import * as tf from '@tensorflow/tfjs'
import { inferenceModelsList } from './brainchop-parameters.js'
import {
addZeroPaddingTo3dTensor,
applyMriThreshold,
binarizeVolumeDataTensor,
convByOutputChannelAndInputSlicing,
draw3dObjBoundingVolume,
firstLastNonZero3D,
generateBrainMask,
generateOutputSlicesV2,
getAllSlicesDataAsTF3D,
getModelNumLayers,
getModelNumParameters,
isModelChnlLast,
load_model,
minMaxNormalizeVolumeData,
quantileNormalizeVolumeData,
removeZeroPaddingFrom3dTensor,
resizeWithZeroPadding,
SequentialConvLayer
} from './tensor-utils.js'
async function inferenceFullVolumeSeqCovLayerPhase2(
opts,
modelEntry,
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
pipeline1_out,
callbackUI,
callbackImg,
statData,
niftiImage
) {
// --Phase-2, After remove the skull try to allocate brain volume and make inferece
console.log(' ---- Start FullVolume Inference with Sequential Conv Layer for phase-II ---- ')
// console.log("BOB", callbackUI); console.log("UNCLE",callbackImg); return
const quantileNorm = modelEntry.enableQuantileNorm
if (quantileNorm) {
// Quantile normalize function needs specific models to be used
console.log('preModel Quantile normalization enabled')
slices_3d = await quantileNormalizeVolumeData(slices_3d)
} else {
// Min Max Nomalize MRI data to be from 0 to 1
console.log('preModel Min Max normalization enabled')
slices_3d = await minMaxNormalizeVolumeData(slices_3d)
}
let mask_3d
if (pipeline1_out == null) {
// preModel is null
// Check if thresholding the MRI to remove noisy voxels for better cropping is needed.
const autoThresholdValue = modelEntry.autoThreshold
if (autoThresholdValue > 0 && autoThresholdValue <= 1) {
// Filtered MRI from noisy voxel below autoThresholdValue
mask_3d = await applyMriThreshold(slices_3d, autoThresholdValue)
} else {
console.log('No valid crop threshold value')
// binarize original image
mask_3d = await slices_3d.greater([0]).asType('bool')
}
} else {
mask_3d = await pipeline1_out.greater([0]).asType('bool')
// -- pipeline1_out.dispose();
}
console.log(' mask_3d shape : ', mask_3d.shape)
const [row_min, row_max, col_min, col_max, depth_min, depth_max] = await firstLastNonZero3D(mask_3d)
mask_3d.dispose()
// -- Reference voxel that cropped volume started slice with it
const refVoxel = [row_min, col_min, depth_min]
// -- Starting form refVoxel, size of bounding volume
const boundVolSizeArr = [row_max - row_min + 1, col_max - col_min + 1, depth_max - depth_min + 1]
// -- Extract 3d object (e.g. brain)
const cropped_slices_3d = await slices_3d.slice(
[row_min, col_min, depth_min],
[row_max - row_min + 1, col_max - col_min + 1, depth_max - depth_min + 1]
)
slices_3d.dispose()
// -- Padding size add to cropped brain
const pad = modelEntry.cropPadding
// Create margin around the bounding volume
let cropped_slices_3d_w_pad = await addZeroPaddingTo3dTensor(cropped_slices_3d, [pad, pad], [pad, pad], [pad, pad])
console.log(' cropped slices_3d with padding shape: ', cropped_slices_3d_w_pad.shape)
cropped_slices_3d.dispose()
if (opts.drawBoundingVolume) {
let testVol = await removeZeroPaddingFrom3dTensor(cropped_slices_3d_w_pad, pad, pad, pad)
console.log(' outLabelVolume without padding shape : ', testVol.shape)
testVol = await resizeWithZeroPadding(testVol, num_of_slices, slice_height, slice_width, refVoxel, boundVolSizeArr)
console.log(' outLabelVolume final shape after resizing : ', testVol.shape)
draw3dObjBoundingVolume(tf.unstack(testVol), opts, modelEntry, callbackImg)
testVol.dispose()
return 0
}
statData.Brainchop_Ver = 'FullVolume'
// model.then(function (res) {
// console.log("--->>>>", opts.drawBoundingVolume); return
const res = await model
try {
let startTime = performance.now()
const inferenceStartTime = performance.now()
// maxLabelPredicted in whole volume of the brain
let maxLabelPredicted = 0
const transpose = modelEntry.enableTranspose
const delay = modelEntry.inferenceDelay
console.log('Inference delay :', delay)
if (transpose) {
cropped_slices_3d_w_pad = await cropped_slices_3d_w_pad.transpose()
console.log('Input transposed for pre-model')
} else {
console.log('Transpose not enabled for pre-model')
}
let i = 1
const layersLength = res.layers.length
console.log('res.layers.length ', layersLength)
const isChannelLast = isModelChnlLast(res)
const batchSize = opts.batchSize
const numOfChan = opts.numOfChan
let adjusted_input_shape
// -- Adjust model input shape
if (isChannelLast) {
res.layers[0].batchInputShape[1] = cropped_slices_3d_w_pad.shape[0]
res.layers[0].batchInputShape[2] = cropped_slices_3d_w_pad.shape[1]
res.layers[0].batchInputShape[3] = cropped_slices_3d_w_pad.shape[2]
adjusted_input_shape = [
batchSize,
res.layers[0].batchInputShape[1],
res.layers[0].batchInputShape[2],
res.layers[0].batchInputShape[3],
numOfChan
]
} else {
res.layers[0].batchInputShape[2] = cropped_slices_3d_w_pad.shape[0]
res.layers[0].batchInputShape[3] = cropped_slices_3d_w_pad.shape[1]
res.layers[0].batchInputShape[4] = cropped_slices_3d_w_pad.shape[2]
adjusted_input_shape = [
batchSize,
numOfChan,
res.layers[0].batchInputShape[2],
res.layers[0].batchInputShape[3],
res.layers[0].batchInputShape[4]
]
}
console.log(' Model batch input shape : ', res.layers[0].batchInputShape)
// -- batchInputShape {Array} input_shape - e.g. [?, D, H, W, Ch] or [?, Ch, D, H, W]
statData.Input_Shape = JSON.stringify(res.layers[0].batchInputShape)
statData.Output_Shape = JSON.stringify(res.output.shape)
statData.Channel_Last = isChannelLast
statData.Model_Param = await getModelNumParameters(res)
statData.Model_Layers = await getModelNumLayers(res)
statData.Model = modelEntry.modelName
statData.Seq_Conv = modelEntry.enableSeqConv
statData.Extra_Info = null
// Determine the number of output channels in the last layer of the model
// e.g. 3, 50, 104
const outputLayer = res.layers[res.layers.length - 1]
console.log('Output Layer : ', outputLayer)
const expected_Num_labels = isChannelLast
? outputLayer.outputShape[outputLayer.outputShape.length - 1]
: outputLayer.outputShape[1]
console.log('Num of output channels : ', expected_Num_labels)
const curTensor = []
curTensor[0] = await cropped_slices_3d_w_pad.reshape(adjusted_input_shape)
const timer = window.setInterval(async function () {
try {
if (res.layers[i].activation.getClassName() !== 'linear') {
curTensor[i] = await res.layers[i].apply(curTensor[i - 1])
} else {
curTensor[i] = await convByOutputChannelAndInputSlicing(
curTensor[i - 1],
res.layers[i].getWeights()[0],
res.layers[i].getWeights()[1],
res.layers[i].strides,
res.layers[i].padding,
res.layers[i].dilationRate,
3
) // important for memory use
}
tf.dispose(curTensor[i - 1])
} catch (err) {
const errTxt = 'Your graphics card (e.g. Intel) may not be compatible with WebGL. ' + err.message
callbackUI(errTxt, -1, errTxt)
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err.message
statData.Extra_Err_Info = 'Failed while model layer ' + i + ' apply'
callbackUI('', -1, '', statData)
return 0
}
console.log('layer output Tensor shape : ', curTensor[i].shape)
console.log('layer count params ', res.layers[i].countParams())
res.layers[i].dispose()
curTensor[i - 1].dispose()
callbackUI('Layer ' + i.toString(), (i + 1) / layersLength)
if (tf.memory().unreliable) {
const unreliableReasons = 'unreliable reasons :' + tf.memory().reasons
callbackUI(unreliableReasons, NaN, unreliableReasons)
}
if (i === layersLength - 2) {
// Stop before the last layer or classification layer.
window.clearInterval(timer)
// // Create an instance of SequentialConvLayer
// The second parameter is important for memory,
// the larger it is, the more memory it uses
// it was 8, but I set it to 3, got a different error
// let seqConvLayer = new SequentialConvLayer(res, 10, isChannelLast);
const seqConvLayer = await new SequentialConvLayer(res, 10, isChannelLast, callbackUI, false)
// Apply the last output tensor to the seq. instance
const outputTensor = await seqConvLayer.apply(curTensor[i])
callbackUI('seqConvLayer Done')
// -- document.getElementById("progressBarChild").style.width = 0 + "%";;
// Dispose the previous layer input tensor
tf.dispose(curTensor[i])
// delete the used class
// ? delete seqConvLayer;
// You can now use 'outputTensor' as needed
console.log(' Output tensor', outputTensor)
console.log(' Output tensor shape : ', outputTensor.shape)
// Array(3) [ 256, 256, 256 ]
if (outputTensor.shape.length !== 3) {
const msg = 'Output tensor shape should be 3 dims but it is ' + outputTensor.shape.length
callbackUI(msg, -1, msg)
}
console.log(' find array max ')
const curBatchMaxLabel = await outputTensor.max().dataSync()[0]
const Inference_t = ((performance.now() - startTime) / 1000).toFixed(4)
if (maxLabelPredicted < curBatchMaxLabel) {
maxLabelPredicted = curBatchMaxLabel
}
const numSegClasses = maxLabelPredicted + 1
console.log('Predicted num of segmentation classes', numSegClasses)
statData.Actual_Labels = numSegClasses
statData.Expect_Labels = expected_Num_labels
statData.NumLabels_Match = numSegClasses === expected_Num_labels
if (numSegClasses !== expected_Num_labels) {
const msg = 'expected ' + expected_Num_labels + ' labels, but the predicted are ' + numSegClasses
callbackUI(msg, -1, msg)
}
// -- Transpose back to original unpadded size
let outLabelVolume = outputTensor.reshape([
cropped_slices_3d_w_pad.shape[0],
cropped_slices_3d_w_pad.shape[1],
cropped_slices_3d_w_pad.shape[2]
])
tf.dispose(outputTensor)
// Transpose MRI data to be match pytorch/keras input output
if (transpose) {
console.log('outLabelVolume transposed')
outLabelVolume = outLabelVolume.transpose()
}
outLabelVolume = await removeZeroPaddingFrom3dTensor(outLabelVolume, pad, pad, pad)
console.log(' outLabelVolume without padding shape : ', outLabelVolume.shape)
outLabelVolume = await resizeWithZeroPadding(
outLabelVolume,
num_of_slices,
slice_height,
slice_width,
refVoxel,
boundVolSizeArr
)
console.log(' outLabelVolume final shape after resizing : ', outLabelVolume.shape)
// let filterOutWithPreMask = inferenceModelsList[$$("selectModel").getValue() - 1]["filterOutWithPreMask"];
const filterOutWithPreMask = modelEntry.filterOutWithPreMask
// To clean the skull area wrongly segmented inphase-2.
if (pipeline1_out != null && opts.isBrainCropMaskBased && filterOutWithPreMask) {
const bin = await binarizeVolumeDataTensor(pipeline1_out)
outLabelVolume = await outLabelVolume.mul(bin)
}
startTime = performance.now()
// Generate output volume or slices
console.log('Generating correct output')
let outimg
try {
const img = await new Uint32Array(outLabelVolume.dataSync())
const Vshape = outLabelVolume.shape
const Vtype = outLabelVolume.dtype
outimg = await generateOutputSlicesV2(
img,
Vshape,
Vtype,
num_of_slices,
numSegClasses,
slice_height,
slice_width,
modelEntry,
opts,
niftiImage
)
console.log(' Phase-2 num of tensors after generateOutputSlicesV2: ', tf.memory().numTensors)
tf.dispose(outLabelVolume)
tf.engine().endScope()
tf.engine().disposeVariables()
} catch (error) {
// -- Timing data to collect
tf.engine().endScope()
tf.engine().disposeVariables()
console.log('Error while generating output: ', error)
const msg = 'Failed while generating output due to limited browser memory available'
callbackUI(msg, -1, msg)
statData.Inference_t = Inference_t
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = error.message
statData.Extra_Err_Info = 'Failed while generating output'
callbackUI('', -1, '', statData)
return 0
}
const Postprocess_t = ((performance.now() - startTime) / 1000).toFixed(4)
console.log(
'Processing the whole brain volume in tfjs for multi-class output mask took : ',
((performance.now() - inferenceStartTime) / 1000).toFixed(4) + ' Seconds'
)
// -- Timing data to collect
statData.Inference_t = Inference_t
statData.Postprocess_t = Postprocess_t
statData.Status = 'OK'
callbackUI('', -1, '', statData)
callbackUI('Segmentation finished', 0)
callbackImg(outimg, opts, modelEntry)
return 0
} else {
i++
}
}, delay)
} catch (err) {
callbackUI(err.message, -1, err.message)
console.log(
'If webgl context is lost, try to restore webgl context by visit the link ' +
'<a href="https://support.biodigital.com/hc/en-us/articles/218322977-How-to-turn-on-WebGL-in-my-browser">here</a>'
)
if (tf.memory().unreliable) {
const unreliableReasons = 'unreliable reasons :' + tf.memory().reasons
callbackUI(unreliableReasons, NaN, unreliableReasons)
}
}
}
async function inferenceFullVolumePhase2(
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
pipeline1_out,
modelEntry,
statData,
opts,
callbackImg,
callbackUI,
niftiImage
) {
let outimg = []
// --Phase-2, After remove the skull try to allocate brain volume and make inferece
console.log(' ---- Start FullVolume inference phase-II ---- ')
const quantileNorm = modelEntry.enableQuantileNorm
if (quantileNorm) {
// Quantile normalize function needs specific models to be used
console.log('preModel Quantile normalization enabled')
slices_3d = await quantileNormalizeVolumeData(slices_3d)
} else {
// Min Max Nomalize MRI data to be from 0 to 1
console.log('preModel Min Max normalization enabled')
slices_3d = await minMaxNormalizeVolumeData(slices_3d)
}
let mask_3d
if (pipeline1_out == null) {
// preModel is null
// Check if thresholding the MRI to remove noisy voxels for better cropping is needed.
const autoThresholdValue = modelEntry.autoThreshold
if (autoThresholdValue > 0 && autoThresholdValue <= 1) {
// Filtered MRI from noisy voxel below autoThresholdValue
mask_3d = await applyMriThreshold(slices_3d, autoThresholdValue)
} else {
console.log('No valid crop threshold value')
// binarize original image
mask_3d = await slices_3d.greater([0]).asType('bool')
}
} else {
mask_3d = pipeline1_out.greater([0]).asType('bool')
// -- pipeline1_out.dispose()
}
console.log(' mask_3d shape : ', mask_3d.shape)
const [row_min, row_max, col_min, col_max, depth_min, depth_max] = await firstLastNonZero3D(mask_3d)
mask_3d.dispose()
// -- Reference voxel that cropped volume started slice with it
const refVoxel = [row_min, col_min, depth_min]
console.log('refVoxel :', refVoxel)
// -- Starting form refVoxel, size of bounding volume
const boundVolSizeArr = [row_max - row_min + 1, col_max - col_min + 1, depth_max - depth_min + 1]
console.log('boundVolSizeArr :', boundVolSizeArr)
// -- Extract 3d object (e.g. brain)
const cropped_slices_3d = slices_3d.slice(
[row_min, col_min, depth_min],
[row_max - row_min + 1, col_max - col_min + 1, depth_max - depth_min + 1]
)
slices_3d.dispose()
// -- Padding size add to cropped brain
const pad = modelEntry.cropPadding
// Create margin around the bounding volume
let cropped_slices_3d_w_pad = await addZeroPaddingTo3dTensor(cropped_slices_3d, [pad, pad], [pad, pad], [pad, pad])
console.log(' cropped slices_3d with padding shape: ', cropped_slices_3d_w_pad.shape)
cropped_slices_3d.dispose()
// -- Test dim after padding ..
// for (let i = 0; i < cropped_slices_3d_w_pad.rank; i++) {
// if(cropped_slices_3d_w_pad.shape[i] > 256) {
// console.log(" cropped_slices_3d_w_pad > 256 ")
// }
// }
if (opts.drawBoundingVolume) {
let testVol = await removeZeroPaddingFrom3dTensor(cropped_slices_3d_w_pad, pad, pad, pad)
console.log(' outLabelVolume without padding shape : ', testVol.shape)
testVol = await resizeWithZeroPadding(testVol, num_of_slices, slice_height, slice_width, refVoxel, boundVolSizeArr)
console.log(' outLabelVolume final shape after resizing : ', testVol.shape)
draw3dObjBoundingVolume(tf.unstack(testVol), opts, modelEntry, callbackImg)
testVol.dispose()
return 0
}
statData.Brainchop_Ver = 'FullVolume'
let startTime = performance.now()
let adjusted_input_shape = []
const res = await model
try {
startTime = performance.now()
const inferenceStartTime = performance.now()
// maxLabelPredicted in whole volume of the brain
let maxLabelPredicted = 0
const transpose = modelEntry.enableTranspose
const delay = modelEntry.inferenceDelay
console.log('Inference delay :', delay)
if (transpose) {
cropped_slices_3d_w_pad = cropped_slices_3d_w_pad.transpose()
console.log('Input transposed for pre-model')
} else {
console.log('Transpose not enabled for pre-model')
}
let i = 1
const layersLength = res.layers.length
console.log('res.layers.length ', layersLength)
const isChannelLast = await isModelChnlLast(res)
const batchSize = opts.batchSize
const numOfChan = opts.numOfChan
// -- Adjust model input shape
if (isChannelLast) {
res.layers[0].batchInputShape[1] = cropped_slices_3d_w_pad.shape[0]
res.layers[0].batchInputShape[2] = cropped_slices_3d_w_pad.shape[1]
res.layers[0].batchInputShape[3] = cropped_slices_3d_w_pad.shape[2]
adjusted_input_shape = [
batchSize,
res.layers[0].batchInputShape[1],
res.layers[0].batchInputShape[2],
res.layers[0].batchInputShape[3],
numOfChan
]
} else {
res.layers[0].batchInputShape[2] = cropped_slices_3d_w_pad.shape[0]
res.layers[0].batchInputShape[3] = cropped_slices_3d_w_pad.shape[1]
res.layers[0].batchInputShape[4] = cropped_slices_3d_w_pad.shape[2]
adjusted_input_shape = [
batchSize,
numOfChan,
res.layers[0].batchInputShape[2],
res.layers[0].batchInputShape[3],
res.layers[0].batchInputShape[4]
]
}
console.log(' Model batch input shape : ', res.layers[0].batchInputShape)
// -- batchInputShape {Array} input_shape - e.g. [?, D, H, W, Ch] or [?, Ch, D, H, W]
statData.Input_Shape = JSON.stringify(res.layers[0].batchInputShape)
statData.Output_Shape = JSON.stringify(res.output.shape)
statData.Channel_Last = isChannelLast
statData.Model_Param = await getModelNumParameters(res)
statData.Model_Layers = await getModelNumLayers(res)
statData.Model = modelEntry.modelName
statData.Extra_Info = null
const curTensor = []
curTensor[0] = cropped_slices_3d_w_pad.reshape(adjusted_input_shape)
const timer = window.setInterval(async function () {
try {
curTensor[i] = res.layers[i].apply(curTensor[i - 1])
} catch (err) {
callbackUI(err.message, -1, err.message)
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err.message
statData.Extra_Err_Info = 'Failed while model layer ' + i + ' apply'
callbackUI('', -1, '', statData)
return 0
}
callbackUI('Layer ' + i.toString(), (i + 1) / layersLength)
console.log('layer output Tensor shape : ', curTensor[i].shape)
console.log('layer count params ', res.layers[i].countParams())
res.layers[i].dispose()
curTensor[i - 1].dispose()
if (tf.memory().unreliable) {
const unreliableReasons = 'unreliable reasons :' + tf.memory().reasons
callbackUI(unreliableReasons, NaN, unreliableReasons)
}
if (i === layersLength - 1) {
window.clearInterval(timer)
const axis = isChannelLast ? -1 : 1
console.log(' find argmax ')
console.log('last Tensor shape : ', curTensor[i].shape)
// -- curTensor[i].shape e.g. [ 1, 256, 256, 256, 3 ]
const expected_Num_labels = isChannelLast ? curTensor[i].shape[4] : curTensor[i].shape[1]
let prediction_argmax
// Try for argMax with model output tensor.
try {
const argMaxTime = performance.now()
console.log(' Try tf.argMax for fullVolume ..')
prediction_argmax = tf.argMax(curTensor[i], axis)
console.log('tf.argMax for fullVolume takes : ', ((performance.now() - argMaxTime) / 1000).toFixed(4))
} catch (err1) {
// if channel last
if (axis === -1) {
try {
const argMaxLargeTime = performance.now()
console.log(' tf.argMax failed .. try argMaxLarge ..')
window.alert('tensor2LightBuffer() is not dead code?')
window.alert('argMaxLarge() is not dead code?')
console.log(
'argMaxLarge for fullVolume takes : ',
((performance.now() - argMaxLargeTime) / 1000).toFixed(4)
)
} catch (err2) {
const errTxt = "argMax buffer couldn't be created due to limited memory resources."
callbackUI(errTxt, -1, errTxt)
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err2.message
statData.Extra_Err_Info = 'prediction_argmax from argMaxLarge failed'
callbackUI('', -1, '', statData)
return 0
}
} else {
// if channel first ..
const errTxt = "argMax buffer couldn't be created due to limited memory resources."
callbackUI(errTxt, -1, errTxt)
prediction_argmax.dispose()
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err1.message
statData.Extra_Err_Info = 'prediction_argmax from argMaxLarge not support yet channel first'
callbackUI('', -1, '', statData)
return 0
}
}
console.log(' prediction_argmax shape : ', prediction_argmax.shape)
// -- prediction_argmax.shape : [ 1, 256, 256, 256]
const Inference_t = ((performance.now() - startTime) / 1000).toFixed(4)
// outputDataBeforArgmx = Array.from(prediction_argmax.dataSync())
tf.dispose(curTensor[i])
// allPredictions.push({"id": allBatches[j].id, "coordinates": allBatches[j].coordinates, "data": Array.from(prediction_argmax.dataSync()) })
const curBatchMaxLabel = await prediction_argmax.max().dataSync()[0]
if (maxLabelPredicted < curBatchMaxLabel) {
maxLabelPredicted = curBatchMaxLabel
}
const numSegClasses = maxLabelPredicted + 1
console.log('numSegClasses', numSegClasses)
statData.Actual_Labels = numSegClasses
statData.Expect_Labels = expected_Num_labels
statData.NumLabels_Match = numSegClasses === expected_Num_labels
if (numSegClasses !== expected_Num_labels) {
// errTxt = "expected " + expected_Num_labels + " labels, but the predicted are " + numSegClasses + ". For possible solutions please refer to <a href='https://github.com/neuroneural/brainchop/wiki/FAQ#Q3' target='_blank'><b> FAQ </b></a>.", "alert-error"
const errTxt = 'expected ' + expected_Num_labels + ' labels, but the predicted are ' + numSegClasses
callbackUI(errTxt, -1, errTxt)
}
// -- Transpose back to original unpadded size
let outLabelVolume = prediction_argmax.reshape([
cropped_slices_3d_w_pad.shape[0],
cropped_slices_3d_w_pad.shape[1],
cropped_slices_3d_w_pad.shape[2]
])
tf.dispose(prediction_argmax)
// Transpose MRI data to be match pytorch/keras input output
if (transpose) {
console.log('outLabelVolume transposed')
outLabelVolume = outLabelVolume.transpose()
}
outLabelVolume = await removeZeroPaddingFrom3dTensor(outLabelVolume, pad, pad, pad)
console.log(' outLabelVolume without padding shape : ', outLabelVolume.shape)
outLabelVolume = await resizeWithZeroPadding(
outLabelVolume,
num_of_slices,
slice_height,
slice_width,
refVoxel,
boundVolSizeArr
)
console.log(' outLabelVolume final shape after resizing : ', outLabelVolume.shape)
const filterOutWithPreMask = modelEntry.filterOutWithPreMask
// To clean the skull area wrongly segmented in phase-2.
if (pipeline1_out != null && opts.isBrainCropMaskBased && filterOutWithPreMask) {
const bin = binarizeVolumeDataTensor(pipeline1_out)
outLabelVolume = outLabelVolume.mul(bin)
}
startTime = performance.now()
// Generate output volume or slices
console.log('Generating correct output')
try {
const img = new Uint32Array(outLabelVolume.dataSync())
const Vshape = outLabelVolume.shape
const Vtype = outLabelVolume.dtype
tf.dispose(outLabelVolume)
tf.engine().endScope()
tf.engine().disposeVariables()
outimg = await generateOutputSlicesV2(
img,
Vshape,
Vtype,
num_of_slices,
numSegClasses,
slice_height,
slice_width,
modelEntry,
opts,
niftiImage
)
console.log(' Phase-2 num of tensors after generateOutputSlicesV2: ', tf.memory().numTensors)
} catch (error) {
// -- Timing data to collect
tf.engine().endScope()
tf.engine().disposeVariables()
const errTxt = 'Failed while generating output due to limited browser memory available'
callbackUI(errTxt, -1, errTxt)
statData.Inference_t = Inference_t
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = error.message
statData.Extra_Err_Info = 'Failed while generating output'
callbackUI('', -1, '', statData)
return 0
}
const Postprocess_t = ((performance.now() - startTime) / 1000).toFixed(4)
// tf.engine().endScope()
tf.engine().disposeVariables()
console.log(
'Processing the whole brain volume in tfjs for multi-class output mask took : ',
((performance.now() - inferenceStartTime) / 1000).toFixed(4) + ' Seconds'
)
// -- Timing data to collect
statData.Inference_t = Inference_t
statData.Postprocess_t = Postprocess_t
statData.Status = 'OK'
callbackUI('', -1, '', statData)
clearInterval(timer)
callbackUI('Segmentation finished', 0)
callbackImg(outimg, opts, modelEntry)
return 0
}
i++
}, delay)
} catch (err) {
callbackUI(err.message, -1, err.message)
console.log(
'If webgl context is lost, try to restore webgl context by visit the link ' +
'<a href="https://support.biodigital.com/hc/en-us/articles/218322977-How-to-turn-on-WebGL-in-my-browser">here</a>'
)
}
// })
}
async function inferenceFullVolumePhase1(
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
isModelFullVol,
modelEntry,
statData,
opts,
callbackImg,
callbackUI,
niftiImage
) {
statData.No_SubVolumes = 1
// load pre-model for inference first, can be null if no pre-model such as GWM models
if (modelEntry.preModelId) {
const preModel = await load_model(opts.rootURL + inferenceModelsList[modelEntry.preModelId - 1].path)
const transpose = inferenceModelsList[modelEntry.preModelId - 1].enableTranspose
const quantileNorm = inferenceModelsList[modelEntry.preModelId - 1].enableQuantileNorm
let preModel_slices_3d = null
// -- If pre-model is not null then slices_3d mask will be generated..
// -- The mask is needed to remove the skull and set noise in background to 0, and get the brain bounding volume properly
const slices_3d_mask = null
if (quantileNorm) {
// Quantile normalize function needs specific models to be used
console.log('preModel Quantile normalization enabled')
preModel_slices_3d = await quantileNormalizeVolumeData(slices_3d)
} else {
// Min Max Nomalize MRI data to be from 0 to 1
console.log('preModel Min Max normalization enabled')
preModel_slices_3d = await minMaxNormalizeVolumeData(slices_3d)
}
// -- Transpose MRI data to be match pytorch/keras input output
// -- Check if pre-model needs transpose..
if (transpose) {
preModel_slices_3d = await preModel_slices_3d.transpose()
console.log('Input transposed for pre-model')
} else {
console.log('Transpose not enabled for pre-model')
}
statData.Brainchop_Ver = 'PreModel_FV' // e.g. "PreModel_FV"
// preModel.then(function (res) {
const res = await preModel
try {
const inferenceStartTime = performance.now()
const preModelObject = res
// read input shape from model.json object
const preModelBatchInputShape = preModelObject.layers[0].batchInputShape
console.log(' Pre-Model batch input shape : ', preModelBatchInputShape)
// -- Verify input shape
if (preModelBatchInputShape.length !== 5) {
const errTxt = 'The pre-model input shape must be 5D '
callbackUI(errTxt, -1, errTxt)
return 0
}
const isPreModelChannelLast = isModelChnlLast(preModelObject)
const batchSize = opts.batchSize
const numOfChan = opts.numOfChan
let batch_D, batch_H, batch_W
let preModel_input_shape
if (isPreModelChannelLast) {
console.log('Pre-Model Channel Last')
if (isNaN(preModelBatchInputShape[4]) || preModelBatchInputShape[4] !== 1) {
const errTxt = 'The number of channels for pre-model input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
batch_D = preModelBatchInputShape[1]
batch_H = preModelBatchInputShape[2]
batch_W = preModelBatchInputShape[3]
preModel_input_shape = [batchSize, batch_D, batch_H, batch_W, numOfChan]
} else {
console.log('Pre-Model Channel First')
if (isNaN(preModelBatchInputShape[1]) || preModelBatchInputShape[1] !== 1) {
const errTxt = 'The number of channels for pre-model input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
batch_D = preModelBatchInputShape[2]
batch_H = preModelBatchInputShape[3]
batch_W = preModelBatchInputShape[4]
preModel_input_shape = [batchSize, numOfChan, batch_D, batch_H, batch_W]
}
statData.Input_Shape = JSON.stringify(preModel_input_shape)
statData.Output_Shape = JSON.stringify(preModelObject.output.shape)
statData.Channel_Last = isPreModelChannelLast
statData.Model_Param = await getModelNumParameters(preModelObject)
statData.Model_Layers = await getModelNumLayers(preModelObject)
// maxLabelPredicted in whole volume of the brain
let maxLabelPredicted = 0
const delay = inferenceModelsList[modelEntry.preModelId - 1].inferenceDelay
let i = 1
const layersLength = res.layers.length
const curTensor = []
// -- reshape MRI to model input shape
curTensor[0] = preModel_slices_3d.reshape(preModel_input_shape)
// Dispose the volume
tf.dispose(preModel_slices_3d)
const timer = window.setInterval(async function () {
try {
curTensor[i] = await res.layers[i].apply(curTensor[i - 1])
} catch (err) {
const errTxt = 'Your graphics card (e.g. Intel) may not be compatible with WebGL. ' + err.message
callbackUI(errTxt, -1, errTxt)
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err.message
statData.Extra_Err_Info = 'PreModel Failed while model layer ' + i + ' apply'
callbackUI('', -1, '', statData)
return 0
}
res.layers[i].dispose()
curTensor[i - 1].dispose()
callbackUI('Layer ' + i.toString(), (i + 1) / layersLength)
if (tf.memory().unreliable) {
const unreliableReasons = 'unreliable reasons :' + tf.memory().reasons
callbackUI(unreliableReasons, NaN, unreliableReasons)
}
if (i === layersLength - 1) {
window.clearInterval(timer)
// -- prediction = res.layers[res.layers.length-1].apply(curTensor[i])
// -- curTensor[i].print()
// -- outputDataBeforArgmx = Array.from(curTensor[i].dataSync())
const axis = isPreModelChannelLast ? -1 : 1
console.log(' find argmax ')
console.log('last Tensor shape : ', curTensor[i].shape)
// -- curTensor[i].shape : [ 1, 256, 256, 256, 3 ]
const expected_Num_labels = isPreModelChannelLast ? curTensor[i].shape[4] : curTensor[i].shape[1]
let prediction_argmax
// Try for argMax with model output tensor.
try {
console.log(' Try tf.argMax for fullVolume ..')
prediction_argmax = await tf.argMax(curTensor[i], axis)
} catch (err1) {
// if channel last
if (axis === -1) {
try {
const argMaxLargeTime = performance.now()
console.log(' tf.argMax failed .. try argMaxLarge ..')
window.alert('tensor2LightBuffer() is not dead code?')
window.alert('argMaxLarge() is not dead code?')
console.log(
'argMaxLarge for fullVolume takes : ',
((performance.now() - argMaxLargeTime) / 1000).toFixed(4)
)
} catch (err2) {
const errTxt = "argMax buffer couldn't be created due to limited memory resources."
callbackUI(errTxt, -1, errTxt)
prediction_argmax.dispose()
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err2.message
statData.Extra_Err_Info = 'preModel prediction_argmax from argMaxLarge failed'
callbackUI('', -1, '', statData)
return 0
}
} else {
// if channel first ..
const errTxt = "argMax buffer couldn't be created due to limited memory resources."
callbackUI(errTxt, -1, errTxt)
prediction_argmax.dispose()
window.clearInterval(timer)
tf.engine().endScope()
tf.engine().disposeVariables()
statData.Inference_t = Infinity
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = err1.message
statData.Extra_Err_Info = 'preModel prediction_argmax from argMaxLarge not support yet channel first'
callbackUI('', -1, '', statData)
return 0
}
}
console.log(' Pre-model prediction_argmax shape : ', prediction_argmax.shape)
// -- prediction_argmax.shape : [ 1, 256, 256, 256]
const Inference_t = ((performance.now() - inferenceStartTime) / 1000).toFixed(4)
tf.dispose(curTensor[i])
console.log(' Pre-model find array max ')
const curBatchMaxLabel = await prediction_argmax.max().dataSync()[0]
if (maxLabelPredicted < curBatchMaxLabel) {
maxLabelPredicted = curBatchMaxLabel
}
const numSegClasses = maxLabelPredicted + 1
console.log('Pre-model numSegClasses', numSegClasses)
statData.Actual_Labels = numSegClasses
statData.Expect_Labels = expected_Num_labels
statData.NumLabels_Match = numSegClasses === expected_Num_labels
// -- Transpose back to original unpadded size
let outLabelVolume = await prediction_argmax.reshape([num_of_slices, slice_height, slice_width])
tf.dispose(prediction_argmax)
// Transpose MRI data to be match pytorch/keras input output
if (transpose) {
console.log('Pre-model outLabelVolume transposed')
outLabelVolume = outLabelVolume.transpose()
}
const startTime = performance.now()
// Generate output volume or slices
console.log('Generating pre-model output')
let slices_3d_mask
try {
const unstackOutVolumeTensor = await tf.unstack(outLabelVolume)
slices_3d_mask = await generateBrainMask(
unstackOutVolumeTensor,
num_of_slices,
slice_height,
slice_width,
modelEntry,
opts,
callbackUI,
callbackImg,
false
)
await tf.dispose(outLabelVolume)
console.log(' Phase-1 num of tensors after generateBrainMask: ', tf.memory().numTensors)
} catch (error) {
// -- Timing data to collect
tf.engine().endScope()
tf.engine().disposeVariables()
const errTxt = 'Failed while generating pre-model output due to limited browser memory available'
callbackUI(errTxt, -1, errTxt)
statData.Inference_t = Inference_t
statData.Postprocess_t = Infinity
statData.Status = 'Fail'
statData.Error_Type = error.message
statData.Extra_Err_Info = 'Pre-model failed while generating output'
callbackUI('', -1, '', statData)
return 0
}
const Postprocess_t = ((performance.now() - startTime) / 1000).toFixed(4)
console.log(
'Pre-model processing the whole brain volume in tfjs tooks for multi-class output mask : ',
((performance.now() - inferenceStartTime) / 1000).toFixed(4) + ' Seconds'
)
// -- Timing data to collect
statData.Inference_t = Inference_t
statData.Postprocess_t = Postprocess_t
statData.Status = 'OK'
callbackUI('', -1, '', statData)
if (slices_3d_mask == null) {
const msg = 'slice_3d_mask failed ...'
callbackUI(msg, -1, msg)
return 0
} else {
// --Phase-2, After remove the skull try to allocate brain volume and make inferece
console.log('--- pre-model done ---')
// --mask_3d = slices_3d_mask.greater([0]).asType('bool')
// --slices_3d_mask.dispose()
if (isModelFullVol) {
if (modelEntry.enableSeqConv) {
// Mask cropping & seq conv
// Non-Atlas model (e.g. GWM) needs sequential convolution layer.
// Sequential convolution layer to be used after cropping - slow but reliable on most machines
console.log('------ Mask Cropping & Seq Convoluton ------')
await inferenceFullVolumeSeqCovLayerPhase2(
opts,
modelEntry,
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
slices_3d_mask,
callbackUI,
callbackImg,
statData,
niftiImage
)
return 0
// inferenceFullVolumeSeqCovLayerPhase2(model, slices_3d.transpose(), num_of_slices, slice_height, slice_width, slices_3d_mask)
} else {
// Mask cropping BUT no seq conv
console.log('------ Mask Cropping - NO Seq Convoluton ------')
await inferenceFullVolumePhase2(
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
slices_3d_mask,
modelEntry,
statData,
opts,
callbackImg,
callbackUI,
niftiImage
)
// inferenceFullVolumePhase2(model, slices_3d.transpose(), num_of_slices, slice_height, slice_width, slices_3d_mask)
}
} else {
// -- In version 3.0.0 this function not used
window.alert('inferenceSubVolumes() is not dead code?')
}
}
}
i++
}, delay)
} catch (err) {
callbackUI(err.message, -1, err.message)
console.log(
'If webgl context is lost, try to restore webgl context by visit the link ' +
'<a href="https://support.biodigital.com/hc/en-us/articles/218322977-How-to-turn-on-WebGL-in-my-browser">here</a>'
)
// document.getElementById("webGl2Status").style.backgroundColor = isWebGL2ContextLost() ? "Red" : "Green"
// document.getElementById("memoryStatus").style.backgroundColor = tf.memory().unreliable ? "Red" : "Green"
}
// })
// -- if(...) end
} else {
// No preModel
// --Phase-2, After remove the skull try to allocate brain volume and make inferece
console.log('--- No pre-model is selected ---')
console.log('------ Run voxel cropping ------')
// -- mask_3d = slices_3d.greater([0]).asType('bool')
if (isModelFullVol) {
if (modelEntry.enableSeqConv) {
// Voxel cropping & seq conv
// Non-Atlas model (e.g. GWM) needs sequential convolution layer.
// Sequential convolution layer to be used after cropping - slow but reliable on most machines
console.log('------ Seq Convoluton ------')
await inferenceFullVolumeSeqCovLayerPhase2(
opts,
modelEntry,
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
null,
callbackUI,
callbackImg,
statData,
niftiImage
)
} else {
// Voxel cropping BUT no seq conv
// todo: we do not use result const outimg = await
inferenceFullVolumePhase2(
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
null,
modelEntry,
statData,
opts,
callbackImg,
callbackUI,
niftiImage
)
}
} else {
// -- In version 3.0.0 this function not used
window.alert('inferenceSubVolumes() is not dead code?')
}
}
}
async function enableProductionMode(textureF16Flag = true) {
// -- tf.setBackend('cpu')
// -- tf.removeBackend('cpu')
// -- Calling enableProdMode() method
await tf.enableProdMode()
// -- Setting debug mode of the environment
tf.env().set('DEBUG', false)
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', -1)
// -- tf.env().set('WEBGL_PACK', false)
// -- Put ready after sets above
await tf.ready()
// -- Printing output
console.log('tf env() flags :', tf.env().flags)
console.log('tf env() features :', tf.env().features)
console.log('tf env total features: ', Object.keys(tf.env().features).length)
console.log(tf.getBackend())
}
export async function runInference(opts, modelEntry, niftiHeader, niftiImage, callbackImg, callbackUI) {
const statData = []
statData.startTime = Date.now() // for common webworker/mainthread do not use performance.now()
callbackUI('Segmentation started', 0)
const startTime = performance.now()
const batchSize = opts.batchSize
const numOfChan = opts.numOfChan
if (isNaN(batchSize) || batchSize !== 1) {
const errTxt = 'The batch Size for input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
if (isNaN(numOfChan) || numOfChan !== 1) {
const errTxt = 'The number of channels for input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
tf.engine().startScope()
console.log('Batch size: ', batchSize)
console.log('Num of Channels: ', numOfChan)
const model = await load_model(opts.rootURL + modelEntry.path)
await enableProductionMode(true)
statData.TF_Backend = tf.getBackend()
const modelObject = model
let batchInputShape = []
// free global variable of 16777216 voxel
// allOutputSlices3DCC1DimArray = []
// outputSceneRendered = false
// read input shape from model.json object
batchInputShape = modelObject.layers[0].batchInputShape
console.log(' Model batch input shape : ', batchInputShape)
// -- Verify input shape
if (batchInputShape.length !== 5) {
const errTxt = 'The model input shape must be 5D'
callbackUI(errTxt, -1, errTxt)
return 0
}
let batch_D, batch_H, batch_W
const slice_width = niftiHeader.dims[1]
const slice_height = niftiHeader.dims[2]
const num_of_slices = niftiHeader.dims[3]
const isChannelLast = await isModelChnlLast(modelObject)
if (isChannelLast) {
console.log('Model Channel Last')
if (isNaN(batchInputShape[4]) || batchInputShape[4] !== 1) {
const errTxt = 'The number of channels for input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
batch_D = batchInputShape[1]
batch_H = batchInputShape[2]
batch_W = batchInputShape[3]
} else {
console.log('Model Channel First')
if (isNaN(batchInputShape[1]) || batchInputShape[1] !== 1) {
const errTxt = 'The number of channels for input shape must be 1'
callbackUI(errTxt, -1, errTxt)
return 0
}
batch_D = batchInputShape[2]
batch_H = batchInputShape[3]
batch_W = batchInputShape[4]
}
// const input_shape = [batchSize, numOfChan, batch_D, batch_H, batch_W]
// //-- Atlas version check
// if ( (batch_D > 30) && (batch_H == 256) && (batch_W == 256) ) {
// const errTxt = "The subvolume dimension in z-axis shouldn't exceed 30 number of slices for browser limitation"
// callbackUI(errTxt, -1, errTxt)
// return 0
// }
// --Check whether the model will make inference at once as FullVolumeModel
let isModelFullVol
if (batch_D === 256 && batch_H === 256 && batch_W === 256) {
isModelFullVol = true
} else {
isModelFullVol = false
}
statData.isModelFullVol = isModelFullVol
// Model output number of segmentations
let slices_3d = await getAllSlicesDataAsTF3D(num_of_slices, niftiHeader, niftiImage)
const transpose = modelEntry.enableTranspose
const enableCrop = modelEntry.enableCrop
if (isModelFullVol) {
if (enableCrop) {
// FullVolume with Crop option before inference ..
// pre-model to mask the volume, can also be null and the cropping will be on the MRI.
await inferenceFullVolumePhase1(
model,
slices_3d,
num_of_slices,
slice_height,
slice_width,
isModelFullVol,
modelEntry,
statData,
opts,
callbackImg,
callbackUI,
niftiImage
)
} else {
// Transpose MRI data to be match pytorch/keras input output
console.log('Cropping Disabled')
if (transpose) {
slices_3d = slices_3d.transpose()
console.log('Input transposed')
} else {
console.log('Transpose NOT Enabled')
}
const enableSeqConv = modelEntry.enableSeqConv
if (enableSeqConv) {
console.log('Seq Convoluton Enabled')
window.alert('inferenceFullVolumeSeqCovLayer() is not dead code?')
} else {
console.log('Seq Convoluton Disabled')
window.alert('inferenceFullVolume() is not dead code?')
}
}
}
}
