv)
mx_idx = np.flatnonzero(sc_reconv == np.max(sc_reconv))
leda2.analysis.peakTime[iPeak] = t[minL[iPeak]] + mx_idx[
0] / leda2.data.samplingrate # SCR peak could be outside of SC time range
negamp_idx = np.flatnonzero(
leda2.analysis.amp < .001
) # criterion removes peaks at end of sc_reconv due to large negative driver-segments
leda2.analysis.impulseOnset = np.delete(leda2.analysis.impulseOnset,
negamp_idx)
leda2.analysis.impulsePeakTime = np.delete(leda2.analysis.impulsePeakTime,
negamp_idx)
leda2.analysis.impulseAmp = np.delete(leda2.analysis.impulseAmp,
negamp_idx)
leda2.analysis.onset = np.delete(leda2.analysis.onset, negamp_idx)
leda2.analysis.amp = np.delete(leda2.analysis.amp, negamp_idx)
leda2.analysis.peakTime = np.delete(leda2.analysis.peakTime, negamp_idx)
def translate_ft(ft):
A = npa([[0, -ft[2], ft[1]], [ft[2], 0, -ft[0]], [-ft[1], ft[0], 0]]).T
b = npa(ft[3:6])
print "det", np.linalg.det(A.T), "multiply", ft[0] * ft[1] * ft[2]
print A
r = np.linalg.solve(A, b)
# calculate new r
print r
newr = r - npa([0, 0, 0.14])
newft = ft[0:3] + np.cross(f, r).tolist()
return newft
def _compute_coords(self, mesh=None):
coords = getattr(self, '_coords', None)
if coords is None:
xl, yl = mesh_bbox(mesh)
y0 = npa(yl).mean()
t = np.linspace(0, 1, self.resolution)
coords = (np.outer(1-t, npa((xl[0], y0))) +
np.outer(t, npa((xl[1], y0))))
self._coords = coords
df = self._df
df['coord_x'] = coords.view()[:,0]
df['coord_y'] = coords.view()[:,1]
return coords
def process_input_image(mask_t_1, jpeg_t, flow_t_1=None):
'''
mask_t_1: PIL Image, mask at time step t-1
jpeg_t: PIL Image, image at time step t
flow_t_1: flo
return: Jpeg PIL Image
'''
mask_t_1_dilated = npa(dilate_and_gaussian_mask(mask_t_1))
jpeg_t = npa(jpeg_t)
#jpeg_t = skimage.util.invert(jpeg_t) #INVERT
jpeg_t = jpeg_t * np.expand_dims((mask_t_1_dilated / 255), 2)
jpeg_t = jpeg_t.astype(np.uint8)
return ifa(jpeg_t)
def trial_wrapper(dft, ls):
if dft.shape[0] != 1:
# errpool.append(dft.copy())
# ii = randint(dft.shape[0])
# dft = dft.iloc[ii:ii+1]
trialError = None
else:
KX = K_se(X, X, ls, SIGVAR)
xObs = npa(dft.xObs.iat[0])
yObs = npa(dft.yObs.iat[0])
xDrill = dft.xDrill.iat[0]
yDrill = dft.yDrill.iat[0]
trialError = get_trialError(xObs, yObs, xDrill, yDrill, X, KX, ls)
def postrun(self):
#get gradients and save them to the pickle files for ASE
path = self.path
for child in self.children:
res = child.results
name = child.name
# don't rely on gradients beeing numpy arrays
f = [ npa(vec) for vec in self.get_grad(res, eUnit='eV', lUnit='Angstrom') ]
force = -1.0 * npa(self.reorder(res, f))
filename = osPJ(path, name+'.pckl')
with open(filename, 'wb') as f:
pickleDump(force, f, protocol=2)
self.results._vib = self._vib
def cgd_linesearch(x, error0, direction, error_fcn, h):
"""
Original location: analyze/cg/cgd_linesearch
"""
direction_n = direction / norm(direction, 2)
error_list = npa(error0)
stepsize = h
maxSteps = 6
count = 0
factor = npa([0])
for iStep in range(1, maxSteps):
factor = np.hstack((factor, pow(2, (iStep - 1))))
xc = x + (direction_n * stepsize) * factor[iStep]
(catVal, xc) = error_fcn(xc) # xc may be changed due to limits
error_list = np.hstack((error_list, catVal))
if error_list[-1] >= error_list[-2]: # end of decline
if iStep == 1: # no success
step = 0
error1 = npa(error0)
else: # parabolic
p = np.polyfit(factor, error_list, 2)
fx = np.arange(factor[0], factor[-1] + .1, .1)
fy = np.polyval(p, fx)
idx = np.argmin(fy)
fxm = fx[idx]
xcm = x + (direction_n * stepsize) * fxm
(error1,
xcm) = error_fcn(xcm) # xc may be changed due to limits
if error1 < error_list[iStep - 1]:
xc = xcm
step = fxm
else: # finding Minimum did not work
xc = x + (direction_n * stepsize
) * factor[iStep - 1] # before last point
(error1, xc) = error_fcn(
xc
) # recalculate error in order to check for limits again
step = factor[iStep - 1]
return (xc, error1, step)
count = iStep
step = factor[count]
error1 = error_list[count]
return (xc, error1, step)
def euler(espacio,velocidad):
espacio=npa(espacio,dtype=np.float32)
velocidad = npa(velocidad,dtype=np.float32)
pt = np.arange(0,time,h)
pe=[]
for t in pt:
aceleracion=(-espacio/(sum(espacio**2))**(1.5))
velocidad+=(aceleracion*h)
espacio+=(velocidad*h)
if(abs(espacio[0])>xlim):break
if(abs(espacio[1])>ylim):break
if((sum(espacio**2))**0.5<=r):break
pe.append(espacio.tolist())
return npa(pe)
def euler2(espacio, velocidad, aceleracion):
pe = []
pv = []
pa = []
for t in pt:
if (t == 3): velocidad += 3
if (t == 8): velocidad = 3
if (t == 10): velocidad += -5
espacio += (velocidad * h)
velocidad += (aceleracion * h)
pe.append(espacio.tolist())
pv.append(velocidad.tolist())
pa.append(aceleracion.tolist())
return npa(pe), npa(pv), npa(pa)
def euler(espacio,velocidad,aceleracion,inicio=True):
espacio=np.array(espacio,dtype=np.float32)
velocidad = np.array(velocidad,dtype=np.float32)
aceleracion = np.array(aceleracion,dtype=np.float32)
pe=[]
pv=[]
pa=[]
a =1 if inicio else -1
for t in pt:
espacio+=(velocidad*h*a)
velocidad+=(aceleracion*h*a)
pe.append(espacio.tolist())
pv.append(velocidad.tolist())
pa.append(aceleracion.tolist())
return npa(pe),npa(pv),npa(pa)
def img_subset(img):
'''Transform a whole img to a set of patches.'''
local_img = img
img_set = []
# 3*3 patches in total , each patch is 14pix*14pix
# rows,cols = local_img.shape
subnum = npa([3,3])
subsize = npa([14,14])
subdist = (local_img.shape - subsize) / (subnum - 1)
for srow in range(subnum[0]):
for scol in range(subnum[1]):
row, col = subdist * (srow, scol)
sub_img = local_img[row : row + subsize[0], col : col + subsize[1]]
img_set.append(sub_img.reshape(1,-1))
return npa(img_set)
def toASE(molecule):
"""Convert a PLAMS |Molecule| to an ASE molecule (``ase.Atoms`` instance). Translate coordinates, atomic numbers, and lattice vectors (if present). The order of atoms is preserved."""
aseMol = aseAtoms()
#iterate over PLAMS atoms
for atom in molecule:
#check if coords only consists of floats or ints
if not all(isinstance(x, (int,float)) for x in atom.coords):
raise ValueError("Non-Number in Atomic Coordinates, not compatible with ASE")
#append atom to aseMol
aseMol.append(aseAtom(atom.atnum, atom.coords))
#get lattice info if any
lattice = npz((3,3))
pbc = [False,False,False]
for i,vec in enumerate(molecule.lattice):
#check if lattice only consists of floats or ints
if not all(isinstance(x, (int,float)) for x in vec):
raise ValueError("Non-Number in Lattice Vectors, not compatible with ASE")
pbc[i] = True
lattice[i] = npa(vec)
#save lattice info to aseMol
if any(pbc):
aseMol.set_pbc(pbc)
aseMol.set_cell(lattice)
return aseMol
def signpeak(data, cccrimin, cccrimax, sigc):
"""
Originally subfunction of segment_driver
data, cccrimin, cccrimax must be row vectors of shape (x,)
"""
if cccrimax is None:
return (None, None)
if not isinstance(data, np.ndarray):
raise ValueError('data is not a numpy array')
if not isinstance(cccrimin, np.ndarray):
raise ValueError('cccrimin is not a numpy array')
if not isinstance(cccrimax, np.ndarray):
raise ValueError('cccrimax is not a numpy array')
dmm = np.vstack((data[cccrimax] - data[cccrimin[:-1]],
data[cccrimax] - data[cccrimin[1:]]))
maxL = npa(cccrimax[np.max(dmm, axis=0) > sigc])
# keep only minima right before and after sign maxima
minL = None
for i in range(len(maxL)):
minm1_idx = np.flatnonzero(cccrimin < maxL[i])
before_smpl = cccrimin[minm1_idx[-1]]
after_smpl = cccrimin[minm1_idx[-1] + 1]
newStack = np.hstack((before_smpl, after_smpl))
if minL is None:
minL = newStack
else:
minL = np.vstack((minL, newStack))
return (minL, maxL)
def get_iea37_cost(n_wt=9):
"""Cost component that wraps the IEA 37 AEP calculator"""
wd = npa(range(16)) * 22.5 # only 16 bins
site = IEA37Site(n_wt)
wind_turbines = IEA37_WindTurbines()
wake_model = IEA37SimpleBastankhahGaussian(site, wind_turbines)
return PyWakeAEPCostModelComponent(wake_model, n_wt, wd=wd)
def parse_day(s):
"""
>>> d = parse_day('Mon Apr 01 13:44:45 +0000 2011')
>>> print d.strftime('%Y-%m-%d')
2011-04-01
"""
return datetime.strptime(' '.join(npa(s.split())[[1, 2, 5]]), '%b %d %Y')
def rod_to_quad(r):
# q = [qx, qy, qz, qw]
rotmat, jacobian = cv2.Rodrigues(npa(r))
rotmat = np.append(rotmat, [[0, 0, 0]], 0)
rotmat = np.append(rotmat, [[0], [0], [0], [1]], 1)
q = tfm.quaternion_from_matrix(rotmat)
return q.tolist()
def smooth_adapt(data, winwidth_max, err_crit):
"""
Original location: main/util/smooth_adapt.m
"""
success = 0
ce = np.sqrt(np.mean(pow(np.diff(data), 2)) / 2)
iterL = np.arange(0, winwidth_max + 4, 4)
if len(iterL) < 2:
iterL = npa([0, 2])
count = 0
for i in range(1, len(iterL)):
count = i
winwidth = iterL[i]
scs = smooth(data, winwidth)
scd = np.diff(scs)
ce = np.hstack(
(ce, np.sqrt(np.mean(pow(scd, 2)) / 2))) # conductance_error
if abs(ce[i] - ce[i - 1]) < err_crit:
success = 1
break
if success: # take before-last result
if count > 1:
scs = smooth(data, iterL[count - 1])
winwidth = iterL[count - 1]
else: # data already satisfy smoothness criteria
scs = data
winwidth = 0
return (scs, winwidth)
def bateman(time, onset, amp, tau1, tau2):
"""
original location: analyze/template/bateman.m
time must be a numpy array
"""
if not isinstance(time, np.ndarray):
time = npa(time)
if tau1 < 0 or tau2 < 0:
raise ValueError('tau1 or tau2 < 0: ({:f}, {:f})'.format(tau1, tau2))
if tau1 == tau2:
raise ValueError('tau1 == tau2 == {:f}'.format(tau1))
conductance = np.zeros(time.shape)
rang = np.flatnonzero(time > onset)
if len(rang) == 0:
return None
xr = time[rang] - onset
if amp > 0:
maxx = tau1 * tau2 * math.log(tau1 / tau2) / (tau1 - tau2) # b' = 0
maxamp = abs(math.exp(-maxx / tau2) - math.exp(-maxx / tau1))
c = amp / maxamp
else: # amp == 0: normalized bateman, area(bateman) = 1/sr
sr = round(1 / np.mean(np.diff(time)))
c = 1 / ((tau2 - tau1) * sr)
if tau1 > 0:
conductance[rang] = c * (np.exp(-xr / tau2) - np.exp(-xr / tau1))
else:
conductance[rang] = c * np.exp(-xr / tau2)
return conductance
def obj_func(self, cam):
c0 = cam[0]
c1 = cam[1]
c2 = cam[2]
diff = []
#print matrix_from_xyzrpy([0,0,0, c,0,0])
for i in xrange(len(self.point3Ds)):
point3D = self.point3Ds[i]
point3D_pc = self.point3Ds_pc[i]
#point3D_pc_trans = np.array(point3D_pc + [1.0]) * c
#import ipdb; ipdb.set_trace()
point3D_pc_trans = np.dot(
matrix_from_xyzrpy([
c2 * point3D_pc[0] / point3D_pc[2],
c2 * point3D_pc[1] / point3D_pc[2], c2, 0, 0, 0
]),
np.array([point3D_pc[0], point3D_pc[1], point3D_pc[2], 1.0]))
#point3D_pc_trans[0] = point3D_pc[0] + c * point3D_pc[0] / point3D_pc[2]
#point3D_pc_trans[1] = point3D_pc[1] + c * point3D_pc[1] / point3D_pc[2]
#point3D_pc_trans[2] = point3D_pc[2] + c
point3D_pc_world = np.dot(self.x0_ext, point3D_pc_trans)
#print point3D, point3D_pc_world[0:3].tolist()
diff_ = npa(point3D,
dtype=np.float) - point3D_pc_world[0:3].tolist()
diff.extend(diff_.tolist())
#import ipdb; ipdb.set_trace()
res = np.linalg.norm(diff)
print res / len(self.point3Ds)
err = res / len(self.point3Ds)
return err
def _section_fire(self): # {{{
fire_origin = self._fire_origin()
times, hrrs = self._draw_fire_development()
fire_properties = self._draw_fire_properties(len(times))
self._fire_obstacle()
area = nround(npa(hrrs) / (self.hrrpua * 1000) + 0.1, decimals=1)
fire_origin = self._fire_origin()
txt = (
'!! FIRE,compa,x,y,z,fire_number,ignition_type,ignition_criterion,ignition_target,?,?,name',
fire_origin,
'',
'!! CHEMI,?,?,?,?',
'CHEMI,1,1.8,0.3,0.05,0,0.283,{}'.format(
fire_properties['heatcom']),
'',
'TIME,' + ','.join(str(i) for i in times),
'HRR,' + ','.join(str(round(i, 3)) for i in hrrs),
fire_properties['sootyield'],
fire_properties['coyield'],
fire_properties['trace'],
'AREA,' + ','.join(str(i) for i in area),
fire_properties['heigh'],
)
return "\n".join(txt) + "\n"
def generate_rand_obs(nExp, nObs, domainBounds, sigvar=None, rng=None):
# create random sets of observations for each experiment
if not sigvar: sigvar = 1.
if not rng: rng = RandomState()
domainBounds = npa(domainBounds)
dimX = domainBounds.shape[0]
minX = domainBounds[:, 0]
maxX = domainBounds[:, 1]
rangeX = maxX - minX
xObs = rng.uniform(size=(nExp, nObs, dimX))
xObs *= rangeX
xObs += minX
yObs = empty(shape=(nExp, nObs))
for iexp in xrange(nExp):
good = False
while not good:
yObs0 = rng.normal(size=(nObs))
if yObs0.max() > 0: good = True
yObs[iexp, :] = yObs0
# yObs = rng.normal(size=(nExp, nObs, 1))
yObs *= sigvar
return {'x': xObs,
'y': yObs}
def unpack_rngstate(json_rngstate):
jrs = loads(json_rngstate)
p0 = jrs[0].encode('ascii') # numpy plays nice with ascii
p1 = npa(jrs[1], dtype=uint32) # unpack into numpy uint32 array
p2 = int(jrs[2])
p3 = int(jrs[3])
p4 = float(jrs[4])
return (p0, p1, p2, p3, p4) # rngstate
def read_obj(filename: str) -> object:
obj = OBJ(path.basename(filename))
def _type(v):
try: return int(v or 0)
except ValueError:
return float(v)
def _update(tar, val):
if len(val) != np.size(getattr(obj.values, tar), 1):
setattr(obj.values, tar, np.empty((0, len(val)), dtype=np.float32))
setattr(obj.values, tar, np.append(getattr(obj.values, tar), [val], axis=0))
parse = lambda t, *v: {
'v' : lambda v: _update('vertex', tuple(map(_type, v))),
'vn': lambda v: _update('normal', tuple(map(_type, v))),
'vt': lambda v: _update('texcoord', tuple(map(_type, v))),
'f' : lambda v: obj.faces.append([tuple(map(_type, z.split('/'))) for z in v]),
}.get(t, lambda v: None)(v)
with open(filename) as file:
any(parse(*line) for line in filter(None, map(str.split, file)))
obj.face_info[0] = len(list(filter(lambda x: len(x) == 3, obj.faces)))
obj.face_info[1] = len(list(filter(lambda x: len(x) == 4, obj.faces)))
obj.face_info[2] = len(list(filter(lambda x: len(x) >= 5, obj.faces)))
newface = list()
for i, face in enumerate(obj.faces):
if len(face) > 3:
face = np.array(face)
# real vertex coord data from parsed vertex
m = npa(lambda x: obj.values.vertex[x-1], 1, np.array([face])[:,:,0].T).squeeze()
# vectorize function to detect plane
f = np.vectorize(lambda x: not np.any(m[:,x]-m[:,x][0]))
# vectorize function to detect index from vertex value
g = lambda t, a: np.where(npa(lambda x: np.allclose(x, t), 1, a) == True)[0][0]
# 2-d vertex array without a plane
p = np.delete(m, (np.where(f(np.arange(3)) == True)[0] or [0])[0], 1)
newface.extend([[[ary[p] for ary in face.T] # new face values
for p in map(partial(g, a=p), tri)] # each triangle (convert vertex to id)
for tri in OBJ.trianglize(p)]) # trianglize given polygon
else:
newface.append(face)
obj.faces = np.asarray(newface)
obj.buffer.vertex = npa(obj.values.vertex.__getitem__, 0, obj.faces[:, :, 0].flatten()-1) if obj.values.vertex.size else None
obj.buffer.normal = npa(obj.values.normal.__getitem__, 0, obj.faces[:, 0, 2]-1) if obj.values.normal.size else None
obj.buffer.texcoord = npa(obj.values.texcoord.__getitem__, 0, obj.faces[:, 0, 0]-1) if obj.values.texcoord.size else None
w, h = obj.buffer.vertex.shape
arange = np.arange(w).reshape(w, 1)
ovn = npa(lambda x: np.stack((x,x,x)), 1, obj.buffer.normal).reshape(w, h)
obj.array = npa(lambda x: np.stack((ovn[x], obj.buffer.vertex[x])), 1, arange).reshape(w*2, h).astype(np.float32)
return obj
def test_alternative_header_field_names():
# some V4.2 files had variant spellings for some of the fields in the
# header. This test reads one such file and verifies that the fields with
# the alternate spelling were read.
with ImageOpener(VARIANT_PAR, 'rt') as _fobj:
HDR_INFO, HDR_DEFS = parse_PAR_header(_fobj)
assert_equal(HDR_INFO['series_type'], 'Image MRSERIES')
assert_equal(HDR_INFO['diffusion_echo_time'], 0.0)
assert_equal(HDR_INFO['repetition_time'], npa([ 21225.76]))
assert_equal(HDR_INFO['patient_position'], 'HFS')
def bayesOpt_trialError(xObs, yObs, xSub, ySub, lenscale, sigvar):
KDOMAIN = K_se(DOMAIN, DOMAIN, lenscale, sigvar)
out = get_trialError(npa(xObs),
npa(yObs),
npa(xSub),
npa(ySub),
DOMAIN,
KDOMAIN,
lenscale)
xerr = out[0]
yerr = out[1]
xhat = out[2]
yhat = out[3]
return {'xerr': xerr,
'yerr': yerr,
'xhat': xhat,
'yhat': yhat}
def load_obj(obj_file):
obj = map(lambda x: x.strip(), open(obj_file).read().split("\n"))
# read vertices
vertices = npa(map(lambda x: map(float, x.split()[1:]), filter(lambda x: x[0:2] == "v ", obj)))
#vertices += K*10
# read in faces
tris = map(lambda x: parse_face(x, vertices), filter(lambda x: x[0:2] == "f ", obj))
print len(tris), "triangles"
return tris
def make_domain_grid(domainBounds, domainRes):
"""takes domainBounds and domainRes for each dim of input space and grids
accordingly"""
#TODO: add sparse version with ndm
domainBounds = npa(domainBounds)
# get domain from bounds and res
dimX = domainBounds.shape[0]
if isscalar(domainRes):
# equal res if scalar
domainRes = repeat(domainRes, dimX)
else:
assert len(domainRes) == dimX
domainRes = npa(domainRes)
domain = npa([linspace(domainBounds[dim][0],
domainBounds[dim][1],
domainRes[dim])
for dim in xrange(dimX)])
domain = cartesian(domain)
return domain
def project_point(pt):
# vector from pt to origin
vv = pt - origin
v = vv/norm(vv)
# real projection shit
vx = npa((v[0], 0, v[2]))
lx = npa((look[0], 0, look[2]))
vy = npa((0, v[1], v[2]))
ly = npa((0, look[1], look[2]))
def ang(v1, v2):
v1 /= norm(v1)
v2 /= norm(v2)
angl = np.dot(v1, v2)
crs = np.cross(v1, v2)
if np.sum(crs) >= 0.0:
return np.arccos(angl)
else:
return -np.arccos(angl)
x = (ang(vx, lx) / arcrad_per_pixel)
y = (ang(vy, ly) / arcrad_per_pixel)
# add z for z-buffering
# z is the distance of the point from the plane formed by look and origin
# project v on to look
z = np.dot(v, look) * norm(vv)
"""
print " *** "
print v, K
print pt, x, y
"""
return int(round(x + X/2)),int(round(Y/2 - y)), z
def test_hebb_learning_vector():
assert len(hebb_learning(Tns.v_in_1, Tns.s_out_1, Tns.v_w_1, 1)) == 5
assert (hebb_learning(Tns.v_in_1, Tns.s_out_1, Tns.v_w_1, 1) == \
Tns.v_w_1 + npa(Tns.s_out_1) * npa(Tns.v_in_1)).all()
assert len(hebb_learning(Tns.v_in_2, Tns.s_out_2, Tns.v_w_2, 0.5)) == 5
assert (hebb_learning(Tns.v_in_2, Tns.s_out_2, Tns.v_w_2, 0.5) == \
Tns.v_w_2 + .5 * npa(Tns.s_out_2) * npa(Tns.v_in_2)).all()
assert len(hebb_learning(Tns.v_in_3, Tns.s_out_3, Tns.v_w_3, 3.5)) == 5
assert (hebb_learning(Tns.v_in_3, Tns.s_out_3, Tns.v_w_3, 3.5) == \
Tns.v_w_3 + 3.5 * npa(Tns.s_out_3) * npa(Tns.v_in_3)).all()
def trainvaltest_split(Xseq, yseq, p_train, p_val, p_test=None, shuffle=False):
ncase, seqlen, nbatch = Xseq.shape
if not p_test: p_test = 1.-(p_train+p_val)
# can be less if don't want to use full dataset
assert npa([p_train, p_val, p_test]).sum() <= 1.
ntrain, nval, ntest = [int(p * ncase) for p in [p_train, p_val, p_test]]
if shuffle:
neworder = rng.permutation(ncase)
Xseq = Xseq[neworder]
yseq = yseq[neworder]
return {'train': {'X': Xseq[:ntrain], 'y': yseq[:ntrain]},
'val': {'X': Xseq[ntrain:ntrain+nval], 'y': yseq[ntrain:ntrain+nval]},
'test': {'X': Xseq[ntrain+nval:ntrain+nval+ntest], 'y': yseq[ntrain+nval:ntrain+nval+ntest]}
}
def make_experiment(nTrial, nPassivePool, nActivePool, rng):
nTrialType = len(nPassivePool) * len(nActivePool)
assert nTrial % nTrialType == 0
nPerNPassive = nTrial / len(nPassivePool)
nPerNActive = nTrial / len(nActivePool)
nPerTrialType = nTrial / nTrialType
# col 0 is nPassive, col 1 is nActive
# pdb.set_trace()
trialTypeTuples = cartesian([nPassivePool, nActivePool])
# get queue of how many obs per round
trialParamsQueue = npa(make_nObsQueue(trialTypeTuples, nTrial, rng))
nPassiveQueue = trialParamsQueue[:, 0]
nActiveQueue = trialParamsQueue[:, 1]
return {'nPassiveObsQueue': nPassiveQueue,
'nActiveObsQueue': nActiveQueue}
def fast_triangle_mesh_drawer(tris, origin, look):
# shouldn't do anything
look /= norm(look)
img = np.zeros((Y, X))
zimg = np.ones((Y, X))*np.inf
def project_point(pt):
# vector from pt to origin
vv = pt - origin
v = vv/norm(vv)
# real projection shit
vx = npa((v[0], 0, v[2]))
lx = npa((look[0], 0, look[2]))
vy = npa((0, v[1], v[2]))
ly = npa((0, look[1], look[2]))
def ang(v1, v2):
v1 /= norm(v1)
v2 /= norm(v2)
angl = np.dot(v1, v2)
crs = np.cross(v1, v2)
if np.sum(crs) >= 0.0:
return np.arccos(angl)
else:
return -np.arccos(angl)
x = (ang(vx, lx) / arcrad_per_pixel)
y = (ang(vy, ly) / arcrad_per_pixel)
# add z for z-buffering
# z is the distance of the point from the plane formed by look and origin
# project v on to look
z = np.dot(v, look) * norm(vv)
"""
print " *** "
print v, K
print pt, x, y
"""
return int(round(x + X/2)),int(round(Y/2 - y)), z
# project the triangles into 2D space
# does this projection preserve the u and v
DRAW_WIREFRAME = False
if DRAW_WIREFRAME:
lines = []
for tr in tris:
p0, p1, p2 = project_point(tr[0]), project_point(tr[1]), project_point(tr[2])
lines.append((p0[0:2], p1[0:2]))
lines.append((p1[0:2], p2[0:2]))
lines.append((p2[0:2], p0[0:2]))
for pt1, pt2 in lines:
rr, cc, val = line_aa(pt1[1], pt1[0], pt2[1], pt2[0])
# filter
rr[np.logical_or(rr < 0, rr >= Y)] = 0
cc[np.logical_or(cc < 0, cc >= X)] = 0
img[rr, cc] = val
else:
# z-buffering, keeping the quality low in line with the rest of the program
polys = []
for tr in tris:
xyz = npa(map(project_point, tr))
# get min and max
xmin, xmax = np.min(xyz[:, 0]), np.max(xyz[:, 0])
ymin, ymax = np.min(xyz[:, 1]), np.max(xyz[:, 1])
# on screen
xmin = np.clip(xmin, 0, X).astype(np.int)
xmax = np.clip(xmax, 0, X).astype(np.int)
ymin = np.clip(ymin, 0, Y).astype(np.int)
ymax = np.clip(ymax, 0, Y).astype(np.int)
# triangle in 3 space
vs1 = xyz[1][0:2] - xyz[0][0:2]
vs2 = xyz[2][0:2] - xyz[0][0:2]
vsx = np.cross(vs1, vs2)
# shade
shade = random.uniform(0.3, 1.0)
for x in range(xmin, xmax):
for y in range(ymin, ymax):
q = npa([x,y]) - xyz[0][0:2]
u = np.cross(q, vs2) / vsx
v = np.cross(vs1, q) / vsx
if u >= 0 and v >= 0 and u+v <= 1.0:
pt_xyz = (1-u-v)*xyz[0] + u*xyz[1] + v*xyz[2]
if pt_xyz[2] < zimg[y,x]:
zimg[y,x] = pt_xyz[2]
img[y,x] = shade
#polys.append((np.mean(xyz[:, 2]), xyz))
"""
polys = sorted(polys, reverse=True, key=lambda x: x[0])
for _, xyz in polys:
rr, cc = polygon(xyz[:, 1], xyz[:, 0])
rr[np.logical_or(rr < 0, rr >= Y)] = 0
cc[np.logical_or(cc < 0, cc >= X)] = 0
img[rr, cc] = random.uniform(0.3, 1.0)
"""
return img
get_ipython().magic(u'pylab inline')
import numpy as np
from numpy import array as npa
def gauss(mean, covar, x):
"""
Bivariate Gaussian distribution, assuming diagonal covariance.
1/(2*pi*v1*v2) * exp(- 1/2 * (x1-mean1)**2/v1 + (x2-mean2)**2/v2)
"""
Xmu = x[0]-mean[0]
Ymu = x[1]-mean[1]
z = Xmu**2 / (covar[0]**2) + Ymu**2 / (covar[1]**2)
denom = 2 * np.pi * covar[0] * covar[1]
return np.exp(-z / 2.) / denom
data = np.array([npa([0.,0.02]), npa([.1,0.005]), npa([-0.1,.01]),
npa([1.01,1.]), npa([.99,0.9]), npa([1.02,1.1])])
mean1 = npa([-.5, -.5])
covar1 = npa([.4, .4])
mean2 = npa([1.5, 1.5])
covar2 = npa([.4, .4])
def plotme(mean1, covar1, mean2, covar2, data):
x, y = np.mgrid[-1.5:2.5:.01, -1.5:2.5:.01]
pos = np.empty(x.shape + (2,))
pos[:, :, 0] = x; pos[:, :, 1] = y
contourf(x, y,
[gauss(mean1, covar1, [xi, yi]) + gauss(mean2, covar2, [xi, yi])
for (xi, yi) in zip(x, y)])
scatter([d[0] for d in data], [d[1] for d in data], marker='v', color='w')
def firstBookLengthN(n):
"""returns the index of the first book of length n"""
# determine how many books with len < lenBook exist
nShorter = npa([cardPool**l for l in xrange(n)]).sum()
return nShorter # no need for +1 bc of the empty book
# Simpler distance
# Get the pairwise comparison vectors
for language in languages:
language.get_pairwise()
# Calculate distance between languages
for l1 in range(lcount):
for l2 in range(l1,lcount):
add = 0
for i in range(len(languages[l1].pairwise_ranking)):
add += languages[l1].pairwise_ranking[i] - languages[l2].pairwise_ranking[i]
distances[l1][l2] = add
# Cluster!
npdistances = npa(distances)
thecluster = fastcluster.linkage(npdistances, method=m)
# Using average as default; options: single, complete, average, weighted
# Output the cluster as a png
# dendrogram = scipy.cluster.hierarchy.dendrogram(thecluster, labels=languagenames)
# plt.savefig('temp.png')
# plt.cla()
# Get labeled nodes from gold tree
goldlabeled = []
for family in families:
goldlabeled += get_nodes(family.languages)
rootall = set(languagenames)
if rootall not in goldlabeled:
goldlabeled.append(rootall)
def ei_trialSeries(trialSeries):
wid = trialSeries.workerid
condition = trialSeries.condition
counterbalance = trialSeries.counterbalance
lenscale = trialSeries.LENSCALE
sigvar = trialSeries.SIGVAR
noisevar2 = 1e-7
DOMAIN = np.linspace(0, 1, 1028)
KDOMAIN = gp.K_se(DOMAIN, DOMAIN, lenscale, sigvar)
# trial by trial fits to expected improvement
nPassiveObs = len(trialSeries.xPassiveObs)
nActiveObs = len(trialSeries.xActiveObs)
xActive = trialSeries.xActiveObs
yActive = trialSeries.yActiveObs
xPassive = trialSeries.xPassiveObs
yPassive = trialSeries.yPassiveObs
minidicts = []
for iActive in xrange(nActiveObs):
# get active obs to this point
xAct = xActive[:iActive]
yAct = yActive[:iActive]
# combine all obs seen to this point
xObs = npa(xAct + xPassive)
yObs = npa(yAct + yPassive)
xBest = xObs.max()
yBest = yObs.max()
# USING TRUE LENSCALE
# get posterior
mu = gp.conditioned_mu(DOMAIN, xObs, yObs, lenscale, sigvar, noisevar2)
cm = gp.conditioned_covmat(DOMAIN, KDOMAIN, xObs, lenscale, sigvar, noisevar2)
sd = np.diag(cm)
# get EI guess
eiout = acq.EI(yBest, mu, sd, DOMAIN)
xEI = eiout['xmax']
yEI = eiout['fmax']
# get subject guess
xSub = xActive[iActive]
ySub = yActive[iActive]
# compare
xDiff = xSub - xEI
# store
minidicts.append({'xEI': xEI,
'yEI': yEI,
'xSub': xSub,
'ySub': ySub,
'xDiff': xDiff,
'iActive': iActive,
'xAct': xAct,
'yAct': yAct,
'xPassive': xPassive,
'yPassive': yPassive,
'exp_ls': lenscale,
'xAct': xAct,
'yAct': yAct,
'workerid': wid,
'condition': condition,
'counterbalance': counterbalance})
return DataFrame(minidicts)
ax1.set_xlim(0, len(bands.kpoints))
# Density of state
# ----------------
ax2.set_yticklabels([])
ax2.grid()
ax2.set_xticks(np.arange(0, 1.5, 0.4))
ax2.set_xticklabels(np.arange(0, 1.5, 0.4))
ax2.set_xlim(1e-6, 1.5)
ax2.hlines(y=0, xmin=0, xmax=1.5, color="k", lw=2)
ax2.set_xlabel("Density of State")
# s contribution
ax2.plot(npa(dosrun.pdos[0][Orbital.s][Spin.up]) +
npa(dosrun.pdos[1][Orbital.s][Spin.up]),
dosrun.tdos.energies - dosrun.efermi,
"r-", label="s", linewidth=2)
# px py contribution
ax2.plot(npa(dosrun.pdos[0][Orbital.px][Spin.up]) +
npa(dosrun.pdos[1][Orbital.px][Spin.up]) +
npa(dosrun.pdos[0][Orbital.py][Spin.up]) +
npa(dosrun.pdos[1][Orbital.py][Spin.up]),
dosrun.tdos.energies - dosrun.efermi,
"g-",
label="(px, py)",
linewidth=2)
# pz contribution
def jsonToNpa(jstr, npa_type=float):
array = loads(jstr)
array = map(npa_type, array)
return npa(array)
LENSCALEPOWSOF2 = [2., 4., 6.]
LENSCALEPOOL = [1./2.**n for n in LENSCALEPOWSOF2]
DOMAINBOUNDS = [[0., 1.]]
DOMAINRES = 1024
DOMAIN = make_domain_grid(DOMAINBOUNDS, DOMAINRES).flatten()
EDGEBUF = 0.05 # samples for 2sams wont be closer than EDGEBUF from screen edge
# how close to domain edges passive observations can occur
XSAM_BOUNDS = [dim[:] for dim in DOMAINBOUNDS] # deep copy of DOMAINBOUNDS
XSAM_BOUNDS[0][0] = EDGEBUF
XSAM_BOUNDS[0][1] -= EDGEBUF
# made with numpy.random.randint(4294967295, size=20) # (number is max allowed on amazon linux)
RNGSEEDPOOL =\
npa([1903799985, 1543581047, 1218602148, 764353219, 1906699770,
951675775, 2101131205, 1792109879, 781776608, 2388543424,
2154736893, 2773127409, 3304953852, 678883645, 3097437001,
3696226994, 242457524, 991216532, 2747458246, 2432174005])
## LOAD GP STUFF INTO WORKSPACE
@custom_code.route('/init_experiment', methods=['GET'])
def init_experiment():
if not request.args.has_key('condition'):
raise ExperimentError('improper_inputs') # i don't like returning HTML to JSON requests... maybe should change this
condition = int(request.args['condition'])
counterbalance = int(request.args['counterbalance'])
## END FREE VARS
lenscale = LENSCALEPOOL[condition]
rngseed = RNGSEEDPOOL[counterbalance]
rng = RandomState(rngseed)
def eiregret_trialSeries(trialSeries, ls=None, firstN=None):
if not ls: ls=trialSeries.LENSCALE # default use experiment lenscale
wid = trialSeries.workerid
itrial = trialSeries.itrial
condition = trialSeries.condition
counterbalance = trialSeries.counterbalance
sigvar = trialSeries.SIGVAR
noisevar2 = 1e-7
DOMAIN = np.linspace(0, 1, 1028)
KDOMAIN = gp.K_se(DOMAIN, DOMAIN, ls, sigvar)
# trial by trial fits to expected improvement
nPassiveObs = len(trialSeries.xPassiveObs)
nActiveObs = len(trialSeries.xActiveObs)
xActive = trialSeries.xActiveObs
yActive = trialSeries.yActiveObs
xPassive = trialSeries.xPassiveObs
yPassive = trialSeries.yPassiveObs
minidicts = []
if firstN: nActiveObs = firstN
for iActive in xrange(nActiveObs): # run analysis for each active choice
# get active obs to this point
xAct = xActive[:iActive]
yAct = yActive[:iActive]
# combine all obs seen to this point
xObs = npa(xAct + xPassive)
yObs = npa(yAct + yPassive)
xBest = xObs.max()
yBest = yObs.max()
# get posterior
mu = gp.conditioned_mu(DOMAIN, xObs, yObs, ls, sigvar, noisevar2)
cm = gp.conditioned_covmat(DOMAIN, KDOMAIN, xObs, ls, sigvar, noisevar2)
sd = np.diag(cm)
# get EI guess
eiout = acq.EI(yBest, mu, sd, DOMAIN, return_whole_domain=True)
xEI = eiout['xmax']
yEI = eiout['fmax']
domainEI = eiout['fall']
iEI = np.where(DOMAIN>=xEI)[0][0]
# get subject guess
xSub = xActive[iActive]
ySub = yActive[iActive]
iSub = np.where(DOMAIN>=xSub)[0][0]
# get regret
evyEI = domainEI[iEI]
evySub = domainEI[iSub]
# compare
regret = evyEI - evySub
# store
minidicts.append({'regret': regret,
'evyEI': evyEI,
'evySub': evySub,
'xEI': xEI,
'yEI': yEI,
'xSub': xSub,
'ySub': ySub,
'iActive': iActive,
'xPassive': xPassive,
'yPassive': yPassive,
'lenscale': ls,
'xAct': xAct,
'yAct': yAct,
'workerid': wid,
'itrial': itrial,
'condition': condition,
'counterbalance': counterbalance})
return DataFrame(minidicts)
[0., -3.75, 0., 115.617 ],
[0.86045705, 0., 7.78655376, -27.91161211],
[0., 0., 0., 1. ]])
# Affine from Philips-created NIfTI
PHILIPS_AFFINE = np.array(
[[ -3.65 , -0.0016, 1.8356, 125.4881],
[ 0.0016, -3.75 , -0.0004, 117.4916],
[ 0.8604, 0.0002, 7.7866, -28.3411],
[ 0. , 0. , 0. , 1. ]])
# Affines generated by parrec.py from test data in many orientations
# Data from http://psydata.ovgu.de/philips_achieva_testfiles/conversion2
PREVIOUS_AFFINES={
"Phantom_EPI_3mm_cor_20APtrans_15RLrot_SENSE_15_1" :
npa([[ -3. , 0. , 0. , 118.5 ],
[ 0. , -0.77645714, -3.18755523, 72.82738377],
[ 0. , -2.89777748, 0.85410285, 97.80720486],
[ 0. , 0. , 0. , 1. ]]),
"Phantom_EPI_3mm_cor_SENSE_8_1" :
npa([[ -3. , 0. , 0. , 118.5 ],
[ 0. , 0. , -3.3 , 64.35],
[ 0. , -3. , 0. , 118.5 ],
[ 0. , 0. , 0. , 1. ]]),
"Phantom_EPI_3mm_sag_15AP_SENSE_13_1" :
npa([[ 0. , 0.77645714, 3.18755523, -92.82738377],
[ -3. , 0. , 0. , 118.5 ],
[ 0. , -2.89777748, 0.85410285, 97.80720486],
[ 0. , 0. , 0. , 1. ]]),
"Phantom_EPI_3mm_sag_15FH_SENSE_12_1" :
npa([[ 0.77645714, 0. , 3.18755523, -92.82738377],
[ -2.89777748, 0. , 0.85410285, 97.80720486],
[ 0. , -3. , 0. , 118.5 ],
# In[162]:
# Plot effect of relevance feedback as we change parameters.
import numpy as np
from numpy import array as npa
import random as rnd
def centroid(docs):
return np.sum(docs, axis=0) / len(docs)
def rocchio(query, relevant, irrelevant, alpha, beta, gamma):
return alpha * query + beta * centroid(relevant) - gamma * centroid(irrelevant)
# Create some documents
relevant = npa([[1, 5], [1.1, 5.1], [0.9, 4.9], [1.0, 4.8]])
irrelevant = npa([[rnd.random()*6, rnd.random()*6] for i in range(30)])
# Create a query
query = npa([.1, .1])
# Compute two different Rocchio updates (beta=0.5, beta=0)
new_query_b5 = rocchio(query, relevant, irrelevant, 1., .75, .5)
new_query_b0 = rocchio(query, relevant, irrelevant, 1., .75, 0.)
# Plot them.
pos = scatter([p[0] for p in relevant], [p[1] for p in relevant])
neg = scatter([p[0] for p in irrelevant], [p[1] for p in irrelevant], marker='+', edgecolor='red')
q = scatter(query[0], query[1], marker='v', c=0.1, s=100)
newq_b5 = scatter([new_query_b5[0]], [new_query_b5[1]], marker='*', s=100, c=.9)
newq_b0 = scatter([new_query_b0[0]], [new_query_b0[1]], marker='d', s=100, c=.8)