void repository::builder::build(const entry &package) {
try {
BUNSAN_LOG_DEBUG << "Starting \"" << package << "\" " << __func__;
const tempfile build_dir_ = local_system_().tempdir_for_build();
const boost::filesystem::path build_dir = build_dir_.path();
const boost::filesystem::path src =
build_dir / m_config.name.dir.get_source();
const boost::filesystem::path build =
build_dir / m_config.name.dir.get_build();
const boost::filesystem::path installation =
build_dir / m_config.name.dir.get_installation();
// create/clean directories
boost::filesystem::create_directory(src);
boost::filesystem::create_directory(build);
boost::filesystem::create_directory(installation);
// unpack source
snapshot snapshot_;
unpack_source(package, src, snapshot_);
get_builder()->install(build_dir / m_config.name.dir.get_source(),
build_dir / m_config.name.dir.get_build(),
build_dir / m_config.name.dir.get_installation());
cache_().pack_build(package,
build_dir / m_config.name.dir.get_installation());
write_snapshot(cache_().build_snapshot_path(package), snapshot_);
} catch (std::exception &) {
BOOST_THROW_EXCEPTION(builder_build_error()
<< builder_build_error::package(package)
<< enable_nested_current());
}
}
void repository::builder::build_installation(const entry &package) {
try {
BUNSAN_LOG_DEBUG << "Starting \"" << package << "\" " << __func__;
const tempfile build_dir = local_system_().tempdir_for_build();
boost::filesystem::path install_dir =
build_dir.path() / m_config.name.dir.get_installation();
// unpack
extractor_().extract_build(package, install_dir);
snapshot snapshot_ = cache_().read_build_snapshot(package);
const index deps = cache_().read_index(package);
for (const auto &i : deps.package.self)
extractor_().extract_source(package, i.source, install_dir / i.path);
for (const auto &i : deps.package.import.source)
unpack_source(i.package, install_dir / i.path, snapshot_);
for (const auto &i : deps.package.import.package) {
extractor_().extract_installation(i.package, install_dir / i.path);
merge_maps(snapshot_, cache_().read_installation_snapshot(i.package));
}
// save
cache_().pack_installation(package, install_dir);
write_snapshot(cache_().installation_snapshot_path(package), snapshot_);
} catch (std::exception &) {
BOOST_THROW_EXCEPTION(builder_build_installation_error()
<< builder_build_installation_error::package(package)
<< enable_nested_current());
}
}
void out_result(void)
{
string out;
if (outstr==NULL) {
out = getparam("out");
outstr = stropen(out, "w");
put_history(outstr);
}
write_snapshot(); /* output testdata results */
}
int main(int argc, char * argv [])
{
const int n = argc > 1 ? atoi(argv[1]) : 1000000;
fprintf(stderr, " -- writing %d particles -- \n", n);
assert(n > 16);
MPI_Init(&argc, &argv);
int rank, nrank;
MPI_Comm_rank (MPI_COMM_WORLD, &rank);
MPI_Comm_size (MPI_COMM_WORLD, &nrank);
const MPI_Comm MPI_WORKING_WORLD = MPI_COMM_WORLD;
std::vector<real4> pos(n), vel(n);
std::vector<int> IDs(n);
for (int i = 0; i < n ; i++)
{
const float fi = i;
pos[i] = (real4){ fi, fi+1.0f, fi-1.0f, -fi-1.0f};
vel[i] = (real4){2.0f*fi, 2.0f*fi+1.0f, 2.0f*fi-1.0f, -2.0f*fi-1.0f};
IDs[i] = 3*i-2;
}
const float time = 0.125;
std::string fileName; fileName.resize(256);
MPI_Barrier(MPI_WORKING_WORLD);
const double t0 = rtc();
#ifndef _SION_
sprintf(&fileName[0], "%s_%010.4f-%d", "naive_test", time, rank);
const size_t nbytes = write_snapshot(
&pos[0], &vel[0], &IDs[0], n, fileName, time,
rank, nrank, MPI_WORKING_WORLD);
#else
sprintf(&fileName[0], "%s_%010.4f-%d", "sion_test", time, nrank);
const size_t nbytes = sion_write_snapshot(
&pos[0], &vel[0], &IDs[0], n, fileName, time,
rank, nrank, MPI_WORKING_WORLD);
#endif
MPI_Barrier(MPI_WORKING_WORLD);
const double t1 = rtc();
if (rank == 0)
fprintf(stderr, " -- writing took %g sec -- BW= %g MB/s\n",
(t1-t0), nbytes/1e6/(t1-t0));
MPI_Finalize();
}
void repository::builder::build_empty(const entry &package) {
try {
BUNSAN_LOG_DEBUG << "Starting \"" << package << "\" " << __func__;
const tempfile build_dir = local_system_().tempdir_for_build();
// create empty archive
cache_().pack_build(package, build_dir.path());
const snapshot snapshot_ = {{package, cache_().read_checksum(package)}};
write_snapshot(cache_().build_snapshot_path(package), snapshot_);
} catch (std::exception &) {
BOOST_THROW_EXCEPTION(builder_build_empty_error()
<< builder_build_empty_error::package(package)
<< enable_nested_current());
}
}
/* Here we load a snapshot file. It can be distributed
* onto several files (for files>1).
* The particles are brought back into the order
* implied by their ID's.
* A unit conversion routine is called to do unit
* conversion, and to evaluate the gas temperature.
*/
int main(int argc, char **argv)
{
char path[200], input_fname[200], output_fname[200], basename[200], basenameout[200];
int j, n, type, snapshot_number, output_number,files, Ngas, random, ncount, ncounthalo1, ncount2;
float x,y,z,x1,y1, z1, delr;
double delx, dely, delz, boxsize;
FILE *outfile;
sprintf(path, "/work/00863/minerva/");
sprintf(basename, "bin_HR10_map");
output_number = 0;
for(j=0; j<=0; j=j+1)
{
snapshot_number=j;
files=1;
boxsize = 140.0;
delx = 512.65800353; //del's used in making bin_zoom10_cut_??? (bin_zoom10_???)
dely = 505.21836888;
delz = 497.39349349;
sprintf(input_fname, "%s/%s_%03d", path, basename, snapshot_number);
if(snapshot_number > 999)
sprintf(input_fname, "%s/%s_%04d", path, basename, snapshot_number);
if(snapshot_number > 9999)
sprintf(input_fname, "%s/%s_%05d", path, basename, snapshot_number);
sprintf(basenameout, "ot");
sprintf(output_fname, "%s/%s_%04d", path, basenameout, output_number);
if(snapshot_number > 999)
sprintf(output_fname, "%s/%s_%04d", path, basenameout, output_number);
if(snapshot_number > 9999)
sprintf(output_fname, "%s/%s_%05d", path, basenameout, output_number);
output_number++;
Ngas = write_snapshot(input_fname, files, output_fname, delx, dely, delz, boxsize);
unit_conversion();
do_what_you_want();
free(P);
}
}
/* Here we load a snapshot file. It can be distributed
* onto several files (for files>1).
* The particles are brought back into the order
* implied by their ID's.
* A unit conversion routine is called to do unit
* conversion, and to evaluate the gas temperature.
*/
int main(int argc, char **argv)
{
char path[200], input_fname[200], input_fname_dm[200], output_fname[200], basename[200], basenameout[200];
int j, n, type, snapshot_number, files, Ngas, random, ncount, ncounthalo1, ncount2;
float x,y,z,x1,y1, z1, delr;
double delx, dely, delz, delx_dm, dely_dm, delz_dm, boxsize;
FILE *outfile;
sprintf(path, "/work/00863/minerva");
sprintf(basename, "ds_ic");
snapshot_number=000; /* number of snapshot */
files=1;
boxsize = 100.0;
delx = 50.339110402;
dely = 50.122129376;
delz = 49.486652655;
delx_dm = 3.4331373996e-06;
dely_dm = 3.4336503546e-06;
delz_dm = 3.432893655e-06;
sprintf(input_fname, "%s/%s_%03d", path, basename, snapshot_number);
sprintf(input_fname_dm, "/work/00863/minerva/minihalo_128");
sprintf(output_fname, "/work/00863/minerva/ds_ng_000");
Ngas = write_snapshot(input_fname, input_fname_dm, files, output_fname, delx, dely, delz, delx_dm, dely_dm, delz_dm, boxsize);
unit_conversion();
ncount = 0;
ncount2 = 0;
printf("ncount = %d.\n", ncount);
printf("ncount2 = %d.\n", ncount2);
do_what_you_want();
}
static void snapshot_save_callback(unsigned int opt) {
const char *snap_exts[] = { "SN0", "SN1", "SN2", "SN3", "SN4",
"SN5", "SN6", "SN7", "SN8", "SN9", NULL };
int selected;
Menu savemenu[2];
char filename[13];
(void)opt; /* unused */
if (save_basename == NULL) {
notify_box("Unable to save snapshot");
return;
}
memset(savemenu, 0, sizeof(savemenu));
savemenu[0].label = save_basename;
savemenu[0].num_opts = 10;
savemenu[0].options = snap_exts;
selected = show_menu(savemenu, 1, 9, 38, 1);
if (selected < 0)
return;
strcpy(filename, save_basename);
strcat(filename, ".");
strcat(filename, snap_exts[selected]);
write_snapshot(filename);
}
/* Here we load a snapshot file. It can be distributed
* onto several files (for files>1).
* The particles are brought back into the order
* implied by their ID's.
* A unit conversion routine is called to do unit
* conversion, and to evaluate the gas temperature.
*/
int main(int argc, char **argv)
{
char path[200], input_fname[200], input_fname_dm[200], output_fname[200], basename[200], basenameout[200];
int j, n, type, snapshot_number, files, Ngas, random, ncount, ncounthalo1, ncount2;
float x,y,z,x1,y1, z1, delr;
double delx, dely, delz, delx_dm, dely_dm, delz_dm, boxsize, dummy=1.0;
FILE *outfile;
sprintf(path, "/nobackupp1/astacy");
sprintf(basename, "dma");
snapshot_number=12; /* number of snapshot */
files=1;
boxsize = 140.0;
delx = dely = delz = dummy;
delx_dm = dely_dm = delz_dm = dummy;
sprintf(input_fname, "%s/%s_%03d", path, basename, snapshot_number);
sprintf(input_fname_dm, "/nobackupp1/astacy/minihalo_256"); //"nfw" denotes an r^-1 profile!
sprintf(output_fname, "/nobackupp1/astacy/dma_prof1_000");
Ngas = write_snapshot(input_fname, input_fname_dm, files, output_fname, delx, dely, delz, delx_dm, dely_dm, delz_dm, boxsize);
unit_conversion();
ncount = 0;
ncount2 = 0;
printf("ncount = %d.\n", ncount);
printf("ncount2 = %d.\n", ncount2);
do_what_you_want();
}
static int
extract_snap( libspectrum_rzx *rzx, size_t where, const char *filename )
{
libspectrum_rzx_iterator it;
libspectrum_snap *snap;
int e;
it = get_block( rzx, where );
if( !it ) {
fprintf( stderr, "%s: not enough blocks in RZX file\n", progname );
return 1;
}
snap = libspectrum_rzx_iterator_get_snap( it );
if( !snap ) {
fprintf( stderr, "%s: not a snapshot block\n", progname );
return 1;
}
e = write_snapshot( snap, filename );
if( e ) return e;
return 0;
}
int
main(int argc, char *argv[])
{
char **av, *source_fname, *target_fname, *out_fname, fname[STRLEN] ;
int ac, nargs, new_transform = 0, pad ;
MRI *mri_target, *mri_source, *mri_orig_source ;
MRI_REGION box ;
struct timeb start ;
int msec, minutes, seconds ;
GCA_MORPH *gcam ;
MATRIX *m_L/*, *m_I*/ ;
LTA *lta ;
/* initialize the morph params */
memset(&mp, 0, sizeof(GCA_MORPH_PARMS));
/* for nonlinear morph */
mp.l_jacobian = 1 ;
mp.min_sigma = 0.4 ;
mp.l_distance = 0 ;
mp.l_log_likelihood = .025 ;
mp.dt = 0.005 ;
mp.noneg = True ;
mp.exp_k = 20 ;
mp.diag_write_snapshots = 1 ;
mp.momentum = 0.9 ;
if (FZERO(mp.l_smoothness))
mp.l_smoothness = 2 ;
mp.sigma = 8 ;
mp.relabel_avgs = -1 ;
mp.navgs = 256 ;
mp.levels = 6 ;
mp.integration_type = GCAM_INTEGRATE_BOTH ;
mp.nsmall = 1 ;
mp.reset_avgs = -1 ;
mp.npasses = 3 ;
mp.regrid = regrid? True : False ;
mp.tol = 0.1 ;
mp.niterations = 1000 ;
TimerStart(&start) ;
setRandomSeed(-1L) ;
DiagInit(NULL, NULL, NULL) ;
ErrorInit(NULL, NULL, NULL) ;
Progname = argv[0] ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 4)
usage_exit(1) ;
source_fname = argv[1] ;
target_fname = argv[2] ;
out_fname = argv[3] ;
FileNameOnly(out_fname, fname) ;
FileNameRemoveExtension(fname, fname) ;
strcpy(mp.base_name, fname) ;
mri_source = MRIread(source_fname) ;
if (!mri_source)
ErrorExit(ERROR_NOFILE, "%s: could not read source label volume %s",
Progname, source_fname) ;
if (mri_source->type == MRI_INT)
{
MRI *mri_tmp = MRIchangeType(mri_source, MRI_FLOAT, 0, 1, 1) ;
MRIfree(&mri_source); mri_source = mri_tmp ;
}
mri_target = MRIread(target_fname) ;
if (!mri_target)
ErrorExit(ERROR_NOFILE, "%s: could not read target label volume %s",
Progname, target_fname) ;
if (mri_target->type == MRI_INT)
{
MRI *mri_tmp = MRIchangeType(mri_target, MRI_FLOAT, 0, 1, 1) ;
MRIfree(&mri_target); mri_target = mri_tmp ;
}
if (erosions > 0)
{
int n ;
for (n = 0 ; n < erosions ; n++)
{
MRIerodeZero(mri_target, mri_target) ;
MRIerodeZero(mri_source, mri_source) ;
}
}
if (scale_values > 0)
{
MRIscalarMul(mri_source, mri_source, scale_values) ;
MRIscalarMul(mri_target, mri_target, scale_values) ;
}
if (transform && transform->type == MORPH_3D_TYPE)
TransformRas2Vox(transform, mri_source,NULL) ;
if (use_aseg == 0)
{
if (match_peak_intensity_ratio)
MRImatchIntensityRatio(mri_source, mri_target, mri_source, .8, 1.2,
100, 125) ;
else if (match_mean_intensity)
MRImatchMeanIntensity(mri_source, mri_target, mri_source) ;
MRIboundingBox(mri_source, 0, &box) ;
pad = (int)ceil(PADVOX *
MAX(mri_target->xsize,MAX(mri_target->ysize,mri_target->zsize)) /
MIN(mri_source->xsize,MIN(mri_source->ysize,mri_source->zsize)));
#if 0
{ MRI *mri_tmp ;
if (pad < 1)
pad = 1 ;
printf("padding source with %d voxels...\n", pad) ;
mri_tmp = MRIextractRegionAndPad(mri_source, NULL, &box, pad) ;
if ((Gdiag & DIAG_WRITE) && DIAG_VERBOSE_ON)
MRIwrite(mri_tmp, "t.mgz") ;
MRIfree(&mri_source) ;
mri_source = mri_tmp ;
}
#endif
}
mri_orig_source = MRIcopy(mri_source, NULL) ;
mp.max_grad = 0.3*mri_source->xsize ;
if (transform == NULL)
transform = TransformAlloc(LINEAR_VOXEL_TO_VOXEL, NULL) ;
if (transform->type != MORPH_3D_TYPE) // initializing m3d from a linear transform
{
new_transform = 1 ;
lta = ((LTA *)(transform->xform)) ;
if (lta->type != LINEAR_VOX_TO_VOX)
{
printf("converting ras xform to voxel xform\n") ;
m_L = MRIrasXformToVoxelXform(mri_source, mri_target, lta->xforms[0].m_L, NULL) ;
MatrixFree(<a->xforms[0].m_L) ;
lta->type = LINEAR_VOX_TO_VOX ;
}
else
{
printf("using voxel xform\n") ;
m_L = lta->xforms[0].m_L ;
}
#if 0
if (Gsx >= 0) // update debugging coords
{
VECTOR *v1, *v2 ;
v1 = VectorAlloc(4, MATRIX_REAL) ;
Gsx -= (box.x-pad) ;
Gsy -= (box.y-pad) ;
Gsz -= (box.z-pad) ;
V3_X(v1) = Gsx ; V3_Y(v1) = Gsy ; V3_Z(v1) = Gsz ;
VECTOR_ELT(v1,4) = 1.0 ;
v2 = MatrixMultiply(m_L, v1, NULL) ;
Gsx = nint(V3_X(v2)) ; Gsy = nint(V3_Y(v2)) ; Gsz = nint(V3_Z(v2)) ;
MatrixFree(&v2) ; MatrixFree(&v1) ;
printf("mapping by transform (%d, %d, %d) --> (%d, %d, %d) for rgb writing\n",
Gx, Gy, Gz, Gsx, Gsy, Gsz) ;
}
#endif
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
write_snapshot(mri_target, mri_source, m_L, &mp, 0, 1, "linear_init");
lta->xforms[0].m_L = m_L ;
printf("initializing GCAM with vox->vox matrix:\n") ;
MatrixPrint(stdout, m_L) ;
gcam = GCAMcreateFromIntensityImage(mri_source, mri_target, transform) ;
#if 0
gcam->gca = gcaAllocMax(1, 1, 1,
mri_target->width, mri_target->height,
mri_target->depth,
0, 0) ;
#endif
GCAMinitVolGeom(gcam, mri_source, mri_target) ;
if (use_aseg)
{
if (ribbon_name)
{
char fname[STRLEN], path[STRLEN], *str, *hemi ;
int h, s, label ;
MRI_SURFACE *mris_white, *mris_pial ;
MRI *mri ;
for (s = 0 ; s <= 1 ; s++) // source and target
{
if (s == 0)
{
str = source_surf ;
mri = mri_source ;
FileNamePath(mri->fname, path) ;
strcat(path, "/../surf") ;
}
else
{
mri = mri_target ;
FileNamePath(mri->fname, path) ;
strcat(path, "/../elastic") ;
str = target_surf ;
}
// sorry - these values come from FreeSurferColorLUT.txt
MRIreplaceValueRange(mri, mri, 1000, 1034, Left_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 1100, 1180, Left_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 2000, 2034, Right_Cerebral_Cortex) ;
MRIreplaceValueRange(mri, mri, 2100, 2180, Right_Cerebral_Cortex) ;
for (h = LEFT_HEMISPHERE ; h <= RIGHT_HEMISPHERE ; h++)
{
if (h == LEFT_HEMISPHERE)
{
hemi = "lh" ;
label = Left_Cerebral_Cortex ;
}
else
{
label = Right_Cerebral_Cortex ;
hemi = "rh" ;
}
sprintf(fname, "%s/%s%s.white", path, hemi, str) ;
mris_white = MRISread(fname) ;
if (mris_white == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface %s", Progname, fname) ;
MRISsaveVertexPositions(mris_white, WHITE_VERTICES) ;
sprintf(fname, "%s/%s%s.pial", path, hemi, str) ;
mris_pial = MRISread(fname) ;
if (mris_pial == NULL)
ErrorExit(ERROR_NOFILE, "%s: could not read surface %s", Progname, fname) ;
MRISsaveVertexPositions(mris_pial, PIAL_VERTICES) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "sb.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "tb.mgz") ;
MRIwrite(mri_target, fname) ;
}
insert_ribbon_into_aseg(mri, mri, mris_white, mris_pial, h) ;
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "sa.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "ta.mgz") ;
MRIwrite(mri_target, fname) ;
}
MRISfree(&mris_white) ; MRISfree(&mris_pial) ;
}
}
if (Gdiag & DIAG_WRITE && DIAG_VERBOSE_ON)
{
sprintf(fname, "s.mgz") ;
MRIwrite(mri_source, fname) ;
sprintf(fname, "t.mgz") ;
MRIwrite(mri_target, fname) ;
}
}
GCAMinitLabels(gcam, mri_target) ;
GCAMsetVariances(gcam, 1.0) ;
mp.mri_dist_map = create_distance_transforms(mri_source, mri_target, NULL, 40.0, gcam) ;
}
}
else /* use a previously create morph and integrate it some more */
{
printf("using previously create gcam...\n") ;
gcam = (GCA_MORPH *)(transform->xform) ;
GCAMrasToVox(gcam, mri_source) ;
if (use_aseg)
{
GCAMinitLabels(gcam, mri_target) ;
GCAMsetVariances(gcam, 1.0) ;
mp.mri_dist_map = create_distance_transforms(mri_source, mri_target, NULL, 40.0, gcam) ;
}
else
GCAMaddIntensitiesFromImage(gcam, mri_target) ;
}
if (gcam->width != mri_source->width ||
gcam->height != mri_source->height ||
gcam->depth != mri_source->depth)
ErrorExit(ERROR_BADPARM, "%s: warning gcam (%d, %d, %d), doesn't match source vol (%d, %d, %d)",
Progname, gcam->width, gcam->height, gcam->depth,
mri_source->width, mri_source->height, mri_source->depth) ;
mp.mri_diag = mri_source ;
mp.diag_morph_from_atlas = 0 ;
mp.diag_write_snapshots = 1 ;
mp.diag_sample_type = use_aseg ? SAMPLE_NEAREST : SAMPLE_TRILINEAR ;
mp.diag_volume = use_aseg ? GCAM_LABEL : GCAM_MEANS ;
if (renormalize)
GCAMnormalizeIntensities(gcam, mri_target) ;
if (mp.write_iterations != 0)
{
char fname[STRLEN] ;
MRI *mri_gca ;
if (getenv("DONT_COMPRESS"))
sprintf(fname, "%s_target.mgh", mp.base_name) ;
else
sprintf(fname, "%s_target.mgz", mp.base_name) ;
if (mp.diag_morph_from_atlas == 0)
{
printf("writing target volume to %s...\n", fname) ;
MRIwrite(mri_target, fname) ;
sprintf(fname, "%s_target", mp.base_name) ;
MRIwriteImageViews(mri_target, fname, IMAGE_SIZE) ;
}
else
{
if (use_aseg)
mri_gca = GCAMwriteMRI(gcam, NULL, GCAM_LABEL) ;
else
{
mri_gca = MRIclone(mri_source, NULL) ;
GCAMbuildMostLikelyVolume(gcam, mri_gca) ;
}
printf("writing target volume to %s...\n", fname) ;
MRIwrite(mri_gca, fname) ;
sprintf(fname, "%s_target", mp.base_name) ;
MRIwriteImageViews(mri_gca, fname, IMAGE_SIZE) ;
MRIfree(&mri_gca) ;
}
}
if (nozero)
{
printf("disabling zero nodes\n") ;
GCAMignoreZero(gcam, mri_target) ;
}
mp.mri = mri_target ;
if (mp.regrid == True && new_transform == 0)
GCAMregrid(gcam, mri_target, PAD, &mp, &mri_source) ;
mp.write_fname = out_fname ;
GCAMregister(gcam, mri_source, &mp) ; // atlas is target, morph target into register with it
if (apply_transform)
{
MRI *mri_aligned ;
char fname[STRLEN] ;
FileNameRemoveExtension(out_fname, fname) ;
strcat(fname, ".mgz") ;
mri_aligned = GCAMmorphToAtlas(mp.mri, gcam, NULL, -1, mp.diag_sample_type) ;
printf("writing transformed output volume to %s...\n", fname) ;
MRIwrite(mri_aligned, fname) ;
MRIfree(&mri_aligned) ;
}
printf("writing warp vector field to %s\n", out_fname) ;
GCAMvoxToRas(gcam) ;
GCAMwrite(gcam, out_fname) ;
GCAMrasToVox(gcam, mri_source) ;
msec = TimerStop(&start) ;
seconds = nint((float)msec/1000.0f) ;
minutes = seconds / 60 ;
seconds = seconds % 60 ;
printf("registration took %d minutes and %d seconds.\n",
minutes, seconds) ;
exit(0) ;
return(0) ;
}
int main(int argc, char** argv) {
char *infile;
infile=argv[1];
char *outfile;
outfile=argv[2];
float clumpx, clumpy, clumpz;
sscanf (argv[3],"%f",&clumpx);
sscanf (argv[4],"%f",&clumpy);
sscanf (argv[5],"%f",&clumpz);
if(argc!=6) {
printf("Usage: ./cutout <infile> <outfile> <x coordinate of clump [Mpc]> <y coordinate> <z coordinate>\n");
return 0;
}
printf("Box centered around x: %g y: %g z: %g [Mpc] \n", clumpx, clumpy, clumpz);
/* load snapshot file */
io_header header;
particle_data * P;
int nTot;
nTot = load_snapshot(infile, &header, &P);
/* output information about the simulation */
printf(">> Output from Header \n");
printf("Boxsize of Simulation: %g\n", header.BoxSize);
printf("Number of gas particles: %i\n", header.npart[0]);
printf("Number of high-res dm particles: %i\n", header.npart[1]);
printf("Number of low-res dm particles: %i\n", header.npart[5]);
printf("Number of star particles: %i\n", header.npart[4]);
/*cutout region around the center */
float extent=20000;
clumpx=clumpx*1000; // Mpc -> kpc
clumpy=clumpy*1000; // Mpc -> kpc
clumpz=clumpz*1000; // Mpc -> kpc
/* check if the cutout region does not extend over boundaries */
if(header.BoxSize-extent/2.<clumpx || extent/2.>clumpx) {
printf("Out of bound in x-dimension - chose a more centered clump \n" );
printf(">> ABORTING \n" );
return 0;
}
if(header.BoxSize-extent/2.<clumpy || extent/2.>clumpy) {
printf("Out of bound in y-dimension - chose a more centered clump \n" );
printf(">> ABORTING \n" );
return 0;
}
if(header.BoxSize-extent/2.<clumpz || extent/2.>clumpz) {
printf("Out of bound in z-dimension - chose a more centered clump \n" );
printf(">> ABORTING \n" );
return 0;
}
int i;
/* loop over all particles */
int counter = 0;
float center = header.BoxSize/2;
for (i=0;i<nTot;i++) {
/* test if particle is within our desired volume */
if(P[i].Pos[0]<clumpx+extent/2 && P[i].Pos[0]>clumpx-extent/2 &&
P[i].Pos[1]<clumpy+extent/2 && P[i].Pos[1]>clumpy-extent/2 &&
P[i].Pos[2]<clumpz+extent/2 && P[i].Pos[2]>clumpz-extent/2) {
/* shift coordinates */
P[i].Pos[0]-= clumpx-extent/2;
P[i].Pos[1]-= clumpy-extent/2;
P[i].Pos[2]-= clumpz-extent/2;
P[counter] = P[i];
counter++;
}
}
int counterType [6] = {0,0,0,0,0,0};
/* get the numbers of the particle types */
for (i=0;i<counter;i++) {
if(P[i].Type==0) {
counterType[0]+=1;
}
if(P[i].Type==1) {
counterType[1]+=1;
}
if(P[i].Type==2) {
counterType[2]+=1;
}
if(P[i].Type==3) {
counterType[3]+=1;
}
if(P[i].Type==4) {
counterType[4]+=1;
}
if(P[i].Type==5) {
counterType[5]+=1;
}
}
header.npart[0]=counterType[0];
header.npartTotal[0]=counterType[0];
header.npart[1]=counterType[1];
header.npartTotal[1]=counterType[1];
header.npart[4]=counterType[4];
header.npartTotal[4]=counterType[4];
header.npart[5]=counterType[5];
header.npartTotal[5]=counterType[5];
header.BoxSize = extent;
/* output information about the simulation */
printf(">> Output Cutout Box\n");
printf("Boxsize: %g\n", header.BoxSize);
printf("Number of gas particles: %i\n", header.npart[0]);
printf("Number of high-res dm particles: %i\n", header.npart[1]);
printf("Number of low-res dm particles: %i\n", header.npart[5]);
printf("Number of star particles: %i\n", header.npart[4]);
printf("Box centered around x: %g y: %g z: %g \n", clumpx, clumpy, clumpz);
/* write reduced snapshot file */
write_snapshot(outfile, &header, P);
return 0;
}
/* Here we load a snapshot file. It can be distributed
* onto several files (for files>1).
* The particles are brought back into the order
* implied by their ID's.
* A unit conversion routine is called to do unit
* conversion, and to evaluate the gas temperature.
*/
int main(int argc, char **argv)
{
char path[200], input_fname[200], output_fname[200], basename[200], basenameout[200];
int j, n, type, snapshot_number, output_number,files, Ngas, random, ncount, ncounthalo1, ncount2;
float x,y,z,x1,y1, z1, delr;
double delx, dely, delz, boxsize;
FILE *outfile;
sprintf(path, "/work/00863/minerva/");
//sprintf(basename, "midres_small");
//sprintf(basename, "midhires/midhires");
//sprintf(basename, "hires_test10");
//sprintf(basename, "dmaH101");
sprintf(basename, "bin_HR10");
//sprintf(basename, "bin_zoom10_new");
//sprintf(basename, "bin_zoom10_new_highN");
//sprintf(basename, "bin_zoom10_new_ref");
//snapshot_number=300; /* number of snapshot */
//snapshot_number=500;
//snapshot_number=800;
//snapshot_number=910;
//snapshot_number=2550;
//snapshot_number=764;
//snapshot_number=442;
//sprintf(basename, "midres");
//snapshot_number=250; /* number of snapshot */
output_number = 6;
for(j=6; j<=6; j=j+1)
{
snapshot_number=j;
files=1;
boxsize = 140.0;
/*
delx = 70.309788381; /del's used in making hires_nf (?) (midhires_920)
dely = 70.290775273;
delz = 69.663477541;
*/
/*
delx = 70.285815369; //del's used in making hires_nf2 (midhires_500)
dely = 70.267684537;
delz = 69.645294964;
*/
/*
delx = 70.285954951; //del's used in making hires_nf3 (midhires_800)
dely = 70.267065424;
delz = 69.645294964;
*/
/*
delx = 70.285976724; //del's used in making hires_nf2 (midhires_910)
dely = 70.266799478;
delz = 69.644071682;
*/
/*
delx = 70.286688899; //del's used in making dma_ (midhires_300)
dely = 70.271233273;
delz = 69.65345084;
*/
/*
delx = 70.285951357; //del's used in making hires_test10_4202 (hires_test10_4201)
dely = 70.2668302;
delz = 69.644059893;
*/
/*
delx = 70.285964359; //del's used in making hires_test10b_2550 (hires_test10_2550)
dely = 70.266825688;
delz = 69.644095683;
*/
/*
delx = 70.285900597; //del's used in making dmaH101_765 (dmaH101_764)
dely = 70.267312791;
delz = 69.645754876;
*/
/*
delx = 512.65800353; //del's used in making bin_HRE10_442 (bin_HRE10_443)
dely = 505.21836888;
delz = 497.39349349;
*/
delx = 512.65800353; //del's used in making bin_zoom10_cut_??? (bin_zoom10_???)
dely = 505.21836888;
delz = 497.39349349;
sprintf(input_fname, "%s/%s_%03d", path, basename, snapshot_number);
if(snapshot_number > 999)
sprintf(input_fname, "%s/%s_%04d", path, basename, snapshot_number);
//sprintf(output_fname, "/nobackupp1/astacy/dma_001");
//sprintf(output_fname, "/nobackupp1/astacy/hires_test10_4202");
//sprintf(output_fname, "/nobackupp1/astacy/hires_test10b_2550");
//sprintf(output_fname, "/nobackupp1/astacy/dmaH101_765");
//sprintf(output_fname, "/nobackupp1/astacy/bin_HRE10_443");
sprintf(basenameout, "bin_HR10_cut");
sprintf(output_fname, "%s/%s_%03d", path, basenameout, output_number);
if(snapshot_number > 999)
sprintf(output_fname, "%s/%s_%04d", path, basenameout, output_number);
output_number++;
Ngas = write_snapshot(input_fname, files, output_fname, delx, dely, delz, boxsize);
unit_conversion();
ncount = 0;
ncount2 = 0;
printf("ncount = %d.\n", ncount);
printf("ncount2 = %d.\n", ncount2);
do_what_you_want();
free(P);
}
}
/* Here we load a snapshot file. It can be distributed
* onto several files (for files>1).
* The particles are brought back into the order
* implied by their ID's.
* A unit conversion routine is called to do unit
* conversion, and to evaluate the gas temperature.
*/
int main(int argc, char **argv)
{
char path[200], input_fname[200], output_fname[200], basename[200], basenameout[200];
int j, n, type, snapshot_number, files, Ngas, random, ncount, ncounthalo1, ncount2;
float x,y,z,x1,y1, z1, delr;
double delx, dely, delz, boxsize;
FILE *outfile;
sprintf(path, "/nobackupp1/astacy/bin_zoom");
//sprintf(basename, "midres_small");
//sprintf(basename, "midhires");
sprintf(basename, "bin_zoom10");
//snapshot_number=90; /* number of snapshot */
//snapshot_number=77;
//snapshot_number=86;
//snapshot_number=127;
//snapshot_number=112;
//snapshot_number=139;
//snapshot_number=101;
//snapshot_number=94;
//snapshot_number=113;
snapshot_number=91;
//snapshot_number=89; //using bin_zoom10 for dma study
files=1;
boxsize = 140.0;
//delx = 70.309788381;
//dely = 70.290775273;
//delz = 69.663477541;
//delx = 50.339110402;
//dely = 50.122129376;
//delz = 49.486652655;
//delx = 501.10837429; //bin_HR1
//dely = 502.63795002;
//delz = 500.57881331;
//delx = 504.74822278; //bin_HR2
//dely = 502.54674042;
//delz = 498.35964366;
//delx = 497.97549715; //bin_HR3
//dely = 478.97623119;
//delz = 533.38658886;
//delx = 492.79124064; //bin_HR4
//dely = 481.69180059;
//delz = 488.42188726;
//delx = 500.7922779; //bin_HR5
//dely = 499.63885791;
//delz = 498.79440875;
//delx = 491.44365517; //bin_HR6
//dely = 524.86976032;
//delz = 504.56886557;
//delx = 500.88344323; //bin_HR7
//dely = 499.58683015;
//delz = 504.99209358;
//delx = 506.01124135; //bin_HR8
//dely = 501.56161969;
//delz = 503.11090611;
//delx = 496.9606639; //bin_HR9
//dely = 497.98016741;
//delz = 514.16669622;
delx = 512.66315335; //bin_HR10
dely = 505.21955922;
delz = 497.39292251;
//delx = 512.70283548; //bin_HR10 (for dma study)
//dely = 505.23514735;
//delz = 497.3872807;
sprintf(input_fname, "%s/%s_%03d", path, basename, snapshot_number);
//sprintf(output_fname, "/nobackupp1/astacy/hires_001a");
//sprintf(output_fname, "/nobackupp1/astacy/bin_HR10_001");
sprintf(output_fname, "/nobackupp1/astacy/bin_HRL10_001");
//sprintf(output_fname, "/nobackupp1/astacy/dma2_001");
Ngas = write_snapshot(input_fname, files, output_fname, delx, dely, delz, boxsize);
unit_conversion();
ncount = 0;
ncount2 = 0;
printf("ncount = %d.\n", ncount);
printf("ncount2 = %d.\n", ncount2);
do_what_you_want();
}