Python numpy.ceil函数代码示例

    def __init__(self, dataset_size, batch_size, num_batches=None, rng=None):
        self._rng = make_np_rng(rng, which_method=["random_integers",
                                                   "shuffle"])
        assert num_batches is None or num_batches >= 0
        self._dataset_size = dataset_size
        if batch_size is None:
            if num_batches is not None:
                batch_size = int(np.ceil(self._dataset_size / num_batches))
            else:
                raise ValueError("need one of batch_size, num_batches "
                                 "for sequential batch iteration")
        elif batch_size is not None:
            if num_batches is not None:
                max_num_batches = np.ceil(self._dataset_size / batch_size)
                if num_batches > max_num_batches:
                    raise ValueError("dataset of %d examples can only provide "
                                     "%d batches with batch_size %d, but %d "
                                     "batches were requested" %
                                     (self._dataset_size, max_num_batches,
                                      batch_size, num_batches))
            else:
                num_batches = np.ceil(self._dataset_size / batch_size)

        self._batch_size = batch_size
        self._num_batches = int(num_batches)
        self._next_batch_no = 0
        self._idx = 0
        self._batch_order = list(range(self._num_batches))
        self._rng.shuffle(self._batch_order)

def max_lm(baselines, wavelengths, uwidth, vwidth=0.0):
    """Get the maximum (l,m) that a baseline is sensitive to.

    Parameters
    ----------
    baselines : np.ndarray
        An array of baselines.
    wavelengths : np.ndarray
        An array of wavelengths.
    uwidth : np.ndarray
        Width of the receiver in the u-direction.
    vwidth : np.ndarray
        Width of the receiver in the v-direction.

    Returns
    -------
    lmax, mmax : array_like
    """

    umax = (np.abs(baselines[:, 0]) + uwidth) / wavelengths
    vmax = (np.abs(baselines[:, 1]) + vwidth) / wavelengths

    mmax = np.ceil(2 * np.pi * umax).astype(np.int64)
    lmax = np.ceil((mmax**2 + (2*np.pi*vmax)**2)**0.5).astype(np.int64)

    return lmax, mmax

def _filter_ridge_lines(cwt, ridge_lines, window_size=None, min_length=None,
                       min_snr=1, noise_perc=10):
    """
    Filter ridge lines according to prescribed criteria. Intended
    to be used for finding relative maxima.

    Parameters
    -------------
    cwt : 2-D ndarray
        Continuous wavelet transform from which
        the ridge_lines were defined
    ridge_lines: 1-D sequence
        Each element should contain 2 sequences, the rows and columns
        of the ridge line (respectively)
    window_size: int, optional
        Size of window to use to calculate noise floor.
        Default is `cwt`.shape[1]/20
    min_length: int, optional
        Minimum length a ridge line needs to be acceptable.
        Default is `cwt`.shape[0]/4, ie 1/4th the number of widths.
    min_snr: float, optional
        Minimum SNR ratio. Default 0. The signal is the value of
        the cwt matrix at the shortest length scale (`cwt`[0,loc]), the noise is
        the `noise_perc`th percentile of datapoints contained within
        a window of `window_size` around `cwt`[0,loc]
    noise_perc: float,optional
        When calculating the noise floor, percentile of data points
        examined below which to consider noise. Calculated using
        scipy.stats.scoreatpercentile.

    References
    ----------
    Bioinformatics (2006) 22 (17): 2059-2065. doi: 10.1093/bioinformatics/btl355
    http://bioinformatics.oxfordjournals.org/content/22/17/2059.long

    """
    num_points = cwt.shape[1]
    if min_length is None:
        min_length = np.ceil(cwt.shape[0] / 4)
    if window_size is None:
        window_size = np.ceil(num_points / 20)
    hf_window = window_size / 2

    #Filter based on SNR
    row_one = cwt[0, :]
    noises = np.zeros_like(row_one)
    for ind, val in enumerate(row_one):
        window = np.arange(max([ind - hf_window, 0]), min([ind + hf_window, num_points]))
        window = window.astype(int)
        noises[ind] = scoreatpercentile(row_one[window], per=noise_perc)

    def filt_func(line):
        if len(line[0]) < min_length:
            return False
        snr = abs(cwt[line[0][0], line[1][0]] / noises[line[1][0]])
        if snr < min_snr:
            return False
        return True

    return filter(filt_func, ridge_lines)

def setupFakePulsar(nodes=range(1, 9), fpgaclk=360e6, frqs=cfs, sideband=-1):
    n = np.arange(8)
    clk = fpgaclk
    if frqs is None:
        frqs = (
            18e9
            - (np.ceil(150e6 / (clk * 4 / 1024.0)) * clk * 4 / 1024.0)
            + ((clk * 2) * (2 * n + 1))
            - ((np.ceil(150e6 / (clk * 4 / 1024.0)) * clk * 4 / 1024.0) * n)
        )
    frqd = dict(zip(n + 1, frqs))
    esr = fpgaclk * 8  # effective sample rate

    pfb_rate = sideband * esr / (2 * 1024.0)
    for node in nodes:
        vsd[node].setParams(
            EFSAMPFR=esr,
            NCHAN=1024,
            EXPOSURE=1e-6,
            SUB0FREQ=frqd[node],
            OBSFREQ=frqd[node],
            CHAN_BW=pfb_rate,
            FPGACLK=fpgaclk,
        )  # exposure should be ~0 to get every single spectrum

    pass

 def affine_grid(self,Hz,rhoz,Lam):
     """
     Get data on regular spatial grid
     """
     #First find dimensionless density params
     Om0 = 8*pi*rhoz[0]/(3*Hz[0]**2)
     OL0 = Lam/(3*Hz[0]**2)
     Ok0 = 1-Om0-OL0
     #Get t0
     t0 = self.get_age(Om0,Ok0,OL0,Hz[0])
     #Set affine parameter vals        
     dvo = uvs(self.z,1/(self.uz**2*Hz),k=3,s=0.0)
     vzo = dvo.antiderivative()
     vz = vzo(self.z)
     vz[0] = 0.0
     #Compute grid sizes that gives num error od err
     NJ = int(ceil(vz[-1]/sqrt(self.err) + 1))
     NI = int(ceil(3.0*(NJ - 1)*(t0 - self.tmin)/vz[-1] + 1))
     #Get functions on regular grid
     v = linspace(0,vz[-1],NJ)
     delv = (v[-1] - v[0])/(NJ-1)
     if delv > sqrt(self.err):
         print 'delv > sqrt(err)'
     Ho = uvs(vz,Hz,s=0.0,k=3)
     H = Ho(v)
     rhoo = uvs(vz,rhoz,s=0.0,k=3)
     rho = rhoo(v)
     uo = uvs(vz,self.uz,s=0.0,k=3)
     u = uo(v)
     u[0] = 1.0
     return v,vzo,H,rho,u,NJ,NI,delv,Om0,OL0,Ok0,t0

def qwtCanvasClip(canvas, canvasRect):
    x1 = np.ceil(canvasRect.left())
    x2 = np.floor(canvasRect.right())
    y1 = np.ceil(canvasRect.top())
    y2 = np.floor(canvasRect.bottom())
    r = QRect(x1, y1, x2-x1-1, y2-y1-1)
    return canvas.borderPath(r)

def each_SASA(sasas,sort_keys,kcat_cut=30,plot=True,meta=None):
    num_sims=len(sort_keys)
    labels=label_maker(sasas,kcat_cut=kcat_cut,name_list=sort_keys)
    base_size = 20.
    wide_factor = 1.5
    color_dict={True:'r', False:'g', 'maybe':'b', 'wt':'m'}
    ncols = int(np.ceil(np.sqrt(num_sims)))
    nrows = int(np.ceil(float(num_sims)/ncols))
    fig = plt.figure(figsize=(base_size,base_size*(float(nrows)/ncols)/wide_factor))
    gs = gridspec.GridSpec(nrows,ncols,hspace=0.65,wspace=0.8)
    axes = [plt.subplot(gs[plot_num/ncols,plot_num%ncols]) for plot_num in range(num_sims)]
    max_SASA=0;ts_scaling=0.02
    for plot_num,ax in enumerate(axes):
        SASA=sasas[sort_keys[plot_num]]
        ts_sasa=np.sum([SASA['base_sasa'][res]['sasa_vals'] for res in SASA['base_sasa']],axis=0)
        name=SASA['name'];activity=labels[plot_num]
        ts = np.array(range(len(ts_sasa)))*ts_scaling
        ax.plot(ts,ts_sasa,color=color_dict[activity])
        ax.set_title(name)
        ax.tick_params(axis='y',which='both',left='off',right='off',labelleft='on')
        ax.tick_params(axis='x',which='both',bottom='off',top='off',labelbottom='on')
        max_SASA=max(max_SASA,max(ts_sasa))

    min_SASA=0
    if meta:
        meta['kcat cut']=kcat_cut
        meta['max sasa']=max_sasa
        meta['ts scaling']=ts_scaling
    else: meta={'kcat cut':kcat_cut,'max sasa':max_SASA,'ts scaling':ts_scaling}
    for plot_num,ax in enumerate(axes):
        ax.set_ylim(min_SASA,max_SASA)
    if plot:
        plt.show(block=False)
    else: picturesave('fig.each-%s'%plotname,work.plotdir,backup=False,version=True,meta=meta)

    def return_unit_round_neighborhood(self, row, col, radius):
        """Return a list with (row, col, distance) of the units around a unit. This version uses a circle as radius, all the element inside the radius are taken as neighborood.

        @param row index of the unit
        @param col the column index of the unit
        @param radius the radius of the distance to consider
        """
        output_list = list()
        if(radius <= 0): output_list.append((row, col, 0)); return output_list #return empty if radius=0

        #Finding the square around the unit
        #with wide=radius using the ceil of radius
        row_range_min = row - int(np.ceil(radius))
        if(row_range_min < 0): row_range_min = 0
        row_range_max = row + int(np.ceil(radius))
        if(row_range_max >= self._matrix_size): row_range_max = self._matrix_size - 1
        col_range_min = col - int(np.ceil(radius))
        if(col_range_min < 0): col_range_min = 0
        col_range_max = col + int(np.ceil(radius))
        if(col_range_max >= self._matrix_size): col_range_max = self._matrix_size - 1

        for row_iter in range(row_range_min, row_range_max+1):
            for col_iter in range(col_range_min, col_range_max+1):
                #Finding the distances from the BMU
                col_distance = np.abs(col - col_iter)
                row_distance = np.abs(row - row_iter)
                #Pitagora's Theorem to estimate distance
                distance = np.sqrt( np.power(col_distance,2) + np.power(row_distance,2) )
                #Store the unit only if the distance is
                #less than the radius
                if(distance <= radius): output_list.append((row_iter, col_iter, distance))

        return output_list

    def init_log_binned_fx_buckets(self):
        # initializes the refex_log_binned_buckets with the vertical log bin values,
        # computed based on p and the number of vertices in the graph

        max_fx_value = np.ceil(np.log2(self.no_of_vertices) + self.TOLERANCE)  # fixing value of p = 0.5,
        # In our experiments, we found p = 0.5 to be a sensible choice:
        # with each bin containing the bottom half of the remaining nodes.
        log_binned_fx_keys = [value for value in xrange(0, int(max_fx_value))]

        fx_bucket_size = []
        starting_bucket_size = self.no_of_vertices

        for idx in np.arange(0.0, max_fx_value):
            starting_bucket_size *= self.p
            fx_bucket_size.append(int(np.ceil(starting_bucket_size)))

        total_slots_in_all_buckets = sum(fx_bucket_size)
        if total_slots_in_all_buckets > self.no_of_vertices:
            fx_bucket_size[0] -= (total_slots_in_all_buckets - self.no_of_vertices)

        log_binned_buckets_dict = dict(zip(log_binned_fx_keys, fx_bucket_size))

        for binned_value in sorted(log_binned_buckets_dict.keys()):
            for count in xrange(0, log_binned_buckets_dict[binned_value]):
                self.refex_log_binned_buckets.append(binned_value)

        if len(self.refex_log_binned_buckets) != self.no_of_vertices:
            raise Exception("Vertical binned bucket size not equal to the number of vertices!")

    def _drawGraticules(self,m,gd):
        par = np.arange(np.ceil(gd.ymin),np.floor(gd.ymax)+1,1.0)
        mer = np.arange(np.ceil(gd.xmin),np.floor(gd.xmax)+1,1.0)
        merdict = m.drawmeridians(mer,labels=[0,0,0,1],fontsize=10,
                                  linewidth=0.5,color='gray',zorder=GRATICULE_ZORDER)
        pardict = m.drawparallels(par,labels=[1,0,0,0],fontsize=10,
                                  linewidth=0.5,color='gray',zorder=GRATICULE_ZORDER)

        #loop over meridian and parallel dicts, change/increase font, draw ticks
        xticks = []
        for merkey,mervalue in merdict.items():
            merline,merlablist = mervalue
            merlabel = merlablist[0]
            merlabel.set_family('sans-serif')
            merlabel.set_fontsize(12.0)
            xticks.append(merline[0].get_xdata()[0])

        yticks = []
        for parkey,parvalue in pardict.items():
            parline,parlablist = parvalue
            parlabel = parlablist[0]
            parlabel.set_family('sans-serif')
            parlabel.set_fontsize(12.0)
            yticks.append(parline[0].get_ydata()[0])

        #plt.tick_params(axis='both',color='k',direction='in')
        plt.xticks(xticks,())
        plt.yticks(yticks,())
        m.ax.tick_params(direction='out')

def sample_size_necessary_under_cph(power, ratio_of_participants, p_exp, p_con,
                                    postulated_hazard_ratio, alpha=0.05):
    """
    This computes the sample size for needed power to compare two groups under a Cox
    Proportional Hazard model.

    References:
        https://cran.r-project.org/web/packages/powerSurvEpi/powerSurvEpi.pdf

    Parameters:
        power: power to detect the magnitude of the hazard ratio as small as that specified by postulated_hazard_ratio.
        ratio_of_participants: ratio of participants in experimental group over control group.
        p_exp: probability of failure in experimental group over period of study.
        p_con: probability of failure in control group over period of study
        postulated_hazard_ratio: the postulated hazard ratio
        alpha: type I error rate

    Returns:
        n_exp, n_con: the samples sizes need for the experiment and control group, respectively, to achieve desired power
    """
    z = lambda p: stats.norm.ppf(p)

    m = 1.0 / ratio_of_participants \
        * ((ratio_of_participants * postulated_hazard_ratio + 1.0) / (postulated_hazard_ratio - 1.0)) ** 2 \
        * (z(1. - alpha / 2.) + z(power)) ** 2

    n_exp = m * ratio_of_participants / (ratio_of_participants * p_exp + p_con)
    n_con = m / (ratio_of_participants * p_exp + p_con)

    return int(np.ceil(n_exp)), int(np.ceil(n_con))

def create_mask(Nx,Ny,frac,
                rmin = 0.5,
                rmax = 2):
    """
    create a mask Nx by Ny pixels
    frac: 0 <= frac <= 1: fraction of pixels to be covered
    """
    mask = numpy.ones((Nx,Ny))

    ncovered = 0
    goal = frac*Nx*Ny

    while ncovered < goal:
        x = Nx*numpy.random.random()
        y = Ny*numpy.random.random()
        r = rmin + numpy.random.random()*(rmax-rmin)
        
        xmin = max(0,int(numpy.floor(x-r)))
        xmax = min(Nx,int(numpy.ceil(x+r)))
        ymin = max(0,int(numpy.floor(y-r)))
        ymax = min(Ny,int(numpy.ceil(y+r)))

        for ix in range(xmin,xmax):
            for iy in range(ymin,ymax):
                if (x-ix)**2 + (y-iy)**2 < r**2:
                    ncovered += mask[ix,iy]
                    mask[ix,iy] = 0
    
    return mask

def dispims_color(M, border=0, bordercolor=[0.0, 0.0, 0.0], savePath=None, *imshow_args, **imshow_keyargs):
    """ Display an array of rgb images. 

    The input array is assumed to have the shape numimages x numpixelsY x numpixelsX x 3
    """
    bordercolor = numpy.array(bordercolor)[None, None, :]
    numimages = len(M)
    M = M.copy()
    for i in range(M.shape[0]):
        M[i] -= M[i].flatten().min()
        M[i] /= M[i].flatten().max()
    height, width, three = M[0].shape
    assert three == 3
    
    n0 = numpy.int(numpy.ceil(numpy.sqrt(numimages)))
    n1 = numpy.int(numpy.ceil(numpy.sqrt(numimages)))
    im = numpy.array(bordercolor)*numpy.ones(
                             ((height+border)*n1+border,(width+border)*n0+border, 1),dtype='<f8')
    for i in range(n0):
        for j in range(n1):
            if i*n1+j < numimages:
                im[j*(height+border)+border:(j+1)*(height+border)+border,
                   i*(width+border)+border:(i+1)*(width+border)+border,:] = numpy.concatenate((
                  numpy.concatenate((M[i*n1+j,:,:,:],
                         bordercolor*numpy.ones((height,border,3),dtype=float)), 1),
                  bordercolor*numpy.ones((border,width+border,3),dtype=float)
                  ), 0)
    imshow_keyargs["interpolation"]="nearest"
    pylab.imshow(im, *imshow_args, **imshow_keyargs)
    
    if savePath == None:
        pylab.show()
    else:
        pylab.savefig(savePath)

    def _scale_to_res(self):
        """Change self._A and _extent to render an image whose
        resolution is matched to the eventual rendering."""

        ax = self.axes
        ext = ax.transAxes.transform([1, 1]) - ax.transAxes.transform([0, 0])
        xlim, ylim = ax.get_xlim(), ax.get_ylim()
        dx, dy = xlim[1] - xlim[0], ylim[1] - ylim[0]

        y0 = max(self.miny, ylim[0] - 5)
        y1 = min(self._full_res.shape[0] + self.miny, ylim[1] + 5)
        x0 = max(self.minx, xlim[0] - 5)
        x1 = min(self._full_res.shape[1] + self.minx, xlim[1] + 5)
        y0, y1, x0, x1 = map(int, [y0, y1, x0, x1])

        sy = int(max(1, min((y1 - y0) / 5., np.ceil(dy / ext[1]))))
        sx = int(max(1, min((x1 - x0) / 5., np.ceil(dx / ext[0]))))

        # have we already calculated what we need?
        if sx == self._sx and sy == self._sy and \
                x0 == self._bounds[0] and x1 == self._bounds[1] and \
                y0 == self._bounds[2] and y1 == self._bounds[3]:
            return

        self._A = self._full_res[y0 - self.miny:y1 - self.miny:sy,
                                 x0 - self.minx:x1 - self.minx:sx]

        x1 = x0 + self._A.shape[1] * sx
        y1 = y0 + self._A.shape[0] * sy

        self.set_extent([x0 - .5, x1 - .5, y0 - .5, y1 - .5])
        self._sx = sx
        self._sy = sy
        self._bounds = (x0, x1, y0, y1)
        self.changed()

def check_orbits(p1, t1, p2, t2, tmn, tmx, tol):
    n1 = t1 + p1 * np.arange(np.floor((tmn-t1)/p1), np.ceil((tmx-t1)/p1))
    n1 = n1[(tmn <= n1) * (n1 <= tmx)]
    n2 = t2 + p2 * np.arange(np.floor((tmn-t2)/p2), np.ceil((tmx-t2)/p2))
    n2 = n2[(tmn <= n2) * (n2 <= tmx)]
    delta = np.fabs(n1[:, None] - n2[None, :])
    return max(len(n1), len(n2)) == np.sum(delta < tol)