Update docs

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
 <SUBSECTION>
 cell_new
 cell_new_from_cell
@@ -173,6 +172,9 @@ ph_lambda_to_eV
 random_flat
 flat_noise
 show_matrix
+likely
+unlikely
+UNUSED
 </SECTION>
 
 <SECTION>
@@ -299,6 +301,7 @@ free_symopmask
 describe_symmetry
 symmetry_name
 set_symmetry_name
+get_matrix_name
 is_centrosymmetric
 is_centric
 </SECTION>
@@ -347,6 +350,7 @@ twod_mapping
 reverse_2d_mapping
 largest_q
 in_bad_region
+mark_resolution_range_as_bad
 </SECTION>
 
 <SECTION>
@@ -426,7 +430,6 @@ LORENTZ_SCALE
 <FILE>peaks</FILE>
 peak_sanity_check
 search_peaks
-integrate_peak
 make_BgMask
 validate_peaks
 </SECTION>
@@ -453,6 +456,7 @@ IntDiag
 integrate_all
 integrate_all_2
 integrate_all_3
+integrate_all_4
 integration_method
 </SECTION>
 
@@ -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
 </SECTION>
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.