aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--config.h.in1
-rw-r--r--libcrystfel/libcrystfel-config.h.meson.in1
-rw-r--r--libcrystfel/meson.build3
-rw-r--r--libcrystfel/src/crystfel-mille.c131
-rw-r--r--libcrystfel/src/crystfel-mille.h6
-rw-r--r--libcrystfel/src/predict-refine.c6
-rw-r--r--src/im-sandbox.c6
-rw-r--r--subprojects/packagefiles/millepede/meson.build8
-rw-r--r--subprojects/packagefiles/millepede/mille_c_wrap.cc47
-rw-r--r--subprojects/packagefiles/millepede/mille_c_wrap.h30
10 files changed, 121 insertions, 118 deletions
diff --git a/config.h.in b/config.h.in
index f0e8c962..c4ac7ebe 100644
--- a/config.h.in
+++ b/config.h.in
@@ -7,4 +7,3 @@
#mesondefine HAVE_HDF5
#mesondefine HAVE_ASAPO
#mesondefine HAVE_SCHED_SETAFFINITY
-#mesondefine HAVE_MILLEPEDE
diff --git a/libcrystfel/libcrystfel-config.h.meson.in b/libcrystfel/libcrystfel-config.h.meson.in
index c788c017..302fae0b 100644
--- a/libcrystfel/libcrystfel-config.h.meson.in
+++ b/libcrystfel/libcrystfel-config.h.meson.in
@@ -11,7 +11,6 @@
#mesondefine HAVE_CLOCK_GETTIME
#mesondefine HAVE_HDF5
#mesondefine HAVE_SEEDEE
-#mesondefine HAVE_MILLEPEDE
#mesondefine HAVE_FORKPTY_PTY_H
#mesondefine HAVE_FORKPTY_UTIL_H
diff --git a/libcrystfel/meson.build b/libcrystfel/meson.build
index 81156b61..23b267c1 100644
--- a/libcrystfel/meson.build
+++ b/libcrystfel/meson.build
@@ -41,9 +41,6 @@ endif
millepededep = dependency('millepede',
required: false,
fallback: ['millepede', 'millepede_dep'])
-if millepededep.found()
- conf_data.set10('HAVE_MILLEPEDE', true)
-endif
xgandalfdep = dependency('xgandalf',
required: false,
diff --git a/libcrystfel/src/crystfel-mille.c b/libcrystfel/src/crystfel-mille.c
index 036848de..aee391ea 100644
--- a/libcrystfel/src/crystfel-mille.c
+++ b/libcrystfel/src/crystfel-mille.c
@@ -37,11 +37,6 @@
#include "predict-refine.h"
#include "profile.h"
-#ifdef HAVE_MILLEPEDE
-#include <mille_c_wrap.h>
-#endif /* HAVE_MILLEPEDE */
-
-
int mille_label(int group_serial, enum gparam param)
{
switch ( param ) {
@@ -72,7 +67,84 @@ enum gparam mille_unlabel(int n)
}
-#ifdef HAVE_MILLEPEDE
+struct mille
+{
+ float *float_arr;
+ int *int_arr;
+ int max_entries;
+ int n;
+ FILE *fh;
+};
+
+typedef struct mille Mille;
+
+
+static void mille_add_measurement(Mille *m,
+ int NLC, float *derLc,
+ int NGL, float *derGl, int *labels,
+ float rMeas, float sigma)
+{
+ int space_required;
+ int i;
+
+ if ( m == NULL ) return;
+
+ /* Allocate extra space if necessary */
+ space_required = m->n + NLC + NGL + 2;
+ if ( space_required > m->max_entries ) {
+
+ float *new_float_arr;
+ int *new_int_arr;
+ int new_max_entries;
+
+ if ( m->max_entries == 0 ) {
+ new_max_entries = 256;
+ } else {
+ new_max_entries = m->max_entries;
+ }
+
+ while ( new_max_entries < space_required ) {
+ new_max_entries *= 2;
+ }
+
+ new_float_arr = realloc(m->float_arr, new_max_entries*sizeof(float));
+ new_int_arr = realloc(m->int_arr, new_max_entries*sizeof(int));
+ if ( (new_float_arr == NULL) || (new_int_arr == NULL) ) return;
+
+ m->float_arr = new_float_arr;
+ m->int_arr = new_int_arr;
+ m->max_entries = new_max_entries;
+ }
+
+ /* The measurement */
+ m->float_arr[m->n] = rMeas;
+ m->int_arr[m->n] = 0;
+ m->n++;
+
+ /* Local gradients */
+ for ( i=0; i<NLC; i++ ) {
+ if ( derLc[i] != 0.0 ) {
+ m->float_arr[m->n] = derLc[i];
+ m->int_arr[m->n] = i+1;
+ m->n++;
+ }
+ }
+
+ /* The measurement error */
+ m->float_arr[m->n] = sigma;
+ m->int_arr[m->n] = 0;
+ m->n++;
+
+ /* Global gradients */
+ for ( i=0; i<NGL; i++ ) {
+ if ( (derGl[i] != 0.0) && (labels[i] > 0) ) {
+ m->float_arr[m->n] = derGl[i];
+ m->int_arr[m->n] = labels[i];
+ m->n++;
+ }
+ }
+}
+
void write_mille(Mille *mille, int n, UnitCell *cell,
struct reflpeak *rps, struct image *image,
@@ -176,29 +248,58 @@ void write_mille(Mille *mille, int n, UnitCell *cell,
}
-Mille *crystfel_mille_new(const char *outFileName,
- int asBinary,
- int writeZero)
+Mille *crystfel_mille_new(const char *outFileName)
{
- return mille_new(outFileName, asBinary, writeZero);
+ Mille *m;
+
+ m = malloc(sizeof(Mille));
+ if ( m == NULL ) return NULL;
+
+ m->max_entries = 0;
+ m->n = 0;
+ m->float_arr = NULL;
+ m->int_arr = NULL;
+
+ m->fh = fopen(outFileName, "wb");
+ if ( m->fh == NULL ) {
+ ERROR("Failed to open Mille file '%s'\n", outFileName);
+ free(m);
+ return NULL;
+ }
+
+
+ return m;
}
void crystfel_mille_free(Mille *m)
{
- mille_free(m);
+ if ( m == NULL ) return;
+ fclose(m->fh);
+ free(m->float_arr);
+ free(m->int_arr);
+ free(m);
}
void crystfel_mille_delete_last_record(Mille *m)
{
- mille_delete_last_record(m);
+ m->n = 0;
}
void crystfel_mille_write_record(Mille *m)
{
- mille_write_record(m);
-}
+ float nf = 0.0;
+ int ni = 0;
+ int nw = (m->n * 2)+2;
+
+ fwrite(&nw, sizeof(int), 1, m->fh);
-#endif /* HAVE_MILLEPEDE */
+ fwrite(&nf, sizeof(float), 1, m->fh);
+ fwrite(m->float_arr, sizeof(float), m->n, m->fh);
+
+ fwrite(&ni, sizeof(int), 1, m->fh);
+ fwrite(m->int_arr, sizeof(int), m->n, m->fh);
+ m->n = 0;
+}
diff --git a/libcrystfel/src/crystfel-mille.h b/libcrystfel/src/crystfel-mille.h
index e3f4553e..a4b83815 100644
--- a/libcrystfel/src/crystfel-mille.h
+++ b/libcrystfel/src/crystfel-mille.h
@@ -31,7 +31,7 @@
#include <gsl/gsl_matrix.h>
-typedef void *Mille;
+typedef struct mille Mille;
#include "cell.h"
#include "image.h"
@@ -42,9 +42,7 @@ typedef void *Mille;
* Detector geometry refinement using Millepede
*/
-extern Mille *crystfel_mille_new(const char *outFileName,
- int asBinary,
- int writeZero);
+extern Mille *crystfel_mille_new(const char *outFileName);
extern void crystfel_mille_free(Mille *m);
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 9ca95bfc..58bf3580 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -868,13 +868,11 @@ int refine_prediction(struct image *image, Crystal *cr, Mille *mille)
pred_residual(rps, n, image->detgeom));
crystal_add_notes(cr, tmp);
- #ifdef HAVE_MILLEPEDE
if ( mille != NULL ) {
profile_start("mille-calc");
write_mille(mille, n, crystal_get_cell(cr), rps, image, Minvs);
profile_end("mille-calc");
}
- #endif
for ( i=0; i<image->detgeom->n_panels; i++ ) {
gsl_matrix_free(Minvs[i]);
@@ -887,21 +885,17 @@ int refine_prediction(struct image *image, Crystal *cr, Mille *mille)
n = pair_peaks(image, cr, NULL, rps);
free_rps_noreflist(rps, n);
if ( n < 10 ) {
- #ifdef HAVE_MILLEPEDE
if ( mille != NULL ) {
crystfel_mille_delete_last_record(mille);
}
- #endif
return 1;
}
- #ifdef HAVE_MILLEPEDE
if ( mille != NULL ) {
profile_start("mille-write");
crystfel_mille_write_record(mille);
profile_end("mille-write");
}
- #endif
return 0;
}
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 6b68326c..27e33b8f 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -366,13 +366,11 @@ static int run_work(const struct index_args *iargs, Stream *st,
}
mille = NULL;
- #ifdef HAVE_MILLEPEDE
if ( iargs->mille ) {
char tmp[64];
snprintf(tmp, 63, "mille-data-%i.bin", cookie);
- mille = crystfel_mille_new(tmp, 1, 0);
+ mille = crystfel_mille_new(tmp);
}
- #endif
while ( !allDone ) {
@@ -547,9 +545,7 @@ static int run_work(const struct index_args *iargs, Stream *st,
free(pargs.event);
}
- #ifdef HAVE_MILLEPEDE
crystfel_mille_free(mille);
- #endif
/* These are both no-ops if argument is NULL */
im_zmq_shutdown(zmqstuff);
diff --git a/subprojects/packagefiles/millepede/meson.build b/subprojects/packagefiles/millepede/meson.build
index 603c709e..2857205f 100644
--- a/subprojects/packagefiles/millepede/meson.build
+++ b/subprojects/packagefiles/millepede/meson.build
@@ -1,5 +1,5 @@
# Meson file for Millepede-II
-project('millepede', ['c', 'cpp','fortran'],
+project('millepede', ['c', 'fortran'],
version: '2.0.0',
license: 'LGPL2+',
default_options: ['buildtype=debugoptimized'])
@@ -11,11 +11,7 @@ if zlibdep.found()
pede_c_args += '-DUSE_ZLIB'
endif
-mille = library('mille', ['Mille.cc', 'mille_c_wrap.cc'],
- install: true)
-
-millepede_dep = declare_dependency(include_directories: '.',
- link_with: mille)
+millepede_dep = declare_dependency()
executable('pede',
['mpdef.f90',
diff --git a/subprojects/packagefiles/millepede/mille_c_wrap.cc b/subprojects/packagefiles/millepede/mille_c_wrap.cc
deleted file mode 100644
index 103754a1..00000000
--- a/subprojects/packagefiles/millepede/mille_c_wrap.cc
+++ /dev/null
@@ -1,47 +0,0 @@
-#include "Mille.h"
-#include "mille_c_wrap.h"
-
-
-extern "C" Mille *mille_new(const char *outFileName,
- int asBinary,
- int writeZero)
-{
- return new Mille(outFileName, asBinary, writeZero);
-}
-
-
-extern "C" void mille_free(Mille *m)
-{
- delete m;
-}
-
-
-extern "C" void mille_add_measurement(Mille *m,
- int NLC, const float *derLc,
- int NGL, const float *derGl,
- const int *label, float rMeas,
- float sigma)
-{
- m->mille(NLC, derLc, NGL, derGl, label, rMeas, sigma);
-}
-
-
-extern "C" void mille_add_special(Mille *m,
- int nSpecial,
- const float *floatings,
- const int *integers)
-{
- m->special(nSpecial, floatings, integers);
-}
-
-
-extern "C" void mille_delete_last_record(Mille *m)
-{
- m->kill();
-}
-
-
-extern "C" void mille_write_record(Mille *m)
-{
- m->end();
-}
diff --git a/subprojects/packagefiles/millepede/mille_c_wrap.h b/subprojects/packagefiles/millepede/mille_c_wrap.h
deleted file mode 100644
index 1f0fc841..00000000
--- a/subprojects/packagefiles/millepede/mille_c_wrap.h
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifdef __cplusplus
-extern "C" {
-#else
-typedef void *Mille;
-#endif
-
-
-extern Mille *mille_new(const char *outFileName,
- int asBinary,
- int writeZero);
-
-extern void mille_add_measurement(Mille *m,
- int NLC, const float *derLc,
- int NGL, const float *derGl,
- const int *label, float rMeas, float sigma);
-
-extern void mille_add_special(Mille *m,
- int nSpecial,
- const float *floatings,
- const int *integers);
-
-extern void mille_delete_last_record(Mille *m);
-
-extern void mille_write_record(Mille *m);
-
-extern void mille_free(Mille *m);
-
-#ifdef __cplusplus
-} /* extern "C" */
-#endif
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-28 18:50:41 +0000