diff --git a/package-lock.json b/package-lock.json index 62a3d34..ee9518d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "alvinn", - "version": "0.2.1", + "version": "0.3.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "alvinn", - "version": "0.2.1", + "version": "0.3.0", "hasInstallScript": true, "license": "UNLICENSED", "dependencies": { diff --git a/src/models/thorax-0.1.0-n640/classes.json b/src/models/thorax-0.1.0-n640/classes.json new file mode 100644 index 0000000..ff6c63d --- /dev/null +++ b/src/models/thorax-0.1.0-n640/classes.json @@ -0,0 +1,43 @@ +[ + "Abdominal diaphragm", + "Aorta", + "Azygous vein", + "Brachiocephalic trunk", + "Caudal vena cava", + "Cranial vena cava", + "Esophagus", + "External abdominal oblique", + "Iliocostalis", + "Latissimus dorsi", + "Left atrium", + "Left auricle", + "Left lung", + "Left subclavian artery", + "Left ventricle", + "Longissimus", + "Pectoralis profundus", + "Pectoralis superficialis", + "Pericardium", + "Phrenic nerve", + "Primary bronchus", + "Pulmonary artery", + "Pulmonary trunk", + "Pulmonary vein", + "Rectus abdominis", + "Rectus thoracis", + "Recurrent laryngeal nerve", + "Rhomboideus", + "Right atrium", + "Right auricle", + "Right lung", + "Right ventricle", + "Scalenus", + "Serratus dorsalis caudalis", + "Serratus dorsalis cranialis", + "Serratus ventralis", + "Spinalis", + "Sympathetic chain", + "Trachea", + "Trapezius", + "Vagus nerve" +] \ No newline at end of file diff --git a/src/models/thorax-0.1.0-n640/group1-shard1of3.bin b/src/models/thorax-0.1.0-n640/group1-shard1of3.bin new file mode 100644 index 0000000..a7d822a Binary files /dev/null and b/src/models/thorax-0.1.0-n640/group1-shard1of3.bin differ diff --git a/src/models/thorax-0.1.0-n640/group1-shard2of3.bin b/src/models/thorax-0.1.0-n640/group1-shard2of3.bin new file mode 100644 index 0000000..e7a09fc Binary files /dev/null and b/src/models/thorax-0.1.0-n640/group1-shard2of3.bin differ diff --git a/src/models/thorax-0.1.0-n640/group1-shard3of3.bin b/src/models/thorax-0.1.0-n640/group1-shard3of3.bin new file mode 100644 index 0000000..8d63b16 Binary files /dev/null and b/src/models/thorax-0.1.0-n640/group1-shard3of3.bin differ diff --git a/src/models/thorax-0.1.0-n640/metadata.yaml b/src/models/thorax-0.1.0-n640/metadata.yaml new file mode 100644 index 0000000..3b05b37 --- /dev/null +++ b/src/models/thorax-0.1.0-n640/metadata.yaml @@ -0,0 +1,54 @@ +description: Ultralytics thorax-0.1.0-n model trained on /data/ALVINN/Thorax/Thorax + 0.1.0/thorax.yaml +author: Ultralytics +license: AGPL-3.0 https://ultralytics.com/license +date: '2024-02-29T21:26:09.903031' +version: 8.1.19 +stride: 32 +task: detect +batch: 1 +imgsz: +- 640 +- 640 +names: + 0: Abdominal diaphragm + 1: Aorta + 2: Azygous vein + 3: Brachiocephalic trunk + 4: Caudal vena cava + 5: Cranial vena cava + 6: Esophagus + 7: External abdominal oblique + 8: Iliocostalis + 9: Latissimus dorsi + 10: Left atrium + 11: Left auricle + 12: Left lung + 13: Left subclavian artery + 14: Left ventricle + 15: Longissimus + 16: Pectoralis profundus + 17: Pectoralis superficialis + 18: Pericardium + 19: Phrenic nerve + 20: Primary bronchus + 21: Pulmonary artery + 22: Pulmonary trunk + 23: Pulmonary vein + 24: Rectus abdominis + 25: Rectus thoracis + 26: Recurrent laryngeal nerve + 27: Rhomboideus + 28: Right atrium + 29: Right auricle + 30: Right lung + 31: Right ventricle + 32: Scalenus + 33: Serratus dorsalis caudalis + 34: Serratus dorsalis cranialis + 35: Serratus ventralis + 36: Spinalis + 37: Sympathetic chain + 38: Trachea + 39: Trapezius + 40: Vagus nerve diff --git a/src/models/thorax-0.1.0-n640/model.json b/src/models/thorax-0.1.0-n640/model.json new file mode 100644 index 0000000..8ffe7a3 --- /dev/null +++ b/src/models/thorax-0.1.0-n640/model.json @@ -0,0 +1 @@ +{"format": "graph-model", "generatedBy": "2.9.0", "convertedBy": "TensorFlow.js Converter v3.15.0", "signature": {"outputs": 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{"name": "PartitionedCall/model/output0/concat/axis", "shape": [], "dtype": "int32"}]}]} \ No newline at end of file diff --git a/src/models/thorax-0.1.0-n960/classes.json b/src/models/thorax-0.1.0-n960/classes.json new file mode 100644 index 0000000..ff6c63d --- /dev/null +++ b/src/models/thorax-0.1.0-n960/classes.json @@ -0,0 +1,43 @@ +[ + "Abdominal diaphragm", + "Aorta", + "Azygous vein", + "Brachiocephalic trunk", + "Caudal vena cava", + "Cranial vena cava", + "Esophagus", + "External abdominal oblique", + "Iliocostalis", + "Latissimus dorsi", + "Left atrium", + "Left auricle", + "Left lung", + "Left subclavian artery", + "Left ventricle", + "Longissimus", + "Pectoralis profundus", + "Pectoralis superficialis", + "Pericardium", + "Phrenic nerve", + "Primary bronchus", + "Pulmonary artery", + "Pulmonary trunk", + "Pulmonary vein", + "Rectus abdominis", + "Rectus thoracis", + "Recurrent laryngeal nerve", + "Rhomboideus", + "Right atrium", + "Right auricle", + "Right lung", + "Right ventricle", + "Scalenus", + "Serratus dorsalis caudalis", + "Serratus dorsalis cranialis", + "Serratus ventralis", + "Spinalis", + "Sympathetic chain", + "Trachea", + "Trapezius", + "Vagus nerve" +] \ No newline at end of file diff --git a/src/models/thorax-0.1.0-n960/group1-shard1of3.bin b/src/models/thorax-0.1.0-n960/group1-shard1of3.bin new file mode 100644 index 0000000..f9a70a2 Binary files /dev/null and b/src/models/thorax-0.1.0-n960/group1-shard1of3.bin differ diff --git a/src/models/thorax-0.1.0-n960/group1-shard2of3.bin b/src/models/thorax-0.1.0-n960/group1-shard2of3.bin new file mode 100644 index 0000000..018027d Binary files /dev/null and b/src/models/thorax-0.1.0-n960/group1-shard2of3.bin differ diff --git a/src/models/thorax-0.1.0-n960/group1-shard3of3.bin b/src/models/thorax-0.1.0-n960/group1-shard3of3.bin new file mode 100644 index 0000000..3494196 Binary files /dev/null and b/src/models/thorax-0.1.0-n960/group1-shard3of3.bin differ diff --git a/src/models/thorax-0.1.0-n960/metadata.yaml b/src/models/thorax-0.1.0-n960/metadata.yaml new file mode 100644 index 0000000..cdbb300 --- /dev/null +++ b/src/models/thorax-0.1.0-n960/metadata.yaml @@ -0,0 +1,53 @@ +description: Ultralytics thorax-0.1.0-n model trained on ./thorax.yaml +author: Ultralytics +license: AGPL-3.0 https://ultralytics.com/license +date: '2024-02-29T23:52:02.571033' +version: 8.1.19 +stride: 32 +task: detect +batch: 1 +imgsz: +- 960 +- 960 +names: + 0: Abdominal diaphragm + 1: Aorta + 2: Azygous vein + 3: Brachiocephalic trunk + 4: Caudal vena cava + 5: Cranial vena cava + 6: Esophagus + 7: External abdominal oblique + 8: Iliocostalis + 9: Latissimus dorsi + 10: Left atrium + 11: Left auricle + 12: Left lung + 13: Left subclavian artery + 14: Left ventricle + 15: Longissimus + 16: Pectoralis profundus + 17: Pectoralis superficialis + 18: Pericardium + 19: Phrenic nerve + 20: Primary bronchus + 21: Pulmonary artery + 22: Pulmonary trunk + 23: Pulmonary vein + 24: Rectus abdominis + 25: Rectus thoracis + 26: Recurrent laryngeal nerve + 27: Rhomboideus + 28: Right atrium + 29: Right auricle + 30: Right lung + 31: Right ventricle + 32: Scalenus + 33: Serratus dorsalis caudalis + 34: Serratus dorsalis cranialis + 35: Serratus ventralis + 36: Spinalis + 37: Sympathetic chain + 38: Trachea + 39: Trapezius + 40: Vagus nerve diff --git a/src/models/thorax-0.1.0-n960/model.json b/src/models/thorax-0.1.0-n960/model.json new file mode 100644 index 0000000..8e48331 --- /dev/null +++ b/src/models/thorax-0.1.0-n960/model.json @@ -0,0 +1 @@ +{"format": "graph-model", "generatedBy": "2.9.0", "convertedBy": "TensorFlow.js Converter v3.15.0", "signature": {"outputs": {"Identity:0": {"name": "Identity:0"}}}, "modelTopology": {"node": [{"name": "ConstantFolding/PartitionedCall/model/tf.math.divide/truediv_recip", "op": "Const", "attr": {"value": {"tensor": {"dtype": "DT_FLOAT", "tensorShape": {"dim": [{"size": "1"}, {"size": "1"}, {"size": "1"}]}}}, "dtype": 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'./submit-mixin' import detectMixin from './local-detect' - import thoraxClasses from '../models/thorax_tfwm/classes.json' + import thoraxClasses from '../models/thorax-0.1.0-n960/classes.json' export default { mixins: [submitMixin, detectMixin], @@ -334,9 +334,9 @@ this.detectorName = 'thorax' this.classesList = thoraxClasses /* VITE setting */ - this.modelLocation = '../models/thorax_tfwm/model.json' + this.modelLocation = '../models/thorax-0.1.0-n960/model.json' /* PWA Build setting */ - //this.modelLocation = './models/thorax_tfwm/model.json' + //this.modelLocation = './models/thorax-0.1.0-n960/model.json' this.modelLocationCordova = 'https://localhost/models/thorax_tfwm/model.json' break; case 'abdomen': diff --git a/src/pages/local-detect.js b/src/pages/local-detect.js index c6fd09e..dbac842 100644 --- a/src/pages/local-detect.js +++ b/src/pages/local-detect.js @@ -8,41 +8,69 @@ export default { model = await tf.loadGraphModel(weights).then(graphModel => { return graphModel }) - }, + }, async localDetect(imageData) { const [modelWidth, modelHeight] = model.inputs[0].shape.slice(1, 3); const input = tf.tidy(() => { return tf.image.resizeBilinear(tf.browser.fromPixels(imageData), [modelWidth, modelHeight]).div(255.0).expandDims(0) }) - var results = model.executeAsync(input).then(res => { - const [boxes, scores, classes, valid_detections] = res; - const boxes_data = boxes.dataSync(); - const scores_data = scores.dataSync(); - const classes_data = classes.dataSync(); - const valid_detections_data = valid_detections.dataSync()[0]; - tf.dispose(res) + const res = model.predict(input) + const detectAttempts = res.shape[2] + const outputSize = res.shape[1] + const rawRes = tf.transpose(res,[0,2,1]).dataSync() + let rawBoxes = [] + let rawScores = [] - var output = { - detections: [] - } - for (var i =0; i < valid_detections_data; i++) { - var [dLeft, dTop, dRight, dBottom] = boxes_data.slice(i * 4, (i + 1) * 4); - output.detections.push({ - "top": dTop, - "left": dLeft, - "bottom": dBottom, - "right": dRight, - "label": this.detectorLabels[classes_data[i]].name, - "confidence": scores_data[i] * 100 - }) + for (var i = 0; i < detectAttempts; i++) { + var getBox = rawRes.slice((i * outputSize),(i * outputSize) + 4) + var boxCalc = [ + (getBox[0] - (getBox[2] / 2)) / modelWidth, + (getBox[1] - (getBox[3] / 2)) / modelHeight, + (getBox[0] + (getBox[2] / 2)) / modelWidth, + (getBox[1] + (getBox[3] / 2)) / modelHeight, + ] + rawBoxes.push(boxCalc) + rawScores.push(rawRes.slice((i * outputSize) + 4,(i + 1) * outputSize)) + } + const tBoxes = tf.tensor2d(rawBoxes) + let tScores = null + let boxes_data = [] + let scores_data = [] + let classes_data = [] + for (var c = 0; c < outputSize - 4; c++) { + tScores = rawScores.map(x => x[c]) + var validBoxes = await tf.image.nonMaxSuppressionAsync(tBoxes,tf.tensor1d(tScores),10,0.5,.05) + validBoxes = validBoxes.dataSync() + if (validBoxes) { + boxes_data.push(...rawBoxes.filter( (_, idx) => validBoxes.includes(idx))) + var outputScores = tScores.filter( (_, idx) => validBoxes.includes(idx)) + scores_data.push(...outputScores) + classes_data.push(...outputScores.fill(c)) } + } - return output - }) + const valid_detections_data = classes_data.length + var output = { + detections: [] + } + for (var i =0; i < valid_detections_data; i++) { + var [dLeft, dTop, dRight, dBottom] = boxes_data[i] + output.detections.push({ + "top": dTop, + "left": dLeft, + "bottom": dBottom, + "right": dRight, + "label": this.detectorLabels[classes_data[i]].name, + "confidence": scores_data[i] * 100 + }) + } - return results + tf.dispose(res) + tf.dispose(tBoxes) + + return output } } } \ No newline at end of file