diff options
| -rw-r--r-- | doc/reference/CrystFEL-docs.sgml | 5 | ||||
| -rw-r--r-- | doc/reference/CrystFEL-sections.txt | 14 | ||||
| -rw-r--r-- | libcrystfel/src/cell-utils.h | 2 | ||||
| -rw-r--r-- | libcrystfel/src/cell.h | 25 | ||||
| -rw-r--r-- | libcrystfel/src/index.h | 16 | ||||
| -rw-r--r-- | libcrystfel/src/integer_matrix.c | 8 | ||||
| -rw-r--r-- | libcrystfel/src/reflist-utils.c | 3 | ||||
| -rw-r--r-- | libcrystfel/src/utils.h | 8 |
8 files changed, 54 insertions, 27 deletions
diff --git a/doc/reference/CrystFEL-docs.sgml b/doc/reference/CrystFEL-docs.sgml index ffff9e9f..348169bd 100644 --- a/doc/reference/CrystFEL-docs.sgml +++ b/doc/reference/CrystFEL-docs.sgml @@ -53,11 +53,6 @@ </chapter> <chapter> - <title>Simulation</title> - <xi:include href="xml/simulation.xml"><xi:fallback /></xi:include> - </chapter> - - <chapter> <title>Indexing</title> <xi:include href="xml/indexing.xml"><xi:fallback /></xi:include> </chapter> diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt index 8da5798c..18a20eb9 100644 --- a/doc/reference/CrystFEL-sections.txt +++ b/doc/reference/CrystFEL-sections.txt @@ -125,7 +125,6 @@ uncenter_cell bravais_lattice right_handed str_lattice -uncenter_cell forbidden_reflection load_cell_from_pdb </SECTION> @@ -152,7 +151,6 @@ safe_basename progress_bar rad2deg is_odd -modulus poisson_noise notrail smallest @@ -209,17 +207,6 @@ stat_scale_intensity </SECTION> <SECTION> -<FILE>simulation</FILE> -clError -cleanup_gpu -GradientMethod -get_cl_dev -get_diffraction -get_diffraction_gpu -setup_gpu -</SECTION> - -<SECTION> <FILE>indexing</FILE> IndexingMethod IndexingPrivate @@ -230,7 +217,6 @@ prepare_indexing index_pattern run_dirax run_mosflm -indexingprivate map_all_peaks </SECTION> diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h index f92ab22d..8eb08ca7 100644 --- a/libcrystfel/src/cell-utils.h +++ b/libcrystfel/src/cell-utils.h @@ -55,7 +55,7 @@ extern int cell_is_sensible(UnitCell *cell); extern int validate_cell(UnitCell *cell); -extern UnitCell *uncenter_cell(UnitCell *in, UnitCellTransformation **tr); +extern UnitCell *uncenter_cell(UnitCell *in, UnitCellTransformation **t); extern int bravais_lattice(UnitCell *cell); diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h index cde25b07..57741b41 100644 --- a/libcrystfel/src/cell.h +++ b/libcrystfel/src/cell.h @@ -40,8 +40,15 @@ #include "utils.h" #include "integer_matrix.h" -/* A 3D vector in reciprocal space. - * Note: Heavily abused to serve as a real space vector as well */ +/** + * rvec: + * @u: x component (in reciprocal space) + * @v: y component (in reciprocal space) + * @w: z component (in reciprocal space) + * + * Structure representing a 3D vector in reciprocal space. + * Note: Heavily abused to serve as a real space vector as well. + **/ struct rvec { double u; @@ -49,6 +56,20 @@ struct rvec double w; }; + +/** + * LatticeType: + * @L_TRICLINIC: Triclinic lattice + * @L_MONOCLINIC: Monoclinic lattice + * @L_ORTHORHOMBIC: Orthorhombic lattice + * @L_TETRAGONAL: Tetragonal lattice + * @L_RHOMBOHEDRAL: Rhombohedral lattice + * @L_HEXAGONAL: Hexagonal lattice + * @L_CUBIC: Cubic lattice + * + * An enumeration of the possible lattice types: triclinic, monoclinic, + * orthorhombic, tetragonal, rhombohedral, hexagonal and cubic. + **/ typedef enum { L_TRICLINIC, diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 9d23f3fb..4a724645 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -43,7 +43,15 @@ #include "detector.h" -/* Indexing methods */ +/** + * IndexingMethod: + * @INDEXING_NONE: No indexing to be performed + * @INDEXING_DIRAX: Invoke DirAx + * @INDEXING_MOSFLM: Invoke MOSFLM + * @INDEXING_REAX: DPS algorithm using known cell parameters + * + * An enumeration of all the available indexing methods. + **/ typedef enum { INDEXING_NONE, INDEXING_DIRAX, @@ -61,6 +69,12 @@ enum { }; +/** + * IndexingPrivate: + * + * This is an opaque data structure containing information needed by the + * indexing method. + **/ typedef struct _indexingprivate IndexingPrivate; extern IndexingPrivate *indexing_private(IndexingMethod indm); diff --git a/libcrystfel/src/integer_matrix.c b/libcrystfel/src/integer_matrix.c index 32784f20..96159cc6 100644 --- a/libcrystfel/src/integer_matrix.c +++ b/libcrystfel/src/integer_matrix.c @@ -62,6 +62,8 @@ struct _integermatrix /** * intmat_new: + * @rows: Number of rows that the new matrix is to have + * @cols: Number of columns that the new matrix is to have * * Allocates a new %IntegerMatrix with all elements set to zero. * @@ -406,7 +408,7 @@ void intmat_print(const IntegerMatrix *m) * intmat_is_identity * @m: An %IntegerMatrix * - * Returns true if @m is an identity matrix. + * Returns: true if @m is an identity matrix. * */ int intmat_is_identity(const IntegerMatrix *m) @@ -439,7 +441,7 @@ int intmat_is_identity(const IntegerMatrix *m) * intmat_is_inversion * @m: An %IntegerMatrix * - * Returns true if @m = -I, where I is an identity matrix. + * Returns: true if @m = -I, where I is an identity matrix. * */ int intmat_is_inversion(const IntegerMatrix *m) @@ -473,7 +475,7 @@ int intmat_is_inversion(const IntegerMatrix *m) * @a: An %IntegerMatrix * @b: An %IntegerMatrix * - * Returns true if @a = @b. + * Returns: true if @a = @b. * */ int intmat_equals(const IntegerMatrix *a, const IntegerMatrix *b) diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c index f2292929..04096ae4 100644 --- a/libcrystfel/src/reflist-utils.c +++ b/libcrystfel/src/reflist-utils.c @@ -437,6 +437,9 @@ double max_intensity(RefList *list) /** * res_cutoff: * @list: A %RefList + * @cell: A %UnitCell with which to calculate 1/d values for @list + * @min: Minimum acceptable value of 1/d + * @max: Maximum acceptable value of 1/d * * Applies a resolution cutoff to @list, returning the new version and freeing * the old version. diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h index 951d9d03..b75693db 100644 --- a/libcrystfel/src/utils.h +++ b/libcrystfel/src/utils.h @@ -100,6 +100,11 @@ extern void show_matrix_eqn(gsl_matrix *M, gsl_vector *v, int r); extern size_t notrail(char *s); extern void chomp(char *s); +/** + * AssplodeFlag: + * @ASSPLODE_NONE: Nothing + * @ASSPLODE_DUPS: Don't merge deliminators + **/ typedef enum { ASSPLODE_NONE = 0, ASSPLODE_DUPS = 1<<0 @@ -141,7 +146,8 @@ static inline double modulus_squared(double x, double y, double z) { static inline double distance3d(double x1, double y1, double z1, double x2, double y2, double z2) { - return modulus(x1-x2, y1-y2, z1-z2); + double d = modulus(x1-x2, y1-y2, z1-z2); + return d; } /* Answer in radians */ |