From 819358977e6eb31182f2ecfaa21e15937ddef3a1 Mon Sep 17 00:00:00 2001
From: Holger Frey <frey@imtek.de>
Date: Tue, 3 Jan 2023 17:43:31 +0100
Subject: [PATCH] fixed test data for upcoming module xml_parser

---
 example_data/defect.xml                       |  29 ++++
 .../Calibration Check 4e.svalg                |  29 ++++
 .../Calibration Check 4e.svary                | 131 ++++++++++++++++++
 .../Calibration Check 4e.svexp                |  21 +++
 .../Parameters/Rack/Calibration Slide.svmpd   |  21 +++
 .../Rack/Microplate (96 wells).svmpd          |  21 ---
 6 files changed, 231 insertions(+), 21 deletions(-)
 create mode 100644 example_data/defect.xml
 create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg
 create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary
 create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp
 create mode 100644 example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd
 delete mode 100644 example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd

diff --git a/example_data/defect.xml b/example_data/defect.xml
new file mode 100644
index 0000000..eac8561
--- /dev/null
+++ b/example_data/defect.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="utf-8"?>
+<?xml-stylesheet type='text/xsl' href='220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xsl'?>
+<ScanJobResult ID="220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1" Rack="Calibration Slide - 4 Slides">
+  <StartTime>3/7/2022 5:31:40 PM</StartTime>
+  <FinishTime>3/7/2022 5:33:45 PM</FinishTime>
+  <ExperimentResults>
+    <AssayResult ID="A01" Type="Calibration Check_v1.2.4.3c">
+      <ReferencePatternResult Status="Valid" Rotation="0.23807670284076057" Scaling="0.998411582643245" PositionTopLeft.X="230.07833862304688" PositionTopLeft.Y="232.07130432128906" />
+      <RelationArrayToRefPattern OffsetMm.X="0.018938772094637457" OffsetMm.Y="-0.0071761016171074665" ScalingFactor="1.001991960802898" RotationAngleDeg="0" />
+      <ChannelConfig1>
+        <Status ErrorID="0" Message="no error" />
+        <ChannelDescription>Cy3/Cy5 Green</ChannelDescription>
+        <Timestamp>3/7/2022 5:31:47 PM</Timestamp>
+        <ImageFileName>220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.tif</ImageFileName>
+        <ImageResolutionPixPerMm>150.3716670323235</ImageResolutionPixPerMm>
+        <SystemImageResolutionPixPerMm>150.6109</SystemImageResolutionPixPerMm>
+        <Transform>
+          <M11>150.66990076589988</M11>
+          <M12>-0.62607054037768517</M12>
+          <M21>0.62607054037768517</M21>
+          <M22>150.66990076589988</M22>
+          <Dx>227.22602466270919</Dx>
+          <Dy>233.1385439330713</Dy>
+        </Transform>
+        <SpotResults>
+          <Spot ID="1">
+            <Result Label="Pos.X" Type="System.Int32" Value="228" />
+            <Result Label="Pos.Y" Type="System.Int32" Value="232" />
+            <Result Label="Bkg.Mean" Type="System.Double" Value="0.23538493173349712" />
\ No newline at end of file
diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg
new file mode 100644
index 0000000..1530523
--- /dev/null
+++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg	
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--Algorithm configuration-->
+<Algorithm>
+  <BrightnessCheck>
+    <Settings Active="False" MinimumBrightnessPercent="70" MaximumBrightnessPercent="100" HistogrammPercent="95" OverrideMaximumPixelValue="0" SubSampleX="2" SubSampleY="2" />
+  </BrightnessCheck>
+  <Shading>
+    <Settings Active="true" />
+  </Shading>
+  <OrientationDetection>
+    <Settings Active="True" HoughCircleSensitivitySliderUsed="True" BlobMethod="Classic,HoughCircle" HoughCircleGamma="1.1" HoughCircleScale="1" HoughCircleMinDist="5" HoughCircleCannyThresh="100" HoughCircleAccumThresh="15" HoughCircleMinRadius="5" HoughCircleMaxRadius="30" HoughCircleSmoothRadius="0" HoughCircleDilationRadius="3" HoughCircleSensitivitySlider="2" RefPatternFittingMethod="ICP" AdvancedMaxMissingSpots="1" BinThresholdPercent="40" JoinRadius="2" OpeningNeighborhoodSizeXY="7" BlobAreaMin="50">
+    </Settings>
+    <DebugSettings ImageDebugAODResult="0" ImageDebugAODBinary="0" ImageDebugAODMorphed="1" ShowResults="1" ShowSearchOrder="1" ShowDistances="1" />
+  </OrientationDetection>
+  <Flip>
+    <Settings Direction="FLIP_NONE" />
+  </Flip>
+  <MicroArraySpotFinding>
+    <Settings Active="True" BkgAvgAreaPix="10" HistogramPerCent="10" BinarizationThresholdOffsetPerc="7" SpotImageSubSampling="1" ApertureWidth="3" MinArea="50" MinSpotDiameterMm="0.15" SpotFindingSensitivity="10" SpotShape="CIRCLE" SelectionPreference="Compactest" InsideGridRectCriteria="Rectangle" BlobbingActive="True" CircleDetectionActive="True" MeanBeforeEdgeDetectionActive="False" CannyThreshold="50" MinMatchQuality="0.35" CircleMatchExponent="1" />
+  </MicroArraySpotFinding>
+  <MicroArrayAnalysis>
+    <Settings Active="True" MinBkgThresholdPerc="1" MaxSpotThresholdPerc="100" AutoAdjustAnalysisDiameter="True" MinSpotSizeMm="0.18" MaxSpotSizeMm="0.28" AutoAdjustTolerancePercentage="10">
+    </Settings>
+  </MicroArrayAnalysis>
+  <Registration>
+    <Settings XmaxDisplacementMm="0.2" YmaxDisplacementMm="0.2" MinWithForStitchingMm="0.5" MinHeightForStitchingMm="0.5" XcutterAreaSizeMm="0.4" YcutterAreaSizeMm="0.4" RegistrationTypeFlair="TMWithSobelAndDustFilter" RegistrationTypeClair="TMWeightEdges" ROIMarginHeight="0.5" ROIMarginWidth="0.5">
+    </Settings>
+  </Registration>
+</Algorithm>
\ No newline at end of file
diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary
new file mode 100644
index 0000000..da00932
--- /dev/null
+++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary	
@@ -0,0 +1,131 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--Definition of the microarray and the-->
+<!--embedded reference pattern-->
+<MicroArray>
+  <Layout NofSpotsX="10" NofSpotsY="10" SpotDistMmX="0.353" SpotDistMmY="0.349" />
+  <ReferencePattern ReferencePointOffsetMm.X="0.689155651736256" ReferencePointOffsetMm.Y="1.5170187539612119">
+    <Features MarkerType="BRIGHT">
+    </Features>
+    <Tolerances ScalePercent="5" RotationPercent="5">
+      <CIRCLE PositionMm="0.06" SizePercent="50" SimpleCompactnessMax="17" EccentricityMax="0.2" />
+      <RECT PositionMm="0.1" SizePercent="30" SimpleCompactnessMin="13" SimpleCompactnessMax="22" EccentricityMin="0.25" EccentricityMax="0.4">
+      </RECT>
+    </Tolerances>
+    <Shapes>
+      <Shape0 ShapeType="CIRCLE" PosMm.X="0" PosMm.Y="0" DiameterMm="0.203">
+      </Shape0>
+      <Shape1 ShapeType="CIRCLE" PosMm.X="3.161" PosMm.Y="3.124" DiameterMm="0.21">
+      </Shape1>
+      <Shape2 ShapeType="CIRCLE" PosMm.X="0.019" PosMm.Y="3.153" DiameterMm="0.203">
+      </Shape2>
+      <Shape3 ShapeType="CIRCLE" PosMm.X="3.129" PosMm.Y="-0.016" DiameterMm="0.21">
+      </Shape3>
+      <Shape4 ShapeType="CIRCLE" PosMm.X="0.013" PosMm.Y="2.794" DiameterMm="0.21">
+      </Shape4>
+    </Shapes>
+  </ReferencePattern>
+  <RelationArrayToRefPattern OffsetMm.X="0.0053912827593903812" OffsetMm.Y="-0.00040235694948398404" ScalingFactor="1.001991960802898" RotationAngleDeg="0">
+  </RelationArrayToRefPattern>
+  <SpotsLayout>
+    <Spot Number="1" Id="" Name="" />
+    <Spot Number="2" Id="" Name="" />
+    <Spot Number="3" Id="" Name="" />
+    <Spot Number="4" Id="" Name="" />
+    <Spot Number="5" Id="" Name="" />
+    <Spot Number="6" Id="" Name="" />
+    <Spot Number="7" Id="" Name="" />
+    <Spot Number="8" Id="" Name="" />
+    <Spot Number="9" Id="" Name="" />
+    <Spot Number="10" Id="" Name="" />
+    <Spot Number="11" Id="" Name="" />
+    <Spot Number="12" Id="" Name="" />
+    <Spot Number="13" Id="" Name="" />
+    <Spot Number="14" Id="" Name="" />
+    <Spot Number="15" Id="" Name="" />
+    <Spot Number="16" Id="" Name="" />
+    <Spot Number="17" Id="" Name="" />
+    <Spot Number="18" Id="" Name="" />
+    <Spot Number="19" Id="" Name="" />
+    <Spot Number="20" Id="" Name="" />
+    <Spot Number="21" Id="" Name="" />
+    <Spot Number="22" Id="" Name="" />
+    <Spot Number="23" Id="" Name="" />
+    <Spot Number="24" Id="" Name="" />
+    <Spot Number="25" Id="" Name="" />
+    <Spot Number="26" Id="" Name="" />
+    <Spot Number="27" Id="" Name="" />
+    <Spot Number="28" Id="" Name="" />
+    <Spot Number="29" Id="" Name="" />
+    <Spot Number="30" Id="" Name="" />
+    <Spot Number="31" Id="" Name="" />
+    <Spot Number="32" Id="" Name="" />
+    <Spot Number="33" Id="" Name="" />
+    <Spot Number="34" Id="" Name="" />
+    <Spot Number="35" Id="" Name="" />
+    <Spot Number="36" Id="" Name="" />
+    <Spot Number="37" Id="" Name="" />
+    <Spot Number="38" Id="" Name="" />
+    <Spot Number="39" Id="" Name="" />
+    <Spot Number="40" Id="" Name="" />
+    <Spot Number="41" Id="" Name="" />
+    <Spot Number="42" Id="" Name="" />
+    <Spot Number="43" Id="" Name="" />
+    <Spot Number="44" Id="" Name="" />
+    <Spot Number="45" Id="" Name="" />
+    <Spot Number="46" Id="" Name="" />
+    <Spot Number="47" Id="" Name="" />
+    <Spot Number="48" Id="" Name="" />
+    <Spot Number="49" Id="" Name="" />
+    <Spot Number="50" Id="" Name="" />
+    <Spot Number="51" Id="" Name="" />
+    <Spot Number="52" Id="" Name="" />
+    <Spot Number="53" Id="" Name="" />
+    <Spot Number="54" Id="" Name="" />
+    <Spot Number="55" Id="" Name="" />
+    <Spot Number="56" Id="" Name="" />
+    <Spot Number="57" Id="" Name="" />
+    <Spot Number="58" Id="" Name="" />
+    <Spot Number="59" Id="" Name="" />
+    <Spot Number="60" Id="" Name="" />
+    <Spot Number="61" Id="" Name="" />
+    <Spot Number="62" Id="" Name="" />
+    <Spot Number="63" Id="" Name="" />
+    <Spot Number="64" Id="" Name="" />
+    <Spot Number="65" Id="" Name="" />
+    <Spot Number="66" Id="" Name="" />
+    <Spot Number="67" Id="" Name="" />
+    <Spot Number="68" Id="" Name="" />
+    <Spot Number="69" Id="" Name="" />
+    <Spot Number="70" Id="" Name="" />
+    <Spot Number="71" Id="" Name="" />
+    <Spot Number="72" Id="" Name="" />
+    <Spot Number="73" Id="" Name="" />
+    <Spot Number="74" Id="" Name="" />
+    <Spot Number="75" Id="" Name="" />
+    <Spot Number="76" Id="" Name="" />
+    <Spot Number="77" Id="" Name="" />
+    <Spot Number="78" Id="" Name="" />
+    <Spot Number="79" Id="" Name="" />
+    <Spot Number="80" Id="" Name="" />
+    <Spot Number="81" Id="" Name="" />
+    <Spot Number="82" Id="" Name="" />
+    <Spot Number="83" Id="" Name="" />
+    <Spot Number="84" Id="" Name="" />
+    <Spot Number="85" Id="" Name="" />
+    <Spot Number="86" Id="" Name="" />
+    <Spot Number="87" Id="" Name="" />
+    <Spot Number="88" Id="" Name="" />
+    <Spot Number="89" Id="" Name="" />
+    <Spot Number="90" Id="" Name="" />
+    <Spot Number="91" Id="" Name="" />
+    <Spot Number="92" Id="" Name="" />
+    <Spot Number="93" Id="" Name="" />
+    <Spot Number="94" Id="" Name="" />
+    <Spot Number="95" Id="" Name="" />
+    <Spot Number="96" Id="" Name="" />
+    <Spot Number="97" Id="" Name="" />
+    <Spot Number="98" Id="" Name="" />
+    <Spot Number="99" Id="" Name="" />
+    <Spot Number="100" Id="" Name="" />
+  </SpotsLayout>
+</MicroArray>
\ No newline at end of file
diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp
new file mode 100644
index 0000000..b62b882
--- /dev/null
+++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp	
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<Assay>
+  <Channels>
+    <ChannelConfig1 IlluminationID="4" Description="Cy3/Cy5 Green" ExposureTimeMs="100" Intensity="100">
+    </ChannelConfig1>
+    <ChannelConfig2 IlluminationID="4" Description="Cy3/Cy5 Green" ExposureTimeMs="10" Intensity="100">
+    </ChannelConfig2>
+    <ChannelConfig3 IlluminationID="3" Description="Cy3/Cy5 Red" ExposureTimeMs="60" Intensity="100">
+    </ChannelConfig3>
+    <ChannelConfig4 IlluminationID="3" Description="Cy3/Cy5 Red" ExposureTimeMs="6" Intensity="100">
+    </ChannelConfig4>
+  </Channels>
+  <Components MicroArray="Calibration Check 4e" AlgoConfig="Calibration Check 4e">
+  </Components>
+  <DebugSwitches DoImageProcessing="True" DoDarkImageCorrection="False" DoFullRangeAdaption="True" RestoreSaturation="True" SaveResultAsCSVFile="True" SaveResultAsXmlFile="True" DoShadingCorrection="True" DoRemap="True">
+  </DebugSwitches>
+  <RefPattern ChannelConfig="Channel1">
+  </RefPattern>
+  <WorkbookAnalysis Active="True" UseSingleWorkbook="YES" TemplateWorkbookName="2022-03-15 Calibration Check v1.2.5.4e.xlsx" PasteWorksheetName="Input_Data" PasteStartingCell="AA300" ParameterWorksheetName="parameter" ResultWorksheetName="Workflow" KeepDataWorkbookOpen="NO">
+  </WorkbookAnalysis>
+</Assay>
\ No newline at end of file
diff --git a/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd b/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd
new file mode 100644
index 0000000..a39226b
--- /dev/null
+++ b/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd	
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<Rack Version="2">
+  <Reference RefPosXMm="103.5" RefPosYMm="67.5" RefPosZMm="3.8" XAxisInverted="True" YAxisInverted="True" ScanAreaValidationActive="True">
+  </Reference>
+  <ChannelSettings>
+    <ChannelSetting1 ExposureTimeMs="30" IlluminationId="3" Intensity="100">
+    </ChannelSetting1>
+    <ChannelSetting2 ExposureTimeMs="30" IlluminationId="4" Intensity="100">
+    </ChannelSetting2>
+  </ChannelSettings>
+  <PlateHolder HolderType="SinglePlateHolder">
+  </PlateHolder>
+  <Layout OffsetXMm="17" OffsetYMm="19" OffsetZMm="5.84" NofWellsX="1" NofWellsY="4" WellDistXMm="9" WellDistYMm="9" WellDiameterMm="5" WellSizeXMm="1" WellSizeYMm="1" WellType="Circle">
+  </Layout>
+  <Flip>
+    <Settings Direction="FLIP_NONE">
+    </Settings>
+  </Flip>
+  <Sharpness XBorderPercent="0.333333343" YBorderPercent="0.333333343">
+  </Sharpness>
+</Rack>
\ No newline at end of file
diff --git a/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd b/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd
deleted file mode 100644
index 5695a27..0000000
--- a/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd	
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<Rack Version="2">
-  <Reference RefPosXMm="103.5" RefPosYMm="67.5" RefPosZMm="3.8" XAxisInverted="True" YAxisInverted="True">
-  </Reference>
-  <ChannelSettings>
-    <ChannelSetting1 ExposureTimeMs="100" IlluminationId="3" Intensity="100">
-    </ChannelSetting1>
-    <ChannelSetting2 ExposureTimeMs="50" IlluminationId="4" Intensity="100">
-    </ChannelSetting2>
-  </ChannelSettings>
-  <PlateHolder HolderType="SinglePlateHolder">
-  </PlateHolder>
-  <Layout OffsetXMm="12.5" OffsetYMm="10" OffsetZMm="3.42" NofWellsX="12" NofWellsY="8" WellDistXMm="9" WellDistYMm="9" WellDiameterMm="5" WellSizeXMm="1" WellSizeYMm="1" WellType="Circle">
-  </Layout>
-  <DigitalPlate Create="False" BkgndColor="Black">
-  </DigitalPlate>
-  <Flip>
-    <Settings Direction="FLIP_NONE">
-    </Settings>
-  </Flip>
-</Rack>
\ No newline at end of file