Python numpy.zeros() Examples

def get_a_datum(self):
        if self._compressed:
            datum = extract_sample(
                self._data[self._cur], self._mean, self._resize)
        else:
            datum = self._data[self._cur]
        # start parsing labels
        label_elems = parse_label(self._label[self._cur])
        label = np.zeros(self._label_dim)
        if not self._multilabel:
            label[0] = label_elems[0]
        else:
            for i in label_elems:
                label[i] = 1
        self._cur = (self._cur + 1) % self._sample_count
        return datum, label 

def wordbag2mat(self, wordbag): #testing
        if self.model==None:
            raise Exception("no model")
        matrix=np.empty((len(wordbag),self.len_vector))
        #如果词典中不存在该词，抛出异常，但暂时还没有自定义词典的办法，所以暂时不那么严格
        #try:
        #    for i in range(len(wordbag)):
        #        matrix[i,:]=self.model[wordbag[i]]
        #except:
        #    raise Exception("'%s' can not be found in dictionary." % wordbag[i])
        #如果词典中不存在该词，则push进一列零向量
        for i in range(len(wordbag)):
            try:
                matrix[i,:]=self.model.wv.__getitem__(wordbag[i])#[wordbag[i]]
            except:
                matrix[i,:]=np.zeros((1,self.len_vector))
        return matrix
################################ problem ##################################### 

def similarity_label(self, words, normalization=True):
        """
        you can calculate more than one word at the same time.
        """
        if self.model==None:
            raise Exception('no model.')
        if isinstance(words, string_types):
            words=[words]
        vectors=np.transpose(self.model.wv.__getitem__(words))
        if normalization:
            unit_vector=unitvec(vectors,ax=0) # 这样写比原来那样速度提升一倍
            #unit_vector=np.zeros((len(vectors),len(words)))
            #for i in range(len(words)):
            #    unit_vector[:,i]=matutils.unitvec(vectors[:,i])
            dists=np.dot(self.Label_vec_u, unit_vector)
        else:
            dists=np.dot(self.Label_vec, vectors)
        return dists 

def load_keypoints(image_filepath, image_height, image_width):
    """Load facial keypoints of one image."""
    fp_keypoints = "%s.cat" % (image_filepath,)
    if not os.path.isfile(fp_keypoints):
        raise Exception("Could not find keypoint coordinates for image '%s'." \
                        % (image_filepath,))
    else:
        coords_raw = open(fp_keypoints, "r").readlines()[0].strip().split(" ")
        coords_raw = [abs(int(coord)) for coord in coords_raw]
        keypoints = []
        #keypoints_arr = np.zeros((9*2,), dtype=np.int32)
        for i in range(1, len(coords_raw), 2): # first element is the number of coords
            x = np.clip(coords_raw[i], 0, image_width-1)
            y = np.clip(coords_raw[i+1], 0, image_height-1)
            keypoints.append((x, y))

        return keypoints 

def wer(self, r, h):
        # initialisation
        d = np.zeros((len(r)+1)*(len(h)+1), dtype=np.uint8)
        d = d.reshape((len(r)+1, len(h)+1))
        for i in range(len(r)+1):
            for j in range(len(h)+1):
                if i == 0:
                    d[0][j] = j
                elif j == 0:
                    d[i][0] = i

        # computation
        for i in range(1, len(r)+1):
            for j in range(1, len(h)+1):
                if r[i-1] == h[j-1]:
                    d[i][j] = d[i-1][j-1]
                else:
                    substitution = d[i-1][j-1] + 1
                    insertion    = d[i][j-1] + 1
                    deletion     = d[i-1][j] + 1
                    d[i][j] = min(substitution, insertion, deletion)

        return d[len(r)][len(h)] 

def compliance_function_fdiff(self, x, dc):
        obj = self.compliance_function(x, dc)

        x0 = x.copy()
        dc0 = dc.copy()
        dcf = np.zeros(dc.shape)
        for i, v in enumerate(x):
            x = x0.copy()
            x[i] += 1e-6
            o1 = self.compliance_function(x, dc)
            x[i] = x0[i] - 1e-6
            o2 = self.compliance_function(x, dc)
            dcf[i] = (o1 - o2) / (2e-6)
        print("finite differences: {:g}".format(np.linalg.norm(dcf - dc0)))
        dc[:] = dc0

        return obj 

def calculate_fdiff_stress(self, x, u, nu, side=1, dx=1e-6):
        """
        Calculate the derivative of the Von Mises stress using finite
        differences given the densities x, displacements u, and young modulus
        nu. Optionally, provide the side length (default: 1) and delta x
        (default: 1e-6).
        """
        ds = self.calculate_diff_stress(x, u, nu, side)
        dsf = numpy.zeros(x.shape)
        x = numpy.expand_dims(x, -1)
        for i in range(x.shape[0]):
            delta = scipy.sparse.coo_matrix(([dx], [[i], [0]]), shape=x.shape)
            s1 = self.calculate_stress((x + delta.A).squeeze(), u, nu, side)
            s2 = self.calculate_stress((x - delta.A).squeeze(), u, nu, side)
            dsf[i] = ((s1 - s2) / (2. * dx))[i]
        print("finite differences: {:g}".format(numpy.linalg.norm(dsf - ds)))
        return dsf 

def compliance_function_fdiff(self, x, dc):
        obj = self.compliance_function(x, dc)

        x0 = x.copy()
        dc0 = dc.copy()
        dcf = np.zeros(dc.shape)
        for i, v in enumerate(x):
            x = x0.copy()
            x[i] += 1e-6
            o1 = self.compliance_function(x, dc)
            x[i] = x0[i] - 1e-6
            o2 = self.compliance_function(x, dc)
            dcf[i] = (o1 - o2) / (2e-6)
        print("finite differences: {:g}".format(np.linalg.norm(dcf - dc0)))
        dc[:] = dc0

        return obj 

def calculate_fdiff_stress(self, x, u, nu, side=1, dx=1e-6):
        """
        Calculate the derivative of the Von Mises stress using finite
        differences given the densities x, displacements u, and young modulus
        nu. Optionally, provide the side length (default: 1) and delta x
        (default: 1e-6).
        """
        ds = self.calculate_diff_stress(x, u, nu, side)
        dsf = numpy.zeros(x.shape)
        x = numpy.expand_dims(x, -1)
        for i in range(x.shape[0]):
            delta = scipy.sparse.coo_matrix(([dx], [[i], [0]]), shape=x.shape)
            s1 = self.calculate_stress((x + delta.A).squeeze(), u, nu, side)
            s2 = self.calculate_stress((x - delta.A).squeeze(), u, nu, side)
            dsf[i] = ((s1 - s2) / (2. * dx))[i]
        print("finite differences: {:g}".format(numpy.linalg.norm(dsf - ds)))
        return dsf 

def test_add_uniform_time_weights():
    time = np.array([15, 46, 74])
    data = np.zeros((3))
    ds = xr.DataArray(data,
                      coords=[time],
                      dims=[TIME_STR],
                      name='a').to_dataset()
    units_str = 'days since 2000-01-01 00:00:00'
    cal_str = 'noleap'
    ds[TIME_STR].attrs['units'] = units_str
    ds[TIME_STR].attrs['calendar'] = cal_str

    with pytest.raises(KeyError):
        ds[TIME_WEIGHTS_STR]

    ds = add_uniform_time_weights(ds)
    time_weights_expected = xr.DataArray(
        [1, 1, 1], coords=ds[TIME_STR].coords, name=TIME_WEIGHTS_STR)
    time_weights_expected.attrs['units'] = 'days'
    assert ds[TIME_WEIGHTS_STR].identical(time_weights_expected) 

def ds_time_encoded_cf():
    time_bounds = np.array([[0, 31], [31, 59], [59, 90]])
    bounds = np.array([0, 1])
    time = np.array([15, 46, 74])
    data = np.zeros((3))
    ds = xr.DataArray(data,
                      coords=[time],
                      dims=[TIME_STR],
                      name='a').to_dataset()
    ds[TIME_BOUNDS_STR] = xr.DataArray(time_bounds,
                                       coords=[time, bounds],
                                       dims=[TIME_STR, BOUNDS_STR],
                                       name=TIME_BOUNDS_STR)
    units_str = 'days since 2000-01-01 00:00:00'
    cal_str = 'noleap'
    ds[TIME_STR].attrs['units'] = units_str
    ds[TIME_STR].attrs['calendar'] = cal_str
    return ds 

def ds_with_time_bounds(alt_lat_str, var_name):
    time_bounds = np.array([[0, 31], [31, 59], [59, 90]])
    bounds = np.array([0, 1])
    time = np.array([15, 46, 74])
    data = np.zeros((3, 1, 1))
    lat = [0]
    lon = [0]
    ds = xr.DataArray(data,
                      coords=[time, lat, lon],
                      dims=[TIME_STR, alt_lat_str, LON_STR],
                      name=var_name).to_dataset()
    ds[TIME_BOUNDS_STR] = xr.DataArray(time_bounds,
                                       coords=[time, bounds],
                                       dims=[TIME_STR, BOUNDS_STR],
                                       name=TIME_BOUNDS_STR)
    units_str = 'days since 2000-01-01 00:00:00'
    ds[TIME_STR].attrs['units'] = units_str
    ds[TIME_BOUNDS_STR].attrs['units'] = units_str
    return ds 

def test_sel_var():
    time = np.array([0, 31, 59]) + 15
    data = np.zeros((3))
    ds = xr.DataArray(data,
                      coords=[time],
                      dims=[TIME_STR],
                      name=convection_rain.name).to_dataset()
    condensation_rain_alt_name, = condensation_rain.alt_names
    ds[condensation_rain_alt_name] = xr.DataArray(data, coords=[ds.time])
    result = _sel_var(ds, convection_rain)
    assert result.name == convection_rain.name

    result = _sel_var(ds, condensation_rain)
    assert result.name == condensation_rain.name

    with pytest.raises(LookupError):
        _sel_var(ds, precip) 

def build(self):
#{{{
        import numpy as np;
        self.W = shared((self.input_dim, 4 * self.output_dim),
                               name='{}_W'.format(self.name))
        self.U = shared((self.output_dim, 4 * self.output_dim),
                                     name='{}_U'.format(self.name))

        self.b = K.variable(np.hstack((np.zeros(self.output_dim),
                                        K.get_value(self.forget_bias_init(
                                                (self.output_dim,))),
                                        np.zeros(self.output_dim),
                                        np.zeros(self.output_dim))),
                                name='{}_b'.format(self.name))
        #self.c_0 = shared((self.output_dim,), name='{}_c_0'.format(self.name)  )
        #self.h_0 = shared((self.output_dim,), name='{}_h_0'.format(self.name)  )
        self.c_0=np.zeros(self.output_dim).astype(theano.config.floatX);
        self.h_0=np.zeros(self.output_dim).astype(theano.config.floatX);
        self.params=[self.W,self.U,
                        self.b,
                    # self.c_0,self.h_0
                    ];
        #}}} 

def ctc_update_log_p(skip_idxs, zeros, active, log_p_curr, log_p_prev):
    active_skip_idxs = skip_idxs[(skip_idxs < active).nonzero()]
    active_next = T.cast(T.minimum(
        T.maximum(
            active + 1,
            T.max(T.concatenate([active_skip_idxs, [-1]])) + 2 + 1
        ), log_p_curr.shape[0]), 'int32')

    common_factor = T.max(log_p_prev[:active])
    p_prev = T.exp(log_p_prev[:active] - common_factor)
    _p_prev = zeros[:active_next]
    # copy over
    _p_prev = T.set_subtensor(_p_prev[:active], p_prev)
    # previous transitions
    _p_prev = T.inc_subtensor(_p_prev[1:], _p_prev[:-1])
    # skip transitions
    _p_prev = T.inc_subtensor(_p_prev[active_skip_idxs + 2], p_prev[active_skip_idxs])
    updated_log_p_prev = T.log(_p_prev) + common_factor

    log_p_next = T.set_subtensor(
        zeros[:active_next],
        log_p_curr[:active_next] + updated_log_p_prev
    )
    return active_next, log_p_next 

def ctc_path_probs(predict, Y, alpha=1e-4):
    smoothed_predict = (1 - alpha) * predict[:, Y] + alpha * np.float32(1.) / Y.shape[0]
    L = T.log(smoothed_predict)
    zeros = T.zeros_like(L[0])
    log_first = zeros

    f_skip_idxs = ctc_create_skip_idxs(Y)
    b_skip_idxs = ctc_create_skip_idxs(Y[::-1])  # there should be a shortcut to calculating this

    def step(log_f_curr, log_b_curr, f_active, log_f_prev, b_active, log_b_prev):
        f_active_next, log_f_next = ctc_update_log_p(f_skip_idxs, zeros, f_active, log_f_curr, log_f_prev)
        b_active_next, log_b_next = ctc_update_log_p(b_skip_idxs, zeros, b_active, log_b_curr, log_b_prev)
        return f_active_next, log_f_next, b_active_next, log_b_next

    [f_active, log_f_probs, b_active, log_b_probs], _ = theano.scan(
        step, sequences=[L, L[::-1, ::-1]], outputs_info=[np.int32(1), log_first, np.int32(1), log_first])

    idxs = T.arange(L.shape[1]).dimshuffle('x', 0)
    mask = (idxs < f_active.dimshuffle(0, 'x')) & (idxs < b_active.dimshuffle(0, 'x'))[::-1, ::-1]
    log_probs = log_f_probs + log_b_probs[::-1, ::-1] - L
    return log_probs, mask 

def _project_im_rois(im_rois, scales):
    """Project image RoIs into the image pyramid built by _get_image_blob.
    Arguments:
        im_rois (ndarray): R x 4 matrix of RoIs in original image coordinates
        scales (list): scale factors as returned by _get_image_blob
    Returns:
        rois (ndarray): R x 4 matrix of projected RoI coordinates
        levels (list): image pyramid levels used by each projected RoI
    """
    im_rois = im_rois.astype(np.float, copy=False)

    if len(scales) > 1:
        widths = im_rois[:, 2] - im_rois[:, 0] + 1
        heights = im_rois[:, 3] - im_rois[:, 1] + 1
        areas = widths * heights
        scaled_areas = areas[:, np.newaxis] * (scales[np.newaxis, :] ** 2)
        diff_areas = np.abs(scaled_areas - 224 * 224)
        levels = diff_areas.argmin(axis=1)[:, np.newaxis]
    else:
        levels = np.zeros((im_rois.shape[0], 1), dtype=np.int)

    rois = im_rois * scales[levels]

    return rois, levels 

def setup_buffer(width, height):
    """Set up the internal pixel buffer.

    :param width: width of buffer, ideally in multiples of 16
    :param height: height of buffer, ideally in multiples of 16

    """
    global _buffer_width, _buffer_height, _buf

    _buffer_width = width
    _buffer_height = height
    _buf = numpy.zeros((_buffer_width, _buffer_height, 3), dtype=int) 

def compute_mfcc(audio, **kwargs):
    """
    Compute the MFCC for a given audio waveform. This is
    identical to how DeepSpeech does it, but does it all in
    TensorFlow so that we can differentiate through it.
    """

    batch_size, size = audio.get_shape().as_list()
    audio = tf.cast(audio, tf.float32)

    # 1. Pre-emphasizer, a high-pass filter
    audio = tf.concat((audio[:, :1], audio[:, 1:] - 0.97*audio[:, :-1], np.zeros((batch_size,1000),dtype=np.float32)), 1)

    # 2. windowing into frames of 320 samples, overlapping
    windowed = tf.stack([audio[:, i:i+400] for i in range(0,size-320,160)],1)

    # 3. Take the FFT to convert to frequency space
    ffted = tf.spectral.rfft(windowed, [512])
    ffted = 1.0 / 512 * tf.square(tf.abs(ffted))

    # 4. Compute the Mel windowing of the FFT
    energy = tf.reduce_sum(ffted,axis=2)+1e-30
    filters = np.load("filterbanks.npy").T
    feat = tf.matmul(ffted, np.array([filters]*batch_size,dtype=np.float32))+1e-30

    # 5. Take the DCT again, because why not
    feat = tf.log(feat)
    feat = tf.spectral.dct(feat, type=2, norm='ortho')[:,:,:26]

    # 6. Amplify high frequencies for some reason
    _,nframes,ncoeff = feat.get_shape().as_list()
    n = np.arange(ncoeff)
    lift = 1 + (22/2.)*np.sin(np.pi*n/22)
    feat = lift*feat
    width = feat.get_shape().as_list()[1]

    # 7. And now stick the energy next to the features
    feat = tf.concat((tf.reshape(tf.log(energy),(-1,width,1)), feat[:, :, 1:]), axis=2)
    
    return feat 

def get_logits(new_input, length, first=[]):
    """
    Compute the logits for a given waveform.

    First, preprocess with the TF version of MFC above,
    and then call DeepSpeech on the features.
    """
    # new_input = tf.Print(new_input, [tf.shape(new_input)])

    # We need to init DeepSpeech the first time we're called
    if first == []:
        first.append(False)
        # Okay, so this is ugly again.
        # We just want it to not crash.
        tf.app.flags.FLAGS.alphabet_config_path = "DeepSpeech/data/alphabet.txt"
        DeepSpeech.initialize_globals()
        print('initialized deepspeech globals')

    batch_size = new_input.get_shape()[0]

    # 1. Compute the MFCCs for the input audio
    # (this is differentable with our implementation above)
    empty_context = np.zeros((batch_size, 9, 26), dtype=np.float32)
    new_input_to_mfcc = compute_mfcc(new_input)[:, ::2]
    features = tf.concat((empty_context, new_input_to_mfcc, empty_context), 1)

    # 2. We get to see 9 frames at a time to make our decision,
    # so concatenate them together.
    features = tf.reshape(features, [new_input.get_shape()[0], -1])
    features = tf.stack([features[:, i:i+19*26] for i in range(0,features.shape[1]-19*26+1,26)],1)
    features = tf.reshape(features, [batch_size, -1, 19*26])

    # 3. Whiten the data
    mean, var = tf.nn.moments(features, axes=[0,1,2])
    features = (features-mean)/(var**.5)

    # 4. Finally we process it with DeepSpeech
    logits = DeepSpeech.BiRNN(features, length, [0]*10)

    return logits 

def evaluate(self, points):
        points = atleast_2d(points)

        d, m = points.shape
        if d != self.d:
            if d == 1 and m == self.d:
                # points was passed in as a row vector
                points = reshape(points, (self.d, 1))
                m = 1
            else:
                msg = "points have dimension %s, dataset has dimension %s" % (d,
                    self.d)
                raise ValueError(msg)

        result = zeros((m,), dtype=np.float)

        if m >= self.n:
            # there are more points than data, so loop over data
            for i in range(self.n):
                diff = self.dataset[:, i, newaxis] - points
                tdiff = dot(self.inv_cov, diff)
                energy = sum(diff*tdiff,axis=0) / 2.0
                result = result + exp(-energy)
        else:
            # loop over points
            for i in range(m):
                diff = self.dataset - points[:, i, newaxis]
                tdiff = dot(self.inv_cov, diff)
                energy = sum(diff * tdiff, axis=0) / 2.0
                result[i] = sum(exp(-energy), axis=0)

        result = result / self._norm_factor

        return result 

def one_hot(y, fill_k=False, one_not=False):
    """Map to one-hot encoding."""
    # Check labels
    labels = np.unique(y)

    # Number of classes
    K = len(labels)

    # Number of samples
    N = y.shape[0]

    # Preallocate array
    if one_not:
        Y = -np.ones((N, K))
    else:
        Y = np.zeros((N, K))

    # Set k-th column to 1 for n-th sample
    for n in range(N):

        # Map current class to index label
        y_n = (y[n] == labels)

        if fill_k:
            Y[n, y_n] = y_n
        else:
            Y[n, y_n] = 1

    return Y, labels 

def psi(self, X, theta, w, K=2):
        """
        Compute psi function.

        Parameters
        ----------
        X : array
            data set (N samples by D features)
        theta : array
            classifier parameters (D features by 1)
        w : array
            importance-weights (N samples by 1)
        K : int
            number of classes (def: 2)

        Returns
        -------
        psi : array
            array with psi function values (N samples by K classes)

        """
        # Number of samples
        N = X.shape[0]

        # Preallocate psi array
        psi = np.zeros((N, K))

        # Loop over classes
        for k in range(K):
            # Compute feature statistics
            Xk = self.feature_stats(X, k*np.ones((N, 1)))

            # Compute psi function
            psi[:, k] = (w*np.dot(Xk, theta))[:, 0]

        return psi 

def posterior(self, psi):
        """
        Class-posterior estimation.

        Parameters
        ----------
        psi : array
            weighted data-classifier output (N samples by K classes)

        Returns
        -------
        pyx : array
            class-posterior estimation (N samples by K classes)

        """
        # Data shape
        N, K = psi.shape

        # Preallocate array
        pyx = np.zeros((N, K))

        # Subtract maximum value for numerical stability
        psi = (psi.T - np.max(psi, axis=1).T).T

        # Loop over classes
        for k in range(K):

            # Estimate posterior p^(Y=y | x_i)
            pyx[:, k] = np.exp(psi[:, k]) / np.sum(np.exp(psi), axis=1)

        return pyx 

def test_fit_semi():
    """Test for fitting the model."""
    X = rnd.randn(10, 2)
    y = np.hstack((np.zeros((5,)), np.ones((5,))))
    Z = rnd.randn(10, 2) + 1
    u = np.array([[0, 0], [9, 1]])
    clf = SemiSubspaceAlignedClassifier()
    clf.fit(X, y, Z, u)
    assert clf.is_trained 

def test_predict_semi():
    """Test for making predictions."""
    X = rnd.randn(10, 2)
    y = np.hstack((np.zeros((5,)), np.ones((5,))))
    Z = rnd.randn(10, 2) + 1
    u = np.array([[0, 0], [9, 1]])
    clf = SemiSubspaceAlignedClassifier()
    clf.fit(X, y, Z, u)
    u_pred = clf.predict(Z)
    labels = np.unique(y)
    assert len(np.setdiff1d(np.unique(u_pred), labels)) == 0 

def test_fit():
    """Test for fitting the model."""
    X = rnd.randn(10, 2)
    y = np.hstack((np.zeros((5,)), np.ones((5,))))
    Z = rnd.randn(10, 2) + 1
    clf = RobustBiasAwareClassifier()
    clf.fit(X, y, Z)
    assert clf.is_trained 

def test_predict():
    """Test for making predictions."""
    X = rnd.randn(10, 2)
    y = np.hstack((np.zeros((5,)), np.ones((5,))))
    Z = rnd.randn(10, 2) + 1
    clf = RobustBiasAwareClassifier()
    clf.fit(X, y, Z)
    u_pred = clf.predict(Z)
    labels = np.unique(y)
    assert len(np.setdiff1d(np.unique(u_pred), labels)) == 0 

def test_fit():
    """Test for fitting the model."""
    X = np.vstack((rnd.randn(5, 2), rnd.randn(5, 2)+1))
    y = np.hstack((np.zeros((5,)), np.ones((5,))))
    Z = np.vstack((rnd.randn(5, 2)-1, rnd.randn(5, 2)+2))
    clf = TargetContrastivePessimisticClassifier(l2=0.1)
    clf.fit(X, y, Z)
    assert clf.is_trained 

def test_init():
    """Test for object type."""
    clf = StructuralCorrespondenceClassifier()
    assert type(clf) == StructuralCorrespondenceClassifier
    assert not clf.is_trained


# def test_fit():
#     """Test for fitting the model."""
#     X = np.vstack((rnd.randn(5, 2), rnd.randn(5, 2)+1))
#     y = np.hstack((np.zeros((5,)), np.ones((5,))))
#     Z = np.vstack((rnd.randn(5, 2)-1, rnd.randn(5, 2)+2))
#     clf = StructuralCorrespondenceClassifier(l2=1.0)
#     clf.fit(X, y, Z)
#     assert clf.is_trained


# def test_predict():
#     """Test for making predictions."""
#     X = np.vstack((rnd.randn(5, 2), rnd.randn(5, 2)+1))
#     y = np.hstack((np.zeros((5,)), np.ones((5,))))
#     Z = np.vstack((rnd.randn(5, 2)-1, rnd.randn(5, 2)+2))
#     clf = StructuralCorrespondenceClassifier(l2=1.0)
#     clf.fit(X, y, Z)
#     u_pred = clf.predict(Z)
#     labels = np.unique(y)
#     assert len(np.setdiff1d(np.unique(u_pred), labels)) == 0