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Diffstat (limited to 'src')
-rw-r--r-- | src/indexamajig.c | 202 |
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" ); } |