Skyline: First draft automation of screenshots for two more tutorials (…

…#3247) * Skyline: First draft automation of screenshots for two more tutorials CEOptimizationTutorialTest and DriftTimePredictorTutorialTest
ProteoWizard · Nov 28, 2024 · 14db3eb · 14db3eb
1 parent 011166e
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Showing 10 changed files with 143 additions and 74 deletions.
diff --git a/pwiz_tools/Skyline/Controls/Graphs/AreaReplicateGraphPane.cs b/pwiz_tools/Skyline/Controls/Graphs/AreaReplicateGraphPane.cs
@@ -209,7 +209,12 @@ protected override int FirstDataIndex
 
         public bool DotProductLabelsVisible
         {
-            get{return CanShowDotProduct && DotProductDisplayOption.label.IsSet(Settings.Default);}
+            get { return CanShowDotProduct && DotProductDisplayOption.label.IsSet(Settings.Default); }
+        }
+
+        public bool DotProductLineVisible
+        {
+            get { return CanShowDotProduct && DotProductDisplayOption.line.IsSet(Settings.Default); }
         }
 
         public bool IsLineGraph
@@ -668,6 +673,8 @@ public override void UpdateGraph(bool selectionChanged)
                 Y2Axis.Scale.Min = 0;
                 Y2Axis.Scale.Max = 1.1;
                 Y2Axis.Title.Text = DotpLabelText;
+                Y2Axis.MajorTic.IsOpposite = false;
+                Y2Axis.MinorTic.IsOpposite = false;
                 var dotpLine = new LineItem(DotpLabelText, graphData.DotpData, Color.DimGray, SymbolType.Circle )
                 {
                     IsY2Axis = true, Line = new Line() { Style = DashStyle.Dash, Color = Color.DimGray, Width = 2.0f},
@@ -682,49 +689,58 @@ public override void UpdateGraph(bool selectionChanged)
                 Y2Axis.IsVisible = false;
             }
 
-            UpdateAxes(resetAxes, aggregateOp, dataScalingOption, normalizeOption);
+            AddDotProductLine(graphData);
 
-            if (Settings.Default.PeakAreaDotpCutoffShow && DotProductDisplayOption.line.IsSet(Settings.Default) && _dotpData != null)
-            {
-                var cutoff = ExpectedVisible.GetDotpValueCutoff(Settings.Default);
-                var highlightValues = new PointPairList(graphData.DotpData.Select(point => point.Y < cutoff ? point : new PointPair(){X = point.X, Y = float.NaN}).ToList());
-                var cutoffHighlightLine = new LineItem("", highlightValues, Color.DimGray, SymbolType.Circle)
-                {
-                    IsY2Axis = true,
-                    Line = new Line() { Color = Color.Transparent},
-                    Symbol = new Symbol() { Type = SymbolType.Diamond, Size = 9f, Fill = new Fill(Color.Red), Border = new Border(Color.Red, 1) }
-                };
-                cutoffHighlightLine.Label.IsVisible = false;
-                CurveList.Insert(Math.Min(CurveList.Count, 1), cutoffHighlightLine); // Add below cutoff highlight markers
-                ToolTip.TargetCurves.Add(cutoffHighlightLine);
+            UpdateAxes(resetAxes, aggregateOp, dataScalingOption, normalizeOption);
+        }
 
+        private void AddDotProductLine(AreaGraphData graphData)
+        {
+            if (!Settings.Default.PeakAreaDotpCutoffShow || !DotProductDisplayOption.line.IsSet(Settings.Default) ||
+                _dotpData == null)
+                return;
 
-                var belowCutoffCount = _dotpData.Count(dotp => dotp <= cutoff);
-                var labelText = string.Format(GraphsResources.AreaReplicateGraphPane_Replicates_Count_Above_Below_Cutoff,
-                    _dotpData.Count - belowCutoffCount, belowCutoffCount, DotpLabelText);
-                var labelObject = new TextObj(labelText, 1, 0, CoordType.ChartFraction, AlignH.Right, AlignV.Top)
-                {
-                    IsClippedToChartRect = true,
-                    ZOrder = ZOrder.E_BehindCurves,
-                    FontSpec = GraphSummary.CreateFontSpec(Color.Black),
-                };
-                labelObject.FontSpec.Fill = new Fill(Color.Transparent);
-                GraphObjList.Add(labelObject);
-                var cutoffLine = new LineObj()
-                {
-                    IsClippedToChartRect = true,
-                    Location = new Location(0, cutoff, CoordType.XChartFractionY2Scale){Rect = new RectangleF(0, cutoff, 1, 0)},
-                    Line = new LineBase(Color.Red)
-                };
-                GraphObjList.Add(cutoffLine);                          // Add  cutoff line
-                //This is a placeholder to make sure the line shows in the legend.
-                CurveList.Insert(0, new LineItem(string.Format(CultureInfo.CurrentCulture,
-                    GraphsResources.AreaReplicateGraphPane_Dotp_Cutoff_Line_Label, DotpLabelText, cutoff))
-                {
-                    Points = new PointPairList(new[] { new PointPair(0, 0) }),
-                    Symbol = new Symbol(SymbolType.None, Color.Transparent)
-                });
-            }
+            var cutoff = ExpectedVisible.GetDotpValueCutoff(Settings.Default);
+            var highlightValues = new PointPairList(graphData.DotpData
+                .Select(point => point.Y < cutoff ? point : new PointPair() { X = point.X, Y = float.NaN }).ToList());
+            var cutoffHighlightLine = new LineItem("", highlightValues, Color.DimGray, SymbolType.Circle)
+            {
+                IsY2Axis = true,
+                Line = new Line() { Color = Color.Transparent },
+                Symbol = new Symbol()
+                    { Type = SymbolType.Diamond, Size = 9f, Fill = new Fill(Color.Red), Border = new Border(Color.Red, 1) }
+            };
+            cutoffHighlightLine.Label.IsVisible = false;
+            CurveList.Insert(Math.Min(CurveList.Count, 1), cutoffHighlightLine); // Add below cutoff highlight markers
+            ToolTip.TargetCurves.Add(cutoffHighlightLine);
+
+            var belowCutoffCount = _dotpData.Count(dotp => dotp <= cutoff);
+            var labelText = string.Format(GraphsResources.AreaReplicateGraphPane_Replicates_Count_Above_Below_Cutoff,
+                _dotpData.Count - belowCutoffCount, belowCutoffCount, DotpLabelText);
+            var labelObject = new TextObj(labelText, 1, 0, CoordType.ChartFraction, AlignH.Right, AlignV.Top)
+            {
+                IsClippedToChartRect = true,
+                ZOrder = ZOrder.E_BehindCurves,
+                FontSpec = GraphSummary.CreateFontSpec(Color.Black),
+            };
+            labelObject.FontSpec.Fill = new Fill(Color.Transparent);
+            GraphObjList.Add(labelObject);
+            _labelHeight = (int)labelObject.FontSpec.GetHeight(CalcScaleFactor());
+            var cutoffLine = new LineObj()
+            {
+                IsClippedToChartRect = true,
+                Location = new Location(0, cutoff, CoordType.XChartFractionY2Scale)
+                    { Rect = new RectangleF(0, cutoff, 1, 0) },
+                Line = new LineBase(Color.Red)
+            };
+            GraphObjList.Add(cutoffLine); // Add  cutoff line
+            //This is a placeholder to make sure the line shows in the legend.
+            CurveList.Insert(0, new LineItem(string.Format(CultureInfo.CurrentCulture,
+                GraphsResources.AreaReplicateGraphPane_Dotp_Cutoff_Line_Label, DotpLabelText, cutoff))
+            {
+                Points = new PointPairList(new[] { new PointPair(0, 0) }),
+                Symbol = new Symbol(SymbolType.None, Color.Transparent)
+            });
         }
 
         public override void PopulateTooltip(int index, CurveItem targetCurve)
@@ -952,9 +968,11 @@ private void UpdateAxes(bool resetAxes, GraphValues.AggregateOp aggregateOp, Dat
 
             // Reformat Y-Axis for labels and whiskers
             var maxY = GraphHelper.GetMaxY(CurveList,this);
-            if (DotProductLabelsVisible)
+            if (DotProductLabelsVisible || DotProductLineVisible)
             {
-                var extraSpace = _labelHeight*(maxY/(Chart.Rect.Height - _labelHeight*2))*2;
+                var reservedSpace = _labelHeight * 2;
+                var unitsPerPixel = maxY / (Chart.Rect.Height - reservedSpace);
+                var extraSpace = reservedSpace*unitsPerPixel;
                 maxY += extraSpace;
             }
 
@@ -1019,6 +1037,7 @@ private void AddDotProductLabels(Graphics g, TransitionGroupDocNode nodeGroup, I
             foreach (GraphObj pa in _dotpLabels)
                 GraphObjList.Remove(pa);
             _dotpLabels.Clear();
+            _labelHeight = 0;
 
             if (visible)
             {
@@ -1042,7 +1061,9 @@ private void AddDotProductLabels(Graphics g, TransitionGroupDocNode nodeGroup, I
                     textObj.FontSpec.Border.IsVisible = false;
                     textObj.FontSpec.Size = pointSize.Value;
                     textObj.FontSpec.Fill = new Fill(Color.Transparent);
-                    _labelHeight =(int) textObj.FontSpec.GetHeight(CalcScaleFactor());
+                    var labelHeight = (int) textObj.FontSpec.GetHeight(CalcScaleFactor());
+                    if (labelHeight > _labelHeight)
+                        _labelHeight = labelHeight;
                     GraphObjList.Add(textObj);
                     _dotpLabels.Add(textObj);
                 }
@@ -1068,7 +1089,9 @@ private string GetDotProductResultsText(int indexResult)
         {
             if (_dotpData?.Count > 0 && indexResult < _dotpData.Count && !float.IsNaN(_dotpData[indexResult]))
             {
-                var separator = DotProductDisplayOption.line.IsSet(Settings.Default) ? (Func<IEnumerable<string>, string>)TextUtil.SpaceSeparate : TextUtil.LineSeparate;
+                var separator = DotProductDisplayOption.line.IsSet(Settings.Default)
+                    ? (Func<IEnumerable<string>, string>)TextUtil.SpaceSeparate
+                    : TextUtil.LineSeparate;
                 return separator(new [] { DotpLabelText , string.Format(@"{0:F02}", _dotpData[indexResult]) } ) ;
             }
             else

diff --git a/pwiz_tools/Skyline/Controls/Graphs/GraphChromatogram.cs b/pwiz_tools/Skyline/Controls/Graphs/GraphChromatogram.cs
@@ -562,7 +562,7 @@ public void UnlockZoom()
 
         public PointF TransformCoordinates(double x, double y, PaneKey? paneKey, CoordType coordType = CoordType.AxisXYScale)
         {
-            var graphPane = _graphHelper.GetGraphPane(paneKey ?? PaneKey.DEFAULT);
+            var graphPane = GetGraphPane(paneKey);
             return graphPane.GeneralTransform(new PointF((float)x, (float)y), coordType);
         }
 
@@ -1626,7 +1626,7 @@ private void DisplayTransitions(AlignmentFunction timeRegressionFunction,
                 iColor++;
             }
 
-            var graphPane = _graphHelper.GetGraphPane(graphPaneKey);
+            var graphPane = GetGraphPane(graphPaneKey);
             if (graphPane == null)
                 _enableTrackingDot = false;
             if (_enableTrackingDot)
@@ -3534,7 +3534,7 @@ public void TestMouseDown(double x, double y, PaneKey? paneKey)
 
         public string TestFullScanSelection(double x, double y, PaneKey? paneKey)
         {
-            var graphPane = _graphHelper.GetGraphPane(paneKey ?? PaneKey.DEFAULT);
+            var graphPane = GetGraphPane(paneKey);
             var selectionDot = graphPane.CurveList[FULLSCAN_SELECTED_INDEX];
             var mouse = TransformCoordinates(x, y, paneKey);
             var dot = TransformCoordinates(selectionDot[0].X, selectionDot[0].Y, paneKey);
@@ -3546,6 +3546,11 @@ public string TestFullScanSelection(double x, double y, PaneKey? paneKey)
             return string.Empty;
         }
 
+        public GraphPane GetGraphPane(PaneKey? paneKey)
+        {
+            return _graphHelper.GetGraphPane(paneKey ?? PaneKey.DEFAULT);
+        }
+
         #endregion Test support
     }
 

diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/index.html b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/index.html
@@ -261,7 +261,7 @@ <h2>Creating Optimization Methods</h2>
         something like the following for your OptimizeCE folder:
     </p>
     <p>
-        <img src="s-05.png" />
+        <img src="s-file-explorer.png" />
     </p>
     <p>
         If you open one of the CSV files in Excel, it should contain a transition list like the one below, with 9 columns in the order precursor m/z,
@@ -490,7 +490,7 @@ <h2>Analyzing Optimization Data</h2>
         Once the data is loaded, Skyline should look something like this:
     </p>
     <p>
-        <img src="s-06.png" />
+        <img src="s-05.png" />
     </p>
     <p>
         The red bar in the middle of the <b>Peak Areas</b> view and the red curve among the chromatograms is the measurement for the
@@ -517,7 +517,7 @@ <h2>Analyzing Optimization Data</h2>
         but not that bad.
     </p>
     <p>
-        <img src="s-07.png" />
+        <img src="s-06.png" />
     </p>
     <p>
         For this tutorial, however, remove this peptide before calculating the new equation for the Thermo TSQ Vantage.
@@ -562,7 +562,7 @@ <h2>Creating a New Equation for CE</h2>
         Skyline will present the following graphs:
     </p>
     <p>
-        <img src="s-08.png" />
+        <img src="s-07.png" />
     </p>
     <p>
         The points correlate very well to the new linear equation, and appear to be on average 3-4 volts below the CE values chosen by the default

diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-05.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-05.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-06.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-06.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-07.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-07.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-08.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-08.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-file-explorer.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/s-file-explorer.png