New subject: [SciPy-dev] reimplementation of lfilter

Sept. 22, 2009

      Looking at this atrocious piece of C:

http://svn.scipy.org/svn/scipy/trunk/scipy/signal/lfilter.c.src

I got some inspiration for reusing some of my other C code to
reimplement scipy.signal.lfilter. I basically just had to write
this small C function + a Cython wrapper:

static void lfilter_1d(double *restrict b, double *restrict a,
    double *x, double *y, double *zi, npy_intp K, npy_intp N)
{
    double Z[K];
    double *restrict pz = zi, *restrict z = Z;
    register npy_intp n, k;
    for (n=0; n<N; n++) {
        register double yn, xn = x[n];
        yn = y[n] = b[0] * xn + pz[0];
        for (k=0; k<K-1; k++)
            z[k] = b[k+1] * xn + pz[k+1] - a[k+1]*yn;
        z[K-1] = b[K]*xn - a[K]*yn;
        double *tmp = pz;
        pz = z;
        z = tmp;
    }
    if (pz != zi)     
        memcpy(zi, pz, K*sizeof(double));       
}

Relative speed compared to scipy.signal.lfilter:

One processor:
1D array, 1000000 floats:              150%
2D array, 1000 x 1000 floats, axis=0:   80%
2D array, 1000 x 1000 floats, axis=1:  150%

It is faster than lfilter except for 2D with axis=0. For
2D with axis=1 it is probably faster than lfilter due to
copy-in copy-out optimization. For arrays with more than
one dimension, multithreading helps as well:

Four processors:
1D array, 1000000 floats:              150%
2D array, 1000 x 1000 floats, axis=0:  160%
2D array, 1000 x 1000 floats, axis=1:  250%

Multithreading obviously does not help for filtering single
vector, as there is no work to share.

Some other improvements over signal.lfilter, apart from readable
Cython code:

* GIL is released. The C code is not littered with Python C
  API calls that prevents this.

* Filtering can be done in reverse, i.e. no need for fliplr or
  flipud for filtering backwards.

* Arrays can be filtered in-place.

* Cleaned up docstring.

Still it only work as a "proof of concept" with double precision
floats. Adding support for other dtypes would be easy, just
replace double with any of:

float
float _Complex
double _Complex
long double
long double _Complex

Regards,
Sturla Molden

# Copyright (C) 2009 Sturla Molden

import numpy as np
cimport numpy as np

cdef extern int _linear_filter( object a, object b, 
                                object x, object y, object z, 
                                int axis, int direction)

def lfilter(object B, object A, object X, 
            object zi=None, 
            object axis = None, 
            int direction=1,
            object inplace=False):

    """
    Filter data along one-dimension with an IIR or FIR filter.

    Description
    ===========

      Filter a data sequence, x, using a digital filter.  This works for many
      fundamental data types (including Object type).  The filter is a direct
      form II transposed implementation of the standard difference equation
      (see "Algorithm").

    Inputs:
    =======    

      b : vector-like  
          The numerator coefficient vector in a 1-D sequence.

      a : vector-like
          The denominator coefficient vector in a 1-D sequence. If a[0]
          is not 1, then both a and b are normalized by a[0].

      x : array-like
          An N-dimensional input array.

      axis : int or None
          The axis of the input data array along which to apply the
          linear filter. The filter is applied to each subarray along
          this axis. If axis is None, the filter is applied to x
          flattened. Default: axis=None.

      zi : array-like
          Initial conditions for the filter delays.  It is a vector
          (or array of vectors for an N-dimensional input) of length
          max(len(a),len(b)). If zi=None or is not given then initial
          rest is assumed. If axis is None, zi should be a vector 
          of length K = max(M,N), where M=len(b)-1 and N=len(a)-1. If 
          an axis is not None, zi should either be a vector of length 
          K, or an array with same shape as x, except for zi.shape[axis] 
          which should be K. If zi is a vector, the same initial 
          conditions are applied to each vector along the specified
          axis. Default: zi=None (initial rest).

          See signal.lfiltic for more information. 

      direction : int
          If negative, the filter is applied in reverse direction
          along the axis. Default: direction=1 (filter forward).

      inplace : bool
          If True, allow x or zi to be modified inplace if possible. 
          Default: False.

    Outputs: (y, {zf})
    =======

      y : ndarray
          The output of the digital filter.

      zf : ndarray
          If zi is None, this is not returned, otherwise, zf holds the
          final filter delay values.

    Algorithm:
    ==========
      The filter function is implemented as a direct II transposed structure.
      This means that the filter implements

      a[0]*y[n] = b[0]*x[n] + b[1]*x[n-1] + ... + b[nb]*x[n-nb]
                            - a[1]*y[n-1] - ... - a[na]*y[n-na]

      using the following difference equations:

      y[m] = b[0]*x[m] + z[0,m-1]
      z[0,m] = b[1]*x[m] + z[1,m-1] - a[1]*y[m]
      ...
      z[n-3,m] = b[n-2]*x[m] + z[n-2,m-1] - a[n-2]*y[m]
      z[n-2,m] = b[n-1]*x[m] - a[n-1]*y[m]

      where m is the output sample number and n=max(len(a),len(b)) is the
      model order.

      The rational transfer function describing this filter in the
      z-transform domain is
                                  -1               -nb
                      b[0] + b[1]z  + ... + b[nb] z
              Y(z) = ---------------------------------- X(z)
                                  -1               -na
                      a[0] + a[1]z  + ... + a[na] z

    """                      

    cdef np.ndarray b, a, x, y, z
    cdef np.npy_intp i, ierr 
    cdef double tmp
    cdef object K, zshape, iaxis

    # get filter coeffs b, a

    A = np.asarray(A)
    B = np.asarray(B)

    if (A.ndim != 1) or (B.ndim != 1): 
        raise ValueError, 'a and b must be vectors'

    K = max(len(A)-1,len(B)-1)

    b = np.zeros(K+1)
    a = np.zeros(K+1)
    a[:A.shape[0]] = A[:]
    b[:B.shape[0]] = B[:]

    # normalize by a[0]
    if a[0] != 1.0:
        tmp = a[0]
        for i in range(a.shape[0]):
            a[i] /= tmp
            b[i] /= tmp            

    # set up input signal
    X = np.asarray(X, dtype=np.float64)
    if axis is None: 
        X = X.ravel()
    elif type(axis) != int:
        raise ValueError, 'axis must be None or an integer >= 0'
    elif axis < 0:
        raise ValueError, 'axis must be None or an integer >= 0'
    x = X

    # set up output signal
    if inplace:
        y = X
    else:
        y = np.zeros(X.shape, dtype=np.float64)

    # set up filter delay buffer

    iaxis = 0 if (axis is None) else axis

    if zi is None:

        # zi not specified, assume initial rest

        zshape = list(X.shape)
        zshape[iaxis] = K
        z = np.zeros(zshape, dtype=np.float64)

    else:

        zi = np.asarray(zi, dtype=np.float64)

        # x and zi are both vectors

        if (x.ndim == 1) and (zi.ndim == 1): 

            if (zi.shape[0] != K):
                raise ValueError, 'length of zi must be K'

            if inplace:
                z = zi
            else:    
                z = zi.copy()

        # x is nd array, zi is vector
        # broadcast zi (cannot modify inplace)

        elif (x.ndim > 1) and (zi.ndim == 1):

            if (zi.shape[0] != K):
                raise ValueError, 'length of zi must be K'

            zshape = list(X.shape)
            zshape[iaxis] = K
            z = np.zeros(zshape, dtype=np.float64)

            zshape = [1] * X.ndim
            zshape[iaxis] = K
            z = z + zi.reshape(zshape) 

        # x and zi are both nd arrays   

        else:

            zshape = list(X.shape)
            zshape[iaxis] = K
            zshape = tuple(zshape)

            if (zi.shape != zshape):
                raise ValueError, ('bad shape of zi: expected %r, got %r' % (zshape,zi.shape))

            if inplace:
                z = zi
            else:    
                z = zi.copy()

    # apply the linear filter

    ierr = _linear_filter(a, b, x, y, z, <int> iaxis, direction)

    # check for error conditions on return

    if ierr == -1:
        raise MemoryError, 'malloc returned NULL'
    if ierr == -2:
        raise ValueError, 'shape of x, y, and z did not match... should never happen, debug please.'
    if ierr == -3:
        raise ValueError, 'shape of a and b did not match... should never happen, debug please.'

    # return y or (y, z) depending on zi

    # return (y if (zi is None) else (y, z)) ## Cython fails on this

    if (zi is None):
       return y
    else:
       return (y,z)

/* Copyright (C) 2009 Sturla Molden */

#include <Python.h>
#include <numpy/arrayobject.h>
#include <string.h>
#include <stdlib.h>

typedef PyArrayObject ndarray;    /* PyArrayObject is an ugly name */
typedef Py_ssize_t    integer;    /* Py_ssize_t of int for 64 bit support, npy_intp is typedef'ed incorrectly. */

/* copy data to and from temporary work arrays  */      

static void copy_in(double *restrict y, double *restrict x, integer n, integer s)
{
    integer i;
    char *tmp;

    if (s == sizeof(double))
        memcpy(y, x, n*sizeof(double));
    else {
        tmp = (char *)x;
        for (i=0; i<n; i++) {
            *y++ = *x;
            tmp += s;
            x = (double *)tmp;
        }    
    }
}            

static void copy_out(double *restrict y, double *restrict x, integer n, integer s)
{
    integer i;
    char *tmp;
    if (s == sizeof(double))
        memcpy(y, x, n*sizeof(double));
    else {
        tmp = (char *)y;
        for (i=0; i<n; i++) {
            *y = *x++;
            tmp += s;
            y = (double *)tmp;
        }    
    }
}

/* this computes the start adress for every vector along a dimension
  (axis) of an ndarray */

inline char *datapointer(ndarray *a, integer *indices)
{
    char *data = a->data;
    int i; 
    integer j;
    for (i=0; i < a->nd; i++) {
        j = indices[i];
        data += j * a->strides[i];
    }
    return data;    
}

static double ** _get_axis_pointer(integer *indices, int axis,
                           ndarray *a, double **axis_ptr_array, int dim)
{                                   
    /* recursive axis pointer search for 4 dimensions or more */
    integer i;
    double *axis_ptr;
    if (dim == a->nd) {
        /* done recursing dimensions,
        compute address of this axis */
        axis_ptr = (double *) datapointer(a, indices);
        *axis_ptr_array = axis_ptr;
        return (axis_ptr_array + 1);
    } else if (dim == axis) {
        /* use first element only */
        indices[dim] = 0;
        axis_ptr_array = _get_axis_pointer(indices, axis, a, axis_ptr_array, dim+1);
        return axis_ptr_array;
    } else {
        /* iterate range of indices */
        integer length = a->dimensions[dim];
        for (i=0; i < length; i++) {
            indices[dim] = i;
            axis_ptr_array = _get_axis_pointer(indices, axis, a, axis_ptr_array, dim+1);
        }
        return axis_ptr_array;
    }
}    

static double **get_axis_pointers(ndarray *a, int axis, integer *count)
{
    integer indices[a->nd];
    double **out, **tmp;
    integer i, j;
    j = 1;    
    for (i=0; i < a->nd; i++) {
        if (i != axis)
            j *= a->dimensions[i];
    }
    *count = j;

    out = (double **) malloc(*count * sizeof(double*));
    if (out == NULL) {
        *count = 0;
        return NULL;
    }
    tmp = out;
    switch (a->nd) {
        /* for one dimension we just return the data pointer */
        case 1:
            *tmp = (double *)a->data;
            break;
        /* specialized for two dimensions */
        case 2:
            switch (axis) {
                case 0:
                    for (i=0; i<a->dimensions[1]; i++)
                        *tmp++ = (double *)(a->data + i*a->strides[1]);
                    break;

                case 1:
                    for (i=0; i<a->dimensions[0]; i++)
                        *tmp++ = (double *)(a->data + i*a->strides[0]);
                    break;
            }
            break;
        /* specialized for three dimensions */
        case 3:
            switch (axis) {
                case 0:
                    for (i=0; i<a->dimensions[1]; i++)
                        for (j=0; j<a->dimensions[2]; j++)
                            *tmp++ = (double *)(a->data + i*a->strides[1] + j*a->strides[2]);
                    break;
                case 1:
                    for (i=0; i<a->dimensions[0]; i++)
                        for (j=0; j<a->dimensions[2]; j++)
                            *tmp++ = (double *)(a->data + i*a->strides[0] + j*a->strides[2]);
                    break;

                case 2:
                    for (i=0; i<a->dimensions[0]; i++)
                        for (j=0; j<a->dimensions[1]; j++)
                            *tmp++ = (double *)(a->data + i*a->strides[0] + j*a->strides[1]);

            }
            break; 
        /* four or more dimensions: use recursion */
        default:
            for (i=0; i<a->nd; i++) indices[i] = 0;
            _get_axis_pointer(indices, axis, a, out, 0);

    }
done:
    return out;
}

/* applies a linear filter along one dimension */

static void lfilter_1d( double *restrict b, double *restrict a,
                        double *x, double *y,
                        double *zi,
                        integer K, integer N)
{
    double Z[K];
    double *restrict pz = zi, *restrict z = Z; 
    register integer n, k;

    for (n=0; n<N; n++) {

        register double yn, xn = x[n];

        yn = y[n] = b[0] * xn + pz[0];

        for (k=0; k<K-1; k++)
            z[k] = b[k+1] * xn + pz[k+1] - a[k+1]*yn;

        z[K-1] = b[K]*xn - a[K]*yn;

        double *tmp = pz;
        pz = z;
        z = tmp;
    }

    if (pz != zi)       
        memcpy(zi, pz, K*sizeof(double));         
}

static void rev_lfilter_1d( double *restrict b, double *restrict a,
                            double *restrict x, double *restrict y,
                            double *zi,
                            integer K, integer N)
{
    double Z[K];
    double *restrict pz = zi, *restrict z = Z; 
    register integer n, k;

    for (n=N-1; n >= 0; n--) {

        register double yn, xn = x[n];

        yn = y[n] = b[0] * xn + pz[0];

        for (k=0; k<K-1; k++)
            z[k] = b[k+1]*xn + pz[k+1] - a[k+1]*yn;

        z[K-1] = b[K]*xn - a[K]*yn;

        double *tmp = pz;
        pz = z;
        z = tmp;
    }

    if (pz != zi)       
        memcpy(zi, pz, K*sizeof(double));         
}

typedef void (*lfilterfun_t)(double *restrict b, double *restrict a,
                            double *restrict x, double *restrict y,
                            double *zi, integer K, integer N);

int _linear_filter(ndarray *a, ndarray *b,
                   ndarray *x, ndarray *y, ndarray *z,
                   int axis,
                   int direction)
{
    int retval = 0;
    double *wx, *wy, *wz, *data_a, *data_b;
    integer xcount, ycount, zcount;
    integer xstride, ystride, zstride; 
    double *xdata, *ydata, *zdata; 
    double **x_axis_ptrs = NULL, **y_axis_ptrs = NULL, **z_axis_ptrs = NULL;
    lfilterfun_t lfilter;
    integer i, K, N;

    /* release the GIL */
    Py_BEGIN_ALLOW_THREADS

    /* sanity check on a and b (these should never fail) */
    if (a->nd != 1) goto error_ab;
    if (b->nd != 1) goto error_ab;
    if (b->dimensions[0] != a->dimensions[0]) goto error_ab;
    data_a = (double *)a->data;
    data_b = (double *)b->data;
    K = a->dimensions[0] - 1;

    /* sanity ckeck on x, y and z */
    if ((x->nd != y->nd) || (y->nd != z->nd)) goto error_xyz;
    for (int d=0; d < a->nd; d++) {
        if (d == axis) continue;     
        if ((x->dimensions[d] != y->dimensions[d]) 
            || (y->dimensions[d] != z->dimensions[d])) goto error_xyz;
    }
    N = x->dimensions[axis];

    /* extract axis pointers */
    x_axis_ptrs = get_axis_pointers(x, axis, &xcount);
    y_axis_ptrs = get_axis_pointers(y, axis, &ycount);
    z_axis_ptrs = get_axis_pointers(z, axis, &zcount);

    /* sanity check */
    if (!x_axis_ptrs) goto error_malloc;
    if (!y_axis_ptrs) goto error_malloc;
    if (!z_axis_ptrs) goto error_malloc;
    if ((xcount != ycount)||(ycount != zcount)) goto error_xyz;

    /* all ok, we can start ... */

    lfilter = direction < 0 ? rev_lfilter_1d : lfilter_1d;

    xstride = x->strides[axis];
    ystride = y->strides[axis];
    zstride = z->strides[axis];

    #pragma omp parallel \
        firstprivate(lfilter, N, K, xcount, x_axis_ptrs, y_axis_ptrs, z_axis_ptrs, \
            xstride, ystride, zstride, data_b, data_a)  \
        private(i, xdata, ydata, zdata, wx, wy, wz) \
        shared(retval) \
        default(none)
    {
        if ((xstride==sizeof(double)) 
             && (ystride==sizeof(double))
             && (xstride==sizeof(double)))
        {

            #pragma omp for schedule(static)
            for (i=0; i < xcount; i++) {
                xdata = x_axis_ptrs[i];
                ydata = y_axis_ptrs[i];
                zdata = z_axis_ptrs[i];
                /* strictly speaking we could be aliasing
                   xdata and ydata here, but it should not matter. */
                lfilter(data_b, data_a, xdata, ydata, zdata, K, N);
            }

        } else {

            /* axis is strided, use copy-in copy-out */

            wx = (double *)malloc((2*N+K)*sizeof(double));
            if (!wx) { 
                #pragma omp critical
                retval = -1; /* error_malloc */
            }
            #pragma omp barrier
            #pragma omp flush(retval)
            if (retval < 0)
                /* malloc failed in some thread */
                goto filtering_complete;
            wy = wx + N;
            wz = wy + N;

            #pragma omp for schedule(static)
            for (i=0; i < xcount; i++) {

                /* get pointe to the first element of the axis */
                xdata = x_axis_ptrs[i];
                ydata = y_axis_ptrs[i];
                zdata = z_axis_ptrs[i];

                /* copy to local contiguous buffers */
                copy_in(wx, xdata, N, xstride);
                copy_in(wz, zdata, K, zstride);

                /* filter */    
                lfilter(data_b, data_a, wx, wy, wz, K, N);

                /* copy data back */
                copy_out(ydata, wy, N, ystride);
                copy_out(zdata, wz, K, zstride);

            }
filtering_complete:    
            if (wx) free(wx);
        }
    }    
    /* we are done... */
    goto done;

/* error conditions */
error_ab:    
    retval = -3;
    goto done;
error_xyz:    
    retval = -2;
    goto done;
error_malloc:
    retval = -1;

/* clean up and exit */
done:

    if (x_axis_ptrs) free(x_axis_ptrs);
    if (y_axis_ptrs) free(y_axis_ptrs);
    if (z_axis_ptrs) free(z_axis_ptrs);

    /* get the GIL back and return */
    Py_END_ALLOW_THREADS

    return retval;
}

reimplementation of lfilter

Sturla Molden

Ralf Gommers

Sturla Molden

Ralf Gommers

Sturla Molden

Sturla Molden

Sturla Molden

Ralf Gommers

Sturla Molden

David Cournapeau

Sturla Molden

Ravi

David Cournapeau

Sturla Molden

Charles R Harris

David Cournapeau

Sturla Molden

David Cournapeau

David Cournapeau

Sturla Molden

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