Merge pull request #441 from mkofarag/ALPIDE_bringingUpToDateTheCode

ALPIDE bringing up to date our code
eutelescope · Oct 4, 2018 · dd3a0e7 · dd3a0e7
2 parents 7debb79 + 54488a4
commit dd3a0e7
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Showing 9 changed files with 781 additions and 324 deletions.
diff --git a/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/align-tmp.xml b/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/align-tmp.xml
@@ -17,11 +17,9 @@
 
    <execute>
       <processor name="AIDA"/>
-      <processor name="LoadRefHitDB"/>
+      <!--processor name="LoadRefHitDB"/-->
       <processor name="LoadPreAlignment"/>
       <processor name="ApplyPreAlignment"/>
-      <!--processor name="LoadAlignment"/-->
-      <!--processor name="ApplyAlignment"/-->
       <processor name="AlignStraight"/>
    </execute>
 
@@ -81,126 +79,14 @@
   <!--parameter name="Verbosity" type="string" value=""/-->
 </processor>
 
- <processor name="ApplyPreAlignment" type="EUTelApplyAlignmentProcessor">
+ <processor name="ApplyPreAlignment" type="EUTelProcessorApplyAlignment">
  <!--Apply to the input hit the alignment corrections-->
   <!--Alignment constant from the condition file-->
   <parameter name="AlignmentConstantName" type="string" lcioInType="LCGenericObject"> prealign </parameter>
   <!--The name of the input hit collection-->
   <parameter name="InputHitCollectionName" type="string" lcioInType="TrackerHit"> hit </parameter>
   <!--The name of the output hit collection-->
   <parameter name="OutputHitCollectionName" type="string" lcioOutType="TrackerHit"> PreAlignedHit </parameter>
-  <!--Rotation Angle around X axis-->
-  <!--parameter name="Alpha" type="double" value="0"/-->
-  <!--Available directinos are:
- 0 --> direct  
- 1 --> reverse -->
-  <parameter name="ApplyAlignmentDirection" type="int" value="0"/>
-  <!--Do you want the reference hit collection to be corrected by the shifts and tilts from the alignment collection? (default - false )-->
-  <parameter name="ApplyToReferenceCollection" type="bool" value="1"/>
-  <!--Rotation Angle around Y axis-->
-  <!--parameter name="Beta" type="double" value="0"/-->
-  <!--Available methods are:
- 0 -.-> shift only 
- 1 -.-> rotation first 
- 2 -.-> shift first -->
-  <parameter name="CorrectionMethod" type="int" value="1"/>
-  <!--Enable or disable DEBUG mode -->
-  <parameter name="DEBUG" type="bool" value="false"/>
-  <!--Implement geometry shifts and rotations as described in alignmentCollectionName -->
-  <parameter name="DoAlignCollection" type="bool" value="true"/>
-  <!--Apply alignment steps in one go. Is supposed to be used for reversealignment in reverse order, like: undoAlignment, undoPreAlignment, undoGear -->
-  <!--parameter name="DoAlignmentInOneGo" type="bool" value="false"/-->
-  <!--Implement geometry shifts and rotations as described in GEAR steering file -->
-  <!--parameter name="DoGear" type="bool" value="false"/-->
-  <!--Rotation Angle around Z axis-->
-  <!--parameter name="Gamma" type="double" value="0"/-->
-  <!--Enable or disable histograms-->
-  <parameter name="HistogramSwitch" type="bool" value="false"/>
-  <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <!--parameter name="OutputReferenceCollection" type="string" value="output_refhit"/-->
-  <!--Events number to have DEBUG1 printed outs (default=10)-->
-  <parameter name="PrintEvents" type="int" value="0"/>
-  <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <parameter name="ReferenceCollection" type="string" value="refhit"/>
-  <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <!--parameter name="ReferenceHitFile" type="string" value="reference.slcio"/-->
-  <!--verbosity level of this processor ("DEBUG0-4,MESSAGE0-4,WARNING0-4,ERROR0-4,SILENT")-->
-  <!--parameter name="Verbosity" type="string" value=""/-->
-  <!--List of alignment collections that were applied to the DUT-->
-  <parameter name="alignmentCollectionNames" type="StringVec" value="prealign"/>
-  <!--List of hit collections. First one is INPUT collection, every subsequent corresponds to applying alignment collection-->
-  <!--<parameter name="hitCollectionNames" type="StringVec" value="hitCollectionNames"/>-->
-  <!--List of refhit collections. First one is INPUT collection, every subsequent corresponds to applying alignment collection-->
-  <!--<parameter name="refhitCollectionNames" type="StringVec" value="hitCollectionNames"/>-->
-</processor>
-
- <processor name="LoadAlignment" type="ConditionsProcessor">
-  <!--ConditionsProcessor provides access to conditions data  transparently from LCIO files or a databases, using LCCD-->
-  <!--Initialization of a conditions database handler-->
-  <!--parameter name="DBCondHandler" type="StringVec"> conditionsName /lccd/myfolder HEAD </parameter-->
-  <!--Initialization of a conditions db file handler-->
-  <!--parameter name="DBFileHandler" type="StringVec"> conditionsName conditions.slcio collectionName </parameter-->
-  <!--Initialization string for conditions database-->
-  <parameter name="DBInit" type="string" value="localhost:lccd_test:align:tel"/>
-    <!--Initialization of a data file handler-->
-  <!--parameter name="DataFileHandler" type="StringVec" value="conditionsName"/-->
-  <!--Initialization of a simple conditions file handler-->
-  <parameter name="SimpleFileHandler" type="StringVec"> align1 @DatabasePath@/@FilePrefix@-alignmentgbl.slcio alignment </parameter>
-    <!--verbosity level of this processor ("DEBUG0-4,MESSAGE0-4,WARNING0-4,ERROR0-4,SILENT")-->
-  <!--parameter name="Verbosity" type="string" value=""/-->
-</processor>
-
- <processor name="ApplyAlignment" type="EUTelApplyAlignmentProcessor">
-  <!--Apply to the input hit the alignment corrections-->
-  <!--Alignment constant from the condition file-->
-  <parameter name="AlignmentConstantName" type="string" lcioInType="LCGenericObject"> align1 </parameter>
-    <!--The name of the input hit collection-->
-  <parameter name="InputHitCollectionName" type="string" lcioInType="TrackerHit"> PreAlignedHit </parameter>
-    <!--The name of the output hit collection-->
-  <parameter name="OutputHitCollectionName" type="string" lcioOutType="TrackerHit"> AlignedHit1 </parameter>
-    <!--Rotation Angle around X axis-->
-  <!--parameter name="Alpha" type="double" value="0"/-->
-  <!--Available directinos are:
-        0 --> direct
- 1 --> reverse -->
-  <parameter name="ApplyAlignmentDirection" type="int" value="0"/>
-    <!--Do you want the reference hit collection to be corrected by the shifts and tilts from the alignment collection? (default - false )-->
-  <parameter name="ApplyToReferenceCollection" type="bool" value="1"/>
-    <!--Rotation Angle around Y axis-->
-  <!--parameter name="Beta" type="double" value="0"/-->
-  <!--Available methods are:
-        0 --> shift only
- 1 --> rotation first
- 2 --> shift first -->
-  <parameter name="CorrectionMethod" type="int" value="1"/>
-    <!--Enable or disable DEBUG mode -->
-  <parameter name="DEBUG" type="bool" value="false"/>
-    <!--Implement geometry shifts and rotations as described in alignmentCollectionName -->
-  <parameter name="DoAlignCollection" type="bool" value="true"/>
-    <!--Apply alignment steps in one go. Is supposed to be used for reversealignment in reverse order, like: undoAlignment, undoPreAlignment, undoGear -->
-  <!--parameter name="DoAlignmentInOneGo" type="bool" value="false"/-->
-  <!--Implement geometry shifts and rotations as described in GEAR steering file -->
-  <!--parameter name="DoGear" type="bool" value="false"/-->
-  <!--Rotation Angle around Z axis-->
-  <!--parameter name="Gamma" type="double" value="0"/-->
-  <!--Enable or disable histograms-->
-  <parameter name="HistogramSwitch" type="bool" value="false"/>
-    <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <!--parameter name="OutputReferenceCollection" type="string" value="output_refhit"/-->
-  <!--Events number to have DEBUG1 printed outs (default=10)-->
-  <parameter name="PrintEvents" type="int" value="0"/>
-    <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <parameter name="ReferenceCollection" type="string" value="refhit"/>
-    <!--This is the name of the reference it collection (init at 0,0,0)-->
-  <!--parameter name="ReferenceHitFile" type="string" value="reference.slcio"/-->
-  <!--verbosity level of this processor ("DEBUG0-4,MESSAGE0-4,WARNING0-4,ERROR0-4,SILENT")-->
-  <!--parameter name="Verbosity" type="string" value=""/-->
-  <!--List of alignment collections that were applied to the DUT-->
-  <parameter name="alignmentCollectionNames" type="StringVec" value="align1"/>
-    <!--List of hit collections. First one is INPUT collection, every subsequent corresponds to applying alignment collection-->
-  <!--<parameter name="hitCollectionNames" type="StringVec" value="hitCollectionNames"/>-->
-  <!--List of refhit collections. First one is INPUT collection, every subsequent corresponds to applying alignment collection-->
-  <!--<parameter name="refhitCollectionNames" type="StringVec" value="hitCollectionNames"/>-->
 </processor>
 
  <processor name="AlignStraight" type="EUTelMille">
@@ -213,7 +99,7 @@
 1 - shifts in the X and Y directions and a rotation around the Z axis,
 2 - only shifts in the X and Y directions
 3 - (EXPERIMENTAL) shifts in the X,Y and Z directions and rotations around all three axis-->
-  <parameter name="AlignMode" type="int" value="1"/>
+  <parameter name="AlignMode" type="string" value="XYShiftsAllRot"/>
   <!--This is the name of the alignment collection to be saved into the slcio file-->
   <!--parameter name="AlignmentConstantCollectionName" type="string" value="alignment"/-->
   <!--This is the name of the LCIO file name with the output alignmentconstants (add .slcio)-->
@@ -232,7 +118,7 @@
   <!--Exclude planes from fit according to their sensor ids.-->
   <parameter name="ExcludePlanes" type="IntVec" value="@ExcludePlanes@"/>
   <!--Fixes the given alignment parameters in the fit if alignMode==3 is used. For each sensor an integer must be specified (If no value is given, then all parameters will be free). bit 0 = x shift, bit 1 = y shift, bit 2 = z shift, bit 3 = alpha, bit 4 = beta, bit 5 = gamma. Note: these numbers are ordered according to the z position of the sensors and NOT according to the sensor id.-->
-  <parameter name="FixParameter" type="IntVec"> 28 28 28 60 28 28 28 </parameter>
+  <!--parameter name="FixParameter" type="IntVec"> 28 28 28 60 28 28 28 </parameter-->
   <!--Fix sensor planes in the fit according to their sensor ids.-->
   <parameter name="FixedPlanes" type="IntVec" value="@FixedPlanes@"/>
   <!--Generate a steering file for the pede program.-->

diff --git a/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/clusterAnalysis-tmp.xml b/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/clusterAnalysis-tmp.xml
@@ -107,6 +107,22 @@
   <parameter name="Irradiation" type="stringVec" value="@IrradiationLevel@"/>
   <!--Data taking rate-->
   <parameter name="Rate" type="string" value="@Rate@"/>
+  <!--Bool to analyze the clusters with a smaller distance allowed between the pixels-->
+  <parameter name="IsDistanceSquareAnalysis" type="bool" value="true"/>
+  <!--Bool to analyze the clusters with empty middle-->
+  <parameter name="IsEmptyMiddleAnalysis" type="bool" value="true"/>
+  <!--Bool to create hit maps with a cut on the cluster size-->
+  <parameter name="IsPlotSizeCutHitmap" type="bool" value="true"/>
+  <!--This cluster size is the cut between the small and the big clusters for the previous bool-->
+  <parameter name="CuttingSize" type="int" value="5"/>
+  <!--Bool to plot the first 100 cluster examples-->
+  <parameter name="IsPlotExampleEvents" type="bool" value="false"/>
+  <!--Bool to do the analysis of clusters appearing in two consecutive events-->
+  <parameter name="IsDoubleFiringAnalysis" type="bool" value="true"/>
+  <!--Distance of the pixels in the clustering to which we compare the original version defined in the clustering step-->
+  <parameter name="SparseMinDistanceSquaredComparison" type="int" value="1"/>
+  <!--Chip version-->
+  <parameter name="ChipVersion" type="int" value="@whichChip@"/>
   <!--parameter name="Verbosity" type="string" value="DEBUG"/-->
 </processor>
 

diff --git a/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/clustering-tmp.xml b/jobsub/examples/pALPIDEfs/steering-templates_pALPIDEfs_7/clustering-tmp.xml
@@ -148,6 +148,8 @@ Available types of the data format:
   <parameter name="SparseClusterCut" type="float" value="0.0"/>
   <!--Minimum distance between sparsified pixel ( touching == sqrt(2)) -->
   <parameter name="SparseMinDistance" type="float" value="1"/>
+  <!--Squared minimum distance between sparsified pixel-->
+  <parameter name="SparseMinDistanceSquared" type="float" value="2"/>
   <!--Threshold in SNR for seed pixel contained in ZS data-->
   <parameter name="SparseSeedCut" type="float" value="0.0"/>
   <!--verbosity level of this processor ("DEBUG0-4,MESSAGE0-4,WARNING0-4,ERROR0-4,SILENT")-->