Offset peak locations from HDF5 or CXI files by 0.5,0.5

CrystFEL considers all peak locations to be distances from the corner of
the detector panel, in pixel units, consistent with its description of
detector geometry.  In contrast, Cheetah considers the peak locations
to be pixel indices in the data array.  Therefore, a half-pixel offset
is needed when importing the peak lists.

For users who need the old behaviour, this commit adds a new option
indexamajig --no-half-pixel-shift to deactivate this offset.

3 files changed, 21 insertions, 13 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 28a7bf85..f48fac17 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -152,16 +152,17 @@ static void show_help(const char *s)
 " --temp-dir=<path>        Put the temporary folder under <path>.\n"
 "\n"
 "\nOptions you probably won't need:\n\n"
-"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
-"     --no-use-saturated   During the initial peak search, reject\n"
-"                           peaks which contain pixels above max_adu.\n"
-"     --no-revalidate      Don't re-integrate and check HDF5 peaks for\n"
-"                           validity.\n"
-"     --no-peaks-in-stream Do not record peak search results in the stream.\n"
-"     --no-refls-in-stream Do not record integrated reflections in the stream.\n"
-"     --int-diag=<cond>    Show debugging information about reflections.\n"
-"     --no-refine          Skip the prediction refinement step.\n"
-"     --profile            Show timing data for performance monitoring.\n"
+"     --no-check-prefix     Don't attempt to correct the --prefix.\n"
+"     --no-use-saturated    During the initial peak search, reject\n"
+"                            peaks which contain pixels above max_adu.\n"
+"     --no-revalidate       Don't re-integrate and check HDF5 peaks for\n"
+"                            validity.\n"
+"     --no-peaks-in-stream  Do not record peak search results in the stream.\n"
+"     --no-refls-in-stream  Do not record integrated reflections in the stream.\n"
+"     --int-diag=<cond>     Show debugging information about reflections.\n"
+"     --no-refine           Skip the prediction refinement step.\n"
+"     --profile             Show timing data for performance monitoring.\n"
+"     --no-half-pixel-shift Don't offset the HDF5 peak locations by 0.5 px.\n"
 "\nLow-level options for the felix indexer:\n\n"
 "     --felix-options      Change the default arguments passed to the indexer.\n"
 "                          Given as a list of comma separated list of \n"
@@ -243,6 +244,7 @@ int main(int argc, char *argv[])
 	iargs.peaks = PEAK_ZAEF;
 	iargs.beam = &beam;
 	iargs.hdf5_peak_path = NULL;
+	iargs.half_pixel_shift = 1;
 	iargs.copyme = NULL;
 	iargs.pk_inn = -1.0;
 	iargs.pk_mid = -1.0;
@@ -297,6 +299,7 @@ int main(int argc, char *argv[])
 		{"check-hdf5-snr",     0, &iargs.check_hdf5_snr,     1},
 		{"no-refine",          0, &no_refine,                1},
 		{"profile",            0, &iargs.profile,            1},
+		{"no-half-pixel-shift",0, &iargs.half_pixel_shift,   0},
 
 		/* Long-only options which don't actually do anything */
 		{"no-sat-corr",        0, &iargs.satcorr,            0},
diff --git a/src/process_image.c b/src/process_image.c
index e6e6d22a..cd5c0866 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -160,7 +160,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
-		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
+		if ( get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
+		                 iargs->half_pixel_shift) )
+		{
 			ERROR("Failed to get peaks from HDF5 file.\n");
 		}
 		if ( !iargs->no_revalidate ) {
@@ -172,8 +174,10 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		break;
 
 		case PEAK_CXI:
-		if ( get_peaks_cxi(&image, hdfile, iargs->hdf5_peak_path,
-		                   pargs->filename_p_e) ) {
+		if ( get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
+		                     pargs->filename_p_e,
+		                     iargs->half_pixel_shift) )
+		{
 			ERROR("Failed to get peaks from CXI file.\n");
 		}
 		if ( !iargs->no_revalidate ) {
diff --git a/src/process_image.h b/src/process_image.h
index bc8b31fd..d63679cf 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -67,6 +67,7 @@ struct index_args
 	float tols[4];
 	struct beam_params *beam;
 	char *hdf5_peak_path;
+	int half_pixel_shift;
 	float pk_inn;
 	float pk_mid;
 	float pk_out;