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authorThomas White <taw@physics.org>2012-03-23 16:30:00 +0100
committerThomas White <taw@physics.org>2012-03-23 16:30:00 +0100
commit685f23322f7a40102f80a41b8dba3a29c8a99ae4 (patch)
tree5c90608989b656bc80864417ee6525fb9a9615cc /libcrystfel
parentdbdc0f4e278dd4f4a6925fc4ecb96c4899c82fa9 (diff)
Add new function hdf5_write_image() to include all relevant information in the file
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/hdf5-file.c109
-rw-r--r--libcrystfel/src/hdf5-file.h2
2 files changed, 110 insertions, 1 deletions
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index c1b38507..206e6295 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -227,6 +227,8 @@ void hdfile_close(struct hdfile *f)
}
+
+/* Deprecated */
int hdf5_write(const char *filename, const void *data,
int width, int height, int type)
{
@@ -281,10 +283,115 @@ int hdf5_write(const char *filename, const void *data,
H5Fclose(fh);
return 1;
}
-
+ H5Dclose(dh);
+ H5Gclose(gh);
H5Pclose(ph);
+ H5Fclose(fh);
+
+ return 0;
+}
+
+
+int hdf5_write_image(const char *filename, struct image *image)
+{
+ hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
+ hid_t ph; /* Property list */
+ herr_t r;
+ hsize_t size[2];
+ double lambda, eV;
+
+ fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ if ( fh < 0 ) {
+ ERROR("Couldn't create file: %s\n", filename);
+ return 1;
+ }
+
+ gh = H5Gcreate2(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if ( gh < 0 ) {
+ ERROR("Couldn't create group\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ /* Note the "swap" here, according to section 3.2.5,
+ * "C versus Fortran Dataspaces", of the HDF5 user's guide. */
+ size[0] = image->height;
+ size[1] = image->width;
+ sh = H5Screate_simple(2, size, NULL);
+
+ /* Set compression */
+ ph = H5Pcreate(H5P_DATASET_CREATE);
+ H5Pset_chunk(ph, 2, size);
+ H5Pset_deflate(ph, 3);
+
+ dh = H5Dcreate2(gh, "data", H5T_NATIVE_FLOAT, sh,
+ H5P_DEFAULT, ph, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ ERROR("Couldn't create dataset\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ /* Muppet check */
+ H5Sget_simple_extent_dims(sh, size, NULL);
+
+ r = H5Dwrite(dh, H5T_NATIVE_FLOAT, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, image->data);
+ if ( r < 0 ) {
+ ERROR("Couldn't write data\n");
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return 1;
+ }
+ H5Dclose(dh);
+
H5Gclose(gh);
+
+ gh = H5Gcreate2(fh, "LCLS", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if ( gh < 0 ) {
+ printf("Couldn't create group\n");
+ H5Fclose(fh);
+ return 1;
+ }
+
+ sh = H5Screate_simple(1, size, NULL);
+
+ dh = H5Dcreate2(gh, "photon_energy_eV", H5T_NATIVE_DOUBLE, sh,
+ H5P_DEFAULT, ph, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ H5Fclose(fh);
+ return 1;
+ }
+ eV = ph_lambda_to_eV(image->lambda);
+ r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, &eV);
+ if ( r < 0 ) {
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return 1;
+ }
+ H5Dclose(dh);
+
+ dh = H5Dcreate2(fh, "/LCLS/photon_wavelength_A", H5T_NATIVE_DOUBLE, sh,
+ H5P_DEFAULT, ph, H5P_DEFAULT);
+ if ( dh < 0 ) {
+ H5Fclose(fh);
+ return 1;
+ }
+ lambda = image->lambda * 1e10;
+ r = H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL,
+ H5S_ALL, H5P_DEFAULT, &lambda);
+ if ( r < 0 ) {
+ H5Dclose(dh);
+ H5Fclose(fh);
+ return 1;
+ }
H5Dclose(dh);
+
+ H5Gclose(gh);
+
+ H5Pclose(ph);
+
H5Fclose(fh);
return 0;
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 2ef76304..f6051c88 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -46,6 +46,8 @@ struct copy_hdf5_field;
extern int hdf5_write(const char *filename, const void *data,
int width, int height, int type);
+extern int hdf5_write_image(const char *filename, struct image *image);
+
extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr);
extern struct hdfile *hdfile_open(const char *filename);