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[feat] accept MeshROI for immc in the JSON input
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@fangq
fangq committed Mar 9, 2024
1 parent dd9b4d5 commit cc3f362
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Showing 2 changed files with 64 additions and 10 deletions.
72 changes: 62 additions & 10 deletions src/mmc_utils.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -336,6 +336,8 @@ void mcx_initcfg(mcconfig* cfg) {
cfg->elemlen = 0;
cfg->node = NULL;
cfg->elem = NULL;
cfg->roitype = 0;
cfg->roidata = NULL;

#ifdef MCX_EMBED_CL
cfg->clsource = (char*)mmc_core_cl;
Expand Down Expand Up @@ -416,6 +418,10 @@ void mcx_clearcfg(mcconfig* cfg) {
free(cfg->elem);
}

if (cfg->roidata) {
free(cfg->roidata);
}

#ifndef MCX_EMBED_CL

if (cfg->clsource && cfg->clsource != (char*)mmc_core_cl) {
Expand Down Expand Up @@ -1261,7 +1267,10 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {

if (subitem) {
strncpy(cfg->meshtag, FIND_JSON_KEY("MeshID", "Mesh.MeshID", Mesh, (MMC_ERROR(-1, "You must specify mesh files"), ""), valuestring), MAX_SESSION_LENGTH - 1);
} else {
}

//< reading mesh node and elem mesh data from JSON file
{
int ndim;
uint dims[3] = {1, 1, 1};
char* type = NULL;
Expand Down Expand Up @@ -1290,7 +1299,7 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {
subitem = subitem->next;
}
} else {
mcx_jdatadecode((void**)&cfg->node, &ndim, dims, 3, &type, subitem, cfg);
mcx_jdatadecode((void**)&cfg->node, &ndim, dims, 2, &type, subitem, cfg);

if (strcmp(type, "single") || ndim != 2 || (ndim >= 2 && dims[1] != 3)) {
if (cfg->node) {
Expand All @@ -1302,8 +1311,6 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {
cfg->nodenum = dims[0];
}
}
} else {
MMC_ERROR(-1, "MeshNode must be provided if MeshID is missing");
}

subitem = FIND_JSON_OBJ("MeshElem", "Mesh.MeshElem", Mesh);
Expand All @@ -1322,7 +1329,7 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {

for (int i = 0; i < cfg->elemnum; i++) {
if (cJSON_GetArraySize(subitem) != 5) {
MMC_ERROR(-1, "Each element in MeshElem must have 3 numbers");
MMC_ERROR(-1, "Each element in MeshElem must have 5 integers");
}

tmp = subitem->child;
Expand All @@ -1335,11 +1342,11 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {
subitem = subitem->next;
}

cfg->elemlen--;
cfg->elemlen--; // to make cfg->elemlen and mesh->elemlen the same - cfg->elem contains 1 extra column for mesh->type
} else {
mcx_jdatadecode((void**)&cfg->elem, &ndim, dims, 3, &type, subitem, cfg);
mcx_jdatadecode((void**)&cfg->elem, &ndim, dims, 2, &type, subitem, cfg);

if (strstr(type, "int32") || ndim != 2 || (ndim >= 2 && dims[1] != 5 && dims[1] != 11)) {
if (!strstr(type, "int32") || ndim != 2 || (ndim >= 2 && dims[1] != 5 && dims[1] != 11)) {
if (cfg->elem) {
free(cfg->elem);
}
Expand All @@ -1350,9 +1357,54 @@ int mcx_loadjson(cJSON* root, mcconfig* cfg) {
cfg->elemlen = dims[1] - 1;
}
}
}

subitem = FIND_JSON_OBJ("MeshROI", "Mesh.MeshROI", Mesh);

if (subitem) {
if (cfg->roidata) {
free(cfg->roidata);
cfg->roidata = NULL;
}

if (cJSON_IsArray(subitem)) {
int collen, rowlen = cJSON_GetArraySize(subitem);
subitem = subitem->child;

if (cJSON_IsArray(subitem)) {
collen = cJSON_GetArraySize(subitem);
} else {
collen = rowlen;
rowlen = 1;
}

} else {
MMC_ERROR(-1, "MeshNode must be provided if MeshID is missing");
cfg->roitype = (collen == 6) ? rtEdge : ((collen == 1 || rowlen == 1) ? rtNode : (collen == 4 ? rtFace : rtNone));
cfg->roidata = (float*)malloc(sizeof(float) * rowlen * collen);

for (int i = 0; i < rowlen; i++) {
if (cJSON_GetArraySize(subitem) != collen) {
MMC_ERROR(-1, "Each element in MeshROI must have the same length");
}

tmp = subitem->child;

for (int j = 0; j < collen; j++) {
cfg->roidata[ i * collen + j ] = tmp->valuedouble;
tmp = tmp->next;
}

subitem = subitem->next;
}
} else {
mcx_jdatadecode((void**)&cfg->roidata, &ndim, dims, 2, &type, subitem, cfg);

if (strcmp(type, "single") || ndim > 2 || (ndim >= 2 && dims[1] != 6 && dims[1] != 4)) {
free(cfg->roidata);
MMC_ERROR(-1, "Mesh.MeshROI JData-annotated array must be in the 'single' format");
} else {
cfg->roitype = (dims[1] == 6) ? rtEdge : ((ndim == 1 || dims[0] == 1 || dims[1] == 1) ? rtNode : (dims[1] == 4 ? rtFace : rtNone));
}
}
}
}

Expand Down
2 changes: 2 additions & 0 deletions src/mmc_utils.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -290,6 +290,8 @@ typedef struct MMC_config {
int* elem; /**<tetrahedron node indices from json input*/
unsigned int elemnum; /**<total number of elem*/
unsigned int elemlen; /**<number of nodes per elem*/
char roitype; /**<mesh roi type: 0: unknown, 1: edge-roi, 2: node-roi, 3: face-roi */
float* roidata; /**<mesh roi (edge/node/face) data*/
char jsonfile[MAX_PATH_LENGTH];/**<if the seed is specified as a file (mch), mcx will replay the photons*/
} mcconfig;

Expand Down

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