Documentation fixes

3 files changed, 45 insertions, 48 deletions

diff --git a/doc/man/geoptimiser.1 b/doc/man/geoptimiser.1
index 10bf6dce..8426f365 100644
--- a/doc/man/geoptimiser.1
+++ b/doc/man/geoptimiser.1
@@ -92,7 +92,6 @@ Sets the minimum number of peaks that should fall within a pixel, across all ind
 Sets the minimum number of pixels that contribute to the geometry opimization (see the \fB--min-num-peaks-per-pixel\fR option above ) that a connected group should have for the group to be optimized independently. The default value is 100.
 
 .PD 0
-.IP "\fB-p\fR \fIn\fR"
 .IP \fB--min-num-peaks-per-panel=\fR\fIn\fR
 .PD
 This option has been renamd to  \fB--min-num-pixels-per-conn-group\fR. It has been deprecated and will soon be removed. It is currently mapped to the \fB--min-num-pixels-per-conn-group\fR option.
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 00157ad1..54d3a9f5 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -344,52 +344,6 @@ You do not have to use all three of these options together.  For example, if the
 .PD
 Skip the prediction refinement step.
 
-.SH IDENTIFYING SINGLE PATTERNS IN THE INPUT FILE
-
-By default indexamajig processes all diffraction patterns ("events") in each of the data files listed in the input list. It is however, possible, to only process single events in a multi-event file, by adding in the list an event description string after the data filename. The event description always includes a first section with alphanumeric strings separated by forward slashes ("/") and a second section with integer numbers also separated by forward slashes. The two sections are in turn separated by a double forward slash ('//'). Any of the two sections can be empty, but the double forward slash separator must always be present.  Indexamajig matches the strings and the numbers in the event description with the event placeholders ('%') present respectively in the 'data' and 'dim' properties defined in the geometry file, and tries to retrieve the full HDF path to the event data and the the its location in a multi-dimensional data space. Consider the following examples:
-
-\fBExample 1:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:
-
-.br
-data = /data/%/rawdata
-.br
-dim0 = ss
-.br
-dim1 = fs
-
-The event list contains the following line:
-.br
-
-filename.h5  event1//
-.br
-
-This identifies an event in the 2-dimensional data block located at /data/event1/rawdata in the HDF5 file called filename.h5.
-
-\fBExample 2:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:
-
-.br
-data = /data/rawdata
-.br
-dim0 = %
-.br
-dim1 = ss
-.br
-dim2 = fs
-
-The event list contains the following line:
-.br
-
-filename.h5  //3
-.br
-
-This identifies an event in the 3-dimensional data block located at /data/rawdata in the HDF5 file called filename.h5, specifically the 2-dimensional data slice defined by the value 3 of the first axis of the data space.
-
-Indexamajig tries to match the alphanumerical strings to the placeholders in the 'dim' property defined in the geometry file. The first string is matched to the first placeholder, the second to
-the second placeholder, and so on. A similar strategy is followed to match integer numbers to the placeholders in the 'dim' property defined in the geometry file.
-For a full explanation of how the internal layout of the data file can be  described in the geometry file, please see \fBman crystfel_geometry\fR.
-
-You can use \fBlist_events\fR to prepare a list of each event in one or more input files.  Note that you only need to do this if you need to perform some sorting or filtering on this list.  If you want to process every event in a file, simply specify the filename in the input file.
-
 .PD 0
 .IP \fB--felix-options\fR
 .PD
@@ -500,7 +454,51 @@ Specify a file from which to read in the ideal gvectors for the crystal.
 Specify a maximum time which Felix is allowed to attempt to index the pattern (seconds)
 (Default: 30 s)
 
+.SH IDENTIFYING SINGLE PATTERNS IN THE INPUT FILE
+
+By default indexamajig processes all diffraction patterns ("events") in each of the data files listed in the input list. It is however, possible, to only process single events in a multi-event file, by adding in the list an event description string after the data filename. The event description always includes a first section with alphanumeric strings separated by forward slashes ("/") and a second section with integer numbers also separated by forward slashes. The two sections are in turn separated by a double forward slash ('//'). Any of the two sections can be empty, but the double forward slash separator must always be present.  Indexamajig matches the strings and the numbers in the event description with the event placeholders ('%') present respectively in the 'data' and 'dim' properties defined in the geometry file, and tries to retrieve the full HDF path to the event data and the the its location in a multi-dimensional data space. Consider the following examples:
+
+\fBExample 1:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:
+
+.br
+data = /data/%/rawdata
+.br
+dim0 = ss
+.br
+dim1 = fs
+
+The event list contains the following line:
+.br
+
+filename.h5  event1//
+.br
+
+This identifies an event in the 2-dimensional data block located at /data/event1/rawdata in the HDF5 file called filename.h5.
+
+\fBExample 2:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:
 
+.br
+data = /data/rawdata
+.br
+dim0 = %
+.br
+dim1 = ss
+.br
+dim2 = fs
+
+The event list contains the following line:
+.br
+
+filename.h5  //3
+.br
+
+This identifies an event in the 3-dimensional data block located at /data/rawdata in the HDF5 file called filename.h5, specifically the 2-dimensional data slice defined by the value 3 of the first axis of the data space.
+
+Indexamajig tries to match the alphanumerical strings to the placeholders in the 'dim' property defined in the geometry file. The first string is matched to the first placeholder, the second to
+the second placeholder, and so on. A similar strategy is followed to match integer numbers to the placeholders in the 'dim' property defined in the geometry file.
+For a full explanation of how the internal layout of the data file can be  described in the geometry file, please see \fBman crystfel_geometry\fR.
+
+You can use \fBlist_events\fR to prepare a list of each event in one or more input files.  Note that you only need to do this if you need to perform some sorting or filtering on this list.  If you want to process every event in a file, simply specify the filename in the input file.
 
 .SH AUTHOR
 This page was written by Thomas White.
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index e11c75e7..88148776 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -147,7 +147,7 @@ Set the central photon energy, in eV, for the incident beam.  The default is \fB
 .PD 0
 .IP \fB--really-random\fR
 .PD
-Seed the random number generator using the kernel random number generator (/dev/urandom).  This means that truly random numbers for the orientation and crystal size, instead of the same sequence being used for each new run.
+Seed the random number generator using the kernel random number generator (/dev/urandom).  This means that truly random (although not "cryptographically random") numbers will be used for the orientation and crystal size, instead of the same sequence being used for each new run.
 .SH AUTHOR
 This page was written by Thomas White.