def make_step(self, signals, dt, rng):
if self.conv.dimensions > 2:
# note: we raise the error here, rather than earlier, because
# other backends might support different convolutions
raise NotImplementedError("Convolution > 2D not supported")
W = signals[self.W]
X = signals[self.X]
Y = signals[self.Y]
pad = self.conv.padding.upper()
stride = self.conv.strides
X = X.reshape(self.conv.input_shape.shape)
Y = Y.reshape(self.conv.output_shape.shape)
if not self.conv.channels_last:
X = np.moveaxis(X, 0, -1)
Y = np.moveaxis(Y, 0, -1)
if self.conv.dimensions == 1:
# add extra dimension to make it a 2D convolution
X = X[None, :, :]
W = W[None, :, :, :]
Y = Y[None, :, :]
stride = (1,) + stride
# add empty batch dimension
X = X[None, ...]
def step_conv():
Y[...] += conv2d.conv2d(X, W, pad=pad, stride=stride)[0]
return step_conv
def get_float_tensor_from_cntk_convolutional_weight_parameter(tensorParameter):
"""Returns an ELL.FloatTensor from a trainable parameter
Note that ELL's ordering is row, column, channel.
4D parameters (e.g. those that represent convolutional weights) are stacked vertically in the row dimension.
CNTK has them in filter, channel, row, column order.
"""
tensorShape = tensorParameter.shape
tensorValue = tensorParameter.value
if (len(tensorShape) == 4):
orderedWeights = np.moveaxis(tensorValue, 1, -1)
orderedWeights = orderedWeights.ravel().astype(np.float).reshape(
tensorShape[0] * tensorShape[2], tensorShape[3], tensorShape[1])
elif (len(tensorShape) == 3):
orderedWeights = np.moveaxis(tensorValue, 0, -1)
orderedWeights = orderedWeights.ravel().astype(np.float).reshape(
tensorShape[1], tensorShape[2], tensorShape[0])
elif (len(tensorShape) == 2):
orderedWeights = np.moveaxis(tensorValue, 0, -1)
orderedWeights = orderedWeights.ravel().astype(
np.float).reshape(tensorShape[1], tensorShape[0], 1)
else:
orderedWeights = tensorValue.ravel().astype(
np.float).reshape(1, 1, tensorValue.size)
return ELL.FloatTensor(orderedWeights)
def weighed_arithmetic_mean_numpy(data, weights=None):
"""
Calculate the weighted mean of an array/list using numpy
"""
# Not weighted
if weights is None: return arithmetic_mean_numpy(data)
import numpy as np
# Get the number of dimensions
ndim_data = len(data.shape)
ndim_weights = len(weights.shape)
#weights = np.array(weights).flatten() / float(sum(weights))
#return np.dot(np.array(data), weights)
if ndim_weights > 1:
weights = np.copy(weights)
divisors = np.sum(weights, axis=-1)
#norm_weights = weights /
norm_weights = np.moveaxis(weights, -1, 0) # move last to first axis
#print("1", norm_weights.shape)
# Loop over
for index in range(norm_weights.shape[0]): norm_weights[index] /= divisors
#print(norm_weights.shape)
norm_weights = np.moveaxis(norm_weights, 0, 1)
#print("2", norm_weights.shape)
else: norm_weights = weights / float(np.sum(weights))
return np.dot(data, norm_weights)
def calc(self, pars, elo, xlo, ylo, ehi, xhi, yhi):
etrue_centers = self.true_energy.log_centers
if self.use_psf:
# Convolve the spatial model * exposure by the psf in etrue
spatial = np.zeros((self.dim_Etrue, self.dim_x, self.dim_y))
a = self.spatial_model.calc(pars[self._spatial_pars], self.xx_lo.ravel(), self.xx_hi.ravel(),
self.yy_lo.ravel(), self.yy_hi.ravel()).reshape(self.xx_lo.shape)
for ind_E in range(self.dim_Etrue):
spatial[ind_E, :, :] = self._fftconvolve(a * self.exposure.data[ind_E, :, :],
self.psf.data[ind_E, :, :] /
(self.psf.data[ind_E, :, :].sum()), mode='same')
# To avoid nan value for the true energy values asked by the user for which the PSF is not defined.
# The interpolation gives nan when you are outside the range and when you sum over all the true energy bin to calculate the expected
# number of counts in the reconstucted energy bin, you get nan whereas you just want the bin in true energy
# for which the PSF is not defined to not count in the sum.
spatial[np.isnan(spatial)] = 0
else:
spatial_2d = self.spatial_model.calc(pars[self._spatial_pars], self.xx_lo.ravel(), self.xx_hi.ravel(),
self.yy_lo.ravel(), self.yy_hi.ravel()).reshape(self.xx_lo.shape)
spatial = np.tile(spatial_2d, (len(etrue_centers), 1, 1))
# Calculate the spectral model in etrue
spectral_1d = self.spectral_model.calc(pars[self._spectral_pars], etrue_centers)
spectral = spectral_1d.reshape(len(etrue_centers), 1, 1) * np.ones_like(self.xx_lo)
# Convolve by the energy resolution
etrue_band = self.true_energy.bands
for ireco in range(self.dim_Ereco):
self.convolve_edisp[:, :, :, ireco] = np.moveaxis(spatial, 0, -1) * np.moveaxis(spectral, 0, -1) * \
self.edisp[:, ireco] * etrue_band
# Integration in etrue
model = np.moveaxis(np.sum(self.convolve_edisp, axis=2), -1, 0)
if not self.select_region:
return model.ravel()
else:
return model[self.index_selected_region].ravel()
def get_float_tensor_from_cntk_dense_weight_parameter(tensorParameter):
"""Returns an ELL.FloatTensor from a trainable parameter
Note that ELL's ordering is row, column, channel.
CNTK has them in channel, row, column, filter order.
4D parameters are converted to ELL Tensor by stacking vertically in the row dimension.
"""
tensorShape = tensorParameter.shape
tensorValue = tensorParameter.value
#orderedWeights = tensorValue
if (len(tensorShape) == 4):
orderedWeights = tensorValue
orderedWeights = np.moveaxis(orderedWeights, 0, -1)
orderedWeights = np.moveaxis(orderedWeights, 2, 0)
orderedWeights = orderedWeights.ravel().astype(np.float).reshape(
tensorShape[3] * tensorShape[1], tensorShape[2], tensorShape[0])
elif (len(tensorShape) == 3):
orderedWeights = np.moveaxis(tensorValue, 0, -1)
orderedWeights = orderedWeights.ravel().astype(np.float).reshape(
tensorShape[1], tensorShape[2], tensorShape[0])
elif (len(tensorShape) == 2):
orderedWeights = np.moveaxis(tensorValue, 0, -1)
orderedWeights = orderedWeights.ravel().astype(
np.float).reshape(tensorShape[1], 1, tensorShape[0])
else:
orderedWeights = tensorValue.ravel().astype(
np.float).reshape(1, 1, tensorValue.size)
return ELL.FloatTensor(orderedWeights)
def test_exceptions(self):
# test axis must be in bounds
for ndim in [1, 2, 3]:
a = np.ones((1,)*ndim)
np.concatenate((a, a), axis=0) # OK
assert_raises(np.AxisError, np.concatenate, (a, a), axis=ndim)
assert_raises(np.AxisError, np.concatenate, (a, a), axis=-(ndim + 1))
# Scalars cannot be concatenated
assert_raises(ValueError, concatenate, (0,))
assert_raises(ValueError, concatenate, (np.array(0),))
# test shapes must match except for concatenation axis
a = np.ones((1, 2, 3))
b = np.ones((2, 2, 3))
axis = list(range(3))
for i in range(3):
np.concatenate((a, b), axis=axis[0]) # OK
assert_raises(ValueError, np.concatenate, (a, b), axis=axis[1])
assert_raises(ValueError, np.concatenate, (a, b), axis=axis[2])
a = np.moveaxis(a, -1, 0)
b = np.moveaxis(b, -1, 0)
axis.append(axis.pop(0))
# No arrays to concatenate raises ValueError
assert_raises(ValueError, concatenate, ())
def coral_numpy(source, target):
n_channels = source.shape[-1]
source = np.moveaxis(source, -1, 0) # HxWxC -> CxHxW
target = np.moveaxis(target, -1, 0) # HxWxC -> CxHxW
source_flatten = source.reshape(n_channels, source.shape[1]*source.shape[2])
target_flatten = target.reshape(n_channels, target.shape[1]*target.shape[2])
source_flatten_mean = source_flatten.mean(axis=1, keepdims=True)
source_flatten_std = source_flatten.std(axis=1, keepdims=True)
source_flatten_norm = (source_flatten - source_flatten_mean) / source_flatten_std
target_flatten_mean = target_flatten.mean(axis=1, keepdims=True)
target_flatten_std = target_flatten.std(axis=1, keepdims=True)
target_flatten_norm = (target_flatten - target_flatten_mean) / target_flatten_std
source_flatten_cov_eye = source_flatten_norm.dot(source_flatten_norm.T) + np.eye(n_channels)
target_flatten_cov_eye = target_flatten_norm.dot(target_flatten_norm.T) + np.eye(n_channels)
source_flatten_norm_transfer = matSqrt_numpy(target_flatten_cov_eye).dot(np.linalg.inv(matSqrt_numpy(source_flatten_cov_eye))).dot(source_flatten_norm)
source_flatten_transfer = source_flatten_norm_transfer * target_flatten_std + target_flatten_mean
coraled = source_flatten_transfer.reshape(source.shape)
coraled = np.moveaxis(coraled, 0, -1) # CxHxW -> HxWxC
return coraled
def test_pick():
group = icosahedral.Pyritohedral()
full = group.group
from pycomplex.math import linalg
N = 128
points = np.moveaxis(np.indices((N, N)).astype(np.float), 0, -1) / (N - 1) * 2 - 1
z = np.sqrt(np.clip(1 - linalg.dot(points, points), 0, 1))
points = np.concatenate([points, z[..., None]], axis=-1)
element_idx, sub_idx, quotient_idx, bary = group.pick(points.reshape(-1, 3))
if False:
col = bary
else:
col = np.array([
sub_idx.astype(np.float) / sub_idx.max(),
sub_idx * 0,
quotient_idx.astype(np.float) / quotient_idx.max()
]).T
plt.figure()
img = np.flip(np.moveaxis(col.reshape(N, N, 3), 0, 1), axis=0)
# img = (img * 255).astype(np.uint8)
plt.imshow(img)
plt.show()
def load_and_subsample(raw_img_path, substep, low_freq_percent):
"""
Loads and subsamples an MR image in Analyze format
Parameters
------------
raw_img_path : str
The path to the MR image
substep : int
The substep to use when subsampling image slices
low_freq_percent : float
The percentage of low frequency data to retain when subsampling slices
Returns
------------
tuple
A triple containing the following ordered numpy arrays:
1. The subsampled MR image (datatype `np.float32`)
2. The k-space representation of the subsampled MR image (datatype `np.complex128`)
3. The original MR image (datatype `np.float32`)
"""
original_img = load_image_data(analyze_img_path=raw_img_path)
subsampled_img, subsampled_k = subsample(
analyze_img_data=original_img,
substep=substep,
low_freq_percent=low_freq_percent)
original_img = np.moveaxis(original_img, -1, 0)
subsampled_img = np.moveaxis(subsampled_img, -1, 0)
subsampled_k = np.moveaxis(subsampled_k, -1, 0)
return subsampled_img, subsampled_k, original_img
def load_data(dirp,nb_classes):
# load the dataset as X_train and as a copy the X_val
X_train = pickle.load( open( os.path.join(dirp,'X_train.pkl'), "rb" ) )
y_train = pickle.load( open(os.path.join(dirp,'y_train.pkl'), "rb" ) )
X_val = pickle.load( open( os.path.join(dirp,'X_val.pkl'), "rb" ) )
y_val = pickle.load( open( os.path.join(dirp,'y_val.pkl'), "rb" ) )
if len(X_train.shape)>3:
X_train=np.moveaxis(X_train,3,1)
X_val=np.moveaxis(X_val,3,1)
else:
X_train = np.expand_dims(X_train,1)
X_val =np.expand_dims(X_val,1)
print ('Xtrain :',X_train.shape)
print 'X_train min max :',X_train.min(),X_train.max()
# labels to categorical vectors
# uniquelbls = np.unique(y_train)
# nb_classes = int( uniquelbls.shape[0])
print ('number of classes :', int(nb_classes))
# zbn = np.min(uniquelbls) # zero based numbering
y_train = np_utils.to_categorical(y_train, nb_classes)
y_val = np_utils.to_categorical(y_val, nb_classes)
return (X_train, y_train), (X_val, y_val)
def test_pick():
group = Cyclic(2)
complex = MultiComplex.generate(group, 6)
from pycomplex.math import linalg
N = 1024
points = np.moveaxis(np.indices((N, N)).astype(np.float), 0, -1) / (N - 1) * 2 - 1
z = np.sqrt(np.clip(1 - linalg.dot(points, points), 0, 1))
points = np.concatenate([points, z[..., None]], axis=-1)
element_idx, sub_idx, quotient_idx, triangle_idx, bary = complex[-1].pick(points.reshape(-1, 3))
print(bary.min(), bary.max())
if True:
col = bary
else:
col = np.array([
sub_idx.astype(np.float) / sub_idx.max(),
sub_idx * 0,
quotient_idx.astype(np.float) / quotient_idx.max()
]).T
plt.figure()
img = np.flip(np.moveaxis(col.reshape(N, N, 3), 0, 1), axis=0)
plt.imshow(img)
plt.show()
def apply_transform(matrix, image, params):
"""
Apply a transformation to an image.
The origin of transformation is at the top left corner of the image.
The matrix is interpreted such that a point (x, y) on the original image is moved to transform * (x, y) in the generated image.
Mathematically speaking, that means that the matrix is a transformation from the transformed image space to the original image space.
Parameters:
matrix: A homogenous 3 by 3 matrix holding representing the transformation to apply.
image: The image to transform.
params: The transform parameters (see TransformParameters)
"""
if params.channel_axis != 2:
image = np.moveaxis(image, params.channel_axis, 2)
output = cv2.warpAffine(
image,
matrix[:2, :],
dsize = (image.shape[1], image.shape[0]),
flags = params.cvInterpolation(),
borderMode = params.cvBorderMode(),
borderValue = params.cval,
)
if params.channel_axis != 2:
output = np.moveaxis(output, 2, params.channel_axis)
return output
def scattering_matrix(vp1, vs1, rho1, vp2, vs2, rho2, theta1=0):
"""
Full Zoeppritz solution, considered the definitive solution.
Calculates the angle dependent p-wave reflectivity of an interface
between two mediums.
Originally written by: Wes Hamlyn, vectorized by Agile.
Returns the complex reflectivity.
Args:
vp1 (float): The upper P-wave velocity.
vs1 (float): The upper S-wave velocity.
rho1 (float): The upper layer's density.
vp2 (float): The lower P-wave velocity.
vs2 (float): The lower S-wave velocity.
rho2 (float): The lower layer's density.
theta1 (ndarray): The incidence angle; float or 1D array length n.
Returns:
ndarray. The exact Zoeppritz solution for all modes at the interface.
A 4x4 array representing the scattering matrix at the incident
angle theta1.
"""
theta1 = np.radians(theta1).astype(complex) * np.ones_like(vp1)
p = np.sin(theta1) / vp1 # Ray parameter.
theta2 = np.arcsin(p * vp2) # Trans. angle of P-wave.
phi1 = np.arcsin(p * vs1) # Refl. angle of converted S-wave.
phi2 = np.arcsin(p * vs2) # Trans. angle of converted S-wave.
# Matrix form of Zoeppritz equations... M & N are matrices.
M = np.array([[-np.sin(theta1), -np.cos(phi1), np.sin(theta2), np.cos(phi2)],
[np.cos(theta1), -np.sin(phi1), np.cos(theta2), -np.sin(phi2)],
[2 * rho1 * vs1 * np.sin(phi1) * np.cos(theta1),
rho1 * vs1 * (1 - 2 * np.sin(phi1) ** 2),
2 * rho2 * vs2 * np.sin(phi2) * np.cos(theta2),
rho2 * vs2 * (1 - 2 * np.sin(phi2) ** 2)],
[-rho1 * vp1 * (1 - 2 * np.sin(phi1) ** 2),
rho1 * vs1 * np.sin(2 * phi1),
rho2 * vp2 * (1 - 2 * np.sin(phi2) ** 2),
-rho2 * vs2 * np.sin(2 * phi2)]])
N = np.array([[np.sin(theta1), np.cos(phi1), -np.sin(theta2), -np.cos(phi2)],
[np.cos(theta1), -np.sin(phi1), np.cos(theta2), -np.sin(phi2)],
[2 * rho1 * vs1 * np.sin(phi1) * np.cos(theta1),
rho1 * vs1 * (1 - 2 * np.sin(phi1) ** 2),
2 * rho2 * vs2 * np.sin(phi2) * np.cos(theta2),
rho2 * vs2 * (1 - 2 * np.sin(phi2) ** 2)],
[rho1 * vp1 * (1 - 2 * np.sin(phi1) ** 2),
-rho1 * vs1 * np.sin(2 * phi1),
- rho2 * vp2 * (1 - 2 * np.sin(phi2) ** 2),
rho2 * vs2 * np.sin(2 * phi2)]])
M_ = np.moveaxis(np.squeeze(M), [0, 1], [-2, -1])
A = np.linalg.inv(M_)
N_ = np.moveaxis(np.squeeze(N), [0, 1], [-2, -1])
Z_ = np.matmul(A, N_)
return np.transpose(Z_, axes=list(range(Z_.ndim - 2)) + [-1, -2])
def test_convinc_2d(
channels_last, stride0, stride1, kernel0, kernel1, padding, rng):
correlate2d = pytest.importorskip("scipy.signal").correlate2d
shape0 = 16
shape1 = 17
in_channels = 32
out_channels = 64
x_shape = (shape0, shape1, in_channels) if channels_last else (
in_channels, shape0, shape1)
x = Signal(rng.randn(*x_shape))
w = Signal(rng.randn(kernel0, kernel1, in_channels, out_channels))
conv = Convolution(out_channels,
x_shape,
kernel_size=(kernel0, kernel1),
strides=(stride0, stride1),
padding=padding,
channels_last=channels_last)
y = Signal(np.zeros(conv.output_shape.shape))
signals = {sig: np.array(sig.initial_value) for sig in (x, w, y)}
step = ConvInc(w, x, y, conv).make_step(signals, None, None)
step()
x0 = x.initial_value
if not channels_last:
x0 = np.moveaxis(x0, 0, -1)
if padding == "same":
strides = np.asarray([stride0, stride1])
padding = np.ceil(np.asarray([shape0, shape1]) / strides)
padding = np.maximum(
(padding - 1) * strides + (kernel0, kernel1) - (shape0, shape1),
0).astype(np.int64)
x0 = np.pad(x0, [
(padding[0] // 2, padding[0] - padding[0] // 2),
(padding[1] // 2, padding[1] - padding[1] // 2),
(0, 0),
], "constant")
y0 = np.stack([
np.sum([
correlate2d(x0[..., j], w.initial_value[..., j, i], mode="valid")
for j in range(in_channels)
], axis=0) for i in range(out_channels)
], axis=-1)
y0 = y0[::stride0, ::stride1, :]
if not channels_last:
y0 = np.moveaxis(y0, -1, 0)
assert np.allclose(signals[y], y0)
def __init__(self):
train = scipy.io.loadmat('/home/roliveira/.keras/datasets/svhn/train_32x32.mat')
test = scipy.io.loadmat('/home/roliveira/.keras/datasets/svhn/test_32x32.mat')
self.X_train = np.moveaxis(train['X'], [0, 1 , 2, 3], [2, 3, 1, 0])
self.y_train = train['y'].reshape(-1)
self.y_train[self.y_train == 10] = 0
self.X_test = np.moveaxis(test['X'], [0, 1 , 2, 3], [2, 3, 1, 0])
self.y_test = test['y']
self.y_test[self.y_test == 10] = 0
def run_same(self, batch, input_support, channels, filters, kernel_support,
corr, strides_down, strides_up, padding, extra_pad_end,
channel_separable, data_format, activation, use_bias):
assert channels == filters == 1
# Create input array.
input_shape = (batch, 1) + input_support
inputs = np.arange(np.prod(input_shape))
inputs = inputs.reshape(input_shape).astype(np.float32)
if data_format != "channels_first":
tf_inputs = tf.constant(np.moveaxis(inputs, 1, -1))
else:
tf_inputs = tf.constant(inputs)
# Create kernel array. This is an identity kernel, so the outputs should
# be equal to the inputs except for up- and downsampling.
tf_kernel = parameterizers.StaticParameterizer(
initializers.IdentityInitializer())
# Run SignalConv* layer.
layer_class = {
3: signal_conv.SignalConv1D,
4: signal_conv.SignalConv2D,
5: signal_conv.SignalConv3D,
}[inputs.ndim]
layer = layer_class(
1, kernel_support, corr=corr, strides_down=strides_down,
strides_up=strides_up, padding=padding, extra_pad_end=extra_pad_end,
channel_separable=channel_separable, data_format=data_format,
activation=activation, use_bias=use_bias,
kernel_parameterizer=tf_kernel)
tf_outputs = layer(tf_inputs)
with self.test_session() as sess:
sess.run(tf.global_variables_initializer())
outputs = sess.run(tf_outputs)
# Check that SignalConv* computes the correct output size.
predicted_shape = layer.compute_output_shape(tf_inputs.shape)
self.assertEqual(outputs.shape, tuple(predicted_shape.as_list()))
# If not using channels_first, convert back to it to compare to input.
if data_format != "channels_first":
outputs = np.moveaxis(outputs, -1, 1)
# Upsample and then downsample inputs.
expected = inputs
if not all(s == 1 for s in strides_up):
expected = self.numpy_upsample(expected, strides_up, extra_pad_end)
slices = (slice(None), slice(None))
slices += tuple(slice(None, None, s) for s in strides_down)
expected = expected[slices]
self.assertAllClose(expected, outputs, rtol=0, atol=1e-3)
def gen(self, snr, x_axis=0, ivar_precision=.05, structure_shape=(1, )):
'''
generate data from full PC basis, and noisify according to snr
'''
if x_axis < 0:
raise ValueError('x axis index must be positive')
# since in this case we're using all PCs to construct fake data
q = self.n
self.x_axis = x_axis
# if SNR is a single number, just return a single spectrum
if not hasattr(snr, '__len__'):
snr = snr * np.ones_like(self.x)
fulldata_shape = (self.n, )
coeffs_shape = (q, )
# if SNR is given as a map (i.e., has an incompatible shape to self.x),
# then add a dimension where specified in x_axis to make shapes compatible
elif self.n not in snr.shape:
# define higher-dimensional data structure shape
# that delimits separate measurements
structure_shape = snr.shape
snr = np.expand_dims(snr, x_axis)
snr = np.repeat(snr, self.n, axis=x_axis)
fulldata_shape = snr.shape
coeffs_shape = tuple_insert(structure_shape, x_axis, q)
else:
structure_shape = tuple_delete(snr.shape, x_axis)
fulldata_shape = snr.shape
coeffs_shape = tuple_insert(structure_shape, x_axis, q)
self.snr = snr
self.A0 = np.random.randn(*coeffs_shape)
# generate centered data, and then add mean
self.obs0_ctrd = np.moveaxis(
(np.moveaxis(self.A0, x_axis, -1) @ self.E_full.T), -1, x_axis)
self.obs0 = np.moveaxis(
np.moveaxis(self.obs0_ctrd, x_axis, -1) + self.M, -1, x_axis)
obs_noise = self.obs0 * np.random.randn(*fulldata_shape) / snr
spectrophotometric_noise = np.moveaxis(
np.random.multivariate_normal(
np.zeros(self.n), self.K_inst.covariance_,
structure_shape),
-1, x_axis)
self.obs = self.obs0 + obs_noise + spectrophotometric_noise
self.ivar0 = (snr / self.obs)**2.
self.ivar = (self.ivar0 * (1. + ivar_precision * \
np.random.randn(*self.ivar0.shape))).clip(min=0.)
def __call__(self, l, flam, ivar=None, axis=0, *args, **kwargs):
if len(l.shape) > 1:
raise ValueError('wavelength array (l) must be 1D')
flam[flam == 0.] = eps
if ivar is None:
ivar = np.ones_like(flam)
ivar[ivar == 0.] = eps
# rearrange axes to make broadcasting work
ivar = np.moveaxis(ivar, axis, -1)
flam = np.moveaxis(flam, axis, -1)
return getattr(self, self._func)(l, flam, ivar, axis, *args, **kwargs)
def run_valid(self, batch, input_support, channels, filters, kernel_support,
corr, strides_down, strides_up, padding, extra_pad_end,
channel_separable, data_format, activation, use_bias):
assert padding == "valid"
# Create input array.
inputs = np.random.randint(32, size=(batch, channels) + input_support)
inputs = inputs.astype(np.float32)
if data_format != "channels_first":
tf_inputs = tf.constant(np.moveaxis(inputs, 1, -1))
else:
tf_inputs = tf.constant(inputs)
# Create kernel array.
kernel = np.random.randint(16, size=kernel_support + (channels, filters))
kernel = kernel.astype(np.float32)
tf_kernel = parameterizers.StaticParameterizer(
tf.constant_initializer(kernel))
# Run SignalConv* layer.
layer_class = {
3: signal_conv.SignalConv1D,
4: signal_conv.SignalConv2D,
5: signal_conv.SignalConv3D,
}[inputs.ndim]
layer = layer_class(
filters, kernel_support, corr=corr, strides_down=strides_down,
strides_up=strides_up, padding="valid", extra_pad_end=extra_pad_end,
channel_separable=channel_separable, data_format=data_format,
activation=activation, use_bias=use_bias,
kernel_parameterizer=tf_kernel)
tf_outputs = layer(tf_inputs)
with self.test_session() as sess:
sess.run(tf.global_variables_initializer())
outputs = sess.run(tf_outputs)
# Check that SignalConv* computes the correct output size.
predicted_shape = layer.compute_output_shape(tf_inputs.shape)
self.assertEqual(outputs.shape, tuple(predicted_shape.as_list()))
# If not using channels_first, convert back to it to compare to SciPy.
if data_format != "channels_first":
outputs = np.moveaxis(outputs, -1, 1)
# Compute the equivalent result using SciPy and compare.
expected = self.scipy_convolve_valid(
corr, inputs, kernel, strides_down, strides_up, extra_pad_end,
channel_separable)
self.assertAllClose(expected, outputs, rtol=0, atol=1e-3)
def run_resample(self, src_data, interp_method='nearest', fill_value=np.nan, nprocs=1, print_msg=True):
"""Run interpolation operation for input 2D/3D data
Parameters: src_data : 2D/3D np.array, source data to be geocoded
interp_method : string, nearest | linear
fill_value : NaN or number
nprocs : int, number of processes to be used
print_msg : bool
Returns: geo_data : 2D/3D np.array
"""
# use pyresample
if self.processor == 'pyresample':
if len(src_data.shape) == 3:
src_data = np.moveaxis(src_data, 0, -1)
if src_data.dtype == np.bool_:
fill_value = False
print('restrict fill value to False for bool type source data')
# resample source data into target data
geo_data = self.run_pyresample(src_data=src_data,
interp_method=interp_method,
fill_value=fill_value,
nprocs=nprocs,
radius=None,
print_msg=True)
if len(geo_data.shape) == 3:
geo_data = np.moveaxis(geo_data, -1, 0)
# use scipy.interpolater.RegularGridInterpolator
else:
if print_msg:
print('resampling using scipy.interpolate.RegularGridInterpolator ...')
if len(src_data.shape) == 3:
geo_data = np.empty((src_data.shape[0], self.length, self.width), src_data.dtype)
prog_bar = ptime.progressBar(maxValue=src_data.shape[0])
for i in range(src_data.shape[0]):
geo_data[i, :, :] = self.run_regular_grid_interpolator(src_data=src_data[i, :, :],
interp_method=interp_method,
fill_value=fill_value,
print_msg=True)
prog_bar.update(i+1)
prog_bar.close()
else:
geo_data = self.run_regular_grid_interpolator(src_data=src_data,
interp_method=interp_method,
fill_value=fill_value,
print_msg=True)
return geo_data
def each_channel(image_filter, image, *args, **kwargs):
"""Return color image by applying `image_filter` on channels of `image`.
Note that this function is intended for use with `adapt_rgb`.
Parameters
----------
image_filter : function
Function that filters a gray-scale image.
image : array
Input image.
"""
c_new = [image_filter(c, *args, **kwargs)
for c in np.moveaxis(image, -1, 0)]
return np.moveaxis(np.array(c_new), 0, -1)
def __getitem__(self, idx):
a = np.load(os.path.join(self.tile_dir, '{}anchor.npy'.format(idx)))
n = np.load(os.path.join(self.tile_dir, '{}neighbor.npy'.format(idx)))
if self.pairs_only:
name = np.random.choice(['anchor', 'neighbor', 'distant'])
d_idx = np.random.randint(0, self.n_triplets)
d = np.load(os.path.join(self.tile_dir, '{}{}.npy'.format(d_idx, name)))
else:
d = np.load(os.path.join(self.tile_dir, '{}distant.npy'.format(idx)))
a = np.moveaxis(a, -1, 0)
n = np.moveaxis(n, -1, 0)
d = np.moveaxis(d, -1, 0)
sample = {'anchor': a, 'neighbor': n, 'distant': d}
if self.transform:
sample = self.transform(sample)
return sample
def _calc_sensib(símismo):
# El diccionario para los resultados
d_sens = {}
matr_t = símismo.res.matr_t
for índs in matr_t.iter_índs(excluir=['días', 'estoc', 'parám']):
ejes_orig = np.argsort([matr_t.í_eje('días'), matr_t.í_eje('estoc'), matr_t.í_eje('parám')])
vals_res = matr_t.obt_valor_t(índs=índs)
vals_res = np.moveaxis(vals_res, ejes_orig, [0, 1, 2])
vals_res = vals_res.reshape(vals_res.shape[:3]).mean(axis=(1, 2))
l_llaves = list(str(ll) for ll in índs.values())
for ll in l_llaves[:-1]:
if ll not in d_sens:
d_sens[ll] = {}
d_sens = d_sens[ll]
d_sensib_índ = {}
for í, vals_t in enumerate(vals_res):
sensib = símismo.func(vals_t)
for egr, m_egr in sensib.items():
# Para cada tipo de egreso del análisis de sensibilidad...
# Crear la matriz de resultados vacía, si necesario
if egr not in d_sensib_índ:
d_sensib_índ[egr] = np.zeros((*m_egr.shape, len(vals_res)))
# Llenar los datos para este día
d_sensib_índ[egr][..., í] = sensib[egr]
d_sens[l_llaves[-1]] = d_sensib_índ
return d_sens
def collapse_psd(psd, kind, index=None, average=False):
"""Collapse a PSD"""
if index is None:
if 'pseudophase' == kind:
psd_selected = (ap[...,None] * psd).sum(axis=tuple(range(psd.ndim - 1))) / ap.sum()
else:
psd_selected = psd.mean(axis=tuple(range(psd.ndim - 1)))
elif isinstance(index, slice):
psd_selected = np.moveaxis(psd[index], -1, 0).squeeze()
else:
index = tuple(index) + (slice(None, None),)
psd_selected = np.moveaxis(psd[index], -1, 0).squeeze()
if average and psd_selected.ndim > 1:
psd_selected = psd_selected.mean(axis=tuple(range(1, psd_selected.ndim)))
return psd_selected
def _comp_samples(self, point=None, size=None,
comp_dist_shapes=None,
broadcast_shape=None):
if self.comp_is_distribution:
samples = self._comp_dists.random(point=point, size=size)
else:
if comp_dist_shapes is None:
comp_dist_shapes = self._comp_dist_shapes
if broadcast_shape is None:
broadcast_shape = self._sample_shape
samples = []
for dist_shape, generator in zip(comp_dist_shapes,
self._generators):
sample = generate_samples(
generator=generator,
dist_shape=dist_shape,
broadcast_shape=broadcast_shape,
point=point,
size=size,
not_broadcast_kwargs={'raw_size_': size},
)
samples.append(sample)
samples = np.array(
broadcast_distribution_samples(samples, size=size)
)
# In the logp we assume the last axis holds the mixture components
# so we move the axis to the last dimension
samples = np.moveaxis(samples, 0, -1)
return samples.astype(self.dtype)
def _import_field_image(filename, hotpixelremove=False):
'''
'''
from ..datahandling import Field, Axis
if filename.lower().endswith('png'):
data = _readpng(filename)
else:
data = _read_image_pil(filename)
if hotpixelremove:
import scipy.ndimage
if data.ndim == 3 and data.shape[2] < 5:
# assume multichannel image file like rgb or rgba
for i in range(data.shape[2]):
data[..., i] = scipy.ndimage.morphology.grey_opening(data[..., i], size=(3, 3))
else:
data = scipy.ndimage.morphology.grey_opening(data, size=(3, 3))
# image data are usually in y-major order, but postpic Fields assume x-major order
# and rows are stored from top to bottom while y axes coordinate grows from bottom to top
data = np.moveaxis(data, 0, 1)[:, ::-1, ...]
axes = []
for i, (name, axlen) in enumerate(zip(['x', 'y', 'channel'], data.shape)):
ax = Axis(name=name, unit='px' if i < 2 else '',
grid=np.linspace(0, axlen-1, axlen))
axes.append(ax)
basename = osp.basename(filename)
return Field(data, unit='counts', name=basename, axes=axes)
def grad(X):
if X.shape==(1,):
shape=(X.dim,)
else:
shape=X.shape+(X.dim,)
name='grad({0})'.format(X.name[:10])
gX=Tensor(name=name, shape=shape, N=X.N,
Fourier=True, fft_form=X.fft_form)
if X.Fourier:
FX=X
else:
F=DFT(N=X.N, fft_form=X.fft_form) # TODO:change to X.fourier()
FX=F(X)
dim=len(X.N)
freq=Grid.get_freq(X.N, X.Y, fft_form=X.fft_form)
strfreq='xyz'
coef=2*np.pi*1j
val=np.empty((X.dim,)+X.shape+X.N_fft, dtype=np.complex)
for ii in range(X.dim):
mul_str='{0},...{1}->...{1}'.format(strfreq[ii], strfreq[:dim])
val[ii]=np.einsum(mul_str, coef*freq[ii], FX.val, dtype=np.complex)
if X.shape==(1,):
gX.val=np.squeeze(val)
else:
gX.val=np.moveaxis(val, 0, X.order)
if not X.Fourier:
iF=DFT(N=X.N, inverse=True, fft_form=gX.fft_form)
gX=iF(gX)
gX.name='grad({0})'.format(X.name[:10])
return gX
def hessian(self, q, t=0.):
"""
Compute the Hessian of the potential at the given position(s).
Parameters
----------
q : `~gala.dynamics.PhaseSpacePosition`, `~astropy.units.Quantity`, array_like
The position to compute the value of the potential. If the
input position object has no units (i.e. is an `~numpy.ndarray`),
it is assumed to be in the same unit system as the potential.
Returns
-------
hess : `~astropy.units.Quantity`
The Hessian matrix of second derivatives of the potential. If the input
position has shape ``q.shape``, the output energy will have shape
``(q.shape[0],q.shape[0]) + q.shape[1:]``. That is, an ``n_dim`` by
``n_dim`` array (matrix) for each position.
"""
if (self.R is not None and
not np.allclose(np.diag(self.R), 1., atol=1e-15, rtol=0)):
raise NotImplementedError("Computing Hessian matrices for rotated "
"potentials is currently not supported.")
q = self._remove_units_prepare_shape(q)
orig_shape,q = self._get_c_valid_arr(q)
t = self._validate_prepare_time(t, q)
ret_unit = 1 / self.units['time']**2
hess = np.moveaxis(self._hessian(q, t=t), 0, -1)
return hess.reshape((orig_shape[0], orig_shape[0]) + orig_shape[1:]) * ret_unit
def test_outer_indexer_consistency_with_broadcast_indexes_vectorized():
def nonzero(x):
if isinstance(x, np.ndarray) and x.dtype.kind == 'b':
x = x.nonzero()[0]
return x
original = np.random.rand(10, 20, 30)
v = Variable(['i', 'j', 'k'], original)
I = ReturnItem() # noqa: E741 # allow ambiguous name
# test orthogonally applied indexers
indexers = [I[:], 0, -2, I[:3], np.array([0, 1, 2, 3]), np.array([0]),
np.arange(10) < 5]
for i, j, k in itertools.product(indexers, repeat=3):
if isinstance(j, np.ndarray) and j.dtype.kind == 'b': # match size
j = np.arange(20) < 4
if isinstance(k, np.ndarray) and k.dtype.kind == 'b':
k = np.arange(30) < 8
_, expected, new_order = v._broadcast_indexes_vectorized((i, j, k))
expected_data = nputils.NumpyVIndexAdapter(v.data)[expected.tuple]
if new_order:
old_order = range(len(new_order))
expected_data = np.moveaxis(expected_data, old_order,
new_order)
outer_index = indexing.OuterIndexer((nonzero(i), nonzero(j),
nonzero(k)))
actual = indexing._outer_to_numpy_indexer(outer_index, v.shape)
actual_data = v.data[actual]
np.testing.assert_array_equal(actual_data, expected_data)
def load_dataset(self):
dataset = self.cfg.dataset
dataset_phase = self.cfg.dataset_phase
dataset_ann = self.cfg.dataset_ann
# initialize COCO api
annFile = '%s/annotations/%s_%s.json'%(dataset,dataset_ann,dataset_phase)
self.coco = COCO(annFile)
imgIds = self.coco.getImgIds()
data = []
# loop through each image
for imgId in imgIds:
item = DataItem()
img = self.coco.loadImgs(imgId)[0]
item.im_path = "%s/images/%s/%s"%(dataset, dataset_phase, img["file_name"])
item.im_size = [3, img["height"], img["width"]]
item.coco_id = imgId
annIds = self.coco.getAnnIds(imgIds=img['id'], iscrowd=False)
anns = self.coco.loadAnns(annIds)
all_person_keypoints = []
masked_persons_RLE = []
visible_persons_RLE = []
all_visibilities = []
# Consider only images with people
has_people = len(anns) > 0
if not has_people and self.cfg.coco_only_images_with_people:
continue
for ann in anns: # loop through each person
person_keypoints = []
visibilities = []
if ann["num_keypoints"] != 0:
for i in range(self.cfg.num_joints):
x_coord = ann["keypoints"][3 * i]
y_coord = ann["keypoints"][3 * i + 1]
visibility = ann["keypoints"][3 * i + 2]
visibilities.append(visibility)
if visibility != 0: # i.e. if labeled
person_keypoints.append([i, x_coord, y_coord])
all_person_keypoints.append(np.array(person_keypoints))
visible_persons_RLE.append(maskUtils.decode(self.coco.annToRLE(ann)))
all_visibilities.append(visibilities)
if ann["num_keypoints"] == 0:
masked_persons_RLE.append(self.coco.annToRLE(ann))
item.joints = all_person_keypoints
item.im_neg_mask = maskUtils.merge(masked_persons_RLE)
if self.cfg.use_gt_segm:
item.gt_segm = np.moveaxis(np.array(visible_persons_RLE), 0, -1)
item.visibilities = all_visibilities
data.append(item)
self.has_gt = self.cfg.dataset is not "image_info"
return data
def test(cfg, net):
_, data = get_data(cfg)
# Initialize the network the right way
# net.train and net.eval account for differences in dropout/batch norm
# during training and testing
net.eval().cuda()
metrics = {'acc_all': [], 'acc_nonzero': [], 'loss': []}
metrics_mean = {'acc_all': [], 'acc_nonzero': [], 'loss': []}
metrics_std = {'acc_all': [], 'acc_nonzero': [], 'loss': []}
durations_mean = {'cuda': [], 'loss': [], 'forward': [], 'acc': []}
durations_std = {'cuda': [], 'loss': [], 'forward': [], 'acc': []}
# Only enable gradients if we are training
# with torch.set_grad_enabled(is_training):
durations, durations_cuda, durations_loss, durations_acc = [], [], [], []
steps = []
print('Listing weights...')
weights = glob.glob(os.path.join(cfg.WEIGHTS_FILE_BASE, "*.ckpt"))
weights.sort()
print('Done.')
blobs = []
print('Fetch data...')
for i in range(cfg.MAX_STEPS):
print("%d/%d" % (i, cfg.MAX_STEPS))
blob = data.forward()
blob.pop('data')
blob['label_voxels'], blob['label_values'] = extract_voxels(
blob['labels'])
blob.pop('labels')
blobs.append(blob)
print('Done.')
for w in weights:
step = int(re.findall(r'model-(\d+)', w)[0])
steps.append(step)
print('Restoring weights from %s...' % w)
with open(w, 'rb') as f:
checkpoint = torch.load(f)
net.load_state_dict(checkpoint['state_dict'])
print('Done.')
for i, blob in enumerate(blobs): # FIXME
print("Step %d/%d" % (i, cfg.MAX_STEPS))
if sparse:
start = time.time()
coords = torch.from_numpy(blob['voxels']).cuda()
features = torch.from_numpy(
np.reshape(blob['voxels_value'], (-1, 1))).cuda()
label_voxels, labels = blob['label_voxels'], blob[
'label_values']
labels = torch.from_numpy(labels).cuda().type(
torch.cuda.LongTensor)
end = time.time()
durations_cuda.append(end - start)
start = time.time()
predictions_raw = net(coords,
features) # size N_voxels x num_classes
end = time.time()
durations.append(end - start)
else:
start = time.time()
image = torch.from_numpy(np.moveaxis(blob['data'], -1,
1)).cuda()
labels = torch.from_numpy(blob['labels']).cuda().type(
torch.cuda.LongTensor)
end = time.time()
durations_cuda.append(end - start)
start = time.time()
predictions_raw = net(image)
end = time.time()
durations.append(end - start)
start = time.time()
loss = criterion(predictions_raw, labels)
end = time.time()
durations_loss.append(end - start)
metrics['loss'].append(loss.item())
print("\tLoss = ", metrics['loss'][-1])
# Accuracy
start = time.time()
predicted_labels = torch.argmax(predictions_raw, dim=1)
acc_all = (predicted_labels == labels).sum().item() / float(
labels.numel())
nonzero_px = labels > 0
nonzero_prediction = predicted_labels[nonzero_px]
nonzero_label = labels[nonzero_px]
acc_nonzero = (nonzero_prediction
== nonzero_label).sum().item() / float(
nonzero_label.numel())
end = time.time()
durations_acc.append(end - start)
metrics['acc_all'].append(acc_all)
metrics['acc_nonzero'].append(acc_nonzero)
print("\tAccuracy = ", metrics['acc_all'][-1],
" - Nonzero accuracy = ", metrics['acc_nonzero'][-1])
metrics_mean['loss'].append(np.array(metrics['loss']).mean())
metrics_std['loss'].append(np.array(metrics['loss']).std())
metrics_mean['acc_all'].append(np.array(metrics['acc_all']).mean())
metrics_std['acc_all'].append(np.array(metrics['acc_all']).std())
metrics_mean['acc_nonzero'].append(
np.array(metrics['acc_nonzero']).mean())
metrics_std['acc_nonzero'].append(
np.array(metrics['acc_nonzero']).std())
durations_mean['cuda'].append(np.array(durations_cuda).mean())
durations_std['cuda'].append(np.array(durations_cuda).std())
durations_mean['loss'].append(np.array(durations_loss).mean())
durations_std['loss'].append(np.array(durations_loss).std())
durations_mean['forward'].append(np.array(durations).mean())
durations_std['forward'].append(np.array(durations).std())
durations_mean['acc'].append(np.array(durations_acc).mean())
durations_std['acc'].append(np.array(durations_acc).std())
durations, durations_cuda, durations_loss, durations_acc = [], [], [], []
metrics = {'acc_all': [], 'acc_nonzero': [], 'loss': []}
print('Mean cuda duration = %f s' % durations_mean['cuda'][-1])
print('Mean loss duration = %f s' % durations_mean['loss'][-1])
print('Mean acc duration = %f s' % durations_mean['acc'][-1])
print('Mean forward duration = %f s' % durations_mean['forward'][-1])
print('Mean acc = %f s' % metrics_mean['acc_nonzero'][-1])
np.savetxt(os.path.join(cfg.OUTPUT_DIR, 'steps_%d.csv' % step),
steps,
delimiter=',')
for attr in metrics:
np.savetxt(os.path.join(cfg.OUTPUT_DIR,
'%s_mean_%d.csv' % (attr, step)),
metrics_mean[attr],
delimiter=',')
np.savetxt(os.path.join(cfg.OUTPUT_DIR,
'%s_std_%d.csv' % (attr, step)),
metrics_std[attr],
delimiter=',')
for attr in durations_mean:
np.savetxt(os.path.join(cfg.OUTPUT_DIR,
'durations_%s_mean_%d.csv' % (attr, step)),
durations_mean[attr],
delimiter=',')
np.savetxt(os.path.join(cfg.OUTPUT_DIR,
'durations_%s_std_%d.csv' % (attr, step)),
durations_std[attr],
delimiter=',')
def img_to_tensor(im, normalize=None):
tensor = torch.from_numpy(np.moveaxis(im / (255.0 if im.dtype == np.uint8 else 1), -1, 0).astype(np.float32))
if normalize is not None:
return F.normalize(tensor, **normalize)
return tensor
def ATL15_write2nc(args):
def make_dataset(field,fieldout,data,field_attrs,file_obj,group_obj,nctype,dimScale=False):
# where field is the name from ATL15_output_attrs.csv file
# where fieldout is the name of the output variable in the .nc file
dimensions = field_attrs[field]['dimensions'].split(',')
dimensions = tuple(x.strip() for x in dimensions)
if field_attrs[field]['datatype'].startswith('int'):
fill_value = np.iinfo(np.dtype(field_attrs[field]['datatype'])).max
elif field_attrs[field]['datatype'].startswith('float'):
fill_value = np.finfo(np.dtype(field_attrs[field]['datatype'])).max
data = np.nan_to_num(data,nan=fill_value)
if dimScale:
group_obj.createDimension(field_attrs[field]['dimensions'],data.shape[0])
dsetvar = group_obj.createVariable(fieldout,
nctype[field_attrs[field]['datatype']],
dimensions,
fill_value=fill_value, zlib=True,
least_significant_digit=ast.literal_eval(field_attrs[field]['least_significant_digit']))
dsetvar[:] = data
for attr in attr_names:
if attr != 'group description':
dsetvar.setncattr(attr,field_attrs[field][attr])
# add attributes for projection
if not field.startswith('time'):
dsetvar.setncattr('grid_mapping','Polar_Stereographic')
if field == 'x':
dsetvar.standard_name = 'projection_x_coordinate'
if field == 'y':
dsetvar.standard_name = 'projection_y_coordinate'
return file_obj
dz_dict ={'time':'t', # for non-lagged vars. {ATL15 outgoing var name: hdf5 incoming var name}
'time_lag1':'t',
'time_lag4':'t',
'time_lag8':'t',
'x':'x',
'y':'y',
'cell_area':'cell_area',
'ice_mask':'mask',
'data_count':'count',
'misfit_rms':'misfit_rms',
'misfit_scaled_rms':'misfit_scaled_rms',
'delta_h':'dz',
'delta_h_sigma':'sigma_dz',
'delta_h_10km':'avg_dz_10000m',
'delta_h_sigma_10km':'sigma_avg_dz_10000m',
'delta_h_20km':'avg_dz_20000m',
'delta_h_sigma_20km':'sigma_avg_dz_20000m',
'delta_h_40km':'avg_dz_40000m',
'delta_h_sigma_40km':'sigma_avg_dz_40000m',
}
nctype = {'float64':'f8',
'float32':'f4',
'int8':'i1'}
lags = {
'file' : ['FH','FH_lag1','FH_lag4','FH_lag8'],
'vari' : ['','_lag1','_lag4','_lag8'],
'varigrp' : ['delta_h','dhdt_lag1','dhdt_lag4','dhdt_lag8']
}
avgs = ['','_10km','_20km','_40km']
# open data attributes file
attrFile = pkg_resources.resource_filename('surfaceChange','resources/ATL15_output_attrs.csv')
with open(attrFile,'r',encoding='utf-8-sig') as attrfile:
reader=list(csv.DictReader(attrfile))
attr_names=[x for x in reader[0].keys() if x != 'field' and x != 'group']
for ave in avgs:
# establish output file, one per average
if ave=='':
fileout = args.base_dir.rstrip('/') + '/ATL15_' + args.region + '_' + args.cycles + '_01km_' + args.Release + '_' + args.version + '.nc'
else:
fileout = args.base_dir.rstrip('/') + '/ATL15_' + args.region + '_' + args.cycles + ave + '_' + args.Release + '_' + args.version + '.nc'
# print('output file:',fileout)
with Dataset(fileout,'w',clobber=True) as nc:
nc.setncattr('GDAL_AREA_OR_POINT','Area')
nc.setncattr('Conventions','CF-1.6')
# make tile_stats group (ATBD 4.1.2.1, Table 3)
tilegrp = nc.createGroup('tile_stats')
tileFile = pkg_resources.resource_filename('surfaceChange','resources/tile_stats_output_attrs.csv')
with open(tileFile,'r', encoding='utf-8-sig') as tilefile:
tile_reader=list(csv.DictReader(tilefile))
tile_attr_names=[x for x in tile_reader[0].keys() if x != 'field' and x != 'group']
tile_field_names = [row['field'] for row in tile_reader]
tile_stats={} # dict for appending data from the tile files
for field in tile_field_names:
if field not in tile_stats:
tile_stats[field] = { 'data': [], 'mapped':np.array(())}
# work through the tiles in all three subdirectories
for sub in ['centers','edges','corners']:
files = os.listdir(os.path.join(args.base_dir,sub))
files = [f for f in files if f.endswith('.h5')]
for file in files:
try:
tile_stats['x']['data'].append(int(re.match(r'^.*E(.*)\_.*$',file).group(1)))
except Exception as e:
print(f"problem with [ {file} ], skipping")
continue
tile_stats['y']['data'].append(int(re.match(r'^.*N(.*)\..*$',file).group(1)))
with h5py.File(os.path.join(args.base_dir,sub,file),'r') as h5:
tile_stats['N_data']['data'].append( np.sum(h5['data']['three_sigma_edit'][:]) )
tile_stats['RMS_data']['data'].append( h5['RMS']['data'][()] ) # use () for getting a scalar.
tile_stats['RMS_bias']['data'].append( np.sqrt(np.mean((h5['bias']['val'][:]/h5['bias']['expected'][:])**2)) )
tile_stats['N_bias']['data'].append( len(h5['bias']['val'][:]) ) #### or all BUT the zeros.
tile_stats['RMS_d2z0dx2']['data'].append( h5['RMS']['grad2_z0'][()] )
tile_stats['RMS_d2zdt2']['data'].append( h5['RMS']['d2z_dt2'][()] )
tile_stats['RMS_d2zdx2dt']['data'].append( h5['RMS']['grad2_dzdt'][()] )
tile_stats['sigma_xx0']['data'].append( h5['E_RMS']['d2z0_dx2'][()] )
tile_stats['sigma_tt']['data'].append( h5['E_RMS']['d2z_dt2'][()] )
tile_stats['sigma_xxt']['data'].append( h5['E_RMS']['d3z_dx2dt'][()] )
# establish output grids from min/max of x and y
for key in tile_stats.keys():
if key == 'N_data' or key == 'N_bias': # key == 'x' or key == 'y' or
tile_stats[key]['mapped'] = np.zeros( [len(np.arange(np.min(tile_stats['y']['data']),np.max(tile_stats['y']['data'])+40,40)),
len(np.arange(np.min(tile_stats['x']['data']),np.max(tile_stats['x']['data'])+40,40))],
dtype=int)
else:
tile_stats[key]['mapped'] = np.zeros( [len(np.arange(np.min(tile_stats['y']['data']),np.max(tile_stats['y']['data'])+40,40)),
len(np.arange(np.min(tile_stats['x']['data']),np.max(tile_stats['x']['data'])+40,40))],
dtype=float)
# put data into grids
for key in tile_stats.keys():
# fact helps convert x,y in km to m
if key == 'x' or key == 'y':
continue
for (yt, xt, dt) in zip(tile_stats['y']['data'], tile_stats['x']['data'], tile_stats[key]['data']):
if not np.isfinite(dt):
print(f"ATL14_write2nc: found bad tile_stats value in field {key} at x={xt}, y={yt}")
continue
row=int((yt-np.min(tile_stats['y']['data']))/40)
col=int((xt-np.min(tile_stats['x']['data']))/40)
tile_stats[key]['mapped'][row,col] = dt
tile_stats[key]['mapped'] = np.ma.masked_where(tile_stats[key]['mapped'] == 0, tile_stats[key]['mapped'])
# make dimensions, fill them as variables
tilegrp.createDimension('y',len(np.arange(np.min(tile_stats['y']['data']),np.max(tile_stats['y']['data'])+40,40)))
tilegrp.createDimension('x',len(np.arange(np.min(tile_stats['x']['data']),np.max(tile_stats['x']['data'])+40,40)))
# create tile_stats/ variables in .nc file
for field in tile_field_names:
tile_field_attrs = {row['field']: {tile_attr_names[ii]:row[tile_attr_names[ii]] for ii in range(len(tile_attr_names))} for row in tile_reader if field in row['field']}
if field == 'x':
dsetvar = tilegrp.createVariable('x', tile_field_attrs[field]['datatype'], ('x',), fill_value=np.finfo(tile_field_attrs[field]['datatype']).max, zlib=True)
dsetvar[:] = np.arange(np.min(tile_stats['x']['data']),np.max(tile_stats['x']['data'])+40,40.) * 1000 # convert from km to meter
elif field == 'y':
dsetvar = tilegrp.createVariable('y', tile_field_attrs[field]['datatype'], ('y',), fill_value=np.finfo(tile_field_attrs[field]['datatype']).max, zlib=True)
dsetvar[:] = np.arange(np.min(tile_stats['y']['data']),np.max(tile_stats['y']['data'])+40,40.) * 1000 # convert from km to meter
elif field == 'N_data' or field == 'N_bias':
dsetvar = tilegrp.createVariable(field, tile_field_attrs[field]['datatype'],('y','x'),fill_value=np.iinfo(tile_field_attrs[field]['datatype']).max, zlib=True)
else:
dsetvar = tilegrp.createVariable(field, tile_field_attrs[field]['datatype'],('y','x'),fill_value=np.finfo(tile_field_attrs[field]['datatype']).max, zlib=True)
if field != 'x' and field != 'y':
dsetvar[:] = tile_stats[field]['mapped'][:]
for attr in ['units','dimensions','datatype','coordinates','description','coordinates','long_name','source']:
dsetvar.setncattr(attr,tile_field_attrs[field][attr])
dsetvar.setncattr('grid_mapping','Polar_Stereographic')
crs_var = projection_variable(args.region,tilegrp)
# # make comfort figures
# extent=[np.min(tile_stats['x']['data'])*fact,np.max(tile_stats['x']['data'])*fact,
# np.min(tile_stats['y']['data'])*fact,np.max(tile_stats['y']['data'])*fact]
# cmap = mpl.cm.get_cmap("viridis").copy()
# cmnan = mpl.cm.get_cmap(cmap)
# cmnan.set_bad(color='white')
#
# for i,key in enumerate(tile_stats.keys()):
# makey = np.ma.masked_where(tile_stats[key]['mapped'] == 0, tile_stats[key]['mapped'])
# fig,ax=plt.subplots(1,1)
# ax = plt.subplot(1,1,1,projection=ccrs.NorthPolarStereo(central_longitude=-45))
# ax.add_feature(cartopy.feature.LAND)
# ax.coastlines(resolution='110m',linewidth=0.5)
# ax.set_extent([-10,90,70,90],crs=ccrs.PlateCarree())
# ax.gridlines(crs=ccrs.PlateCarree())
# h=ax.imshow(makey,extent=extent,vmin=np.min(makey.ravel()),vmax=np.max(makey.ravel()),cmap=cmnan,origin='lower')
# fig.colorbar(h,ax=ax)
# ax.set_title(f'{key}')
# fig.savefig(f"{os.path.join(args.base_dir,'tile_stats_' + key + '.png')}",format='png')
#
# plt.show(block=False)
# plt.pause(0.001)
# input('Press enter to end.')
# plt.close('all')
# exit(-1)
# loop over dz*.h5 files for one ave
for jj in range(len(lags['file'])):
filein = args.base_dir.rstrip('/')+'/dz'+ave+lags['vari'][jj]+'.h5'
if not os.path.isfile(filein):
print('No file:',args.base_dir.rstrip('/')+'/'+os.path.basename(filein))
continue
else:
print('Reading file:',args.base_dir.rstrip('/')+'/'+os.path.basename(filein))
lags['file'][jj] = h5py.File(filein,'r') # file object
dzg=list(lags['file'][jj].keys())[0] # dzg is group in input file
nc.createGroup(lags['varigrp'][jj])
# print(lags['varigrp'][jj])
# make projection variable for each group
crs_var = projection_variable(args.region,nc.groups[lags['varigrp'][jj]])
# dimension scales for each group
for field in ['x','y']:
data = np.array(lags['file'][jj][dzg][dz_dict[field]])
if field == 'x':
x = data
xll = np.min(x)
dx = x[1]-x[0]
if field == 'y':
y = data
yll = np.max(y)
dy = y[0]-y[1]
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field in row['field'] if row['group']=='height_change'+ave}
make_dataset(field,field,data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=True)
crs_var.GeoTransform = (xll,dx,0,yll,0,dy)
if jj==0: # no lag
field = 'time'
data = np.array(lags['file'][jj][dzg]['t'])
# convert to decimal days from 1/1/2018
data = (data-2018.)*365.25
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field in row['field'] if row['group']=='height_change'+ave}
make_dataset(field,field,data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=True)
for fld in ['cell_area','delta_h','delta_h_sigma','ice_mask','data_count','misfit_rms','misfit_scaled_rms']: # fields that can be ave'd but not lagged
if (len(ave) > 0) and (fld.startswith('misfit') or fld=='ice_mask' or fld=='data_count'): # not in ave'd groups
break
field = fld+ave
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field == row['field'] if row['group']=='height_change'+ave}
if fld.startswith('delta_h'): # fields with complicated name changes
data = np.array(lags['file'][jj][dzg][dz_dict[field]])
for tt in range(data.shape[-1]):
data[:,:,tt][np.isnan(cell_area_mask)] = np.nan
if fld=='delta_h': # add group description
nc.groups[lags['varigrp'][jj]].setncattr('description',field_attrs[field]['group description'])
else:
data = np.array(lags['file'][jj][dzg][dz_dict[fld]])
if len(data.shape)==3:
data = np.moveaxis(data,2,0) # t, y, x
if fld == 'cell_area':
data[data==0.0] = np.nan
cell_area_mask = data # where cell_area is invalid, so are delta_h and dhdt variables.
make_dataset(field,fld,data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=False)
else: # one of the lags
field = 'time'+lags['vari'][jj]
data = np.array(lags['file'][jj][dzg]['t'])
# convert to decimal days from 1/1/2018
data = (data-2018.)*365.25
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field in row['field'] if row['group']=='height_change'+ave}
make_dataset(field,'time',data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=True)
field = 'dhdt'+lags['vari'][jj]+ave
data = np.array(lags['file'][jj][dzg][dzg])
for tt in range(data.shape[-1]):
data[:,:,tt][np.isnan(cell_area_mask)] = np.nan
data = np.moveaxis(data,2,0) # t, y, x
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field in row['field'] if row['group']=='height_change'+ave}
make_dataset(field,'dhdt',data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=False)
# add group description
nc.groups[lags['varigrp'][jj]].setncattr('description',field_attrs[field]['group description'])
field = 'dhdt'+lags['vari'][jj]+'_sigma'+ave
data = np.array(lags['file'][jj][dzg]['sigma_'+dzg])
for tt in range(data.shape[-1]):
data[:,:,tt][np.isnan(cell_area_mask)] = np.nan
data = np.moveaxis(data,2,0) # t, y, x
field_attrs = {row['field']: {attr_names[ii]:row[attr_names[ii]] for ii in range(len(attr_names))} for row in reader if field in row['field'] if row['group']=='height_change'+ave}
make_dataset(field,'dhdt_sigma',data,field_attrs,nc,nc.groups[lags['varigrp'][jj]],nctype,dimScale=False)
for jj in range(len(lags['file'])):
try:
lags['file'][jj].close()
except:
pass
ncTemplate=pkg_resources.resource_filename('surfaceChange','resources/atl15_metadata_template.nc')
write_atl14meta(nc, fileout, ncTemplate, args)
return fileout
def collect_images_and_labels(directory):
"""
This function collects the images and labels of these images located in
a directory. The contents of the directory must be organized into folders
where images under said folder are labeled as that folder.
example:
-my_directory/
|----A/
| |- image1.jpg
| |- image2.jpg
|
|----B/
| |- image3.jpg
|
|----C/
|- image4.jpg
|- image5.jpg
|- image6.jpg
The images get classified as follows
class file_name
A image1.jpg
A image2.jpg
B image3.jpg
C image4.jpg
C image5.jpg
C image6.jpg
@returns:
@labels - list of strings of corresponding labels to each file in @file_names
@file_names - list of strings corresponding to the file names of each image
@grayscale_images - 3D numpy array of grayscale images where each image is indexed
using axis 3. grayscale_images[:,:,i] indexes the i'th image.
dtype is uint8, values range from 0 to 255.
Images normalized using the mean_filter_normalize function
@saturation_images - 3D numpy array of saturation images where each image is indexed
using axis 3. saturation_images[:,:,i] indexes the i'th image.
dtype is uint8, values range from 0 to 255.
Images normalized using the mean_filter_normalize function
"""
labels = []
file_names = []
grayscale_images = []
saturation_images = []
# collect images and labels
for label in os.listdir(directory):
path = '{}/{}'.format(directory, label)
image_names = os.listdir(path) # names of images in label folder
# record labels and names
labels.extend([label]*len(image_names))
file_names.extend(image_names)
for file_nm in image_names:
name = '{}/{}'.format(path, file_nm) # name of file of image
img = skimio.imread(name) # read image
img = img[:-128,:,:] # crop scalebar
img_gray = cv.cvtColor(img, cv.COLOR_RGB2GRAY) # grayscale
img_sat = cv.cvtColor(img, cv.COLOR_RGB2HSV)[:,:,1] # saturation
# collect images
grayscale_images.append(img_gray)
saturation_images.append(img_sat)
# convert to numpy arrays
grayscale_images = np.moveaxis(np.array(grayscale_images), 0, -1)
saturation_images = np.moveaxis(np.array(saturation_images), 0, -1)
# normalize images, this removes artifacts
grayscale_images = mean_filter_normalize(grayscale_images)
saturation_images = mean_filter_normalize(saturation_images)
return labels, file_names, grayscale_images, saturation_images
def MDD(G,
d,
dt=0.004,
dr=1.,
nfmax=None,
wav=None,
twosided=True,
causality_precond=False,
adjoint=False,
psf=False,
dtype='float64',
dottest=False,
saveGt=True,
add_negative=True,
smooth_precond=0,
**kwargs_solver):
r"""Multi-dimensional deconvolution.
Solve multi-dimensional deconvolution problem using
:py:func:`scipy.sparse.linalg.lsqr` iterative solver.
Parameters
----------
G : :obj:`numpy.ndarray`
Multi-dimensional convolution kernel in time domain of size
:math:`[n_s \times n_r \times n_t]` for ``twosided=False`` or
``twosided=True`` and ``add_negative=True``
(with only positive times) or size
:math:`[n_s \times n_r \times 2*n_t-1]` for ``twosided=True`` and
``add_negative=False``
(with both positive and negative times)
d : :obj:`numpy.ndarray`
Data in time domain :math:`[n_s (\times n_{vs}) \times n_t]` if
``twosided=False`` or ``twosided=True`` and ``add_negative=True``
(with only positive times) or size
:math:`[n_s (\times n_{vs}) \times 2*n_t-1]` if ``twosided=True``
dt : :obj:`float`, optional
Sampling of time integration axis
dr : :obj:`float`, optional
Sampling of receiver integration axis
nfmax : :obj:`int`, optional
Index of max frequency to include in deconvolution process
wav : :obj:`numpy.ndarray`, optional
Wavelet to convolve to the inverted model and psf
(must be centered around its index in the middle of the array).
If ``None``, the outputs of the inversion are returned directly.
twosided : :obj:`bool`, optional
MDC operator and data both negative and positive time (``True``)
or only positive (``False``)
add_negative : :obj:`bool`, optional
Add negative side to MDC operator and data (``True``) or not
(``False``)- operator and data are already provided with both positive
and negative sides. To be used only with ``twosided=True``.
causality_precond : :obj:`bool`, optional
Apply causality mask (``True``) or not (``False``)
smooth_precond : :obj:`int`, optional
Lenght of smoothing to apply to causality preconditioner
adjoint : :obj:`bool`, optional
Compute and return adjoint(s)
psf : :obj:`bool`, optional
Compute and return Point Spread Function (PSF) and its inverse
dtype : :obj:`bool`, optional
Type of elements in input array.
dottest : :obj:`bool`, optional
Apply dot-test
saveGt : :obj:`bool`, optional
Save ``G`` and ``G^H`` to speed up the computation of adjoint of
:class:`pylops.signalprocessing.Fredholm1` (``True``) or create
``G^H`` on-the-fly (``False``) Note that ``saveGt=True`` will be
faster but double the amount of required memory
**kwargs_solver
Arbitrary keyword arguments for chosen solver
(:py:func:`scipy.sparse.linalg.cg` and
:py:func:`pylops.optimization.solver.cg` are used as default for numpy
and cupy `data`, respectively)
Returns
-------
minv : :obj:`numpy.ndarray`
Inverted model of size :math:`[n_r (\times n_{vs}) \times n_t]`
for ``twosided=False`` or
:math:`[n_r (\times n_vs) \times 2*n_t-1]` for ``twosided=True``
madj : :obj:`numpy.ndarray`
Adjoint model of size :math:`[n_r (\times n_{vs}) \times n_t]`
for ``twosided=False`` or
:math:`[n_r (\times n_r) \times 2*n_t-1]` for ``twosided=True``
psfinv : :obj:`numpy.ndarray`
Inverted psf of size :math:`[n_r \times n_r \times n_t]`
for ``twosided=False`` or
:math:`[n_r \times n_r \times 2*n_t-1]` for ``twosided=True``
psfadj : :obj:`numpy.ndarray`
Adjoint psf of size :math:`[n_r \times n_r \times n_t]`
for ``twosided=False`` or
:math:`[n_r \times n_r \times 2*n_t-1]` for ``twosided=True``
See Also
--------
MDC : Multi-dimensional convolution
Notes
-----
Multi-dimensional deconvolution (MDD) is a mathematical ill-solved problem,
well-known in the image processing and geophysical community [1]_.
MDD aims at removing the effects of a Multi-dimensional Convolution
(MDC) kernel or the so-called blurring operator or point-spread
function (PSF) from a given data. It can be written as
.. math::
\mathbf{d}= \mathbf{D} \mathbf{m}
or, equivalently, by means of its normal equation
.. math::
\mathbf{m}= (\mathbf{D}^H\mathbf{D})^{-1} \mathbf{D}^H\mathbf{d}
where :math:`\mathbf{D}^H\mathbf{D}` is the PSF.
.. [1] Wapenaar, K., van der Neut, J., Ruigrok, E., Draganov, D., Hunziker,
J., Slob, E., Thorbecke, J., and Snieder, R., "Seismic interferometry
by crosscorrelation and by multi-dimensional deconvolution: a
systematic comparison", Geophyscial Journal International, vol. 185,
pp. 1335-1364. 2011.
"""
ncp = get_array_module(d)
ns, nr, nt = G.shape
if len(d.shape) == 2:
nv = 1
else:
nv = d.shape[1]
if twosided:
if add_negative:
nt2 = 2 * nt - 1
else:
nt2 = nt
nt = (nt2 + 1) // 2
nfmax_allowed = int(np.ceil((nt2 + 1) / 2))
else:
nt2 = nt
nfmax_allowed = nt
# Fix nfmax to be at maximum equal to half of the size of fft samples
if nfmax is None or nfmax > nfmax_allowed:
nfmax = nfmax_allowed
logging.warning('nfmax set equal to ceil[(nt+1)/2=%d]' % nfmax)
# Add negative part to data and model
if twosided and add_negative:
G = np.concatenate((ncp.zeros((ns, nr, nt - 1)), G), axis=-1)
d = np.concatenate((np.squeeze(np.zeros((ns, nv, nt - 1))), d),
axis=-1)
# Bring kernel to frequency domain
Gfft = np.fft.rfft(G, nt2, axis=-1)
Gfft = Gfft[..., :nfmax]
# Bring frequency/time to first dimension
Gfft = np.moveaxis(Gfft, -1, 0)
d = np.moveaxis(d, -1, 0)
if psf:
G = np.moveaxis(G, -1, 0)
# Define MDC linear operator
MDCop = MDC(Gfft,
nt2,
nv=nv,
dt=dt,
dr=dr,
twosided=twosided,
transpose=False,
saveGt=saveGt)
if psf:
PSFop = MDC(Gfft,
nt2,
nv=nr,
dt=dt,
dr=dr,
twosided=twosided,
transpose=False,
saveGt=saveGt)
if dottest:
Dottest(MDCop,
nt2 * ns * nv,
nt2 * nr * nv,
verb=True,
backend=get_module_name(ncp))
if psf:
Dottest(PSFop,
nt2 * ns * nr,
nt2 * nr * nr,
verb=True,
backend=get_module_name(ncp))
# Adjoint
if adjoint:
madj = MDCop.H * d.flatten()
madj = np.squeeze(madj.reshape(nt2, nr, nv))
madj = np.moveaxis(madj, 0, -1)
if psf:
psfadj = PSFop.H * G.flatten()
psfadj = np.squeeze(psfadj.reshape(nt2, nr, nr))
psfadj = np.moveaxis(psfadj, 0, -1)
# Inverse
if twosided and causality_precond:
P = np.ones((nt2, nr, nv))
P[:nt - 1] = 0
if smooth_precond > 0:
P = filtfilt(np.ones(smooth_precond) / smooth_precond,
1,
P,
axis=0)
P = to_cupy_conditional(d, P)
Pop = Diagonal(P)
minv = PreconditionedInversion(MDCop,
Pop,
d.flatten(),
returninfo=False,
**kwargs_solver)
else:
if ncp == np:
minv = lsqr(MDCop, d.flatten(), **kwargs_solver)[0]
else:
minv = cgls(MDCop, d.flatten(),
ncp.zeros(int(MDCop.shape[1]), dtype=MDCop.dtype),
**kwargs_solver)[0]
minv = np.squeeze(minv.reshape(nt2, nr, nv))
minv = np.moveaxis(minv, 0, -1)
if wav is not None:
wav1 = wav.copy()
for _ in range(minv.ndim - 1):
wav1 = wav1[ncp.newaxis]
minv = get_fftconvolve(d)(minv, wav1, mode='same')
if psf:
if ncp == np:
psfinv = lsqr(PSFop, G.flatten(), **kwargs_solver)[0]
else:
psfinv = cgls(PSFop, G.flatten(),
ncp.zeros(int(PSFop.shape[1]), dtype=PSFop.dtype),
**kwargs_solver)[0]
psfinv = np.squeeze(psfinv.reshape(nt2, nr, nr))
psfinv = np.moveaxis(psfinv, 0, -1)
if wav is not None:
wav1 = wav.copy()
for _ in range(psfinv.ndim - 1):
wav1 = wav1[np.newaxis]
psfinv = get_fftconvolve(d)(psfinv, wav1, mode='same')
if adjoint and psf:
return minv, madj, psfinv, psfadj
elif adjoint:
return minv, madj
elif psf:
return minv, psfinv
else:
return minv
running_tar_loss / ite_num4val))
#save entire model
# torch.save(net, "saved_models/u2netp/itr_%d_train_%3f_tar_%3f.pth" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val))
running_loss = 0.0
running_tar_loss = 0.0
net.train() # resume train
# middle_output = (d0[0][0] + d1[0][0] + d2[0][0] + d3[0][0] + d4[0][0] + d5[0][0] + d6[0][0]) / 7 * 255
middle_output = d0[0][0] * 255
middle_output = middle_output.cpu().detach().numpy()
middle_input = inputs.cpu().detach().numpy()[0][:3]
middle_input = np.moveaxis(middle_input, 0, 2) * 255
middle_prior = inputs.cpu().detach().numpy()[0][3] * 255
middle_label = labels.cpu().detach().numpy()[0][0] * 255
# print('middle_input', middle_input.shape)
# print('middle_prior', middle_prior.shape)
# cv2.imwrite(model_dir + "saved_models/u2netp/_output_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), middle_output)
# cv2.imwrite(model_dir + "_input_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), cv2.cvtColor(middle_input, cv2.COLOR_BGR2RGB))
# cv2.imwrite(model_dir + "_prior_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), middle_prior)
# cv2.imwrite(model_dir + "_difference_prior_output_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), middle_prior - middle_output)
# cv2.imwrite(model_dir + "_difference_prior_label_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), middle_prior - middle_label)
# cv2.imwrite(model_dir + "_difference_output_label_bce_itr_%d_train_%3f_tar_%3f.png" % (ite_num, running_loss / ite_num4val, running_tar_loss / ite_num4val), middle_output - middle_label)
cv2.imwrite("saved_models/u2netp/output_itr_%d.png" % (ite_num),
#print(Y)
#print('*************************************************************************************')
# remove unphysical values
X[X < 1e-6] = 0
X_train, X_test, y_train, y_test = train_test_split(X,
y,
train_size=0.05,
test_size=0.05)
# tensorflow ordering
X_train = np.expand_dims(X_train, axis=-1)
X_test = np.expand_dims(X_test, axis=-1)
print(X_train.shape)
X_train = np.moveaxis(X_train, -1, 1)
X_test = np.moveaxis(X_test, -1, 1)
y_train = y_train / 100
y_test = y_test / 100
print(X_train.shape)
print(X_test.shape)
print(y_train.shape)
print(y_test.shape)
print(
'*************************************************************************************'
)
nb_train, nb_test = X_train.shape[0], X_test.shape[0]
X_train = X_train.astype(np.float32)
def Detect(img, model):
transform = tv.transforms.Compose(
[tv.transforms.Resize(224),
tv.transforms.ToTensor()])
img = transform(img)
device = torch.device(
'cuda') if torch.cuda.is_available() else torch.device('cpu')
thre = 0.5 # confidence threshold
class_names = [
'aeroplane', 'bicycle', 'bird', 'boat', 'bottle', 'bus', 'car', 'cat',
'chair', 'cow', 'diningtable', 'dog', 'horse', 'motorbike', 'person',
'pottedplant', 'sheep', 'sofa', 'train', 'tvmonitor'
]
model.eval()
with torch.no_grad():
prediction = model([img.to(device)])
prediction = prediction[0]
img = np.array(img)
img = np.moveaxis(img, [0, 1, 2], [2, 0, 1])
plt.figure()
fig, ax = plt.subplots(1, figsize=(12, 12))
ax.imshow(img)
# prediction items
boxes = prediction['boxes']
scores = prediction['scores']
labels = prediction['labels']
# Bounding-box colors
cmap = plt.get_cmap("tab20b")
colors = [cmap(i) for i in np.linspace(0, 1, 20)]
#
unique_labels = labels.cpu().unique()
n_cls_preds = len(unique_labels)
bbox_colors = random.sample(colors, n_cls_preds)
for row in range(len(scores[scores > thre])):
box = boxes[row, :].reshape(1, -1)
box = box[0]
x1 = box[0]
y1 = box[1]
box_w = box[2] - box[0]
box_h = box[3] - box[1]
cls_pred = labels[row]
cls_conf = scores[row]
color = bbox_colors[int(np.where(unique_labels == int(cls_pred))[0])]
bbox = patches.Rectangle((x1, y1),
box_w,
box_h,
linewidth=2,
edgecolor=color,
facecolor="none")
ax.add_patch(bbox)
plt.text(x1,
y1,
fontsize=14,
s=class_names[int(cls_pred) - 1] + ' ' + ('%.4f' % cls_conf),
color="white",
verticalalignment="top",
bbox={
"color": color,
"pad": 0
})
plt.show()
os.makedirs(log_dir) # # load the data # fds = xr.open_dataset(feature_data) lds = xr.open_dataset(label_data) feature = fds.QRAIN.values label = lds.W.values # # move the channels from position 1 to position 3 # goes from [time,channel,height,width] to [time, height, width, channel] # which is the default for Conv2D. # feature = np.moveaxis(feature, 1, 3) label = np.moveaxis(label, 1, 3) # # random shuffle # s = np.arange(feature.shape[0]) np.random.shuffle(s) # # # num_images = feature.shape[0] train_data_start = 0 train_data_end = int(
def verify_ell_model(self,
onnx_model_path,
verify_compiled=True,
arg_max_only=False):
"""
Test each operation in the onnx graph by creating a custom pytorch layer for each node then
run forward with the onnx node weight on both ell and pytorch node. If verify_compiled is
True then also test compiled ELL model.
"""
self._logger.info("Model verification started")
try:
# install debug hooks into torch model so we capture output of every layer.
info = LayerInfo(self.torch_model)
# get the pytorch model output
self.torch_model.eval()
model_name = os.path.basename(onnx_model_path)
model_name = os.path.splitext(model_name)[0]
ell_map, ordered_importer_nodes = onnx_to_ell.convert_onnx_to_ell(
onnx_model_path)
ell_map.Save(model_name + ".ell")
# Get compiled ELL result
if verify_compiled:
self._logger.info("Getting compiled ELL results")
compiler_options = ell.model.MapCompilerOptions()
compiler_options.useBlas = True
compiled_ell_map = ell_map.Compile(
"host",
"model",
"predict",
compilerOptions=compiler_options,
dtype=np.float32)
input_index = 0
for test_input in self.input_tensors:
# get torch model output
info.clear()
torch_out = self.torch_model.forward(
test_input).data.numpy().ravel()
test_input = test_input.detach().cpu().numpy(
) # convert to numpy
order = self.get_order(test_input.shape)
ell_input_tensor = memory_shapes.get_tensor_in_ell_order(
test_input, order)
ell_flat_input = ell_input_tensor.ravel().astype(np.float32)
if verify_compiled:
ell_out_compiled = np.array(
compiled_ell_map.Compute(ell_flat_input,
dtype=np.float32))
# must come after the compiled Compute so that map contains valid outputs for layer by layer test
ell_out = np.array(
ell_map.Compute(ell_input_tensor, dtype=np.float32))
ell_nodes = get_nodes(ell_map)
if not arg_max_only:
# Compare the layers of the torch model with the coorresponding layers of the ELL model
for key in info.layers.keys():
if input_index == 0:
self._logger.info(
"----- Comparing Layer {} output -----".format(
key))
torch_output = info.layers[key]["output"].detach(
).numpy().ravel()
node = get_matching_node_output(ell_nodes, key)
if node is not None:
port = node.GetOutputPort("output")
shape = tuple(port.GetMemoryLayout().size)
extent = tuple(port.GetMemoryLayout().extent)
offset = tuple(port.GetMemoryLayout().offset)
# padding = tuple(port.GetMemoryLayout().padding) # output shape includes padding
ell_output = np.array(
port.GetDoubleOutput()).astype(np.float32)
# now to compare ell (row,col,channel) with torch (channel,row,col) we have to reorder
ell_output = get_active_region(
ell_output, shape, extent, offset)
ell_output = np.moveaxis(ell_output, 2, 0).ravel()
# close = np.allclose(torch_output, ell_output, atol=1e-3)
np.testing.assert_almost_equal(
torch_output,
ell_output,
decimal=3,
err_msg=
('results for ELL layer {} do not match torch output for row {}'
.format(node.GetRuntimeTypeName(),
input_index)))
# compare whole model output but only the argmax of it,
# because sometimes model has Softmax but ELL does not.
torch_prediction = np.argmax(torch_out)
ell_prediction = np.argmax(ell_out)
if verify_compiled:
compiled_prediction = np.argmax(ell_out_compiled)
msg = "argmax of ELL result {}, ELL compiled result {} and argmax of torch output {} on row {}"
msg = msg.format(ell_prediction, compiled_prediction,
torch_prediction, input_index)
else:
msg = "argmax of ELL result {} and argmax of torch output {} on row {}".format(
ell_prediction, torch_prediction, input_index)
self._logger.info(msg)
np.testing.assert_equal(torch_prediction, ell_prediction, msg)
if verify_compiled:
np.testing.assert_equal(torch_prediction,
compiled_prediction, msg)
input_index += 1
except BaseException as exception:
self._logger.error("Verification of model output failed: " +
str(exception))
raise
self._logger.info("Verification of model output complete")
def reverse_channels(img):
return np.moveaxis(img, 0, -1) # source, dest
np.tensordot(B, A) np.tensordot(A, A) np.tensordot(A, A, axes=0) np.tensordot(A, A, axes=(0, 1)) np.isscalar(i8) np.isscalar(A) np.isscalar(B) np.roll(A, 1) np.roll(A, (1, 2)) np.roll(B, 1) np.rollaxis(A, 0, 1) np.moveaxis(A, 0, 1) np.moveaxis(A, (0, 1), (1, 2)) np.cross(B, A) np.cross(A, A) np.indices([0, 1, 2]) np.indices([0, 1, 2], sparse=False) np.indices([0, 1, 2], sparse=True) np.binary_repr(1) np.base_repr(1) np.allclose(i8, A) np.allclose(B, A)
def skeletonize(imgs, cases, args, skelDir, miFile):
target = load(args.template)
targetData = target.get_data()
X, Y, Z = targetData.shape[0], targetData.shape[1], targetData.shape[2]
# provide the user with allFA sequence so he knows which volume he is looking at while scrolling through allFA
seqFile = pjoin(args.statsDir, f'all_{args.modality}_sequence.txt')
with open(seqFile, 'w') as f:
f.write('index,caseid\n')
for i, c in enumerate(cases):
f.write(f'{i},{c}\n')
print(f'Calculating mean {args.modality} over all the cases ...')
allFAdata, cumsumFA = calc_mean(imgs, (X, Y, Z), args.qc)
if args.qc:
allFA = pjoin(args.statsDir, f'all_{args.modality}.nii.gz')
save_nifti(allFA, np.moveaxis(allFAdata, 0, -1), target.affine,
target.header)
print(
f'''\n\nQC the warped {args.modality} images: {allFA}, view {seqFile} for index of volumes in all_FA.nii.gz.
You may use fsleyes/fslview to load {allFA}.
MI metric b/w the warped images and target are stored in {miFile}
It might be helpful to re-run registration for warped images that are bad.
Moving images are : {args.outDir}/preproc/
Target is : {args.template}
Transform files are : {args.xfrmDir}/
Warped images are : {args.outDir}/warped/
Save any re-registered images in {args.outDir}/warped/ with the same name as before
For re-registration of any subject, output the transform files to a temporary directory:
mkdir /tmp/badRegistration/
antsRegistrationSyNQuick.sh -d 3 \\
-f TEMPLATE \\
-m FA/preproc/caseid_FA.nii.gz \\
-o /tmp/badRegistration/caseid_FA
antsApplyTransforms -d 3 \\
-i FA/preproc/caseid_FA.nii.gz \\
-o FA/warped/caseid_[FA/MD/AD/RD]_to_target.nii.gz \\
-r TEMPLATE \\
-t /tmp/badRegistration/caseid_FA1Warp.nii.gz /tmp/badRegistration/caseid_FA0GenericAffine.mat
Finally, if wanted, you can copy the transform files to {args.xfrmDir}/ directory.
Note: Replace all the above directories with absolute paths.\n\n''')
while input('Press Enter when you are done with QC/re-registration: '):
pass
allFAdata, cumsumFA = calc_mean(imgs, targetData.shape, args.qc)
meanFAdata = cumsumFA / len(imgs)
meanFA = pjoin(args.statsDir, 'mean_FA.nii.gz')
# outDir should contain
# all_{modality}.nii.gz
# mean_FA.nii.gz
# mean_FA_mask.nii.gz
# mean_FA_skeleton.nii.gz
# mean_FA_skeleton_mask.nii.gz
# mean_FA_skeleton_mask_dst.nii.gz
if args.modality == 'FA':
if not args.templateMask:
print('Creating template mask ...')
args.templateMask = pjoin(args.statsDir, 'mean_FA_mask.nii.gz')
meanFAmaskData = (meanFAdata > 0) * 1
save_nifti(args.templateMask, meanFAmaskData.astype('uint8'),
target.affine, target.header)
else:
meanFAmaskData = load(args.templateMask).get_data()
meanFAdata = meanFAdata * meanFAmaskData
save_nifti(meanFA, meanFAdata, target.affine, target.header)
# if skeleton is not given:
# create all three of skeleton, skeletonMask, and skeletonMaskDst
# if skeleton is given and (neither skeletonMask nor skeletonMaskDst is given):
# create skeletonMask and skeletonMaskDst
# if skeleton and skeletonMask is given and skeletonMaskDst is not given:
# create skeletonMaskDst
if not args.skeleton:
print(
'Creating all three of skeleton, skeletonMask, and skeletonMaskDst ...'
)
args.skeleton = pjoin(args.statsDir, 'mean_FA_skeleton.nii.gz')
args.skeletonMask = pjoin(args.statsDir,
'mean_FA_skeleton_mask.nii.gz')
args.skeletonMaskDst = pjoin(args.statsDir,
'mean_FA_skeleton_mask_dst.nii.gz')
_create_skeleton(meanFA, args.skeleton)
_create_skeletonMask(args.skeleton, args.SKEL_THRESH,
args.skeletonMask)
_create_skeletonMaskDst(args.templateMask, args.skeletonMask,
args.skeletonMaskDst)
if args.skeleton and not (args.skeletonMask or args.skeletonMaskDst):
print('Creating skeletonMask and skeletonMaskDst ...')
args.skeletonMask = pjoin(args.statsDir,
'mean_FA_skeleton_mask.nii.gz')
args.skeletonMaskDst = pjoin(args.statsDir,
'mean_FA_skeleton_mask_dst.nii.gz')
_create_skeletonMask(args.skeleton, args.SKEL_THRESH,
args.skeletonMask)
_create_skeletonMaskDst(args.templateMask, args.skeletonMask,
args.skeletonMaskDst)
if args.skeleton and not args.skeletonMask and args.skeletonMaskDst:
print('Creating skeletonMask ...')
args.skeletonMask = pjoin(args.statsDir,
'mean_FA_skeleton_mask.nii.gz')
_create_skeletonMask(args.skeleton, args.SKEL_THRESH,
args.skeletonMask)
if (args.skeleton and args.skeletonMask) and not args.skeletonMaskDst:
print('Creating skeletonMaskDst ...')
args.skeletonMaskDst = pjoin(args.statsDir,
'mean_FA_skeleton_mask_dst.nii.gz')
_create_skeletonMaskDst(args.templateMask, args.skeletonMask,
args.skeletonMaskDst)
# mask allFA, this step does not seem to have any effect on the pipeline, it should help the user to visualize only
if args.qc:
check_call(
(' ').join(['fslmaths', allFA, '-mas', args.templateMask, allFA]),
shell=True)
# projecting all {modality} data onto skeleton
pool = Pool(args.ncpu)
for c, imgPath in zip(cases, imgs):
pool.apply_async(project_skeleton, (c, imgPath, args, skelDir),
error_callback=RAISE)
pool.close()
pool.join()
if not args.noAllSkeleton:
allFAskeletonized = pjoin(args.statsDir,
f'all_{args.modality}_skeletonized.nii.gz')
print('Creating ', allFAskeletonized)
# this loop has been moved out of multiprocessing block to prevent memroy error
allFAskeletonizedData = np.zeros((len(imgs), X, Y, Z), dtype='float32')
for i, c in enumerate(cases):
allFAskeletonizedData[i, :] = load(
pjoin(
skelDir,
f'{c}_{args.modality}_to_target_skel.nii.gz')).get_data()
save_nifti(allFAskeletonized, np.moveaxis(allFAskeletonizedData, 0,
-1), target.affine,
target.header)
print(
f'Created {allFAskeletonized} and corresponding index file: {seqFile}'
)
return args
def scattering_matrix(vp1, vs1, rho1, vp2, vs2, rho2, theta1=0):
"""
Full Zoeppritz solution, considered the definitive solution.
Calculates the angle dependent p-wave reflectivity of an interface
between two mediums.
Originally written by: Wes Hamlyn, vectorized by Agile.
Returns the complex reflectivity.
Args:
vp1 (float): The upper P-wave velocity.
vs1 (float): The upper S-wave velocity.
rho1 (float): The upper layer's density.
vp2 (float): The lower P-wave velocity.
vs2 (float): The lower S-wave velocity.
rho2 (float): The lower layer's density.
theta1 (ndarray): The incidence angle; float or 1D array length n.
Returns:
ndarray. The exact Zoeppritz solution for all modes at the interface.
A 4x4 array representing the scattering matrix at the incident
angle theta1.
"""
theta1 *= np.ones_like(vp1)
p = np.sin(theta1) / vp1 # Ray parameter.
theta2 = np.arcsin(p * vp2) # Trans. angle of P-wave.
phi1 = np.arcsin(p * vs1) # Refl. angle of converted S-wave.
phi2 = np.arcsin(p * vs2) # Trans. angle of converted S-wave.
# Matrix form of Zoeppritz equations... M & N are matrices.
M = np.array(
[[-np.sin(theta1), -np.cos(phi1),
np.sin(theta2),
np.cos(phi2)],
[np.cos(theta1), -np.sin(phi1),
np.cos(theta2), -np.sin(phi2)],
[
2 * rho1 * vs1 * np.sin(phi1) * np.cos(theta1),
rho1 * vs1 * (1 - 2 * np.sin(phi1)**2),
2 * rho2 * vs2 * np.sin(phi2) * np.cos(theta2),
rho2 * vs2 * (1 - 2 * np.sin(phi2)**2)
],
[
-rho1 * vp1 * (1 - 2 * np.sin(phi1)**2),
rho1 * vs1 * np.sin(2 * phi1),
rho2 * vp2 * (1 - 2 * np.sin(phi2)**2),
-rho2 * vs2 * np.sin(2 * phi2)
]])
N = np.array(
[[np.sin(theta1),
np.cos(phi1), -np.sin(theta2), -np.cos(phi2)],
[np.cos(theta1), -np.sin(phi1),
np.cos(theta2), -np.sin(phi2)],
[
2 * rho1 * vs1 * np.sin(phi1) * np.cos(theta1),
rho1 * vs1 * (1 - 2 * np.sin(phi1)**2),
2 * rho2 * vs2 * np.sin(phi2) * np.cos(theta2),
rho2 * vs2 * (1 - 2 * np.sin(phi2)**2)
],
[
rho1 * vp1 * (1 - 2 * np.sin(phi1)**2),
-rho1 * vs1 * np.sin(2 * phi1),
-rho2 * vp2 * (1 - 2 * np.sin(phi2)**2),
rho2 * vs2 * np.sin(2 * phi2)
]])
M_ = np.moveaxis(np.squeeze(M), [0, 1], [-2, -1])
A = np.linalg.inv(M_)
N_ = np.moveaxis(np.squeeze(N), [0, 1], [-2, -1])
Z_ = np.matmul(A, N_)
return np.transpose(Z_, axes=list(range(Z_.ndim - 2)) + [-1, -2])
def lime_segmentation(self,forward_func, inp_image, inp_transform_flag,transform_func, device,
output_path, input_file, tran_func, is_3d, target, batch_dim_present,
top_labels, num_samples, num_features, depth=None):
self.device = device
indx = 0
target = target if type(target) == int else int(target[0])
if inp_transform_flag:
ip = transform_func(inp_image).to(device)
else:
ip = inp_image.to(device)
if not batch_dim_present:
ip = ip.unsqueeze(0)
def batch_func(imgs):
forward_func.to(device)
imgs = torch.from_numpy(imgs).transpose(-1,1).float().to(device)
op = forward_func(imgs).detach().cpu().numpy()
return op
def batch_func_3d(imgs):
forward_func.to(device)
outputArray = []
for i in range(imgs.shape[0]):
ip[0,0,indx]= torch.from_numpy(imgs[i,:,:,0]).float().to(device)
outputArray.append(forward_func(ip).detach().cpu().numpy().transpose())
return np.array(outputArray).squeeze(-1)
explainer = lime_image.LimeImageExplainer()
if not is_3d:
if type(inp_image) == torch.Tensor:
input = np.array(inp_image.squeeze().type(torch.DoubleTensor).cpu())
if input.shape[0] == 3:
input = np.moveaxis(input, 0, -1)
else:
input = np.array(tran_func(inp_image))
explanation = explainer.explain_instance(input,
batch_func,
top_labels=top_labels,
hide_color=0,
num_samples=num_samples,)
temp, mask = explanation.get_image_and_mask(target, positive_only=True,
num_features=num_features, hide_rest=True)
img_boundry1 = mark_boundaries(temp / 255.0, mask)
save_im = Image.fromarray((img_boundry1 * 255).astype(np.uint8))
save_im.save(output_path + "/" + input_file + '_lime_' + "_towards_prediction_class_" + str(target) + ".png",
format='png')
temp, mask = explanation.get_image_and_mask(target, positive_only=False,
num_features=num_features, hide_rest=False)
img_boundry2 = mark_boundaries(temp / 255.0, mask)
save_im = Image.fromarray((img_boundry2 * 255).astype(np.uint8))
save_im.save(output_path + "/" + input_file + '_lime_' + "_against_prediction_class_" + str(target) + ".png",
format='png')
else:
#print(target, type(target))
if not batch_dim_present:
inp_image = inp_image.unsqueeze(0)
if not os.path.exists(output_path + '/Lime_'+input_file):
os.mkdir(output_path + '/Lime_'+input_file)
while indx< depth:
explanation = explainer.explain_instance(np.array(inp_image[0,0,indx].type(torch.DoubleTensor)),
batch_func_3d,
top_labels=top_labels,
hide_color=0,
num_samples=num_samples)
temp, mask = explanation.get_image_and_mask(target, positive_only=False,
num_features=num_features, hide_rest=False)
img_boundry1 = mark_boundaries(temp / 255.0, mask)
save_im = Image.fromarray((img_boundry1 * 255).astype(np.uint8))
save_im.save(output_path + '/Lime_'+input_file +"/" + str(indx)+"_towards_prediction_class_" + str(target) + ".png",
format='png')
indx +=1
# Load Dataset
if dataset_name.lower() in ["mnist", "mnist_digits", "mnistdigits"]:
X, y = mnist.load_data()[0]
selected_idx = mnist_idx
elif dataset_name.lower() in ["cifar", "cifar10"]:
X, y = cifar10.load_data()[0]
selected_idx = cifar_idx
elif dataset_name.lower() in ['cifar_gray', 'cifar10_gray', 'cifargray']:
from skimage.color import rgb2gray
X, y = cifar10.load_data()[0]
selected_idx = cifar_idx
X = np.moveaxis(X, 1, 3)
X = rgb2gray(X) * 255
print("Array Shape:", X.shape)
elif dataset_name.lower() in ["fashion", "fashion_mnist", "fashionmnist"]:
X, y = fashion_mnist.load_data()[0]
selected_idx = fashion_idx
else:
print("Dataset not found.")
sys.exit(1)
y = np.array([selected_idx[int(val)] for val in y])
print("Dataset loaded.")
def f_lut(array):
if len(axis) > 1 and axis != np.arange(len(axis)):
array = np.moveaxis(array,
source=axis,
destination=np.arange(len(axis)))
elif add_empty_axis:
array = array.reshape((1, ) + array.shape)
# if 'int' not in str(array.dtype):
# log.warn('Array passed to apply_lut was converted to int32. Numeric precision may have been lost.')
# Read array shape
a_source_shape = array.shape[:n_axis]
map_shape = array.shape[n_axis:]
map_size = int(np.prod(map_shape))
# Check source shape
if a_source_shape != source_shape:
raise ValueError(
'Invalid dimensions on axis: %s. (expected: %s, received: %s)'
% (str(axis), str(source_shape), str(a_source_shape)))
# Prepare table
array = np.moveaxis(array.reshape(source_shape + (map_size, )), -1,
0).reshape((map_size, source_size))
if isinstance(sampling, str):
id_mapped = None
else:
if sampling != 1:
array = (array / sampling).astype(np.int32)
id_mapped = np.logical_not(
np.any(np.logical_or(array > maxs, array < mins), axis=1))
array = np.sum((array - mins) * stride, axis=1).astype(np.uint32)
# Map values
if isinstance(lut_sources, str): # and lut_sources == 'nearest':
a = np.sum(
(array[np.newaxis, :, :] - sources[:, np.newaxis, :])**2,
axis=-1)
a = np.argmin(a, axis=0) + 1
elif lut_sources is not None:
a = np.zeros(shape=(map_size, ), dtype=np.uint32)
if lut_sources is not None:
a[id_mapped] = lut_sources[array[id_mapped]]
else:
a[id_mapped] = array[id_mapped] + 1
else:
if lut_sources is not None:
a = lut_sources[array]
else:
a = array + 1
array = lut_dests[a]
del a
del id_mapped
# Reshape
array = array.reshape(map_shape + dest_shape)
array = np.moveaxis(
array, np.arange(len(map_shape), array.ndim),
np.arange(dest_axis, dest_axis + len(dest_shape))
if len(dest_shape) != len(axis) else axis)
if not keep_dims and dest_shape == (1, ):
array = array.reshape(map_shape)
return array
def train_demo(cfg, net, criterion, optimizer, lr_scheduler):
# Data generator
train_data, test_data = get_data(cfg)
if is_training:
data = train_data
else:
data = test_data
# Initialize the network the right way
# net.train and net.eval account for differences in dropout/batch norm
# during training and testing
start = 0
if is_training:
net.train().cuda()
else:
net.eval().cuda()
if cfg.WEIGHTS_FILE_BASE is not None and cfg.WEIGHTS_FILE_BASE != '':
print('Restoring weights from %s...' % cfg.WEIGHTS_FILE_BASE)
with open(cfg.WEIGHTS_FILE_BASE, 'rb') as f:
checkpoint = torch.load(f)
net.load_state_dict(checkpoint['state_dict'])
# print(checkpoint['state_dict'])
optimizer.load_state_dict(checkpoint['optimizer'])
lr_scheduler.load_state_dict(checkpoint['lr_scheduler'])
start = checkpoint['epoch'] + 1
print('Done.')
print('Done.')
metrics = {'acc_all': [], 'acc_nonzero': [], 'loss': []}
# Only enable gradients if we are training
# with torch.set_grad_enabled(is_training):
durations = []
for i in range(cfg.MAX_STEPS): # use with torch.no_grad() for test network
# Check parameters for nan
# print('Check for nan...')
# had_nan = False
# for p in net.parameters():
# if torch.isnan(p).any():
# print(i, p)
# had_nan = True
#
# for name in net.state_dict():
# tensor = net.state_dict()[name]
# if name == 'sparseModel.2.4.1.2.4.1.2.4.1.2.4.1.2.0.1.0.runningVar':
# print(i, name, tensor)
# if torch.isnan(tensor).any():
# print(i, name, tensor)
# had_nan = True
# if had_nan:
# break
# print('Done.')
# inputs, label = dataloader(i)
print("Step %d/%d" % (i, cfg.MAX_STEPS))
blob = data.forward()
print(blob['voxels'].shape, blob['voxels_value'].shape,
blob['data'].shape, blob['labels'].shape)
if sparse:
coords = torch.from_numpy(blob['voxels']).cuda()
features = torch.from_numpy(
np.reshape(blob['voxels_value'], (-1, 1))).cuda()
# print(coords.type(), features.type())
start = time.time()
predictions_raw = net(coords,
features) # size N_voxels x num_classes
end = time.time()
durations.append(end - start)
# print(predictions_raw.size())
label_voxels, labels = extract_voxels(blob['labels'])
labels = torch.from_numpy(labels).cuda().type(
torch.cuda.LongTensor)
# print(labels, label_voxels, blob['voxels'])
# print(net.parameters())
else:
image = torch.from_numpy(np.moveaxis(blob['data'], -1, 1)).cuda()
labels = torch.from_numpy(blob['labels']).cuda().type(
torch.cuda.LongTensor)
start = time.time()
predictions_raw = net(image)
end = time.time()
durations.append(end - start)
loss = criterion(predictions_raw, labels)
if is_training:
lr_scheduler.step() # Decay learning rate
optimizer.zero_grad() # Clear previous gradients
loss.backward() # Compute gradients of all variables wrt loss
nn.utils.clip_grad_norm_(net.parameters(), 1.0) # Clip gradient
optimizer.step() # update using computed gradients
metrics['loss'].append(loss.item())
print("\tLoss = ", metrics['loss'][-1])
# Accuracy
predicted_labels = torch.argmax(predictions_raw, dim=1)
acc_all = (predicted_labels == labels).sum().item() / float(
labels.numel())
nonzero_px = labels > 0
nonzero_prediction = predicted_labels[nonzero_px]
nonzero_label = labels[nonzero_px]
acc_nonzero = (nonzero_prediction
== nonzero_label).sum().item() / float(
nonzero_label.numel())
metrics['acc_all'].append(acc_all)
metrics['acc_nonzero'].append(acc_nonzero)
print("\tAccuracy = ", metrics['acc_all'][-1],
" - Nonzero accuracy = ", metrics['acc_nonzero'][-1])
if is_training and i % 100 == 0:
for attr in metrics:
np.savetxt(os.path.join(cfg.OUTPUT_DIR,
'%s_%d.csv' % (attr, i)),
metrics[attr],
delimiter=',')
# metrics[attr] = []
if is_training and i % 100 == 0:
filename = os.path.join(cfg.OUTPUT_DIR, 'model-%d.ckpt' % i)
# with open(filename, 'wb'):
torch.save(
{
'epoch': i,
'state_dict': net.state_dict(),
'optimizer': optimizer.state_dict(),
'lr_scheduler': lr_scheduler.state_dict()
}, filename)
if not is_training:
print('Display...')
if sparse:
final_predictions = np.zeros(
(1, cfg.IMAGE_SIZE, cfg.IMAGE_SIZE, cfg.IMAGE_SIZE))
indices = label_voxels.T
final_predictions[
0, indices[0], indices[1],
indices[2]] = predicted_labels.cpu().data.numpy()
display_uresnet(blob,
cfg,
index=i,
predictions=final_predictions)
else:
display_uresnet(
blob,
cfg,
index=i,
predictions=predicted_labels.cpu().data.numpy())
print('Done.')
print("Average duration = %f s" % np.array(durations).mean())
def load_h5(fpath,
clip_flyscan=True,
xbic_on_dsic=False,
quant_scaler="us_ic"):
"""
Loads a MAPS-generated .h5 file (raw + fitted data from 2IDD, fitted from 26IDC)
fpath: path to file
clip_flyscan: boolean, removes last two columns of map (which are corrupted when running flyscans)
xbic_on_dsic: boolean. if True, considers the downstream ion chamber to be connected in an XBIC setup, adds to output['maps']['XBIC']
quant_scaler: one of ['sr_current', 'us_ic', 'ds_ic']. quantification is normalized to some metric of beam power deposited in sample. typically we use upstream ion chamber
returns a dictionary with scan info and maps.
"""
quant_scaler_key = {
"sr_current": 0, # storage ring current
"us_ic": 1, # upstream ion chamber (incident flux)
"ds_ic":
2, # downstream ion chamber (transmitted flux - make sure this sensor was not used for XBIC!)
}
if quant_scaler not in quant_scaler_key:
raise ValueError(
f"Quantification normalization must be by either sr_current, us_ic, or ds_ic! user provided {quant_scaler}."
)
output = {"filepath": fpath}
if clip_flyscan:
xmask = slice(
0, -2) # last two columns are garbage from flyscan, omit here
else:
xmask = slice(0, None) # no clipping
with h5py.File(fpath, "r") as dat:
output["x"] = dat["MAPS"]["x_axis"][()]
output["y"] = dat["MAPS"]["y_axis"][()]
output["spectra"] = np.moveaxis(
dat["MAPS"]["mca_arr"][()], 0,
2)[:, xmask] # y by x by energy, full XRF spectra
output["energy"] = dat["MAPS"]["energy"][:output["spectra"].shape[
-1]] # specmap only has 2000 bins sometimes, match energy to that
output["intspectra"] = dat["MAPS"][
"int_spec"][:output["spectra"].shape[-1]] # integrated spectra
output["extent"] = [
output["x"][0],
output["x"][-1],
output["y"][0],
output["y"][-1],
]
scaler_names = dat["MAPS"]["scaler_names"][()].astype("U13").tolist()
quant_scaler_values = np.array(
dat["MAPS"]["scalers"][scaler_names.index(quant_scaler)])[:, xmask]
fillval = np.nanmean(quant_scaler_values[quant_scaler_values > 0])
quant_scaler_values = np.where(
quant_scaler_values == 0.0,
fillval,
quant_scaler_values,
) # change all values that are 0.0 to mean, avoid divide by 0
if "/MAPS/XRF_fits" in dat:
xrf = []
raw = dat["MAPS"][
"XRF_fits"][:, :,
xmask] # xrf elemental maps, elements by y by x
quant = np.moveaxis(
dat["MAPS"]["XRF_fits_quant"][()], 2, 0
) # quantification factors from MAPS fitting, elements by factors
for x, q in zip(raw, quant):
x = np.divide(
x,
quant_scaler_values) # normalize to quantification scaler
quantfactor = q[quant_scaler_key[quant_scaler]]
xrf.append(
x / quantfactor / 4
) # factor of 4 came from discussion w/ Arthur Glowacki @ APS, and brings this value in agreement with MAPS displayed value. not sure why it is necessary though...
# update 20221228: this factor changes from run to run, but is always a round number (have seen 1, 4, and 10). I expect it could be related to usic amplifier settings or similar, but cant find a related value in the h5 file REK
output["fitted"] = True
else:
xrf = dat["MAPS"]["XRF_roi"][:, :, xmask]
output["fitted"] = False
allchan = dat["MAPS"]["channel_names"][()].astype("U13").tolist()
if xbic_on_dsic:
xrf.append(dat["MAPS"]["scalers"][scaler_names.index("ds_ic")]
[:, xmask]) # append DSIC to channels, used for xbic
allchan.append("XBIC") # label for DSIC
output["maps"] = {}
for channel, xrf_ in zip(allchan, xrf):
output["maps"][channel] = np.array(xrf_)
return output
def load_fan_data(return_crlb=False, data_name='supersampled'):
if data_name == 'fan':
file_name = 'runs_2017_01_07_lineardet'
elif data_name == 'supersampled':
file_name = '10_Jan_2017_17_51_44_simulation_forbild_head'
elif data_name == 'fan_circ':
file_name = 'simulated_images_2017_01_06'
else:
assert False
current_path = os.path.dirname(os.path.realpath(__file__))
data_path = os.path.join(current_path, 'data', file_name, 'head_image.mat')
try:
data_mat = sio.loadmat(data_path)
except IOError:
raise IOError('{} missing, '
'contact '
'developers for a copy of the data or use another data '
'source.'.format(data_path))
# print(sorted(data_mat.keys()))
data = data_mat['decomposedbasisProjectionsmm']
data = data.swapaxes(0, 2)
if data_name == 'fan':
det_size = 853
angle_partition = odl.uniform_partition(0.5 * np.pi,
2.5 * np.pi,
360,
nodes_on_bdry=[[True, False]])
detector_partition = odl.uniform_partition(-det_size / 2.0,
det_size / 2.0, 853)
geometry = odl.tomo.FanFlatGeometry(angle_partition,
detector_partition,
src_radius=500,
det_radius=500)
data[:] = data[:, ::-1]
if not return_crlb:
return data, geometry
else:
crlb = data_mat['CRLB']
crlb = crlb.swapaxes(0, 1)
crlb[:] = crlb[::-1]
crlb = swap_axes(crlb)
# Negative correlation
#crlb[0, 1] *= -1
#crlb[1, 0] *= -1
return data, geometry, crlb
if data_name == 'supersampled':
det_size = 853
angle_partition = odl.uniform_partition(0 * np.pi, 2 * np.pi, 360)
detector_partition = odl.uniform_partition(-det_size / 2.0,
det_size / 2.0, 853)
geometry = odl.tomo.FanFlatGeometry(angle_partition,
detector_partition,
src_radius=500,
det_radius=500)
#data[:] = data[:, ::-1]
if not return_crlb:
return data, geometry
else:
crlb = data_mat['CRLB']
crlb = crlb.swapaxes(0, 1)
#crlb[:] = crlb[::-1]
crlb = swap_axes(crlb)
# Negative correlation
#crlb[0, 1] *= -1
#crlb[1, 0] *= -1
return data, geometry, crlb
elif data_name == 'fan_circ':
# Create approximate fan flat geometry.
det_size = 883 * (500 + 500)
angle_partition = odl.uniform_partition(0.5 * np.pi,
2.5 * np.pi,
360,
nodes_on_bdry=[[True, False]])
detector_partition = odl.uniform_partition(-det_size / 2.0,
det_size / 2.0, 883)
geometry = odl.tomo.FanFlatGeometry(angle_partition,
detector_partition,
src_radius=500,
det_radius=500)
# Convert to true fan flat geometry
data[0][:] = fan_to_fan_flat(geometry, data[0])
data[1][:] = fan_to_fan_flat(geometry, data[1])
if not return_crlb:
return data, geometry
else:
crlb = data_mat['CRLB']
crlb = crlb.swapaxes(0, 1)
crlb = np.moveaxis(crlb, [-2, -1], [0, 1])
crlb[0, 0][:] = fan_to_fan_flat(geometry, crlb[0, 0])
crlb[0, 1][:] = fan_to_fan_flat(geometry, crlb[0, 1])
crlb[1, 0][:] = fan_to_fan_flat(geometry, crlb[1, 0])
crlb[1, 1][:] = fan_to_fan_flat(geometry, crlb[1, 1])
# Negative correlation
# crlb[0, 1] *= -1
# crlb[1, 0] *= -1
return data, geometry, crlb
def find_block(a,
axis=0,
ignore_masked=True,
as_slice=False,
block_value=None):
"""Find blocks of contiguous values along a given dimension of a.
This function will identify the index ranges for which there are contiguous values in a and the values themselves.
For example, for::
a = np.array([0, 1, 1, 1, 2, 3, 3, 4, 5])
then ``find_block(a)`` would return ``[(1, 4), (5, 7)]`` and ``[1, 3]``. Note that the index ranges follow the
Python convention that the last index is exclusive, so that ``a[1:4]`` would give ``[1, 1, 1]``.
If ``a`` is a 2D or higher array, then the whole slice ``a[i+1, :]`` must equal ``a[i, :]`` to be considered
contiguous. For::
a = [[1, 2, 3],
[1, 2, 3],
[1, 2, 4]]
the first two rows only would be considered a contiguous block because all their values are identical, while the
third row is not. Finally, if ``a`` is a masked array, then by default the masked *values* are ignored but the masks
themselves must be the same. With the same 2D ``a`` as above, if all the values in the last column were masked:
a = [[1, 2, --],
[1, 2, --],
[1, 2, --]]
then all three rows would be considered a block, but if only the bottom right element was masked:
a = [[1, 2, 3],
[1, 2, 3],
[1, 2, --]]
then the third row would *not* be part of the block, because even though its unmasked values are identical to the
corresponding values in the previous row, the mask is not.
Parameters
----------
a : array-like
the array or array-like object to find contiguous values in. Can be given as anything that `numpy.array`
can turn into a proper array.
axis : int
which axis of ``a`` to operate along.
ignore_masked : bool
setting this to ``False`` modifies the behavior described above regarding masked arrays. When
this is ``False``, then the underlying values are considered for equality. In the example where the entire last
column of ``a`` was masked, setting ``ignore_masked = True`` would cause the third row to be excluded from the
block again, because the values under the mask are compared.
as_slice : bool
set to ``True`` to return the indices as slice instances instead; these can be used directly in
``a`` retrieve the contiguous blocks.
block_value : array-like
if given, this will only look for blocks matching this value. In the first example where ``a``
was a vector, setting this to ``1`` would only return the indices (1, 4) since only the first block has values of
1. If ``a`` if multidimensional, keep in mind that the explicit check is that ``np.all(a[i,:] == block_value)``,
so this may be a scalar or an array, as long as each slice passes that test. If this is a masked array, then the
mask of each slice of ``a`` must also match its mask.
Returns
-------
list[tuple[int]]
A list of block start/end indices as two-element tuples (or slices, if ``as_slice = True``)
list[numpy.ndarray]
a list of the values of each block.
Notes
-----
Even if you pass ``a`` in as something other than a numpy array (e.g. a list of lists) the second return value will
be numpy arrays. This is due to how ``a`` is handled internally.
If ``block_value`` is a masked array and ``a`` is not, then most likely nothing will match. However, you should
not rely on this behavior, since there may be some corner cases where this is not true, particularly if
``block_value`` and ``a`` are boolean arrays.
"""
if not isinstance(a, np.ndarray):
a = np.array(a)
block_mask = None
if block_value is not None:
if not isinstance(block_value, np.ndarray):
block_value = np.array(block_value)
elif isinstance(
block_value, np.ma.masked_array
): # and not isinstance(row.mask, np.bool_): # TODO: figure out why I'd needed the extra isinstance check here and for the rows
block_mask = block_value.mask
if ignore_masked:
# If ignoring masked values, we cut down the value the block is supposed to equal just like we cut
# down each row
block_value = block_value[~block_mask]
a = np.moveaxis(a, axis, 0)
last_row = None
last_mask = None
blocks = []
values = []
block_start = None
for idx, row in enumerate(a):
if isinstance(
row,
np.ma.masked_array): # and not isinstance(row.mask, np.bool_):
mask = row.mask
if ignore_masked:
# Ignoring masked values: masked values do not contribute one way or another to determining if two rows
# are equal, *however*, rows must have the *same* mask, so we store the mask but remove masked values.
# If the whole row was masked, then the last row will have to have been the same. That's why we extract
# the mask before cutting row down.
row = row[~mask]
# If we're not ignoring masked values, then don't cut down row: np.array_equal will test the underlying data
# even under masked values
else:
# Not a masked array? Just make the mask equal to the row so they are both equal or not together - this
# removes the need for logic to determine whether or not to test the masks
mask = row
if last_row is None:
# On the first row. Can't do anything yet.
pass
elif block_start is not None and not (np.array_equal(row, last_row) and
np.array_equal(mask, last_mask)):
# End of block. Add to the list of blocks. The current index is not in the block, but since Python's
# convention is that the ending index is exclusive, we make the end of the block the first index not
# included in it.
blocks.append((block_start, idx))
block_start = None
elif block_start is None and np.array_equal(
row, last_row) and np.array_equal(mask, last_mask):
# If the current row equals the last row, then we're in a block.
if block_value is None:
# If no value to check against the block was given, then set the start of the block to the last index
# (where the block actually started).
block_start = idx - 1
values.append(row)
elif np.all(row.shape == block_value.shape) and np.all(
row == block_value):
# If a value to check against the block was given, then only start the block if the current row
# matches that value. If that value was a masked array, then the masks must be equal as well.
if block_mask is None or np.all(
block_mask == mask
): # if the row is the same shape, then the mask will be too
block_start = idx - 1
values.append(row)
last_row = row
last_mask = mask
if block_start is not None:
# If block_start isn't None after we're done with the for loop, then there's a block that goes to the end of
# the array, so add that.
blocks.append((block_start, a.shape[0]))
if as_slice:
blocks = [slice(*b) for b in blocks]
return blocks, values
field_data,
analytic_data,
chop_size=chop_size,
chunk_size=chunk_size,
network_sequence_size=network_time_sequence)
#field_data = GIGANTIC_DATA_PROCESSOR.rescale_arr(field_data, 1, 255)
#test = field_data.astype(np.uint8)
#imsave('test2.tif', test[0:500, : , :, 3 ])
mean_version = False
if mean_version:
analytic_data = GIGANTIC_DATA_PROCESSOR.analysis_mean_calculation(
analytic_data)
field_data = np.moveaxis(field_data, 3, 1)
#analytic_data = np.moveaxis(analytic_data, 3, 1)
field_data = np.expand_dims(field_data, axis=4)
analytic_data = np.expand_dims(analytic_data, axis=1)
#field_data = np.expand_dims(field_data, axis=1) # [ amount, 1, :, : , 25 ]
#analytic_data = np.expand_dims(analytic_data, axis=1)
freq_set = 3
input_data = field_data[freq_set, :, :, :]
input_data = np.expand_dims(input_data, axis=0)
from keras.models import load_model
model = load_model('test.hdf5')
output = model.predict(input_data)
print(output.shape)
import numpy as np
from numpy.random import seed
from numpy.random import rand
import argparse
parser = argparse.ArgumentParser(description='Run experiment on data')
parser.add_argument('-n', type=int, default=10000)
args = parser.parse_args()
l = 20
randstart = rand(args.n) * 0.5
randterm = rand(args.n) * (1.03 - 0.77) + 0.77
v1 = np.arange(l).reshape(1, -1).repeat(args.n * 2, axis=0).reshape(args.n, 2, l)
v1 = v1 * randterm.reshape(-1, 1, 1) + randstart.reshape(-1, 1, 1)
v1[:, 0, :] = np.sin(v1[:, 0, :])
v1[:, 1, :] = np.cos(v1[:, 1, :])
v1 = np.moveaxis(v1, 1, 2)
np.savetxt("generate_iterative_multijump.dat",v1.reshape(args.n, -1),fmt="%.3f")
def tensorboard_image(name, image, iteration, writer):
out_im = np.moveaxis(image.data.cpu().numpy(), 0, 2)
writer.add_image(name, out_im, iteration)
def push_datas(self, datas, axis=0):
if axis != 0:
datas = np.moveaxis(datas, axis, 0)
assert datas.shape[1:] == self._accum.shape_data
for data in datas:
self._values.append(data)
def test_moveaxis(source, destination):
x = sparse.random((2, 3, 4, 5), density=0.25)
y = x.todense()
xx = sparse.moveaxis(x, source, destination)
yy = np.moveaxis(y, source, destination)
assert_eq(xx, yy)
def _prepare_grating(self):
'''Create temporospatial grating
'''
spatial_frequency = self.options["spatial_frequency"]
temporal_frequency = self.options["temporal_frequency"]
fps = self.options["fps"]
duration_seconds = self.options["duration_seconds"]
orientation = self.options["orientation"]
if not spatial_frequency:
print('Spatial_frequency missing, setting to 1')
spatial_frequency = 1
if not temporal_frequency:
print('Temporal_frequency missing, setting to 1')
temporal_frequency = 1
# Create sine wave
one_cycle = 2 * np.pi
cycles_per_degree = spatial_frequency
#image_width_in_degrees = self.options["image_width_in_deg"]
image_width = self.options["image_width"]
image_height = self.options["image_height"]
image_width_in_degrees = image_width / self.options["pix_per_deg"]
# Calculate larger image size to allow rotations
diameter = np.ceil(np.sqrt(image_height**2 + image_width**2)).astype(
np.int)
image_width_diameter = diameter
image_height_diameter = diameter
image_width_diameter_in_degrees = image_width_diameter / self.options[
"pix_per_deg"]
# Draw temporospatial grating
# NB! one_cycle * cycles_per_degree needs to be multiplied with the scaled width to have
# the desired number of cpd in output image
image_position_vector = np.linspace(
0, one_cycle * cycles_per_degree * image_width_diameter_in_degrees,
image_width_diameter)
n_frames = self.frames.shape[2]
# Recycling large_frames and self.frames below, instead of descriptive variable names for the evolving video, saves a lot of memory
# Create large 3D frames array covering the most distant corner when rotated
large_frames = np.tile(image_position_vector,
(image_height_diameter, n_frames, 1))
# Correct dimensions to image[0,1] and time[2]
large_frames = np.moveaxis(large_frames, 2, 1)
total_temporal_shift = temporal_frequency * one_cycle * duration_seconds
one_frame_temporal_shift = (temporal_frequency * one_cycle) / fps
temporal_shift_vector = np.arange(0, total_temporal_shift,
one_frame_temporal_shift)
# Shift grating phase in time. Broadcasting temporal vector automatically to correct dimension.
large_frames = large_frames + temporal_shift_vector
# Rotate to desired orientation
large_frames = ndimage.rotate(large_frames, orientation, reshape=False)
# Cut back to original image dimensions
marginal_height = (diameter - image_height) / 2
marginal_width = (diameter - image_width) / 2
marginal_height = np.round(marginal_height).astype(np.int)
marginal_width = np.round(marginal_width).astype(np.int)
self.frames = large_frames[marginal_height:-marginal_height,
marginal_width:-marginal_width, :]
# remove rounding error
self.frames = self.frames[0:image_height, 0:image_width, :]
def train(self, epochs, batch_size=4):
# Load the LFW dataset
print("Loading the dataset: this step can take a few minutes.")
# Complete LFW dataset
# lfw_people = fetch_lfw_people(color=True, resize=1.0, \
# slice_=(slice(0, 250), slice(0, 250)))
# Smaller dataset used for implementation evaluation
lfw_people = fetch_lfw_people(color=True, resize=1.0, \
slice_=(slice(0, 250), slice(0, 250)), \
min_faces_per_person=3)
images_rgb = lfw_people.images
images_rgb = np.moveaxis(images_rgb, -1, 1)
# Zero pad them to get 256 x 256 inputs
images_rgb = np.pad(images_rgb, ((0,0), (0,0), (3,3), (3,3)), 'constant')
self.images_lfw = images_rgb
# Convert images from RGB to YCbCr and from RGB to grayscale
images_ycc = np.zeros(images_rgb.shape)
secret_gray = np.zeros((images_rgb.shape[0], 1, images_rgb.shape[2], images_rgb.shape[3]))
for k in range(images_rgb.shape[0]):
images_ycc[k, :, :, :] = rgb2ycc(images_rgb[k, :, :, :])
secret_gray[k, 0, :, :] = rgb2gray(images_rgb[k, :, :, :])
# Rescale to [-1, 1]
X_train_ycc = (images_ycc.astype(np.float32) - 127.5) / 127.5
X_train_gray = (secret_gray.astype(np.float32) - 127.5) / 127.5
# Adversarial ground truths
original = np.ones((batch_size, 1))
encrypted = np.zeros((batch_size, 1))
for epoch in range(epochs):
# Select a random batch of cover images
idx = np.random.randint(0, X_train_ycc.shape[0], batch_size)
imgs_cover = X_train_ycc[idx]
# Idem for secret images
idx = np.random.randint(0, X_train_ycc.shape[0], batch_size)
imgs_gray = X_train_gray[idx]
# Predict the generator output for these images
imgs_stego, _ = self.base_model.predict([imgs_cover, imgs_gray])
# imgs_stego, _, _ = self.adversarial.predict([imgs_cover, imgs_gray])
# Train the discriminator
d_loss_real = self.discriminator.train_on_batch(imgs_cover, original)
d_loss_encrypted = self.discriminator.train_on_batch(imgs_stego, encrypted)
d_loss = 0.5 * np.add(d_loss_real, d_loss_encrypted)
# Train the generator
g_loss = self.adversarial.train_on_batch([imgs_cover, imgs_gray], [imgs_cover, imgs_gray, original])
# Print the progress
print("{} [D loss: {}] [G loss: {}]".format(epoch, d_loss, g_loss[0]))
self.adversarial.save('adversarial.h5')
self.discriminator.save('discriminator.h5')
self.base_model.save('base_model.h5')
C3 = np.exp(-(X - 0.1)**2 - (Y + 1)**2) - 0.8 * np.exp(-(X + 1)**2 -
(Y + 1)**2)
C3 = C3 - C3.min()
test_compositions = [C1, C2, C3]
if __name__ == "__main__":
import matplotlib.pyplot as plt
from matplotlib import cm
C1 = (C1 - C1.min()) / (C1.max() - C1.min())
C2 = (C2 - C2.min()) / (C2.max() - C2.min())
C3 = (C3 - C3.min()) / (C3.max() - C3.min())
RGB_style = np.array([C1, C2, C3])
RGB_style = np.moveaxis(RGB_style, 0, -1)
fig, axes = plt.subplots(ncols=4)
axes[0].set_title('Red')
axes[0].imshow(C1,
vmax=1.0,
vmin=0,
cmap=cm.gray,
origin='lower',
extent=[-imsize, imsize, -imsize, imsize])
axes[1].set_title('Green')
axes[1].imshow(C2,
vmax=1.0,
vmin=0,
cmap=cm.gray,
# Get meta to pass to input data
meta = src.meta.copy()
meta['transform'] = src.transform
# Reset meta for our outputs
meta['count'] = 3
meta['dtype'] = 'uint8'
# Build API call and request our image
url = f'https://api.mapbox.com/styles/v1/{STYLE_USER}/{STYLE_ID}/static/{im_bounds}/{src.width}x{src.height}?access_token={MAPBOX_API_KEY}&attribution=false&logo=false'
r = requests.get(url)
# Read in our data and convert it to RGB
map_im = Image.open(BytesIO(r.content))
map_conv = map_im.convert(mode='RGB')
# Get our image as an np array and set axes for rio
a = np.asarray(map_conv)
move = np.moveaxis(np.asarray(a), [0, 1, 2], [1, 2, 0])
# Add geospatial data and write
with rasterio.open(new_file, 'w', **meta) as outds:
outds.write(move)
# Sleep to prevent getting rate limited (1,250/hr)
sleep(.05)
elapsed = timeit.default_timer() - t0
print(f'Run complete in {elapsed / 60:.3f} min')