sdeSelections.js

function openDatasetLabels() {
    const datasetLabels = document.getElementById('datasetLabels');
    datasetLabels.style.display = 'block';
    let form = document.getElementById('datasetLabelsForm');
    form.innerHTML = '';
    let index = 0;
    for (dataset in selectedSampleInfo) {
        // Create a label
        let label = document.createElement('label');
        label.setAttribute('for', `dataset-${index}`);
        label.textContent = `Enter alternate name for ${dataset}: `;

        // Create an input field
        let input = document.createElement('input');
        input.type = 'text';
        input.id = `dataset-${index}`;
        input.name = `dataset-${index}`;
        input.placeholder = `Alternate name for ${dataset}`;

        // Append the label and input to the form
        form.appendChild(label);
        form.appendChild(input);

        // Add a line break for spacing
        form.appendChild(document.createElement('br'));
        index += 1;
    }
}

function updateDatasetLabels() {
    let form = document.getElementById('datasetLabelsForm');
    let formData = new FormData(form); // Collect form data
//    let result = {};
    let index = 0;

    // Iterate through form entries and collect values
    for (dataset in selectedSampleInfo) {
        let altName = formData.get(`dataset-${index}`);
//console.log(`dataset-${index}`);
//console.log('altName ',altName);
        if (!(altName === '')) {
//            result[dataset] = altName;
            selectedSampleInfo[dataset].label = altName;
        }
        index += 1;
    }
    closeDatasetLabels();
//    console.log(result); // Log the result to the console
}

function closeDatasetLabels() {
    const datasetLabels = document.getElementById('datasetLabels');
    datasetLabels.style.display = 'none';
}

function openSampleLabels() {
    const sampleLabels = document.getElementById('sampleLabels');
    sampleLabels.style.display = 'block';
    let form = document.getElementById('sampleLabelsForm');
    form.innerHTML = '';
    let index = 0;
    for (dataset in selectedSampleInfo) {
        for (sample in selectedSampleInfo[dataset].position) {
            // Create a label
            let label = document.createElement('label');
            label.setAttribute('for', `sample-${index}`);
            label.textContent = `Enter alternate name for ${sample}: `;

            // Create an input field
            let input = document.createElement('input');
            input.type = 'text';
            input.id = `sample-${index}`;
            input.name = `sample-${index}`;
            input.placeholder = `Alternate name for ${sample}`;

            // Append the label and input to the form
            form.appendChild(label);
            form.appendChild(input);

            // Add a line break for spacing
            form.appendChild(document.createElement('br'));
            index += 1;
        }
    }
}

function updateSampleLabels() {
    let form = document.getElementById('sampleLabelsForm');
    let formData = new FormData(form); // Collect form data
//    let result = {};
    let index = 0;

    // Iterate through form entries and collect values
    for (dataset in selectedSampleInfo) {
        for (sample in selectedSampleInfo[dataset].position) {
            let altName = formData.get(`sample-${index}`);
//console.log(`sample-${index}`);
//console.log('altName ',altName);
            if (!(altName === '')) {
//                result[sample] = altName;
                selectedSampleInfo[dataset].position[sample].label = altName;
            }
            index += 1;
        }
    }
    closeSampleLabels();
//    console.log(result); // Log the result to the console
}

function closeSampleLabels() {
    const sampleLabels = document.getElementById('sampleLabels');
    sampleLabels.style.display = 'none';
}

function openChemicalSelection(sampleMeasurements) {
    const chemicalModal = document.getElementById('chemicalModal');
    chemicalModal.style.display = 'block';

    const chemicalCheckboxes = document.getElementById('chemicalCheckboxes');
    chemicalCheckboxes.innerHTML = '';

    const datesSampled = Object.keys(selectedSampleMeasurements);

    for (chemicalType in selectedSampleMeasurements[datesSampled[0]]) {
        if (chemicalType !== 'Physical Data') {
            const chemicals = Object.keys(selectedSampleMeasurements[datesSampled[0]][chemicalType].chemicals);

            const checkboxContainer = document.createElement('div');
            checkboxContainer.className = 'checkbox-container';

            chemicals.forEach(chemical => {
                const checkbox = document.createElement('input');
                checkbox.type = 'checkbox';
                checkbox.id = `chemical`;
                checkbox.name = 'chemical';
                checkbox.value = chemical;
                checkbox.checked = true; // Initially all chemicals are checked

                const label = document.createElement('label');
                label.htmlFor = `chemical_${chemical}`;
                label.appendChild(document.createTextNode(chemical));

                checkboxContainer.appendChild(checkbox);
                checkboxContainer.appendChild(label);
                checkboxContainer.appendChild(document.createElement('br'));
            });

            chemicalCheckboxes.appendChild(checkboxContainer);
        }
    }
}

function flipChemicalSelections(selection) {
    const checkboxes = document.querySelectorAll('#chemicalCheckboxes input[type="checkbox"]');
    checkboxes.forEach(checkbox => {
        if (selection) {
            checkbox.checked = true;
        } else {
            checkbox.checked = false;
        };
    });
}

function applyChemicalFilter() {
    const containsText = document.getElementById('containsTextChemical').value.toLowerCase();
    const checkboxes = document.querySelectorAll('#chemicalCheckboxes input[type="checkbox"]');
    checkboxes.forEach(checkbox => {
        if (containsText.length > 0) {
            if (checkbox.nextSibling.textContent.toLowerCase().includes(containsText)) {
                checkbox.checked = true;
            } else {
                checkbox.checked = false;
            }
        }
    });
}

function closeChemicalSelection() {
    selectChemicals();
    const chemicalModal = document.getElementById('chemicalModal');
    chemicalModal.style.display = 'none';
}

function selectChemicals() {
    const checkboxes = document.querySelectorAll('input[name="chemical"]:checked');
    const selectedChemicals = Array.from(checkboxes)
        .filter(checkbox => checkbox.checked)
        .map(checkbox => checkbox.value);
    selectedSampleMeasurements = getSelectedChemicalSampleMeasurements(selectedChemicals);
    selectedSampleInfo = getSelectedChemicalSampleInfo(selectedChemicals);
    updateChart();
}

function getSelectedChemicalSampleMeasurements(selectedChemicals) {
//console.log(selectedChemicals);
//console.log(selectedSampleInfo);
//console.log(selectedSampleMeasurements);
    selectedMeas = {};
    for (dateSampled in selectedSampleMeasurements) {
        for (const chemicalType in selectedSampleMeasurements[dateSampled]) {
            if ('Physical Data' != chemicalType) {
                for (const chemical in selectedSampleMeasurements[dateSampled][chemicalType].chemicals) {
                    if (selectedChemicals.includes(chemical)) {
                        // Put here as if no chemicals selected then don't need chemical type
                        if (!selectedMeas[dateSampled]) {
                            selectedMeas[dateSampled] = {};
                        }
                        if (!(chemicalType in selectedMeas[dateSampled])) {
                            selectedMeas[dateSampled][chemicalType] = {};
                            selectedMeas[dateSampled][chemicalType].chemicals = {};
                            selectedMeas[dateSampled][chemicalType]['Unit of measurement'] = sampleMeasurements[dateSampled][chemicalType]['Unit of measurement'];
                            if (chemicalType == 'PAH data') {
                                // Just copy all common data even if only 1 PAH is selected
                                if (sampleMeasurements[dateSampled][chemicalType].gorhamTest !== undefined) selectedMeas[dateSampled][chemicalType].gorhamTest = sampleMeasurements[dateSampled][chemicalType].gorhamTest;
                                if (sampleMeasurements[dateSampled][chemicalType].total !== undefined) selectedMeas[dateSampled][chemicalType].total = sampleMeasurements[dateSampled][chemicalType].total;
                                if (sampleMeasurements[dateSampled][chemicalType].totalHC !== undefined) selectedMeas[dateSampled][chemicalType].totalHC = sampleMeasurements[dateSampled][chemicalType].totalHC;
                                if (sampleMeasurements[dateSampled][chemicalType].totalHCUnit !== undefined) selectedMeas[dateSampled][chemicalType].totalHCUnit = sampleMeasurements[dateSampled][chemicalType].totalHCUnit;
                            }
                            if (chemicalType == 'PCB data') {
                                //console.log('Create ', dateSampled, chemicalType,'Gorham Test');
/*                                selectedMeas[dateSampled][chemicalType].congenerTest = {};
                                selectedMeas[dateSampled][chemicalType].congenerTest[sample] = sampleMeasurements[dateSampled][chemicalType].congenerTest[sample];*/
//                                selectedMeas[dateSampled][chemicalType].congenerTest = {};
                                if (sampleMeasurements[dateSampled][chemicalType].congenerTest !== undefined) selectedMeas[dateSampled][chemicalType].congenerTest = sampleMeasurements[dateSampled][chemicalType].congenerTest;
                                if (sampleMeasurements[dateSampled][chemicalType].total !== undefined) selectedMeas[dateSampled][chemicalType].total = sampleMeasurements[dateSampled][chemicalType].total;
                            }
                        }
                        for (sample in selectedSampleInfo[dateSampled].position) {
//console.log(selectedSampleMeasurements,dateSampled,chemicalType,chemical);
//console.log(selectedMeas[dateSampled][chemicalType].chemicals[chemical]);
                           if (!selectedMeas[dateSampled][chemicalType]?.chemicals[chemical]) {
                                selectedMeas[dateSampled][chemicalType].chemicals[chemical] = {};
                                selectedMeas[dateSampled][chemicalType].chemicals[chemical].samples = {};
                            }
/*                            if (!selectedMeas[dateSampled][chemicalType].chemicals[chemical]?.samples) {
                                selectedMeas[dateSampled][chemicalType].chemicals[chemical].samples = {};
                            }*/
//console.log(selectedMeas[dateSampled][chemicalType].chemicals[chemical]);
                            selectedMeas[dateSampled][chemicalType].chemicals[chemical].samples[sample] = selectedSampleMeasurements[dateSampled][chemicalType].chemicals[chemical].samples[sample];
/*                           if (!selectedMeas[dateSampled]?.["Physical Data"]) {
                                selectedMeas[dateSampled]["Physical Data"] = {};
                                selectedMeas[dateSampled]["Physical Data"]["Date analysed"] = selectedSampleMeasurements[dateSampled]["Physical Data"]["Date analysed"]
                                selectedMeas[dateSampled]["Physical Data"]["Laboratory/contractor"] = selectedSampleMeasurements[dateSampled]["Physical Data"]["Laboratory/contractor"];
                                selectedMeas[dateSampled]["Physical Data"]["Unit of measurement"] = selectedSampleMeasurements[dateSampled]["Physical Data"]["Unit of measurement"];
                                selectedMeas[dateSampled]["Physical Data"].sizes = selectedSampleMeasurements[dateSampled]["Physical Data"].sizes;
                                selectedMeas[dateSampled]["Physical Data"].samples = {};
                            }*/
                            if (selectedSampleMeasurements[dateSampled]["Physical Data"]?.samples[sample] !== undefined) {
                                selectedMeas[dateSampled]["Physical Data"].samples[sample] = selectedSampleMeasurements[dateSampled]["Physical Data"].samples[sample];
                            }
                        }
                    }
                }
            }
        }
    }
    for (dateSampled in selectedMeas) {
        if ('Physical Data' in selectedSampleMeasurements[dateSampled]){
            for (sample in selectedSampleInfo[dateSampled].position) {
                selectedMeas[dateSampled]['Physical Data'] = selectedSampleMeasurements[dateSampled]['Physical Data'];
            }
        }
    }
    return selectedMeas;
}

function getSelectedChemicalSampleInfo(selectedChemicals) {
    let selectedSamps = {};
    for (const dateSampled in selectedSampleMeasurements) {
        selectedSamps[dateSampled] = {};
        selectedSamps[dateSampled]['Date sampled'] = selectedSampleInfo[dateSampled]['Date sampled'];
        selectedSamps[dateSampled].fileURL = selectedSampleInfo[dateSampled].fileURL;
        selectedSamps[dateSampled].Applicant = selectedSampleInfo[dateSampled].Applicant;
        selectedSamps[dateSampled]['Application number'] = selectedSampleInfo[dateSampled]['Application number'];
        selectedSamps[dateSampled]['Application title'] = selectedSampleInfo[dateSampled]['Application title'];
        selectedSamps[dateSampled]['label'] = selectedSampleInfo[dateSampled]['label'];
        for (const chemicalType in selectedSampleMeasurements[dateSampled]) {
            if (!('position' in selectedSamps[dateSampled])) {
//console.log('setting up position');
                selectedSamps[dateSampled].position = {};
            }
            if ('Physical Data' != chemicalType) {
//console.log('getting positions',chemicalType,chemical);
                for (const chemical in selectedSampleMeasurements[dateSampled][chemicalType].chemicals) {
                    if (selectedChemicals.includes(chemical)) {
                        for (const sample in selectedSampleMeasurements[dateSampled][chemicalType].chemicals[chemical].samples) {
//if (sample.includes('Scar')) {
//    console.log('Sample',sample);
//}
                            selectedSamps[dateSampled].position[sample] = selectedSampleInfo[dateSampled].position[sample];
                        }
                    }
                }
            }
        }
    }
    return selectedSamps;
}

function openDatasetSelection(selectedSampleMeasurements) {
    const sampleModal = document.getElementById('datasetModal');
    sampleModal.style.display = 'block';

}

function yourapplyDatasetFilter() {
    const sampleModal = document.getElementById('datasetModal');
    sampleModal.style.display = 'none';

    let sheetsToSelect = {}; // Use an object
    for (let i = 0; i < dataSheetNames.length; i++) {
        let sheetName = dataSheetNames[i]; // Declare sheetName with let
        sheetsToSelect[sheetName] = document.getElementById(dataSheetNamesCheckboxes[i] + 'set').checked;
    }

    console.log(sheetsToSelect);
    console.log(Object.keys(sheetsToSelect));

    let datasetsToKeep = {}; // Use an object
    for (let dateSelected in selectedSampleInfo) {
        datasetsToKeep[dateSelected] = true;

        for (let sheetName in sheetsToSelect) {
            if (sheetsToSelect[sheetName]) {
                console.log(sheetName);

                if (!(sheetName in selectedSampleMeasurements[dateSelected])) {
                    datasetsToKeep[dateSelected] = false;
                    console.log(dateSelected, ' has no ', sheetName);
                    break;
                }
            }
        }
        console.log(dateSelected, ' has ', sheetName);
    }

    console.log(datasetsToKeep);

    selectedSampleInfo = {};
    selectedSampleMeasurements = {};

    for (let dateSelected in datasetsToKeep) {
        if (datasetsToKeep[dateSelected]) {
            selectedSampleInfo[dateSelected] = sampleInfo[dateSelected];
            selectedSampleMeasurements[dateSelected] = sampleMeasurements[dateSelected];
        }
    }
    
    updateChart();
}

function applyDatasetFilter() {
    const sampleModal = document.getElementById('datasetModal');
    sampleModal.style.display = 'none';
    let sheetsToSelect = {};
    for (let i = 0; i < dataSheetNames.length; i++) {
        //sheetName = dataSheetNames[i];
        sheetsToSelect[dataSheetNames[i]] = document.getElementById(dataSheetNamesCheckboxes[i]+'set').checked ? true : false; // Check the checkbox state
    }
//console.log(sheetsToSelect);
//console.log(Object.keys(sheetsToSelect));
    let datasetsToKeep = {};
    for (let dateSelected in selectedSampleInfo) {
        datasetsToKeep[dateSelected] = true;
        for (let sheetName in sheetsToSelect) {
//console.log(sheetName);
            if (sheetsToSelect[sheetName]) {
//console.log(sheetName);
                if (!(sheetName in selectedSampleMeasurements[dateSelected])) {
                    datasetsToKeep[dateSelected] = false;
//console.log(dateSelected,' has no ',sheetName);
                    break;
                }
//                keepInfo = sampleInfo[dateSelected];
//                keepSample = sampleMeasurements[dateSelected]
            }
        }
//console.log(dateSelected,' has ',sheetName);
    }
//console.log(datasetsToKeep);
    selectedSampleInfo = {};
    selectedSampleMeasurements = {};
    for (let dateSelected in datasetsToKeep) {
        if (datasetsToKeep[dateSelected]) {
            selectedSampleInfo[dateSelected] = sampleInfo[dateSelected];
            selectedSampleMeasurements[dateSelected] = sampleMeasurements[dateSelected];
        }
    }
    updateChart();
}
    

function openSampleSelection(sampleMeasurements) {
    const sampleModal = document.getElementById('sampleModal');
    sampleModal.style.display = 'block';

    const sampleCheckboxes = document.getElementById('sampleCheckboxes');
    sampleCheckboxes.innerHTML = '';

    //    const datesSampled = Object.keys(sampleInfo);
    const datesSampled = Object.keys(selectedSampleInfo);


    datesSampled.sort();
    datesSampled.forEach(dateSampled => {

        //    for (dateSampled in sampleInfo) {
        const samples = Object.keys(selectedSampleInfo[dateSampled].position);
        samples.sort();
        const checkboxContainer = document.createElement('div');
        checkboxContainer.className = 'checkbox-container';

        samples.forEach(sample => {
            const checkbox = document.createElement('input');
            checkbox.type = 'checkbox';
            checkbox.id = `sample_${dateSampled + ': ' + sample}`;
            checkbox.name = 'sample';
            checkbox.value = dateSampled + ': ' + sample;
            checkbox.checked = true; // Initially all samples are checked

            const label = document.createElement('label');
            label.htmlFor = `sample_${sample}`;
            label.appendChild(document.createTextNode(dateSampled + ': ' + sample));

            checkboxContainer.appendChild(checkbox);
            checkboxContainer.appendChild(label);
            checkboxContainer.appendChild(document.createElement('br'));
        });

        sampleCheckboxes.appendChild(checkboxContainer);
    });
    createStandardFilterUI();
    populateAreaFilter();
}

function flipSampleSelections(selection) {
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
    checkboxes.forEach(checkbox => {
        if (selection) {
            checkbox.checked = true;
        } else {
            checkbox.checked = false;
        };
    });
}

/*function selectHighlighted(selection) {
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
    index = 0;
    //        for (ds in selectedSampleInfo) {
    //            for (s in selectedSampleInfo[ds]) {
    checkboxes.forEach(checkbox => {
        checkbox.checked = highlighted[index];
        index += 1;
    });
    //            }
    //        }
}*/

function selectHighlighted(selection) {
    // 1. Create the master list of all samples and sort it EXACTLY as in createHighlights.
    // This list correctly corresponds to the indices in the 'highlighted' array.
    const masterSampleList = [];
    const datesSampled = Object.keys(selectedSampleInfo);
    datesSampled.forEach(date => {
        const samplesForDate = Object.keys(selectedSampleInfo[date].position);
        samplesForDate.forEach(sampleName => {
            masterSampleList.push(date + ': ' + sampleName);
        });
    });
    masterSampleList.sortComplexSamples(); // Use the same custom sort function

    // 2. Get all checkboxes from the modal.
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');

    // 3. Create a map of checkboxes by their value (which is the unique sample ID) for fast lookups.
    const checkboxMap = new Map();
    checkboxes.forEach(cb => checkboxMap.set(cb.value, cb));

    // 4. Iterate through the master sorted list. For each sample, check if it should be highlighted.
    masterSampleList.forEach((sampleId, index) => {
        const checkbox = checkboxMap.get(sampleId);
        if (checkbox) {
            // Use the index from the sorted list to check the 'highlighted' array.
            // This ensures the correct checkbox is updated.
            checkbox.checked = highlighted[index] || false; // Default to false if undefined
        }
    });
}

function applySampleFilter() {
    let sheetsToSelect = [];
    selectBySheet = false;
    for (i = 0; i < dataSheetNames.length; i++) {
        sheetName = dataSheetNames[i];
console.log('sheetName',sheetName,dataSheetNamesCheckboxes[i]);
        sheetsToSelect[dataSheetNames[i]] = document.getElementById(dataSheetNamesCheckboxes[i]+'sample').checked ? true : false; // Check the checkbox state
        if (sheetsToSelect[dataSheetNames[i]]) {
            selectBySheet = true;
        }
    }
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
    const checkboxesIn = document.querySelectorAll('input[name="sample"]:checked');
//console.log(checkboxes,checkboxesIn);
//console.log(Object.keys(checkboxes));
let checkboxesNames = [];
for (let i = 0; i < checkboxes.length; i++) {
    checkboxesNames[i] = checkboxes[i].value;
}
    if (selectBySheet) {
        index = 0;
        samplesToKeep = {};
//        for (const sheetName in sheetsToSelect) {
//            for (const dateSelected in selectedSampleMeasurements) {
        for (const dateSelected in selectedSampleMeasurements) {
            for (const sample in selectedSampleInfo[dateSelected].position) {
//a            for (const sample in sampleInfo[dateSelected].position) {
                samplesToKeep[dateSelected + ': ' + sample] = true;
            }
            for (const sheetName in sheetsToSelect) {
//console.log('Should I check for',sheetName);
                if (sheetsToSelect[sheetName]) {
//console.log('I should check for',sheetName);
                    if (sheetName in selectedSampleMeasurements[dateSelected]) {
//console.log(dateSelected,'has',sheetName,'so setting all false');
                        for (const sample in selectedSampleInfo[dateSelected].position) {
//a                        for (const sample in sampleInfo[dateSelected].position) {
                                samplesToKeep[dateSelected + ': ' + sample] = false;
                            }
                            for (const chemical in selectedSampleMeasurements[dateSelected][sheetName].chemicals) {
                                for (const sample in selectedSampleMeasurements[dateSelected][sheetName].chemicals[chemical].samples) {
//console.log(dateSelected,sheetName,chemical);
/*                                    if (sample === 'CSA 2.00') {
        index += 1;
        console.log(index,sample,chemical);
    }*/
                                    if (!samplesToKeep[dateSelected + ': ' + sample]) {
                                        if (selectedSampleMeasurements[dateSelected][sheetName].chemicals[chemical].samples[sample] > 0) {
//console.log('keeping',dateSelected,sample);
                                            samplesToKeep[dateSelected + ': ' + sample] = true;
                                        }
                                    }
                                }
                            }
                        } else {
                            if (!(sheetName === 'Physical Data')) {
                                for (const sample in selectedSampleInfo[dateSelected].position) {
//a                                for (const sample in sampleInfo[dateSelected].position) {
//console.log(dateSelected,'has no',sheetName,'so setting all false');
                                                                    samplesToKeep[dateSelected + ': ' + sample] = false;
                            }
                        }
                            }
                }

            }
        }
//console.log(samplesToKeep);
        for (const sampleName in samplesToKeep) {
            if(samplesToKeep[sampleName]) {
//console.log('keeping ',sampleName);
                    const checkName = `sample_${sampleName}`;
                    const checkbox = document.getElementById(checkName);
                    checkbox.checked = true;
            }
        }
    }
//console.log(checkboxes);
    const containsText = document.getElementById('containsText').value.toLowerCase();
    const minDepth = parseFloat(document.getElementById('minDepth').value);
    const maxDepth = parseFloat(document.getElementById('maxDepth').value);
    centreLat = parseFloat(document.getElementById('centreLat').value);
    centreLon = parseFloat(document.getElementById('centreLon').value);
    const centreDist = parseFloat(document.getElementById('centreDist').value);
//    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
//    const checkboxesIn = document.querySelectorAll('input[name="sample"]:checked');
    checkboxes.forEach(checkbox => {
        if (containsText.length > 0) {
            if (checkbox.nextSibling.textContent.toLowerCase().includes(containsText)) {
                checkbox.checked = true;
            } else {
                checkbox.checked = false;
            }
        }
    });
    if (!(isNaN(minDepth) || isNaN(maxDepth)) && (minDepth <= maxDepth)) {
        checkboxes.forEach(checkbox => {
            checkbox.checked = false;
        });
        for (const dateSelected in selectedSampleInfo) {
            for (const sample in selectedSampleInfo[dateSelected].position) {
                const minSample = selectedSampleInfo[dateSelected].position[sample]['Sampling depth (m)'].minDepth;
                if (minDepth <= minSample) {
                    const maxSample = selectedSampleInfo[dateSelected].position[sample]['Sampling depth (m)'].maxDepth;
/*a        for (const dateSelected in sampleInfo) {
            for (const sample in sampleInfo[dateSelected].position) {
                const minSample = sampleInfo[dateSelected].position[sample]['Sampling depth (m)'].minDepth;
                if (minDepth <= minSample) {
                    const maxSample = sampleInfo[dateSelected].position[sample]['Sampling depth (m)'].maxDepth;*/
                    if (maxDepth >= maxSample) {
                        const checkName = `sample_${dateSelected + ': ' + sample}`;
                        const checkbox = document.getElementById(checkName);
                        checkbox.checked = true;
                    }
                }
            }
        }
    }
    // going to find samples close to a set of coordinates
    if (!isNaN(centreDist)) {
        // latitude and longitude not supplied
        if ((isNaN(centreLat) || isNaN(centreLon))) {
            // so assuming only one checkbox is ticked then find all samples near to that position
            const selectedSamples = Array.from(checkboxesIn)
                .filter(checkbox => checkbox.checked)
                .map(checkbox => checkbox.value);
            if (selectedSamples.length === 1) {
                for (const dateSampled in selectedSampleInfo) {
                    for (const sample in selectedSampleInfo[dateSampled].position) {
                        if (selectedSamples.includes(dateSampled + ': ' + sample)) {
                            centreLat = selectedSampleInfo[dateSampled].position[sample]['Position latitude'];
                            centreLon = selectedSampleInfo[dateSampled].position[sample]['Position longitude'];
/*a                for (const dateSampled in sampleInfo) {
                    for (const sample in sampleInfo[dateSampled].position) {
                        if (selectedSamples.includes(dateSampled + ': ' + sample)) {
                            centreLat = sampleInfo[dateSampled].position[sample]['Position latitude'];
                            centreLon = sampleInfo[dateSampled].position[sample]['Position longitude'];*/
                        }
                    }
                }
            } else {
                return
            }
        }
        checkboxes.forEach(checkbox => {
            checkbox.checked = false;
        });
        for (const dateSelected in selectedSampleInfo) {
            for (const sample in selectedSampleInfo[dateSelected].position) {
                const sampleLat = selectedSampleInfo[dateSelected].position[sample]['Position latitude'];
                const sampleLon = selectedSampleInfo[dateSelected].position[sample]['Position longitude'];
/*a        for (const dateSelected in sampleInfo) {
            for (const sample in sampleInfo[dateSelected].position) {
                const sampleLat = sampleInfo[dateSelected].position[sample]['Position latitude'];
                const sampleLon = sampleInfo[dateSelected].position[sample]['Position longitude'];*/
                distance = 1000 * haversineDistance(sampleLat, sampleLon, centreLat, centreLon);
                if (distance <= centreDist) {
                    const checkName = `sample_${dateSelected + ': ' + sample}`;
                    const checkbox = document.getElementById(checkName);
                    checkbox.checked = true;
                }
            }
        }
    }
    // going to find sample with specific measurements
/*    for (const dateSelected in selectedSampleMeasurements) {
        for (const sheetName in selectedSampleMeasurements[dateSelected]) {
            const mustChemicalType = document.getElementById((sheetName + 'sample').replace(/\s/g, '').toLowerCase()).checked;
            if (mustChemicalType) {
                for (const chemical in selectedSampleMeasurements[dateSelected][sheetName].chemicals) {
                    for (const sample in selectedSampleInfo[dateSelected].position) {
                        const conc = selectedSampleMeasurements[dateSelected][sheetName].chemicals[chemical].samples[sample];
console.log(dateSelected,sheetName,chemical,sample,conc);
                        if (conc === null || conc == undefined) {
                            const checkName = `sample_${dateSelected + ': ' + sample}`;
                            const checkbox = document.getElementById(checkName);
                            checkbox.checked = false;
                        }
                    }
                }
            }
        }
    }*/
    for (let i = 0; i < dataSheetNames.length; i++) {
        sheetName = dataSheetNames[i];
        const mustChemicalType = document.getElementById((sheetName + 'sample').replace(/\s/g, '').toLowerCase()).checked;
        if(mustChemicalType) {
            for (let j = 0; j < checkboxesNames.length; j++) {
                let parts = checkboxesNames[j].split(": ");
                if (parts.length > 2) parts[1] = parts[1] + ': ' + parts[2];
                const dateSampled = parts[0];
                const sample = parts[1];
                const checkName = `sample_${dateSampled + ': ' + sample}`;
                const checkbox = document.getElementById(checkName);
                if (!(sheetName in selectedSampleMeasurements[dateSampled])) {
                    checkbox.checked = false;
                } else {
                    // Assume no chemicals are present for this sample
                    checkbox.checked = false;
                    for (const chemical in selectedSampleMeasurements[dateSampled][sheetName].chemicals) {
                        const conc = selectedSampleMeasurements[dateSampled][sheetName].chemicals[chemical].samples[sample];
//        console.log(dateSampled,sheetName,chemical,sample,conc);
  /*                          if (conc === null || conc == undefined) {
                                const checkName = `sample_${dateSampled + ': ' + sample}`;
                                const checkbox = document.getElementById(checkName);
                                checkbox.checked = false;
                            }*/
                           // If any chemical has a concentration > 0 then keep the sample
                        if (conc > 0) {
                            checkbox.checked = true;
                            break;
                        }
                    }
                }
            }
        }
    }
}

function haversineDistance(lat1, lon1, lat2, lon2) {
    const R = 6371; // Radius of the Earth in kilometers
    const dLat = toRadians(lat2 - lat1);
    const dLon = toRadians(lon2 - lon1);
    const a =
        Math.sin(dLat / 2) * Math.sin(dLat / 2) +
        Math.cos(toRadians(lat1)) * Math.cos(toRadians(lat2)) * Math.sin(dLon / 2) * Math.sin(dLon / 2);
    const c = 2 * Math.atan2(Math.sqrt(a), Math.sqrt(1 - a));
    const distance = R * c; // Distance in kilometers
    return distance;
}

function toRadians(degrees) {
    return degrees * (Math.PI / 180);
}


function closeSampleSelection() {
    selectSamples();
    const sampleModal = document.getElementById('sampleModal');
    sampleModal.style.display = 'none';
}

function selectSamples() {
    const checkboxes = document.querySelectorAll('input[name="sample"]:checked');
    //console.log(checkboxes);
    const selectedSamples = Array.from(checkboxes)
        .filter(checkbox => checkbox.checked)
        .map(checkbox => checkbox.value);
    //console.log(selectedSamples);
    selectedSampleMeasurements = getSelectedSampleMeasurements(selectedSamples);
    selectedSampleInfo = getSelectedSamples(selectedSamples);
console.log(selectedSampleInfo);
    updateChart();
}


function getSelectedSampleMeasurements(selectedSamples) {
//console.log('getSelectedSampleMeasurements',selectedSamples,selectedSamples.length);
    selectedMeas = {};
    for (let i=0; i < selectedSamples.length; i++) {
        let parts = selectedSamples[i].split(": ");
        if (parts.length>2) {
            parts[1] = parts[1] + ': ' + parts[2];
        }
        dateSampled = parts[0];
        sample = parts[1];
        let dataset = sampleMeasurements[dateSampled];
        if (!selectedMeas[dateSampled]) {
            selectedMeas[dateSampled] = {};
        }
        const chemicalTypes = Object.keys(sampleMeasurements[dateSampled]);
        for (const chemicalType in sampleMeasurements[dateSampled]) {
            if (!selectedMeas[dateSampled][chemicalType]) {
                //console.log('Create ', dateSampled);
                selectedMeas[dateSampled][chemicalType] = {};
            }
//console.log(dateSampled,sample,chemicalType);
            if (chemicalType === 'Physical Data') {
                if (!selectedMeas[dateSampled][chemicalType].samples) {
                    selectedMeas[dateSampled][chemicalType].samples = {};
                    selectedMeas[dateSampled][chemicalType]['Unit of measurement'] = sampleMeasurements[dateSampled][chemicalType]['Unit of measurement'];
                    selectedMeas[dateSampled][chemicalType].sizes = sampleMeasurements[dateSampled][chemicalType].sizes;
//console.log('1 psd selectedMeas ',dateSampled,chemicalType,selectedMeas);
//console.log('2 psd selectedMeas ',dateSampled,chemicalType,selectedMeas);
                }
                if (sampleMeasurements[dateSampled][chemicalType].samples[sample] !== undefined) {
                    selectedMeas[dateSampled][chemicalType].samples[sample] = sampleMeasurements[dateSampled][chemicalType].samples[sample];
                }
            } else {
                        //    						for (const chemicalType in sampleMeasurements[dateSampled]) {
                let newData = {};
                if (selectedMeas[dateSampled]?.[chemicalType]) {
                    newData = selectedMeas[dateSampled][chemicalType];
                } else {
                    newData = {};
                }
console.log(chemicalType, dataset, newData);
                for (const key in dataset[chemicalType]) {
                    let currentData = dataset[chemicalType][key];
console.log(chemicalType,key,currentData);
                    if (key === 'chemicals') {
                        if (!newData.chemicals) {
                            newData.chemicals = {};
                            for (const chemical in dataset[chemicalType].chemicals) {
                                    //console.log('Create ', dateSampled, chemicalType,chemical);
                                newData.chemicals[chemical] = {};
                                newData.chemicals[chemical].samples = {};
                                if (currentData[chemical].samples[sample] !== undefined) {
                                    newData.chemicals[chemical].samples[sample] = currentData[chemical].samples[sample];
                                }
                            }
                        } else {
                            newData.chemicals = selectedMeas[dateSampled][chemicalType].chemicals;
                            for (const chemical in dataset[chemicalType].chemicals) {
//console.log('Create ', dateSampled, chemicalType, chemical,newData, currentData);
                                if (currentData[chemical].samples[sample] !== undefined) {
                                    newData.chemicals[chemical].samples[sample] = currentData[chemical].samples[sample];
                                }
                            }
                        }
                    } else {
                        if (isSingleValue(currentData)) {
                            if (!newData[key]) {
                                newData[key] = currentData;
                            }
                        } else {
//if (key === 'gorhamTest') {
console.log(dateSampled,sample,key,currentData,newData);
//}
                            if (currentData) {
                                if (!newData[key]) {
                                    newData[key] = {};
                                }
                                if (currentData[sample] !== undefined) {
                                    newData[key][sample] = currentData[sample];
                                }
                            }
                        }
                    }
                }
//console.log(newData);
                selectedMeas[dateSampled][chemicalType] = newData;
            }
        }
    }
//console.log(selectedMeas); // Output each cell value to console
    return selectedMeas;
}

function getSelectedSamples(selectedSamples) {
    let selectedSamps = {};
//let numberNow = 0;
    for (let i=0; i < selectedSamples.length; i++) {
        let parts = selectedSamples[i].split(": ");
        if (parts.length>2) {
            parts[1] = parts[1] + ': ' + parts[2];
        }
        dateSampled = parts[0];
        sample = parts[1];

//    for (const dateSampled in selectedSampleInfo) {
//        for (const sample in selectedSampleInfo[dateSampled].position) {
//numberNow += 1;
//            if (selectedSamples.includes(dateSampled + ': ' + sample)) {
                // console.log('a point ' + dateSampled + ': ' + sample);
        if (!selectedSamps[dateSampled]) {
            selectedSamps[dateSampled] = {};
        }
        for (const key in selectedSampleInfo[dateSampled]) {
            currentData = selectedSampleInfo[dateSampled][key];
            if (isSingleValue(currentData)) {
                selectedSamps[dateSampled][key] = currentData;
            } else {
                if (!selectedSamps[dateSampled][key]) {
                    selectedSamps[dateSampled][key] = {};
                }
//console.log(dateSampled, sample, currentData, selectedSamps);
                selectedSamps[dateSampled][key][sample] = currentData[sample];
            }
        }
    }
//    selectedSampleInfo = selectedSamps;
//console.log(selectedSamps); // Output each cell value to console
//console.log('numberNow',numberNow);
fred=selectedSamps;
    return selectedSamps;
}

function clearSelections() {
    selectedSampleMeasurements = sampleMeasurements;
    selectedSampleInfo = sampleInfo;
    updateChart();
}

function populateAreaFilter() {
    const areaSelect = document.getElementById('areaSelect');

    if (!areaSelect) return;

    // Clear existing options except the first "Select an Area"
    areaSelect.innerHTML = '<option value="">-- Select an Area --</option>';    

    // Check if we have shapes loaded (allShapeLayers is global from sdeMaps.js)
    if (typeof allShapeLayers === 'undefined' || allShapeLayers.length === 0) {
        const option = document.createElement('option');
        option.text = "No shapes loaded";
        option.disabled = true;
        areaSelect.appendChild(option);
        return;
    }

    allShapeLayers.forEach((layer, index) => {
        // 1. Extract Name
        // We try standard properties, then the tooltip if properties are missing
        let name = layer.options?.name || layer.name || layer.feature?.properties?.name || "Unnamed Area";
        
        // If name is still generic, try to parse it from the binded Tooltip content
        if ((name === "Unnamed Area" || name === "") && layer.getTooltip()) {
            const tooltipContent = layer.getTooltip().getContent();
            // Regex to strip HTML tags like <b>Name</b>
            const div = document.createElement("div");
            div.innerHTML = tooltipContent;
            name = div.innerText.split('\n')[0] || "Unnamed Area";
        }

        // 2. Extract Area
        // We recalculate it here to be safe, ensuring consistency with sdeMaps.js
        let areaHa = 0;
        const latLngs = layer.getLatLngs();
        if (Array.isArray(latLngs) && latLngs.length > 0) {
             // Handle simple polygons vs polygons with holes/multipolygons
             if (Array.isArray(latLngs[0]) && !Array.isArray(latLngs[0][0]) && typeof latLngs[0][0] !== 'number') {
                // Polygon with holes or simple nested array
                let areaM2 = L.GeometryUtil.geodesicArea(latLngs[0]);
                for (let i = 1; i < latLngs.length; i++) {
                    areaM2 -= L.GeometryUtil.geodesicArea(latLngs[i]);
                }
                areaHa = areaM2 / 10000;
            } else {
                // Simple Polygon
                areaHa = L.GeometryUtil.geodesicArea(latLngs) / 10000;
            }
        }

        // 3. Create Option
        const option = document.createElement('option');
        option.value = index; // We use the index in allShapeLayers array as the value
        option.text = `${name} (${areaHa.toFixed(2)} ha)`;
        areaSelect.appendChild(option);
    });
}

/**
 * Triggered when the user selects an area from the dropdown.
 * Unchecks all samples, then checks only those falling inside the selected polygon.
 */
function applyAreaFilter() {
    const areaSelect = document.getElementById('areaSelect');
    const selectedIndex = areaSelect.value;

    // If no area selected, do nothing (or reset? usually better to do nothing so other filters work)
    if (selectedIndex === "") return;

    const selectedLayer = allShapeLayers[parseInt(selectedIndex)];
    if (!selectedLayer) return;

    // 1. Deselect all checkboxes first
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
    checkboxes.forEach(cb => cb.checked = false);

    // 2. Iterate all samples and check if inside polygon
    // Note: selectedSampleInfo is global from the main app
    for (const dateSampled in selectedSampleInfo) {
        for (const sample in selectedSampleInfo[dateSampled].position) {
            
            // Get Sample Coordinates
            const lat = parseFloat(selectedSampleInfo[dateSampled].position[sample]['Position latitude']);
            const lon = parseFloat(selectedSampleInfo[dateSampled].position[sample]['Position longitude']);

            if (isNaN(lat) || isNaN(lon)) continue;

            // Check if point is inside the selected layer
            if (isPointInLayer(lat, lon, selectedLayer)) {
                // Check the specific checkbox
                // ID format from openSampleSelection: `sample_${dateSampled + ': ' + sample}`
                const checkBoxId = `sample_${dateSampled}: ${sample}`;
                const checkbox = document.getElementById(checkBoxId);
                if (checkbox) checkbox.checked = true;
            }
        }
    }
}

/**
 * Helper: Checks if a Lat/Lon is inside a Leaflet Polygon Layer.
 * Handles Polygons, Polygons with holes, and MultiPolygons.
 */
function isPointInLayer(lat, lon, layer) {
    const point = [lat, lon];
    const latlngs = layer.getLatLngs();

    // Leaflet stores LatLngs differently depending on shape complexity:
    // 1. Simple Polygon: [ [Lat,Lon], [Lat,Lon] ... ]  (Wait, Leaflet uses objects usually, but we need points)
    //    Actually Leaflet .getLatLngs() returns [ L.LatLng, L.LatLng... ] for simple,
    //    or [ [L.LatLng...], [L.LatLng...] ] for holes/multipolygons.
    
    // Helper to run Ray Casting on a ring of L.LatLng objects
    function isInsideRing(pt, ring) {
        let x = pt[0], y = pt[1];
        let inside = false;
        for (let i = 0, j = ring.length - 1; i < ring.length; j = i++) {
            let xi = ring[i].lat, yi = ring[i].lng;
            let xj = ring[j].lat, yj = ring[j].lng;
            
            let intersect = ((yi > y) != (yj > y)) &&
                (x < (xj - xi) * (y - yi) / (yj - yi) + xi);
            if (intersect) inside = !inside;
        }
        return inside;
    }

    // Determine structure depth
    // Case A: Simple Polygon (Level 1 array of objects) - Leaflet often wraps this in an array too [[...]]
    // Case B: Polygon with holes (Level 2 array: [OuterRing, Hole1, Hole2])
    // Case C: MultiPolygon (Level 3 array)

    // We normalize to handle the specific Leaflet structure
    let rings = latlngs;
    
    // If it's a flat array of LatLng objects (rare in imported KMLs, usually wrapped), wrap it
    if (latlngs[0] && ('lat' in latlngs[0])) {
        rings = [latlngs];
    }

    // Check Outer Ring (Index 0)
    // For MultiPolygons, we might need deeper iteration, but usually KML import results in
    // distinct Polygon layers. Assuming Simple Polygon or Polygon w/ Holes here.
    
    // If MultiPolygon (array of arrays of arrays), we need to check if it's in ANY of them
    if (Array.isArray(rings[0]) && Array.isArray(rings[0][0])) {
         // It is likely a MultiPolygon or just deeply nested. 
         // We iterate all top-level shapes.
         for (let i = 0; i < rings.length; i++) {
             // For each polygon in the multipolygon, check inside outer ring (index 0)
             // ignoring holes for simplicity or recurse if strictness needed
             if (isInsideRing(point, rings[i][0] || rings[i])) return true;
         }
         return false;
    }
    
    // Standard Polygon (Index 0 is outer boundary, 1+ are holes)
    const insideOuter = isInsideRing(point, rings[0]);
    if (!insideOuter) return false;

    // If inside outer, check holes (if any exist)
    if (rings.length > 1) {
        for (let i = 1; i < rings.length; i++) {
            if (isInsideRing(point, rings[i])) {
                return false; // It's in a hole, so it's outside
            }
        }
    }

    return true;
}

function createStandardFilterUI() {
    const sampleCheckboxes = document.getElementById('sampleCheckboxes');
    if (!sampleCheckboxes) return;

    let container = document.getElementById('standardFilterContainer');
    if (!container) {
        container = document.createElement('div');
        container.id = 'standardFilterContainer';
        container.style.marginBottom = '10px';
        container.style.padding = '5px';
        container.style.borderBottom = '1px solid #ccc';
        sampleCheckboxes.parentNode.insertBefore(container, sampleCheckboxes);
    } else {
        container.innerHTML = '';
    }

    const title = document.createElement('div');
    title.innerHTML = '<strong>Filter by ' + chosenStandard + ':</strong>';
    container.appendChild(title);

    if (typeof standards === 'undefined' || !standards[chosenStandard]) return;
    const std = standards[chosenStandard];

    const options = [
        { label: "None", value: -1 },
        { label: "Above " + (std.levelNames && std.levelNames[0] ? std.levelNames[0] : "Action Level 1"), value: 0 },
        { label: "Above " + (std.levelNames && std.levelNames[1] ? std.levelNames[1] : "Action Level 2"), value: 1 }
    ];

    options.forEach(opt => {
        const wrapper = document.createElement('div');
        wrapper.style.display = 'inline-block';
        wrapper.style.marginRight = '15px';

        const radio = document.createElement('input');
        radio.type = 'radio';
        radio.name = 'standardFilter';
        radio.id = 'stdFilter_' + opt.value;
        radio.value = opt.value;
        if (opt.value === -1) radio.checked = true;
        
        radio.addEventListener('change', () => applyStandardFilter(opt.value));

        const label = document.createElement('label');
        label.htmlFor = 'stdFilter_' + opt.value;
        label.textContent = opt.label;
        label.style.marginLeft = '5px';

        wrapper.appendChild(radio);
        wrapper.appendChild(label);
        container.appendChild(wrapper);
    });
}

function applyStandardFilter(levelIndex) {
    levelIndex = parseInt(levelIndex);
    const checkboxes = document.querySelectorAll('#sampleCheckboxes input[type="checkbox"]');
    
    if (levelIndex === -1) {
        checkboxes.forEach(cb => cb.checked = true);
        return;
    }

    if (typeof standards === 'undefined' || !standards[chosenStandard]) return;
    const std = standards[chosenStandard];
    const stdUnit = extractUnit(std.unit);

    checkboxes.forEach(cb => cb.checked = false);
    const samplesToKeep = new Set();

    for (const ds in selectedSampleMeasurements) {
        const dataset = selectedSampleMeasurements[ds];
        for (const sheetName in dataset) {
            const sheet = dataset[sheetName];
            if (!sheet.chemicals) continue;
            const sheetUnit = extractUnit(sheet['Unit of measurement']);
            const factor = factorUnit(sheetUnit, stdUnit);

            for (const chemName in sheet.chemicals) {
                let limit = null;
                if (std.chemicals && std.chemicals[chemName] && Array.isArray(std.chemicals[chemName])) {
                    limit = std.chemicals[chemName][levelIndex];
                }
                if (limit !== null && limit !== undefined) {
                    const samples = sheet.chemicals[chemName].samples;
                    for (const sampleName in samples) {
                        const val = samples[sampleName];
                        if (val !== undefined && val !== null && (val * factor) > limit) {
                            samplesToKeep.add(ds + ': ' + sampleName);
                        }
                    }
                }
            }
        }
    }
    checkboxes.forEach(cb => {
        if (samplesToKeep.has(cb.value)) cb.checked = true;
    });
}