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authorThomas White <taw@physics.org>2017-10-02 03:58:55 +0200
committerThomas White <taw@physics.org>2017-10-02 03:58:55 +0200
commit8ed0757a113059dca55ad795a231dfe4eb6f452b (patch)
tree92f5f35c08c633e77e3b419f79295368ec419969 /src/indexamajig.c
parent4253d35e56bb7bc76b30a770dda2fc8168ac47f6 (diff)
indexamajig: Tidy up --help
Diffstat (limited to 'src/indexamajig.c')
-rw-r--r--src/indexamajig.c202
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"
);
}