Merge pull request #129 from fact-project/fixSourceTrafo

Merge fixSourceTrafo in Master, new Version 0.14.0

CHANGELOG.md

@@ -1,5 +1,16 @@
 #Changelog for the fact-tools
 
+## Version 0.14.0 -- 03.05.2016
+
+* Bug fix for the calculation of the source position (and position of stars in the camera):
+  * There was an arcsin in the calculation of the az of a given ra/dec coordinate, causing the calculated az to be in -90 to 90 degree.
+  * This was not a problem for Crab Nebula data (or at least for most of it, so that a clear signal could be achieved) but for Mrk 421 data. For this data, there was no signal of the source visible.
+  * New calculation formulas are now implemented, which are using the atan2 method for this.
+  * The new calculated coordinate transformation were checked against python implementation and also checked by Max Ahnen, who could clearly see a signal of Mrk 421 after the bugfix.
+  * Corresponding tests were adapted.
+* There is now also an example file for the erna std analysis (this is work in progress)
+
+
 ## Version 0.13.3 -- 06.04.2016
 
 * new Processor: `fact.ApplyModel` which applies a .pmml model to data in the data item. The model can be written with SciKit learn.

examples/forErna/std_analysis_erna.xml

@@ -0,0 +1,98 @@
+<container>
+    <!--
+    This Process contains the standard analysis for FACT, with modifications to be used with the SGE/TORQUE cluster
+    execution tool ERNA (Easy RuN Access) https://github.com/fact-project/erna
+    -->
+    <properties url="classpath:/default/settings.properties" />
+
+    <property name="db" value="file:./2015.sqlite" />
+
+    <property name="integralGainFile" value="classpath:/default/gain_sorted_20131127.csv" />
+    <property name="pixelDelayFile" value="classpath:/default/delays_lightpulser_20150217.csv" />
+
+    <service id="auxService" class="fact.auxservice.SqliteService" url="${db}" />
+    <service id="calibService" class="fact.calibrationservice.ConstantCalibService" />
+
+    <!-- Has to be a  FactFileListMultiStream in order to work on tasks from gridmap and the executor script.-->
+    <stream id="fact" class="fact.io.FactFileListMultiStream"   url="${input}">
+        <stream class="fact.io.zfits.ZFitsStream" id="_" />
+    </stream>
+
+    <process id="1" input="fact">
+        <!-- prevEventAndSkip: -->
+        <!-- PreviousEventInfo, Skip(no Data Trigger) -->
+        <include url="classpath:/default/data/prevEventAndSkip.xml" />
+        <!-- Output: Data -->
+
+        <!-- Calibration: -->
+        <fact.datacorrection.DrsCalibration
+                key="Data"
+                outputKey="DataCalibrated"
+        />
+        <fact.datacorrection.PatchJumpRemoval
+                dataKey="DataCalibrated"
+                outputKey="DataCalibrated"
+                prevEventsKey="prevEvents"
+                startCellKey="StartCellData"
+                jumpLimit="${patchJumpRemoval_jumpLimit}"
+        />
+        <fact.datacorrection.RemoveSpikes
+                dataKey="DataCalibrated"
+                outputKey="DataCalibrated"
+                startCellKey="StartCellData"
+                leftBorder="${removeSpikes_leftBorder}"
+                spikeLimit="${removeSpikes_spikeLimit}"
+                topSlopeLimit="${removeSpikes_topSlopeLimit}"
+                maxSpikeLength="${removeSpikes_maxSpikeLength}"
+        />
+        <fact.filter.DrsTimeCalibration
+                outputKey="timeCalibConst"
+        />
+        <fact.filter.ArrayTimeCorrection
+                dataKey="DataCalibrated"
+                timeCalibConstKey="timeCalibConst"
+                outputKey="DataCalibrated"
+        />
+        <fact.datacorrection.InterpolateTimeSeries
+                calibService="calibService"
+                dataKey="DataCalibrated"
+                dataOutputKey="DataCalibrated"
+        />
+
+        <!-- Extraction -->
+        <!-- BasicExtraction, RisingEdgeForPositions, RisingEdgePolynomFit, TimeOverThreshold,
+        PhotonChargeTimeOverThreshold, HandleSaturation, CorrectPixelDelays-->
+        <include url="classpath:/default/data/extraction.xml" />
+        <!-- Output: photoncharge, arrivalTime -->
+
+        <!-- Cleaning -->
+        <!-- SourcePosition(Cetatauri), CoreNeighborCleanTimeNeighbor-->
+        <include url="classpath:/default/data/cleaning.xml" />
+        <!-- Output: shower -->
+
+        <!-- Parameter calculation (only source independent) -->
+        <!-- ArrayMean(photoncharge,arrivalTime), ArrayStatistics(photoncharge,arrivalTime,maxSlopes,
+        arrivalTimePos,maxSlopesPos,maxAmplitudePosition,photonchargeSaturated,arrivalTimeTOT),
+        Size, DistributionFromShower, M3Long, Length, Width, NumberOfIslands, TimeGraident,
+        Concentration, ConcentrationCore, ConcentrationAtCenterOfGravity, Leakage, TimeSpread,
+        ShowerSlope, Disp -->
+        <include url="classpath:/default/data/parameterCalc.xml" />
+        <!-- Output: source independent parameters -->
+
+        <!-- Parameter calculation (only source dependent) -->
+        <!-- SourcePosition(${sourcename}), AntiSourcePosition(5), Alpha(for 6 Sources),
+        Distance(for 6 Sources), CosDeltaAlpha(for 6 Sources), Theta(for 6 Sources) -->
+        <include url="classpath:/default/data/sourceParameter.xml" />
+        <!-- Output: source dependent parameters -->
+
+        <!-- its important that you output a valid json file for this to work in conjuction with gridmap -->
+	<fact.io.JSONWriter keys="${keysForOutput}" 
+		url="${output}" 
+		writeListOfItems="True" 
+		specialDoubleValuesAsString="True"
+		pixelSetsAsInt="True"
+		/>
+	<!-- <PrintData/> -->
+	<!-- <fact.io.PrintKeysOnConsole keys="${keysForOutput}" /> -->
+    </process>
+</container>

pom.xml

@@ -4,7 +4,7 @@
   <groupId>de.sfb876</groupId>
   <artifactId>fact-tools</artifactId>
   <name>fact-tools</name>
-  <version>0.13.3</version>
+  <version>0.14.0</version>
   <url>http://sfb876.de/fact-tools/</url>
 
 	<description>

src/main/java/fact/auxservice/SqliteService.java

@@ -162,8 +162,8 @@ private TreeSet<AuxPoint> getSourceDataFromCursor(ISqlJetCursor cursor) throws S
                 m.put("Angle", cursor.getFloat("Angle"));
                 m.put("Ra_src", cursor.getFloat("Ra_src"));
                 m.put("Dec_src", cursor.getFloat("Dec_src"));
-                m.put("Ra_cmd", cursor.getFloat("Ra_cmd"));
-                m.put("Dec_cmd", cursor.getFloat("Dec_cmd"));
+                // m.put("Ra_cmd", cursor.getFloat("Ra_cmd"));
+                // m.put("Dec_cmd", cursor.getFloat("Dec_cmd"));
                 m.put("Offset", cursor.getFloat("Offset"));
 
                 DateTimeFormatter formatter = DateTimeFormat.forPattern("YYYY-MM-DD HH:mm:ss.SSSSSS");