From d53d140090f4132d8bb53b95bd192cedc47a6283 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 4 Jul 2013 15:28:19 +0200
Subject: Update docs

---
 doc/reference/libcrystfel/CrystFEL-docs.sgml    |  5 +++++
 doc/reference/libcrystfel/CrystFEL-sections.txt | 18 +++++++++++++++++-
 libcrystfel/src/integration.h                   |  2 +-
 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
@@ -82,6 +82,11 @@
         <xi:include href="xml/indexing.xml"><xi:fallback /></xi:include>
   </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>
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.
  **/
-- 
cgit v1.2.3