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fix paper bib
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@Mmasoud1
Mmasoud1 committed Jan 13, 2024
1 parent ad7cc00 commit cab91ac
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145 changes: 129 additions & 16 deletions js/histojs/designFunctionsv4.js
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Original file line number Diff line number Diff line change
Expand Up @@ -44,20 +44,26 @@
{id: "2", value: "Styx", hostAPI: "https://styx.neurology.emory.edu/girder/api/v1/"}]
*
* findObjectByKeyValue( dict, 'id', "2");
* // => Object { id: "2", value: "Styx", hostAPI: "https://styx.neurology.emory.edu/girder/api/v1/" }
*
* => Object { id: "2", value: "Styx", hostAPI: "https://styx.neurology.emory.edu/girder/api/v1/" }
*
* findObjectByKeyValue( dict, 'id', "2", 'INDEX');
* => 1
*
*
* await findObjectByKeyValueTFJS( dict, 'id', "2")
* => Object { id: "2", value: "Styx", hostAPI: "https://styx.neurology.emory.edu/girder/api/v1/" }
*/

findObjectByKeyValue = (array, key, value, returnType='DATA') => {
const obj = array.filter( entry => entry[key] === value)[0];
return obj ? ( returnType === 'DATA' ? obj : ( returnType === 'INDEX' ? array.indexOf(obj) : null )) : null;
findObjectByKeyValue = (arr, key, value, returnType = 'DATA') => {
const obj = arr.filter( entry => entry[key] === value)[0];
return obj ? ( returnType === 'DATA' ? obj : ( returnType === 'INDEX' ? arr.indexOf(obj) : null )) : null;
}


findObjectByKeyValueTFJS = async (arr, key, value) => {
const result = await tf.data.array(arr).filter( entry => entry[key] === value).toArray();
return (result.length > 1) ? result : result.length ? result[0] : null;
}


/**
* Remove element or record from array
*
Expand All @@ -74,6 +80,9 @@
* removeArrayElem(['a', 'b', 'c', 'd'], 'c')
* => ['a', 'b', 'd']
*
* await removeArrayElemTFJS([1, 2, 3, 4], 3)
* => [1, 2, 4]
* NOTE: TFJS version for numbers only
*/

removeArrayElem = (array, element) => {
Expand All @@ -83,6 +92,17 @@
}
}

removeArrayElemTFJS = async (array, element) => {
const tensor = tf.tensor(array);
const mask = tf.notEqual(tensor, element);
const result = await tf.booleanMaskAsync(tensor, mask);
return result.arraySync();
}

removeArrayElem_v2 = (array, element) => {
return array.filter(elm => elm !== element);
}


/**
* Insert element or record into array at specific index
Expand Down Expand Up @@ -143,11 +163,22 @@
* @returns {Array} arrOfObj2 - The second array of objects to be merged.
* @example
*
* mergeArrayOfObjByKey( "id", [ {id:"spx-1", Type:"Tumor"},
* {id:"spx-7", Type:"Immune"} ],
* mergeArrayOfObjByKey( "id", [ {id:"spx-1", Type:"Tumor" },
* {id:"spx-7", Type:"Immune"} ],
* [{id : "spx-1", area: 250, solidity: 0.95},
* {id : "spx-3", area: 150, solidity: 0.85},
* {id : "spx-7", area: 100, solidity: 0.80} ])
*
* => [{ id: "spx-1", Type:"Tumor", area: 250, solidity: 0.95 },
* { id: "spx-7", Type: "immune", area: 100, solidity: 0.80 }]
*
*
* await mergeArrayOfObjByKeyTFJS( "id", [ {id:"spx-1", Type:"Tumor" },
* {id:"spx-7", Type:"Immune"} ],
* [{id : "spx-1", area: 250, solidity: 0.95},
* {id : "spx-3", area: 150, solidity: 0.85},
* {id : "spx-7", area: 100, solidity: 0.80} ])
*
* => [{ id: "spx-1", Type:"Tumor", area: 250, solidity: 0.95 },
* { id: "spx-7", Type: "immune", area: 100, solidity: 0.80 }]
*
Expand All @@ -167,18 +198,47 @@
// Create hash for the larger array
let largerArrHashByKey = {};

largerArrayOfObjs.forEach((object, idx) => {
largerArrayOfObjs.forEach(object => {
largerArrHashByKey[ object[objKey] ] = object;
});
});

// Merge both arrays of objects
let mergedArrayOfObjs = [];

smallerArrayOfObjs.forEach((object, idx) => {
smallerArrayOfObjs.forEach(object => {
mergedArrayOfObjs.push({ ...object, ...largerArrHashByKey[ object[objKey] ]});
});

return mergedArrayOfObjs;
return mergedArrayOfObjs;
}


mergeArrayOfObjByKeyTFJS = async(objKey, arrOfObj1, arrOfObj2) => {
let largerArrayOfObjs, smallerArrayOfObjs;

if( arrOfObj1.length < arrOfObj2.length) {
largerArrayOfObjs = arrOfObj2;
smallerArrayOfObjs = arrOfObj1;
} else {
largerArrayOfObjs = arrOfObj1;
smallerArrayOfObjs = arrOfObj2;
}

// Create hash for the larger array
let largerArrHashByKey = {};

await tf.data.array(largerArrayOfObjs).forEachAsync(object => {
largerArrHashByKey[ object[objKey] ] = object;
});

// Merge both arrays of objects
let mergedArrayOfObjs = [];

await tf.data.array(smallerArrayOfObjs).forEachAsync(object => {
mergedArrayOfObjs.push({ ...object, ...largerArrHashByKey[ object[objKey] ]});
});

return mergedArrayOfObjs;
}

/**
Expand Down Expand Up @@ -232,14 +292,23 @@
* arrayUniqueValues( [1, 1, 2, 3, 2, 5])
*
* => [1, 2, 3, 5]
*
* arrayUniqueValuesTFJS( [1, 1, 2, 3, 2, 5])
*
* => [1, 2, 3, 5]
*/

arrayUniqueValues = (array) => {

return array.filter((value, index, self) => {
return self.indexOf(value) === index;
});

}


arrayUniqueValuesTFJS = (array) => {
const tensor = tf.tensor(array);
const {values, indices} = tf.unique(tensor);
return values.arraySync();
}


Expand All @@ -253,18 +322,62 @@
* @category Array
* @param {Array} array1 - The array of values.
* @param {Array} array2 - The array of values.
* @returns {Array} array of concatenation
* @returns {Array | promise} array of concatenation, fastArraysConcatTFJSData fun returns promise
* @example
*
* array1 = [{ Type: "1", val: 1}, { Type: "2", val: 2}]
* array2 = [{ Type: "3", val: 3}, { Type: "4", val: 4}]
*
* fastArraysConcat( [1, 1, 2, 3], [5, 2, 5])
*
* => [1, 1, 2, 3, 5, 2, 5]
*
* fastArraysConcat( array1, array2)
*
* => [{ Type: "1", val: 1}, { Type: "2", val: 2}, { Type: "3", val: 3}, { Type: "4", val: 4}]
*********************************************************************************************
* fastArraysConcatTFJS( [1, 1, 2, 3], [5, 2, 5])
*
* => [1, 1, 2, 3, 5, 2, 5]
*
* NOTE: fastArraysConcatTFJS can not concate Array of objects.
*
* fastArraysConcatTFJS( array1, array2)
*
* => [ NaN, NaN, NaN, NaN ]
**********************************************************************************************
* NOTE: fastArraysConcatTFJSData returns promise
*
* await fastArraysConcatTFJSData( [1, 1, 2, 3], [5, 2, 5])
* OR
* fastArraysConcatTFJSData([1, 1, 2, 3], [5, 2, 5]).then(function(res) { console.log(res) })
*
* => [1, 1, 2, 3, 5, 2, 5]
*
* await fastArraysConcatTFJSData( array1, array2)
* OR
* fastArraysConcatTFJSData(array1,array2).then(function(res) { console.log(res) })
*
* => [{ Type: "1", val: 1}, { Type: "2", val: 2}, { Type: "3", val: 3}, { Type: "4", val: 4}]
*/

fastArraysConcat = (array1, array2) => {
return [...array1, ... array2];
}

fastArraysConcatTFJS = (array1, array2) => {
const tensor1 = tf.tensor1d(array1);
const tensor2 = tf.tensor1d(array2);
return tf.concat([tensor1, tensor2]).arraySync();
}


fastArraysConcatTFJSData = (array1, array2) => {
const dataArr1 = tf.data.array(array1);
const dataArr2 = tf.data.array(array2);
return dataArr1.concatenate(dataArr2).toArray();
}


/**
* Find if two arrays are identical.
Expand Down
9 changes: 8 additions & 1 deletion paper/paper.bib
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ @article{gutman2017digital
volume={77},
number={21},
pages={e75--e78},
doi = {10.1158/0008-5472.CAN-17-0629},
year={2017},
publisher={AACR}
}
Expand All @@ -26,6 +27,7 @@ @article{lin2015highly
volume={6},
number={1},
pages={8390},
doi={10.1038/ncomms9390},
year={2015},
publisher={Nature Publishing Group UK London}
}
Expand All @@ -36,6 +38,7 @@ @article{lin2018highly
author={Lin, Jia-Ren and Izar, Benjamin and Wang, Shu and Yapp, Clarence and Mei, Shaolin and Shah, Parin M and Santagata, Sandro and Sorger, Peter K},
journal={elife},
volume={7},
doi={10.7554/eLife.31657},
year={2018},
publisher={eLife Sciences Publications, Ltd}
}
Expand All @@ -48,6 +51,7 @@ @article{gerdes2013highly
volume={110},
number={29},
pages={11982--11987},
doi = {10.1073/pnas.1300136110},
year={2013},
publisher={National Acad Sciences}
}
Expand All @@ -57,6 +61,7 @@ @inproceedings{schmidt2018cell
author={Schmidt, Uwe and Weigert, Martin and Broaddus, Coleman and Myers, Gene},
booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2018: 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II 11},
pages={265--273},
doi={10.1007/978-3-030-00934-2_30},
year={2018},
organization={Springer}
}
Expand All @@ -70,7 +75,7 @@ @article{gabriel1969new
volume={18},
number={3},
pages={259--278},
doi = {https://doi.org/10.2307/2412323},
doi = {10.2307/2412323},
year={1969},
publisher={Society of Systematic Zoology}
}
Expand All @@ -83,6 +88,7 @@ @article{goltsev2018deep
volume={174},
number={4},
pages={968--981},
doi={10.1016/j.cell.2018.07.010},
year={2018},
publisher={Elsevier}
}
Expand All @@ -94,6 +100,7 @@ @article{angelo2014multiplexed
volume={20},
number={4},
pages={436--442},
doi = {10.1038/nm.3488},
year={2014},
publisher={Nature Publishing Group US New York}
}
Expand Down

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