mirror of https://github.com/jlizier/jidt
Added stub JNI function for KSG CMI.
This commit is contained in:
Pedro Martinez Mediano
parent
6a13b80531
commit
9248005de5
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@ -5,6 +5,7 @@
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#define check(ans) { _check((ans), __FILE__, __LINE__); }
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#include "gpuMILibrary.h"
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#include "gpuCMILibrary.h"
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#include "ctimer.h"
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#ifdef __cplusplus
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@ -196,6 +197,198 @@ JNIEXPORT jdoubleArray JNICALL
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} // End of function MIKraskov
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/*
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* Class: infodynamics_measures_continuous_kraskov_ConditionalMutualInfoCalculatorMultiVariateKraskov
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* Method: CMIKraskov
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* Signature: (I[DI[DI[DIIIZZZIZ[I)[D
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*/
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JNIEXPORT jdoubleArray JNICALL
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Java_infodynamics_measures_continuous_kraskov_ConditionalMutualInfoCalculatorMultiVariateKraskov_CMIKraskov(
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JNIEnv *env, jobject thisObj, jint j_N,
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jobjectArray j_sourceArray, jint j_dimx,
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jobjectArray j_destArray, jint j_dimy,
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jobjectArray j_condArray, jint j_dimz,
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jint j_k, jint j_theiler, jboolean j_returnLocals,
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jboolean j_useMaxNorm, jboolean j_isAlgorithm1, jint j_nbSurrogates,
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jboolean j_reorderingsGiven, jobjectArray j_orderings) {
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// Check that incoming data has correct size
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// =====================
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jsize sourceLength = (*env)->GetArrayLength(env, j_sourceArray);
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jsize destLength = (*env)->GetArrayLength(env, j_destArray);
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jsize condLength = (*env)->GetArrayLength(env, j_condArray);
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// if (sourceLength != j_N || destLength != j_N || (j_N%(j_nbSurrogates+1) != 0)) {
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if (sourceLength != j_N || destLength != j_N || condLength != j_N) {
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jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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(*env)->ThrowNew(env, Exception, "Data has wrong length.");
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}
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if (!j_isAlgorithm1) {
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jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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(*env)->ThrowNew(env, Exception, "Only algorithm 1 is supported.");
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}
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if ((j_returnLocals || !j_isAlgorithm1) && (j_nbSurrogates > 0)) {
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jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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(*env)->ThrowNew(env, Exception, "Surrogates only supported for average MI with KSG1.");
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}
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// // Copy variables from Java
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// // =====================
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// int N = j_N;
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// int k = j_k;
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// int dimx = j_dimx;
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// int dimy = j_dimy;
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// int theiler = j_theiler;
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// int returnLocals = j_returnLocals ? 1 : 0;
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// int useMaxNorm = j_useMaxNorm ? 1 : 0;
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// int isAlgorithm1 = j_isAlgorithm1 ? 1 : 0;
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// int nb_surrogates = j_nbSurrogates;
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// int reorderingsGiven = j_reorderingsGiven ? 1 : 0;
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//
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// CPerfTimer pt = startTimer("Java array copy");
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// float *source = (float *) malloc(N * dimx * sizeof(float));
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// float *dest = (float *) malloc(N * dimy * sizeof(float));
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// if (NULL == source || NULL == dest) {
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// jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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// (*env)->ThrowNew(env, Exception, "Error allocating data.");
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// }
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// for (int i = 0; i < N; i++) {
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// jdoubleArray j_sourceRow = (jdoubleArray) (*env)->GetObjectArrayElement(env, j_sourceArray, i);
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// jdoubleArray j_destRow = (jdoubleArray) (*env)->GetObjectArrayElement(env, j_destArray, i);
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// jdouble *sourceRow = (*env)->GetDoubleArrayElements(env, j_sourceRow, NULL);
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// jdouble *destRow = (*env)->GetDoubleArrayElements(env, j_destRow, NULL);
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// // Data in java are doubles, but GPUs need floats.
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// // We have to cast them manually, so we can't memcopy
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// // The following two for-loops get two matrices in T-by-D indexing (i.e.
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// // first dimension is time, second is variable) and return the data in
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// // column-major form
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// for (int j = 0; j < dimx; j++) {
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// source[N*j + i] = (float) sourceRow[j];
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// }
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// for (int j = 0; j < dimy; j++) {
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// dest[N*j + i] = (float) destRow[j];
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// }
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// // // The following two for-loops get the same matrices but return arrays
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// // // in row-major form. Code is left here for future development purposes.
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// // for (j = 0; j < dimx; j++) {
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// // register float x = (float) sourceRow[j];
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// // source[dimx*i + j] = x;
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// // pointset[dims*i + j] = x;
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// // }
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// // for (j = 0; j < dimy; j++) {
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// // register float x = (float) destRow[j];
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// // dest[dimy*i + j] = x
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// // pointset[i*dims + dimx + j] = x;
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// // }
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// (*env)->ReleaseDoubleArrayElements(env, j_sourceRow, sourceRow, 0);
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// (*env)->ReleaseDoubleArrayElements(env, j_destRow, destRow, 0);
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// (*env)->DeleteLocalRef(env, j_sourceRow);
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// (*env)->DeleteLocalRef(env, j_destRow);
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// // FIXME: I'm not entirely sure I'm freeing all the memory here. I should
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// // check for memory leaks more carefully.
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// }
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// int **reorderings = NULL;
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// if (reorderingsGiven) {
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// reorderings = (int **) malloc(nb_surrogates * sizeof(int *));
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// for (int i = 0; i < nb_surrogates; i++) {
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// jintArray j_order = (jdoubleArray) (*env)->GetObjectArrayElement(env, j_orderings, i);
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// jint *order = (*env)->GetIntArrayElements(env, j_order, NULL);
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// reorderings[i] = (int *) malloc(N * sizeof(int));
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// for (int j = 0; j < N; j++) {
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// reorderings[i][j] = order[j];
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// }
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// (*env)->ReleaseIntArrayElements(env, j_order, order, 0);
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// (*env)->DeleteLocalRef(env, j_order);
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// }
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// }
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// stopTimer(pt);
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// // Call C function
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// // =========================
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// int resultSize;
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// if (returnLocals) {
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// resultSize = N;
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// } else if (nb_surrogates > 0) {
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// resultSize = nb_surrogates + 1;
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// } else {
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// resultSize = 3;
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// }
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// float *result = (float *) malloc(resultSize * sizeof(float));
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// jidt_error_t ret;
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// if (!reorderingsGiven) {
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// ret = MIKraskov_C(N, source, dimx, dest, dimy,
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// k, theiler, nb_surrogates, returnLocals, useMaxNorm,
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// isAlgorithm1, result);
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// } else {
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// ret = MIKraskovWithReorderings(N, source, dimx, dest, dimy, k, theiler,
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// nb_surrogates, returnLocals, useMaxNorm,
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// isAlgorithm1, result, reorderingsGiven,
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// reorderings);
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// }
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// if (JIDT_ERROR == ret) {
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// jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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// (*env)->ThrowNew(env, Exception, "Error in GPU execution.");
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// }
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// // Free memory and return
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// // =========================
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// if (source) free(source);
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// if (dest) free(dest);
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// if (reorderingsGiven) {
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// for (int i = 0; i < nb_surrogates; i++) {
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// if (reorderings[i]) free(reorderings[i]);
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// }
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// if (reorderings) free (reorderings);
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// }
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// jdouble outCArray[resultSize];
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// for (int i = 0; i < resultSize; i++) {
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// outCArray[i] = result[i];
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// }
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int resultSize = 1;
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jdouble outCArray[resultSize];
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outCArray[0] = 0.0;
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// Set Java array for return
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jdoubleArray outJNIArray = (*env)->NewDoubleArray(env, resultSize); // allocate
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if (NULL == outJNIArray) {
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jclass Exception = (*env)->FindClass(env, "java/lang/Exception");
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(*env)->ThrowNew(env, Exception, "Error creating return array.");
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}
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(*env)->SetDoubleArrayRegion(env, outJNIArray, 0 , resultSize, outCArray); // copy
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// if (result) { free(result); }
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return outJNIArray;
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} // End of function MIKraskov
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#ifdef __cplusplus
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}
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#endif
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