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Merge branch 'Skyline/work/20250127_NoIterativeLeakTesting' of https:…
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…//github.com/ProteoWizard/pwiz into Skyline/work/20250127_NoIterativeLeakTesting
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@bspratt
bspratt committed Feb 18, 2025
2 parents 18eb8d4 + 50fff5a commit c54b7c2
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Showing 6 changed files with 162 additions and 31 deletions.
7 changes: 7 additions & 0 deletions pwiz_tools/Shared/zedgraph/ZedGraph/GraphPane.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,10 @@ public class GraphPane : PaneBase, ICloneable, ISerializable

private LabelLayout _labelLayout;

/// <summary>
/// Indicates if this graph pane has the LabelLayout object attached.
/// Setting it to false removes the layout object.
/// </summary>
public bool EnableLabelLayout
{
get => _labelLayout != null;
Expand Down Expand Up @@ -1561,7 +1565,10 @@ public void AdjustLabelSpacings(List<LabeledPoint> labPoints, List<LabeledPoint.
labeledPoint.Label.IsVisible = true;
}
else
{
labeledPoint.Label.IsVisible = false;
GraphObjList.Remove(labeledPoint.Connector);
}
}

if (visiblePoints.Any())
Expand Down
119 changes: 106 additions & 13 deletions pwiz_tools/Shared/zedgraph/ZedGraph/LabelLayout.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ private class GridCell
public float _density;
// public PointF _gradient;
public static Dictionary<Color, Brush> _brushes = new Dictionary<Color, Brush>();
public Point _indices;
}

// First index row, second index line
Expand All @@ -100,6 +101,7 @@ private void FillDensityGrid()
{
_location = location,
_bounds = new RectangleF(location, new SizeF(_cellSize, _cellSize)),
_indices = new Point(j, i)
};
}
}
Expand Down Expand Up @@ -129,15 +131,40 @@ private void FillDensityGrid()
}
}

private bool GetPointMarkerRectangle(PointF pt, out RectangleF rect)
{
rect = RectangleF.Empty;
foreach (var line in _graph.CurveList.OfType<LineItem>().Where(c => c.Symbol.Type != SymbolType.None))
{
for (var i = 0; i < line.Points.Count; i++)
{
var screenPt = _graph.TransformCoord(line.Points[i].X, line.Points[i].Y, CoordType.AxisXYScale);
if (Math.Abs(screenPt.X - pt.X) < 1 && Math.Abs(screenPt.Y - pt.Y) < 1 )

{
if (!line.GetCoords(this._graph, i, out var coords))
{
continue;
}
var sides = Array.ConvertAll(coords.Split(','), int.Parse);
rect = new Rectangle(sides[0], sides[1], sides[2] - sides[0], sides[3] - sides[1]);
return true;
} }
}
return false;
}

/// <summary>
/// Calculates goal function for a labeled point and a suggested label position.
/// All coordinates are in screen pixels.
/// </summary>
/// <param name="pt">Center of the label box, in pixels</param>
/// <param name="targetPoint">point being labeled.</param>
/// <param name="targetPoint">data point being labeled.</param>
/// <param name="labelSize"> in pixels </param>
/// <param name="targetMarkerRect"> enclosing rectangle of the target point marker. We want to avoid
/// overlaps with it as much as possible.</param>
/// <returns>goal function value.</returns>
private float GoalFuncion(PointF pt, PointF targetPoint, SizeF labelSize)
private float GoalFunction(PointF pt, PointF targetPoint, SizeF labelSize, RectangleF targetMarkerRect)
{
var pathCellCoord = CellIndexesFromXY(targetPoint);
if (!IndexesWithinGrid(pathCellCoord))
Expand All @@ -147,12 +174,16 @@ private float GoalFuncion(PointF pt, PointF targetPoint, SizeF labelSize)
// Distance to the label is measured from the center or right/left ends, whichever is closer.
var distPoints = new[]
{ pt - new SizeF(labelSize.Width / 2, 0), pt, pt + new SizeF(labelSize.Width / 2, 0) };
var graphWidth = _graph.Chart.Rect.Width;
var graphHeight = _graph.Chart.Rect.Height;
var dist = distPoints.Min(p =>
{
var diff = new SizeF(p.X - targetPoint.X, p.Y - targetPoint.Y);
return diff.Width * diff.Width + diff.Height * diff.Height;
// calculate the distance relative to the chart size to make sure it works
// for both large and small graphs
return diff.Width * diff.Width / (graphWidth * graphWidth) + diff.Height * diff.Height / (graphHeight * graphHeight);
});
var rect = new RectangleF(pt.X - labelSize.Width / 2, pt.Y - labelSize.Height / 2, labelSize.Width,
var rect = new RectangleF(pt.X - labelSize.Width / 2, pt.Y, labelSize.Width,
labelSize.Height);
var totalOverlap = 0.0;
foreach (var cell in GetRectangleCells(rect))
Expand All @@ -161,6 +192,9 @@ private float GoalFuncion(PointF pt, PointF targetPoint, SizeF labelSize)
totalOverlap += 1.0 * intersect.Height * intersect.Width / (_cellSize * _cellSize) * cell._density;
}

// overlap with the target point is bad, we should penalize it heavily
if (RectangleF.Intersect(rect, targetMarkerRect) != RectangleF.Empty)
totalOverlap += 1500;
// penalize this point if there is more points between it and its label
// we find the cells between the two points by traversing the vector intersection
// with the grid
Expand Down Expand Up @@ -218,7 +252,13 @@ private float GoalFuncion(PointF pt, PointF targetPoint, SizeF labelSize)
penalty += 2000;
}

return (float)((0.025 * dist + totalOverlap) + penalty + 0.2 * pathDensity);
// penalize the goal if the label is completely or partially outside of the chart area
var visibleArea = RectArea(RectangleF.Intersect(rect, _graph.Chart.Rect));
var clipPenalty = 0.0f;
if (visibleArea > 0)
clipPenalty = (1 - visibleArea / RectArea(rect)) * 500.0f;

return (float)((20000 * dist + totalOverlap) + penalty + 0.2 * pathDensity) + clipPenalty;
}

private IEnumerable<GridCell> GetRectangleCells(RectangleF rect)
Expand Down Expand Up @@ -256,16 +296,24 @@ private bool IndexesWithinGrid(Point pt)
return pt.X >= 0 && pt.X < _densityGridSize.Width && pt.Y >= 0 && pt.Y < _densityGridSize.Height;
}

/// <summary>
/// Uniform distribution searches the available area more efficiently.
/// </summary>
private int GetRandom(float range)
{
return (int)((_randGenerator.NextDouble() - 0.5) * (_randGenerator.NextDouble() - 0.5) * range * 1.5);
return (int)((_randGenerator.NextDouble() - 0.5) * range * 0.75);
}

private static Rectangle ToRectangle(RectangleF rect)
{
return new Rectangle((int)rect.X, (int)rect.Y, (int)rect.Width, (int)rect.Height);
}

private float RectArea(RectangleF rect) { return rect.Width * rect.Height; }

public const int SEARCH_COUNT_COARSE = 80;
public const int SEARCH_COUNT_FINE = 15;

/**
* Algorighm overview:
* Divide the graph into a grid with cell size equals the label height (the smallest dimension).
Expand All @@ -276,23 +324,41 @@ private static Rectangle ToRectangle(RectangleF rect)
* of the label relative to it's data point.
* The algorighm works in screen coordinates (pixels). There is no need to use user coordinates here.
* Returns true if the label has been successfully placed, false otherwise.
* Note that TextObj location is top-center, not top-left
*/
public bool PlaceLabel(LabeledPoint labPoint, Graphics g)
{
var labelRect = _graph.GetRectScreen(labPoint.Label, g);
// do not attempt placement if the chart is too small
if (labelRect.Height > _graph.Chart.Rect.Height)
return false;
if ((labelRect.Width / 2) > _graph.Chart.Rect.Width)
return false;

var targetPoint = _graph.TransformCoord(labPoint.Point.X, labPoint.Point.Y, CoordType.AxisXYScale);
var labelLength = (int)Math.Ceiling(1.0 * labelRect.Width / _cellSize);
var labelLength = (int)Math.Ceiling(1.0 * labelRect.Width / _cellSize); // label length in grid units

var pointCell = new Point((int)((targetPoint.X - _chartOffset.X) / _cellSize),
(int)((targetPoint.Y - _chartOffset.Y) / _cellSize));
if (!new Rectangle(Point.Empty, _densityGridSize).Contains(pointCell))
return false;
var goal = float.MaxValue;
var goalCell = Point.Empty;
var gridRect = new Rectangle(Point.Empty, _densityGridSize);
var gridRect = Rectangle.Empty;
// 4 is more or less arbitrary here, just to avoid search area 1 cell wide and make the search more efficient.
if (labelLength < _densityGridSize.Width - 4)
gridRect = new Rectangle(labelLength / 2 + 1, 0, _densityGridSize.Width - labelLength, _densityGridSize.Height - 1);
else
gridRect = new Rectangle(labelLength / 2 + 1, 0, _densityGridSize.Width - labelLength/2 - 1, _densityGridSize.Height - 1);
var points = new List<Point>();
for (var count = 80; count > 0; count--)

GetPointMarkerRectangle(targetPoint, out var targetMarkerRect);
var totalCount = SEARCH_COUNT_COARSE * 5;
for (var count = SEARCH_COUNT_COARSE; count > 0; count--)
{
// make sure we are not stuck in this loop if the search area is exhausted.
if (totalCount-- <= 0)
break;
var randomGridPoint = pointCell +
new Size(GetRandom(_densityGridSize.Width), GetRandom(_densityGridSize.Height));

Expand All @@ -308,7 +374,7 @@ public bool PlaceLabel(LabeledPoint labPoint, Graphics g)
}

points.Add(randomGridPoint);
var goalEstimate = GoalFuncion(CellFromPoint(randomGridPoint)._location, targetPoint, labelRect.Size);
var goalEstimate = GoalFunction(CellFromPoint(randomGridPoint)._location, targetPoint, labelRect.Size, targetMarkerRect);
if (goalEstimate < goal)
{
goal = goalEstimate;
Expand All @@ -319,12 +385,24 @@ public bool PlaceLabel(LabeledPoint labPoint, Graphics g)
var roughGoal = goal;
// Search the cell neighborhood for a better position
var goalPoint = _densityGrid[goalCell.Y][goalCell.X]._location;
for (var count = 15; count > 0; count--)
var chartRect = _graph.Chart.Rect;
var allowedRect = RectangleF.Empty;
if (chartRect.Width > labelRect.Width * 1.2)
{
allowedRect = new RectangleF(chartRect.X + labelRect.Width / 2, chartRect.Y,
chartRect.Width - labelRect.Width, chartRect.Height - labelRect.Height);
}
else
{
allowedRect = new RectangleF(chartRect.X + labelRect.Width / 2, chartRect.Y,
chartRect.Width - labelRect.Width / 2, chartRect.Height - labelRect.Height);
}
for (var count = SEARCH_COUNT_FINE; count > 0; count--)
{
var p = goalPoint + new Size(GetRandom(_cellSize * 2), GetRandom(_cellSize * 2));
if (!_graph.Chart.Rect.Contains(p))
if (!allowedRect.Contains(p)) // label should not overlap chart's borders
continue;
var goalEstimate1 = GoalFuncion(p, targetPoint, labelRect.Size);
var goalEstimate1 = GoalFunction(p, targetPoint, labelRect.Size, targetMarkerRect);
if (goalEstimate1 < goal)
{
goal = goalEstimate1;
Expand Down Expand Up @@ -354,6 +432,21 @@ public bool PlaceLabel(LabeledPoint labPoint, Graphics g)
return true;
}

// mostly for debugging support
public float CalculateGoalFunction(LabeledPoint labPoint)
{
if (labPoint == null)
return 0;
var targetPoint = _graph.TransformCoord(labPoint.Point.X, labPoint.Point.Y, CoordType.AxisXYScale);
var hasTargetMarker = GetPointMarkerRectangle(targetPoint, out var targetMarkerRect);
RectangleF labelRect;
using (var g = Graphics.FromHwnd(IntPtr.Zero))
labelRect = _graph.GetRectScreen(labPoint.Label, g);
var labScreenCoords = _graph.TransformCoord(labPoint.Label.Location.X, labPoint.Label.Location.Y, CoordType.AxisXYScale);
labScreenCoords = new PointF(labScreenCoords.X, labScreenCoords.Y - labelRect.Height/2);
return GoalFunction(labScreenCoords, targetPoint, labelRect.Size, targetMarkerRect);
}

/// <summary>
/// Places the label at the specified coordinates and updates the density grid so that
/// the future calls to PlaceLabel take avoid overlaps and crossovers with this label
Expand Down
5 changes: 4 additions & 1 deletion pwiz_tools/Shared/zedgraph/ZedGraph/ZedGraphControl.Events.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@

using System;
using System.ComponentModel;
using System.Diagnostics;
using System.Drawing;
using System.Drawing.Drawing2D;
using System.Windows.Forms;
Expand Down Expand Up @@ -1232,7 +1233,9 @@ private void HandleLabelDrag(Point mousePt)
_dragText.UpdateLabelLocation(xScale.AddInterval(_dragText.LabelPosition.X, startX, mouseX),
yScale.AddInterval(_dragText.LabelPosition.Y, startY, mouseY), _dragPane);

Invalidate();
if (_dragPane.Layout != null)
Trace.WriteLine(string.Format(@"Goal function: {0}", _dragPane.Layout.CalculateGoalFunction(_dragText)));
Invalidate();
}

private void HandleLabelDragFinish(MouseEventArgs e)
Expand Down
29 changes: 21 additions & 8 deletions pwiz_tools/Skyline/Controls/Graphs/SummaryRelativeAbundanceGraphPane.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -157,9 +157,21 @@ private void UpdateFormatting(IEnumerable<MatchRgbHexColor> colorRows)
/// </summary>
public void OnLabelOverlapPropertyChange(object sender, PropertyChangedEventArgs e)
{
if (e.PropertyName == @"GroupComparisonAvoidLabelOverlap")
if (e.PropertyName == nameof(Settings.Default.GroupComparisonAvoidLabelOverlap))
{
try
{
Settings.Default.PropertyChanged -= OnLabelOverlapPropertyChange;
Settings.Default.GroupComparisonSuspendLabelLayout = false;
}
finally
{
Settings.Default.PropertyChanged += OnLabelOverlapPropertyChange;
}
_labelsLayout = null;
GraphSummary.UpdateUI();
else if (e.PropertyName == @"GroupComparisonSuspendLabelLayout")
}
else if (e.PropertyName == nameof(Settings.Default.GroupComparisonSuspendLabelLayout))
{
if (!Settings.Default.GroupComparisonSuspendLabelLayout)
{
Expand Down Expand Up @@ -364,14 +376,15 @@ public override void UpdateGraph(bool selectionChanged)
UpdateAxes();
if (Settings.Default.GroupComparisonAvoidLabelOverlap)
{
if (Settings.Default.GroupComparisonSuspendLabelLayout)
{
AdjustLabelSpacings(_labeledPoints, _labelsLayout);
_labelsLayout = GraphSummary.GraphControl.GraphPane.Layout?.PointsLayout;
}
AdjustLabelSpacings(_labeledPoints, _labelsLayout);
_labelsLayout = GraphSummary.GraphControl.GraphPane.Layout?.PointsLayout;
}
else
DotPlotUtil.AdjustLabelLocations(_labeledPoints, GraphSummary.GraphControl.GraphPane.YAxis.Scale, GraphSummary.GraphControl.GraphPane.Rect.Height);
{
EnableLabelLayout = false;
DotPlotUtil.AdjustLabelLocations(_labeledPoints, GraphSummary.GraphControl.GraphPane.YAxis.Scale,
GraphSummary.GraphControl.GraphPane.Rect.Height);
}
}

private void this_AxisChangeEvent(GraphPane pane)
Expand Down
5 changes: 4 additions & 1 deletion pwiz_tools/Skyline/Controls/GroupComparison/FoldChangeForm.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ public partial class FoldChangeForm : DockableFormEx
private IDocumentUIContainer _documentContainer;
private string _groupComparisonName;
private Form _owner;
protected bool _dataChanged = true;
public FoldChangeForm()
{
InitializeComponent();
Expand Down Expand Up @@ -86,7 +87,9 @@ protected override void OnShown(EventArgs e)
{
if (null != _documentContainer)
{
FoldChangeBindingSource = FindOrCreateBindingSource(_documentContainer, _groupComparisonName);
var newBindingSource = FindOrCreateBindingSource(_documentContainer, _groupComparisonName);
_dataChanged = newBindingSource != FoldChangeBindingSource;
FoldChangeBindingSource = newBindingSource;
if (IsHandleCreated)
{
FoldChangeBindingSource.AddRef();
Expand Down
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