diff options
Diffstat (limited to 'doc/man/crystfel_geometry.5')
| -rw-r--r-- | doc/man/crystfel_geometry.5 | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5 index 44fe4450..974d602b 100644 --- a/doc/man/crystfel_geometry.5 +++ b/doc/man/crystfel_geometry.5 @@ -55,14 +55,13 @@ Information about the layout of the file data can be included in the geometry fi 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\fB/\fIproperty\fB = \fIvalue\fR +\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" (in lower case), because this is used to identify bad regions. +\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: @@ -133,7 +132,7 @@ The range of pixels in the data block specified by the 'data' property that corr .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. +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. .PD 0 .IP \fBbadrow_direction\fR @@ -149,7 +148,7 @@ The resolution (in pixels per metre) for this panel. This is one over the pixel .PD 0 .IP \fBclen\fR .PD -The camera length (in metres) for this panel. You can also specify the HDF path to a floating point data block containing the camera length in millimetres. For example: "panel0/clen = /LCLS/detectorPosition". If the HDF file contains more than one event, and the data block is scalar, the camera length value +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. @@ -187,7 +186,7 @@ Set this to 1 or "true" to ignore this panel completely. .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: -.br +.IP mask = /processing/hitfinder/masks .br mask_good = 0x27 @@ -197,7 +196,9 @@ mask_bad = 0x00 .SH BAD REGIONS -You can also specify bad regions. Peaks with centroid locations within such a region will not be integrated nor used for indexing. 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". +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 @@ -218,6 +219,8 @@ badregionB/max_fs = 160 badregionB/min_ss = 256 .br badregionB/max_ss = 512 +.br +badregionB/panel = q0a1 .SH RIGID GROUPS AND RIGID GROUP COLLECTIONS @@ -248,7 +251,7 @@ The geometry file can include information about beam characteristics, using gene .PD 0 .IP \fBphoton_energy\fR .PD -The beam photon energy in eV. You can also specify the HDF path to a floating point data block value containing the photon energy in eV. For example: "photon_energy = /LCLS/photon_energy_eV". If the HDF file contains more than one event, and the data block is scalar, the photon energy value +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. |