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Add model
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@Mmasoud1
Mmasoud1 committed Mar 30, 2024
1 parent 391699b commit 0fe66a3
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Showing 2 changed files with 50 additions and 33 deletions.
25 changes: 9 additions & 16 deletions js/brainchop/mainMeshNetFunctions.js
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,6 @@
=========================================================
Brainchop for 3D Brain Segmentation
=========================================================*/
// Set the WEBGL_FORCE_F16_TEXTURES flag
tf.env().set('WEBGL_FORCE_F16_TEXTURES', true);

(function() {

Expand Down Expand Up @@ -4280,6 +4278,7 @@ class SequentialConvLayer {
*/

async apply(inputTensor) {

let oldDeleteTextureThreshold = tf.ENV.get('WEBGL_DELETE_TEXTURE_THRESHOLD');
tf.ENV.set('WEBGL_DELETE_TEXTURE_THRESHOLD', 0);

Expand Down Expand Up @@ -4374,6 +4373,7 @@ class SequentialConvLayer {
const endTime = performance.now();
const executionTime = endTime - startTime;
console.log(`Execution time for output layer: ${executionTime} milliseconds`);
tf.ENV.set('WEBGL_DELETE_TEXTURE_THRESHOLD', oldDeleteTextureThreshold);
resolve(outC);
} else {

Expand All @@ -4388,7 +4388,7 @@ class SequentialConvLayer {
}, 0);
});

tf.ENV.set('WEBGL_DELETE_TEXTURE_THRESHOLD', oldDeleteTextureThreshold);

}


Expand Down Expand Up @@ -6968,7 +6968,7 @@ checkInferenceModelList = () => {
*
*/

enableProductionMode = async() => {
enableProductionMode = async(textureF16Flag = true) => {

//-- tf.setBackend('cpu');
//-- tf.removeBackend('cpu')
Expand All @@ -6979,7 +6979,7 @@ checkInferenceModelList = () => {
tf.env().set('DEBUG', false);


tf.env().set('WEBGL_FORCE_F16_TEXTURES', true);
tf.env().set('WEBGL_FORCE_F16_TEXTURES', textureF16Flag);
//-- set this flag so that textures are deleted when tensors are disposed.
tf.env().set("WEBGL_DELETE_TEXTURE_THRESHOLD", 0);
//-- tf.env().set('WEBGL_PACK', false);
Expand Down Expand Up @@ -7047,6 +7047,10 @@ resetMainParameters = () => {
model = load_browser_model( modelEntry.modelFile, modelEntry.weightFile);
}

// Enable production model:
// true enable F16 bit, false enable F32 bit processing
await enableProductionMode(true);

let modelObject = {};
// get model object data e.g. layers etc
model.then(function(res) {
Expand Down Expand Up @@ -7153,19 +7157,8 @@ resetMainParameters = () => {
// }




let Preprocess_t = ((performance.now() - startTime)/1000).toFixed(4);

console.log(tf.getBackend());
//-- set this flag so that textures are deleted when tensors are disposed.
tf.env().set("WEBGL_DELETE_TEXTURE_THRESHOLD", 0);

console.log("tf env() features :", tf.env().features);
console.log("tf env total features: ", Object.keys(tf.env().features).length);
// tf.env().set('WEBGL_PACK', false);

// enableProductionMode();

//-- Timing data to collect
let today = new Date();
Expand Down
58 changes: 41 additions & 17 deletions js/brainchop/mainParameters.js
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Original file line number Diff line number Diff line change
Expand Up @@ -113,8 +113,8 @@
isBatchOverlapEnable: false, //create extra overlap batches for inference
numOverlapBatches: 0, //Number of extra overlap batches for inference
enableTranspose : true, // Keras and tfjs input orientation may need a tranposing step to be matched
enableCrop: false, // For speed-up inference, crop brain from background before feeding to inference model to lower memory use.
cropPadding: 0, // Padding size add to cropped brain
enableCrop: true, // For speed-up inference, crop brain from background before feeding to inference model to lower memory use.
cropPadding: 2, // Padding size add to cropped brain
autoThreshold: 0, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
enableQuantileNorm: false, // Some models needs Quantile Normaliztion.
filterOutWithPreMask: false, // Can be used to multiply final output with premodel output mask to crean noisy areas
Expand Down Expand Up @@ -180,8 +180,8 @@
type: "Atlas",
path:"./models/model30chan18cls/model.json",
modelName:"\u{1FA93} Subcortical + GWM (High Mem, Fast)",
labelsPath: "./models/model18cls/labels.json",
colorsPath: "./models/model18cls/colorLUT.json",
labelsPath: "./models/model30chan18cls/labels.json",
colorsPath: "./models/model30chan18cls/colorLUT.json",
preModelId: null,// Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, //create extra overlap batches for inference
Expand All @@ -204,8 +204,8 @@
type: "Atlas",
path:"./models/model30chan18cls/model.json",
modelName:"\u{1FA93} Subcortical + GWM (Low Mem, Slow)",
labelsPath: "./models/model18cls/labels.json",
colorsPath: "./models/model18cls/colorLUT.json",
labelsPath: "./models/model30chan18cls/labels.json",
colorsPath: "./models/model30chan18cls/colorLUT.json",
preModelId: null,// Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, //create extra overlap batches for inference
Expand All @@ -228,8 +228,8 @@
type: "Atlas",
path:"./models/model18cls/model.json",
modelName:"\u{1FA93} Subcortical + GWM (Low Mem, Faster)",
labelsPath: "./models/model30chan18cls/labels.json",
colorsPath: "./models/model30chan18cls/colorLUT.json",
labelsPath: "./models/model18cls/labels.json",
colorsPath: "./models/model18cls/colorLUT.json",
preModelId: null, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, //create extra overlap batches for inference
Expand All @@ -250,6 +250,30 @@
,{
id: 7,
type: "Atlas",
path:"./models/model30chan18cls/model.json",
modelName:"\u{1F52A}\u{1FA93} Subcortical + GWM (Failsafe, Less Acc)",
labelsPath: "./models/model30chan18cls/labels.json",
colorsPath: "./models/model30chan18cls/colorLUT.json",
preModelId: 1, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, //create extra overlap batches for inference
numOverlapBatches: 200, //Number of extra overlap batches for inference
enableTranspose : true, // Keras and tfjs input orientation may need a tranposing step to be matched
enableCrop: true, // For speed-up inference, crop brain from background before feeding to inference model to lower memory use.
cropPadding: 0, // Padding size add to cropped brain
autoThreshold: 0, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
enableQuantileNorm: false, // Some models needs Quantile Normaliztion.
filterOutWithPreMask: false, // Can be used to multiply final output with premodel output mask to crean noisy areas
enableSeqConv: false, // For low memory system and low configuration, enable sequential convolution instead of last layer
textureSize: 0, // Requested Texture size for the model, if unknown can be 0.
warning: "This model may need dedicated graphics card. For more info please check with Browser Resources <i class='fa fa-cogs'></i>.", // Warning message to show when select the model.
inferenceDelay: 100, // Delay in ms time while looping layers applying.
description: "Parcellation of the brain into 17 regions: gray and white matter plus subcortical areas. This is not a robust model, it may work on low data quality, including varying saturation, and even clinical scans. It may work also on infant brains, but your mileage may vary."
}

,{
id: 8,
type: "Atlas",
path:"./models/model30chan50cls/model.json",
modelName:"\u{1F52A} Aparc+Aseg 50 (High Mem, Fast)",
labelsPath: "./models/model30chan50cls/labels.json",
Expand All @@ -272,7 +296,7 @@
}

,{
id: 8,
id: 9,
type: "Atlas",
path:"./models/model30chan50cls/model.json",
modelName:"\u{1F52A} Aparc+Aseg 50 (Low Mem, Slow)",
Expand All @@ -297,7 +321,7 @@


,{
id: 9,
id: 10,
type: "Brain_Extraction",
path: "./models/model5_gw_ae/model.json",
modelName:"\u26A1 Extract the Brain (FAST)",
Expand All @@ -310,7 +334,7 @@
enableTranspose : true, // Keras and tfjs input orientation may need a tranposing step to be matched
enableCrop: true, // For speed-up inference, crop brain from background before feeding to inference model to lower memory use.
cropPadding: 2, // Padding size add to cropped brain
autoThreshold: 0.1, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
autoThreshold: 0, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
enableQuantileNorm: false, // Some models needs Quantile Normaliztion.
filterOutWithPreMask: false, // Can be used to multiply final output with premodel output mask to crean noisy areas
enableSeqConv: false, // For low memory system and low configuration, enable sequential convolution instead of last layer
Expand All @@ -321,7 +345,7 @@
}

,{
id: 10,
id: 11,
type: "Brain_Extraction",
path: "./models/model11_gw_ae/model.json",
modelName:"\u{1F52A} Extract the Brain (High Acc, Slow)",
Expand All @@ -345,7 +369,7 @@
}

,{
id: 11,
id: 12,
type: "Brain_Masking",
path: "./models/model5_gw_ae/model.json",
modelName:"\u26A1 Brain Mask (FAST)",
Expand All @@ -358,7 +382,7 @@
enableTranspose : true, // Keras and tfjs input orientation may need a tranposing step to be matched
enableCrop: true, // For speed-up inference, crop brain from background before feeding to inference model to lower memory use.
cropPadding: 2, // Padding size add to cropped brain
autoThreshold: 0.1, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
autoThreshold: 0, // Threshold between 0 and 1, given no preModel and tensor is normalized either min-max or by quantiles. Will remove noisy voxels around brain
enableQuantileNorm: false, // Some models needs Quantile Normaliztion.
filterOutWithPreMask: false, // Can be used to multiply final output with premodel output mask to crean noisy areas
enableSeqConv: false, // For low memory system and low configuration, enable sequential convolution instead of last layer
Expand All @@ -369,7 +393,7 @@
}

,{
id: 12,
id: 13,
type: "Brain_Masking",
path: "./models/model11_gw_ae/model.json",
modelName:"\u{1F52A} Brain Mask (High Acc, Low Mem)",
Expand All @@ -393,7 +417,7 @@
}

,{
id: 13,
id: 14,
type: "Atlas",
path:"./models/model21_104class/model.json",
modelName:"\u{1F52A} Aparc+Aseg 104 (High Mem, Fast)",
Expand All @@ -417,7 +441,7 @@
}

,{
id: 14,
id: 15,
type: "Atlas",
path:"./models/model21_104class/model.json",
modelName:"\u{1F52A} Aparc+Aseg 104 (Low Mem, Slow)",
Expand Down

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