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Simple HDF5 reader in clojure
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(ns hdf5 | |
(:import [org.bytedeco.javacpp | |
DoublePointer FloatPointer | |
LongPointer IntPointer | |
ShortPointer BytePointer] | |
[org.bytedeco.javacpp hdf5 hdf5$H5File])) | |
;; Using maven dependency: | |
;; [org.bytedeco.javacpp-presets/hdf5-platform "1.10.0-patch1-1.3"] | |
;; C++ API Reference | |
;; https://support.hdfgroup.org/HDF5/doc/cpplus_RM/ | |
;; Example: discovering contents of file | |
;; https://support.hdfgroup.org/ftp/HDF5/examples/misc-examples/h5_info.c | |
(defn hdf5-file [path] | |
(hdf5$H5File. path hdf5/H5F_ACC_RDONLY)) | |
(defn dataset-names [file] | |
(let [fg (.asCommonFG file) | |
num-objs (.getNumObjs fg)] | |
(map #(-> fg (.getObjnameByIdx %) .getString) (range num-objs)))) | |
(defn dataset [file name] | |
(-> file .asCommonFG (.openDataSet name))) | |
(defn- ptr->array [ptr] | |
(let [buf-fn (condp instance? ptr | |
DoublePointer double-array | |
FloatPointer float-array | |
LongPointer long-array | |
IntPointer int-array | |
ShortPointer short-array | |
BytePointer byte-array) | |
buf (buf-fn (.capacity ptr))] | |
(.get ptr buf) | |
buf)) | |
(defn- with-ptr [^long capacity type f] | |
(let [ptr (condp = type | |
double (DoublePointer. capacity) | |
float (FloatPointer. capacity) | |
long (LongPointer. capacity) | |
int (IntPointer. capacity) | |
short (ShortPointer. capacity) | |
byte (BytePointer. capacity))] | |
(f ptr) | |
ptr)) | |
(defn dimensions [dataset] | |
(let [ndim (-> dataset .getSpace .getSimpleExtentNdims) | |
dims #(-> dataset .getSpace (.getSimpleExtentDims %)) | |
type (case hdf5/H5_SIZEOF_HSIZE_T | |
8 long | |
4 int)] | |
(ptr->array (with-ptr ndim type dims)))) | |
(defn ->array [dataset] | |
(let [mem-size (.getInMemDataSize dataset) | |
abs-dataset (.asAbstractDs dataset) | |
data-type (.getTypeClass abs-dataset) | |
nelem (reduce * (dimensions dataset)) | |
dtype-size (quot mem-size nelem) | |
type (condp = [data-type dtype-size] | |
[hdf5/H5T_FLOAT 8] double | |
[hdf5/H5T_FLOAT 4] float | |
[hdf5/H5T_INTEGER 8] long | |
[hdf5/H5T_INTEGER 4] int | |
[hdf5/H5T_INTEGER 2] short | |
[hdf5/H5T_INTEGER 1] byte)] | |
(ptr->array | |
(with-ptr nelem type #(.read dataset % (.getDataType abs-dataset)))))) |
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