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-rw-r--r--silx/math/fit/filters/src/smoothnd.c317
-rw-r--r--silx/math/fit/filters/src/snip1d.c149
-rw-r--r--silx/math/fit/filters/src/snip2d.c96
-rw-r--r--silx/math/fit/filters/src/snip3d.c186
-rw-r--r--silx/math/fit/filters/src/strip.c118
5 files changed, 866 insertions, 0 deletions
diff --git a/silx/math/fit/filters/src/smoothnd.c b/silx/math/fit/filters/src/smoothnd.c
new file mode 100644
index 0000000..cb96961
--- /dev/null
+++ b/silx/math/fit/filters/src/smoothnd.c
@@ -0,0 +1,317 @@
+#/*##########################################################################
+#
+# Copyright (c) 2004-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+#############################################################################*/
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define MIN(x, y) (((x) < (y)) ? (x) : (y))
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+
+#define MAX_SAVITSKY_GOLAY_WIDTH 101
+#define MIN_SAVITSKY_GOLAY_WIDTH 3
+
+/* Wrapped functions */
+void smooth1d(double *data, int size);
+void smooth2d(double *data, int size0, int size1);
+void smooth3d(double *data, int size0, int size1, int size2);
+int SavitskyGolay(double* input, long len_input, int npoints, double* output);
+
+/* Internal functions */
+long index2d(long row_idx, long col_idx, long ncols);
+long index3d(long x_idx, long y_idx, long z_idx, long ny, long nz);
+void smooth1d_rows(double *data, long nrows, long ncols);
+void smooth1d_cols(double *data, long nrows, long ncols);
+void smooth1d_x(double *data, long nx, long ny, long nz);
+void smooth1d_y(double *data, long nx, long ny, long nz);
+void smooth1d_z(double *data, long nx, long ny, long nz);
+void smooth2d_yzslice(double *data, long nx, long ny, long nz);
+void smooth2d_xzslice(double *data, long nx, long ny, long nz);
+void smooth2d_xyslice(double *data, long nx, long ny, long nz);
+
+
+/* Simple smoothing of a 1D array */
+void smooth1d(double *data, int size)
+{
+ long i;
+ double prev_sample;
+ double next_sample;
+
+ if (size < 3)
+ {
+ return;
+ }
+ prev_sample = data[0];
+ for (i=0; i<(size-1); i++)
+ {
+ next_sample = 0.25 * (prev_sample + 2 * data[i] + data[i+1]);
+ prev_sample = data[i];
+ data[i] = next_sample;
+ }
+ data[size-1] = 0.25 * prev_sample + 0.75 * data[size-1];
+ return;
+}
+
+/* Smoothing of a 2D array*/
+void smooth2d(double *data, int nrows, int ncols)
+{
+ /* smooth the first dimension (rows) */
+ smooth1d_rows(data, nrows, ncols);
+
+ /* smooth the 2nd dimension */
+ smooth1d_cols(data, nrows, ncols);
+}
+
+/* Smoothing of a 3D array */
+void smooth3d(double *data, int nx, int ny, int nz)
+{
+ smooth2d_xyslice(data, nx, ny, nz);
+ smooth2d_xzslice(data, nx, ny, nz);
+ smooth2d_yzslice(data, nx, ny, nz);
+}
+
+/* 1D Savitsky-Golay smoothing */
+int SavitskyGolay(double* input, long len_input, int npoints, double* output)
+{
+
+ //double dpoints = 5.;
+ double coeff[MAX_SAVITSKY_GOLAY_WIDTH];
+ int i, j, m;
+ double dhelp, den;
+ double *data;
+
+ memcpy(output, input, len_input * sizeof(double));
+
+ if (!(npoints % 2)) npoints +=1;
+
+ if((npoints < MIN_SAVITSKY_GOLAY_WIDTH) || (len_input < npoints) || \
+ (npoints > MAX_SAVITSKY_GOLAY_WIDTH))
+ {
+ /* do not smooth data */
+ return 1;
+ }
+
+ /* calculate the coefficients */
+ m = (int) (npoints/2);
+ den = (double) ((2*m-1) * (2*m+1) * (2*m + 3));
+ for (i=0; i<= m; i++){
+ coeff[m+i] = (double) (3 * (3*m*m + 3*m - 1 - 5*i*i ));
+ coeff[m-i] = coeff[m+i];
+ }
+
+ /* simple smoothing at the beginning */
+ for (j=0; j<=(int)(npoints/3); j++)
+ {
+ smooth1d(output, m);
+ }
+
+ /* simple smoothing at the end */
+ for (j=0; j<=(int)(npoints/3); j++)
+ {
+ smooth1d((output+len_input-m-1), m);
+ }
+
+ /*one does not need the whole spectrum buffer, but code is clearer */
+ data = (double *) malloc(len_input * sizeof(double));
+ memcpy(data, output, len_input * sizeof(double));
+
+ /* the actual SG smoothing in the middle */
+ for (i=m; i<(len_input-m); i++){
+ dhelp = 0;
+ for (j=-m;j<=m;j++) {
+ dhelp += coeff[m+j] * (*(data+i+j));
+ }
+ if(dhelp > 0.0){
+ *(output+i) = dhelp / den;
+ }
+ }
+ free(data);
+ return (0);
+}
+
+/*********************/
+/* Utility functions */
+/*********************/
+
+long index2d(long row_idx, long col_idx, long ncols)
+{
+ return (row_idx*ncols+col_idx);
+}
+
+/* Apply smooth 1d on all rows in a 2D array*/
+void smooth1d_rows(double *data, long nrows, long ncols)
+{
+ long row_idx;
+
+ for (row_idx=0; row_idx < nrows; row_idx++)
+ {
+ smooth1d(&data[row_idx * ncols], ncols);
+ }
+}
+
+/* Apply smooth 1d on all columns in a 2D array*/
+void smooth1d_cols(double *data, long nrows, long ncols)
+{
+ long row_idx, col_idx;
+ long this_idx2d, next_idx2d;
+ double prev_sample;
+ double next_sample;
+
+ for (col_idx=0; col_idx < ncols; col_idx++)
+ {
+ prev_sample = data[index2d(0, col_idx, ncols)];
+ for (row_idx=0; row_idx<(nrows-1); row_idx++)
+ {
+ this_idx2d = index2d(row_idx, col_idx, ncols);
+ next_idx2d = index2d(row_idx+1, col_idx, ncols);
+
+ next_sample = 0.25 * (prev_sample + \
+ 2 * data[this_idx2d] + \
+ data[next_idx2d]);
+ prev_sample = data[this_idx2d];
+ data[this_idx2d] = next_sample;
+ }
+
+ this_idx2d = index2d(nrows-1, col_idx, ncols);
+ data[this_idx2d] = 0.25 * prev_sample + 0.75 * data[this_idx2d];
+ }
+}
+
+long index3d(long x_idx, long y_idx, long z_idx, long ny, long nz)
+{
+ return ((x_idx*ny + y_idx) * nz + z_idx);
+}
+
+/* Apply smooth 1d along first dimension in a 3D array*/
+void smooth1d_x(double *data, long nx, long ny, long nz)
+{
+ long x_idx, y_idx, z_idx;
+ long this_idx3d, next_idx3d;
+ double prev_sample;
+ double next_sample;
+
+ for (y_idx=0; y_idx < ny; y_idx++)
+ {
+ for (z_idx=0; z_idx < nz; z_idx++)
+ {
+ prev_sample = data[index3d(0, y_idx, z_idx, ny, nz)];
+ for (x_idx=0; x_idx<(nx-1); x_idx++)
+ {
+ this_idx3d = index3d(x_idx, y_idx, z_idx, ny, nz);
+ next_idx3d = index3d(x_idx+1, y_idx, z_idx, ny, nz);
+
+ next_sample = 0.25 * (prev_sample + \
+ 2 * data[this_idx3d] + \
+ data[next_idx3d]);
+ prev_sample = data[this_idx3d];
+ data[this_idx3d] = next_sample;
+ }
+
+ this_idx3d = index3d(nx-1, y_idx, z_idx, ny, nz);
+ data[this_idx3d] = 0.25 * prev_sample + 0.75 * data[this_idx3d];
+ }
+ }
+}
+
+/* Apply smooth 1d along second dimension in a 3D array*/
+void smooth1d_y(double *data, long nx, long ny, long nz)
+{
+ long x_idx, y_idx, z_idx;
+ long this_idx3d, next_idx3d;
+ double prev_sample;
+ double next_sample;
+
+ for (x_idx=0; x_idx < nx; x_idx++)
+ {
+ for (z_idx=0; z_idx < nz; z_idx++)
+ {
+ prev_sample = data[index3d(x_idx, 0, z_idx, ny, nz)];
+ for (y_idx=0; y_idx<(ny-1); y_idx++)
+ {
+ this_idx3d = index3d(x_idx, y_idx, z_idx, ny, nz);
+ next_idx3d = index3d(x_idx, y_idx+1, z_idx, ny, nz);
+
+ next_sample = 0.25 * (prev_sample + \
+ 2 * data[this_idx3d] + \
+ data[next_idx3d]);
+ prev_sample = data[this_idx3d];
+ data[this_idx3d] = next_sample;
+ }
+
+ this_idx3d = index3d(x_idx, ny-1, z_idx, ny, nz);
+ data[this_idx3d] = 0.25 * prev_sample + 0.75 * data[this_idx3d];
+ }
+ }
+}
+
+/* Apply smooth 1d along third dimension in a 3D array*/
+void smooth1d_z(double *data, long nx, long ny, long nz)
+{
+ long x_idx, y_idx;
+ long idx3d_first_sample;
+
+ for (x_idx=0; x_idx < nx; x_idx++)
+ {
+ for (y_idx=0; y_idx < ny; y_idx++)
+ {
+ idx3d_first_sample = index3d(x_idx, y_idx, 0, ny, nz);
+ /*We can use regular 1D smoothing function because z samples
+ are contiguous in memory*/
+ smooth1d(&data[idx3d_first_sample], nz);
+ }
+ }
+}
+
+/* 2D smoothing of a YZ slice in a 3D volume*/
+void smooth2d_yzslice(double *data, long nx, long ny, long nz)
+{
+ long x_idx;
+ long slice_size = ny * nz;
+
+ /* a YZ slice is a "normal" 2D array of memory-contiguous data*/
+ for (x_idx=0; x_idx < nx; x_idx++)
+ {
+ smooth2d(&data[x_idx*slice_size], ny, nz);
+ }
+}
+
+/* 2D smoothing of a XZ slice in a 3D volume*/
+void smooth2d_xzslice(double *data, long nx, long ny, long nz)
+{
+
+ /* smooth along the first dimension */
+ smooth1d_x(data, nx, ny, nz);
+
+ /* smooth along the third dimension */
+ smooth1d_z(data, nx, ny, nz);
+}
+
+/* 2D smoothing of a XY slice in a 3D volume*/
+void smooth2d_xyslice(double *data, long nx, long ny, long nz)
+{
+ /* smooth along the first dimension */
+ smooth1d_x(data, nx, ny, nz);
+
+ /* smooth along the second dimension */
+ smooth1d_y(data, nx, ny, nz);
+}
+
diff --git a/silx/math/fit/filters/src/snip1d.c b/silx/math/fit/filters/src/snip1d.c
new file mode 100644
index 0000000..994a272
--- /dev/null
+++ b/silx/math/fit/filters/src/snip1d.c
@@ -0,0 +1,149 @@
+#/*##########################################################################
+# Copyright (c) 2004-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+#############################################################################*/
+/*
+ Implementation of the algorithm SNIP in 1D described in
+ Miroslav Morhac et al. Nucl. Instruments and Methods in Physics Research A401 (1997) 113-132.
+
+ The original idea for 1D and the low-statistics-digital-filter (lsdf) come from
+ C.G. Ryan et al. Nucl. Instruments and Methods in Physics Research B34 (1988) 396-402.
+*/
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+
+#define MIN(x, y) (((x) < (y)) ? (x) : (y))
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+
+void lls(double *data, int size);
+void lls_inv(double *data, int size);
+void snip1d(double *data, int n_channels, int snip_width);
+void snip1d_multiple(double *data, int n_channels, int snip_width, int n_spectra);
+void lsdf(double *data, int size, int fwhm, double f, double A, double M, double ratio);
+
+void lls(double *data, int size)
+{
+ int i;
+ for (i=0; i< size; i++)
+ {
+ data[i] = log(log(sqrt(data[i]+1.0)+1.0)+1.0);
+ }
+}
+
+void lls_inv(double *data, int size)
+{
+ int i;
+ double tmp;
+ for (i=0; i< size; i++)
+ {
+ /* slightly different than the published formula because
+ with the original formula:
+
+ tmp = exp(exp(data[i]-1.0)-1.0);
+ data[i] = tmp * tmp - 1.0;
+
+ one does not recover the original data */
+
+ tmp = exp(exp(data[i])-1.0)-1.0;
+ data[i] = tmp * tmp - 1.0;
+ }
+}
+
+void lsdf(double *data, int size, int fwhm, double f, double A, double M, double ratio)
+{
+ int channel, i, j;
+ double L, R, S;
+ int width;
+ double dhelp;
+
+ width = (int) (f * fwhm);
+ for (channel=width; channel<(size-width); channel++)
+ {
+ i = width;
+ while(i>0)
+ {
+ L=0;
+ R=0;
+ for(j=channel-i; j<channel; j++)
+ {
+ L += data[j];
+ }
+ for(j=channel+1; j<channel+i; j++)
+ {
+ R += data[j];
+ }
+ S = data[channel] + L + R;
+ if (S<M)
+ {
+ data[channel] = S /(2*i+1);
+ break;
+ }
+ dhelp = (R+1)/(L+1);
+ if ((dhelp < ratio) && (dhelp > (1/ratio)))
+ {
+ if (S<(A*sqrt(data[channel])))
+ {
+ data[channel] = S /(2*i+1);
+ break;
+ }
+ }
+ i=i-1;
+ }
+ }
+}
+
+
+void snip1d(double *data, int n_channels, int snip_width)
+{
+ snip1d_multiple(data, n_channels, snip_width, 1);
+}
+
+void snip1d_multiple(double *data, int n_channels, int snip_width, int n_spectra)
+{
+ int i;
+ int j;
+ int p;
+ int offset;
+ double *w;
+
+ i = (int) (0.5 * snip_width);
+ /* lsdf(data, size, i, 1.5, 75., 10., 1.3); */
+
+ w = (double *) malloc(n_channels * sizeof(double));
+
+ for (j=0; j < n_spectra; j++)
+ {
+ offset = j * n_channels;
+ for (p = snip_width; p > 0; p--)
+ {
+ for (i=p; i<(n_channels - p); i++)
+ {
+ w[i] = MIN(data[i + offset], 0.5*(data[i + offset - p] + data[ i + offset + p]));
+ }
+ for (i=p; i<(n_channels - p); i++)
+ {
+ data[i+offset] = w[i];
+ }
+ }
+ }
+ free(w);
+}
diff --git a/silx/math/fit/filters/src/snip2d.c b/silx/math/fit/filters/src/snip2d.c
new file mode 100644
index 0000000..235759c
--- /dev/null
+++ b/silx/math/fit/filters/src/snip2d.c
@@ -0,0 +1,96 @@
+#/*##########################################################################
+#
+# The PyMca X-Ray Fluorescence Toolkit
+#
+# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF by the Software group.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+#############################################################################*/
+/*
+ Implementation of the algorithm SNIP in 2D described in
+ Miroslav Morhac et al. Nucl. Instruments and Methods in Physics Research A401 (1997) 113-132.
+*/
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define MIN(x, y) (((x) < (y)) ? (x) : (y))
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+
+void lls(double *data, int size);
+void lls_inv(double *data, int size);
+
+void snip2d(double *data, int nrows, int ncolumns, int width)
+{
+ int i, j;
+ int p;
+ int size;
+ double *w;
+ double P1, P2, P3, P4;
+ double S1, S2, S3, S4;
+ double dhelp;
+ int iminuspxncolumns; /* (i-p) * ncolumns */
+ int ixncolumns; /* i * ncolumns */
+ int ipluspxncolumns; /* (i+p) * ncolumns */
+
+ size = nrows * ncolumns;
+ w = (double *) malloc(size * sizeof(double));
+
+ for (p=width; p > 0; p--)
+ {
+ for (i=p; i<(nrows-p); i++)
+ {
+ iminuspxncolumns = (i-p) * ncolumns;
+ ixncolumns = i * ncolumns;
+ ipluspxncolumns = (i+p) * ncolumns;
+ for (j=p; j<(ncolumns-p); j++)
+ {
+ P4 = data[ iminuspxncolumns + (j-p)]; /* P4 = data[i-p][j-p] */
+ S4 = data[ iminuspxncolumns + j]; /* S4 = data[i-p][j] */
+ P2 = data[ iminuspxncolumns + (j+p)]; /* P2 = data[i-p][j+p] */
+ S3 = data[ ixncolumns + (j-p)]; /* S3 = data[i][j-p] */
+ S2 = data[ ixncolumns + (j+p)]; /* S2 = data[i][j+p] */
+ P3 = data[ ipluspxncolumns + (j-p)]; /* P3 = data[i+p][j-p] */
+ S1 = data[ ipluspxncolumns + j]; /* S1 = data[i+p][j] */
+ P1 = data[ ipluspxncolumns + (j+p)]; /* P1 = data[i+p][j+p] */
+ dhelp = 0.5*(P1+P3);
+ S1 = MAX(S1, dhelp) - dhelp;
+ dhelp = 0.5*(P1+P2);
+ S2 = MAX(S2, dhelp) - dhelp;
+ dhelp = 0.5*(P3+P4);
+ S3 = MAX(S3, dhelp) - dhelp;
+ dhelp = 0.5*(P2+P4);
+ S4 = MAX(S4, dhelp) - dhelp;
+ w[ixncolumns + j] = MIN(data[ixncolumns + j], 0.5 * (S1+S2+S3+S4) + 0.25 * (P1+P2+P3+P4));
+ }
+ }
+ for (i=p; i<(nrows-p); i++)
+ {
+ ixncolumns = i * ncolumns;
+ for (j=p; j<(ncolumns-p); j++)
+ {
+ data[ixncolumns + j] = w[ixncolumns + j];
+ }
+ }
+ }
+ free(w);
+}
diff --git a/silx/math/fit/filters/src/snip3d.c b/silx/math/fit/filters/src/snip3d.c
new file mode 100644
index 0000000..cf48ee4
--- /dev/null
+++ b/silx/math/fit/filters/src/snip3d.c
@@ -0,0 +1,186 @@
+#/*##########################################################################
+#
+# The PyMca X-Ray Fluorescence Toolkit
+#
+# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
+#
+# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
+# the ESRF by the Software group.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+#############################################################################*/
+/*
+ Implementation of the algorithm SNIP in 3D described in
+ Miroslav Morhac et al. Nucl. Instruments and Methods in Physics Research A401 (1997) 113-132.
+*/
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#define MIN(x, y) (((x) < (y)) ? (x) : (y))
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+
+void lls(double *data, int size);
+void lls_inv(double *data, int size);
+
+void snip3d(double *data, int nx, int ny, int nz, int width)
+{
+ int i, j, k;
+ int p;
+ int size;
+ double *w;
+ double P1, P2, P3, P4, P5, P6, P7, P8;
+ double R1, R2, R3, R4, R5, R6;
+ double S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12;
+ double dhelp;
+ long ioffset;
+ long iplus;
+ long imin;
+ long joffset;
+ long jplus;
+ long jmin;
+
+ size = nx * ny * nz;
+ w = (double *) malloc(size * sizeof(double));
+
+ for (p=width; p > 0; p--)
+ {
+ for (i=p; i<(nx-p); i++)
+ {
+ ioffset = i * ny * nz;
+ iplus = (i + p) * ny * nz;
+ imin = (i - p) * ny * nz;
+ for (j=p; j<(ny-p); j++)
+ {
+ joffset = j * nz;
+ jplus = (j + p) * nz;
+ jmin = (j - p) * nz;
+ for (k=p; k<(nz-p); k++)
+ {
+ P1 = data[iplus + jplus + k-p]; /* P1 = data[i+p][j+p][k-p] */
+ P2 = data[imin + jplus + k-p]; /* P2 = data[i-p][j+p][k-p] */
+ P3 = data[iplus + jmin + k-p]; /* P3 = data[i+p][j-p][k-p] */
+ P4 = data[imin + jmin + k-p]; /* P4 = data[i-p][j-p][k-p] */
+ P5 = data[iplus + jplus + k+p]; /* P5 = data[i+p][j+p][k+p] */
+ P6 = data[imin + jplus + k+p]; /* P6 = data[i-p][j+p][k+p] */
+ P7 = data[imin + jmin + k+p]; /* P7 = data[i-p][j-p][k+p] */
+ P8 = data[iplus + jmin + k+p]; /* P8 = data[i+p][j-p][k+p] */
+
+ S1 = data[iplus + joffset + k-p]; /* S1 = data[i+p][j][k-p] */
+ S2 = data[ioffset + jmin + k-p]; /* S2 = data[i][j+p][k-p] */
+ S3 = data[imin + joffset + k-p]; /* S3 = data[i-p][j][k-p] */
+ S4 = data[ioffset + jmin + k-p]; /* S4 = data[i][j-p][k-p] */
+ S5 = data[imin + joffset + k+p]; /* S5 = data[i-p][j][k+p] */
+ S6 = data[ioffset + jplus + k+p]; /* S6 = data[i][j+p][k+p] */
+ S7 = data[imin + joffset + k+p]; /* S7 = data[i-p][j][k+p] */
+ S8 = data[ioffset + jmin + k+p]; /* S8 = data[i][j-p][k+p] */
+ S9 = data[imin + jplus + k]; /* S9 = data[i-p][j+p][k] */
+ S10 = data[imin + jmin + k]; /* S10 = data[i-p][j-p][k] */
+ S11 = data[iplus + jmin + k]; /* S11 = data[i+p][j-p][k] */
+ S12 = data[iplus + jplus + k]; /* S12 = data[i+p][j+p][k] */
+
+ R1 = data[ioffset + joffset + k-p]; /* R1 = data[i][j][k-p] */
+ R2 = data[ioffset + joffset + k+p]; /* R2 = data[i][j][k+p] */
+ R3 = data[imin + joffset + k]; /* R3 = data[i-p][j][k] */
+ R4 = data[iplus + joffset + k]; /* R4 = data[i+p][j][k] */
+ R5 = data[ioffset + jplus + k]; /* R5 = data[i][j+p][k] */
+ R6 = data[ioffset + jmin + k]; /* R6 = data[i][j-p][k] */
+
+ dhelp = 0.5*(P1+P3);
+ S1 = MAX(S1, dhelp) - dhelp;
+
+ dhelp = 0.5*(P1+P2);
+ S2 = MAX(S2, dhelp) - dhelp;
+
+ dhelp = 0.5*(P2+P4);
+ S3 = MAX(S3, dhelp) - dhelp;
+
+ dhelp = 0.5*(P3+P4);
+ S4 = MAX(S4, dhelp) - dhelp;
+
+ dhelp = 0.5*(P5+P8); /* Different from paper (P5+P7) but according to drawing */
+ S5 = MAX(S5, dhelp) - dhelp;
+
+ dhelp = 0.5*(P5+P6);
+ S6 = MAX(S6, dhelp) - dhelp;
+
+ dhelp = 0.5*(P6+P7); /* Different from paper (P6+P8) but according to drawing */
+ S7 = MAX(S7, dhelp) - dhelp;
+
+ dhelp = 0.5*(P7+P8);
+ S8 = MAX(S8, dhelp) - dhelp;
+
+ dhelp = 0.5*(P2+P6);
+ S9 = MAX(S9, dhelp) - dhelp;
+
+ dhelp = 0.5*(P4+P7); /* Different from paper (P4+P8) but according to drawing */
+ S10 = MAX(S10, dhelp) - dhelp;
+
+ dhelp = 0.5*(P3+P8); /* Different from paper (P1+P5) but according to drawing */
+ S11 = MAX(S11, dhelp) - dhelp;
+
+ dhelp = 0.5*(P1+P5); /* Different from paper (P3+P7) but according to drawing */
+ S12 = MAX(S12, dhelp) - dhelp;
+
+ /* The published formulae correspond to have:
+ P7 and P8 interchanged, and S11 and S12 interchanged
+ with respect to the published drawing */
+
+ dhelp = 0.5 * (S1+S2+S3+S4) + 0.25 * (P1+P2+P3+P4);
+ R1 = MAX(R1, dhelp) - dhelp;
+
+ dhelp = 0.5 * (S5+S6+S7+S8) + 0.25 * (P5+P6+P7+P8);
+ R2 = MAX(R2, dhelp) - dhelp;
+
+ dhelp = 0.5 * (S3+S7+S9+S10) + 0.25 * (P2+P4+P6+P7); /* Again same P7 and P8 change */
+ R3 = MAX(R3, dhelp) - dhelp;
+
+ dhelp = 0.5 * (S1+S5+S11+S12) + 0.25 * (P1+P3+P5+P8); /* Again same P7 and P8 change */
+ R4 = MAX(R4, dhelp) - dhelp;
+
+ dhelp = 0.5 * (S2+S6+S9+S12) + 0.25 * (P1+P2+P5+P6); /* Again same S11 and S12 change */
+ R5 = MAX(R5, dhelp) - dhelp;
+
+ dhelp = 0.5 * (S4+S8+S10+S11) + 0.25 * (P3+P4+P7+P8); /* Again same S11 and S12 change */
+ R6 = MAX(R6, dhelp) - dhelp;
+
+ dhelp = 0.5 * (R1 + R2 + R3 + R4 + R5 + R6) +\
+ 0.25 * (S1 + S2 + S3 + S4 + S5 + S6) +\
+ 0.25 * (S7 + S8 + S9 + S10 + S11 + S12) +\
+ 0.125 * (P1 + P2 + P3 + P4 + P5 + P6 + P7 + P8);
+ w[ioffset + joffset + k] = MIN(data[ioffset + joffset + k], dhelp);
+ }
+ }
+ }
+ for (i=p; i<(nx-p); i++)
+ {
+ ioffset = i * ny * nz;
+ for (j=p; j<(ny-p); j++)
+ {
+ joffset = j * nz;
+ for (k=p; k<(nz-p); j++)
+ {
+ data[ioffset + joffset + k] = w[ioffset + joffset + k];
+ }
+ }
+ }
+ }
+ free(w);
+}
diff --git a/silx/math/fit/filters/src/strip.c b/silx/math/fit/filters/src/strip.c
new file mode 100644
index 0000000..dec0742
--- /dev/null
+++ b/silx/math/fit/filters/src/strip.c
@@ -0,0 +1,118 @@
+#/*##########################################################################
+# Copyright (c) 2004-2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+#############################################################################*/
+/*
+ This file provides a background strip function, to isolate low frequency
+ background signal from a spectrum (and later substact it from the signal
+ to be left only with the peaks to be fitted).
+
+ It is adapted from PyMca source file "SpecFitFuns.c". The main difference
+ with the original code is that this code does not handle the python
+ wrapping, which is done elsewhere using cython.
+
+ Authors: V.A. Sole, P. Knobel
+ License: MIT
+ Last modified: 17/06/2016
+*/
+
+#include <string.h>
+
+#include <stdio.h>
+
+/* strip(double* input, double c, long niter, double* output)
+
+ The strip background is probably PyMca's most popular background model.
+
+ In its simplest implementation it is just as an iterative procedure depending
+ on two parameters. These parameters are the strip background width w, and the
+ strip background number of iterations. At each iteration, if the contents of
+ channel i, y(i), is above the average of the contents of the channels at w
+ channels of distance, y(i-w) and y(i+w), y(i) is replaced by the average.
+ At the end of the process we are left with something that resembles a spectrum
+ in which the peaks have been "stripped".
+
+ Parameters:
+
+ - input: Input data array
+ - c: scaling factor applied to the average of y(i-w) and y(i+w) before
+ comparing to y(i)
+ - niter: number of iterations
+ - deltai: operator width (in number of channels)
+ - anchors: Array of anchors, indices of points that will not be
+ modified during the stripping procedure.
+ - output: output array
+
+*/
+int strip(double* input, long len_input,
+ double c, long niter, int deltai,
+ long* anchors, long len_anchors,
+ double* output)
+{
+ long iter_index, array_index, anchor_index, anchor;
+ int anchor_nearby_flag;
+ double t_mean;
+
+ memcpy(output, input, len_input * sizeof(double));
+
+ if (deltai <=0) deltai = 1;
+
+ if (len_input < (2*deltai+1)) return(-1);
+
+ if (len_anchors > 0) {
+ for (iter_index = 0; iter_index < niter; iter_index++) {
+ for (array_index = deltai; array_index < len_input - deltai; array_index++) {
+ /* if index is within +- deltai of an anchor, don't do anything */
+ anchor_nearby_flag = 0;
+ for (anchor_index=0; anchor_index<len_anchors; anchor_index++)
+ {
+ anchor = anchors[anchor_index];
+ if (array_index > (anchor - deltai) && array_index < (anchor + deltai))
+ {
+ anchor_nearby_flag = 1;
+ break;
+ }
+ }
+ /* skip this array_index index */
+ if (anchor_nearby_flag) {
+ continue;
+ }
+
+ t_mean = 0.5 * (input[array_index-deltai] + input[array_index+deltai]);
+ if (input[array_index] > (t_mean * c))
+ output[array_index] = t_mean;
+ }
+ memcpy(input, output, len_input * sizeof(double));
+ }
+ }
+ else {
+ for (iter_index = 0; iter_index < niter; iter_index++) {
+ for (array_index=deltai; array_index < len_input - deltai; array_index++) {
+ t_mean = 0.5 * (input[array_index-deltai] + input[array_index+deltai]);
+
+ if (input[array_index] > (t_mean * c))
+ output[array_index] = t_mean;
+ }
+ memcpy(input, output, len_input * sizeof(double));
+ }
+ }
+ return(0);
+}
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