pyfast 4.12.0__cp36-abi3-macosx_11_0_arm64.whl

fast/kernels/Algorithms/TemporalSmoothing/ImageMovingAverage.cl

@@ -0,0 +1,66 @@
+__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP | CLK_FILTER_NEAREST;
+
+float getPixelAsFloat(__read_only image2d_t image, int2 pos) {
+    float value;
+    int dataType = get_image_channel_data_type(image);
+    if(dataType == CLK_FLOAT) {
+        value = read_imagef(image, sampler, pos).x;
+    } else if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+        value = read_imageui(image, sampler, pos).x;
+    } else {
+        value = read_imagei(image, sampler, pos).x;
+    }
+    return value;
+}
+
+__kernel void MAinitialize(
+        __read_only image2d_t input,
+        __write_only image2d_t output,
+        __write_only image2d_t memoryOut,
+        __private int frameCount
+    ) {
+    const int2 pos = {get_global_id(0), get_global_id(1)};
+
+    float value = getPixelAsFloat(input, pos);
+    write_imagef(memoryOut, pos, value);
+    int dataType = get_image_channel_data_type(output);
+    if(dataType == CLK_FLOAT) {
+        write_imagef(output, pos, value);
+    } else {
+        // output image is of integer type, have to apply rounding
+        if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+            write_imageui(output, pos, (uint)value);
+        } else {
+            write_imagei(output, pos, (int)value);
+        }
+    }
+}
+
+__kernel void MAiteration(
+        __read_only image2d_t input,
+        __read_only image2d_t memoryIn,
+        __read_only image2d_t last,
+        __write_only image2d_t output,
+        __write_only image2d_t memoryOut,
+        __private int frameCount
+    ) {
+    const int2 pos = {get_global_id(0), get_global_id(1)};
+
+    float newValue = getPixelAsFloat(input, pos);
+    float oldMemory = read_imagef(memoryIn, sampler, pos).x;
+    float lastValue = getPixelAsFloat(last, pos);
+    float result = oldMemory + 1.0f/(float)frameCount * (newValue - lastValue);
+    write_imagef(memoryOut, pos, result);
+
+    int dataType = get_image_channel_data_type(output);
+    if(dataType == CLK_FLOAT) {
+        write_imagef(output, pos, result);
+    } else {
+        // output image is of integer type, have to apply rounding
+        if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+            write_imageui(output, pos, (uint)round(result));
+        } else {
+            write_imagei(output, pos, (int)round(result));
+        }
+    }
+}

fast/kernels/Algorithms/TemporalSmoothing/ImageWeightedMovingAverage.cl

@@ -0,0 +1,74 @@
+__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP | CLK_FILTER_NEAREST;
+
+float getPixelAsFloat(__read_only image2d_t image, int2 pos) {
+    float value;
+    int dataType = get_image_channel_data_type(image);
+    if(dataType == CLK_FLOAT) {
+        value = read_imagef(image, sampler, pos).x;
+    } else if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+        value = read_imageui(image, sampler, pos).x;
+    } else {
+        value = read_imagei(image, sampler, pos).x;
+    }
+    return value;
+}
+
+__kernel void WMAinitialize(
+        __read_only image2d_t input,
+        __write_only image2d_t output,
+        __write_only image2d_t memoryOut,
+        __private int frameCount
+    ) {
+    const int2 pos = {get_global_id(0), get_global_id(1)};
+
+    float value = getPixelAsFloat(input, pos);
+    float sum = value*frameCount;
+    float numerator = 0.0f;
+    for(int i = 0; i < frameCount; ++i) {
+        numerator += (i+1)*value;
+    }
+    float result = numerator / (frameCount*(frameCount + 1.0f)/2.0f);
+
+    write_imagef(memoryOut, pos, (float4)(sum, numerator, 0, 0));
+
+    int dataType = get_image_channel_data_type(output);
+    if(dataType == CLK_FLOAT) {
+        write_imagef(output, pos, result);
+    } else {
+        // output image is of integer type, have to apply rounding
+        if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+            write_imageui(output, pos, (uint)round(result));
+        } else {
+            write_imagei(output, pos, (int)round(result));
+        }
+    }
+}
+
+__kernel void WMAiteration(
+        __read_only image2d_t input,
+        __read_only image2d_t memoryIn,
+        __read_only image2d_t last,
+        __write_only image2d_t output,
+        __write_only image2d_t memoryOut,
+        __private int frameCount
+    ) {
+    const int2 pos = {get_global_id(0), get_global_id(1)};
+
+    float newValue = getPixelAsFloat(input, pos);
+    float2 oldMemory = read_imagef(memoryIn, sampler, pos).xy;
+    float newTotal = oldMemory.x + newValue - getPixelAsFloat(last, pos);
+    float newNumerator = oldMemory.y + frameCount*newValue - oldMemory.x;
+    write_imagef(memoryOut, pos, (float4)(newTotal, newNumerator, 0, 0));
+
+    int dataType = get_image_channel_data_type(output);
+    if(dataType == CLK_FLOAT) {
+        write_imagef(output, pos, newNumerator / (frameCount*(frameCount + 1.0f)/2.0f));
+    } else {
+        // output image is of integer type, have to apply rounding
+        if(dataType == CLK_UNSIGNED_INT8 || dataType == CLK_UNSIGNED_INT16 || dataType == CLK_UNSIGNED_INT32) {
+            write_imageui(output, pos, (uint)round(newNumerator / (frameCount*(frameCount + 1.0f)/2.0f)));
+        } else {
+            write_imagei(output, pos, (int)round(newNumerator / (frameCount*(frameCount + 1.0f)/2.0f)));
+        }
+    }
+}

fast/kernels/Algorithms/TissueSegmentation/TissueSegmentation.cl

@@ -0,0 +1,18 @@
+__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_NONE | CLK_FILTER_NEAREST;
+
+__kernel void segment(
+            __read_only image2d_t input,
+            __write_only image2d_t output,
+            __private int m_thresh,
+            __private int m_filterZeros
+    ) {
+    const int2 pos = {get_global_id(0), get_global_id(1)};
+    float3 color = convert_float4(read_imageui(input, sampler, pos)).xyz;
+
+    uchar result = 0;
+    if ((!(m_filterZeros && all(color == 0))) && (length(color - (float3)(255, 255, 255)) > m_thresh)) {
+        result = 1;
+    }
+
+    write_imageui(output, pos, result);
+}

fast/kernels/Algorithms/TubeSegmentationAndCenterlineExtraction/InverseGradientSegmentation.cl

@@ -0,0 +1,203 @@
+__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;
+
+#define LPOS(pos) pos.x+pos.y*get_global_size(0)+pos.z*get_global_size(0)*get_global_size(1)
+
+__kernel void initGrowing(
+        __read_only image3d_t centerline,
+#ifdef fast_3d_image_writes
+        __write_only image3d_t initSegmentation
+#else
+    __global uchar * initSegmentation
+#endif
+    ) {
+    int4 pos = {get_global_id(0), get_global_id(1), get_global_id(2), 0};
+    if(read_imageui(centerline, sampler, pos).x > 0) {
+        uint radius = read_imageui(centerline, sampler, pos).x;
+        int N;
+        if(radius > 7) {
+            N = min(max(1, (int)(radius)), 5);
+        } else {
+            N = 1;
+        }
+
+        for(int a = -N; a < N+1; a++) {
+        for(int b = -N; b < N+1; b++) {
+        for(int c = -N; c < N+1; c++) {
+            int4 n;
+            n.x = pos.x + a;
+            n.y = pos.y + b;
+            n.z = pos.z + c;
+            if(read_imageui(centerline, sampler, n).x == 0 && length((float3)(a,b,c)) <= N) {
+#ifdef fast_3d_image_writes
+                write_imageui(initSegmentation, n, 2);
+#else
+                if(n.x >= 0 && n.y >= 0 && n.z >= 0 &&
+                    n.x < get_global_size(0) && n.y < get_global_size(1) && n.z < get_global_size(2))
+                    initSegmentation[LPOS(n)] = 2; 
+#endif
+        }
+        }}}
+    }
+
+}
+
+__kernel void grow(
+        __read_only image3d_t currentSegmentation,
+        __read_only image3d_t gvf,
+#ifdef fast_3d_image_writes
+        __write_only image3d_t nextSegmentation,
+#else
+        __global uchar* nextSegmentation,
+#endif
+        __global int * stop
+    ) {
+
+    int4 X = {get_global_id(0), get_global_id(1), get_global_id(2), 0};
+    char value = read_imageui(currentSegmentation, sampler, X).x;
+    // value of 2, means to check it, 1 means it is already accepted
+    if(value == 1) {
+#ifdef fast_3d_image_writes
+        write_imageui(nextSegmentation, X, 1);
+#else
+        nextSegmentation[LPOS(X)] = 1;
+#endif
+    } else if(value == 2){
+        float4 FNX = read_imagef(gvf, sampler, X);
+        float FNXw = length(FNX.xyz);
+
+        bool continueGrowing = false;
+        for(int a = -1; a < 2; a++) {
+        for(int b = -1; b < 2; b++) {
+        for(int c = -1; c < 2; c++) {
+            if(a == 0 && b == 0 && c == 0)
+                continue;
+
+            int4 Y;
+            Y.x = X.x + a;
+            Y.y = X.y + b;
+            Y.z = X.z + c;
+            
+            char valueY = read_imageui(currentSegmentation, sampler, Y).x;
+            if(valueY != 1) {
+                float4 FNY = read_imagef(gvf, sampler, Y);
+                FNY.w = length(FNY.xyz);
+                FNY.x /= FNY.w;
+                FNY.y /= FNY.w;
+                FNY.z /= FNY.w;
+                if(FNY.w > FNXw /*|| FNXw < 0.1f*/) {
+                    int4 Z;
+                    float maxDotProduct = -2.0f;
+                    for(int a2 = -1; a2 < 2; a2++) {
+                    for(int b2 = -1; b2 < 2; b2++) {
+                    for(int c2 = -1; c2 < 2; c2++) {
+                        if(a2 == 0 && b2 == 0 && c2 == 0)
+                            continue;
+                        int4 Zc;
+                        Zc.x = Y.x+a2;
+                        Zc.y = Y.y+b2;
+                        Zc.z = Y.z+c2;
+                        float3 YZ;
+                        YZ.x = Zc.x-Y.x;
+                        YZ.y = Zc.y-Y.y;
+                        YZ.z = Zc.z-Y.z;
+                        YZ = normalize(YZ);
+                        if(dot(FNY.xyz, YZ) > maxDotProduct) {
+                            maxDotProduct = dot(FNY.xyz, YZ);
+                            Z = Zc;
+                        }
+                    }}}
+
+                    if(Z.x == X.x && Z.y == X.y && Z.z == X.z) {
+#ifdef fast_3d_image_writes
+                        write_imageui(nextSegmentation, X, 1);
+                        write_imageui(nextSegmentation, Y, 2);
+#else
+                        nextSegmentation[LPOS(X)] = 1;
+                        // Check if in bounds
+                        if(Y.x >= 0 && Y.y >= 0 && Y.z >= 0 && 
+                            Y.x < get_global_size(0) && Y.y < get_global_size(1) && Y.z < get_global_size(2)) {
+                            nextSegmentation[LPOS(Y)] = 2; 
+                        }
+#endif
+                      
+                        continueGrowing = true;
+                    }
+                }
+            }
+        }}}
+
+        if(continueGrowing) {
+            // Added new items to list (values of 2)
+            stop[0] = 0;
+        } else {
+            // X was not accepted
+#ifdef fast_3d_image_writes
+            write_imageui(nextSegmentation, X, 0);
+#else
+            nextSegmentation[LPOS(X)] = 0;
+#endif
+        }
+    }
+}
+
+__kernel void dilate(
+        __read_only image3d_t volume, 
+#ifdef fast_3d_image_writes
+        __write_only image3d_t result
+#else
+        __global uchar * result
+#endif
+    ) {
+    int4 pos = {get_global_id(0), get_global_id(1), get_global_id(2), 0};
+
+    if(read_imageui(volume, sampler, pos).x == 1) {
+        for(int a = -1; a < 2 ; a++) {
+            for(int b = -1; b < 2 ; b++) {
+                for(int c = -1; c < 2 ; c++) {
+                    int4 nPos = pos + (int4)(a,b,c,0);
+#ifdef fast_3d_image_writes
+                    write_imageui(result, nPos, 1);
+#else
+                    // Check if in bounds
+                    if(nPos.x >= 0 && nPos.y >= 0 && nPos.z >= 0 &&
+                        nPos.x < get_global_size(0) && nPos.y < get_global_size(1) && nPos.z < get_global_size(2))
+                    result[LPOS(nPos)] = 1;
+#endif
+                }
+            }
+        }
+    }
+}
+
+__kernel void erode(
+        __read_only image3d_t volume, 
+#ifdef fast_3d_image_writes
+        __write_only image3d_t result
+#else
+        __global uchar * result
+#endif
+    ) {
+    int4 pos = {get_global_id(0), get_global_id(1), get_global_id(2), 0};
+
+    int value = read_imageui(volume, sampler, pos).x;
+    if(value == 1) {
+        bool keep = true;
+        for(int a = -1; a < 2 ; a++) {
+            for(int b = -1; b < 2 ; b++) {
+                for(int c = -1; c < 2 ; c++) {
+                    keep = (read_imageui(volume, sampler, pos + (int4)(a,b,c,0)).x == 1 && keep);
+                }
+            }
+        }
+#ifdef fast_3d_image_writes
+        write_imageui(result, pos, keep ? 1 : 0);
+    } else {
+        write_imageui(result, pos, 0);
+    }
+#else
+        result[LPOS(pos)] = keep ? 1 : 0;
+    } else {
+        result[LPOS(pos)] = 0;
+    }
+#endif
+}