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Core.hpp
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Core.hpp
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/**
* Simple Image Processing Library
* Copyright Erik Smistad 2012
* See LICENSE file for information on use
*/
#ifndef SIPL_H_
#define SIPL_H_
#define _USE_MATH_DEFINES // windows crap
#include <cmath>
#include "Exceptions.hpp"
#include "Types.hpp"
#include <gtk/gtk.h>
#include <gdk-pixbuf/gdk-pixbuf.h>
#include <gdk/gdkkeysyms.h>
#include <fstream>
#include <typeinfo>
#include <string>
#include <stdlib.h>
namespace SIPL {
void Init();
bool isInit();
void Quit();
void destroyWindow(GtkWidget * widget, gpointer window) ;
void quitProgram(GtkWidget * widget, gpointer window) ;
void signalDestroyWindow(GtkWidget * widget, gpointer window) ;
void saveFileSignal(GtkWidget * widget, gpointer data) ;
void saveDialog(GtkWidget * widget, gpointer image) ;
int increaseWindowCount() ;
int getWindowCount() ;
template <class T>
class Window;
template <class T>
class Dataset {
public:
Dataset();
~Dataset();
int getWidth() const;
int getHeight() const;
T * getData();
void setData(T * data);
virtual int getTotalSize() const=0;
void fill(T value);
protected:
T * data;
int width, height;
};
template <class T>
class Image : public Dataset<T> {
public:
Image(const char * filepath);
Image(unsigned int width, unsigned int height);
Image(int2 size);
template <class U>
Image(Image<U> * otherImage);
T get(int i) const;
T get(int x, int y) const;
T get(int2 pos) const;
void set(int x, int y, T value);
void set(int2, T value);
void set(int i, T v);
void set(Region region, T value);
int2 getSize() const;
Window<T> * show();
Window<T> * show(float level, float window);
void save(const char * filepath, const char * imageType = "jpeg");
void dataToPixbuf(GtkWidget * image);
void dataToPixbuf(GtkWidget * image, float level, float wdinow);
void pixbufToData(GtkImage * image);
static gboolean setupGUI(gpointer data);
template <class U>
Image<T> & operator=(const Image<U> &otherImage);
bool inBounds(int x, int y) const;
bool inBounds(int i) const;
int getTotalSize() const;
};
template <class T>
class Volume : public Dataset<T> {
public:
Volume(std::string filename); // for reading mhd files
Volume(const char * filename, int width, int height, int depth); // for reading raw files
Volume(int width, int height, int depth);
Volume(int3 size);
template <class U>
Volume(Volume<U> * otherVolume);
T get(int x, int y, int z) const;
T get(int3 pos) const;
T get(int i) const;
void set(int x, int y, int z, T value);
void set(int3 pos, T v);
void set(int i, T v);
void set(Region region, T value);
int getDepth() const;
int3 getSize() const;
Window<T> * show();
Window<T> * show(int slice, slice_plane direction);
Window<T> * show(int slice, slice_plane direction, float level, float window);
Window<T> * show(float level, float window);
Window<T> * showMIP();
Window<T> * showMIP(slice_plane direction);
Window<T> * showMIP(slice_plane direction, float level, float window);
Window<T> * showMIP(float level, float window);
void save(const char * filepath);
void saveSlice(int slice, slice_plane direction, const char * filepath, const char * imageType);
void dataToPixbuf(GtkWidget * image, int slice, slice_plane direction);
void dataToPixbuf(GtkWidget * image, int slice, slice_plane direction, float level, float window);
void MIPToPixbuf(GtkWidget * image, float angle, slice_plane direction);
void MIPToPixbuf(GtkWidget * image, float angle, slice_plane direction, float level, float window);
static gboolean setupGUI(gpointer data);
template <class U>
Volume<T> & operator=(const Volume<U> &otherVolume);
bool inBounds(int x, int y, int z) const;
bool inBounds(int3 pos) const;
bool inBounds(int i) const;
template <class U>
void convert(Volume<U> * otherImage) ;
int getTotalSize() const;
float3 getSpacing() const;
void setSpacing(float3 spacing);
private:
int depth;
float3 spacing;
};
template <class T>
class Window {
public:
Window(GtkWidget * gtkWindow, GtkWidget * gtkImage, Image<T> * image);
Window(GtkWidget * gtkWindow, GtkWidget * gtkImage, Volume<T> * volume);
void key_pressed(GtkWidget * widget, GdkEventKey * event, gpointer user_data) ;
static void wrapper_key_pressed(GtkWidget * widget, GdkEventKey * event, gpointer user_data);
void zoomOut();
void zoomIn();
void draw();
void destroy();
void update();
void hide();
int currentSlice;
slice_plane currentDirection;
float level, window;
~Window();
private:
GtkWidget * gtkWindow;
GtkWidget * gtkImage;
GtkWidget * scaledImage;
Dataset<T> * dataset;
bool isVolume;
bool isMIP;
float angle;
float scale;
int windowNr;
friend class Image<T>;
friend class Volume<T>;
};
template <class T>
Window<T>::~Window() {
}
/* --- Spesialized conversion functions --- */
void toGuchar(bool value, guchar * pixel) ;
void toGuchar(uchar value, guchar * pixel) ;
void toGuchar(char value, guchar * pixel) ;
void toGuchar(ushort value, guchar * pixel) ;
void toGuchar(short value, guchar * pixel) ;
void toGuchar(uint value, guchar * pixel) ;
void toGuchar(int value, guchar * pixel) ;
void toGuchar(float value, guchar * pixel) ;
void toGuchar(color_uchar value, guchar * pixel) ;
void toGuchar(color_float value, guchar * pixel) ;
void toGuchar(float2 value, guchar * pixel) ;
void toGuchar(float3 value, guchar * pixel) ;
// Conversion from bool
void convertImageType(bool *, bool);
void convertImageType(uchar *, bool);
void convertImageType(char *, bool);
void convertImageType(ushort *, bool);
void convertImageType(short *, bool);
void convertImageType(uint *, bool);
void convertImageType(int *, bool);
void convertImageType(float *, bool);
void convertImageType(color_uchar *, bool);
void convertImageType(color_float *, bool);
void convertImageType(float2 *, bool);
void convertImageType(float3 *, bool);
// Conversion from uchar
void convertImageType(bool *, uchar);
void convertImageType(uchar *, uchar);
void convertImageType(char *, uchar);
void convertImageType(ushort *, uchar);
void convertImageType(short *, uchar);
void convertImageType(uint *, uchar);
void convertImageType(int *, uchar);
void convertImageType(float *, uchar);
void convertImageType(color_uchar *, uchar);
void convertImageType(color_float *, uchar);
void convertImageType(float2 *, uchar);
void convertImageType(float3 *, uchar);
// Conversion from char
void convertImageType(bool *, char);
void convertImageType(uchar *, char);
void convertImageType(char *, char);
void convertImageType(ushort *, char);
void convertImageType(short *, char);
void convertImageType(uint *, char);
void convertImageType(int *, char);
void convertImageType(float *, char);
void convertImageType(color_uchar *, char);
void convertImageType(color_float *, char);
void convertImageType(float2 *, char);
void convertImageType(float3 *, char);
// Conversion from ushort
void convertImageType(bool *, ushort);
void convertImageType(uchar *, ushort);
void convertImageType(char *, ushort);
void convertImageType(ushort *, ushort);
void convertImageType(short *, ushort);
void convertImageType(uint *, ushort);
void convertImageType(int *, ushort);
void convertImageType(float *, ushort);
void convertImageType(color_uchar *, ushort);
void convertImageType(color_float *, ushort);
void convertImageType(float2 *, ushort);
void convertImageType(float3 *, ushort);
// Conversion from short
void convertImageType(bool *, short);
void convertImageType(uchar *, short);
void convertImageType(char *, short);
void convertImageType(ushort *, short);
void convertImageType(short *, short);
void convertImageType(uint *, short);
void convertImageType(int *, short);
void convertImageType(float *, short);
void convertImageType(color_uchar *, short);
void convertImageType(color_float *, short);
void convertImageType(float2 *, short);
void convertImageType(float3 *, short);
// Conversion from uint
void convertImageType(bool *, uint);
void convertImageType(uchar *, uint);
void convertImageType(char *, uint);
void convertImageType(ushort *, uint);
void convertImageType(short *, uint);
void convertImageType(uint *, uint);
void convertImageType(int *, uint);
void convertImageType(float *, uint);
void convertImageType(color_uchar *, uint);
void convertImageType(color_float *, uint);
void convertImageType(float2 *, uint);
void convertImageType(float3 *, uint);
// Conversion from int
void convertImageType(bool *, int);
void convertImageType(uchar *, int);
void convertImageType(char *, int);
void convertImageType(ushort *, int);
void convertImageType(short *, int);
void convertImageType(uint *, int);
void convertImageType(int *, int);
void convertImageType(float *, int);
void convertImageType(color_uchar *, int);
void convertImageType(color_float *, int);
void convertImageType(float2 *, int);
void convertImageType(float3 *, int);
// Conversion from float
void convertImageType(bool *, float);
void convertImageType(uchar *, float);
void convertImageType(char *, float);
void convertImageType(ushort *, float);
void convertImageType(short *, float);
void convertImageType(uint *, float);
void convertImageType(int *, float);
void convertImageType(float *, float);
void convertImageType(color_uchar *, float);
void convertImageType(color_float *, float);
void convertImageType(float2 *, float);
void convertImageType(float3 *, float);
// Conversion from color_uchar
void convertImageType(bool *, color_uchar);
void convertImageType(uchar *, color_uchar);
void convertImageType(char *, color_uchar);
void convertImageType(ushort *, color_uchar);
void convertImageType(short *, color_uchar);
void convertImageType(uint *, color_uchar);
void convertImageType(int *, color_uchar);
void convertImageType(float *, color_uchar);
void convertImageType(color_uchar *, color_uchar);
void convertImageType(color_float *, color_uchar);
void convertImageType(float2 *, color_uchar);
void convertImageType(float3 *, color_uchar);
// Conversion from color_float
void convertImageType(bool *, color_float);
void convertImageType(uchar *, color_float);
void convertImageType(char *, color_float);
void convertImageType(ushort *, color_float);
void convertImageType(short *, color_float);
void convertImageType(uint *, color_float);
void convertImageType(int *, color_float);
void convertImageType(float *, color_float);
void convertImageType(color_uchar *, color_float);
void convertImageType(color_float *, color_float);
void convertImageType(float2 *, color_float);
void convertImageType(float3 *, color_float);
// Conversion from float2
void convertImageType(bool *, float2);
void convertImageType(uchar *, float2);
void convertImageType(char *, float2);
void convertImageType(ushort *, float2);
void convertImageType(short *, float2);
void convertImageType(uint *, float2);
void convertImageType(int *, float2);
void convertImageType(float *, float2);
void convertImageType(color_uchar *, float2);
void convertImageType(color_float *, float2);
void convertImageType(float2 *, float2);
void convertImageType(float3 *, float2);
// Conversion from float3
void convertImageType(bool *, float3);
void convertImageType(uchar *, float3);
void convertImageType(char *, float3);
void convertImageType(ushort *, float3);
void convertImageType(short *, float3);
void convertImageType(uint *, float3);
void convertImageType(int *, float3);
void convertImageType(float *, float3);
void convertImageType(color_uchar *, float3);
void convertImageType(color_float *, float3);
void convertImageType(float2 *, float3);
void convertImageType(float3 *, float3);
/* --- Spesialized level/window --- */
void toGuchar(uchar value, guchar * pixel, float level, float window) ;
void toGuchar(char value, guchar * pixel, float level, float window) ;
void toGuchar(ushort value, guchar * pixel, float level, float window) ;
void toGuchar(short value, guchar * pixel, float level, float window) ;
void toGuchar(uint value, guchar * pixel, float level, float window) ;
void toGuchar(int value, guchar * pixel, float level, float window) ;
void toGuchar(float value, guchar * pixel, float level, float window) ;
void toGuchar(color_float value, guchar * pixel, float level, float window) ;
void toGuchar(color_uchar value, guchar * pixel, float level, float window) ;
void toGuchar(float2 value, guchar * pixel, float level, float window) ;
void toGuchar(float3 value, guchar * pixel, float level, float window) ;
inline double round( double d ) {
return floor( d + 0.5 );
}
template <class T>
uchar levelWindow(T value, float level, float window) {
float result;
if(value < level-window*0.5f) {
result = 0.0f;
} else if(value > level+window*0.5f) {
result = 1.0f;
} else {
result = (float)(value-(level-window*0.5f)) / window;
}
result = round(result*255);
return result;
}
/* --- Spesialized toT functions --- */
void toT(bool * r, uchar * p) ;
void toT(uchar * r, uchar * p) ;
void toT(char * r, uchar * p) ;
void toT(ushort * r, uchar * p) ;
void toT(short * r, uchar * p) ;
void toT(uint * r, uchar * p) ;
void toT(int * r, uchar * p) ;
void toT(float * r, uchar * p) ;
void toT(color_uchar * r, uchar * p) ;
void toT(color_float * r, uchar * p) ;
void toT(float2 * r, uchar * p) ;
void toT(float3 * r, uchar * p) ;
template <class T>
void Image<T>::pixbufToData(GtkImage * image) {
gdk_threads_enter ();
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
for(int i = 0; i < this->width*this->height; i++) {
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
unsigned char * c = (unsigned char *)((pixels + i * gdk_pixbuf_get_n_channels(pixBuf)));
toT(&this->data[i], c);
}
gdk_threads_leave();
}
template <class T>
void Image<T>::dataToPixbuf(GtkWidget * image) {
gdk_threads_enter();
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
for(int i = 0; i < this->width*this->height; i++) {
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
guchar * p = pixels + i * gdk_pixbuf_get_n_channels(pixBuf);
toGuchar(this->data[i], p);
}
gdk_threads_leave();
}
template <class T>
void Image<T>::dataToPixbuf(GtkWidget * image, float level, float window) {
gdk_threads_enter();
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
for(int i = 0; i < this->width*this->height; i++) {
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
guchar * p = pixels + i * gdk_pixbuf_get_n_channels(pixBuf);
toGuchar(this->data[i], p, level, window);
}
gdk_threads_leave();
}
int validateSlice(int slice, slice_plane direction, int3 size);
template <class T>
void Volume<T>::dataToPixbuf(GtkWidget * image, int slice, slice_plane direction) {
//gdk_threads_enter();
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
validateSlice(slice, direction, getSize());
int xSize = 0;
int ySize = 0;
switch(direction) {
case X:
// x direction
xSize = this->height;
ySize = this->depth;
break;
case Y:
// y direction
xSize = this->width;
ySize = this->depth;
break;
case Z:
// z direction
xSize = this->width;
ySize = this->height;
break;
}
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
int n = gdk_pixbuf_get_n_channels(pixBuf);
int rowstride = gdk_pixbuf_get_rowstride(pixBuf);
for(int y = 0; y < ySize; y++) {
for(int x = 0; x < xSize; x++) {
int i = x*n+y*rowstride;
guchar * p = pixels + i;;
T intensity;
switch(direction) {
case X:
intensity = this->data[slice + x*this->width + (ySize-1-y)*this->width*this->height];
break;
case Y:
intensity = this->data[x + slice*this->width + (ySize-1-y)*this->width*this->height];
break;
case Z:
intensity = this->data[x + y*this->width + slice*this->width*this->height];
break;
}
toGuchar(intensity, p);
}}
//gdk_threads_leave();
}
template <class T>
void Volume<T>::dataToPixbuf(GtkWidget * image, int slice, slice_plane direction, float level, float window) {
//gdk_threads_enter();
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
int xSize = 0;
int ySize = 0;
switch(direction) {
case X:
// x direction
xSize = this->height;
ySize = this->depth;
break;
case Y:
// y direction
xSize = this->width;
ySize = this->depth;
break;
case Z:
// z direction
xSize = this->width;
ySize = this->height;
break;
}
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
int n = gdk_pixbuf_get_n_channels(pixBuf);
int rowstride = gdk_pixbuf_get_rowstride(pixBuf);
for(int x = 0; x < xSize; x++) {
for(int y = 0; y < ySize; y++) {
int i = x*n + y*rowstride;
guchar * p = pixels + i;
T intensity;
switch(direction) {
case X:
intensity = this->data[slice + x*this->width + (ySize-1-y)*this->width*this->height];
break;
case Y:
intensity = this->data[x + slice*this->width + (ySize-1-y)*this->width*this->height];
break;
case Z:
intensity = this->data[x + y*this->width + slice*this->width*this->height];
break;
}
toGuchar(intensity, p, level, window);
}}
}
template <class T>
T maximum(T a, T b, bool * change) {
*change = a < b;
return a > b ? a : b;
}
template <>
inline float2 maximum<float2>(float2 a, float2 b, bool * change) {
float2 c;
c.x = a.x > b.x ? a.x : b.x;
c.y = a.y > b.y ? a.y : b.y;
*change = a.x < b.x || a.y < b.y;
return c;
}
template <>
inline float3 maximum<float3>(float3 a, float3 b, bool * change) {
float3 c;
c.x = a.x > b.x ? a.x : b.x;
c.y = a.y > b.y ? a.y : b.y;
c.z = a.z > b.z ? a.z : b.z;
*change = a.x < b.x || a.y < b.y || a.z < b.z;
return c;
}
template <>
inline color_uchar maximum<color_uchar>(color_uchar a, color_uchar b, bool * change) {
color_uchar c;
c.red = a.red > b.red ? a.red : b.red;
c.green = a.green > b.green ? a.green : b.green;
c.blue = a.blue > b.blue ? a.blue : b.blue;
*change = a.red < b.red || a.green < b.green || a.blue < b.blue;
return c;
}
template <class T>
void Volume<T>::MIPToPixbuf(GtkWidget * image, float angle, slice_plane direction) {
int xSize;
int ySize;
int zSize;
switch(direction) {
case X:
// x direction
xSize = this->height;
ySize = this->depth;
zSize = this->width;
break;
case Y:
// y direction
xSize = this->width;
ySize = this->depth;
zSize = this->height;
break;
case Z:
// z direction
xSize = this->width;
ySize = this->height;
zSize = this->depth;
break;
}
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
float cangle = cos(angle);
float sangle = sin(angle);
int xMultiple, yMultiple, zMultiple;
switch(direction) {
case X:
xMultiple = this->width;
yMultiple = this->width*this->height;
zMultiple = 1;
break;
case Y:
xMultiple = 1;
yMultiple = this->width*this->height;
zMultiple = this->width;
break;
case Z:
xMultiple = 1;
yMultiple = this->width;
zMultiple = this->width*this->height;
break;
}
T * mip = new T[xSize*ySize]();
int n = gdk_pixbuf_get_n_channels(pixBuf);
int rowstride = gdk_pixbuf_get_rowstride(pixBuf);
// Initialize image to black
for(int i = 0; i < n*xSize*ySize; i++)
pixels[i] = 0;
#pragma omp parallel for
for(int x = 0; x < xSize; x++) {
int nu = (x-(float)xSize/2.0f)*sangle + (float)xSize/2.0f;
for(int y = 0; y < ySize; y++) {
int v = y;
for(int z = 0; z < zSize; z++) {
int u = round((z-(float)zSize/2.0f)*cangle + nu);
if(u >= 0 && u < xSize) {
bool change;
T newValue = maximum<T>(mip[u+v*xSize], this->data[x*xMultiple+y*yMultiple+z*zMultiple], &change);
if(change) {
// New maximum
mip[u+v*xSize] = newValue;
guchar * p = pixels + (u*n+(ySize-1-v)*rowstride);
toGuchar(newValue, p);
}
}
}}}
}
template <class T>
void Volume<T>::MIPToPixbuf(GtkWidget * image, float angle, slice_plane direction, float level, float window) {
int xSize;
int ySize;
int zSize;
switch(direction) {
case X:
// x direction
xSize = this->height;
ySize = this->depth;
zSize = this->width;
break;
case Y:
// y direction
xSize = this->width;
ySize = this->depth;
zSize = this->height;
break;
case Z:
// z direction
xSize = this->width;
ySize = this->height;
zSize = this->depth;
break;
}
GdkPixbuf * pixBuf = gtk_image_get_pixbuf((GtkImage *) image);
guchar * pixels = gdk_pixbuf_get_pixels(pixBuf);
T * mip = new T[xSize*ySize]();
float cangle = cos(angle);
float sangle = sin(angle);
int xMultiple, yMultiple, zMultiple;
switch(direction) {
case X:
xMultiple = this->width;
yMultiple = this->width*this->height;
zMultiple = 1;
break;
case Y:
xMultiple = 1;
yMultiple = this->width*this->height;
zMultiple = this->width;
break;
case Z:
xMultiple = 1;
yMultiple = this->width;
zMultiple = this->width*this->height;
break;
}
int n = gdk_pixbuf_get_n_channels(pixBuf);
int rowstride = gdk_pixbuf_get_rowstride(pixBuf);
// Initialize image to black
for(int i = 0; i < n*xSize*ySize; i++)
pixels[i] = 0;
#pragma omp parallel for
for(int x = 0; x < xSize; x++) {
int nu = round((x-(float)xSize/2.0f)*sangle) + (float)xSize/2.0f;
for(int y = 0; y < ySize; y++) {
int v = y;
for(int z = 0; z < zSize; z++) {
int u = round((z-(float)zSize/2.0f)*cangle) + nu;
if(u >= 0 && u < xSize) {
bool change;
T newValue = maximum<T>(mip[u+v*xSize], this->data[x*xMultiple+y*yMultiple+z*zMultiple], &change);
if(change) {
// New maximum
mip[u+v*xSize] = newValue;
guchar * p = pixels + (u*n+(ySize-1-v)*rowstride);
toGuchar(newValue, p, level, window);
}
}
}}}
}
/* --- Constructors & destructors --- */
template <class T>
Dataset<T>::Dataset() {
if(!isInit()) {
Init();
}
}
template <class T>
Image<T>::Image(const char * filename) {
// Check if file exists
FILE * file = fopen(filename, "r");
if(file == NULL)
throw FileNotFoundException(filename, __LINE__, __FILE__);
fclose(file);
gdk_threads_enter ();
GtkWidget * image = gtk_image_new_from_file(filename);
gdk_threads_leave ();
this->height = gdk_pixbuf_get_height(gtk_image_get_pixbuf((GtkImage *) image));
this->width = gdk_pixbuf_get_width(gtk_image_get_pixbuf((GtkImage *) image));
this->data = new T[this->height*this->width];
this->pixbufToData((GtkImage *)image);
}
template <class T>
template <class U>
Image<T>::Image(Image<U> * otherImage) {
this->width = otherImage->getWidth();
this->height = otherImage->getHeight();
this->data = new T[this->height*this->width];
// Convert image with type U to this with type T
for(int i = 0; i < this->width*this->height; i++) {
T value;
convertImageType(&value, otherImage->get(i));
this->data[i] = value;
}
}
template <class T>
template <class U>
Image<T>& Image<T>::operator=(const Image<U> &otherImage) {
if(this->width != otherImage.getWidth() || this->height != otherImage.getHeight())
throw ConversionException("image size mismatch in assignment", __LINE__, __FILE__);
// Convert image with type U to this with type T
for(int i = 0; i < this->width*this->height; i++) {
T value;
convertImageType(&value, otherImage.get(i));
this->data[i] = value;
}
return *this;
}
template <class T>
template <class U>
void Volume<T>::convert(Volume<U> * otherImage) {
// Convert image with type U to this with type T
for(int i = 0; i < this->width*this->height*this->depth; i++) {
T value;
convertImageType(&value, otherImage->get(i));
this->data[i] = value;
}
}
template <class T>
template <class U>
Volume<T>::Volume(Volume<U> * otherImage) {
this->width = otherImage->getWidth();
this->height = otherImage->getHeight();
this->depth = otherImage->getDepth();
this->spacing = otherImage->getSpacing();
this->data = new T[this->height*this->width*this->depth];
this->convert(otherImage);
}
template <class T>
template <class U>
Volume<T>& Volume<T>::operator=(const Volume<U> &otherImage) {
if(this->width != otherImage.getWidth() ||
this->height != otherImage.getHeight() ||
this->depth != otherImage.getDepth())
throw ConversionException("volume size mismatch in assignment", __LINE__, __FILE__);
this->convert(otherImage);
return *this;
}
template <class T>
Volume<T>::Volume(const char * filename, int width, int height, int depth) {
// Read raw file
this->data = new T[width*height*depth];
FILE * file = fopen(filename, "rb");
if(file == NULL)
throw FileNotFoundException(filename, __LINE__, __FILE__);
fread(this->data, sizeof(T), width*height*depth, file);
fclose(file);
this->width = width;
this->height = height;
this->depth = depth;
this->spacing = float3(1.0f,1.0f,1.0f);
}
template <class T>
Volume<T>::Volume(std::string filename) {
// Current limits of this method: T and the data type to be read has to be the same. Does not handle space after strings
// Read mhd file
std::fstream mhdFile;
mhdFile.open(filename.c_str(), std::fstream::in);
std::string line;
std::string rawFilename;
bool sizeFound = false,
rawFilenameFound = false,
typeFound = false,
dimensionsFound = false;
std::string typeName;
this->spacing = float3(1.0f,1.0f,1.0f);
do{
std::getline(mhdFile, line);
if(line.substr(0, 7) == "DimSize") {
std::string sizeString = line.substr(7+3);
std::string sizeX = sizeString.substr(0,sizeString.find(" "));
sizeString = sizeString.substr(sizeString.find(" ")+1);
std::string sizeY = sizeString.substr(0,sizeString.find(" "));
sizeString = sizeString.substr(sizeString.find(" ")+1);
std::string sizeZ = sizeString.substr(0,sizeString.find(" "));
this->width = atoi(sizeX.c_str());
this->height = atoi(sizeY.c_str());
this->depth = atoi(sizeZ.c_str());
sizeFound = true;
} else if(line.substr(0, 15) == "ElementDataFile") {
rawFilename = line.substr(15+3);
rawFilenameFound = true;
// Remove any trailing spaces
int pos = rawFilename.find(" ");
if(pos > 0)
rawFilename = rawFilename.substr(0,pos);
// Get path name
pos = filename.rfind('/');
if(pos > 0)
rawFilename = filename.substr(0,pos+1) + rawFilename;
} else if(line.substr(0, 11) == "ElementType") {
typeFound = true;
typeName = line.substr(11+3);
// Remove any trailing spaces
int pos = typeName.find(" ");
if(pos > 0)
typeName = typeName.substr(0,pos);
if(typeName == "MET_SHORT") {
} else if(typeName == "MET_USHORT") {
} else if(typeName == "MET_CHAR") {
} else if(typeName == "MET_UCHAR") {
} else if(typeName == "MET_INT") {
} else if(typeName == "MET_UINT") {
} else if(typeName == "MET_FLOAT") {
} else {
throw IOException("Trying to read volume of unsupported data type", __LINE__, __FILE__);
}
} else if(line.substr(0, 5) == "NDims") {
if(line.substr(5+3, 1) == "3")
dimensionsFound = true;
} else if(line.substr(0, 14) == "ElementSpacing") {
std::string sizeString = line.substr(14+3);
std::string sizeX = sizeString.substr(0,sizeString.find(" "));
sizeString = sizeString.substr(sizeString.find(" ")+1);
std::string sizeY = sizeString.substr(0,sizeString.find(" "));
sizeString = sizeString.substr(sizeString.find(" ")+1);
std::string sizeZ = sizeString.substr(0,sizeString.find(" "));
spacing.x = atof(sizeX.c_str());
spacing.y = atof(sizeY.c_str());
spacing.z = atof(sizeZ.c_str());
}
} while(!mhdFile.eof());
mhdFile.close();
if(!sizeFound || !rawFilenameFound || !typeFound || !dimensionsFound)
throw IOException("Error reading the mhd file", __LINE__, __FILE__);
this->data = new T[this->width*this->height*this->depth];
if(typeName == "MET_SHORT") {
Volume<short> * volume = new Volume<short>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_USHORT") {
Volume<ushort> * volume = new Volume<ushort>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_CHAR") {
Volume<char> * volume = new Volume<char>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_UCHAR") {
Volume<uchar> * volume = new Volume<uchar>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_INT") {
Volume<int> * volume = new Volume<int>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_UINT") {
Volume<uint> * volume = new Volume<uint>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
} else if(typeName == "MET_FLOAT") {
Volume<float> * volume = new Volume<float>(rawFilename.c_str(), this->width, this->height, this->depth);
this->convert(volume); // Convert to wanted type
}
}
template <class T>
Volume<T>::Volume(int width, int height, int depth) {
this->data = new T[width*height*depth];
this->width = width;
this->height = height;
this->depth = depth;
this->spacing = float3(1.0f,1.0f,1.0f);
}
template <class T>
Volume<T>::Volume(int3 size) {
this->data = new T[size.x*size.y*size.z];
this->width = size.x;
this->height = size.y;
this->depth = size.z;
this->spacing = float3(1.0f,1.0f,1.0f);
}
template <class T>
Image<T>::Image(unsigned int width, unsigned int height) {
this->data = new T[width*height];
this->width = width;
this->height = height;
}
template <class T>
Image<T>::Image(int2 size) {
this->data = new T[size.x*size.y];
this->width = size.x;
this->height = size.y;
}
template <class T>
Dataset<T>::~Dataset() {
delete[] this->data;
}
template <class T>
void Image<T>::save(const char * filepath, const char * imageType) {
GtkWidget * image = gtk_image_new_from_pixbuf(gdk_pixbuf_new(GDK_COLORSPACE_RGB, false,
8, this->width, this->height));
this->dataToPixbuf(image);
gdk_pixbuf_save(gtk_image_get_pixbuf((GtkImage *) image), filepath, imageType,
NULL, NULL);
}
template <class T>
void Volume<T>::save(const char * filepath) {
// This might not work for the defined struct types?
std::string filename = filepath;
if(filename.substr(filename.size()-3) == "mhd") {
// Create MHD file
std::ofstream file;
file.open(filename.c_str());
file << "ObjectType = Image\n";
file << "NDims = 3\n";
file << "DimSize = " << this->width << " " <<
this->height << " " << this->depth << "\n";
std::string type;
if(typeid(T) == typeid(uchar)) {