Update and fix some bugs.

.gitignore

@@ -6,4 +6,5 @@ packages/*
 primer/*
 #Files to ignore
 *.pdb
-*.p7s
+*.p7s
+*.xcf

DoseGradient.csproj

@@ -180,6 +180,9 @@
       <Generator>ResXFileCodeGenerator</Generator>
       <LastGenOutput>Resources.Designer.cs</LastGenOutput>
     </EmbeddedResource>
+    <None Include="LICENSE">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Include="packages.config" />
     <None Include="Properties\Settings.settings">
       <Generator>SettingsSingleFileGenerator</Generator>
@@ -224,5 +227,23 @@
   <ItemGroup>
     <Resource Include="icon.ico" />
   </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\2grad.png" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\2grad2.png" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\0grad.png" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\1grad1.png" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\2grad3.png" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="images\1grad2.png" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
 </Project>

HelpWindow.xaml

@@ -54,19 +54,7 @@
                 <LineBreak/>
                 Save the new dose matrix. Import the original data with the new dose file into the TPS. On some systems you have to delete the original plan 
                 before you can import the data back. The program changes the SOPInstanceUID of the dose file, but other files are left untouched.<LineBreak/><LineBreak/>
-                <Bold>LICENSE</Bold>
-                <LineBreak/>
-                The DoseGradient program is published under the MIT license. The Microsoft NuGet libraries are published under the Appache 2.0 license.<LineBreak/>
-                <LineBreak/>
-                THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-                IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-                FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-                AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-                LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-                OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-                SOFTWARE.
-                <LineBreak/> <LineBreak/>
-                Denis Brojan
+
             </TextBlock>
         </Grid>
     </ScrollViewer>

MainWindow.xaml

@@ -43,9 +43,12 @@
                 <StackPanel Grid.Column="0" Orientation="Horizontal" Height="Auto" VerticalAlignment="Center">
                     <Button Grid.Column="0" Content="Open..." Width="100" Height="30" Click="Button_Click" VerticalAlignment="Center"></Button>
                     <Button Content="Save..." Width="100"  Height="30" Margin="10,0,0,0" VerticalAlignment="Center" Click="Button_Click_5"></Button>
-                    <CheckBox x:Name="CheckBoxOverwriteZeroVoxels" Height="30" VerticalContentAlignment="Center" VerticalAlignment="Center" Margin="15,0,0,0" Checked="CheckBox_Checked" Unchecked="CheckBox_Checked">
+                    <CheckBox x:Name="CheckBoxOverwriteZeroVoxels" Height="30" VerticalContentAlignment="Center" VerticalAlignment="Center" Margin="15,0,0,0">
                         <Label Content="Overwrite all voxels" VerticalAlignment="Top" ToolTip="Using this option will overwrite all elements of the dose matrix (in each z-slice), regardless of their value."></Label>
                     </CheckBox>
+                    <CheckBox x:Name="CheckBoxChangeUID" Height="30" VerticalContentAlignment="Center" VerticalAlignment="Center" Margin="15,0,0,0" IsChecked="True">
+                        <Label Content="Change UID" VerticalAlignment="Top" ToolTip="Using this option will change SOPInstanceUID of the RT dose file."></Label>
+                    </CheckBox>
                 </StackPanel>
                 <StackPanel Grid.Column="1" Orientation="Horizontal" HorizontalAlignment="Right" Height="Auto" VerticalAlignment="Center">
                     <Label Content="Select plot type:"  Height="30" VerticalAlignment="Center"></Label>
@@ -66,10 +69,24 @@
                 <GroupBox.Header>
                     <DockPanel HorizontalAlignment="Stretch">
                         <Label Content="Gradient regions" HorizontalAlignment="Left"></Label>
-                        <Button Content="0 gradients" HorizontalAlignment="Right" Height="20" Width="80" Margin="5,0,0,0" Click="Button_Click_2"/>
-                        <Button Content="1 gradient" HorizontalAlignment="Right" Height="20" Width="80" Margin="5,0,0,0" Click="Button_Click_3"/>
-                        <Button Content="2 gradients" HorizontalAlignment="Right" Height="20" Width="80" Margin="5,0,0,0" Click="Button_Click_4"/>
-                        <Button Content="Default" HorizontalAlignment="Right" Height="20" Width="60" Margin="5,0,0,0" Click="Button_Click_1"/>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_2">
+                            <Image Source="/images/0grad.png"></Image>
+                        </Button>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_3">
+                            <Image Source="/images/1grad1.png"></Image>
+                        </Button>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_8">
+                            <Image Source="/images/1grad2.png"></Image>
+                        </Button>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_4">
+                            <Image Source="/images/2grad.png"></Image>
+                        </Button>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_7">
+                            <Image Source="/images/2grad2.png"></Image>
+                        </Button>
+                        <Button HorizontalAlignment="Right" Height="20" Width="25" Margin="5,0,0,0" Click="Button_Click_1">
+                            <Image Source="/images/2grad3.png"></Image>
+                        </Button>
                     </DockPanel>
                 </GroupBox.Header>
                 <Grid HorizontalAlignment="Stretch">

MainWindow.xaml.cs

@@ -412,7 +412,7 @@ private void SetGradientStartingValues()
 
             for (int i = 0; i < this.gradientXPositions.Count; i++)
             {
-                this.gradientXPositions[i] = x0 + i * dx;
+                this.gradientXPositions[i] = Math.Round(x0 + i * dx, 2);
             }
         }
 
@@ -563,12 +563,69 @@ private void Button_Click_4(object sender, RoutedEventArgs e)
             SetTextBoxes();
         }
 
+
+        private void Button_Click_7(object sender, RoutedEventArgs e)
+        {
+            // 2 gradients upside down
+            if (this.DoseMatrix == null)
+            {
+                return;
+            }
+            double xmin = this.DoseImageHeatMapSeries.X0;
+            double xmax = this.DoseImageHeatMapSeries.X1;
+            SetGradientStartingValues();
+            this.gradientXPositions[0] = xmin;
+            this.gradientXPositions[1] = xmin;
+            this.gradientXPositions[2] = xmin;
+            this.gradientXPositions[3] = xmin + (xmax - xmin) / 3.0 - 0.5;
+            this.gradientXPositions[4] = xmin + (xmax - xmin) / 3.0 + 0.5;
+            this.gradientXPositions[5] = xmin + 2 * (xmax - xmin) / 3.0 - 0.5;
+            this.gradientXPositions[6] = xmin + 2 * (xmax - xmin) / 3.0 + 0.5;
+            this.gradientXPositions[7] = xmax;
+            this.gradientXPositions[8] = xmax;
+            this.gradientXPositions[9] = xmax;
+
+            this.gradientDoses = new List<double>() { 30.6, 30.6, 30.6, 30.6, 0, 0, 30.6, 30.6, 30.6, 30.6 };
+
+            CreateLineSeriesProfilePlot();
+            SetTextBoxes();
+        }
+
+
+        private void Button_Click_8(object sender, RoutedEventArgs e)
+        {
+            // 1 gradient left to right
+            if (this.DoseMatrix == null)
+            {
+                return;
+            }
+            double xmin = this.DoseImageHeatMapSeries.X0;
+            double xmax = this.DoseImageHeatMapSeries.X1;
+            SetGradientStartingValues();
+
+            this.gradientXPositions[0] = xmin;
+            this.gradientXPositions[1] = xmin;
+            this.gradientXPositions[2] = xmin;
+            this.gradientXPositions[3] = (xmin + xmax) / 2.0 - 0.5;
+            this.gradientXPositions[4] = (xmin + xmax) / 2.0 + 0.5;
+            this.gradientXPositions[5] = xmax;
+            this.gradientXPositions[6] = xmax;
+            this.gradientXPositions[7] = xmax;
+            this.gradientXPositions[8] = xmax;
+            this.gradientXPositions[9] = xmax;
+
+            this.gradientDoses = new List<double>() { 30.6, 30.6, 30.6, 30.6, 0, 0, 0, 0, 0, 0 };
+
+            CreateLineSeriesProfilePlot();
+            SetTextBoxes();
+        }
+
         private bool CheckProfileValidity()
         {
             // All X must be increasing. Dose must be non-negative.
             for (int i = 1; i < this.gradientXPositions.Count; i++)
             {
-                if (this.gradientXPositions[i - 1] > this.gradientXPositions[i])
+                if (Math.Round(this.gradientXPositions[i - 1], 2) > Math.Round(this.gradientXPositions[i], 2))
                 {
                     return false;
                 }
@@ -772,34 +829,38 @@ private double GetDoseFromProfileAtPosition(double t)
         {
             List<double> x = this.gradientXPositions;
             List<double> y = this.gradientDoses;
+            double dose;
 
             if (t <= x.First())
             {
-                return y.First();
+                dose = y.First();
             }
-            else if (t >= y.Last())
+            else if (t >= x.Last())
             {
-                return y.Last();
+                dose = y.Last();
             }
             else
             {
                 int i;
-                for (i = 0; i < x.Count - 2; i++)
+                for (i = 0; i < x.Count - 1; i++)
                 {
-                    if (x[i] <= t && t < x[i + 1])
+                    if (t >= x[i] && t < x[i + 1])
                     {
                         break;
                     }
                 }
                 if (Math.Abs(x[i + 1] - x[i]) < 1e-8)
                 {
-                    return (y[i] + y[i + 1]) / 2.0;
+                    dose = (y[i] + y[i + 1]) / 2.0;
                 }
                 else
                 {
-                    return y[i] + ((y[i + 1] - y[i]) / (x[i + 1] - x[i])) * (t - x[i]);
+                    dose = y[i] + ((y[i + 1] - y[i]) / (x[i + 1] - x[i])) * (t - x[i]);
                 }
+
             }
+            return dose;
+
         }
 
 
@@ -1327,7 +1388,7 @@ private void SaveToDicom(string oldfilePath, string filePath, Tuple<uint[,,], ui
 
             dcm.FindFirst(TagHelper.PixelData).DData_ = byteArray;
 
-            dcm.FindFirst(TagHelper.DoseGridScaling).DData = Double.Parse(newData.Item4.ToString("E6"));
+            dcm.FindFirst(TagHelper.DoseGridScaling).DData = newData.Item4;
 
             var _smallestImagePixelValue = dcm.FindFirst(TagHelper.SmallestImagePixelValue) as AbstractElement<ushort>;
             if (_smallestImagePixelValue != null)
@@ -1341,7 +1402,10 @@ private void SaveToDicom(string oldfilePath, string filePath, Tuple<uint[,,], ui
             }
             // Since Eclipse is using 32 bit voxels, setting the true largest pixel value would not work because only unsigned short is allowed.
             // However, Eclipse is not writing this tag to dicom. Ha ha ...
-            dcm.FindFirst(TagHelper.SOPInstanceUID).DData = UIDHelper.GenerateUID();
+            if ((bool)this.CheckBoxChangeUID.IsChecked == true)
+            {
+                dcm.FindFirst(TagHelper.SOPInstanceUID).DData = UIDHelper.GenerateUID();
+            }
             dcm.WriteAddMeta(filePath);
             // using dcm.Write() doesn't work with Monaco, it works only with Eclipse
         }
@@ -1357,5 +1421,6 @@ private void Button_Click_6(object sender, RoutedEventArgs e)
             HelpWindow helpwindow = new HelpWindow();
             helpwindow.Show();
         }
+
     }
 }