Patient Flow Sankey Particles

.block

license: CC0-1.0
border: none

.gitignore

node_modules

README.md

a Sankey Particles visualization of patient flow through an orthopaedic clinic

paper Enabling measuring of the patient flow in an orthopaedic clinic [abstract] [pdf] [data]

This research enables measuring of the patient flow in the orthopaedic clinic
in the Sint Maartenskliniek (SMK). An in-depth understanding of
the patient flow process is required in order to identify areas for improvement
and by that make the patient flow process more efficient.

Figure 17 presents the Sankey diagram of the patient flow. Data from the period
2012-2016 is used.

100% of the patients is initially referred to the first consult outpatient clinic
where the 100% arrives.

64% of the patients do not receive an OR-receipt against the other
36% of patients that receive an OR-receipt.

From the patients that receive an OR-receipt only 67% percent receives surgery.
The other 33% cannot receive surgery based on the results of the screening.

16% of the patients that receive surgery are patients within one of the
four emergency categories.

84% of the patients that receive surgery are not emergency patients.

this bl.ock forks the City of Oakland Budget Proposal Sankey Particles bl.ock which in turn is an iteration on the bl.ock Sankey Particles III by @Elijah_Meeks

---

Original README.md:

Using particles to indicate flow between reservoirs in a sankey diagram. This time with particles moving at varying speeds and maintaining the color of the source node. You can drag the reservoirs (the rectangles) to adjust the path of the flows.

Other examples of sankeys with particles:

• Fixed speed particles transitioning in color from source node color to target node color.

• Particles of differing sizes and differing speeds moving in "bursts" between nodes.

d3.sankey.js

d3.sankey = function() {
  var sankey = {},
      nodeWidth = 24,
      nodePadding = 8,
      size = [1, 1],
      nodes = [],
      links = [];

  sankey.nodeWidth = function(_) {
    if (!arguments.length) return nodeWidth;
    nodeWidth = +_;
    return sankey;
  };

  sankey.nodePadding = function(_) {
    if (!arguments.length) return nodePadding;
    nodePadding = +_;
    return sankey;
  };

  sankey.nodes = function(_) {
    if (!arguments.length) return nodes;
    nodes = _;
    return sankey;
  };

  sankey.links = function(_) {
    if (!arguments.length) return links;
    links = _;
    return sankey;
  };

  sankey.size = function(_) {
    if (!arguments.length) return size;
    size = _;
    return sankey;
  };

  sankey.layout = function(iterations) {
    computeNodeLinks();
    computeNodeValues();
    computeNodeBreadths();
    computeNodeDepths(iterations);
    computeLinkDepths();
    return sankey;
  };

  sankey.relayout = function() {
    computeLinkDepths();
    return sankey;
  };

  sankey.link = function() {
    var curvature = .5;

    function link(d) {
      var x0 = d.source.x + d.source.dx,
          x1 = d.target.x,
          xi = d3.interpolateNumber(x0, x1),
          x2 = xi(curvature),
          x3 = xi(1 - curvature),
          y0 = d.source.y + d.sy + d.dy / 2,
          y1 = d.target.y + d.ty + d.dy / 2;
      return "M" + x0 + "," + y0
           + "C" + x2 + "," + y0
           + " " + x3 + "," + y1
           + " " + x1 + "," + y1;
    }

    link.curvature = function(_) {
      if (!arguments.length) return curvature;
      curvature = +_;
      return link;
    };

    return link;
  };

  // Populate the sourceLinks and targetLinks for each node.
  // Also, if the source and target are not objects, assume they are indices.
  function computeNodeLinks() {
    nodes.forEach(function(node) {
      node.sourceLinks = [];
      node.targetLinks = [];
    });
    links.forEach(function(link) {
      var source = link.source,
          target = link.target;
      if (typeof source === "number") source = link.source = nodes[link.source];
      if (typeof target === "number") target = link.target = nodes[link.target];
      source.sourceLinks.push(link);
      target.targetLinks.push(link);
    });
  }

  // Compute the value (size) of each node by summing the associated links.
  function computeNodeValues() {
    nodes.forEach(function(node) {
      node.value = Math.max(
        d3.sum(node.sourceLinks, value),
        d3.sum(node.targetLinks, value)
      );
    });
  }

  // Iteratively assign the breadth (x-position) for each node.
  // Nodes are assigned the maximum breadth of incoming neighbors plus one;
  // nodes with no incoming links are assigned breadth zero, while
  // nodes with no outgoing links are assigned the maximum breadth.
  function computeNodeBreadths() {
    var remainingNodes = nodes,
        nextNodes,
        x = 0;

    while (remainingNodes.length) {
      nextNodes = [];
      remainingNodes.forEach(function(node) {
        node.x = x;
        node.dx = nodeWidth;
        node.sourceLinks.forEach(function(link) {
          if (nextNodes.indexOf(link.target) < 0) {
            nextNodes.push(link.target);
          }
        });
      });
      remainingNodes = nextNodes;
      ++x;
    }

    //
    moveSinksRight(x);
    scaleNodeBreadths((size[0] - nodeWidth) / (x - 1));
  }

  function moveSourcesRight() {
    nodes.forEach(function(node) {
      if (!node.targetLinks.length) {
        node.x = d3.min(node.sourceLinks, function(d) { return d.target.x; }) - 1;
      }
    });
  }

  function moveSinksRight(x) {
    nodes.forEach(function(node) {
      if (!node.sourceLinks.length) {
        node.x = x - 1;
      }
    });
  }

  function scaleNodeBreadths(kx) {
    nodes.forEach(function(node) {
      node.x *= kx;
    });
  }

  function computeNodeDepths(iterations) {
    var nodesByBreadth = d3.nest()
        .key(function(d) { return d.x; })
        .sortKeys(d3.ascending)
        .entries(nodes)
        .map(function(d) { return d.values; });

    //
    initializeNodeDepth();
    resolveCollisions();
    for (var alpha = 1; iterations > 0; --iterations) {
      relaxRightToLeft(alpha *= .99);
      resolveCollisions();
      relaxLeftToRight(alpha);
      resolveCollisions();
    }

    function initializeNodeDepth() {
      var ky = d3.min(nodesByBreadth, function(nodes) {
        return (size[1] - (nodes.length - 1) * nodePadding) / d3.sum(nodes, value);
      });

      nodesByBreadth.forEach(function(nodes) {
        nodes.forEach(function(node, i) {
          node.y = i;
          node.dy = node.value * ky;
        });
      });

      links.forEach(function(link) {
        link.dy = link.value * ky;
      });
    }

    function relaxLeftToRight(alpha) {
      nodesByBreadth.forEach(function(nodes, breadth) {
        nodes.forEach(function(node) {
          if (node.targetLinks.length) {
            var y = d3.sum(node.targetLinks, weightedSource) / d3.sum(node.targetLinks, value);
            node.y += (y - center(node)) * alpha;
          }
        });
      });

      function weightedSource(link) {
        return center(link.source) * link.value;
      }
    }

    function relaxRightToLeft(alpha) {
      nodesByBreadth.slice().reverse().forEach(function(nodes) {
        nodes.forEach(function(node) {
          if (node.sourceLinks.length) {
            var y = d3.sum(node.sourceLinks, weightedTarget) / d3.sum(node.sourceLinks, value);
            node.y += (y - center(node)) * alpha;
          }
        });
      });

      function weightedTarget(link) {
        return center(link.target) * link.value;
      }
    }

    function resolveCollisions() {
      nodesByBreadth.forEach(function(nodes) {
        var node,
            dy,
            y0 = 0,
            n = nodes.length,
            i;

        // Push any overlapping nodes down.
        nodes.sort(ascendingDepth);
        for (i = 0; i < n; ++i) {
          node = nodes[i];
          dy = y0 - node.y;
          if (dy > 0) node.y += dy;
          y0 = node.y + node.dy + nodePadding;
        }

        // If the bottommost node goes outside the bounds, push it back up.
        dy = y0 - nodePadding - size[1];
        if (dy > 0) {
          y0 = node.y -= dy;

          // Push any overlapping nodes back up.
          for (i = n - 2; i >= 0; --i) {
            node = nodes[i];
            dy = node.y + node.dy + nodePadding - y0;
            if (dy > 0) node.y -= dy;
            y0 = node.y;
          }
        }
      });
    }

    function ascendingDepth(a, b) {
      return a.y - b.y;
    }
  }

  function computeLinkDepths() {
    nodes.forEach(function(node) {
      node.sourceLinks.sort(ascendingTargetDepth);
      node.targetLinks.sort(ascendingSourceDepth);
    });
    nodes.forEach(function(node) {
      var sy = 0, ty = 0;
      node.sourceLinks.forEach(function(link) {
        link.sy = sy;
        sy += link.dy;
      });
      node.targetLinks.forEach(function(link) {
        link.ty = ty;
        ty += link.dy;
      });
    });

    function ascendingSourceDepth(a, b) {
      return a.source.y - b.source.y;
    }

    function ascendingTargetDepth(a, b) {
      return a.target.y - b.target.y;
    }
  }

  function center(node) {
    return node.y + node.dy / 2;
  }

  function value(link) {
    return link.value;
  }

  return sankey;
};

graph.json

{
  "nodes": [
    {
      "name": "All referred patients",
      "id": 0
    },
    {
      "name": "First consult outpatient clinic",
      "id": 1
    },
    {
      "name": "No OR-receipt",
      "id": 2
    },
    {
      "name": "OR-receipt",
      "id": 3
    },
    {
      "name": "No surgery",
      "id": 4
    },
    {
      "name": "Start surgery",
      "id": 5
    },
    {
      "name": "Emergency",
      "id": 6
    },
    {
      "name": "No emergency",
      "id": 7
    }
  ],
  "links": [
    {
      "source": 0,
      "target": 1,
      "value": 1,
      "label": 1
    },
    {
      "source": 1,
      "target": 2,
      "value": 0.64,
      "label": 0.64
    },    
    {
      "source": 1,
      "target": 3,
      "value": 0.36,
      "label": 0.36
    },
    {
      "source": 3,
      "target": 4,
      "value": 0.1188,
      "label": 0.33
    },
    {
      "source": 3,
      "target": 5,
      "value": 0.2412,
      "label": 0.67
    },
    {
      "source": 5,
      "target": 6,
      "value": 0.038592,
      "label": 0.16
    },
    {
      "source": 5,
      "target": 7,
      "value": 0.20260799999999998,
      "label": 0.84
    }
  ]
}

index.html

<!DOCTYPE html>

<html lang='en'>
<head>
<meta charset='utf-8' />
<title>Sankey Particles</title>
</head>
<body>
<canvas width='1000' height='1000' ></canvas>
<svg width='1000' height='1000' ></svg>

<script src='https://d3js.org/d3.v3.min.js' charset='utf-8' type='text/javascript'></script>
<script src='d3.sankey.js' charset='utf-8' type='text/javascript'></script>
<script src='https://npmcdn.com/babel-core@5.8.34/browser.min.js'></script>
<script lang='babel' type='text/babel'>
  /* const canvas = */ d3.select('canvas')
    .style('position', 'absolute');

  const margin = { top: 1, right: 1, bottom: 6, left: 1 };
  const width = 960 - margin.left - margin.right;
  const height = 500 - margin.top - margin.bottom;

  const formatNumber = d3.format('.0%');
  const format = d => `${formatNumber(d)}`;
  const color = d3.scale.category20();

  const svg = d3.select('svg')
    .style('position', 'absolute')
    .attr('width', width + margin.left + margin.right)
    .attr('height', height + margin.top + margin.bottom)
    .append('g')
      .attr('transform', `translate(${margin.left}, ${margin.top})`);

  const sankey = d3.sankey()
    .nodeWidth(15)
    .nodePadding(10)
    .size([width, height]);

  const path = sankey.link();

  /* let freqCounter = 1; */


  d3.json('graph.json', graph => {
    sankey
      .nodes(graph.nodes)
      .links(graph.links)
      .layout(32);

    const link = svg.append('g').selectAll('.link')
      .data(graph.links)
      .enter().append('path')
        .attr('class', 'link')
        .attr('d', path)
        .style('stroke-width', d => Math.max(1, d.dy))
        .style({
          fill: 'none',
          stroke: '#000',
          'stroke-opacity': 0.15
        })
        .sort((a, b) => b.dy - a.dy)

    link
      .on('mouseover', function () {
        d3.select(this)
          .style('stroke-opacity', 0.25);
      })
      .on('mouseout', function () {
        d3.select(this)
          .style('stroke-opacity', 0.15);
      });

    link.append('title')
      .text(d => `${format(d.label)} of ${d.source.name} → ${d.target.name}\n${format(d.value)} of ${graph.nodes[0].name}`)

    const node = svg.append('g').selectAll('.node')
      .data(graph.nodes)
      .enter().append('g')
        .attr('class', 'node')
        .attr('transform', d => `translate(${d.x}, ${d.y})`)
        .call(d3.behavior.drag()
        .origin(d => d)
        .on('dragstart', function () { this.parentNode.appendChild(this); })
        .on('drag', dragmove));

    node.append('rect')
      .attr('height', d => d.dy)
      .attr('width', sankey.nodeWidth())
      .style('fill', (d, i) => {
        // d.color = color(d.name.replace(/ .*/, ''));
        d.color = color(i);
        return d.color;
      })
      .style({
        stroke: 'none',
        cursor: 'move',
        'fill-opacity': 0.9,
        'shape-rendering': 'crispEdges'
      })
      .append('title')
        .text(d => `${format(d.value)} ${d.name}`);

    node.append('text')
      .attr('x', -6)
      .attr('y', d => d.dy / 2)
      .attr('dy', '.35em')
      .attr('text-anchor', 'end')
      .attr('transform', null)
      .style({
        'pointer-events': 'none',
        'text-shadow': '0 1px 0 #fff',
        'font-size': '12px'

      })
      .text(d => d.name)
      .filter(d => d.x < width / 2)
        .attr('x', 6 + sankey.nodeWidth())
        .attr('text-anchor', 'start')
        .style('font-size', '12px');

    function dragmove(d) {
      d3.select(this)
        .attr('transform', `translate(${d.x}, ${(d.y = Math.max(0, Math.min(height - d.dy, d3.event.y)))})`);
      sankey.relayout();
      link.attr('d', path);
    }

    const linkExtent = d3.extent(graph.links, d => d.value);

    const frequencyScale = d3.scale.linear()
      .domain(linkExtent)
      .range([0.05, 1]);

    /* const particleSize = */ d3.scale.linear()
      .domain(linkExtent)
      .range([1, 5]);

    graph.links.forEach(currentLink => {
      currentLink.freq = frequencyScale(currentLink.value);
      currentLink.particleSize = 2;
      currentLink.particleColor = d3.scale.linear().domain([0, 1])
      .range([currentLink.source.color, currentLink.target.color]);
    });

    /* const t = */ d3.timer(tick, 1000);
    let particles = [];

    function tick(elapsed /* , time */) {
      particles = particles.filter(d => d.current < d.path.getTotalLength());

      d3.selectAll('path.link')
      .each(
        function (d) {
  //        if (d.freq < 1) {
          for (let x = 0; x < 2; x++) {
            const offset = (Math.random() - 0.5) * (d.dy - 4);
            if (Math.random() < d.freq) {
              const length = this.getTotalLength();
              particles.push({
                link: d,
                time: elapsed,
                offset,
                path: this,
                length,
                animateTime: length,
                speed: 0.5 + (Math.random())
              });
            }
          }
  //        }
  /*        else {
            for (let x = 0; x<d.freq; x++) {
              let offset = (Math.random() - .5) * d.dy;
              particles.push({link: d, time: elapsed, offset: offset, path: this})
            }
          } */
        });

      particleEdgeCanvasPath(elapsed);
    }

    function particleEdgeCanvasPath(elapsed) {
      const context = d3.select('canvas').node().getContext('2d');

      context.clearRect(0, 0, 1000, 1000);

      context.fillStyle = 'gray';
      context.lineWidth = '1px';
      for (const x in particles) {
        if ({}.hasOwnProperty.call(particles, x)) {
          const currentTime = elapsed - particles[x].time;
  //        let currentPercent = currentTime / 1000 * particles[x].path.getTotalLength();
          particles[x].current = currentTime * 0.15 * particles[x].speed;
          const currentPos = particles[x].path.getPointAtLength(particles[x].current);
          context.beginPath();
          context.fillStyle = particles[x].link.particleColor(0);
          context.arc(
            currentPos.x,
            currentPos.y + particles[x].offset,
            particles[x].link.particleSize,
            0,
            2 * Math.PI
          );
          context.fill();
        }
      }
    }
  });
</script>
</body>
</html>

preview.png

preview.xcf

thumbnail.png