CODE EXAMPLE FOR JAVASCRIPT

jstree select all visible node only

var nodes = $('#tree').jstree(true).get_json("#", { flat: true });
         $.each(nodes, function (index, value) {
             var node = $("#schema").jstree().get_node(this.id);
             if (!node.state.hidden) {
                 $("#tree").jstree("select_node", node.id);
             }          

});