Support colormaps in mrd2gif

kspaceKelvin · Mar 1, 2025 · 9b4a499 · 9b4a499
1 parent 2b1cff3
commit 9b4a499
Showing 1 changed file with 42 additions and 5 deletions.
diff --git a/mrd2gif.py b/mrd2gif.py
@@ -152,6 +152,26 @@ def main(args):
                 minVal = float(meta['GADGETRON_WindowCenter']) - float(meta['GADGETRON_WindowWidth'])/2
                 maxVal = float(meta['GADGETRON_WindowCenter']) + float(meta['GADGETRON_WindowWidth'])/2
 
+            if ('LUTFileName' in meta) or ('GADGETRON_ColorMap' in meta):
+                LUTFileName = meta['LUTFileName'] if 'LUTFileName' in meta else meta['GADGETRON_ColorMap']
+
+                # Replace extension with '.npy'
+                LUTFileName = os.path.splitext(LUTFileName)[0] + '.npy'
+
+                # LUT file is a (256,3) numpy array of RGB values between 0 and 255
+                if os.path.exists(LUTFileName):
+                    palette = np.load(LUTFileName)
+                    palette = palette.flatten().tolist()  # As required by PIL
+                # Look in subdirectory 'colormaps' if not found in current directory
+                elif os.path.exists(os.path.join('colormaps', LUTFileName)):
+                    palette = np.load(os.path.join('colormaps', LUTFileName))
+                    palette = palette.flatten().tolist()  # As required by PIL
+                else:
+                    print("LUT file %s specified by MetaAttributes, but not found" % (LUTFileName))
+                    palette = None
+            else:
+                palette = None
+
             if img.mode != 'RGB':
                 if hasRois:
                     # Convert to RGB mode to allow colored ROI overlays
@@ -160,23 +180,34 @@ def main(args):
                     if maxVal != minVal:
                         data *= 255/(maxVal - minVal)
                     data = np.clip(data, 0, 255)
-                    tmpImg = Image.fromarray(np.repeat(data[:,:,np.newaxis],3,axis=2).astype(np.uint8), mode='RGB')
+                    if palette is not None:
+                        tmpImg = Image.fromarray(data.astype(np.uint8), mode='P')
+                        tmpImg.putpalette(palette)
+                        tmpImg = tmpImg.convert('RGB')  # Needed in order to draw ROIs
+                    else:
+                        tmpImg = Image.fromarray(np.repeat(data[:,:,np.newaxis],3,axis=2).astype(np.uint8), mode='RGB')
 
                     if args.rescale != 1:
                         tmpImg = tmpImg.resize(tuple(args.rescale*x for x in tmpImg.size))
                         for i in range(len(roi)):
                             roi[i] = tuple(([args.rescale*x for x in roi[i][0]], [args.rescale*y for y in roi[i][1]], roi[i][2], roi[i][3]))
 
-                    draw = ImageDraw.Draw(tmpImg)
                     for (x, y, rgb, thickness) in roi:
-                        draw.line(list(zip(x, y)), fill=(int(rgb[0]*255), int(rgb[1]*255), int(rgb[2]*255), 0), width=int(thickness))
+                        draw = ImageDraw.Draw(tmpImg)
+                        draw.line(list(zip(x, y)), fill=(int(rgb[0]*255), int(rgb[1]*255), int(rgb[2]*255), 255), width=int(thickness))
                     imagesWL.append(tmpImg)
                 else:
                     data = np.array(img).astype(float)
                     data -= minVal
                     data *= 255/(maxVal - minVal)
                     data = np.clip(data, 0, 255)
-                    imagesWL.append(Image.fromarray(data))
+
+                    if palette is not None:
+                        tmpImg = Image.fromarray(data.astype(np.uint8), mode='P')
+                        tmpImg.putpalette(palette)
+                        imagesWL.append(tmpImg)
+                    else:
+                        imagesWL.append(Image.fromarray(data))
             else:
                 imagesWL.append(img)
 
@@ -198,7 +229,13 @@ def main(args):
                     # Loop over non-slice dimension
                     imagesWLMosaic = []
                     for idx in range(len(imagesWLSplit[0])):
-                        imagesWLMosaic.append(Image.fromarray(np.hstack([img[idx] for img in imagesWLSplit])))
+                        imgMode = imagesWLSplit[0][idx].mode
+                        tmpImg = Image.fromarray(np.hstack([img[idx] for img in imagesWLSplit]), mode=imgMode)
+                        if imgMode == 'P':
+                            palette = imagesWLSplit[0][0].getpalette()
+                            tmpImg.putpalette(palette)
+                        imagesWLMosaic.append(tmpImg)
+
                     imagesWL = imagesWLMosaic
 
         # Add SequenceDescriptionAdditional to filename, if present