From acbc6aec2f192189659975503717a8ac3d1226f0 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 5 Sep 2014 13:36:08 +0200 Subject: Update docs --- doc/man/indexamajig.1 | 2 +- doc/reference/libcrystfel/CrystFEL-sections.txt | 12 ++++++++++-- libcrystfel/src/detector.c | 2 +- libcrystfel/src/image.h | 9 +++++++++ libcrystfel/src/integration.h | 17 +++++++++++++++++ libcrystfel/src/stream.c | 3 +++ libcrystfel/src/symmetry.c | 6 +++--- libcrystfel/src/utils.c | 3 ++- 8 files changed, 46 insertions(+), 8 deletions(-) diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 51c44ded..0dd31e3e 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -321,7 +321,7 @@ Do not record integrated reflections in the stream. The resulting output won't .PD 0 .IP \fB--int-diag=\fIcondition\fR .PD -Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR. \fBrandom\fR means to show information about a random 1% of the peaks. \fBnegative\fR means to show peaks with intensities which are negative by more than 3 sigma. \fBimplausible\fR means to show peaks with intensities which are negative by more than 5 sigma. The default is \fB--int-diag=none\fR. +Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR. \fBrandom\fR means to show information about a random 1% of the peaks. \fBnegative\fR means to show peaks with intensities which are negative by more than 3 sigma. \fBimplausible\fR means to show peaks with intensities which are negative by more than 5 sigma. \fBstrong\fR means to show peaks with intensities which are positive by more than 3 sigma The default is \fB--int-diag=none\fR. .PD 0 .IP \fB--push-res=\fIn\fR diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 035ab935..6d966a68 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -80,7 +80,6 @@ max_intensity UnitCell LatticeType UnitCellTransformation -rvec cell_new cell_new_from_cell @@ -173,6 +172,9 @@ ph_lambda_to_eV random_flat flat_noise show_matrix +likely +unlikely +UNUSED
@@ -299,6 +301,7 @@ free_symopmask describe_symmetry symmetry_name set_symmetry_name +get_matrix_name is_centrosymmetric is_centric
@@ -347,6 +350,7 @@ twod_mapping reverse_2d_mapping largest_q in_bad_region +mark_resolution_range_as_bad
@@ -426,7 +430,6 @@ LORENTZ_SCALE peaks peak_sanity_check search_peaks -integrate_peak make_BgMask validate_peaks
@@ -453,6 +456,7 @@ IntDiag integrate_all integrate_all_2 integrate_all_3 +integrate_all_4 integration_method @@ -468,9 +472,12 @@ PEAK_LIST_END_MARKER PEAK_LIST_START_MARKER REFLECTION_END_MARKER REFLECTION_START_MARKER +GEOM_END_MARKER +GEOM_START_MARKER open_stream_fd_for_write open_stream_for_read open_stream_for_write +open_stream_for_write_2 get_stream_fd close_stream read_chunk @@ -479,4 +486,5 @@ write_chunk rewind_stream is_stream write_command +write_geometry_file diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c index eb5890b5..537f1f30 100644 --- a/libcrystfel/src/detector.c +++ b/libcrystfel/src/detector.c @@ -1408,7 +1408,7 @@ int write_detector_geometry(const char *filename, struct detector *det) /** - * mark_resolution_range_as_bad() + * mark_resolution_range_as_bad: * @image: An image structure * @min: Minimum value of 1/d to be marked as bad * @max: Maximum value of 1/d to be marked as bad diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index f19a7427..69edb768 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -48,6 +48,15 @@ struct image; #include "crystal.h" #include "index.h" +/** + * SpectrumType: + * @SPECTRUM_TOPHAT: A top hat distribution of wavelengths + * @SPECTRUM_SASE: A simulated SASE spectrum + * @SPECTRUM_TWOCOLOUR: A spectrum containing two peaks + * + * A %SpectrumType represents a type of X-ray energy spectrum to use for + * generating simulated data. + **/ typedef enum { SPECTRUM_TOPHAT, SPECTRUM_SASE, diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h index 9e1c8ee1..ca04157a 100644 --- a/libcrystfel/src/integration.h +++ b/libcrystfel/src/integration.h @@ -36,6 +36,23 @@ #include "geometry.h" +/** + * IntDiag: + * @INTDIAG_NONE: Never show diagnostics + * @INTDIAG_RANDOM: Show diagnostics for a randomly selected 1% of reflections + * @INTDIAG_ALL: Show diagnostics for all reflections + * @INTDIAG_INDICES: Show diagnostics when the Miller indices of the reflection + * are the ones specified + * @INTDIAG_NEGATIVE: Show diagnostics when the measured intensity is less than + * minus three times its estimated error. + * @INTDIAG_IMPLAUSIBLE: Show diagnostics when the measured intensity is les + * than minus five times its estimated error. + * @INTDIAG_STRONG: Show diagnostics when the measured intensity is more than + * three times its estimated error. + * + * An %IntDiag describes the condition under which the integration subsystem + * should display diagnostic information to the user. + **/ typedef enum { INTDIAG_NONE, diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index fd051884..f50d2a2b 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -899,6 +899,9 @@ Stream *open_stream_fd_for_write(int fd) /** * open_stream_for_write_2 * @filename: Filename of new stream + * @geom_filename: The geometry filename to copy + * @argc: The number of arguments to the program + * @argv: The arguments to the program * * Creates a new stream with name @filename, and adds the stream format * and version header, plus a verbatim copy of the geometry file diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c index 266ada66..48d5004e 100644 --- a/libcrystfel/src/symmetry.c +++ b/libcrystfel/src/symmetry.c @@ -212,9 +212,9 @@ static void add_symop_v(SymOpList *ops, * @m: A %SymOpMask * @idx: Index of the operation to get * - * Returns a pointer to an integer matrix specifying a symmetry operation - * contained in the symmetry operator list, and identified by the specified - * index. + * This function returns a pointer to an integer matrix specifying a symmetry + * operation contained in the symmetry operator list, and identified by the + * specified index. **/ IntegerMatrix *get_symop(const SymOpList *ops, const SymOpMask *m, int idx) { diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c index 0972c710..e09b53c3 100644 --- a/libcrystfel/src/utils.c +++ b/libcrystfel/src/utils.c @@ -283,6 +283,7 @@ struct quaternion normalise_quaternion(struct quaternion q) /** * random_quaternion: + * @rng: A GSL random number generator to use * * Returns: a randomly generated, normalised, quaternion. **/ @@ -328,7 +329,7 @@ int quaternion_valid(struct quaternion q) /** * quat_rot - * @q: A vector (in the form of an %rvec) + * @q: A vector (in the form of a "struct rvec") * @z: A %quaternion * * Rotates a vector according to a quaternion. -- cgit v1.2.3