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assets/img/volume/README.adoc

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+:toc:
+
+== Data from BrainWeb: Simulated Brain Database
+
+In the "Volume Rendering - Texture 3D" sample, the implementation uses simulated brain data from BrainWeb. The render results, as seen in the sample, were validated to be representative of standard visualization with VTK.
+
+=== Reproduction
+
+1. Go to https://brainweb.bic.mni.mcgill.ca/brainweb/selection_normal.html
+2. Set modality to T1.
+3. Set slice thickness to 1mm.
+4. Set noise to 0%.
+5. Set RF to 0%.
+6. Click Download.
+7. Set file format to raw byte.
+8. Set compression to none.
+9. Follow other instructions on the website according to your situation.
+10. Click Start Download.
+11. Copy the downloaded *.rawb data to this directory.
+12. Activate a Python environment with at least Python 3.12, Numpy, Scipy, and Pillow.
+13. Start a terminal in this directory.
+14. Run t1_icbm_normal_1mm_pn0_rf0.py script.
+
+=== References
+
+* http://www.bic.mni.mcgill.ca/brainweb/[`http://www.bic.mni.mcgill.ca/brainweb/`]
+
+* C.A. Cocosco, V. Kollokian, R.K.-S. Kwan, A.C. Evans : 
+  __"BrainWeb: Online Interface to a 3D MRI Simulated Brain Database"__ +
+  NeuroImage, vol.5, no.4, part 2/4, S425, 1997 -- Proceedings of 3-rd International Conference on Functional Mapping of the Human Brain, Copenhagen, May 1997.
+  ** abstract available in
+    http://www.bic.mni.mcgill.ca/users/crisco/HBM97_abs/HBM97_abs.html[html],
+    http://www.bic.mni.mcgill.ca/users/crisco/HBM97_abs/HBM97_abs.pdf[pdf (500Kb)],
+    or http://www.bic.mni.mcgill.ca/users/crisco/HBM97_abs/HBM97_abs.ps.gz[gnuzip-ed postscript (500Kb)].
+  ** poster available in
+    http://www.bic.mni.mcgill.ca/users/crisco/HBM97_poster/HBM97_poster.pdf[pdf (1.1Mb)],
+    or http://www.bic.mni.mcgill.ca/users/crisco/HBM97_poster/HBM97_poster.ps.gz[gnuzip-ed postscript (850Kb)].
+
+* R.K.-S. Kwan, A.C. Evans, G.B. Pike :
+  __"MRI simulation-based evaluation of image-processing and classification methods"__ +
+  IEEE Transactions on Medical Imaging. 18(11):1085-97, Nov 1999.
+
+* R.K.-S. Kwan, A.C. Evans, G.B. Pike :
+  __"An Extensible MRI Simulator for Post-Processing Evaluation"__ +
+  Visualization in Biomedical Computing (VBC'96). Lecture Notes in Computer Science, vol. 1131. Springer-Verlag, 1996. 135-140.
+  ** paper available in
+    http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/paper/vbc96.html[html],
+    http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/paper/vbc96.ps[postscript (1Mb)],
+    or http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/paper/vbc96.ps.gz[gnuzip-ed postscript (380Kb)].
+  ** poster available in
+    http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/poster/vbc96bw.ps[grey-scale postscript (5.3Mb)],
+    http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/poster/vbc96bw.ps.gz[grey-scale, gnuzip-ed postscript (536Kb)],
+    or http://www.bic.mni.mcgill.ca/users/rkwan/vbc96/poster/vbc96.poster.ps.gz[colour, gnuzip-ed postscript (597Kb)].  
+
+* D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes, A.C. Evans :
+  __"Design and Construction of a Realistic Digital Brain Phantom"__ +
+  IEEE Transactions on Medical Imaging, vol.17, No.3, p.463--468, June 1998.
+  ** paper available in http://www.bic.mni.mcgill.ca/users/louis/papers/phantom/[html].

assets/img/volume/t1_icbm_normal_1mm_pn0_rf0.py

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+import gzip
+import os
+
+import numpy as np
+from PIL import Image
+from scipy.ndimage import zoom
+
+
+def resample_volume_lanczos(byte_array, original_shape, new_shape):
+    volume = np.frombuffer(byte_array, dtype=np.uint8).reshape(original_shape)
+    zoom_factors = [n / o for n, o in zip(new_shape, original_shape)]
+    resampled_volume = zoom(volume, zoom_factors, order=4)
+    return resampled_volume
+
+
+def load_byte_array_from_file(file_path):
+    with open(file_path, "rb") as file:
+        byte_array = file.read()
+    return byte_array
+
+
+file_path = "t1_icbm_normal_1mm_pn0_rf0.rawb"
+byte_array = load_byte_array_from_file(file_path)
+original_shape = (181, 217, 181)
+new_shape = (180, 216, 180)
+resampled_volume = resample_volume_lanczos(byte_array, original_shape, new_shape)
+
+np.save("t1_icbm_normal_1mm_pn0_rf0.npy", resampled_volume)
+
+
+file_path = "t1_icbm_normal_1mm_pn0_rf0.npy"
+data = np.load(file_path)
+os.makedirs("slices", exist_ok=True)
+
+for i, slice in enumerate(data):
+    img = Image.fromarray(slice)
+    if img.mode != "L":
+        img = img.convert("L")
+    img.save(f"slices/slice_{i:03d}.png")
+
+print(f"Exported {len(data)} slices.")
+
+source_directory = "slices"
+final_file_path = "t1_icbm_normal_1mm_pn0_rf0_180x216x180_uint8_1x1.bin"
+
+with open(final_file_path, "wb") as output_file:
+    for file_name in sorted(os.listdir(source_directory)):
+        if file_name.lower().endswith(".png"):
+            source_path = os.path.join(source_directory, file_name)
+            img = Image.open(source_path).convert("L")
+            img_data = np.array(img, dtype=np.uint8)
+            img_data.tofile(output_file)
+
+print("Images have been successfully converted and concatenated.")
+
+with open("t1_icbm_normal_1mm_pn0_rf0_180x216x180_uint8_1x1.bin", "rb") as f:
+    bytes_data = f.read()
+
+gzip_filename = "t1_icbm_normal_1mm_pn0_rf0_180x216x180_uint8_1x1.bin-gz"
+
+with gzip.open(gzip_filename, "wb", compresslevel=9) as f:
+    f.write(bytes_data)
+
+print(f"File compressed and saved as {gzip_filename}")

main.js

@@ -517,6 +517,23 @@ var videoUploading = {
     ],
 };
 
+var volumeRenderingTexture3D = {
+    name: 'Volume Rendering - Texture 3D',
+    description: `This example shows how to render volumes with WebGPU using a 3D
+texture. It demonstrates simple direct volume rendering for photometric content
+through ray marching in a fragment shader, where a full-screen triangle
+determines the color from ray start and step size values as set in the vertex
+shader. This implementation employs data from the BrainWeb Simulated Brain
+Database, with decompression streams, to save disk space and network traffic.
+
+The original raw data is generated using
+[the BrainWeb Simulated Brain Database](https://brainweb.bic.mni.mcgill.ca/brainweb/)
+before processing in
+[a custom Python script](https://github.com/webgpu/webgpu-samples/tree/main/public/assets/img/volume/t1_icbm_normal_1mm_pn0_rf0.py).`,
+    filename: "sample/volumeRenderingTexture3D",
+    sources: [{ path: 'main.ts' }, { path: 'volume.wgsl' }],
+};
+
 var worker = {
     name: 'WebGPU in a Worker',
     description: `This example shows one method of using WebGPU in a web worker and presenting to
@@ -601,6 +618,7 @@ const pageCategories = [
             'a-buffer': aBuffer,
             skinnedMesh,
             textRenderingMsdf,
+            volumeRenderingTexture3D,
         },
     },
     // Samples that demonstrate how to integrate WebGPU and/or WebGPU render operations with other

sample/volumeRenderingTexture3D/index.html

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+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+    <title>webgpu-samples: volumeRenderingTexture3D</title>
+    <style>
+      :root {
+        color-scheme: light dark;
+      }
+      html, body {
+        margin: 0;      /* remove default margin */
+        height: 100%;   /* make body fill the browser window */
+        display: flex;
+        place-content: center center;
+      }
+      canvas {
+        width: 600px;
+        height: 600px;
+        max-width: 100%;
+        display: block;
+      }
+    </style>
+    <script defer src="main.js" type="module"></script>
+    <script defer type="module" src="../../js/iframe-helper.js"></script>
+  </head>
+  <body>
+    <canvas></canvas>
+  </body>
+</html>