/// <summary>
/// Divide by a scaled 16-bit stack pixel-wise
/// </summary>
/// <param name="ims">The stack to divide by</param>
/// <param name="outMax">65535 will be assigned to this value</param>
public void Divide(ImageStack16 ims, float outMax = ushort.MaxValue)
{
DisposeGuard();
if (ims.IsDisposed)
{
throw new ArgumentException("Can't divide by disposed image");
}
if (!IsCompatible(ims))
{
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
}
for (int z = 0; z < ZPlanes; z++)
{
for (int t = 0; t < TimePoints; t++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
*this[x, y, z, t] /= (float)*ims[x, y, z, t] / ushort.MaxValue * outMax;
}
}
}
}
}
/// <summary>
/// Constructs a new floating point image stack with a 16 bit stack as
/// a source, optionally rescaling the maximum
/// </summary>
/// <param name="ims">The 8bit source stack</param>
/// <param name="outMax">65535 will be assigned to this value in the float stack</param>
public ImageStack32F(ImageStack16 ims, float outMax = ushort.MaxValue)
{
if (ims == null)
{
throw new ArgumentNullException(nameof(ims));
}
if (ims.IsDisposed)
{
throw new ArgumentException("Can't copy disposed stack");
}
//initialize buffer and dimension properties according to source stack
InitializeImageBuffer(ims.ImageWidth, ims.ImageHeight, ims.ZPlanes, ims.TimePoints, 4);
//loop over pixels, assigning values
for (int z = 0; z < ZPlanes; z++)
{
for (int t = 0; t < TimePoints; t++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
float temp = *ims[x, y, z, t];
temp = temp / ushort.MaxValue * outMax;
if (temp > outMax)
{
temp = outMax;
}
*this[x, y, z, t] = temp;
}
}
}
}
}
/// <summary>
/// Copy constructor
/// </summary>
/// <param name="ims">The image to copy</param>
public ImageStack16(ImageStack16 ims)
{
if (ims == null)
throw new ArgumentNullException(nameof(ims));
if (ims.IsDisposed)
throw new ArgumentException("Can't copy disposed stack");
InitializeAsCopy(ims);
}
/// <summary>
/// Performs pixel-by-pixel subtraction of the given image
/// stack from the current stack clipping at 0
/// </summary>
/// <param name="ims">The stack to subtract</param>
public void Subtract(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
{
throw new ArgumentException("Can't add disposed image");
}
if (!IsCompatible(ims))
{
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
}
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint *iData = (uint *)ImageData;
uint *iSub = (uint *)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = SubShortAsUint(iData[i], iSub[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ushort prev = ImageData[i];
ImageData[i] -= ims.ImageData[i];
if (ImageData[i] > prev)
{
ImageData[i] = 0;
}
}
}
else
{
for (int t = 0; t < TimePoints; t++)
{
for (int z = 0; z < ZPlanes; z++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
ushort *pixel = this[x, y, z, t];
ushort prev = *pixel;
* pixel -= *ims[x, y, z, t];
if (*pixel > prev)//indicates that wrap-around occured
{
*pixel = ushort.MinValue;
}
}
}
}
}
}
}
/// <summary>
/// Compares every pixel in an image to a given value
/// </summary>
/// <param name="value">The value each pixel should have</param>
/// <param name="image">The image to compare</param>
private void CompareValImage(ushort value, ImageStack16 image)
{
ushort* imStart = image.ImageData;
//only compare outside of stride padding
for (long i = 0; i < image.ImageNB / 2; i++)
{
if (i % image.Stride < image.ImageWidth)
Assert.AreEqual(value, imStart[i], "Found non-matching pixel at position {0}", i);
}
}
/// <summary>
/// Copy constructor
/// </summary>
/// <param name="ims">The image to copy</param>
public ImageStack16(ImageStack16 ims)
{
if (ims == null)
{
throw new ArgumentNullException(nameof(ims));
}
if (ims.IsDisposed)
{
throw new ArgumentException("Can't copy disposed stack");
}
InitializeAsCopy(ims);
}
public void ShallowConstruction_OddStride()
{
ushort* buffer = (ushort*)Marshal.AllocHGlobal(51);
try
{
var ims = new ImageStack16(buffer, 51, 51, 1, 1, 1, ImageStack.SliceOrders.TBeforeZ);
}
finally
{
Marshal.FreeHGlobal((IntPtr)buffer);
}
}
public void Construction_WithValidArguments_DimCorrect()
{
int w = 20;
int h = 30;
int z = 40;
int t = 50;
var ims = new ImageStack16(w, h, z, t, ImageStack.SliceOrders.TBeforeZ);
Assert.AreEqual(ims.ImageWidth, w, "Image width not correct.");
Assert.AreEqual(ims.ImageHeight, h, "Image height not correct.");
Assert.AreEqual(ims.ZPlanes, z, "Image z plane number not correct.");
Assert.AreEqual(ims.TimePoints, t, "Number of timepoints not correct.");
ims.Dispose();
}
/// <summary>
/// Performs pixel-by-pixel division of the given image
/// stack to the current stack clipping at 255
/// </summary>
/// <param name="ims">The stack to divide by element-wise</param>
public void Divide(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
{
throw new ArgumentException("Can't add disposed image");
}
if (!IsCompatible(ims))
{
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
}
//if the strides of the two images aren't equal (pixels not aligned in memory) we have
//to laboriously loop over individual pixels otherwise we can move through the buffer in 32bit blocks
//for all images created using this code stride should always be the same if the width is the same
//but we could be dealing with a foreign memory block via shallow copy
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint *iData = (uint *)ImageData;
uint *iDiv = (uint *)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = DivShortAsUint(iData[i], iDiv[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ImageData[i] /= ims.ImageData[i];
}
}
else
{
for (int z = 0; z < ZPlanes; z++)
{
for (int t = 0; t < TimePoints; t++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
*this[x, y, z, t] /= *ims[x, y, z, t];//no chance of roll-over on this division
}
}
}
}
}
}
/// <summary>
/// Constructs an 8bit stack via rescaling of a 16bit stack
/// </summary>
/// <param name="ims">The source stack to be copied</param>
/// <param name="min">This value and below will be set to 0</param>
/// <param name="max">This value and above will be set to 255</param>
public ImageStack8(ImageStack16 ims, ushort min = ushort.MinValue, ushort max = ushort.MaxValue)
{
if (ims == null)
{
throw new ArgumentNullException(nameof(ims));
}
if (ims.IsDisposed)
{
throw new ArgumentException("Can't copy disposed stack");
}
if (max <= min)
{
throw new ArgumentException("max has to be strictly greater than min");
}
SliceOrder = ims.SliceOrder;
//initialize buffer and dimension properties according to source stack
InitializeImageBuffer(ims.ImageWidth, ims.ImageHeight, ims.ZPlanes, ims.TimePoints, 1);
//loop over pixels, assigning values
for (int z = 0; z < ZPlanes; z++)
{
for (int t = 0; t < TimePoints; t++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
float temp = *ims[x, y, z, t];
temp = (temp - min) / (max - min) * byte.MaxValue;
if (temp < 0)
{
temp = 0;
}
else if (temp > byte.MaxValue)
{
temp = byte.MaxValue;
}
*this[x, y, z, t] = (byte)temp;
}
}
}
}
}
public void Downscale_Construction_Correct()
{
var rnd = new Random();
ImageStack16 source = new ImageStack16(50, 50, 50, 50, ImageStack.SliceOrders.TBeforeZ);
//quickly fill image with random values
int* buffer = (int*)source.ImageData;
long iter = source.ImageNB / 4;
for (long i = 0; i < iter; i++)
{
buffer[i] = rnd.Next();
}
ushort rangeMin = 10;
ushort rangeMax = 1000;
ImageStack8 ims8 = new ImageStack8(source, rangeMin, rangeMax);
Assert.AreEqual(source.SliceOrder, ims8.SliceOrder);
for (int z = 0; z < source.ZPlanes; z++)
for (int t = 0; t < source.TimePoints; t++)
for (int y = 0; y < source.ImageHeight; y++)
for (int x = 0; x < source.ImageWidth; x++)
{
float pixel = *source[x, y, z, t];
pixel = pixel - rangeMin;
pixel = pixel / (rangeMax - rangeMin) * byte.MaxValue;
pixel = pixel < 0 ? 0 : pixel;
pixel = pixel > byte.MaxValue ? byte.MaxValue : pixel;
Assert.AreEqual((byte)pixel, *ims8[x, y, z, t]);
}
source.Dispose();
ims8.Dispose();
}
/// <summary>
/// Performs pixel-by-pixel subtraction of the given image
/// stack from the current stack clipping at 0
/// </summary>
/// <param name="ims">The stack to subtract</param>
public void Subtract(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
throw new ArgumentException("Can't add disposed image");
if (!IsCompatible(ims))
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint* iData = (uint*)ImageData;
uint* iSub = (uint*)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = SubShortAsUint(iData[i], iSub[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ushort prev = ImageData[i];
ImageData[i] -= ims.ImageData[i];
if (ImageData[i] > prev)
ImageData[i] = 0;
}
}
else
{
for (int t = 0; t < TimePoints; t++)
for (int z = 0; z < ZPlanes; z++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
{
ushort* pixel = this[x, y, z, t];
ushort prev = *pixel;
*pixel -= *ims[x, y, z, t];
if (*pixel > prev)//indicates that wrap-around occured
*pixel = ushort.MinValue;
}
}
}
/// <summary>
/// Performs pixel-by-pixel division of the given image
/// stack to the current stack clipping at 255
/// </summary>
/// <param name="ims">The stack to divide by element-wise</param>
public void Divide(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
throw new ArgumentException("Can't add disposed image");
if (!IsCompatible(ims))
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
//if the strides of the two images aren't equal (pixels not aligned in memory) we have
//to laboriously loop over individual pixels otherwise we can move through the buffer in 32bit blocks
//for all images created using this code stride should always be the same if the width is the same
//but we could be dealing with a foreign memory block via shallow copy
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint* iData = (uint*)ImageData;
uint* iDiv = (uint*)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = DivShortAsUint(iData[i], iDiv[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ImageData[i] /= ims.ImageData[i];
}
}
else
{
for (int z = 0; z < ZPlanes; z++)
for (int t = 0; t < TimePoints; t++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
{
*this[x, y, z, t] /= *ims[x, y, z, t];//no chance of roll-over on this division
}
}
}
public void From16bit_Constructor_Correct()
{
Random rnd = new Random();
var ims16 = new ImageStack16(43, 43, 41, 41, ImageStack.SliceOrders.ZBeforeT);
//quickly fill image with random values
int* buffer = (int*)ims16.ImageData;
long iter = ims16.ImageNB / 4;
for (long i = 0; i < iter; i++)
{
buffer[i] = rnd.Next();
}
var ims32 = new ImageStack32F(ims16);
Assert.AreEqual(ims16.SliceOrder, ims32.SliceOrder);
for (int z = 0; z < ims16.ZPlanes; z++)
for (int t = 0; t < ims16.TimePoints; t++)
for (int y = 0; y < ims16.ImageHeight; y++)
for (int x = 0; x < ims16.ImageWidth; x++)
Assert.AreEqual(*ims16[x, y, z, t], *ims32[x, y, z, t], *ims16[x, y, z, t] / 1000);
ims16.Dispose();
ims32.Dispose();
}
/// <summary>
/// Performs pixel-by-pixel addition of the given image
/// stack to the current stack clipping at 65535
/// </summary>
/// <param name="ims">The stack to add</param>
public void Add(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
throw new ArgumentException("Can't add disposed image");
//NOTE: Not clear whether we should require same z/t ordering for compatibility
if (!IsCompatible(ims))
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
//if the strides of the two images aren't equal (pixels not aligned in memory) we have
//to laboriously loop over individual pixels otherwise we can move through the buffer in 32bit blocks
//for all images created using this code stride should always be the same if the width is the same
//but we could be dealing with a foreign memory block via shallow copy
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint* iData = (uint*)ImageData;
uint* iAdd = (uint*)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = AddShortAsUint(iData[i], iAdd[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ushort prev = ImageData[i];
ImageData[i] += ims.ImageData[i];
if (ImageData[i] < prev)
ImageData[i] = ushort.MaxValue;
}
}
else
{
for (int z = 0; z < ZPlanes; z++)
for (int t = 0; t < TimePoints; t++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
{
ushort* pixel = this[x, y, z, t];
ushort prev = *pixel;
*pixel += *ims[x, y, z, t];
if (*pixel < prev)//indicates that wrap-around occured
*pixel = ushort.MaxValue;
}
}
}
public void CopyConstructor_Correct()
{
var ims = CreateDefaultStack();
ims.SetAll(3337);
var copy = new ImageStack16(ims);
Assert.IsFalse(ims.ImageData == copy.ImageData, "Source and its copy point to the same buffer");
ushort* sourceStart = ims.ImageData;
ushort* copyStart = copy.ImageData;
for (long i = 0; i < ims.ImageNB / 2; i++)
Assert.AreEqual(sourceStart[i], copyStart[i], "Found non-matching pixel");
ims.Dispose();
copy.Dispose();
}
public void RangeCheck_OnPixelAccess()
{
var ims = new ImageStack16(5, 5, 5, 5, ImageStack.SliceOrders.ZBeforeT);
var p = ims[5, 0, 0, 0];
ims.Dispose();
}
public void UpscaleConstructor_Correct()
{
Random rnd = new Random();
var ims8 = new ImageStack8(43, 43, 41, 41, ImageStack.SliceOrders.ZBeforeT);
//quickly fill image with random values
int* buffer = (int*)ims8.ImageData;
long iter = ims8.ImageNB / 4;
for (long i = 0; i < iter; i++)
{
buffer[i] = rnd.Next();
}
var ims16 = new ImageStack16(ims8, true);
Assert.AreEqual(ims8.SliceOrder, ims16.SliceOrder);
for (int z = 0; z < ims8.ZPlanes; z++)
for (int t = 0; t < ims8.TimePoints; t++)
for (int y = 0; y < ims8.ImageHeight; y++)
for (int x = 0; x < ims8.ImageWidth; x++)
{
float value = *ims8[x, y, z, t];
value = (value / 255) * ushort.MaxValue;
Assert.AreEqual((ushort)Math.Floor(value), *ims16[x, y, z, t]);
}
ims8.Dispose();
ims16.Dispose();
}
/// <summary>
/// Performs pixel-by-pixel addition of the given image
/// stack to the current stack clipping at 65535
/// </summary>
/// <param name="ims">The stack to add</param>
public void Add(ImageStack16 ims)
{
DisposeGuard();
if (ims.IsDisposed)
{
throw new ArgumentException("Can't add disposed image");
}
//NOTE: Not clear whether we should require same z/t ordering for compatibility
if (!IsCompatible(ims))
{
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
}
//if the strides of the two images aren't equal (pixels not aligned in memory) we have
//to laboriously loop over individual pixels otherwise we can move through the buffer in 32bit blocks
//for all images created using this code stride should always be the same if the width is the same
//but we could be dealing with a foreign memory block via shallow copy
if (this.Stride == ims.Stride)
{
long intIter = ImageNB / 4;
uint *iData = (uint *)ImageData;
uint *iAdd = (uint *)ims.ImageData;
for (long i = 0; i < intIter; i++)
{
iData[i] = AddShortAsUint(iData[i], iAdd[i]);
}
//For all images we create, we expect the following to be 0 because of the 4-byte aligned stride
int restIter = (int)(ImageNB % 4) / 2;
System.Diagnostics.Debug.Assert(restIter < 2);//there can be only either 0 or 1 ushort left!
for (long i = ImageNB / 2 - restIter; i < ImageNB / 2; i++)
{
ushort prev = ImageData[i];
ImageData[i] += ims.ImageData[i];
if (ImageData[i] < prev)
{
ImageData[i] = ushort.MaxValue;
}
}
}
else
{
for (int z = 0; z < ZPlanes; z++)
{
for (int t = 0; t < TimePoints; t++)
{
for (int y = 0; y < ImageHeight; y++)
{
for (int x = 0; x < ImageWidth; x++)
{
ushort *pixel = this[x, y, z, t];
ushort prev = *pixel;
* pixel += *ims[x, y, z, t];
if (*pixel < prev)//indicates that wrap-around occured
{
*pixel = ushort.MaxValue;
}
}
}
}
}
}
}
/// <summary>
/// Constructs an 8bit stack via rescaling of a 16bit stack
/// </summary>
/// <param name="ims">The source stack to be copied</param>
/// <param name="min">This value and below will be set to 0</param>
/// <param name="max">This value and above will be set to 255</param>
public ImageStack8(ImageStack16 ims, ushort min=ushort.MinValue, ushort max=ushort.MaxValue)
{
if (ims == null)
throw new ArgumentNullException(nameof(ims));
if (ims.IsDisposed)
throw new ArgumentException("Can't copy disposed stack");
if (max <= min)
throw new ArgumentException("max has to be strictly greater than min");
SliceOrder = ims.SliceOrder;
//initialize buffer and dimension properties according to source stack
InitializeImageBuffer(ims.ImageWidth, ims.ImageHeight, ims.ZPlanes, ims.TimePoints, 1);
//loop over pixels, assigning values
for (int z = 0; z < ZPlanes; z++)
for (int t = 0; t < TimePoints; t++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
{
float temp = *ims[x, y, z, t];
temp = (temp - min) / (max- min) * byte.MaxValue;
if (temp < 0)
temp = 0;
else if (temp > byte.MaxValue)
temp = byte.MaxValue;
*this[x, y, z, t] = (byte)temp;
}
}
/// <summary>
/// Constructs a new floating point image stack with a 16 bit stack as
/// a source, optionally rescaling the maximum
/// </summary>
/// <param name="ims">The 8bit source stack</param>
/// <param name="outMax">65535 will be assigned to this value in the float stack</param>
public ImageStack32F(ImageStack16 ims, float outMax = ushort.MaxValue)
{
if (ims == null)
throw new ArgumentNullException(nameof(ims));
if (ims.IsDisposed)
throw new ArgumentException("Can't copy disposed stack");
//initialize buffer and dimension properties according to source stack
InitializeImageBuffer(ims.ImageWidth, ims.ImageHeight, ims.ZPlanes, ims.TimePoints, 4);
//loop over pixels, assigning values
for (int z = 0; z < ZPlanes; z++)
for (int t = 0; t < TimePoints; t++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
{
float temp = *ims[x, y, z, t];
temp = temp / ushort.MaxValue * outMax;
if (temp > outMax)
temp = outMax;
*this[x, y, z, t] = temp;
}
}
public void Construction_WithInvalidHeight()
{
var ims = new ImageStack16(20, 0, 40, 50, ImageStack.SliceOrders.TBeforeZ);
ims.Dispose();
}
/// <summary>
/// Divide by a scaled 16-bit stack pixel-wise
/// </summary>
/// <param name="ims">The stack to divide by</param>
/// <param name="outMax">65535 will be assigned to this value</param>
public void Divide(ImageStack16 ims, float outMax = ushort.MaxValue)
{
DisposeGuard();
if (ims.IsDisposed)
throw new ArgumentException("Can't divide by disposed image");
if (!IsCompatible(ims))
throw new ArgumentException("Given image has wrong dimensions or z versus t ordering");
for (int z = 0; z < ZPlanes; z++)
for (int t = 0; t < TimePoints; t++)
for (int y = 0; y < ImageHeight; y++)
for (int x = 0; x < ImageWidth; x++)
*this[x, y, z, t] /= (float)*ims[x, y, z, t] / ushort.MaxValue * outMax;
}
public void PixelPointerNull_AfterDispose()
{
var ims = new ImageStack16(5, 5, 5, 5, ImageStack.SliceOrders.ZBeforeT);
ims.Dispose();
Assert.IsTrue(ims[4, 0, 0, 0] == null);
}
