[feat] support 1x1x1 volume, add onecube/twocube benchmarks, det not …

…working

src/mcx_bench.c

@@ -36,7 +36,7 @@
 
 #define MSTR(...) #__VA_ARGS__
 
-const char *benchname[MAX_MCX_BENCH]={"cube60","cube60b","cube60planar","cubesph60b","skinvessel","sphshells","spherebox",
+const char *benchname[MAX_MCX_BENCH]={"cube60","cube60b","cube60planar","cubesph60b","onecube","twocube","skinvessel","sphshells","spherebox",
 #ifndef _MSC_VER
 			 "colin27",""};
 #else
@@ -266,6 +266,114 @@ MSTR(
 }),
 
 
+MSTR(
+{
+    "Session":{
+        "ID":"onecube",
+        "DoSaveVolume":0,
+        "DoAutoThread":1,
+        "SaveDataMask":"xv",
+        "Photons":1000000
+    },
+    "Forward":{
+        "T0":0,
+        "T1":5e-09,
+        "Dt":5e-09
+    },
+    "Optode":{
+        "Source":{
+            "Pos":[0.5,0.5,0],
+            "Dir":[0,0,1]
+        },
+        "Detector":[
+            {
+                "Pos":[0.5,0.45,1],
+                "R":0.016667
+            }
+        ]
+    },
+    "Domain":{
+        "OriginType":1,
+        "LengthUnit":60,
+        "Media":[
+            {
+                "mua":0,
+                "mus":0,
+                "g":1,
+                "n":1
+            },
+            {
+                "mua":0.005,
+                "mus":1,
+                "g":0,
+                "n":1.37
+            }
+        ],
+        "MediaFormat":"byte",
+        "Dim":[1,1,1]
+    },
+    "Shapes": {
+        "_ArraySize_": [1,1,1],
+        "_ArrayType_": "uint8",
+        "_ArrayData_": [1]
+    }
+}),
+
+
+MSTR(
+{
+    "Session":{
+        "ID":"twocube",
+        "DoSaveVolume":0,
+        "DoAutoThread":1,
+        "SaveDataMask":"xv",
+        "Photons":1000000
+    },
+    "Forward":{
+        "T0":0,
+        "T1":5e-09,
+        "Dt":5e-09
+    },
+    "Optode":{
+        "Source":{
+            "Pos":[1,1,0],
+            "Dir":[0,0,1]
+        },
+        "Detector":[
+            {
+                "Pos":[1,0.9,1],
+                "R":0.0333333
+            }
+        ]
+    },
+    "Domain":{
+        "OriginType":1,
+        "LengthUnit":30,
+        "Media":[
+            {
+                "mua":0,
+                "mus":0,
+                "g":1,
+                "n":1
+            },
+            {
+                "mua":0.005,
+                "mus":1,
+                "g":0,
+                "n":1.37
+            }
+        ],
+        "MediaFormat":"byte",
+        "Dim":[2,2,2]
+    },
+    "Shapes": {
+        "_ArraySize_": [2,2,2],
+        "_ArrayType_": "uint8",
+        "_ArrayData_": [1,1,1,1,1,1,1,1]
+    }
+}),
+
+
 MSTR(
 {
 	"Session":	{

src/mcx_bench.h

@@ -35,7 +35,7 @@
 #ifndef _MCEXTREME_BENCHMARK_H
 #define _MCEXTREME_BENCHMARK_H
 
-#define MAX_MCX_BENCH  9                           /**< Total number of built-in benchmarks */
+#define MAX_MCX_BENCH  11                          /**< Total number of built-in benchmarks */
 extern const char* benchname[MAX_MCX_BENCH];       /**< String list defining the names of each built-in benchmark */
 extern const char* benchjson[MAX_MCX_BENCH];       /**< JSON-formatted input configuration for each built-in benchmark */
 

src/mcx_core.cu

@@ -2678,7 +2678,8 @@ void mcx_run_simulation(Config* cfg, GPUInfo* gpu) {
     float4 s0 = (float4)cfg->srciquv;
 
     float3 maxidx = float3(cfg->dim.x, cfg->dim.y, cfg->dim.z);
-    int timegate = 0, totalgates, gpuid, threadid = 0;
+    uint timegate = 0, totalgates, threadid = 0;
+    int gpuid;
 
     /** \c gpuphoton - number of photons to be simulated per thread, determined by total workload and thread number */
     size_t gpuphoton = 0;
@@ -2792,6 +2793,14 @@ void mcx_run_simulation(Config* cfg, GPUInfo* gpu) {
         param.skipradius2 = 0.f;
     }
 
+    if (is2d) {
+        /**
+         *  is2d is only turn 1 if only 1 of the 3 dimension has a length of 1; if 2x or 3x of the dimension have a length of 1, use 3D mode
+         */
+        is2d = is2d * ((cfg->dim.x > 1) + (cfg->dim.y > 1) + (cfg->dim.z > 1) == 2);
+        param.is2d = is2d;
+    }
+
     /** Start multiple CPU threads using OpenMP, one thread for each GPU device to run simultaneously, \c threadid returns the current thread ID */
 #ifdef _OPENMP
     threadid = omp_get_thread_num();
@@ -2944,7 +2953,7 @@ void mcx_run_simulation(Config* cfg, GPUInfo* gpu) {
 
     /** Here we determine if the GPU memory of the current device can store all time gates, if not, disabling normalization */
     if (totalgates > gpu[gpuid].maxgate && cfg->isnormalized) {
-        MCX_FPRINTF(cfg->flog, S_RED "WARNING: GPU memory can not hold all time gates, disabling normalization to allow multiple runs\n" S_RESET);
+        MCX_FPRINTF(cfg->flog, S_RED "WARNING: %d %d %d [%d %d %d] GPU memory can not hold all time gates, disabling normalization to allow multiple runs\n" S_RESET, totalgates, gpu[gpuid].maxgate, cfg->isnormalized, cfg->dim.x, cfg->dim.y, cfg->dim.z);
         cfg->isnormalized = 0;
     }
 
@@ -3706,7 +3715,7 @@ is more than what your have specified (%d), please use the -H option to specify
                 } else {
                     int j;
 
-                    for (iter = 0; iter < gpu[gpuid].maxgate; iter++)
+                    for (iter = 0; iter < (int)gpu[gpuid].maxgate; iter++)
                         for (j = 0; j < (int)dimlen.z; j++) {
                             mcx_kahanSum(&energyabs[i], &kahanc, cfg->exportfield[iter * dimxyz + (j * cfg->srcnum + i)]*mcx_updatemua((uint)cfg->vol[j], cfg));
                         }

src/mcx_utils.h

@@ -160,7 +160,7 @@ typedef struct MCXGPUInfo {
     int core;                     /**< number of stream processors */
     int autoblock;                /**< optimized number of blocks to launch */
     int autothread;               /**< optimized number of threads to launch */
-    int maxgate;                  /**< max number of time gates that can be saved in one call */
+    unsigned int maxgate;         /**< max number of time gates that can be saved in one call */
     int maxmpthread;              /**< maximum thread number per multi-processor */
 } GPUInfo;
 

src/mcxlab.cpp

@@ -737,7 +737,7 @@ void mcx_set_field(const mxArray* root, const mxArray* item, int idx, Config* cf
         cfg->mediabyte = 0;
         arraydim = mxGetDimensions(item);
 
-        if (mxGetNumberOfDimensions(item) == 3) {
+        if (mxGetNumberOfDimensions(item) <= 3) {
             if (mxIsUint8(item) || mxIsInt8(item)) { // input is a 3D byte array
                 cfg->mediabyte = 1;
             } else if (mxIsUint16(item) || mxIsInt16(item)) { // input is a 3D short array
@@ -750,9 +750,14 @@ void mcx_set_field(const mxArray* root, const mxArray* item, int idx, Config* cf
                 cfg->mediabyte = 14;
             }
 
-            for (i = 0; i < 3; i++) {
+            for (i = 0; i < mxGetNumberOfDimensions(item); i++) {
                 ((unsigned int*)(&cfg->dim))[i] = arraydim[i];
             }
+
+            if (i < 3) {
+                cfg->dim.z = 1;
+            }
+
         } else if (mxGetNumberOfDimensions(item) == 4) { // if dimension is 4D, 1st dim is the property records: mua/mus/g/n
             if ((mxIsUint8(item) || mxIsInt8(item)) && arraydim[0] == 4) { // if 4D byte array has a 1st dim of 4
                 cfg->mediabyte = MEDIA_ASGN_BYTE;