diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/indexamajig.c | 10 | ||||
| -rw-r--r-- | src/process_image.c | 18 | ||||
| -rw-r--r-- | src/process_image.h | 1 |
3 files changed, 21 insertions, 8 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 9b868b9f..27ec31fc 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -111,6 +111,10 @@ static void show_help(const char *s) " pixels in each 3x3 region to zero if any of them\n" " have negative values. Intensity measurement will\n" " be performed on the image as it was before this.\n" +" --median-filter=<n> Apply a median filter to the image data. Intensity\n" +" measurement will be performed on the image as it\n" +" was before this. The side length of the median\n" +" filter box will be <n>. Default: 0 (no filter).\n" " --no-sat-corr Don't correct values of saturated peaks using a\n" " table included in the HDF5 file.\n" " --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n" @@ -183,6 +187,7 @@ int main(int argc, char *argv[]) iargs.cell = NULL; iargs.cmfilter = 0; iargs.noisefilter = 0; + iargs.median_filter = 0; iargs.satcorr = 1; iargs.closer = 0; iargs.bgsub = 1; @@ -266,6 +271,7 @@ int main(int argc, char *argv[]) {"min-integration-snr",1, NULL, 12}, {"tolerance", 1, NULL, 13}, {"int-radius", 1, NULL, 14}, + {"median-filter", 1, NULL, 15}, {0, 0, NULL, 0} }; @@ -386,6 +392,10 @@ int main(int argc, char *argv[]) intrad = strdup(optarg); break; + case 15 : + iargs.median_filter = atoi(optarg); + break; + case 0 : break; diff --git a/src/process_image.c b/src/process_image.c index 010054c8..a8eeb663 100644 --- a/src/process_image.c +++ b/src/process_image.c @@ -136,23 +136,25 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, if ( iargs->cmfilter ) filter_cm(&image); - /* Take snapshot of image after CM subtraction but before - * the aggressive noise filter. */ + /* Take snapshot of image after CM subtraction but before applying + * horrible noise filters to it */ data_size = image.width * image.height * sizeof(float); data_for_measurement = malloc(data_size); + memcpy(data_for_measurement, image.data, data_size); + + if ( iargs->median_filter > 0 ) { + filter_median(&image, iargs->median_filter); + } if ( iargs->noisefilter ) { - filter_noise(&image, data_for_measurement); - } else { - memcpy(data_for_measurement, image.data, data_size); + filter_noise(&image); } switch ( iargs->peaks ) { case PEAK_HDF5: - // Get peaks from HDF5 - if (get_peaks(&image, hdfile, - iargs->hdf5_peak_path)) { + /* Get peaks from HDF5 */ + if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) { ERROR("Failed to get peaks from HDF5 file.\n"); } if ( !iargs->no_revalidate ) { diff --git a/src/process_image.h b/src/process_image.h index f2f034d9..5fe11e33 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -46,6 +46,7 @@ struct index_args UnitCell *cell; int cmfilter; int noisefilter; + int median_filter; int satcorr; int closer; int bgsub; |