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authorThomas White <taw@physics.org>2013-07-04 15:28:19 +0200
committerThomas White <taw@physics.org>2013-07-04 15:29:16 +0200
commitd53d140090f4132d8bb53b95bd192cedc47a6283 (patch)
tree841b6b01a49dc5535ff3204cace5cd47f782a438
parent11e82cc07b8fc31c660079189e45ffd5528c9e45 (diff)
Update docs
-rw-r--r--doc/reference/libcrystfel/CrystFEL-docs.sgml5
-rw-r--r--doc/reference/libcrystfel/CrystFEL-sections.txt18
-rw-r--r--libcrystfel/src/integration.h2
3 files changed, 23 insertions, 2 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml
index 413d2c50..4e527253 100644
--- a/doc/reference/libcrystfel/CrystFEL-docs.sgml
+++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml
@@ -83,6 +83,11 @@
</chapter>
<chapter>
+ <title>Integration</title>
+ <xi:include href="xml/integration.xml"><xi:fallback /></xi:include>
+ </chapter>
+
+ <chapter>
<title>Detector</title>
<xi:include href="xml/detector.xml"><xi:fallback /></xi:include>
</chapter>
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index 47516ea3..51e2930c 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -75,6 +75,7 @@ max_intensity
UnitCell
LatticeType
UnitCellTransformation
+rvec
<SUBSECTION>
cell_new
cell_new_from_cell
@@ -132,6 +133,7 @@ right_handed
str_lattice
forbidden_reflection
load_cell_from_pdb
+lattice_from_str
</SECTION>
<SECTION>
@@ -316,6 +318,7 @@ get_q
get_q_for_panel
get_tt
smallest_q
+twod_mapping
reverse_2d_mapping
largest_q
in_bad_region
@@ -388,13 +391,15 @@ PartialityModel
find_intersections
select_intersections
update_partialities
+polarisation_correction
</SECTION>
<SECTION>
<FILE>peaks</FILE>
peak_sanity_check
search_peaks
-integrate_reflections
+integrate_peak
+make_BgMask
validate_peaks
</SECTION>
@@ -407,6 +412,17 @@ render_scale
<FILE>filter</FILE>
filter_cm
filter_noise
+filter_median
+</SECTION>
+
+<SECTION>
+<FILE>integration</FILE>
+INTEGRATION_DEFAULTS_PROF2D
+INTEGRATION_DEFAULTS_RINGS
+INTEGRATION_METHOD_MASK
+IntegrationMethod
+integrate_all
+integration_method
</SECTION>
<SECTION>
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index b438e090..1273348d 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -41,8 +41,8 @@
* @INTEGRATION_NONE: No integration at all
* @INTEGRATION_RINGS: Summation of pixel values inside ring, minus background
* @INTEGRATION_PROF2D: Two dimensional profile fitting
- *
* @INTEGRATION_SATURATED: Integrate saturated reflections
+ * @INTEGRATION_CENTER: Center the peak in the box prior to integration
*
* An enumeration of all the available integration methods.
**/