path: root/doc/man/crystfel_geometry.5

.\"
.\" Geometry man page
.\"
.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
.\"                       a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"

.TH CRYSTFEL\_GEOMETRY 5
.SH NAME
CRYSTFEL DETECTOR GEOMETRY DESCRIPTION FILES

.SH CRYSTFEL DETECTOR GEOMETRY FILES
The detector geometry is taken from a text file rather than hardcoded into the
program.  Programs which care about the geometry (particularly
\fBindexamajig\fR and \fBpattern_sim\fR) take an argument
\fB--geometry=\fR\fIfilename\fR, where \fIfilename\fR contains the geometry.
.PP
A flexible (and pedantic) representation of the detector has been developed to
avoid all possible sources of ambiguity.  CrystFEL's representation of a
detector is broken down into one or more "panels", each of which has its own
camera length, geometry, resolution and so on.  Each panel fits into an overall
data block taken from the HDF5 file, defined by minimum and maximum coordinates in
the "fast scan" and "slow scan" directions.  "Fast scan" refers to the direction
whose coordinate changes most quickly as the bytes in the HDF5 file are moved
through.  The coordinates are specified inclusively, meaning that a minimum of 0
and a maximum of 9 results in a width of ten pixels.  Counting begins from zero.
All pixels in the image must be assigned to a panel - gaps are not permitted.
.PP
The job of the geometry file is to establish a relationship an array
of pixel values in the HDF5 file, defined in terms only of the "fast scan" and
"slow scan" directions, and the laboratory coordinate system defined as follows:

.IP
+z is the beam direction, and points along the beam (i.e. away from the source)

.IP
+y points towards the zenith (ceiling).

.IP
+x completes the right-handed coordinate system.

.PP
Naively speaking, this means that CrystFEL looks at the images from the "into the
beam" perspective, but please avoid thinking of things in this way.  It's much
better to consider the precise way in which the coordinates are mapped.

Some file formats store data for multiple patterns ("events") within a single file.
Information about the layout of the file data can be included in the geometry file.
This allows CrystFEL to unambigously identify data blocks which contain
data for a specific event, and to determine the number of events that each file contains.

The geometry file should contain lines of the following form:

.IP
\fIpanel\fR/clen = 0.560

.PP
\fIpanel\fR can be any name of your choosing.  You can make up names for your panels however you please, as long as the first three letters are not "\fBbad\fR" or "rigid_group" (in lower case), because these are used for special purposes (see below).

.PP
You can also specify values without a panel name, for example:

.IP
clen = 0.560

.PP
In this case, the value will be used for all \fBsubsequent\fR panels appearing in the file which do not have their own specific values for the property, or until you specify another default value further down the file.  Panel-specific values always have priority over default values, and changing the default value has no effect for panels which had already be mentioned at the point in the file where the default value was specified.

.PP
Lines which should be ignored start with a semicolon.

.PP
The properties which can be set are:

.PD 0
.IP \fBdata\fR
.PD
The location in the HDF5 file of the data block that contains the panel's data. If this property is not set, the first 2-dimensional data block in the file hierarchy will be used as data source. If the HDF5 file contains multiple events, and each event is stored in a different data block, the variable part of the path can be represented using the % character placeholder.

Example:
.IP
data = /data/%/rawdata

The CrystFEL programs will look for the first event at /data/\fIevent1_name\fR/rawdata, for the second at /data/\fIevent2_name\fR/rawdata, etc., where \fIevent_name\fR and \fIevent2_name\fR are simply whatever the program could find in the HDF5 file which matched the pattern you gave.

.PD 0
.IP \fBdim\fIn\fR\fR
.PD
Information about the layout of the data block identified by the 'data' property. \fIn\fR is an integer number identifying an axis in a multidimensional HDF5 data block. The property value defines the kind of information encoded by the axis. Possible values are:
.RS
.IP %
.PD
event placeholder,the axis encodes events
.IP ss
.PD
the axis encoding the slow scan index
.IP fs
.PD
the axis encodes the fast scan index
.IP \fInumber\fR
.PD
the index in this dimension should be fixed at \fInumber\fR.
.RE
.IP
CrystFEL assumes that the data block defined by the 'data' property has a dimensionality equal to the axis with the highest value of \fIn\fR defined by the 'dim' property, and requires the user to provide information about each of the axes in the data block. When no 'dim' property is defined in the geometry file, CrystFEL assumes the data block to be 2-dimensional, with the two axes encoding slow scan and fast scan information respectively.
.IP
Note that this does indeed mean that you can assign the fast scan coordinates to the slow scan axis of the data block, and vice versa!  This "quirk" helps backwards compatibility with geometry files from older versions of CrystFEL.

Example:
.RS
.PD 0
.IP
dim0 = %
.IP
dim1 = ss
.IP
dim2 = fs
.IP
dim3 = 4
.RE
.IP
The above snippet specifies that the data block is 3-dimensional. The first axis represents the event number, the second the slow scan panel coordinate, the third the fast scan panel coordinate, and the index in the final axis is always 4.

.PD 0
.IP \fBmin_fs\fR
.IP \fBmin_ss\fR
.IP \fBmax_fs\fR
.IP \fBmax_ss\fR
.PD
The range of pixels in the data block specified by the 'data' property that corresponds to the panel, in fast scan/slow scan coordinates, specified \fBinclusively\fR.

.PD 0
.IP \fBadu_per_eV\fR
.PD
The number of detector intensity units (ADU) which will arise from one electron-Volt of photon energy.  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, but if you use both then \fBadu_per_photon\fR will have priority.

.PD 0
.IP \fBadu_per_photon\fR
.PD
The number of detector intensity units (ADU) which will arise from 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, but if you use both then \fBadu_per_photon\fR will have priority.

.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.

.PD 0
.IP \fBclen\fR
.PD
The camera length (in metres) for this panel. You can also specify the HDF5 path to a floating point data block containing the camera length in millimetres.  For example: "panel0/clen = /LCLS/detectorPosition".  If the HDF5 file contains more than one event, and the data block is scalar, the camera length value
it contains will be used for all events. If, however, the data block is multidimensional and the second dimension is bigger than one, the CrystFEL programs will try to match the content of the data block with the events in the file, assigning the first value in the data block to the first event in the file,
the second value in the data block to the second event in the file, etc. See \fBcoffset\fR as well.

.PD 0
.IP \fBcoffset\fR
.PD
The camera length offset (in metres) for this panel.  This number will be added to the camera length (\fBclen\fR).  This can be useful if the camera length is taken from the HDF5 file and you need to make an adjustment, such as that from a calibration experiment.

.PD 0
.IP \fBfs\fR
.IP \fBss\fR
.PD
For this panel, the fast and slow scan directions correspond to the given directions in the lab coordinate system described above, measured in pixels.  Example: "panel0/fs = 0.5x+0.5y-0.0001z".  Including a component in the z direction means that the panel is not perpendicular to the X-ray beam.

.PD 0
.IP \fBcorner_x\fR
.IP \fBcorner_y\fR
.PD
The corner of this panel, defined as the first point in the panel to appear in the HDF5 file, is now given a position in the lab coordinate system. The units are pixel widths of the current panel.  Note that "first point in the panel" is a conceptual simplification.  We refer to that corner, and to the very corner of the pixel - not, for example, to the centre of the first pixel to appear.

.PD 0
.IP \fBmax_adu\fR
The maximum value, in ADU, before the pixel will be considered as bad.  That is, the saturation value for the panel.

.PD 0
.IP \fBmask\fR
If you have a bad pixel mask, you can include it in the HDF5 file as data blocks with the same structure and size as the panel data.  You need to specify the location of each panel's mask data block using this property, and two bitmasks (see below).  The number of placeholders ('%') in the \fBmask\fR must be the same for all panels.  They will be substituted with the same values as used for the placeholders in the \fBdata\fR fields, although there may be fewer of them for \fBmask\fR than for \fBdata\fR.

.PD 0
.IP \fBmask_file\fR
Use this option to specify that the bad pixel mask should be read from a different file to the image data.  The \fBmask\fR field, if it contains placeholders, will be expanded in exactly the same way as normal, it's just that the data will be read from the file you specify instead of the image data file.  The \fBmask_file\fR may be specified as an absolute filename, or relative to the working directory.

.PD 0
.IP \fBsaturation_map\fR
This specifies the location of the per-pixel saturation map in the HDF5 file.  This works just like \fBmask\fR in that it can come from the current file or a separate one (see \fBsaturation_map_file\fR).  Reflections will be rejected if they contain any pixel above the per-pixel values, \fBin addition\fR to the other checks (see \fBmax_adu\fR).

.PD
.IP \fBsaturation_map_file\fR
Specifies that the saturation map should come from the HDF5 file named here, instead of the HDF5 file being processed.  It can be an absolute filename or relative to the working directory.

.PD 0
.IP \fBmask_good\fR
.IP \fBmask_bad\fR
.PD
Bitmasks for bad pixel masks. The pixel is considered good if all of the bits which are set in \fBmask_good\fR are set, \fIand\fR if none of the bits which are set in \fBmask_bad\fR are set. Example:
.IP
mask = /processing/hitfinder/masks
.br
mask_good = 0x27
.br
mask_bad = 0x00

.PD 0
.IP \fBno_index\fR
Set this to 1 or "true" to ignore this panel completely.

.PD 0
.IP \fBrail_direction\fR
.IP \fBclen_for_centering\fR
.PD
Specify the direction in which the panel should move when the camera length is increased.  \fBclen_for_centering\fR is the camera length at which the central beam intersects the centre of the detector.  If you've only calibrated the detector at one camera length, perhaps using prior known values for the rail direction, then this should be the camera length at which you calibrated the detector.  \fBclen_for_centering\fR is the camera length \fBbefore\fR applying the \fBcoffset\fR, i.e. for CSPAD/CXI/LCLS data this value should be an "encoder value" in metres. If you specify the rail direction, you must also specify clen_for_centering.  The default is for the panel to move in the +z direction, so rail_direction = z and clen_for_centering is irrelevant.  The modulus of the "rail vector" should normally be equal to one.  Otherwise, the camera length changes from the centering value will be correspondingly scaled (which might sometimes be what you want!).

.SH BAD REGIONS

You can also specify bad regions.  Bad regions will be completely ignored by CrystFEL.  Bad regions are specified 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).

Examples:
.br
.br
badregionA/min_x = -20.0
.br
badregionA/max_x = +20.0
.br
badregionA/min_y = -100.0
.br
badregionA/max_y = +100.0

.br
badregionB/min_fs = 128
.br
badregionB/max_fs = 160
.br
badregionB/min_ss = 256
.br
badregionB/max_ss = 512
.br
badregionB/panel = q0a1


.SH RIGID GROUPS AND RIGID GROUP COLLECTIONS

Some operations in CrystFEL, such as refining the detector geometry, need a group of panels to be treated as a single rigid body.  Such "rigid groups" might describe the fact that certain panels are physically connected to one another, for example, a pair of adjacent ASICs in the CSPAD detector.  Rigid groups can be defined in the geometry file by listing the panels belonging to each group and assigning the group a name, like this:
.RS
.IP "\fBrigid_group_\fIname\fR = \fIpanel1\fR,\fIpanel2\fR"
.RE
.PP
This creates a rigid group called \fIname\fR, containing panels \fIpanel1\fR and \fIpanel2\fR.
.PP
You can specify multiple sets of rigid groups.  For example, as well as specifying the relationships between pairs of ASICs mentioned above, you may also want to specify that certain groups of panels belong to an independently-movable quadrant of the detector.  You can declare and name such "rigid group collections" as follows:
.RS
.IP "\fBrigid_group_collection_\fIname\fR = \fIrigidgroup1\fR,\fIrigidgroup2\fR"
.RE
.PP
This creates a rigid group collection called \fIname\fR, containing rigid groups \fIrigidgroup1\fR and \fIrigidgroup2\fR.
.PP
Definitions of rigid groups and rigid group collections can appear at any place in the geometry file and can be declared using the following global properties.  They are not panel properties, and therefore don't follow the usual panel/property syntax.  You can assign any number of panels to a rigid group, and any number of rigid groups to a rigid group collection.  A panel can be a member of any number of rigid groups.

.PP
See the "examples" folder for some examples (look at the ones ending in .geom).

.SH BEAM CHARACTERISTICS

The geometry file can include information about beam characteristics, using general properties, that can appear anywhere in the geometry file and do not follow the usual panel/property syntax. The following beam properties are supported:

.PD 0
.IP \fBphoton_energy\fR
.PD
The beam photon energy in eV. You can also specify the HDF5 path to a floating point data block value containing the photon energy in eV.  For example: "photon_energy = /LCLS/photon_energy_eV".  If the HDF5 file contains more than one event, and the data block is scalar, the photon energy value
it contains will be used for all events. If, however, the data block is multidimensional and the second dimension is bigger than one, the CrystFEL programs will try to match the content of the data block with the events in the file, assigning the first value in the data block to the first event in the file,
the second value in the data block to the second event in the file, etc. See also \fBphoton_energy_scale\fR.

.PD 0
.IP \fBphoton_energy_scale\fR
.PD
Sometimes the photon energy value recorded in an HDF5 file differs from the true photon energy value by a multiplication factor. This property defines a correction factor that is applied by the CrystFEL programs. The photon energy value read from a file is multiplied by the value of this property if the property is defined in the geometry file.


.SH PEAK INFO LOCATION

Finally, the geometry file can include information about where to look in the HDF5 or CXI files for the table of peak positions.  CrystFEL can use these peak locations for indexing.  Simply include \fBpeak_info_location\fR = \fIlocation\fR, where \fIlocation\fR could be something like /processing/hitfinder/peakinfo.  A peak location given on the indexamajig command line, e.g. \fB--hdf5-peaks=/some/location\fR, has priority over the location in the geometry file.  If neither the geometry file nor the command line specify a location, the default is \fB/processing/hitfinder/peakinfo\fR when \fB--peaks=hdf5\fR is used, and \fB/entry_1/result_1\fR when \fB--peaks=cxi\fR is used.

.SH AUTHOR
This page was written by Thomas White and Valerio Mariani.

.SH REPORTING BUGS
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.

.SH COPYRIGHT AND DISCLAIMER
Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
.P
CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
.P
You should have received a copy of the GNU General Public License along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.

.SH SEE ALSO
.BR crystfel (7),
.BR pattern_sim (1),
.BR indexamajig (1)