Added GaussianDistribution Tests

README.md

@@ -31,8 +31,12 @@ This installation guide is for ISIS3 users interested in installing ISIS3 (3.6.0
 
         #Activate the environment
         #Depending on your version of Anaconda use one of the following:
-          Anaconda 3.4 and up - conda activate isis3
-          prior to Anaconda 3.4 - source activate isis3
+
+        #Anaconda 3.4 and up:
+        conda activate isis3
+
+        #Prior to Anaconda 3.4:
+        source activate isis3
 
         #Add the following channels to the environment
         conda config --env --add channels conda-forge

isis/scripts/isis3VarInit.py

@@ -113,6 +113,8 @@ def mkdir( p ):
 setenv ISISROOT {}
 setenv ISIS3DATA {}
 setenv ISIS3TESTDATA {}
+
+source $CONDA_PREFIX/scripts/tabCompletion.csh
 """.format(os.environ['CONDA_PREFIX'], args.data_dir, args.test_dir)
     a.write(script)
 print( 'Wrote '+activate_vars_csh )

isis/scripts/tabCompletion.csh

@@ -0,0 +1,25 @@
+#!/bin/csh
+
+
+# Setup tab completion
+if ( -f $ISISROOT/bin/isiscomplete ) then
+  set newBinaries = `/bin/ls $ISISROOT/bin/xml | grep -v qt.conf | sed s%\.xml%%`
+  set i = 0
+  set loop = 0
+  set chunk = ""
+  foreach app ($newBinaries)
+    @ i = $i + 1
+    @ loop = $loop + 1
+    set chunk = "$chunk $app"
+    if ( "$i" == 100 || "$loop" == $#newBinaries) then
+      eval `$ISISROOT/bin/isiscomplete $chunk`
+      set i = 1
+      set chunk = ""
+    endif
+  end
+  unset i
+  unset loop
+  unset chunk
+  unset app
+  unset newBinaries
+endif

isis/src/base/objs/GaussianDistribution/GaussianDistribution.cpp

@@ -38,6 +38,7 @@ namespace Isis {
     p_stdev = standardDeviation;
   }
 
+
   /**
    * Computes and returns the probability of the specified value
    * on the gaussian distribution.
@@ -51,6 +52,7 @@ namespace Isis {
     return std::exp(-0.5 * std::pow((value - p_mean) / p_stdev, 2)) / (std::sqrt(2 * PI) * p_stdev);
   }
 
+
   /**
    * Computes and returns the cumulative distribution up to the
    * specified value on the gaussian distribution.

isis/src/base/objs/ProcessImport/ProcessImport.h

@@ -163,7 +163,7 @@ namespace Isis {
    *                           was made to accomodate Rosetta VIRTIS-m calibrated data files and
    *                           has no impact on other supported BIP files.
    *                           Fixes #5398.
-   *   @history 208-07-19 Tyler Wilson - Added support for 4-byte UnsignedInteger special pixel
+   *   @history 2018-07-19 Tyler Wilson - Added support for 4-byte UnsignedInteger special pixel
    *                            values.
    *
    */

isis/src/galileo/apps/gllssi2isis/gllssi2isis.xml

@@ -8,19 +8,19 @@
 
   <description>
     Converts a PDS formatted Galileo solid state imager (SSI) image EDR
-    into an Isis Cube.  The required instrument labels will be propagated 
-    into the instrument group.  The user must choose an input image label, 
-    output cube name, and frame mode, or summing mode.  Galileo SSI images have 
-    a summing mode of FULL (800 x 800 pixels) or SUMMED (400 x 400 pixels).  
+    into an Isis Cube.  The required instrument labels will be propagated
+    into the instrument group.  The user must choose an input image label,
+    output cube name, and frame mode, or summing mode.  Galileo SSI images have
+    a summing mode of FULL (800 x 800 pixels) or SUMMED (400 x 400 pixels).
     <p>
-      <strong> Note: </strong> For the I24 encounter (found in volume go_0022), 
-      many Galileo SSI images of Io were originally  "garbled".  These images 
-      were reconstructed and released with the filename ####s where ####r is the 
-      name of the original garbled file and #### is the last four digits of the 
-      SPACECRAFT_CLOCK_START_COUNT.  These images will have Most of the original 
-      images were 400 x 400 (i.e. SUMMED). However, the reconstructed files are 
-      800 x 800 and must be imported as FULL to get the entire image.  If the 
-      user imports a reconstructed image with FRAMEMODE = AUTO, it will be 
+      <strong> Note: </strong> For the I24 encounter (found in volume go_0022),
+      many Galileo SSI images of Io were originally  "garbled".  These images
+      were reconstructed and released with the filename ####s where ####r is the
+      name of the original garbled file and #### is the last four digits of the
+      SPACECRAFT_CLOCK_START_COUNT.  These images will have Most of the original
+      images were 400 x 400 (i.e. SUMMED). However, the reconstructed files are
+      800 x 800 and must be imported as FULL to get the entire image.  If the
+      user imports a reconstructed image with FRAMEMODE = AUTO, it will be
       treated as a FULL image, even if the original was SUMMED.
     </p>
   </description>
@@ -33,15 +33,15 @@
       Converted to Isis 3.0
     </change>
     <change name="Steven Koechle" date="2007-10-30">
-      Added Summing Keyword. Moved most hardcoded translations into a 
-      translation table.  Modified tests to check the lables. Removed ImageID 
+      Added Summing Keyword. Moved most hardcoded translations into a
+      translation table.  Modified tests to check the lables. Removed ImageID
       keyword.
     </change>
     <change name="Steven Lambright" date="2007-12-31">
       Removed the hard coded Instrument Mode ID keyword translation.
     </change>
     <change name="Steven Lambright" date="2007-01-08">
-      Added summing options. Output summed images will now only be a quarter of 
+      Added summing options. Output summed images will now only be a quarter of
       the size for calibration (the upper-left data in the input is preserved).
     </change>
     <change name="Christopher Austin" date="2008-03-18">
@@ -52,7 +52,7 @@
     </change>
     <change name="Jeannie Walldren" date="2009-06-08">
        Added valid DATA_SET_ID value for reconstructed images (i.e. value
-       contains "SSI-4-REDR-V1.0").  Modified code to set as FULL summing 
+       contains "SSI-4-REDR-V1.0").  Modified code to set as FULL summing
        mode if FRAMEMODE=AUTO and the image is reconstructed.
     </change>
     <change name="Tyler Wilson" date="2015-10-02">
@@ -64,6 +64,10 @@
       Changed documentation to have the correct link to the Planetary Science Data
       Dictionary Document.  Fixes #3867
     </change>
+    <change name="Adam Paquette" date="2019-04-16">
+      Fixed original label not being written to cubes ingested using the summed
+      option. Fixes #3207
+    </change>
 
 
   </history>
@@ -129,7 +133,7 @@
       <parameter name="FRAMEMODE">
         <type>string</type>
         <brief>Summing mode of the input image</brief>
-        <description>Summing mode of the input image.  The user 
+        <description>Summing mode of the input image.  The user
           may specify the summing mode or choose to allow the program to
           determine this.
         </description>
@@ -138,15 +142,15 @@
           <option value="AUTO">
             <brief>Automatically Detect</brief>
             <description>
-              This will attempt to automatically detect the summing mode of the 
-              input image based on the DATA_SET_ID and/or FRAME_DURATION keyword 
+              This will attempt to automatically detect the summing mode of the
+              input image based on the DATA_SET_ID and/or FRAME_DURATION keyword
               values from the input image labels.
             </description>
           </option>
           <option value="SUMMED">
             <brief>The image is summed</brief>
             <description>
-              This will treat the input image as if it has a summing mode of 2 
+              This will treat the input image as if it has a summing mode of 2
               in both the sample and line direction.
             </description>
           </option>
@@ -182,8 +186,8 @@
               Example GUI
             </brief>
             <description>
-              Screenshot of GUI with parameters filled in to perform the 
-              gllssi2isis application.  Input label and output cubes are always 
+              Screenshot of GUI with parameters filled in to perform the
+              gllssi2isis application.  Input label and output cubes are always
               required.  The FRAMEMODE radio button AUTO is chosen as default.
             </description>
             <thumbnail width="200" height="177" caption="Gllssi2isis GUI using defaults." src="assets/thumbs/gllssi2isisGuiAutoThumb.jpg"/>
@@ -214,7 +218,7 @@
           <thumbnail width="187" height="200" caption="Output cube imported with defaults" src="assets/thumbs/gllssi2isisOutputAutoThumb.jpg" />
           <parameterName>
             TO
-          </parameterName> 
+          </parameterName>
         </image>
       </outputImages>
     </example>

isis/src/galileo/apps/gllssi2isis/main.cpp

@@ -5,6 +5,7 @@
 #include "IException.h"
 #include "iTime.h"
 #include "ProcessImportPds.h"
+#include "OriginalLabel.h"
 #include "UserInterface.h"
 
 #include <cstdio>
@@ -14,9 +15,6 @@
 #include <QFile>
 
 
-
-
-
 using namespace std;
 using namespace Isis;
 bool summed;
@@ -28,25 +26,19 @@ void translateLabels(Pvl &pdsLabel, Cube *ocube);
 void fixPvl(QString fileName);
 
 void IsisMain() {
-
   //initialize globals
   summed = false;
   summedOutput = NULL;
   // Grab the file to import
   ProcessImportPds p;
   UserInterface &ui = Application::GetUserInterface();
   FileName inFile = ui.GetFileName("FROM");
-  FileName out = ui.GetFileName("TO");
-
-
+  FileName outFile = ui.GetFileName("TO");
 
+  // Apply a fix to the gallileo pds labels so they can be read
   fixPvl(inFile.toString());
 
-
-
-
   // Make sure it is a Galileo SSI image
-
   Pvl lab(inFile.expanded());
 
   //Checks if in file is rdr
@@ -102,35 +94,34 @@ void IsisMain() {
   Pvl pdsLabel;
   p.SetPdsFile(inFile.expanded(), "", pdsLabel);
 
-  //Set up the output file
-  Cube *ocube;
-
+  // If summed handle the image similarly to pds2isis
+  // with an extra translation step
   if (!summed) {
-    ocube = p.SetOutputCube("TO");
+    Cube *ocube = p.SetOutputCube("TO");
     p.StartProcess();
+    translateLabels(pdsLabel, ocube);
+    p.EndProcess();
   }
   else {
+  // Otherwise the dimensions of the cube need to be cut in half before
+  // processsing. Since we didn't set the output cube we need to take care
+  // of writting the original label ourselves
     summedOutput = new Cube();
     summedOutput->setDimensions(p.Samples() / 2, p.Lines() / 2, p.Bands());
     summedOutput->setPixelType(p.PixelType());
-    summedOutput->create(ui.GetFileName("TO"));
-    p.StartProcess(translateData);
-    ocube = summedOutput;
-  }
+    summedOutput->create(outFile.expanded());
 
-  translateLabels(pdsLabel, ocube);
-  p.EndProcess();
+    p.StartProcess(translateData);
+    translateLabels(pdsLabel, summedOutput);
 
-  if (summed) {
+    OriginalLabel ol(Pvl(inFile.expanded()));
+    summedOutput->write(ol);
     summedOutput->close();
     delete summedOutput;
   }
-
   return;
 }
 
-
-
 /**
   * This fixes a problem with some of the Pvl files where a comment
   * was left open.  If the file has this error, the comment is closed
@@ -141,9 +132,6 @@ void IsisMain() {
   *     being checked
   *
   */
-
-
-
 void fixPvl(QString fileName){
 
     QFile pvlFile;
@@ -174,15 +162,7 @@ void fixPvl(QString fileName){
 
 }
 
-
-
-
-
-
-
-
-
-void translateData(Buffer &inData) {
+void translateData(Isis::Buffer &inData) {
   summedOutput->write(inData);
 }