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@Mmasoud1
Mmasoud1 committed Dec 30, 2023
1 parent e540588 commit cd83f4f
Showing 1 changed file with 216 additions and 19 deletions.
235 changes: 216 additions & 19 deletions js/histojs/analysisFunctionsv12.js
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Original file line number Diff line number Diff line change
Expand Up @@ -38,31 +38,97 @@
return lastItemSelectionStates.grpIndex != null ? lastItemSelectionStates.grpIndex : null;
}


/**
* check if a group selected to enter the analysis phase
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {boolean}
*/

isGrpSelected = () => {
return lastItemSelectionStates.grpIndex != null ? true : false;
}

////////////////-- For Chart Operations --///////////////
//Check if a group saved its Tumor-immune-Stromal selected channels
//Check if a group saved its Tumor-immune-Stromal selected channels
/**
* Check if a group saved its Tumor-immune-Stromal selected channels
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {boolean}
*/
isGrpChannelsNameTypeExist = (grpIndex) => {
return currentItemInfo.omeDataset.Groups[grpIndex].Channel_Types ?
( currentItemInfo.omeDataset.Groups[grpIndex].Channel_Types.length ? true : false ) : false;
}



/**
* Get the type of channel names if they are Tumor/Immune/Stromal etc
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {Array} array of Objects
*
* @example
*
* getGrpChannelsNameType( 1)
*
* // => [{"channel_name": "CD45", "channel_type" : "Immune"}, ...]
*/

getGrpChannelsNameType = (grpIndex) => {
return isGrpChannelsNameTypeExist(grpIndex) ?
currentItemInfo.omeDataset.Groups[grpIndex].Channel_Types : null;
}

/**
* Set a value to the variable
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

setGrpChannelsNameType = (grpIndex, chnlNameType) => {
currentItemInfo.omeDataset.Groups[grpIndex].Channel_Types = chnlNameType;
}

/**
* Set the variable to null
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetGrpChannelsNameType = (grpIndex) => {
currentItemInfo.omeDataset.Groups[grpIndex].Channel_Types = null;
}

///////////////////////////////

/**
* Check if Dapi channel selected during the design phase (i.e., channel grouping)
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {boolean}
*/
isDAPIChannelSelected = () => {
return lastItemSelectionStates.DAPIChannelIndex != null ? true : false;
}
Expand All @@ -71,14 +137,43 @@
lastItemSelectionStates.DAPIChannelIndex = DAPIChannelIndex;
}

/**
* Get Dapi channel index
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {number}
*/

getSelectedDAPIChannelIndex = () => {
return lastItemSelectionStates.DAPIChannelIndex;
}

/**
* Get Dapi channel name
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
* @returns {String}
*/

getSelectedDAPIChannelName = () => {
return isDAPIChannelSelected() ? getDAPIChannelObj()[0].channel_name : null;
}

/**
* Set the variable to null
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetSelectedDAPIChannelIndex = () => {
lastItemSelectionStates.DAPIChannelIndex = null ;
}
Expand Down Expand Up @@ -490,18 +585,36 @@

}

resetCellFilterDependencies = () => {
allValidTiles = [];
allValidPhenotypes = [];
filteredValidPhenotypes = [];
resetNavigatorValidCells();
/**
* Set the variable to null
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetCellFilterDependencies = () => {
allValidTiles = [];
allValidPhenotypes = [];
filteredValidPhenotypes = [];
resetNavigatorValidCells();

}
}

getNavigatorValue = () => {
return cellFiltersAndPhenotypesStates.navigatorPointer;
}

/**
* Set the variable to zero
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetNavigatorValue = () => {
cellFiltersAndPhenotypesStates.navigatorPointer = 0;
}
Expand All @@ -514,6 +627,15 @@
cellFiltersAndPhenotypesStates.validCells = validCellsArray;
}

/**
* Set the variable to null
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetNavigatorValidCells = () => {
cellFiltersAndPhenotypesStates.validCells = null;
}
Expand Down Expand Up @@ -1482,16 +1604,25 @@ cellClassifications = (cellsWithTypes, callback) => {
}
}

// future use
resetCellTypeDependencies = () => {
if(! isViewBarEmpty("grpFeaturesViewBar") ) {
clearViewBar("grpFeaturesViewBar");
}

cellBasicClassification = [];
resetGrpChannelsNameType( getSelectedGrpIndex() );
setAllChannelsOpacity();
}
/**
* Future use
* reset the variable
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/
resetCellTypeDependencies = () => {
if(! isViewBarEmpty("grpFeaturesViewBar") ) {
clearViewBar("grpFeaturesViewBar");
}

cellBasicClassification = [];
resetGrpChannelsNameType( getSelectedGrpIndex() );
setAllChannelsOpacity();
}


//----------------------------------------------------------------------------------------------------//
Expand Down Expand Up @@ -1999,6 +2130,15 @@ getPhenotypeNamesFormField = (fieldId) => {
return document.getElementById(fieldId).value;
}

/**
* reset the variable
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetPhenotypeNamesFormField = (fieldId) => {
document.getElementById(fieldId).value = "";
}
Expand Down Expand Up @@ -2173,7 +2313,15 @@ initPhenotypeNamesForm = () => {

}

// future use
/**
* Future use
* reset the variable
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/
resetCellPhenotypeDependencies = () => {
if(! isViewBarEmpty("grpFeaturesViewBar") ) {
clearViewBar("grpFeaturesViewBar");
Expand Down Expand Up @@ -2210,7 +2358,14 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {
return phenotypesColorsArray;
}

// Turn Off all channels
/**
* Turn Off all channels
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/
resetAllChannelsOpacity = () => {
const curGroup = getSelectedGroup();
curGroup.Channels.forEach((channelName,idx) => {
Expand All @@ -2220,6 +2375,15 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {
})
}

/**
* Turn On all channels
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

setAllChannelsOpacity = () => {
const curGroup = getSelectedGroup();
curGroup.Channels.forEach((channelName,idx) => {
Expand Down Expand Up @@ -2250,6 +2414,14 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {

}

/**
* Reset all cell filters
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetAllCellFilters = () => {
const curGroup = getSelectedGroup();
Expand Down Expand Up @@ -2354,6 +2526,14 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {
return document.getElementById("cellPositiveSwitch." + channelName).checked ? true : false;
}

/**
* Turn off cell postive switch
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/
resetCellPositiveSwitch = (channelName) => {
document.getElementById("cellPositiveSwitch." + channelName).checked = false;
}
Expand Down Expand Up @@ -2416,6 +2596,15 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {
return document.getElementById("cellNegativeSwitch." + channelName).checked ? true : false;
}

/**
* Turn off cell negative switch
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/

resetCellNegativeSwitch = (channelName) => {
document.getElementById("cellNegativeSwitch." + channelName).checked = false;
}
Expand Down Expand Up @@ -2812,6 +3001,14 @@ createCellPhenotypesColorsArray = (numOfValidPhenotypes) => {
freezeBoundaryDependentControls(freezeFlag);
}

/**
* Turn off boundary switch
*
* @function
* @memberof HistoJS
* @since 1.0.0
* @version 1.0.0
*/
resetBoundarySwitch = () => {
document.getElementById("boundarySwitch").checked = false;
boundarySwitchClicked();
Expand Down Expand Up @@ -3619,7 +3816,7 @@ downloadUserData = (data, fileName) =>{
}



/*------------------------------------------------------------------------------------------------------------------*/
/*--------------------------------------------------Right Panel-----------------------------------------------------*/
/*---------------------------------------------- Features Section---------------------------------------------------*/
/*------------------------------------------------------------------------------------------------------------------*/
Expand Down

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