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-rw-r--r--doc/man/indexamajig.14
-rw-r--r--libcrystfel/meson.build22
-rw-r--r--meson.build20
-rw-r--r--src/indexamajig.c8
-rw-r--r--src/process_image.c10
5 files changed, 35 insertions, 29 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index b8fed6d4..a9d80175 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -336,7 +336,7 @@ Normally, peaks which contain one or more pixels above max_adu (defined in the d
.PD 0
.IP \fB--no-revalidate\fR
.PD
-When using \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR, the peaks will be put through some of the same checks as if you were using \fB--peaks=zaef\fR. These checks reject peaks which are too close to panel edges, are saturated (unless you use \fB--use-saturated\fR), have other nearby peaks (closer than twice the inner integration radius, see \fB--int-radius\fR), or have any part in a bad region. Using this option skips this validation step, and uses the peaks directly.
+When using \fB--peaks=hdf5\fR, \fB--peaks=cxi\fR or \fB--peaks=msgpack\fR, the peaks will be put through some of the same checks as if you were using \fB--peaks=zaef\fR. These checks reject peaks which are too close to panel edges, are saturated (unless you use \fB--use-saturated\fR), have other nearby peaks (closer than twice the inner integration radius, see \fB--int-radius\fR), or have any part in a bad region. Using this option skips this validation step, and uses the peaks directly.
.PD 0
.IP \fB--no-half-pixel-shift\fR
@@ -346,7 +346,7 @@ CrystFEL considers all peak locations to be distances from the corner of the det
.PD 0
.IP \fB--check-hdf5-snr\fR
.PD
-With this option with \fB--peaks=hdf5\fR, the peaks will additionally be checked to see that they satisfy the minimum SNR specified with \fB--min-snr\fR.
+With this option with \fB--peaks=hdf5\fR (or \fBcxi\fR or \fBmsgpack\fR), the peaks will additionally be checked to see that they satisfy the minimum SNR specified with \fB--min-snr\fR.
.SH INDEXING OPTIONS
.PD 0
diff --git a/libcrystfel/meson.build b/libcrystfel/meson.build
index d333d554..b5005aa5 100644
--- a/libcrystfel/meson.build
+++ b/libcrystfel/meson.build
@@ -5,7 +5,7 @@ if zlibdep.found()
if cc.has_function('gzbuffer',
prefix: '#include <zlib.h>',
dependencies: zlibdep)
- conf_data.set10('HAVE_GZBUFFER', 1)
+ conf_data.set10('HAVE_GZBUFFER', true)
endif
else
zlibproj = subproject('zlib')
@@ -13,49 +13,49 @@ else
# Cannot check for gzbuffer in this case, because Zlib won't be built
# until compile time. However, we already know that the wrap version is
# new enough
- conf_data.set10('HAVE_GZBUFFER', 1)
+ conf_data.set10('HAVE_GZBUFFER', true)
endif
if zlibdep.found()
- conf_data.set10('HAVE_ZLIB', 1)
+ conf_data.set10('HAVE_ZLIB', true)
endif
fftwdep = dependency('fftw3', required: false)
if fftwdep.found()
- conf_data.set10('HAVE_FFTW', 1)
+ conf_data.set10('HAVE_FFTW', true)
endif
xgandalfdep = dependency('xgandalf',
required: false,
fallback: ['xgandalf', 'xgandalf_dep'])
if xgandalfdep.found()
- conf_data.set10('HAVE_XGANDALF', 1)
+ conf_data.set10('HAVE_XGANDALF', true)
endif
pinkindexerdep = dependency('pinkIndexer',
required: false,
fallback: ['pinkindexer', 'pinkindexer_dep'])
if pinkindexerdep.found()
- conf_data.set10('HAVE_PINKINDEXER', 1)
+ conf_data.set10('HAVE_PINKINDEXER', true)
endif
fdipdep = dependency('fdip',
required: false,
fallback: ['fdip', 'fdip_dep'])
if fdipdep.found()
- conf_data.set10('HAVE_FDIP', 1)
+ conf_data.set10('HAVE_FDIP', true)
endif
ccp4dep = dependency('libccp4c',
required: false,
fallback: ['libccp4c', 'libccp4c_dep'])
if ccp4dep.found()
- conf_data.set10('HAVE_LIBCCP4', 1)
+ conf_data.set10('HAVE_LIBCCP4', true)
endif
msgpackdep = dependency('msgpack', required: false)
if msgpackdep.found()
- conf_data.set10('HAVE_MSGPACK', 1)
+ conf_data.set10('HAVE_MSGPACK', true)
endif
@@ -68,9 +68,9 @@ libcrystfel_includes = include_directories('src')
# Find forkpty()
utildep = cc.find_library('util', required: true)
if cc.has_function('forkpty', dependencies: utildep, prefix: '#include <pty.h>')
- conf_data.set10('HAVE_FORKPTY_PTY_H', 1)
+ conf_data.set10('HAVE_FORKPTY_PTY_H', true)
elif cc.has_function('forkpty', dependencies: utildep, prefix: '#include <util.h>')
- conf_data.set10('HAVE_FORKPTY_UTIL_H', 1)
+ conf_data.set10('HAVE_FORKPTY_UTIL_H', true)
else
error('Couldn\'t find forkpty()')
endif
diff --git a/meson.build b/meson.build
index d7b04aae..be0f6477 100644
--- a/meson.build
+++ b/meson.build
@@ -24,7 +24,7 @@ pthreaddep = dependency('threads', required: true)
# Find HDF5 using inbuilt Meson methods. Requires Meson >= 0.50.0
hdf5dep = dependency('hdf5', language: 'c', required: get_option('hdf5'))
if hdf5dep.found()
- conf_data.set10('HAVE_HDF5', 1)
+ conf_data.set10('HAVE_HDF5', true)
# Request HDF5 1.10-style API
add_project_arguments('-DH5_USE_110_API', language: 'c')
add_project_arguments('-DH5O_GET_INFO_BY_IDX1', language: 'c')
@@ -32,45 +32,45 @@ endif
fftwdep = dependency('fftw3', required: false)
if fftwdep.found()
- conf_data.set10('HAVE_FFTW', 1)
+ conf_data.set10('HAVE_FFTW', true)
endif
gtkdep = dependency('gtk+-3.0', required: false)
if gtkdep.found()
add_project_arguments('-Wno-deprecated-declarations', language: 'c')
- conf_data.set10('HAVE_GTK', 1)
+ conf_data.set10('HAVE_GTK', true)
endif
gdkdep = dependency('gdk-3.0', required: false)
if gdkdep.found()
- conf_data.set10('HAVE_GDK', 1)
+ conf_data.set10('HAVE_GDK', true)
endif
gdkpixbufdep = dependency('gdk-pixbuf-2.0', required: false)
if gdkpixbufdep.found()
- conf_data.set10('HAVE_GDKPIXBUF', 1)
+ conf_data.set10('HAVE_GDKPIXBUF', true)
endif
cairodep = dependency('cairo', required: false)
if cairodep.found()
- conf_data.set10('HAVE_CAIRO', 1)
+ conf_data.set10('HAVE_CAIRO', true)
endif
opencldep = dependency('OpenCL', required: get_option('opencl'))
if opencldep.found()
- conf_data.set10('HAVE_OPENCL', 1)
+ conf_data.set10('HAVE_OPENCL', true)
if cc.has_header('CL/cl.h', dependencies: opencldep)
- conf_data.set10('HAVE_CL_CL_H', 1)
+ conf_data.set10('HAVE_CL_CL_H', true)
endif
endif
zmqdep = dependency('libzmq', required: false)
if zmqdep.found()
- conf_data.set10('HAVE_ZMQ', 1)
+ conf_data.set10('HAVE_ZMQ', true)
endif
if cc.has_function('clock_gettime', prefix: '#include <time.h>')
- conf_data.set10('HAVE_CLOCK_GETTIME', 1)
+ conf_data.set10('HAVE_CLOCK_GETTIME', true)
endif
# ************************ libcrystfel (subdir) ************************
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 75c7a2d5..fc22a562 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -229,7 +229,7 @@ static void write_harvest_file(struct index_args *args,
fprintf(fh, " },\n");
if ( args->ipriv == NULL ) {
- fprintf(fh, " \"indexing\": null\n");
+ fprintf(fh, " \"indexing\": null,\n");
fprintf(fh, " \"integration\": null\n");
} else {
@@ -970,11 +970,11 @@ int main(int argc, char *argv[])
"highest pixel and neighbours (peakfinder9 only, just for speed)"},
{"no-use-saturated", 318, NULL, OPTION_NO_USAGE, "Reject saturated peaks"},
{"no-revalidate", 319, NULL, OPTION_NO_USAGE, "Don't re-integrate and check HDF5 "
- "peaks"},
+ "or MsgPack peaks"},
{"no-half-pixel-shift", 320, NULL, OPTION_NO_USAGE, "Don't offset HDF5 peak "
"locations by 0.5 pixels"},
- {"check-hdf5-snr", 321, NULL, OPTION_NO_USAGE, "Check SNR for peaks from HDF5 or "
- "CXI (see --min-snr)"},
+ {"check-hdf5-snr", 321, NULL, OPTION_NO_USAGE, "Check SNR for peaks from HDF5, "
+ "CXI or MsgPack (see --min-snr)"},
{NULL, 0, 0, OPTION_DOC, "Indexing options:", 4},
{"indexing", 400, "method", 0, "List of indexing methods"},
diff --git a/src/process_image.c b/src/process_image.c
index 5282e135..9151528d 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -3,11 +3,11 @@
*
* The processing pipeline for one image
*
- * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2022 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2020 Thomas White <taw@physics.org>
+ * 2010-2022 Thomas White <taw@physics.org>
* 2014-2017 Valerio Mariani <valerio.mariani@desy.de>
* 2017 Stijn de Graaf
*
@@ -319,6 +319,12 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
pargs->zmq_data,
pargs->zmq_data_size,
iargs->half_pixel_shift);
+ if ( !iargs->no_revalidate ) {
+ validate_peaks(image, iargs->min_snr,
+ iargs->pk_inn, iargs->pk_mid,
+ iargs->pk_out, iargs->use_saturated,
+ iargs->check_hdf5_snr);
+ }
break;
case PEAK_NONE:
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 17:34:19 +0000