diff options
| author | Thomas White <taw@physics.org> | 2017-03-31 16:27:13 +0200 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2017-03-31 16:30:13 +0200 |
| commit | 3746b4dbed15569764ec6de473806468951748b8 (patch) | |
| tree | 6539282693783345105809166fa58fc9b25cb943 /src/indexamajig.c | |
| parent | 10fd97e6f88bd4d28ffc2bff56aa5ff19ca436ae (diff) | |
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.
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 23 |
1 files changed, 13 insertions, 10 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}, |