ImportHPAImagesJS.imjoy.html

<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>

<config lang="json">
{
  "name": "ImportHPAImagesJS",
  "type": "web-worker",
  "version": "0.1.0",
  "description": "[TODO: describe this plugin with one sentence.]",
  "tags": [],
  "ui": "",
  "cover": "",
  "inputs": null,
  "outputs": null,
  "flags": [],
  "icon": "extension",
  "api_version": "0.1.6",
  "env": "",
  "permissions": [],
  "requirements": [],
  "dependencies": []
}
</config>

<script lang="javascript">
const images_train = [
    'https://images.proteinatlas.org/48363/780_E12_2',
    'https://images.proteinatlas.org/41082/733_D4_2',
    'https://images.proteinatlas.org/3733/992_A2_1',
    'https://images.proteinatlas.org/41082/721_D4_1',
    'https://images.proteinatlas.org/50418/816_E1_1',
    'https://images.proteinatlas.org/50418/777_E1_2',
    'https://images.proteinatlas.org/3733/1432_H3_1',
    'https://images.proteinatlas.org/58509/1039_A5_1',
    'https://images.proteinatlas.org/41082/684_C4_2',
    'https://images.proteinatlas.org/44227/747_G1_2',
    'https://images.proteinatlas.org/14060/105_G9_1',
    'https://images.proteinatlas.org/48363/788_E12_1',
    'https://images.proteinatlas.org/44227/713_G1_1',
    'https://images.proteinatlas.org/3733/992_A2_2',
    'https://images.proteinatlas.org/58509/1037_A5_3',
    'https://images.proteinatlas.org/50418/790_E1_2',
    'https://images.proteinatlas.org/14060/107_G9_2',
    'https://images.proteinatlas.org/44227/714_G1_2',
    'https://images.proteinatlas.org/44227/si31_G10_7',
    'https://images.proteinatlas.org/14060/107_G9_1'    
]

const images_test = [
    'https://images.proteinatlas.org/41082/860_D8_1',
    'https://images.proteinatlas.org/44227/713_G1_3',
    'https://images.proteinatlas.org/44227/si31_G12_11',
    'https://images.proteinatlas.org/41082/684_C4_1'
]

const more_images = [
    'https://images.proteinatlas.org/16562/132_D2_1',
    'https://images.proteinatlas.org/19589/175_B12_1',
    'https://images.proteinatlas.org/50306/789_D9_1',
    'https://images.proteinatlas.org/50306/789_D9_2',
    'https://images.proteinatlas.org/63553/1226_A7_3',
    'https://images.proteinatlas.org/16562/132_D2_2',
    'https://images.proteinatlas.org/41219/557_E9_2',
    'https://images.proteinatlas.org/41219/493_E9_2',
    'https://images.proteinatlas.org/63553/1226_A7_5',
    'https://images.proteinatlas.org/19589/175_B12_2',
    'https://images.proteinatlas.org/41219/557_E9_1',
    'https://images.proteinatlas.org/41227/485_D12_3',
    'https://images.proteinatlas.org/19589/174_B12_2',
    'https://images.proteinatlas.org/19589/174_B12_1',
    'https://images.proteinatlas.org/41227/485_D12_2',
    'https://images.proteinatlas.org/16562/164_D2_1',
    'https://images.proteinatlas.org/63553/1139_C2_1',
    'https://images.proteinatlas.org/16562/131_D2_1',
    'https://images.proteinatlas.org/41219/493_E9_1',
    'https://images.proteinatlas.org/41227/494_D12_1',
    'https://images.proteinatlas.org/41227/488_D12_1',
    'https://images.proteinatlas.org/16562/164_D2_2',
    'https://images.proteinatlas.org/63553/1132_C2_2',
    'https://images.proteinatlas.org/41227/488_D12_2',
    'https://images.proteinatlas.org/63553/1132_C2_1',
    'https://images.proteinatlas.org/41227/494_D12_3',
    'https://images.proteinatlas.org/63553/1139_C2_2',
    'https://images.proteinatlas.org/41219/502_E9_2',
    'https://images.proteinatlas.org/19589/176_B12_1',
    'https://images.proteinatlas.org/16562/131_D2_2'
]

new_images = [
    'https://images.proteinatlas.org/40758/557_C6_1_blue_red_green.jpg',
    'https://images.proteinatlas.org/40758/557_C6_2_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/862_B4_1_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/862_B4_2_blue_red_green.jpg',
    'https://images.proteinatlas.org/64645/1873_H8_2_blue_red_green.jpg',
    'https://images.proteinatlas.org/64645/1873_H8_5_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/867_A2_1_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/867_A2_2_blue_red_green.jpg',
    'https://images.proteinatlas.org/40758/493_C6_1_blue_red_green.jpg',
    'https://images.proteinatlas.org/40758/493_C6_2_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/859_B4_1_blue_red_green.jpg',
    'https://images.proteinatlas.org/41824/859_B4_3_blue_red_green.jpg',
    'https://images.proteinatlas.org/64645/1199_C12_5_blue_red_green.jpg',
    'https://images.proteinatlas.org/64645/1199_C12_6_blue_red_green.jpg',
    'https://images.proteinatlas.org/40758/502_C6_3_blue_red_green.jpg' 
    ]

function filter_images(new_images){
    const seged_images = more_images.concat(images_test).concat(images_train)
    for(let i=0;i<new_images.length;i++){
        new_images[i] = new_images[i].split('_').slice(0,3).join('_')
    }
    new_images = seged_images.concat(new_images)
    return new_images
}


function format_path(path){
    const arr = path.split('/');
    return arr.slice(arr.length-2).join('_')
}
function link_name(path){
    //"""find the link and path to images"""
    links_names = {}
    links_names['name'] = format_path(path)
    links_names['data'] = {'All': {}, 'Microtubules': {}, 'Antibody': {}, 'Nucleus': {}, 'ER': {}}
    links_names['data']['All']['url'] = path + '_blue_red_green_yellow.jpg'
    links_names['data']['All']['file_name'] = format_path(links_names['data']['All']['url'])

    links_names['data']['Microtubules']['url'] = path + '_red.jpg'
    links_names['data']['Microtubules']['file_name'] = format_path(links_names['data']['Microtubules']['url'])

    links_names['data']['Antibody']['url'] = path + '_green.jpg'
    links_names['data']['Antibody']['file_name'] = format_path(links_names['data']['Antibody']['url'])

    links_names['data']['Nucleus']['url'] = path + '_blue.jpg'
    links_names['data']['Nucleus']['file_name'] = format_path(links_names['data']['Nucleus']['url'])

    links_names['data']['ER']['url'] = path + '_yellow.jpg'
    links_names['data']['ER']['file_name'] = format_path(links_names['data']['ER']['url'])

    links_names['group'] = 'train'
    return links_names

}

function samples_generate(images_train){
    return images_train.map(item=>link_name(item))
}

const True = true;

const default_dataset = {
    'api_version': '0.1.6',
    'version': 5,
    'name': 'hap-segmentation',
    'root_folder': '/home/hap-segmentation',
    'samples': samples_generate(filter_images(new_images)),

    'annotation_types':{
        "cell":{
            "label":"cell",
            "color":"#3f51b5",
            "line_width":4,
            "type":"Polygon",
            "freehand":True,
            "checked":True
        },
        "nuclei":{
            "label":"nuclei",
            "color":"#ff9800",
            "line_width":4,
            "type":"Polygon",
            "freehand":True,
            "checked":True
        }
    },
    'channel_config': {
        "All": {
            'filter': '_blue_red_green_yellow.jpg',
            'name': 'All'
        },
        "Microtubules": {
            'filter': '_red.jpg',
            'name': 'Microtubules'
        },
        "Antibody": {
            'filter': '_green.jpg',
            'name': 'Antibody'
        },
        "Nucleus": {
            'filter': '_blue.jpg',
            'name': 'Nucleus'
        },
        "ER": {
            'filter': '_yellow.jpg',
            'name': 'ER'
        }
    }
}

console.log('====================>', default_dataset)

class ImJoyPlugin{
    setup(){
        api.log('initialized')
    }
        
    loadData(win){
        win.importSampleComplete(default_dataset, True)
    }
        
    async run(ctx){
        const window = await api.createWindow({'name': 'Annotator', 'type': 'ImageAnnotator', 'data': {}})
        await this.loadData(window)
    }
}

api.export(new ImJoyPlugin())
</script>