Python numpy.require函数代码示例

  def read_wfsx(self, fname, **kw):
    """ An occasional reading of the SIESTA's .WFSX file """
    from pyscf.nao.m_siesta_wfsx import siesta_wfsx_c
    from pyscf.nao.m_siesta2blanko_denvec import _siesta2blanko_denvec
    from pyscf.nao.m_fermi_dirac import fermi_dirac_occupations

    self.wfsx = siesta_wfsx_c(fname=fname, **kw)
    
    assert self.nkpoints == self.wfsx.nkpoints
    assert self.norbs == self.wfsx.norbs 
    assert self.nspin == self.wfsx.nspin
    orb2m = self.get_orb2m()
    for k in range(self.nkpoints):
      for s in range(self.nspin):
        for n in range(self.norbs):
          _siesta2blanko_denvec(orb2m, self.wfsx.x[k,s,n,:,:])

    self.mo_coeff = np.require(self.wfsx.x, dtype=self.dtype, requirements='CW')
    self.mo_energy = np.require(self.wfsx.ksn2e, dtype=self.dtype, requirements='CW')
    self.telec = kw['telec'] if 'telec' in kw else self.hsx.telec
    self.nelec = kw['nelec'] if 'nelec' in kw else self.hsx.nelec
    self.fermi_energy = kw['fermi_energy'] if 'fermi_energy' in kw else self.fermi_energy
    ksn2fd = fermi_dirac_occupations(self.telec, self.mo_energy, self.fermi_energy)
    self.mo_occ = (3-self.nspin)*ksn2fd
    return self

    def check_distance(self, parent_ix, coords):
        '''Check to ensure that the distance between the coordinates `coords`
        and the parent_ix is less than the distance to any other center in the parent level'''
        if parent_ix is None:
            return True

        try:
            passed_coord_dtype = coords.dtype
        except AttributeError:
            coords = np.require(coords, dtype=coord_dtype)
        else:
            if passed_coord_dtype != coord_dtype:
                coords = np.require(coords, dtype=coord_dtype)

        coords = coords.reshape((1, -1))

        assert len(coords) == 1
        parent_level = self.bin_graph.node[parent_ix]['level']
        level_indices = self.level_indices[parent_level]
        parent_centers = self.fetch_centers(level_indices)

        mask = np.ones((1,), dtype=np.bool_)
        output = np.empty((1,), dtype=index_dtype)
        min_dist = np.empty((1,), dtype=coord_dtype)
        self._assign_level(coords, parent_centers, mask, output, min_dist)

        res = output[0] == level_indices.index(parent_ix)

        return res

 def compute_v_without_derivs(self, Xs, Yinvs, Ts):
     #Turn the parts of omega into gpuarrays
     Xs = np.require(Xs, dtype = np.double, requirements=['A', 'W', 'O', 'C'])
     Yinvs = np.require(Yinvs, dtype = np.double, requirements=['A', 'W', 'O', 'C'])
     Ts = np.require(Ts, dtype = np.double, requirements=['A', 'W', 'O', 'C'])
     Xs_d = gpuarray.to_gpu(Xs)
     Yinvs_d = gpuarray.to_gpu(Yinvs)
     Ts_d = gpuarray.to_gpu(Ts)
     #Determine N = the number of integer points to sum over
     #          K = the number of different omegas to compute the function at
     N = self.Sd.size/self.g
     K = Xs.size/(self.g**2)
     #Create room on the gpu for the real and imaginary finite sum calculations
     fsum_reald = gpuarray.zeros(N*K, dtype=np.double)
     fsum_imagd = gpuarray.zeros(N*K, dtype=np.double)
     #Turn all scalars into numpy data types
     Nd = np.int32(N)
     Kd = np.int32(K)
     gd = np.int32(self.g)
     blocksize = (self.tilewidth, self.tileheight, 1)
     gridsize = (N//self.tilewidth + 1, K//self.tileheight + 1, 1)
     self.finite_sum_without_derivs(fsum_reald, fsum_imagd, Xs_d, Yinvs_d, Ts_d,
                                    self.Sd, gd, Nd, Kd,
                                    block = blocksize,
                                    grid = gridsize)
     cuda.Context.synchronize()
     fsums_real = self.sum_reduction(fsum_reald, N, K, Kd, Nd)
     fsums_imag = self.sum_reduction(fsum_imagd, N, K, Kd, Nd)
     return fsums_real + 1.0j*fsums_imag

    def load_data(self, model_data, callback=None):
        t_start = time.time()

        vertices, normals = model_data
        # convert python lists to numpy arrays for constructing vbos
        self.vertices = numpy.require(vertices, 'f')
        self.normals  = numpy.require(normals, 'f')

        self.scaling_factor = 1.0
        self.rotation_angle = {
            self.AXIS_X: 0.0,
            self.AXIS_Y: 0.0,
            self.AXIS_Z: 0.0,
        }

        self.mat_specular   = (1.0, 1.0, 1.0, 1.0)
        self.mat_shininess  = 50.0
        self.light_position = (20.0, 20.0, 20.0)

        self.initialized = False

        t_end = time.time()

        logging.info('Initialized STL model in %.2f seconds' % (t_end - t_start))
        logging.info('Vertex count: %d' % len(self.vertices))

def setdiff_rows(A, B, return_index=False):
    """
    Similar to MATLAB's setdiff(A, B, 'rows'), this returns C, I
    where C are the row of A that are not in B and I satisfies
    C = A[I,:].

    Returns I if return_index is True.
    """
    A = np.require(A, requirements='C')
    B = np.require(B, requirements='C')

    assert A.ndim == 2, "array must be 2-dim'l"
    assert B.ndim == 2, "array must be 2-dim'l"
    assert A.shape[1] == B.shape[1], \
           "arrays must have the same number of columns"
    assert A.dtype == B.dtype, \
           "arrays must have the same data type"

    # NumPy provides setdiff1d, which operates only on one dimensional
    # arrays. To make the array one-dimensional, we interpret each row
    # as being a string of characters of the appropriate length.
    orig_dtype = A.dtype
    ncolumns = A.shape[1]
    dtype = np.dtype((np.character, orig_dtype.itemsize*ncolumns))
    C = np.setdiff1d(A.view(dtype), B.view(dtype)) \
        .view(A.dtype) \
        .reshape((-1, ncolumns), order='C')
    if return_index:
        raise NotImplementedError
    else:
        return C

    def get_next_batch(self):
        self.advance_batch()

        epoch = self.curr_epoch        
        batchnum = self.curr_batchnum
        
        datadic = leveldb.LevelDB(self.data_dir + '/batch-%d' % batchnum)
        img_raw = []
        label_raw = []
        for k, pickled in datadic.RangeIter():
          imgdata = cPickle.loads(pickled)
          img_raw.append(Image.open(c.StringIO(imgdata['data'])))
          label_raw.append(imgdata['label'])
        
        labels = n.array(label_raw)
        images = n.ndarray((len(img_raw), 64 * 64 * 3), dtype=n.single)
        for idx, jpegdata in enumerate(img_raw):
          images[idx] = n.array(img_raw)
     
        print labels.shape
        print images.shape

        images = n.require(images, dtype=n.single, requirements='C')
        labels = labels.reshape((1, images.shape[1]))
        labels = n.require(labels, dtype=n.single, requirements='C')

        return epoch, batchnum, [images, labels]

def bench():
    size    = 256
    nframes = 4000
    lag     = 24

    X       = N.random.randn(nframes, size)
    X       = N.require(X, requirements = 'C')

    niter   = 10

    # Contiguous
    print "Running optimized with ctypes"
    def contig(*args, **kargs):
        return autocorr_oneside_nofft(*args, **kargs)
    for i in range(niter):
        Yt  = contig(X, lag, axis = 1)

    Yr  = _autocorr_oneside_nofft_py(X, lag, axis = 1)
    N.testing.assert_array_almost_equal(Yt, Yr, 10)

    # Non contiguous
    print "Running optimized with ctypes (non contiguous)"
    def ncontig(*args, **kargs):
        return autocorr_oneside_nofft(*args, **kargs)
    X       = N.require(X, requirements = 'F')
    for i in range(niter):
        Yt  = ncontig(X, lag, axis = 1)

    Yr  = _autocorr_oneside_nofft_py(X, lag, axis = 1)
    N.testing.assert_array_almost_equal(Yt, Yr, 10)

    print "Benchmark func done"

def make_predictions(net, data, labels, num_classes):
    data = np.require(data, requirements='C')
    labels = np.require(labels, requirements='C')

    preds = np.zeros((data.shape[1], num_classes), dtype=np.single)
    softmax_idx = net.get_layer_idx('probs', check_type='softmax')

    t0 = time.time()
    net.libmodel.startFeatureWriter(
        [data, labels, preds], softmax_idx)
    net.finish_batch()
    print "Predicted %s cases in %.2f seconds." % (
        labels.shape[1], time.time() - t0)

    if net.multiview_test:
        #  We have to deal with num_samples * num_views
        #  predictions.
        num_views = net.test_data_provider.num_views
        num_samples = labels.shape[1] / num_views
        split_sections = range(
            num_samples, num_samples * num_views, num_samples)
        preds = np.split(preds, split_sections, axis=0)
        labels = np.split(labels, split_sections, axis=1)
        preds = reduce(np.add, preds)
        labels = labels[0]

    return preds, labels

    def __init__(self, data_dir, 
            img_size, num_colors,  # options i've add to cifar data provider
            batch_range=None, 
            init_epoch=1, init_batchnum=None, dp_params=None, test=False):
        LabeledMemoryDataProvider.__init__(self, data_dir, batch_range, init_epoch, init_batchnum, dp_params, test)

        self.num_colors = num_colors
        self.img_size = img_size
        self.border_size = dp_params['crop_border']
        self.inner_size = self.img_size - self.border_size*2
        self.multiview = dp_params['multiview_test'] and test

        self.img_flip = dp_params['img_flip']
        if self.img_flip:
            self.num_views = 5*2
        else :
            self.num_views = 5;
        self.data_mult = self.num_views if self.multiview else 1
        
        for d in self.data_dic:
            d['data'] = n.require(d['data'], requirements='C')
            d['labels'] = n.require(n.tile(d['labels'].reshape((1, d['data'].shape[1])), (1, self.data_mult)), requirements='C')
        
        self.cropped_data = [n.zeros((self.get_data_dims(), self.data_dic[0]['data'].shape[1]*self.data_mult), dtype=n.single) for x in xrange(2)]

        self.batches_generated = 0
        self.data_mean = self.batch_meta['data_mean'].reshape((self.num_colors,self.img_size,self.img_size))[:,self.border_size:self.border_size+self.inner_size,self.border_size:self.border_size+self.inner_size].reshape((self.get_data_dims(), 1))

def _lpc2_py(signal, order, axis = -1):
    """python implementation of lpc for rank 2., Do not use, for testing purpose only"""
    if signal.ndim > 2:
        raise NotImplemented("only for rank <=2")
    
    if signal.ndim < 2:
        return lpc(_N.require(signal, requirements = 'C'), order)

    # For each array of direction axis, compute levinson durbin
    if axis  % 2 == 0:
        # Prepare output arrays
        coeff   = _N.zeros((order+1, signal.shape[1]), signal.dtype)
        kcoeff  = _N.zeros((order, signal.shape[1]), signal.dtype)
        err     = _N.zeros(signal.shape[1], signal.dtype)
        for i in range(signal.shape[1]):
            coeff[:, i], err[i], kcoeff[:, i] = \
                    lpc(_N.require(signal[:, i], requirements = 'C'), order)
    elif axis % 2 == 1:
        # Prepare output arrays
        coeff   = _N.zeros((signal.shape[0], order+1), signal.dtype)
        kcoeff  = _N.zeros((signal.shape[0], order), signal.dtype)
        err     = _N.zeros(signal.shape[0], signal.dtype)
        for i in range(signal.shape[0]):
            coeff[i], err[i], kcoeff[i] = \
                lpc(_N.require(signal[i], requirements = 'C'), order)
    else:
        raise RuntimeError("this should not happen, please fill a bug")

    return coeff, err, kcoeff

    def print_predictions(self):
        data = self.get_next_batch(train=False)[2] # get a test batch
        num_classes = self.test_data_provider.get_num_classes()
        softmax_idx = self.get_layer_idx('probs', check_type='softmax')
        NUM_IMGS = 1
        NUM_TOP_CLASSES = min(num_classes, 4) # show this many top labels
        label_names = self.test_data_provider.batch_meta['label_names']
        preds = n.zeros((NUM_IMGS, num_classes), dtype=n.single)
        rand_idx = nr.randint(0, data[0].shape[1], NUM_IMGS)
        data[0] = n.require(data[0][:,rand_idx], requirements='C')
        data[1] = n.require(data[1][:,rand_idx], requirements='C')
        data += [preds]

        # Run the model
        self.libmodel.startFeatureWriter(data, softmax_idx)
        self.finish_batch()

        data[0] = self.test_data_provider.get_plottable_data(data[0])
        img_idx = 0
        true_label = int(data[1][0,img_idx])

        img_labels = sorted(zip(preds[img_idx,:], label_names), key=lambda x: x[0])[-NUM_TOP_CLASSES:]
        print "true_label=%s" % (label_names[true_label])
        for l in img_labels:
          print "l=%s" % (str(l))

        binary_checkpoint_file = "binary_%d.%d.ntwk" % (self.epoch, self.batchnum)
        self.save_as_binary(binary_checkpoint_file)

  def get_next_batch(self):
    self.get_next_index()
    epoch = self.curr_epoch
    filename = os.path.join(self.data_dir, 'data_batch_%d' % (self.curr_batch))
    start = time.time()
    if os.path.isdir(filename):
      images = []
      labels = []

      for sub_filename in os.listdir(filename):
        path = os.path.join(filename, sub_filename)
        data = util.load(path)
        images.extend(data['data'])
        labels.extend(data['labels'])
      data['data'] = images
      data['labels'] = labels
    else:
      data = util.load(filename)
    data = self.__multigpu_seg(data)
    images = data['data']

    cropped = np.ndarray((3, self.inner_size, self.inner_size, len(images) * self.num_view), dtype = np.float32)
    self.__decode_trim_images2(images, cropped)

    cropped = garray.reshape_last(cropped) - self.data_mean
    cropped = np.require(cropped.reshape((3, self.inner_size, self.inner_size, len(images) * self.num_view)), dtype = np.single, requirements='C')

    labels = np.array(labels)
    labels = labels.reshape(labels.size, )
    labels = np.require(labels, dtype=np.single, requirements='C')
    return BatchData(cropped, labels, epoch)

    def get_next_batch(self):
        epoch, batchnum, d = LabeledDataProvider.get_next_batch(self)
	#print(datadic)
        # This converts the data matrix to single precision and makes sure that it is C-ordered
        d['data'] = n.require((d['data'].transpose()), dtype=n.single, requirements='C')
        d['labels'] = n.require(d['labels'].reshape((1, d['data'].shape[1])), dtype=n.single, requirements='C')
        return epoch, batchnum, [d['data'], d['labels']]

def slit_uniform_psf(n, seeing, mu_x, mu_y, tau_0, slit_width, slit_height, plot=False):
    """Returns x- and y- coordinate arrays of a 2D random uniformly distributed
    circle.

    Parameters
    ----------
    n : int
        Size of coordinate arrays.
    seeing: double
        Seeing of source psf in arcseconds.
    mu_x : double
        Center of PSF in x-coords.
    mu_y : double
        Center of PSF in y-coords.
    tau_0 : double
        Rotation about z-axis (tilt).
    slit_width : double
        Width of slit in arcseconds.
    slit_height : double
        Height of slit in arcseconds.

    Returns
    -------
    slit_x : array_like
        Array of x-coordinates.
    slit_y : array_like
        Array of y-coordinates.

    """
    desc = "Source psf: uniform, mux=%.2f muy=%.2f seeing=%.2f arcsec" % (mu_x, mu_y, seeing)
    log.info(desc)
    # initialize output arrays to send to c function
    slit_x = np.empty(n, dtype=np.float64)
    slit_y = np.empty(n, dtype=np.float64)
    slit_x = np.require(slit_x, requirements=ci.req_out, dtype=np.float64)
    slit_y = np.require(slit_y, requirements=ci.req_out, dtype=np.float64)
    func = ci.slitc.slit_uniform_psf
    func.argtypes = [
        ct.c_int,             # n
        ct.c_double,          # seeing
        ct.c_double,          # mu_x
        ct.c_double,          # mu_y
        ct.c_double,          # tau_0
        ct.c_double,          # slit_width
        ct.c_double,          # slit_height
        ci.array_1d_double,   # slit_x
        ci.array_1d_double]   # slit_y
    func.restype = None
    log.info("Slit Rejection Sampling: %s rays...", n)
    func(n, seeing, mu_x, mu_y, tau_0, slit_width, slit_height, slit_x, slit_y)
    # preview slit
    if plot:
        log.info("Opening preview plot of 2D uniformly random psf.")
        import matplotlib.pylab as plt
        fig = plt.figure()
        ax = fig.add_subplot(111)#, aspect='equal')
        ax.scatter(slit_x, slit_y, s=20, edgecolor=None)
        plt.title("0D Point Source PSF")
        plt.show()
    return slit_x, slit_y

 def comp_apair_pp_libint(self, a1,a2):
   """ Get's the vertex coefficient and conversion coefficients for a pair of atoms given by their atom indices """
   from operator import mul
   from pyscf.nao.m_prod_biloc import prod_biloc_c
   if not hasattr(self, 'sv_pbloc_data') : raise RuntimeError('.sv_pbloc_data is absent')
   assert a1>=0
   assert a2>=0
   
   t1 = timer()
   sv = self.sv
   aos = self.sv.ao_log
   sp12 = np.require( np.array([sv.atom2sp[a] for a in (a1,a2)], dtype=c_int64), requirements='C')
   rc12 = np.require( np.array([sv.atom2coord[a,:] for a in (a1,a2)]), requirements='C')
   icc2a = np.require( np.array(self.ls_contributing(a1,a2), dtype=c_int64), requirements='C')
   npmx = aos.sp2norbs[sv.atom2sp[a1]]*aos.sp2norbs[sv.atom2sp[a2]]
   npac = sum([self.prod_log.sp2norbs[sv.atom2sp[ia]] for ia in icc2a ])
   nout = c_int64(npmx**2+npmx*npac+10)
   dout = np.require( zeros(nout.value), requirements='CW')
   
   libnao.vrtx_cc_apair( sp12.ctypes.data_as(POINTER(c_int64)), rc12.ctypes.data_as(POINTER(c_double)), icc2a.ctypes.data_as(POINTER(c_int64)), c_int64(len(icc2a)), dout.ctypes.data_as(POINTER(c_double)), nout )    
   if dout[0]<1: return None
   
   nnn = np.array(dout[0:3], dtype=int)
   nnc = np.array([dout[8],dout[7]], dtype=int)
   ncc = int(dout[9])
   if ncc!=len(icc2a): raise RuntimeError('ncc!=len(icc2a)')
   s = 10; f=s+np.prod(nnn); vrtx  = dout[s:f].reshape(nnn)
   s = f;  f=s+np.prod(nnc); ccoe  = dout[s:f].reshape(nnc)
   icc2s = np.zeros(len(icc2a)+1, dtype=np.int64)
   for icc,a in enumerate(icc2a): icc2s[icc+1] = icc2s[icc] + self.prod_log.sp2norbs[sv.atom2sp[a]]
   pbiloc = prod_biloc_c(atoms=array([a2,a1]),vrtx=vrtx,cc2a=icc2a,cc2s=icc2s,cc=ccoe)
   
   return pbiloc