Updates for manual pages

6 files changed, 9 insertions, 27 deletions

diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7
index 73c4e0f3..243d8d1b 100644
--- a/doc/man/crystfel.7
+++ b/doc/man/crystfel.7
@@ -57,9 +57,6 @@ Tools for calculating figures of merit, such as completeness and R-factors.
 .IP \fBpartial_sim\fB
 A tool for calculating partial reflection intensities, perhaps for testing the convergence of Monte Carlo merging.
 
-.IP \fBhdfsee\fR
-A simple viewer for images stored in HDF5 format.
-
 .IP \fBrender_hkl\fR
 A tool for rendering slices of reciprocal space in two dimensions.
 
@@ -168,7 +165,6 @@ You should have received a copy of the GNU General Public License along with Cry
 .BR compare_hkl (1),
 .BR check_hkl (1),
 .BR render_hkl (1),
-.BR hdfsee (1),
 .BR get_hkl (1),
 .BR cell_tool (1),
 .BR geoptimiser (1),
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index 7a92f631..541d729e 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -156,7 +156,7 @@ dim2 = ss
 dim3 = fs
 .RE
 .IP
-The above snippet specifies that the data block is 3-dimensional. The first axis represents the event number, the index in the second axis is always 4, and the remaining two axes are the image coordinates.
+The above snippet specifies that the data block is 4-dimensional. The first axis represents the event number, the index in the second axis is always 4, and the remaining two axes are the image coordinates.
 
 .PD 0
 .IP \fBmin_fs\fR
@@ -173,13 +173,6 @@ The range of pixels in the data block specified by the 'data' property that corr
 The number of detector intensity units (ADU) which will arise from either one electron-Volt of photon energy, or one photon.  This is used to estimate Poisson errors.  Note that setting different values for this parameter for different panels does \fBnot\fR result in the intensities being scaled accordingly when integrating data, but it does affect the intensities calculated by \fBpattern_sim\fR.  You should only specify one out of \fBadu_per_eV\fR and \fBadu_per_photon\fR.
 
 .PD 0
-.IP \fBbadrow_direction\fR
-.PD
-This is the readout direction of a CCD panel, and can be \fBf\fR, \fBs\fR or \fB-\fR.
-If more than three peaks are found in the same readout region with similar coordinates perpendicular to the readout direction, they will all be discarded.  This helps to avoid problems due to streaks appearing along the readout direction, which has happened in the past with pnCCD detectors.
-If the badrow direction is '-', then the culling will not be performed for this panel.
-
-.PD 0
 .IP \fBres\fR
 The resolution (in pixels per metre) for this panel.  This is one over the pixel size in metres.
 
@@ -223,7 +216,7 @@ Mark pixels as "bad" if their values are respectively less than, more than or eq
 .IP \fBmaskN_goodbits\fR
 .IP \fBmaskN_badbits\fR
 .PD
-These specify the parameters for bad pixel mask number \fIN\fR.  You can have up to 8 bad pixel masks, numbered from 0 to 7 inclusive.  Placeholders ('%') in the location (\fBmaskN_data\fR) will be substituted with the same values as used for the placeholders in the image data, although there may be fewer of them for the masks than from the image data.
+These specify the parameters for bad pixel mask number \fIN\fR.  You can have up to 8 bad pixel masks, numbered from 0 to 7 inclusive.  Placeholders ('%') in the location (\fBmaskN_data\fR) will be substituted with the same values as used for the placeholders in the image data, although there may be fewer of them for the masks than for the image data.
 .IP
 You can optionally give a filename for each mask with \fBmaskN_file\fR.  The filename may be specified as an absolute filename, or relative to the working directory.  If you don't specify a filename, the mask will be read from the same file as the image data.
 .IP
@@ -278,7 +271,9 @@ Specify the direction in which the panel should move when the camera length is i
 
 Bad regions will be completely ignored by CrystFEL.  You can specify the pixels to exclude in pixel units, either in the lab coordinate system (see above) or in fast scan/slow scan coordinates (mixtures are not allowed).   In the latter case, the range of pixels is specified \fIinclusively\fR.  Bad regions are distinguished from normal panels by the fact that they begin with the three letters "bad".
 .PP
-You can specify a panel name for the bad region, in which case the pixels will only be considered bad if they are within the range you specify \fIand\fR in the panel you specify.  This might be necessary if your HDF5 file layout has overlapping ranges of fs/ss coordinates for different panels (e.g. if the data blocks for the panels are in different HDF5 datasets).
+If you specify a bad region in fs/ss (image data) coordinates, you must also specify which panel name you are referring to.
+.PP
+Note that bad regions specified in x/y (lab frame) coordinates take longer to process (when loading images) than regions specified in fs/ss (image data) coordinates.  You should use fs/ss coordinates unless the convenience of x/y coordinates outweighs the speed reduction.
 
 Examples:
 .br
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index d3ed3091..4e67f234 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -41,7 +41,7 @@ Indexamajig requires an input file with a list of diffraction patterns ("events"
 
 .SH PEAK DETECTION
 
-You can control the peak detection on the command line.  Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR will take the peak locations from the input file.  See the documentation for \fBpeak_list\fR and \fBpeak_list_type\fR in crystfel_geometry(5) for details.
+You can control the peak detection on the command line.  First, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR will take the peak locations from the input file.  See the documentation for \fBpeak_list\fR and \fBpeak_list_type\fR in crystfel_geometry(5) for details.
 
 If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000).  You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-squared-gradient\fR.  The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units.  Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below).  They will also be rejected if the peak is closer than twice the inner integration radius from another peak.
 
@@ -149,14 +149,6 @@ Normally, reflections which contain one or more pixels above max_adu (defined in
 .PD
 Fit the background around the reflection using gradients in two dimensions.  This was the default until version 0.6.1.  Without the option (or with its opposite, \fB-nograd\fR, which is the default), the background will be considered to have the same value across the entire integration box.
 
-.SH OPTIMISING THE INTEGRATION RADII
-To determine appropriate values for the integration radii, index some patterns with the default values and view the results using \fBcheck-near-bragg\fR (in the scripts folder).  Set the binning in \fBhdfsee\fR to 1, and adjust the ring radius until none of the rings overlap for any of the patterns.  This ring radius is the outer radius to use. Then reduce the radius until the circles match the sizes of the peaks as closely as possible.  This value is the inner radius.  The middle radius should be between the two, ideally between two and three pixels smaller than the outer radius.
-.PP
-If it's difficult to do this without setting the middle radius to the
-same value as the inner radius, then the peaks are too close together to be
-accurately integrated.  Perhaps you got greedy with the resolution and put the
-detector too close to the interaction region?
-
 .SH BASIC OPTIONS
 .PD 0
 .IP "\fB-i\fR \fIfilename\fR"
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 7cd8df03..817fd7ed 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -95,7 +95,7 @@ Run \fIn\fR analyses in parallel.
 .PD 0
 .IP \fB--polarisation=\fItype\fR
 .PD
-Specify the polarisation of the incident radiation.  \fItype\fR can be \fBhoriz\fR or \fBvert\fR to indicate 100% polarisation of the electric field in the horizontal plane or vertical plane respectively.  Setting \fItype\fR to \fBnone\fR completely disables the polarisation correction (see the note below).  Alternatively, \fItype\fR can be a direction followed by a percentage polarisation fraction.  For example, \fB45deg90\fR means that 90% of the radiation is polarised with its electric field in a direction 45 degrees from horizontal, and \fB10deg100\fR means that all the radiation is polarised at 10 degrees from horizontal.  The angle is specified clockwise from horizontal as viewed along the beam direction, i.e. as shown by \fBhdfsee\fR.  The beam is unpolarised when the fraction is 50% (equal parts of the radiation have their electric field in the specified plane).  If the polarisation fraction is 100%, it can be omitted.  For example \fB10deg\fR or \fBhoriz\fR.
+Specify the polarisation of the incident radiation.  \fItype\fR can be \fBhoriz\fR or \fBvert\fR to indicate 100% polarisation of the electric field in the horizontal plane or vertical plane respectively.  Setting \fItype\fR to \fBnone\fR completely disables the polarisation correction (see the note below).  Alternatively, \fItype\fR can be a direction followed by a percentage polarisation fraction.  For example, \fB45deg90\fR means that 90% of the radiation is polarised with its electric field in a direction 45 degrees from horizontal, and \fB10deg100\fR means that all the radiation is polarised at 10 degrees from horizontal.  The angle is specified clockwise from horizontal as viewed along the beam direction, i.e. as shown by the CrystFEL GUI.  The beam is unpolarised when the fraction is 50% (equal parts of the radiation have their electric field in the specified plane).  If the polarisation fraction is 100%, it can be omitted.  For example \fB10deg\fR or \fBhoriz\fR.
 
 Note that \fB--polarisation=none\fR is not the same as, for example, \fB--polarisation=vert50\fR.  In the first case, the polarisation correction will be completely disabled.  In the other case, the incident beam will be unpolarised, but the polarisation of the diffracted radiation will still be corrected for (the factor of (1+cos^2(2theta))/2 or, equivalently, (2-sin^2(2theta))/2).
 
diff --git a/doc/man/process_hkl.1 b/doc/man/process_hkl.1
index ff1933ab..a9b5e2dd 100644
--- a/doc/man/process_hkl.1
+++ b/doc/man/process_hkl.1
@@ -86,7 +86,7 @@ Use \fBpartialator\fR if you need more advanced merging techniques.
 .PD 0
 .IP \fB--polarisation=\fItype\fR
 .PD
-Specify the polarisation of the incident radiation.  \fItype\fR can be \fBhoriz\fR or \fBvert\fR to indicate 100% polarisation of the electric field in the horizontal plane or vertical plane respectively.  Setting \fItype\fR to \fBnone\fR completely disables the polarisation correction (see the note below).  Alternatively, \fItype\fR can be a direction followed by a percentage polarisation fraction.  For example, \fB45deg90\fR means that 90% of the radiation is polarised with its electric field in a direction 45 degrees from horizontal, and \fB10deg100\fR means that all the radiation is polarised at 10 degrees from horizontal.  The angle is specified clockwise from horizontal as viewed along the beam direction, i.e. as shown by \fBhdfsee\fR.  The beam is unpolarised when the fraction is 50% (equal parts of the radiation have their electric field in the specified plane).  If the polarisation fraction is 100%, it can be omitted.  For example \fB10deg\fR or \fBhoriz\fR.
+Specify the polarisation of the incident radiation.  \fItype\fR can be \fBhoriz\fR or \fBvert\fR to indicate 100% polarisation of the electric field in the horizontal plane or vertical plane respectively.  Setting \fItype\fR to \fBnone\fR completely disables the polarisation correction (see the note below).  Alternatively, \fItype\fR can be a direction followed by a percentage polarisation fraction.  For example, \fB45deg90\fR means that 90% of the radiation is polarised with its electric field in a direction 45 degrees from horizontal, and \fB10deg100\fR means that all the radiation is polarised at 10 degrees from horizontal.  The angle is specified clockwise from horizontal as viewed along the beam direction, i.e. as shown by the CrystFEL GUI.  The beam is unpolarised when the fraction is 50% (equal parts of the radiation have their electric field in the specified plane).  If the polarisation fraction is 100%, it can be omitted.  For example \fB10deg\fR or \fBhoriz\fR.
 
 Note that \fB--polarisation=none\fR is not the same as, for example, \fB--polarisation=vert50\fR.  In the first case, the polarisation correction will be completely disabled.  In the other case, the incident beam will be unpolarised, but the polarisation of the diffracted radiation will still be corrected for (the factor of (1+cos^2(2theta))/2 or, equivalently, (2-sin^2(2theta))/2).
 
diff --git a/doc/man/render_hkl.1 b/doc/man/render_hkl.1
index 3c248c28..7afd8727 100644
--- a/doc/man/render_hkl.1
+++ b/doc/man/render_hkl.1
@@ -137,5 +137,4 @@ You should have received a copy of the GNU General Public License along with Cry
 
 .SH SEE ALSO
 .BR crystfel (7),
-.BR check_hkl (1),
-.BR hdfsee (1)
+.BR check_hkl (1)