Merge branch 'release/2.12.0'

.travis.yml

@@ -0,0 +1,17 @@
+language: cpp
+sudo: required
+dist: trusty
+compiler:
+    - clang
+os:
+    - osx
+osx_image: xcode9.3
+ruby: 2.2.0
+before_install:
+    - if [ $TRAVIS_OS_NAME == osx ]; then rm '/usr/local/include/c++' && brew update && brew upgrade python && brew install root hdf5 fftw libmatio ; fi
+script:
+    - if [ $TRAVIS_OS_NAME == osx ]; then source CI/build.sh ; fi
+    - if [ $TRAVIS_OS_NAME == osx ]; then source CI/test.sh ; fi
+notifications:
+    slack:
+        secure: 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

AUTHORS

@@ -3,26 +3,29 @@ Authors and Copyright Holders for Katydid
 
 Individuals
 -----------
-Christine Claessens [4]
-Mathieu Guigue [2]
-Jiarui Huang [1]*
-Brittney Johnson [1]*
-Jared Kofron [5]*
-Benjamin LaRoque [3]
-Noah S. Oblath [2]
-Devyn Rysewyk [1]*
-Luis Saldaña [6]
-Penny Slocum [6]
-Evan Zayas [1]
+Nick Buzinsky [2]
+Christine Claessens [5]
+Laura Gladstone [1]
+Mathieu Guigue [3]
+Jiarui Huang [2]*
+Brittney Johnson [2]*
+Jared Kofron [6]*
+Benjamin LaRoque [4]
+Noah S. Oblath [3]
+Devyn Rysewyk [2]*
+Luis Saldaña [7]
+Penny Slocum [7]
+Evan Zayas [2]
 
 
 Institutions
 ------------
-1. Massachusetts Institute of Technology, Cambridge, MA
-2. Pacific Northwest National Laboratory, Richland, WA
-3. University of California at Santa Barbara, Santa Barbara, CA
-4. University of Mainz, Mainz, Germany
-5. University of Washington, Seattle, WA
-6. Yale University, New Haven, CT
+1. Case Western Reserve University, Cleveland, OH
+2. Massachusetts Institute of Technology, Cambridge, MA
+3. Pacific Northwest National Laboratory, Richland, WA
+4. University of California at Santa Barbara, Santa Barbara, CA
+5. University of Mainz, Mainz, Germany
+6. University of Washington, Seattle, WA
+7. Yale University, New Haven, CT
 
 * Former institutional association

CI/build.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+mkdir build
+cd build
+cmake -DKatydid_ENABLE_TESTING=TRUE -DCMAKE_BUILD_TYPE=STANDARD ..
+make -j3 
+make install
+cd ..

CI/test.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# Miscalleneous 
+./build/bin/TestRandom
+
+# Spectrum Analysis
+./build/bin/TestTrackProcessing
+
+# Event Analysis
+./build/bin/TestDBScanTrackClustering
+./build/bin/TestSequentialTrackFinder
+./build/bin/TestSpectrumDiscriminator

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required (VERSION 3.1)
 
 # Define the project
 cmake_policy( SET CMP0048 NEW ) # version in project()
-project (Katydid VERSION 2.11.1)
+project (Katydid VERSION 2.12.0)
 
 list( APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/Nymph/Scarab/cmake )
 include( PackageBuilder )

Documentation/validation_log.rst

@@ -12,7 +12,7 @@ Guidelines
   * Indicate in this log what tests were performed, and where to find a writeup of the results.
 * Fixes to existing features should also be validated.
   * Perform tests to show that the fix solves the problem that had been indicated.
-  * Perform tests to shwo that the fix does not cause other problems.
+  * Perform tests to show that the fix does not cause other problems.
   * Indicate in this log what tests were performed and how you know the problem was fixed.
 
 Template
@@ -43,6 +43,41 @@ Fixes:
 Log
 ---
 
+Version: 2.12.0
+~~~~~~~~~~~~~~~
+
+Release Date: July 5, 2018
+'''''''''''''''''''''''''''''''
+
+New Features
+''''''''''''
+
+* Moving the default object name from the Katydid Writer into Cicada:
+      * TMultiTrackEventData
+      * TProcessedTrackData
+      * TProcessedMPTData
+      * TClassifierResultsData
+* Continuous Integration with Travis:
+      * Automatic build of libraries and validation executable
+      * Test of one executable (TestRandom)
+      * Slack message upon success or failure
+* Track SNR and NUP:
+      * Adding a KTDiscriminatedPoint structure that would be common to data objects using points obtained by discrimination.
+      * Propagating the new structure to SparseWaterfallCandidateData and related classes (tested with TestDBScanTrackClustering)
+      * KTSpectrumDiscriminator and KTVariableSpectrumDiscriminator: new member variables of KTDiscriminatedPoints1DData are calculated and set.
+      * KTTrackProcessing: split the KTProcessingTrack processor into two processors: KTTrackProcessingDoubleCuts and KTTrackProcessingWeightedSlope.
+      * KTTrackProcessingWeightedSlope handles both SequentialLineData and SparseWaterfallCandidateData; while KTTrackProcessingDoubleCuts only connects to SparseWaterfallCandidateData (with HoughData).
+      * Adding new track properties to the KTProcessedTrackData result (Tested with TestTrackProcessing).
+      * KTMultiTrackEventData and KTProcessedTrackData: added member variables for SNR and NUP quantities.
+      * KTSequentialLineData: new version of KTSeqLine. Has SNR and NUP member variables. LineTrimming now uses SNR instead of Power.
+      * KTSequentialTrackFinder: new slot for KTDiscriminatedPoints1DData only. Signal is now KTSequentialLineData.
+      * KTOverlappingTrackClustering and KTIterativeTrrackClustering: new slot and singal for KTSequentialLineData. Both Processors can no longer apply cuts.
+      * KTSequentialLineSNRCut and KTSequentialLineNUPCut: can be used to apply cuts on total and average SNR and NUP of KTSequentialLineData.
+      * KTEventFirstTrackSNR and KTEventFirstTrackNUPCut: can be used to apply cuts on total and average SNR and NUP of KTMultiTrackEventData.
+* Writers update:
+      * KTSparseWaterfallCandidateData objects: TDiscriminatedPoint and TSparseWaterfallCandidateData classes have been added.
+
+
 Version: 2.11.1
 ~~~~~~~~~~~~~~~
 
@@ -55,7 +90,6 @@ Fixes:
 * Nymph upgraded to v1.4.5
 * Commented out incorrect calculation of variance in KTGainVariationProcessor.
 
-
 Version: 2.11.0
 ~~~~~~~~~~~~~~~
 

Source/Data/CMakeLists.txt

@@ -7,6 +7,7 @@ set (DATA_HEADERFILES
     SpectrumAnalysis/KTCluster1DData.hh
     SpectrumAnalysis/KTCorrelationData.hh
     SpectrumAnalysis/KTCorrelationTSData.hh
+    SpectrumAnalysis/KTDiscriminatedPoint.hh
     SpectrumAnalysis/KTDiscriminatedPoints1DData.hh
     SpectrumAnalysis/KTDiscriminatedPoints2DData.hh
     SpectrumAnalysis/KTGainVarChi2Data.hh
@@ -16,7 +17,7 @@ set (DATA_HEADERFILES
     SpectrumAnalysis/KTKDTreeData.hh
     SpectrumAnalysis/KTNormalizedFSData.hh
     SpectrumAnalysis/KTPointCloud.hh
-    SpectrumAnalysis/KTSeqLine.hh
+    SpectrumAnalysis/KTSequentialLineData.hh
     SpectrumAnalysis/KTTimeSeriesDist.hh
     SpectrumAnalysis/KTTimeSeriesDistData.hh
     SpectrumAnalysis/KTWV2DData.hh
@@ -80,7 +81,7 @@ set (DATA_SOURCEFILES
     SpectrumAnalysis/KTHoughData.cc
     SpectrumAnalysis/KTKDTreeData.cc
     SpectrumAnalysis/KTNormalizedFSData.cc
-    SpectrumAnalysis/KTSeqLine.cc
+    SpectrumAnalysis/KTSequentialLineData.cc
     SpectrumAnalysis/KTTimeSeriesDist.cc
     SpectrumAnalysis/KTTimeSeriesDistData.cc
     SpectrumAnalysis/KTWV2DData.cc

Source/Data/EventAnalysis/KTMultiTrackEventData.cc

@@ -45,6 +45,13 @@ namespace Katydid
             fFirstTrackSlope(0.),
             fFirstTrackIntercept(0.),
             fFirstTrackTotalPower(0.),
+            fFirstTrackNTrackBins(0),
+            fFirstTrackTotalSNR(0.),
+            fFirstTrackMaxSNR(0.),
+            fFirstTrackTotalNUP(0.),
+            fFirstTrackMaxNUP(0.),
+            fFirstTrackTotalWideSNR(0.),
+            fFirstTrackTotalWideNUP(0.),
             fUnknownEventTopology(false),
             fTracks()
     {
@@ -77,6 +84,13 @@ namespace Katydid
             fFirstTrackSlope(orig.fFirstTrackSlope),
             fFirstTrackIntercept(orig.fFirstTrackIntercept),
             fFirstTrackTotalPower(orig.fFirstTrackTotalPower),
+            fFirstTrackNTrackBins(orig.fFirstTrackNTrackBins),
+            fFirstTrackTotalSNR(orig.fFirstTrackTotalSNR),
+            fFirstTrackMaxSNR(orig.fFirstTrackMaxSNR),
+            fFirstTrackTotalNUP(orig.fFirstTrackTotalNUP),
+            fFirstTrackMaxNUP(orig.fFirstTrackMaxNUP),
+            fFirstTrackTotalWideSNR(orig.fFirstTrackTotalWideSNR),
+            fFirstTrackTotalWideNUP(orig.fFirstTrackTotalWideNUP),
             fUnknownEventTopology(orig.fUnknownEventTopology),
             fTracks()
     {
@@ -253,6 +267,14 @@ namespace Katydid
         fFirstTrackIntercept = trackIt->fProcTrack.GetIntercept();
         fFirstTrackTotalPower = trackIt->fProcTrack.GetTotalPower();
 
+        fFirstTrackNTrackBins = trackIt->fProcTrack.GetNTrackBins();
+        fFirstTrackTotalSNR = trackIt->fProcTrack.GetTotalTrackSNR();
+        fFirstTrackMaxSNR = trackIt->fProcTrack.GetMaxTrackSNR();
+        fFirstTrackTotalNUP = trackIt->fProcTrack.GetTotalTrackNUP();
+        fFirstTrackMaxNUP = trackIt->fProcTrack.GetMaxTrackNUP();
+        fFirstTrackTotalWideSNR = trackIt->fProcTrack.GetTotalWideTrackSNR();
+        fFirstTrackTotalWideNUP = trackIt->fProcTrack.GetTotalWideTrackNUP();
+
         for (++trackIt; trackIt != fTracks.end(); ++trackIt)
         {
             KTDEBUG(evlog, "Track " << trackIt->fProcTrack.GetTrackID());
@@ -271,6 +293,13 @@ namespace Katydid
                 fFirstTrackSlope = trackIt->fProcTrack.GetSlope();
                 fFirstTrackIntercept = trackIt->fProcTrack.GetIntercept();
                 fFirstTrackTotalPower = trackIt->fProcTrack.GetTotalPower();
+                fFirstTrackNTrackBins = trackIt->fProcTrack.GetNTrackBins();
+                fFirstTrackTotalSNR = trackIt->fProcTrack.GetTotalTrackSNR();
+                fFirstTrackTotalNUP = trackIt->fProcTrack.GetTotalTrackNUP();
+                fFirstTrackMaxSNR = trackIt->fProcTrack.GetMaxTrackSNR();
+                fFirstTrackMaxNUP = trackIt->fProcTrack.GetMaxTrackNUP();
+                fFirstTrackTotalWideSNR = trackIt->fProcTrack.GetTotalWideTrackSNR();
+                fFirstTrackTotalWideNUP = trackIt->fProcTrack.GetTotalWideTrackNUP();
             }
 
             if (trackIt->fProcTrack.GetEndTimeInRunC() > fEndTimeInRunC)
@@ -330,6 +359,13 @@ namespace Katydid
         fFirstTrackSlope = 0.;
         fFirstTrackIntercept = 0.;
         fFirstTrackTotalPower = 0.;
+        fFirstTrackNTrackBins = 0;
+        fFirstTrackTotalSNR = 0.;
+        fFirstTrackTotalNUP = 0.;
+        fFirstTrackMaxSNR = 0.;
+        fFirstTrackMaxNUP = 0.;
+        fFirstTrackTotalWideSNR = 0.;
+        fFirstTrackTotalWideNUP = 0.;
 
         return;
     }

Source/Data/EventAnalysis/KTMultiTrackEventData.hh

@@ -64,6 +64,13 @@ namespace Katydid
             MEMBERVARIABLE(double, FirstTrackSlope);
             MEMBERVARIABLE(double, FirstTrackIntercept);
             MEMBERVARIABLE(double, FirstTrackTotalPower);
+            MEMBERVARIABLE(int, FirstTrackNTrackBins);
+            MEMBERVARIABLE(double, FirstTrackTotalSNR);
+            MEMBERVARIABLE(double, FirstTrackMaxSNR);
+            MEMBERVARIABLE(double, FirstTrackTotalNUP);
+            MEMBERVARIABLE(double, FirstTrackMaxNUP);
+            MEMBERVARIABLE(double, FirstTrackTotalWideSNR);
+            MEMBERVARIABLE(double, FirstTrackTotalWideNUP);
 
             // this member variable is set by event building
             MEMBERVARIABLE(bool, UnknownEventTopology); // if True, indicates that the reconstruction was unable to deal with the event

Source/Data/EventAnalysis/KTProcessedTrackData.cc

@@ -31,6 +31,13 @@ namespace Katydid
             fSlope(0.),
             fIntercept(0.),
             fTotalPower(0.),
+            fNTrackBins(0.),
+            fTotalTrackSNR(0.),
+            fMaxTrackSNR(0.),
+            fTotalTrackNUP(0.),
+            fMaxTrackNUP(0.),
+            fTotalWideTrackSNR(0.),
+            fTotalWideTrackNUP(0.),
             fStartTimeInRunCSigma(0.),
             fEndTimeInRunCSigma(0.),
             fTimeLengthSigma(0.),
@@ -63,6 +70,13 @@ namespace Katydid
             fSlope(orig.fSlope),
             fIntercept(orig.fIntercept),
             fTotalPower(orig.fTotalPower),
+            fNTrackBins(orig.fNTrackBins),
+            fTotalTrackSNR(orig.fTotalTrackSNR),
+            fMaxTrackSNR(orig.fMaxTrackSNR),
+            fTotalTrackNUP(orig.fTotalTrackNUP),
+            fMaxTrackNUP(orig.fMaxTrackNUP),
+            fTotalWideTrackSNR(orig.fTotalWideTrackSNR),
+            fTotalWideTrackNUP(orig.fTotalWideTrackNUP),
             fStartTimeInRunCSigma(orig.fStartTimeInRunCSigma),
             fEndTimeInRunCSigma(orig.fEndTimeInRunCSigma),
             fTimeLengthSigma(orig.fTimeLengthSigma),
@@ -98,6 +112,13 @@ namespace Katydid
         fSlope = rhs.fSlope;
         fIntercept = rhs.fIntercept;
         fTotalPower = rhs.fTotalPower;
+        fNTrackBins = rhs.fNTrackBins,
+        fTotalTrackSNR = rhs.fTotalTrackSNR;
+        fMaxTrackSNR = rhs.fMaxTrackSNR;
+        fTotalTrackNUP = rhs.fTotalTrackNUP;
+        fMaxTrackNUP = rhs.fMaxTrackNUP;
+        fTotalWideTrackSNR = rhs.fTotalWideTrackSNR;
+        fTotalWideTrackNUP = rhs.fTotalWideTrackNUP;
         fStartTimeInRunCSigma = rhs.fStartTimeInRunCSigma;
         fEndTimeInRunCSigma = rhs.fEndTimeInRunCSigma;
         fTimeLengthSigma = rhs.fTimeLengthSigma;

Source/Data/EventAnalysis/KTProcessedTrackData.hh

@@ -46,6 +46,13 @@ namespace Katydid
             MEMBERVARIABLE(double, Slope);
             MEMBERVARIABLE(double, Intercept);
             MEMBERVARIABLE(double, TotalPower);
+            MEMBERVARIABLE(unsigned, NTrackBins);
+            MEMBERVARIABLE(double, TotalTrackSNR);
+            MEMBERVARIABLE(double, MaxTrackSNR);
+            MEMBERVARIABLE(double, TotalTrackNUP);
+            MEMBERVARIABLE(double, MaxTrackNUP);
+            MEMBERVARIABLE(double, TotalWideTrackSNR);
+            MEMBERVARIABLE(double, TotalWideTrackNUP);
 
             MEMBERVARIABLE(double, StartTimeInRunCSigma);
             MEMBERVARIABLE(double, EndTimeInRunCSigma);

Source/Data/EventAnalysis/KTSparseWaterfallCandidateData.cc

@@ -24,8 +24,8 @@ namespace Katydid
             fTimeInAcq(0.),
             //fFirstSliceNumber(0),
             //fLastSliceNumber(0),
-            fMinimumFrequency(0.),
-            fMaximumFrequency(0.),
+            fMinFrequency(0.),
+            fMaxFrequency(0.),
             //fMeanStartFrequency(0.),
             //fMeanEndFrequency(0.),
             fFrequencyWidth(0.)
@@ -40,7 +40,7 @@ namespace Katydid
     {
     }
 
-    void KTSparseWaterfallCandidateData::AddPoint(const Point& point)
+    void KTSparseWaterfallCandidateData::AddPoint(const KTDiscriminatedPoint& point)
     {
         fPoints.insert(point);
         return;