Merge branch 'master' of github.com:Infogosoft/jsdicom

README.md

@@ -2,7 +2,7 @@
 Dicom library and viewer written in javascript.
 
 ##Dicom parsing
-The dicom parser can handle Implicit VR Little-endian, Explicit VR Little-endian and Explicit VR Big-endian. Sequences are not yet handled correctly.
+The dicom parser can handle Implicit VR Little-endian, Explicit VR Little-endian and Explicit VR Big-endian. ~~Sequences are not yet handled correctly.~~
 
 Parsing files:
 

js/app.js

@@ -261,8 +261,8 @@ DcmApp.prototype.draw_image = function() {
     $("#sliceidx_info").text(this.curr_file_idx+1 + "/" + this.files.length);
     $("#slider").slider("option", "value", this.curr_file_idx);
     var windowing = this.painter.get_windowing();
-    $("#ww_info").text(windowing[0]);
-    $("#wl_info").text(windowing[1]);
+    $("#ww_info").text(windowing[1]);
+    $("#wl_info").text(windowing[0]);
     this.painter.set_file(curr_file);
     this.painter.set_cluts(this.curr_clut_r, this.curr_clut_g, this.curr_clut_b);
     this.painter.draw_image();

js/glpainter.js

@@ -11,7 +11,8 @@
 */
 var FRAG_SHADER_8 = 0;
 var FRAG_SHADER_16 = 1;
-var FRAG_SHADER_RGB_8 = 2;
+var FRAG_SHADER_16_TWO_COMPLEMENTS = 2;
+var FRAG_SHADER_RGB_8 = 3;
 
 function ImageSlice(file, texture, rs, ri, alpha) {
     this.file = file;
@@ -78,6 +79,7 @@ GLPainter.prototype.set_file = function(dcmfile) {
 
 GLPainter.prototype.file_to_texture = function(dcmfile) {
     var internalFormat;
+    raw_data = dcmfile.get_element(dcmdict.PixelData).data;
     switch(jQuery.trim(dcmfile.PhotometricInterpretation)) {
     case "MONOCHROME1":
         // TODO: MONOCHROME1 should use inverse cluts.
@@ -86,6 +88,16 @@ GLPainter.prototype.file_to_texture = function(dcmfile) {
             internalFormat = this.gl.LUMINANCE;
         } else {
             internalFormat = this.gl.LUMINANCE_ALPHA;
+            if(dcmfile.PixelRepresentation == 0x01) {
+                if(!dcmfile.PixelRepresentationPatched) {
+                    //var view16bit = new Uint16Array(dcmfile.PixelData.data.buffer, dcmfile.PixelData.data.byteOffset, dcmfile.PixelData.length/2);
+                    console.log("Patching");
+                    for(var i=0;i<dcmfile.PixelData.length;++i) {
+                        dcmfile.PixelData[i] = dcmfile.PixelData[i] ^ 0x8000;
+                    }
+                    dcmfile.PixelRepresentationPatched = true;
+                }
+            }
         }
         break;
     case "RGB":
@@ -107,10 +119,9 @@ GLPainter.prototype.file_to_texture = function(dcmfile) {
                        0,                        // border
                        internalFormat,           // format
                        this.gl.UNSIGNED_BYTE,    // type
-                       new Uint8Array(dcmfile.PixelData.buffer, dcmfile.PixelData.byteOffset)); // data
-                       //Uint8Array(dcmfile.PixelData.buffer, dcmfile.PixelData.byteOffset)); // TODO: type conversion instead of new array?
-    this.gl.texParameteri(this.gl.TEXTURE_2D, this.gl.TEXTURE_MAG_FILTER, this.gl.LINEAR);
+                       dcmfile.get_element(dcmdict.PixelData).data);// Get raw Uint8array
     this.gl.texParameteri(this.gl.TEXTURE_2D, this.gl.TEXTURE_MIN_FILTER, this.gl.LINEAR);
+    this.gl.texParameteri(this.gl.TEXTURE_2D, this.gl.TEXTURE_MAG_FILTER, this.gl.LINEAR);
     this.gl.texParameteri(this.gl.TEXTURE_2D, this.gl.TEXTURE_WRAP_S, this.gl.CLAMP_TO_EDGE);
     this.gl.texParameteri(this.gl.TEXTURE_2D, this.gl.TEXTURE_WRAP_T, this.gl.CLAMP_TO_EDGE);
 
@@ -188,8 +199,8 @@ GLPainter.prototype.set_cluts = function(clut_r, clut_g, clut_b) {
 }
 
 GLPainter.prototype.set_windowing = function(wl, ww) {
-    this.ww = ww;
     this.wl = wl;
+    this.ww = ww;
 }
 GLPainter.prototype.get_windowing = function() {
     return [this.wl, this.ww];
@@ -350,12 +361,14 @@ GLPainter.prototype.draw_image = function() {
 
         this.set_matrix_uniforms(shaderProgram);
         this.set_window_uniforms(shaderProgram, image);
+
         this.gl.bindBuffer(this.gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
         this.gl.drawElements(this.gl.TRIANGLES, this.vertexIndexBuffer.numItems, this.gl.UNSIGNED_SHORT, 0);
     }
 
 
 }
+off = (1 << (15 - 1));
 
 GLPainter.prototype.init = function(canvasid) {
     try {
@@ -447,7 +460,11 @@ GLPainter.prototype.set_matrix_uniforms = function(shaderProgram) {
 }
 
 GLPainter.prototype.set_window_uniforms = function(shaderProgram, image) {
-    this.gl.uniform1f(shaderProgram.wlUniform, this.wl);
+    // Hack for files with pixel representation in two complements
+    var wl = this.wl;
+    if(image.file.PixelRepresentation == 0x01)
+        wl += 32768.0;
+    this.gl.uniform1f(shaderProgram.wlUniform, wl);
     this.gl.uniform1f(shaderProgram.wwUniform, this.ww);
     this.gl.uniform1f(shaderProgram.rsUniform, image.rs);
     this.gl.uniform1f(shaderProgram.riUniform, image.ri);

js/shaders.js

@@ -23,10 +23,8 @@ uniform sampler2D uClutSampler;\
 void main(void) {  \
     highp vec4 texcolor = texture2D(uSampler, vTextureCoord); \
     highp float intensity = texcolor.r*65536.0;\
-    highp float wl = uWL;\
-    highp float ww = uWW;\
-    highp float lower_bound = wl - ww/2.0;\
-    highp float upper_bound = wl + ww/2.0;\
+    highp float lower_bound = uWL - uWW/2.0;\
+    highp float upper_bound = uWL + uWW/2.0;\
     intensity = (intensity - lower_bound)/(upper_bound - lower_bound);\
 \
     gl_FragColor = vec4(intensity, intensity, intensity, uAlpha);\
@@ -49,14 +47,11 @@ void main(void) {  \
     highp float rescaleIntercept = uRI;\
     highp float rescaleSlope = uRS;\
     intensity = intensity * rescaleSlope + rescaleIntercept;\
-    highp float wl = uWL;\
-    highp float ww = uWW;\
-    highp float lower_bound = wl - ww/2.0;\
-    highp float upper_bound = wl + ww/2.0;\
+    highp float lower_bound = uWL - uWW/2.0;\
+    highp float upper_bound = uWL + uWW/2.0;\
     intensity = (intensity - lower_bound)/(upper_bound - lower_bound);\
     highp vec4 clutcolor = texture2D(uClutSampler, vec2(intensity, intensity)); \
     gl_FragColor = vec4(clutcolor.r, clutcolor.g, clutcolor.b, uAlpha);\
-\
 }";
 
 var fragment_shader_rgb_8 = "\