indexamajig: Tidy up --help

1 files changed, 88 insertions, 114 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index e986e0c7..691d6e11 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -70,120 +70,94 @@ static void show_help(const char *s)
 {
 	printf("Syntax: %s [options]\n\n", s);
 	printf(
-"Process and index FEL diffraction images.\n"
-"\n"
-" -h, --help               Display this help message.\n"
-"     --version            Print CrystFEL version number and exit.\n"
-"\n"
-" -i, --input=<filename>   Filename of list of images to process.\n"
-" -o, --output=<filename>  Output stream filename.\n"
-"\n"
-"     --indexing=<methods> Use 'methods' for indexing.  Provide one or more\n"
-"                           methods separated by commas.\n"
-"                           See 'man indexamajig' for details.\n"
-" -g. --geometry=<file>    Get detector geometry from file.\n"
-" -p, --pdb=<file>         File (PDB or CrystFEL unit cell format) from which\n"
-"                           to get the unit cell.  Default: 'molecule.pdb'.\n"
-"     --basename           Remove the directory parts of the filenames.\n"
-" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
-"     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
-"                           zaef  : Use Zaefferer (2000) gradient detection.\n"
-"                                    This is the default method.\n"
-"                           peakfinder8: Use Peakfinder8 algorithm.\n"
-"                           hdf5  : Get from a table in HDF5 file.\n"
-"                           cxi   : Get from CXI format HDF5 file.\n"
-"     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
-"                           Default: /processing/hitfinder/peakinfo\n"
-"     --integration=<meth> Perform final pattern integration using <meth>.\n"
-"\n\n"
-"For more control over the process, you might need:\n\n"
-"    --tolerance=<tol>     Set the tolerances for cell comparison.\n"
-"                            Default: 5,5,5,1.5.\n"
-"    --filter-noise        Apply an aggressive noise filter which sets all\n"
-"                           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 2<n>+1.\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 in both the\n"
-"	                    Zaefferer and Peakfinder8 algorithms.\n"
-"                           Default: 800.\n"
-"    --min-gradient=<n>    Minimum squared gradient for Zaefferer peak\n"
-"                           search. Default: 100,000.\n"
-"    --min-snr=<n>         Minimum signal-to-noise ratio for peaks, with both\n"
-"                           Zaefferer and Peakfinder8 algorithms.\n"
-"                           Default: 5.\n"
-"    --min-pix-count=<n>   Only accept peaks if they include more than <n>\n"
-"                           pixels, in the Peakfinder8 algorithm.\n"
-"                           Default: 2.\n"
-"    --max-pix-count=<n>   Only accept peaks if they include less than <n>\n"
-"                           pixels, in the Peakfinder8 algorithm.\n"
-"                           Default: 200.\n"
-"    --min-peaks=<n>       Minimum number of peaks for indexing.\n"
-"    --local-bg-radius=<n> Radius (in pixels) to use for the estimation of\n"
-"	                    local background in the Peakfinder8 algorithm.\n"
-"                           Default: 3.\n"
-"    --min-res=<n>         Only accept peaks if they lay at more than <n>\n"
-"	                    pixels from the center of the detector, in the\n"
-"                           peakfinder8 algorithm. Default: 0.\n"
-"    --max-res=<n>         Only accept peaks if they lay at less than <n>\n"
-"	                    pixels from the center of the detector, in the\n"
-"                           peakfinder8 algorithm. Default: 1200.\n"
-"    --check-hdf5-snr      Check SNR for peaks from --peaks=hdf5.\n"
-"    --peak-radius=<r>     Integration radii for peak search.\n"
-"    --int-radius=<r>      Set the integration radii.  Default: 4,5,7.\n"
-"    --push-res=<n>        Integrate higher than apparent resolution cutoff.\n"
-"    --highres=<n>         Absolute resolution cutoff in Angstroms.\n"
-"    --fix-profile-radius  Fix the reciprocal space profile radius for spot\n"
-"                           prediction (default: automatically determine.\n"
-"    --fix-bandwidth       Set the bandwidth for spot prediction.\n"
-"    --fix-divergence      Set the divergence (full angle) for spot prediction.\n"
-"\n"
-"\nFor time-resolved stuff, you might want to use:\n\n"
-"     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
-"                             can use this option as many times as you need.\n"
-"\n"
-"\nOverall control of the indexing process:\n\n"
-"     --no-check-cell        Don't check lattice parameters against input cell.\n"
-"     --no-cell-combinations Don't use axis combinations when checking cell.\n"
-"     --no-multi             Don't repeat indexing to index multiple hits.\n"
-"     --no-retry             Don't repeat indexing to increase indexing rate.\n"
-"     --no-refine            Skip the prediction refinement step.\n"
-"     --check-peaks          Check that most of the peaks can be accounted for\n"
-"                             by the indexing solution.\n"
-"\n"
-"\nOptions for greater performance:\n\n"
-" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
-" --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"
-"     --no-non-hits-in-stream  Do not include non-hit frames in the stream.\n"
-"                               (see --min-peaks)\n"
-"     --int-diag=<cond>     Show debugging information about reflections.\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"
-"                            indexer specific, key word arguments.\n"
-"                          Example: \"arg1=10,arg2=500\" \n"
-"\nLow-level options for the TakeTwo indexer:\n\n"
-"     --taketwo-member-threshold Minimum number of members in network\n"
-"     --taketwo-len-tolerance    Reciprocal space length tolerance (1/A)\n"
-"     --taketwo-angle-tolerance  Reciprocal space angle tolerance (in degrees)\n"
-"     --taketwo-trace-tolerance  Rotation matrix equivalence tolerance (in degrees)\n"
+"Index and integrate snapshot diffraction images.\n\n"
+" -h, --help                Display this help message\n"
+"     --version             Print CrystFEL version number and exit\n"
+"\nBasic options:\n\n"
+" -i, --input=<filename>    List of images to process.\n"
+" -o, --output=<filename>   Output stream filename\n"
+" -g  --geometry=<file>     Detector geometry filename\n"
+"     --basename            Remove the directory parts of the filenames\n"
+" -x, --prefix=<p>          Prefix filenames from input file with <p>\n"
+"     --no-check-prefix     Don't attempt to correct the --prefix\n"
+" -j <n>                    Run <n> analyses in parallel  Default 1\n"
+"     --highres=<n>         Absolute resolution cutoff in Angstroms\n"
+"     --profile             Show timing data for performance monitoring\n"
+"     --temp-dir=<path>     Put the temporary folder under <path>\n"
+"\nPeak search options:\n\n"
+"     --peaks=<method>      Peak search method (zaef,peakfinder8,hdf5,cxi)\n"
+"                            Default: zaef\n"
+"     --peak-radius=<r>     Integration radii for peak search\n"
+"     --min-peaks=<n>       Minimum number of peaks for indexing\n"
+"     --hdf5-peaks=<p>      Find peaks table in HDF5 file here\n"
+"                            Default: /processing/hitfinder/peakinfo\n"
+"     --median-filter=<n>   Apply a median filter to the image data\n"
+"                            Default: 0 (no filter)\n"
+"     --filter-noise        Apply noise filter to image data\n"
+"     --threshold=<n>       Threshold for peak detection\n"
+"                            (zaef,peakfinder8 only) Default: 800\n"
+"     --min-gradient=<n>    Minimum squared gradient\n"
+"                            (zaef only) Default: 100,000\n"
+"     --min-snr=<n>         Minimum signal/noise ratio for peaks\n"
+"                            (zaef,pekafinder8 only) Default: 5\n"
+"     --min-pix-count=<n>   Minimum number of pixels per peak\n"
+"                            (peakfinder8 only) Default: 2\n"
+"     --max-pix-count=<n>   Maximum number of pixels per peak\n"
+"                            (peakfinder8 only) Default: 200\n"
+"     --local-bg-radius=<n> Radius (pixels) for local background estimation\n"
+"                            (peakfinder8 only) Default: 3\n"
+"     --min-res=<n>         Minimum resolution for peak search (in pixels)\n"
+"                            (peakfinder8 only) Default: 0\n"
+"     --max-res=<n>         Maximum resolution for peak search (in pixels)\n"
+"                            (peakfinder8 only) Default: 1200\n"
+"     --no-use-saturated    Reject saturated peaks\n"
+"     --no-revalidate       Don't re-integrate and check HDF5 peaks\n"
+"     --no-half-pixel-shift\n"
+"                           Don't offset the HDF5 peak locations by 0.5 px\n"
+"     --check-hdf5-snr      Check SNR for peaks from hdf5 or cxi (see --min-snr)\n"
+"\nIndexing options:\n\n"
+"     --indexing=<methods>  Indexing method list, comma separated\n"
+" -p, --pdb=<file>          Unit cell file (PDB or CrystFEL unit cell format)\n"
+"                             Default: 'molecule.pdb'\n"
+"     --tolerance=<tol>     Tolerances for cell comparison\n"
+"                              Default: 5,5,5,1.5\n"
+"     --no-check-cell       Don't check lattice parameters against input cell\n"
+"     --no-cell-combinations\n"
+"                           Don't use axis combinations when checking cell\n"
+"     --no-multi            Don't repeat indexing to index multiple hits\n"
+"     --no-retry            Don't repeat indexing to increase indexing rate\n"
+"     --no-refine           Skip the prediction refinement step\n"
+"     --check-peaks         Check that most of the peaks can be accounted for\n"
+"                            by the indexing solution\n"
+"     --taketwo-member-threshold\n"
+"                           Minimum number of members in network\n"
+"     --taketwo-len-tolerance\n"
+"                           Reciprocal space length tolerance (1/A)\n"
+"     --taketwo-angle-tolerance\n"
+"                           Reciprocal space angle tolerance (in degrees)\n"
+"     --taketwo-trace-tolerance\n"
+"                           Rotation matrix equivalence tolerance (in degrees)\n"
+"     --felix-options       Change the default arguments passed to the indexer\n"
+"                           Comma-separated list of options, key=val\n"
+"\nIntegration options:\n\n"
+"     --integration=<meth>  Integration method (rings,prof2d)-(cen,nocen)\n"
+"                            Default: rings-nocen\n"
+"     --fix-profile-radius  Fix the reciprocal space profile radius for spot\n"
+"                            prediction (default: automatically determine\n"
+"     --fix-bandwidth       Set the bandwidth for spot prediction\n"
+"     --fix-divergence      Set the divergence (full angle) for spot prediction\n"
+"     --int-radius=<r>      Set the integration radii.  Default: 4,5,7.\n"
+"     --int-diag=<cond>     Show debugging information about reflections\n"
+"     --push-res=<n>        Integrate higher than apparent resolution cutoff\n"
+"\nOutput options:\n\n"
+"     --no-non-hits-in-stream\n"
+"                           Do not include non-hit frames in the stream\n"
+"                            (see --min-peaks)\n"
+"     --copy-hdf5-field=<f> Copy the value of HDF5 field <f> into the stream\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"
+"\nHistorical options:\n\n"
+"     --no-sat-corr         Don't correct values of saturated peaks\n"
 );
 }