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Custom read zero outside image #301

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Custom read zero outside image #301

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031d524
use custom read for pixels outside image = zero
haesleinhuepf Apr 23, 2023
45fbb3b
make sure input image is of type uint8
haesleinhuepf Apr 23, 2023
3ac5524
fix brackets in tests
haesleinhuepf Apr 23, 2023
feca0c6
modify test to have zeros around all ones
haesleinhuepf Apr 23, 2023
c7854c8
added test directly comparing with skimage
haesleinhuepf Apr 23, 2023
26221bb
more tests comparing with skimage
haesleinhuepf Apr 23, 2023
8c00111
updated demo
haesleinhuepf Apr 23, 2023
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42 changes: 20 additions & 22 deletions demo/smoothing.ipynb
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4 changes: 4 additions & 0 deletions pyclesperanto_prototype/_tier1/_inferior_superior.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,10 @@ def inferior_superior(source : Image, destination : Image = None) -> Image:
Implemented in inf_sup function in scikit morphological snakes:
.. [1] https://github.com/scikit-image/scikit-image/blob/00177e14097237ef20ed3141ed454bc81b308f82/skimage/segmentation/morphsnakes.py
"""
import numpy as np
if source.dtype != np.uint8:
# the read function in the kernel below is custom and only supports images of type uint8
source = source.astype(np.uint8)

parameters = {
"src":source,
Expand Down
4 changes: 4 additions & 0 deletions pyclesperanto_prototype/_tier1/_superior_inferior.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,10 @@ def superior_inferior(source : Image, destination : Image = None) -> Image:
Implemented in sup_inf function in scikit morphological snakes:
.. [1] https://github.com/scikit-image/scikit-image/blob/00177e14097237ef20ed3141ed454bc81b308f82/skimage/segmentation/morphsnakes.py
"""
import numpy as np
if source.dtype != np.uint8:
# the read function in the kernel below is custom and only supports images of type uint8
source = source.astype(np.uint8)

parameters = {
"src":source,
Expand Down
30 changes: 21 additions & 9 deletions pyclesperanto_prototype/_tier1/inferior_superior_2d_x.cl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,17 @@
__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;

#define READ_IMAGE_ZERO_OUTSIDE(a,b,c) read_buffer2duc_zero_outside(GET_IMAGE_WIDTH(a),GET_IMAGE_HEIGHT(a),GET_IMAGE_DEPTH(a),a,b,c)

inline uchar2 read_buffer2duc_zero_outside(int read_buffer_width, int read_buffer_height, int read_buffer_depth, __global uchar * buffer_var, sampler_t sampler, int2 position )
{
int2 pos = (int2){position.x, position.y};
int pos_in_buffer = pos.x + pos.y * read_buffer_width;
if (pos.x < 0 || pos.x >= read_buffer_width || pos.y < 0 || pos.y >= read_buffer_height) {
return (uchar2){0, 0};
}
return (uchar2){buffer_var[pos_in_buffer],0};
}

__kernel void inferior_superior_2d (
IMAGE_src_TYPE src,
IMAGE_dst_TYPE dst
Expand All @@ -10,7 +22,7 @@ __kernel void inferior_superior_2d (

const int2 pos = (int2){x,y};

float value = READ_src_IMAGE(src, sampler, pos).x;
float value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, pos).x;

// if value is already 1, dilate will return 1
if (value == 1) {
Expand All @@ -21,9 +33,9 @@ __kernel void inferior_superior_2d (
/* Dilate with kernel [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, 1})).x;
if (value == 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, -1})).x;
if (value == 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(0));
return;
Expand All @@ -33,9 +45,9 @@ __kernel void inferior_superior_2d (
/* Dilate with kernel [[0, 1, 0],
[0, 1, 0],
[0, 1, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){0, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){0, 1})).x;
if (value == 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){0, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){0, -1})).x;
if (value == 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(0));
return;
Expand All @@ -45,9 +57,9 @@ __kernel void inferior_superior_2d (
/* Dilate with kernel [[0, 0, 1],
[0, 1, 0],
[1, 0, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, 1})).x;
if (value == 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, -1})).x;
if (value == 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(0));
return;
Expand All @@ -57,9 +69,9 @@ __kernel void inferior_superior_2d (
/* Dilate with kernel [[0, 0, 0],
[1, 1, 1],
[0, 0, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, 0})).x;
if (value == 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, 0})).x;
if (value == 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(0));
return;
Expand Down
33 changes: 23 additions & 10 deletions pyclesperanto_prototype/_tier1/inferior_superior_3d_x.cl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,18 @@
__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;


#define READ_IMAGE_ZERO_OUTSIDE(a,b,c) read_buffer3duc_zero_outside(GET_IMAGE_WIDTH(a),GET_IMAGE_HEIGHT(a),GET_IMAGE_DEPTH(a),a,b,c)

inline uchar2 read_buffer3duc_zero_outside(int read_buffer_width, int read_buffer_height, int read_buffer_depth, __global uchar * buffer_var, sampler_t sampler, int4 position )
{
int4 pos = (int4){position.x, position.y, position.z, 0};
int pos_in_buffer = pos.x + pos.y * read_buffer_width + pos.z * read_buffer_width * read_buffer_height;
if (pos.x < 0 || pos.x >= read_buffer_width || pos.y < 0 || pos.y >= read_buffer_height || pos.z < 0 || pos.z >= read_buffer_depth) {
return (uchar2){0, 0};
}
return (uchar2){buffer_var[pos_in_buffer],0};
}

__kernel void inferior_superior_3d (
IMAGE_src_TYPE src,
IMAGE_dst_TYPE dst
Expand All @@ -11,7 +24,7 @@ __kernel void inferior_superior_3d (

const int4 pos = (int4){x, y, z, 0};

float value = READ_src_IMAGE(src, sampler, pos).x;
float value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, pos).x;

// if value is already 0, erode will return 0
if (value != 0) {
Expand All @@ -25,7 +38,7 @@ __kernel void inferior_superior_3d (
// P0
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, 0, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, 0, 0})).x;
// printf("value %i\n", value);
if (value != 0) {
break;
Expand All @@ -43,7 +56,7 @@ __kernel void inferior_superior_3d (
// P1
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, 0, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, 0, j, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -60,7 +73,7 @@ __kernel void inferior_superior_3d (
// P2
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){0, i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){0, i, j, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -77,7 +90,7 @@ __kernel void inferior_superior_3d (
// P3
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, j, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -94,7 +107,7 @@ __kernel void inferior_superior_3d (
// P4
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){j, i, -i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){j, i, -i, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -111,7 +124,7 @@ __kernel void inferior_superior_3d (
// P5
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, i, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -128,7 +141,7 @@ __kernel void inferior_superior_3d (
// P6
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, -i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, -i, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -145,7 +158,7 @@ __kernel void inferior_superior_3d (
// P7
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, i, j, 0})).x;
if (value != 0) {
break;
}
Expand All @@ -162,7 +175,7 @@ __kernel void inferior_superior_3d (
// P8
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, -i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, -i, j, 0})).x;
if (value != 0) {
break;
}
Expand Down
32 changes: 23 additions & 9 deletions pyclesperanto_prototype/_tier1/superior_inferior_2d_x.cl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,19 @@
__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;


#define READ_IMAGE_ZERO_OUTSIDE(a,b,c) read_buffer2duc_zero_outside(GET_IMAGE_WIDTH(a),GET_IMAGE_HEIGHT(a),GET_IMAGE_DEPTH(a),a,b,c)

inline uchar2 read_buffer2duc_zero_outside(int read_buffer_width, int read_buffer_height, int read_buffer_depth, __global uchar * buffer_var, sampler_t sampler, int2 position )
{
int2 pos = (int2){position.x, position.y};
int pos_in_buffer = pos.x + pos.y * read_buffer_width;
if (pos.x < 0 || pos.x >= read_buffer_width || pos.y < 0 || pos.y >= read_buffer_height) {
return (uchar2){0, 0};
}
return (uchar2){buffer_var[pos_in_buffer],0};
}


__kernel void superior_inferior_2d (
IMAGE_src_TYPE src,
IMAGE_dst_TYPE dst
Expand All @@ -10,7 +24,7 @@ __kernel void superior_inferior_2d (

const int2 pos = (int2){x,y};

float value = READ_src_IMAGE(src, sampler, pos).x;
float value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, pos).x;

// if value is already 0, erode will return 0
if (value == 0) {
Expand All @@ -21,9 +35,9 @@ __kernel void superior_inferior_2d (
/* Erode with kernel [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, 1})).x;
if (value != 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, -1})).x;
if (value != 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(1));
return;
Expand All @@ -33,9 +47,9 @@ __kernel void superior_inferior_2d (
/* Erode with kernel [[0, 1, 0],
[0, 1, 0],
[0, 1, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){0, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){0, 1})).x;
if (value != 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){0, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){0, -1})).x;
if (value != 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(1));
return;
Expand All @@ -45,9 +59,9 @@ __kernel void superior_inferior_2d (
/* Erode with kernel [[0, 0, 1],
[0, 1, 0],
[1, 0, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, 1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, 1})).x;
if (value != 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, -1})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, -1})).x;
if (value != 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(1));
return;
Expand All @@ -57,9 +71,9 @@ __kernel void superior_inferior_2d (
/* Erode with kernel [[0, 0, 0],
[1, 1, 1],
[0, 0, 0]] */
value = READ_src_IMAGE(src, sampler, (pos + (int2){1, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){1, 0})).x;
if (value != 0) {
value = READ_src_IMAGE(src, sampler, (pos + (int2){-1, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int2){-1, 0})).x;
if (value != 0) {
WRITE_dst_IMAGE(dst, pos, CONVERT_dst_PIXEL_TYPE(1));
return;
Expand Down
30 changes: 21 additions & 9 deletions pyclesperanto_prototype/_tier1/superior_inferior_3d_x.cl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,17 @@
__constant sampler_t sampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;

#define READ_IMAGE_ZERO_OUTSIDE(a,b,c) read_buffer3duc_zero_outside(GET_IMAGE_WIDTH(a),GET_IMAGE_HEIGHT(a),GET_IMAGE_DEPTH(a),a,b,c)

inline uchar2 read_buffer3duc_zero_outside(int read_buffer_width, int read_buffer_height, int read_buffer_depth, __global uchar * buffer_var, sampler_t sampler, int4 position )
{
int4 pos = (int4){position.x, position.y, position.z, 0};
int pos_in_buffer = pos.x + pos.y * read_buffer_width + pos.z * read_buffer_width * read_buffer_height;
if (pos.x < 0 || pos.x >= read_buffer_width || pos.y < 0 || pos.y >= read_buffer_height || pos.z < 0 || pos.z >= read_buffer_depth) {
return (uchar2){0, 0};
}
return (uchar2){buffer_var[pos_in_buffer],0};
}

__kernel void superior_inferior_3d (
IMAGE_src_TYPE src,
IMAGE_dst_TYPE dst
Expand All @@ -25,7 +37,7 @@ __kernel void superior_inferior_3d (
// P0
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, 0, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, 0, 0})).x;
// printf("value %i\n", value);
if (value == 0) {
break;
Expand All @@ -43,7 +55,7 @@ __kernel void superior_inferior_3d (
// P1
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, 0, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, 0, j, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -60,7 +72,7 @@ __kernel void superior_inferior_3d (
// P2
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){0, i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){0, i, j, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -77,7 +89,7 @@ __kernel void superior_inferior_3d (
// P3
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, j, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -94,7 +106,7 @@ __kernel void superior_inferior_3d (
// P4
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){j, i, -i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){j, i, -i, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -111,7 +123,7 @@ __kernel void superior_inferior_3d (
// P5
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, i, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -128,7 +140,7 @@ __kernel void superior_inferior_3d (
// P6
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, j, -i, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, j, -i, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -145,7 +157,7 @@ __kernel void superior_inferior_3d (
// P7
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, i, j, 0})).x;
if (value == 0) {
break;
}
Expand All @@ -162,7 +174,7 @@ __kernel void superior_inferior_3d (
// P8
for (int i = -1; i <= 1; i++) {
for (int j = -1; j <= 1; j++) {
value = READ_src_IMAGE(src, sampler, (pos + (int4){i, -i, j, 0})).x;
value = READ_IMAGE_ZERO_OUTSIDE(src, sampler, (pos + (int4){i, -i, j, 0})).x;
if (value == 0) {
break;
}
Expand Down
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