Omero utility scripts

omero_figure_channel_names.js

javascript:(function(){
 let infotab = document.getElementById('infoTab').children[0].children[2];
 let channels = infotab.children[0].children[1].children[0].lastElementChild.textContent.trim().split(', ');
 let channelsliders = document.getElementById('channel_sliders').children[0];
 for(i=0;i<channels.length;i++) {
     let p = document.createTextNode(channels[i]);
     let br = document.createElement('br');
     channelsliders.children[i].insertBefore(br,channelsliders.children[i].firstChild);
     channelsliders.children[i].insertBefore(p,channelsliders.children[i].firstChild);
 }
})();

omero_grouping.js

javascript: (function () {
    const channel_headers = document.getElementsByClassName('channel-group-headers');
    let ic = Object.keys(angular.element(channel_headers).scope().model.indexedChannels).length;
    let n_channel_per_cycle = 4;
    let channel_colors = ['#0000FF', '#00FF00', '#FFFFFF', '#FF0000'];
    console.assert(channel_colors.length === n_channel_per_cycle);

    for (i = 0; i < ic / n_channel_per_cycle; i++) {
        angular.element(document.getElementsByClassName('btn-add-channel-group')).click();
        angular.element(channel_headers).scope().model.channelGroups[i].name = 'Cycle' + (i + 1);
        let curr_channels = [...Array(ic).keys()].slice(n_channel_per_cycle * i, n_channel_per_cycle * (i + 1));
        angular.element(channel_headers).scope().model.channelGroups[i].channels = curr_channels;

        curr_channels.forEach((el, idx) => {
            angular.element(channel_headers).scope().model.channels[el].color = channel_colors[idx];
        });
    }
    angular.element(channel_headers).scope().model.channelGroups[ic / n_channel_per_cycle].channels = [];
})();

omero_groupings_2.js

javascript: (function () {
    const channel_headers = document.getElementsByClassName('channel-group-headers');
    let n_channels = Object.keys(angular.element(channel_headers).scope().model.indexedChannels).length;
    let n_channel_per_cycle = [4, 5, 5, 4, 4, 4, 4, 4, 4, 4];

    let channel_colors = ['#0000FF', '#00FF00', '#FFFFFF', '#FF0000', '#00FFFF'];
    let _n_channels = n_channel_per_cycle.reduce((a, b) => a+b, 0);
    if (n_channels !== _n_channels) {
        alert(`Number of channel specified (${_n_channels}) does not match number of channels in the image (${n_channels})`);
        return;
    }

    for (i of n_channel_per_cycle.keys()) {
        let start = n_channel_per_cycle.slice(0, i).reduce((a, b) => a + b, 0);
        let end = n_channel_per_cycle.slice(0, i+1).reduce((a, b) => a + b, 0);
        let curr_channels = [...Array(n_channels).keys()].slice(start, end);
        
        angular.element(document.getElementsByClassName('btn-add-channel-group')).click();
        angular.element(channel_headers).scope().model.channelGroups[i].name = 'Cycle ' + (i + 1);
        angular.element(channel_headers).scope().model.channelGroups[i].channels = curr_channels;

        curr_channels.forEach((el, idx) => {
            angular.element(channel_headers).scope().model.channels[el].color = channel_colors[idx];
        });
    }

    let last_group = angular.element(channel_headers).scope().model.channelGroups.length - 1;
    angular.element(channel_headers).scope().model.channelGroups[last_group].channels = [];
})();

omero_roi_extraction.js

javascript:(function(){
 var imgId = parseInt(document.getElementById('info').children[0].children[3].children[0].children[0].textContent.split(': ')[1]);
 var headers = ['Name', 'X', 'Y', 'RadiusX', 'RadiusY', 'Width', 'Height'];
 var url = `https://omero.hms.harvard.edu/api/v0/m/images/${imgId}/`;
 var urlRoi = `https://omero.hms.harvard.edu/api/v0/m/rois/?image=${imgId}`;
 var imgName;
 fetch(url)
     .then(res => res.json())
     .then(resJson =>
         imgName = resJson.data.Name
     )
     .then(() => fetch(urlRoi)
         .then(res => res.json())
         .then(resJson =>
             resJson.data
                 .map(data => {
                     data.shapes[0].Name = data.Name || 'undefined';
                      return data.shapes
                 })
                 .reduce((acc, val) => acc.concat(val), [])
                 .map(shape => headers.map(header => shape[header] || -1))
         )
         .then(rois => rois.map(e => e.join(",")).join("\n"))
         .then(roisStr =>
              "data:text/csv;charset=utf-8," +
              headers.join(',') + '\n' +
             roisStr)
         .then(fullStr => encodeURI(fullStr))
         .then(uri => {
             let link = document.createElement("a");
             link.setAttribute("href", uri);
             link.setAttribute("download", `${imgName}-${imgId}-rois.csv`);
             document.body.appendChild(link);
              link.click();
         })
     )
 })();