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report.cxx
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#include "report.h"
#include "gdcmAnonymizer.h"
#include "gdcmAttribute.h"
#include "gdcmDefs.h"
#include "gdcmGlobal.h"
#include "gdcmImage.h"
#include "gdcmImageChangeTransferSyntax.h"
#include "gdcmImageHelper.h"
#include "gdcmImageReader.h"
#include "gdcmImageWriter.h"
#include "gdcmPhotometricInterpretation.h"
#include "gdcmUIDGenerator.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionIteratorWithIndex.h"
#include <algorithm>
#include <boost/filesystem.hpp>
#include <boost/math/special_functions/erf.hpp>
#include <gdcmFile.h>
#include <gdcmImage.h>
#include <math.h>
#include <codecvt>
#include <sstream>
#include <boost/date_time.hpp>
#include <boost/math/distributions/lognormal.hpp>
#include <ft2build.h>
#include FT_FREETYPE_H
#define WIDTH 2400
#define HEIGHT 2400
unsigned char image_buffer[HEIGHT][WIDTH];
//unsigned char image_buffer512[512][512];
//unsigned char image_buffer828[512][828];
unsigned int image_buffer_gen_size[2] = {0,0};
unsigned char **image_buffer_gen = NULL;
Report *getDefaultReportStruct() {
Report *report = new Report;
// create some example UIDs for the report
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->SeriesInstanceUID = fuid.Generate();
}
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->StudyInstanceUID = fuid.Generate();
}
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->SOPInstanceUID = fuid.Generate();
}
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->FrameOfReferenceUID = fuid.Generate();
}
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->StudyID = fuid.Generate();
report->StudyID = report->StudyID.substr(0, 16);
}
{
gdcm::UIDGenerator fuid;
fuid.SetRoot("1.3.6.1.4.1.45037");
report->AccessionNumber = fuid.Generate();
report->AccessionNumber = report->AccessionNumber.substr(0, 16);
}
report->SeriesDescription = std::string("Report");
report->StudyDate = std::string("");
report->StudyTime = std::string("");
report->measures = std::vector<std::map<std::string, std::string>>();
report->key_fact = std::string("");
report->key_unit = std::string("");
report->VersionString = std::string("");
report->TitleText = std::string("MMIV.no report. Made with AI");
return report;
}
// provide string as str.c_str()
// return if conversion was successful
int stdstring2stdwstring(std::wstring *wstr, const char* ptr) {
wstr->clear();
std::mbtowc(nullptr, 0, 0); // reset the conversion state
const char* end = ptr + std::strlen(ptr);
int ret{};
for (wchar_t wc; (ret = std::mbtowc(&wc, ptr, end - ptr)) > 0; ptr += ret) {
//std::wcout << wc;
wstr->push_back(wc);
}
std::wcout << '\n';
return ret;
}
// draws into image_buffer
void draw_bitmap(FT_Bitmap *bitmap, int width, int height, FT_Int x, FT_Int y) {
FT_Int i, j, p, q;
FT_Int x_max = x + bitmap->width;
FT_Int y_max = y + bitmap->rows;
for (i = x, p = 0; i < x_max; i++, p++) {
for (j = y, q = 0; j < y_max; j++, q++) {
if (i < 0 || j < 0 || i >= width || j >= height)
continue;
image_buffer[j][i] |= bitmap->buffer[q * bitmap->width + p];
}
}
}
void addBar(CImageType::Pointer img, int height) {
CImageType::RegionType kregion = img->GetLargestPossibleRegion();
using ImageSizeType = typename CImageType::SizeType;
ImageSizeType regionSize;
regionSize[0] = kregion.GetSize()[0];
regionSize[1] = height;
kregion.SetSize(regionSize);
itk::ImageRegionIteratorWithIndex<CImageType> kIterator(img, kregion);
kIterator.GoToBegin();
while(!kIterator.IsAtEnd()) {
CPixelType value = kIterator.Value();
value.SetRed((int)(255));
value.SetGreen((int)(77));
value.SetBlue((int)(5));
kIterator.Set(value);
++kIterator;
}
CImageType::RegionType::IndexType regionStart;
regionStart = kregion.GetIndex();
regionStart[1] = height;
regionSize[0] = kregion.GetSize()[0];
regionSize[1] = 1;
kregion.SetSize(regionSize);
kregion.SetIndex(regionStart);
itk::ImageRegionIteratorWithIndex<CImageType> kIterator2(img, kregion);
kIterator2.GoToBegin();
while(!kIterator2.IsAtEnd()) {
CPixelType value = kIterator.Value();
value.SetRed(0); //(int)(255));
value.SetGreen(0); //(int)(255));
value.SetBlue(0); //(int)(255));
//value.SetGreen((int)(77));
//value.SetBlue((int)(5));
kIterator2.Set(value);
++kIterator2;
}
}
void draw_bitmap_gen(FT_Bitmap *bitmap, int width, int height, FT_Int x, FT_Int y) {
FT_Int i, j, p, q;
FT_Int x_max = x + bitmap->width;
FT_Int y_max = y + bitmap->rows;
for (i = x, p = 0; i < x_max; i++, p++) {
for (j = y, q = 0; j < y_max; j++, q++) {
if (i < 0 || j < 0 || i >= width || j >= height)
continue;
image_buffer_gen[j][i] |= bitmap->buffer[q * bitmap->width + p];
}
}
}
void addMarker(char *buffer, int posx, int posy, int fontSize) {
unsigned char *bvals = (unsigned char *)buffer;
// draw 4 lines to highlight the location (fontSize was 9 before)
int line_length = fontSize/2.0; // in pixel
int offset = 7.0/9.0*fontSize; // in pixel away from that location
int line_width = 3.0/9.0*fontSize; // one pixel wide
// top bar
for (int j = -floor(line_width/2.0); j < floor(line_width/2.0); j++) {
for (int i = 0; i < line_length; i++) {
int idx = (posx+j) + (posy - offset - i) * image_buffer_gen_size[0];
if (idx < 0 || idx > image_buffer_gen_size[1]*image_buffer_gen_size[0])
continue;
bvals[idx] = 255; //(unsigned char)std::max(0.0f, std::min(current_image_max_value, 1.0f));
}
}
// bottom bar
for (int j = -floor(line_width/2.0); j < floor(line_width/2.0); j++) {
for (int i = 0; i < line_length; i++) {
int idx = (posx+j) + (posy + offset + i - 1) * image_buffer_gen_size[0];
if (idx < 0 || idx > image_buffer_gen_size[1]*image_buffer_gen_size[0])
continue;
bvals[idx] = 255; //(unsigned char)std::max(0.0f, std::min(current_image_max_value, 1.0f));
}
}
// left bar
for (int j = -floor(line_width/2.0); j < floor(line_width/2.0); j++) {
for (int i = 0; i < line_length; i++) {
int idx = (posx - offset - i) + (posy + j) * image_buffer_gen_size[0];
if (idx < 0 || idx > image_buffer_gen_size[1]*image_buffer_gen_size[0])
continue;
bvals[idx] = 255; //(unsigned char)std::max(0.0f, std::min(current_image_max_value, 1.0f));
}
}
// right bar
for (int j = -floor(line_width/2.0); j < floor(line_width/2.0); j++) {
for (int i = 0; i < line_length; i++) {
int idx = (posx + offset + i - 1) + (posy + j) * image_buffer_gen_size[0];
if (idx < 0 || idx > image_buffer_gen_size[1]*image_buffer_gen_size[0])
continue;
bvals[idx] = 255; //(unsigned char)std::max(0.0f, std::min(current_image_max_value, 1.0f));
}
}
}
// return one character at position num in wc2
int get_mb(wchar_t *wc2, const char* ptr, int num) {
std::mbtowc(nullptr, 0, 0); // reset the conversion state
const char* end = ptr + std::strlen(ptr);
int ret{};
int n = 0;
for (wchar_t wc; (ret = std::mbtowc(&wc, ptr, end - ptr)) > 0; ptr += ret) {
if (n++ == num) {
*wc2 = wc;
break;
}
}
return ret;
}
// generic method using dynamic array for image_buffer_gen
void addToReportGen(char *buffer, std::string font_file, int font_size, std::string sstext, int posx, int posy, float radiants) {
FT_Library library;
//std::wstring stext;
std::wstring_convert<std::codecvt_utf8_utf16<wchar_t>, wchar_t> convert;
std::wstring stext = convert.from_bytes(sstext);
//if (!stdstring2stdwstring(&stext, sstext.c_str())) {
// fprintf(stderr, "Error converting string to wstring\n");
// return;
//}
bool verbose = 1;
if (verbose) {
fprintf(stdout, " addToReportGen: \"%s\"\n", sstext.c_str());
}
double angle;
int target_height;
int n, num_chars;
// int font_length = 20;
std::string font_path = font_file;
// int font_size = 42;
int face_index = 0;
FT_Face face;
FT_GlyphSlot slot;
FT_Matrix matrix; /* transformation matrix */
FT_Vector pen; /* untransformed origin */
FT_Error error;
// gdcm::ImageReader reader;
// unsigned long len = WIDTH * HEIGHT * 8;
// char *buffer = new char[len];
error = FT_Init_FreeType(&library); /* initialize library */
if (error != 0) {
fprintf(stderr, "\033[0;31mError\033[0m: The freetype library could not be initialized with this font.\n");
return;
}
int start_px = 40;
int start_py = 40;
int text_lines = 1;
float repeat_spacing = 1.0f;
int xmax = image_buffer_gen_size[0];
int ymax = image_buffer_gen_size[1];
num_chars = stext.size();
int px = posx;
// WIDTH - ((num_chars + 2) * font_size - start_px);
// int py = start_py + (text_lines * font_size + text_lines * (repeat_spacing * 0.5 * font_size));
int py = posy;
// start_py + 2.0 * (font_size);
// our image is not of that size but much larger (repeated mosaic tiles in y)
// reset image_buffer_gen now
for (int i = 0; i < image_buffer_gen_size[1]; i++) {
if (image_buffer_gen[i])
memset(image_buffer_gen[i], 0, sizeof(unsigned char) * image_buffer_gen_size[0]);
}
angle = radiants;
target_height = 512;
error = FT_New_Face(library, font_file.c_str(), face_index, &face); /* create face object */
if (face == NULL) {
fprintf(stderr, "\033[0;31mError\033[0m: no face found, provide the filename of a ttf file...\n");
return;
}
int font_size_in_pixel = font_size;
error = FT_Set_Char_Size(face, font_size_in_pixel * 64, 0, 150, 150); // font_size_in_pixel * 64, 0, 96, 0); /* set character size */
/* error handling omitted */
if (error != 0) {
fprintf(stderr, "\033[0;31mError\033[0;31m: FT_Set_Char_Size returned error, could not set size %d.\n", font_size_in_pixel);
return;
}
slot = face->glyph;
/* set up matrix */
matrix.xx = (FT_Fixed)(cos(angle) * 0x10000L);
matrix.xy = (FT_Fixed)(-sin(angle) * 0x10000L);
matrix.yx = (FT_Fixed)(sin(angle) * 0x10000L);
matrix.yy = (FT_Fixed)(cos(angle) * 0x10000L);
/* the pen position in 26.6 cartesian space coordinates; */
/* start at (300,200) relative to the upper left corner */
//pen.x = (num_chars * 1 * 64);
pen.x = (1 * 64);
pen.y = (target_height - 40) * 64; // the 60 here is related to the font size!
/* const char *text = sstext.c_str();
for (n = 0; n < num_chars; n++) {
if (text[n] == '\n') {
continue; // ignore newlines
}
FT_Set_Transform(face, &matrix, &pen);
error = FT_Load_Char(face, stext[n], FT_LOAD_RENDER);
if (error) {
fprintf(stdout, "\033[0;31mError\033[0m:: [addToReportGen] could not load character: '%c'\n", text[n]);
continue;
}
draw_bitmap_gen(&slot->bitmap, image_buffer_gen_size[0], image_buffer_gen_size[1], slot->bitmap_left, target_height - slot->bitmap_top);
pen.x += slot->advance.x;
pen.y += slot->advance.y;
} */
int nn = 0;
for (std::wstring::iterator it = stext.begin(); it != stext.end(); it++) {
//wchar_t c = *it;
wchar_t c;
int ret = get_mb(&c, sstext.c_str(), nn);
nn++;
if (c == '\n') {
continue; // ignore newlines
}
//fprintf(stdout, "char: %s\n", c);
FT_Set_Transform(face, &matrix, &pen);
FT_UInt glyph_index = FT_Get_Char_Index( face, *it );
error = FT_Load_Glyph(face, glyph_index, FT_LOAD_RENDER);
if (error) {
fprintf(stdout, "\033[0;31mError\033[0m:: [addToReportGen] could not load character: '%ls'\n", &c);
continue;
}
/*FT_Glyph glyph;
error = FT_Get_Glyph( face->glyph, &glyph );
if (error) {
fprintf(stdout, "\033[0;31mError\033[0m:: [addToReportGen] could not get glyph: '%ls'\n", it);
continue;
} */
// add here
// FT_Get_Glyph(face->glyph, &glyph);
// FT_Glyph_To_Bitmap(&glyph, FT_RENDER_MODE_NORMAL, 0, 1);
draw_bitmap_gen(&slot->bitmap, image_buffer_gen_size[0], image_buffer_gen_size[1], slot->bitmap_left, target_height - slot->bitmap_top);
pen.x += slot->advance.x;
pen.y += slot->advance.y;
}
FT_Done_Face(face);
// int px = start_px;
// int py = start_py + 10.0 * (font_size);
// (text_lines * font_size + text_lines * (repeat_spacing * 0.5 * font_size));
float current_image_min_value = 0.0f;
float current_image_max_value = 255.0f;
unsigned char *bvals = (unsigned char *)buffer;
for (int yi = 0; yi < image_buffer_gen_size[1]; yi++) {
for (int xi = 0; xi < image_buffer_gen_size[0]; xi++) {
if (image_buffer_gen[yi][xi] == 0)
continue;
// I would like to copy the value from image over to
// the buffer. At some good location...
int newx = px + xi;
int newy = py + yi;
int idx = newy * xmax + newx;
if (newx < 0 || newx >= xmax || newy < 0 || newy >= ymax)
continue;
//if (image_buffer828[yi][xi] == 0)
// continue;
// instead of blending we need to use a fixed overlay color
// we have image information between current_image_min_value and current_image_max_value
// we need to scale the image_buffer by those values.
float f = 1.0;
float v = 1.0f * image_buffer_gen[yi][xi] / 255.0; // 0 to 1 for color, could be inverted if we have a white background
float w = f * 1.0f * bvals[idx] / current_image_max_value;
float alpha_blend = (v + w * (1.0f - v));
// fprintf(stdout, "%d %d: %d\n", xi, yi, bvals[idx]);
bvals[idx] = (unsigned char)std::max(
0.0f, std::min(current_image_max_value, current_image_min_value + (alpha_blend) * (current_image_max_value - current_image_min_value)));
}
}
}
void addToReport(char *buffer, std::string font_file, int font_size, std::string stext, int posx, int posy, float radiants) {
FT_Library library;
double angle;
int target_height;
int n, num_chars;
// int font_length = 20;
std::string font_path = font_file;
// int font_size = 42;
int face_index = 0;
FT_Face face;
FT_GlyphSlot slot;
FT_Matrix matrix; /* transformation matrix */
FT_Vector pen; /* untransformed origin */
FT_Error error;
// gdcm::ImageReader reader;
// unsigned long len = WIDTH * HEIGHT * 8;
// char *buffer = new char[len];
error = FT_Init_FreeType(&library); /* initialize library */
if (error != 0) {
fprintf(stderr, "\033[0;31mError\033[0m: The freetype library could not be initialized with this font.\n");
return;
}
int start_px = -10;
int start_py = -10;
int text_lines = 1;
float repeat_spacing = 2.0f;
int xmax = WIDTH;
int ymax = HEIGHT;
num_chars = stext.size();
int px = posx;
// WIDTH - ((num_chars + 2) * font_size - start_px);
// int py = start_py + (text_lines * font_size + text_lines * (repeat_spacing * 0.5 * font_size));
int py = posy;
// start_py + 2.0 * (font_size);
memset(image_buffer, 0, sizeof(unsigned char) * HEIGHT * WIDTH);
angle = radiants;
target_height = HEIGHT;
error = FT_New_Face(library, font_file.c_str(), face_index, &face); /* create face object */
if (face == NULL) {
fprintf(stderr, "\033[0;31mError\033[0m: no face found, provide the filename of a ttf file...\n");
return;
}
int font_size_in_pixel = font_size;
error = FT_Set_Char_Size(face, font_size_in_pixel * 64, 0, 150, 150); // font_size_in_pixel * 64, 0, 96, 0); /* set character size */
/* error handling omitted */
if (error != 0) {
fprintf(stderr, "\033[0;31mError\033[0;31m: FT_Set_Char_Size returned error, could not set size %d.\n", font_size_in_pixel);
return;
}
slot = face->glyph;
/* set up matrix */
matrix.xx = (FT_Fixed)(cos(angle) * 0x10000L);
matrix.xy = (FT_Fixed)(-sin(angle) * 0x10000L);
matrix.yx = (FT_Fixed)(sin(angle) * 0x10000L);
matrix.yy = (FT_Fixed)(cos(angle) * 0x10000L);
/* the pen position in 26.6 cartesian space coordinates; */
/* start at (300,200) relative to the upper left corner */
pen.x = (num_chars * 1 * 64);
pen.y = (target_height - 80) * 64; // the 60 here is related to the font size!
const char *text = stext.c_str();
for (n = 0; n < num_chars; n++) {
if (text[n] == '\n') {
continue; // ignore newlines
}
/* set transformation */
FT_Set_Transform(face, &matrix, &pen);
error = FT_Load_Char(face, text[n], FT_LOAD_RENDER);
if (error) {
fprintf(stdout, "\033[0;31mError\033[0m: Could not load character: '%c'\n", text[n]);
continue; /* ignore errors */
}
/* now, draw to our target surface (convert position) draws into image_buffer */
draw_bitmap(&slot->bitmap, WIDTH, HEIGHT, slot->bitmap_left, target_height - slot->bitmap_top);
/* increment pen position */
pen.x += slot->advance.x;
pen.y += slot->advance.y;
}
FT_Done_Face(face);
// int px = start_px;
// int py = start_py + 10.0 * (font_size);
// (text_lines * font_size + text_lines * (repeat_spacing * 0.5 * font_size));
float current_image_min_value = 0.0f;
float current_image_max_value = 255.0f;
unsigned char *bvals = (unsigned char *)buffer;
for (int yi = 0; yi < HEIGHT; yi++) {
for (int xi = 0; xi < WIDTH; xi++) {
if (image_buffer[yi][xi] == 0)
continue;
// I would like to copy the value from image over to
// the buffer. At some good location...
int newx = px + xi;
int newy = py + yi;
int idx = newy * xmax + newx;
if (newx < 0 || newx >= xmax || newy < 0 || newy >= ymax)
continue;
if (image_buffer[yi][xi] == 0)
continue;
// instead of blending we need to use a fixed overlay color
// we have image information between current_image_min_value and current_image_max_value
// we need to scale the image_buffer by those values.
float f = 0;
float v = 1.0f * image_buffer[yi][xi] / 255.0; // 0 to 1 for color, could be inverted if we have a white background
float w = 1.0f * bvals[idx] / current_image_max_value;
float alpha_blend = (v + w * (1.0f - v));
// fprintf(stdout, "%d %d: %d\n", xi, yi, bvals[idx]);
bvals[idx] = (unsigned char)std::max(
0.0f, std::min(current_image_max_value, current_image_min_value + (alpha_blend) * (current_image_max_value - current_image_min_value)));
}
}
}
// Create a report image
// distribution can be eiter "norm" or "lognorm"
void saveReport(Report *report, std::string distribution, float mean_mean, float mean_stds, bool verbose) {
std::string font_file = "Menlo.ttf";
if (const char *env_p = std::getenv("REPORT_FONT_PATH")) {
font_file = std::string(env_p);
}
if (!boost::filesystem::exists(font_file)) {
fprintf(stderr, "\033[0;31mError\033[0m: no font provided. Set the environment variable REPORT_FONT_PATH to the location of a ttf file.\n");
fflush(stderr);
return;
}
FT_Library library;
double angle = 0.0;
int target_height = HEIGHT;
int n, num_chars;
// int font_length = 20;
std::string font_path = font_file;
int font_size = 11;
int face_index = 0;
FT_Face face;
FT_GlyphSlot slot;
FT_Matrix matrix; /* transformation matrix */
FT_Vector pen; /* untransformed origin */
FT_Error error;
// gdcm::ImageReader reader;
unsigned long len = WIDTH * HEIGHT; // in bytes
char *buffer = new char[len];
char *buffer_color = new char[WIDTH * HEIGHT * 3];
error = FT_Init_FreeType(&library); /* initialize library */
if (error != 0) {
fprintf(stderr, "\033[0;31mError\033[0m: The freetype library could not be initialized with this font.\n");
return;
}
// add the key image
if (report->keyImage) {
// for that keyImage
CImageType::RegionType kregion = report->keyImage->GetLargestPossibleRegion();
int KWIDTH = kregion.GetSize()[0];
int KHEIGHT = kregion.GetSize()[1];
char *kbuffer = new char[KWIDTH * KHEIGHT];
char *kbuffer_color = new char[KWIDTH * KHEIGHT * 3];
memset(&kbuffer[0], 0, sizeof(char)*KWIDTH*KHEIGHT);
memset(&kbuffer_color[0], 0, sizeof(char)*KWIDTH*KHEIGHT*3);
// create space for image_buffer unsigned char image_buffer828[512][828];
if (image_buffer_gen) {
// delete its memory before we create a new array
for (int i = 0; i < image_buffer_gen_size[1]; i++) {
if (image_buffer_gen[i])
free(image_buffer_gen[i]);
}
if (image_buffer_gen)
free(image_buffer_gen);
image_buffer_gen_size[0] = 0;
image_buffer_gen_size[1] = 0;
}
// allocate new space for the image buffer
image_buffer_gen = (unsigned char**) malloc(KHEIGHT * sizeof(unsigned char*));
if (image_buffer_gen) {
for (int i = 0; i < KHEIGHT; i++) {
image_buffer_gen[i] = (unsigned char*)malloc(KWIDTH * sizeof(unsigned char));
if (!image_buffer_gen[i]) {
fprintf(stderr, "Error allocating memory for report image\n");
fflush(stderr);
exit(-1); // give up
}
}
}
// remember that size for the next free
image_buffer_gen_size[0] = KWIDTH;
image_buffer_gen_size[1] = KHEIGHT;
if (0) {
// to compute a z-score we can use the publication:
// W.Limthongkul et al. The Spine Journal 10 (2010) pages 153-158
// combine male and female, combine all L1 - L5, L1 - L5
std::vector<float> means = {38.15, 41.48, 44.21, 44.61, 42.52, 25.18, 27.37, 29.54, 30.19, 28.80 };
std::vector<float> stds = { 9.25, 7.78, 10.14, 9.96, 10.14, 4.31, 4.53, 4.4, 3.07, 2.63 };
float mean_mean = means[0];
float mean_stds = stds[0];
int sum_n = 10; // Algorithm described by Cochrane
for (int i = 1; i < means.size(); i++) {
// assume 10 for each group, we don't know how many participants participated in each measurement group
float tmp_mean_mean = (sum_n * mean_mean + 10 * means[i]) / (sum_n + 10);
// use the old mean for this computation
// sqrt(((n1-1)*s1*s1 + (n2-1)*s2*s2 + n1 * n2 / (n1 + n2) * (m1*m1 + m2*m2 - 2 * m1 * m2)) / (n1 + n2 -1));
mean_stds = sqrt(((sum_n-1)*mean_stds*mean_stds + (10-1)*stds[i]*stds[i] + (sum_n * 10) /
(sum_n + 10) * (mean_mean*mean_mean + means[i]*means[i] - 2 * mean_mean * means[i])) / (sum_n + 10 -1));
sum_n += 10;
mean_mean = tmp_mean_mean;
if (verbose)
fprintf(stdout, "model used for z-score is: %f %f\n", mean_mean, mean_stds);
}
if (verbose) {
fprintf(stdout, "model used for z-score is: %f %f\n", mean_mean, mean_stds);
fflush(stdout);
}
// a better setting for mean and std is - based on some example runs in BackToBasic
mean_mean = 23.31783;
mean_stds = 4.539313;
}
// add the physical size to each label
for (int i = 0; i < report->keyImageTexts.size(); i++) {
for (int j = 0; j < report->measures.size(); j++) {
if ( atoi(report->keyImageTexts[i].c_str())-1 == j ) {
// remember what keyImageText is what label
// orderOfRegions.insert(std::pair<int, int>(i, j));
// TODO: measures needs to be organized like the text after a resorting
float a = atof(report->measures[j].find("physical_size")->second.c_str()) / 1000.0;
// If we do a log-normal distribution we need to compute the cdf (prob of being smaller than a)
// and the survival function (compelemnt of the cdf, prob of being larger than a), we should report the smaller of the two.
// z-score is
float perc = 0.0f;
float zscore = 0.0f;
if (distribution == "norm") {
zscore = (a - mean_mean) / mean_stds;
//perc = 100.0f * 0.5f * (1.0f + (boost::math::erf(zscore / sqrtf(2.0)))); // or, better behaving distribution
//perc = 100*(/*0.5f * */ boost::math::erfc(- zscore / sqrtf(2.0)));
perc = 100.0f * (1.0f + (boost::math::erf(- abs(zscore) / sqrtf(2.0))));
} else if (distribution == "lognorm") {
zscore = (log(a) - mean_mean) / mean_stds;
//zscore = boost::math::pdf(boost::math::lognormal(mean_mean, mean_stds), a);
perc = 100.0 * fmin(1.0-boost::math::cdf(boost::math::lognormal(mean_mean, mean_stds), a), boost::math::cdf(boost::math::lognormal(mean_mean, mean_stds), a));
} else {
fprintf(stderr, "Error: unknown distribution %s specified, only norm and lognorm are supported\n", distribution.c_str());
return;
}
// create the message string
char str2[256];
snprintf(str2, 256, "%.02f", zscore);
//std::stringstream stream2;
//stream2 << std::fixed << std::setprecision(2) << zscore;
char str3[256];
//std::stringstream stream3;
if (perc < 1)
snprintf(str3, 256, "<1");
else {
if (perc > 99) {
snprintf(str3, 256, ">99");
} else {
snprintf(str3, 256, "%d", (int)perc);
}
}
char str[256];
snprintf(str, 256, "%.03f", a);
//std::stringstream stream;
//stream << std::fixed << std::setprecision(3) << a;
// meaning of p is: probability of randomly drawing a volume that is further away from the mean than the z-score
report->keyImageTexts[i] += std::string(": ") + std::string(str) + std::string(" cm3 ") + std::string("z: ") + std::string(str2) + std::string(" p: ") + std::string(str3) + std::string(" %");
if (verbose) {
fprintf(stdout, " overlay: \"%s\"\n", report->keyImageTexts[i].c_str());
}
}
}
}
// debug orderOfRegions
if (0) {
//std::map<int, int>::iterator it;
//for (it = orderOfRegions.begin(); it != orderOfRegions.end(); it++) {
// fprintf(stdout, "Key: %d, Value: %d\n", it->first, it->second);
// fflush(stdout);
//}
}
// use the generic method to draw text using image_buffer_gen
// mark the top of the image as "Generated by AI"
// what is the size of the keyImage?
int kw = report->keyImage->GetLargestPossibleRegion().GetSize()[0];
int barHeight = 0.04 * kw;
int fontSize = 0.012 * kw;
addBar(report->keyImage, barHeight); // in dark yellow/orange
addToReportGen(kbuffer, font_file, fontSize, report->TitleText, 10, (barHeight/2)-(fontSize), 0);
addToReportGen(kbuffer, font_file, fontSize, std::string("[area") + (report->keyImagePositions.size()!=1?std::string("s"):std::string("")) + std::string(" of interest: ") + std::to_string(report->keyImageTexts.size()) + std::string("]"), 5, 15+barHeight, 0);
if (report->VersionString.size() > 0)
addToReportGen(kbuffer, font_file, fontSize, report->VersionString, 10, (barHeight+5)*2, 0);
for (int k = 0; k < report->keyImagePositions.size(); k++) {
//fprintf(stdout, "print %s at %d %d\n", report->keyImageTexts[k].c_str(), report->keyImagePositions[k][0], report->keyImagePositions[k][1]);
//fflush(stdout);
std::string::size_type pos = 0;
if ( ( pos = report->keyImageTexts[k].find("z:") ) != std::string::npos) {
std::string piece1 = report->keyImageTexts[k].substr(0, pos);
std::string piece2 = report->keyImageTexts[k].substr(pos);
//fprintf(stdout, "string: %s <-> %s", piece1.c_str(), piece2.c_str());
// add a marker for the exact location, need to know how large the character is...
addMarker(kbuffer, report->keyImagePositions[k][0], report->keyImagePositions[k][1], fontSize);
addToReportGen(kbuffer, font_file, fontSize, piece1, report->keyImagePositions[k][0]-(5.0/9.0*fontSize) + (20/9.0*fontSize), report->keyImagePositions[k][1]-(30.0/9.0*fontSize), 0);
addToReportGen(kbuffer, font_file, fontSize/2, piece2, report->keyImagePositions[k][0]+(35.0/9.0*fontSize) + (20/9.0*fontSize), report->keyImagePositions[k][1]-(50.0/9.0*fontSize), 0);
// add TextTopRight
std::istringstream f(report->TextTopRight);
int c = 0;
for (std::string line; std::getline(f, line, '\n'); c++) {
addToReportGen(kbuffer, font_file, fontSize/2, line, KWIDTH-(fontSize*line.size()), k*(KHEIGHT / report->keyImagePositions.size())+(c * 1.5*fontSize)+(3.0*fontSize), 0);
}
// un-changeable text "Not for clinical use"
addToReportGen(kbuffer, font_file, fontSize/2, "For Research Use Only – Not for use in diagnostic procedures.", 10, (k+1)*(KHEIGHT / report->keyImagePositions.size())-(2.5*fontSize), 0);
} else {
addToReportGen(kbuffer, font_file, fontSize/2, report->keyImageTexts[k], report->keyImagePositions[k][0]-5, report->keyImagePositions[k][1]-(30.0/9.0*fontSize), 0);
}
}
//itk::ImageRegionIterator<CImageType> kIterator(report->keyImage, kregion);
itk::ImageRegionIteratorWithIndex<CImageType> kIterator(report->keyImage, kregion);
kIterator.GoToBegin();
while(!kIterator.IsAtEnd()) {
CPixelType val = kIterator.Value();
CImageType::IndexType kidx = kIterator.GetIndex();
//fprintf(stdout, "idx %d %d: %d %d %d\n", kidx[0], kidx[1], val[0], val[1], val[2]);
//fflush(stdout);
int ttt = (unsigned char)kbuffer[kidx[1]*KWIDTH+kidx[0]]; // a text color other than white is 255/255,255/237,255/160 (yellowish-orange)
int c1 = (int)val[0];
int c2 = (int)val[1];
int c3 = (int)val[2];
// now use alpha blending instead of |=
// kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+0] = (c1 |= ttt);
// kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+1] = (c2 |= ttt);
// kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+2] = (c3 |= ttt);
float alpha_a = (float)(ttt/255.0);
float alpha_b = 0.5;
float alpha = alpha_a + alpha_b*(1.0 - alpha_a); // alpha of text is ttt/255, alpha of b is 0
float C_a_r = 1.0;
float C_a_g = 237.0/255.0;
float C_a_b = 160.0/255.0;
float C_b_r = c1/255.0;
float C_b_g = c2/255.0;
float C_b_b = c3/255.0;
float Cr = (C_a_r * alpha_a + (C_b_r * alpha_b *(1.0 - alpha_a)))/alpha;
float Cg = (C_a_g * alpha_a + (C_b_g * alpha_b *(1.0 - alpha_a)))/alpha;
float Cb = (C_a_b * alpha_a + (C_b_b * alpha_b *(1.0 - alpha_a)))/alpha;
Cr = std::min<float>(1, std::max<float>(0,Cr));
Cg = std::min<float>(1, std::max<float>(0,Cg));
Cb = std::min<float>(1, std::max<float>(0,Cb));
kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+0] = 255.0 * Cr;
kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+1] = 255.0 * Cg;
kbuffer_color[3*(kidx[1]*KWIDTH+kidx[0])+2] = 255.0 * Cb;
++kIterator;
}
gdcm::DataElement pixeldata(gdcm::Tag(0x7fe0, 0x0010));
pixeldata.SetByteValue(kbuffer_color, KWIDTH * KHEIGHT * 3); // in bytes
gdcm::SmartPointer<gdcm::Image> im = new gdcm::Image;
im->SetNumberOfDimensions(2);
im->SetDimension(0, KWIDTH);
im->SetDimension(1, KHEIGHT);
im->SetPhotometricInterpretation(gdcm::PhotometricInterpretation::RGB); // change_image.GetPhotometricInterpretation());
im->GetPixelFormat().SetSamplesPerPixel(3);
im->SetTransferSyntax(gdcm::TransferSyntax::ExplicitVRLittleEndian);
// gdcm::Image im = change_image;
gdcm::File *filePtr = new gdcm::File;
gdcm::Anonymizer anon;
anon.SetFile(*filePtr);
anon.Replace(gdcm::Tag(0x0008, 0x0008), "DERIVED\\SECONDARY\\OTHER"); // ImageType
anon.Replace(gdcm::Tag(0x0028, 0x0002), "3"); // SamplesperPixel
anon.Replace(gdcm::Tag(0x0028, 0x0004), "RGB"); // PhotometricInterpretation
anon.Replace(gdcm::Tag(0x0028, 0x0010), std::to_string(KHEIGHT).c_str()); // Rows
anon.Replace(gdcm::Tag(0x0028, 0x0011), std::to_string(KWIDTH).c_str()); // Columns
anon.Replace(gdcm::Tag(0x0028, 0x0030), "1\\1"); // PixelSpacing
anon.Replace(gdcm::Tag(0x0008, 0x0050), report->AccessionNumber.c_str());
// anon.Replace(gdcm::Tag(0x0020, 0x0010), report->StudyID.c_str()); // we might get the wrong StudyID here from PACS, lets use the StudyInstanceUID value here
anon.Replace(gdcm::Tag(0x0020, 0x0010), report->StudyInstanceUID.c_str());
anon.Replace(gdcm::Tag(0x0020, 0x0052), report->FrameOfReferenceUID.c_str());
anon.Replace(gdcm::Tag(0x0010, 0x0010), report->PatientName.c_str());
anon.Replace(gdcm::Tag(0x0010, 0x0020), report->PatientID.c_str());
anon.Replace(gdcm::Tag(0x0020, 0x000d), report->StudyInstanceUID.c_str());
anon.Replace(gdcm::Tag(0x0008, 0x0090), report->ReferringPhysician.c_str());
anon.Replace(gdcm::Tag(0x0008, 0x0020), report->StudyDate.c_str());
anon.Replace(gdcm::Tag(0x0008, 0x0030), report->StudyTime.c_str());
anon.Replace(gdcm::Tag(0x0008, 0x0080), report->InstitutionName.c_str());
anon.Replace(gdcm::Tag(0x0008, 0x1030), report->StudyDescription.c_str());
anon.Replace(gdcm::Tag(0x0020, 0x0011), std::to_string(1000).c_str());
anon.Replace(gdcm::Tag(0x0020, 0x0013), std::to_string(0).c_str()); // InstanceNumber
anon.Replace(gdcm::Tag(0x0008, 0x103e), std::string("Biomarker report (research PACS)").c_str());
boost::posix_time::ptime timeLocal = boost::posix_time::second_clock::local_time();
char dateOfReport[9];
int year = timeLocal.date().year();
int month = timeLocal.date().month();
int day = timeLocal.date().day();
snprintf(dateOfReport, 9, "%04d%02d%02d", year, month, day);
std::string DateOfSecondaryCapture = std::string(dateOfReport);
// std::to_string(timeLocal.date().year()) + std::to_string(timeLocal.date().month()) + std::to_string(timeLocal.date().day());
char timeOfReport[7];
snprintf(timeOfReport, 7, "%02d%02d%02d", (int)(timeLocal.time_of_day().hours()), (int)(timeLocal.time_of_day().minutes()),
(int)(timeLocal.time_of_day().seconds()));
std::string TimeOfSecondaryCapture = std::string(timeOfReport);
// std::to_string(timeLocal.time_of_day().hours()) + std::to_string(timeLocal.time_of_day().minutes()) + std::to_string(timeLocal.time_of_day().seconds());
anon.Replace(gdcm::Tag(0x0018, 0x1012), DateOfSecondaryCapture.c_str());
anon.Replace(gdcm::Tag(0x0018, 0x1014), TimeOfSecondaryCapture.c_str());
anon.Replace(gdcm::Tag(0x0018, 0x1016), std::string("pr2mask").c_str());
anon.Replace(gdcm::Tag(0x0020, 0x4000), std::string("Region of interest shape, intensity and texture measures").c_str());
gdcm::DataSet &ds = filePtr->GetDataSet(); // ds = reader.GetFile().GetDataSet();
im->SetDataElement(pixeldata);
gdcm::Attribute<0x0008, 0x18> ss;
// adjust the SOPInstanceUID string in case we have more than one report to write
// int size_num = std::to_string(report->summary.size()).size()+1;
std::string marker = report->SOPInstanceUID.substr(report->SOPInstanceUID.find_last_of(".") + 1);
std::string newMarker = marker + std::to_string(report->summary.size());
std::string newSOPInstanceUID = report->SOPInstanceUID.substr(0,report->SOPInstanceUID.find_last_of("."));
if (newSOPInstanceUID.size() + newMarker.size() > 62) {
newSOPInstanceUID = newSOPInstanceUID.substr(0, newSOPInstanceUID.size()-newMarker.size()-1);
}
newSOPInstanceUID = newSOPInstanceUID + std::string(".") + newMarker;
//fprintf(stdout, "%s %s\n", report->SOPInstanceUID.c_str(), newSOPInstanceUID.c_str());
ss.SetValue(newSOPInstanceUID.c_str()); // TODO: we need a different SOPInstanceUID for each roi
ds.Replace(ss.GetAsDataElement());
gdcm::Attribute<0x0020, 0x000e> ss2;
ss2.SetValue(report->SeriesInstanceUID.c_str());
ds.Replace(ss2.GetAsDataElement());
gdcm::Attribute<0x0010, 0x0010> ss3;
ss3.SetValue(report->PatientName.c_str());
ds.Replace(ss3.GetAsDataElement());
gdcm::Attribute<0x0010, 0x0020> ss4;
ss4.SetValue(report->PatientID.c_str());
ds.Replace(ss4.GetAsDataElement());
gdcm::Attribute<0x0020, 0x000d> ss5;
ss5.SetValue(report->StudyInstanceUID.c_str());
ds.Replace(ss5.GetAsDataElement());
// we would like to store the numeric information in some kind of sequence here as well - step towards a structured report
if (0) {
//static const gdcm::Global &g = gdcm::Global::GetInstance();
//static const gdcm::Dicts &dicts = g.GetDicts();
//static const gdcm::Dict &pubdict = dicts.GetPublicDict();
//const gdcm::DictEntry &dictentry = pubdict.GetDictEntry(gdcm::Tag);
gdcm::DataElement entry;
entry.SetTag(gdcm::Tag(0x0040, 0x0100)); // CODE VALUE
entry.SetByteValue("44", (uint32_t)strlen("44"));
gdcm::DataElement code;
code.SetTag(gdcm::Tag(0x0008, 0x0104));
code.SetByteValue("Volume", (uint32_t)strlen("Volume")); // CODE MEANING
gdcm::SmartPointer<gdcm::SequenceOfItems> sq = new gdcm::SequenceOfItems();
sq->SetLengthToUndefined();
for (int measure_idx = 0; measure_idx < report->measures.size(); measure_idx++) {
auto m = report->measures[measure_idx];
std::string labelName = std::string("region ") + std::to_string(measure_idx);
if (strlen(labelName.c_str()) % 2 != 0)
labelName += std::string(" ");
for (std::map<std::string, std::string>::iterator iter = m.begin(); iter != m.end(); ++iter) {
gdcm::Item it;
it.SetVLToUndefined();
gdcm::DataSet &nds = it.GetNestedDataSet();
// resultJSON["measures"].push_back(*iter);
std::string code_meaning = iter->first;
std::string code_value = iter->second;
if (strlen(code_meaning.c_str()) % 2 != 0)
code_meaning += std::string(" ");
if (strlen(code_value.c_str()) % 2 != 0)
code_value += std::string(" ");
gdcm::DataElement entry;
entry.SetTag(gdcm::Tag(0x0008, 0x0100)); // CODE VALUE
entry.SetByteValue(code_value.c_str(), (uint32_t)strlen(code_value.c_str()));
gdcm::DataElement code;
code.SetTag(gdcm::Tag(0x0008, 0x0104));
code.SetByteValue(code_meaning.c_str(), (uint32_t)strlen(code_meaning.c_str())); // CODE MEANING
gdcm::DataElement region;
region.SetTag(gdcm::Tag(0x0008, 0x0103));
region.SetByteValue(labelName.c_str(), (uint32_t)strlen(labelName.c_str()));
nds.Insert(entry);
nds.Insert(code);
nds.Insert(region);
sq->AddItem(it);
}
}
gdcm::DataElement nn;
nn.SetTag(gdcm::Tag(0x0040, 0x0a730));
nn.SetValue(*sq);
nn.SetVLToUndefined();