corrects for all but 16 bit compression

organize template files and add 8bit version use 8bit template when 8bit Delete .nfs00000001d83de60d0000003e remove accidental file Updated equalizer output (DOI-USGS#4000) * Fixed equalizer output * Added changelog * Added issue number Stats Docs (DOI-USGS#3923) * Updated stats documentation * Updated stats docs based on feedback isis2raw pure export update (DOI-USGS#4002) * Changed check and set range logic/removed duplicate code * Added history comment and moved function outside of if statement * Fixed pixel type prapogation and boolean logic * Addressed PR feedback * Updated the changelog Add GUI helper to hist so user can see what the minimum and maximum DN values are of the specified band of the cube Update CHANGELOG.md update CHANGELOG and rebase to upstream dev documentation update CHANGELOG and rebase to upstream dev documentation
tgiroux · Sep 8, 2020 · 7e140c9 · 7e140c9
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diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -55,6 +55,7 @@ ISIS3 Contributors
 - Steven Lambright 
 - Stuart Sides 
 - Summer Stapleton 
+- Timothy Giroux
 - Tracie Sucharski 
 - Travis Addair 
 - Tyler Wilson 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,19 @@ update the Unreleased link so that it compares against the latest release tag.
 
 ## [Unreleased]
 
+### Changed
+
+ - Isis2raw will now output straight to a 32bit file (no stretch) when stretch is set to None and bittype is set to 32bit. [#3878](https://github.com/USGS-Astrogeology/ISIS3/issues/3878)
+
+### Fixed
+
+ - Equalizer now reports the correct equation and values used to perform the adjustment. [#3987](https://github.com/USGS-Astrogeology/ISIS3/issues/3987)
+ - mro/hideal2pds app now writes the correct SAMPLE_BIT_MASK values to the output label. [#3978](https://github.com/USGS-Astrogeology/ISIS3/issues/3978)
+
+ ### Added
+
+ - A Gui Helper gear was added to hist to fill in the minimum and maximum parameters with what would have been automatically calculated. [#3880](https://github.com/USGS-Astrogeology/ISIS3/issues/3880) 
+
 ## [4.2.0] - 2020-07-27
 
 ### Added

diff --git a/isis/src/base/apps/equalizer/equalizer.xml b/isis/src/base/apps/equalizer/equalizer.xml
@@ -246,6 +246,10 @@
       Changed pvl.DIFF of input for app tests nonOverlapRecalculate and nonOverlapRetryBoth to
       ignore file names. Allows test to pass when not using default data area. Fixes #4738.
     </change>
+    <change name="Jesse Mapel" date="2020-09-01">
+      Reported formula and variables now match the formula selected by the ADJUST
+      argument. Fixes #3987.
+    </change>
   </history>
 
   <groups>

diff --git a/isis/src/base/apps/hist/hist.xml b/isis/src/base/apps/hist/hist.xml
@@ -88,6 +88,9 @@
       Re-added the ability to set number of bins without setting min/max values after the last update. 
       Follow-on to #3881.
     </change>
+    <change name="Stuart Sides" date="2020-09-02">
+      Added GUI helper for filling in computed min/max. Fixed #3880.
+    </change>
   </history>
 
   <oldName>
@@ -138,6 +141,17 @@
         <description>
           Minimum DN value in histogram.  If not entered it will automatically be computed.
         </description>
+        <helpers>
+          <helper name="H1">
+            <function>helperButtonCalcMinMax</function>
+            <brief>Fill in the auto calculated MINIMUM and MAXIMUM for the input cube</brief>
+            <description>
+              This button will calculate what the default MINIMUM and MAXIMUM values would be
+              and fills the respective GUI fields with them.
+            </description>
+            <icon>$ISISROOT/appdata/images/icons/exec.png</icon>
+          </helper>
+        </helpers>
         <lessThan>
           <item>MAXIMUM</item>
         </lessThan>

diff --git a/isis/src/base/apps/hist/main.cpp b/isis/src/base/apps/hist/main.cpp
@@ -1,3 +1,4 @@
+#define GUIHELPERS
 #include "Isis.h"
 
 #include <QDockWidget>
@@ -18,6 +19,15 @@
 using namespace std;
 using namespace Isis;
 
+void helperButtonCalcMinMax();
+
+map <QString, void *> GuiHelpers() {
+  map <QString, void *> helper;
+  helper ["helperButtonCalcMinMax"] = (void *) helperButtonCalcMinMax;
+  return helper;
+}
+
+
 void IsisMain() {
   Process p;
   Cube *icube = p.SetInputCube("FROM");
@@ -29,7 +39,7 @@ void IsisMain() {
   }
 
   Histogram *hist;
-  if (ui.WasEntered("MINIMUM") && ui.WasEntered("MAXIMUM")){
+  if (ui.WasEntered("MINIMUM") && ui.WasEntered("MAXIMUM")) {
     int nbins = 0;
 
     if (ui.WasEntered("NBINS")){
@@ -71,7 +81,7 @@ void IsisMain() {
   p.Progress()->CheckStatus();
   LineManager line(*icube);
 
-  for(int i = 1; i <= icube->lineCount(); i++) {
+  for (int i = 1; i <= icube->lineCount(); i++) {
     line.SetLine(i);
     icube->read(line);
     hist->AddData(line.DoubleBuffer(), line.size());
@@ -236,3 +246,41 @@ void IsisMain() {
   delete hist;
   p.EndProcess();
 }
+
+
+// Helper function to fill in the auto calculated min/max.
+void helperButtonCalcMinMax() {
+
+  UserInterface &ui = Application::GetUserInterface();
+
+  // Setup a cube for gathering stats from the user requested band
+  QString file = ui.GetFileName("FROM");
+
+  Cube inCube;
+  CubeAttributeInput attrib = ui.GetInputAttribute("FROM");
+  if (attrib.bands().size() != 0) {
+     vector<QString> bands = attrib.bands();
+     inCube.setVirtualBands(bands);
+  }
+
+  inCube.open(file, "r");
+
+  LineManager line(inCube);
+  Statistics cubeStats;
+
+  for (int i = 1; i <= inCube.lineCount(); i++) {
+    line.SetLine(i);
+    inCube.read(line);
+    cubeStats.AddData(line.DoubleBuffer(), line.size());
+  }  
+
+  inCube.close();
+
+  // Write ranges to the GUI
+  ui.Clear("MINIMUM");
+  ui.PutDouble("MINIMUM", cubeStats.Minimum());
+  ui.Clear("MAXIMUM");
+  ui.PutDouble("MAXIMUM", cubeStats.Maximum());
+
+}
+
diff --git a/isis/src/base/apps/isis2raw/isis2raw.xml b/isis/src/base/apps/isis2raw/isis2raw.xml
@@ -11,12 +11,12 @@
     The raw image may be output into an 8-bit, 16-bit unsigned, 16-bit signed
     or 32-bit raw image.  This raw image can be in BSQ, BIL, or BIP format, and
     can include or exclude Null, LRS, LIS, HIS, and/or HRS specific DN values.
-    If no special pixel parameters are selected, then Low Saturation values and 
+    If no special pixel parameters are selected, then Low Saturation values and
     Null values are set to black and High Saturation values are set to white.
-    To ensure acceptable contrast in the output file, the user may select from 
+    To ensure acceptable contrast in the output file, the user may select from
     three stretch options are given 1) no stretch 2) linear, and 3) manual.
-    A custom maximum and minimum DN value can be specified for all output 
-    bittypes.  For example, if a range of 0 to 1023 is selected in a 16-bit 
+    A custom maximum and minimum DN value can be specified for all output
+    bittypes.  For example, if a range of 0 to 1023 is selected in a 16-bit
     unsigned raw image, the DNs are stretched to an effective 10-bit format.
   </description>
 
@@ -57,7 +57,7 @@
       Fixed problem where the valid data range overlapped the null value.
     </change>
     <change name="Christopher Austin" date ="2007-12-17">
-      Created options to ouput BIL and BIP formats, making BSQ the default, as 
+      Created options to ouput BIL and BIP formats, making BSQ the default, as
       well as added preserve special pixel (NULL) option.
     </change>
     <change name="Christopher Austin" date="2008-06-10">
@@ -72,6 +72,11 @@
       output image. OMIN and OMAX are now calculated based on the stretch if 32-bit
       is chosen and the OMIN and OMAX fields are left blank. Fixes #2194.
     </change>
+    <change name="Adam Paquette" date="2020-09-04">
+      Updated application logic to not generate a histogram if stretch is None
+      and the output bit type is 32-bit. Also removes duplicate calls to checkRange
+      and setRangeAndPixels. Closes #3878 (github).
+    </change>
   </history>
 
   <category>
@@ -173,15 +178,15 @@
           The minimum output DN value including special pixels.
         </brief>
         <description>
-          If a value is provided, the value will be the minimum DN used (including special 
-          pixels). If left blank and the BITTYPE is not 32BIT, the minimum DN value 
-          will default to the smallest value possible for the provided 
+          If a value is provided, the value will be the minimum DN used (including special
+          pixels). If left blank and the BITTYPE is not 32BIT, the minimum DN value
+          will default to the smallest value possible for the provided
           BITTYPE. If the BITTYPE is 32BIT and OMIN is left blank, the value
-          of OMIN will depend on the STRETCH type chosen. If LINEAR is 
-          chosen, the value for OMIN will be the DN value at the value 
-          entered for MINPERCENT on the data. If MANUAL is chosen, the OMIN 
-          will equal to the value of MINIMUM. If NONE is chosen, the value 
-          will default to the smallest value possible for 32 bit data. 
+          of OMIN will depend on the STRETCH type chosen. If LINEAR is
+          chosen, the value for OMIN will be the DN value at the value
+          entered for MINPERCENT on the data. If MANUAL is chosen, the OMIN
+          will equal to the value of MINIMUM. If NONE is chosen, the value
+          will default to the smallest value possible for 32 bit data.
         </description>
         <internalDefault>
           Refer to Documentation
@@ -193,14 +198,14 @@
           The maximum output DN value including special pixels.
         </brief>
         <description>
-          If a value is provided, the value will be the maximum DN used (including special 
-          pixels). If left blank and the BITTYPE is not 32BIT, the maximum DN value 
-          will default to the largest value possible for the provided 
+          If a value is provided, the value will be the maximum DN used (including special
+          pixels). If left blank and the BITTYPE is not 32BIT, the maximum DN value
+          will default to the largest value possible for the provided
           BITTYPE. If the BITTYPE is 32BIT and OMAX is left blank, the value
-          of OMAX will depend on the STRETCH type chosen. If LINEAR is 
-          chosen, the value for OMAX will be the DN value at the value 
-          entered for MAXPERCENT on the data. If MANUAL is chosen, the OMIN 
-          will equal to the value of MAXIMUM. If NONE is chosen, the value 
+          of OMAX will depend on the STRETCH type chosen. If LINEAR is
+          chosen, the value for OMAX will be the DN value at the value
+          entered for MAXPERCENT on the data. If MANUAL is chosen, the OMIN
+          will equal to the value of MAXIMUM. If NONE is chosen, the value
           will default to the largest value possible for 32 bit data.
         </description>
         <internalDefault>
@@ -212,7 +217,7 @@
         <default><item>true</item></default>
         <brief>Dedicates the minimum DN value for null pixels.</brief>
         <description>
-          If set to true, the minimum value of the raw output data will be 
+          If set to true, the minimum value of the raw output data will be
           reserved for null pixels.  The actual value used for null pixels will
           be denoted in the print.prt file and displayed onscreen.
         </description>
@@ -403,7 +408,7 @@
         </default>
         <brief>Storage order of output file.</brief>
         <description>
-          Sets the storage order of the raw ouput file to BSQ, BIL, or 
+          Sets the storage order of the raw ouput file to BSQ, BIL, or
           BIP.
         </description>
         <list>

diff --git a/isis/src/base/apps/isis2raw/main.cpp b/isis/src/base/apps/isis2raw/main.cpp
@@ -37,39 +37,42 @@ void IsisMain() {
 //    if(ui.GetString("BITTYPE") != "32BIT")
     p.SetInputRange();
   }
-  if(ui.GetString("STRETCH") == "MANUAL")
+  if(ui.GetString("STRETCH") == "MANUAL") {
     p.SetInputRange(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"));
+  }
 
   //  Determine bit size, output range, and calculate number of bytes to write
   //  for each line.
   double min = -DBL_MAX;
   double max = DBL_MAX;
+  Pixtype pixType = NONE;
   if(ui.GetString("BITTYPE") == "8BIT") {
     p.SetOutputType(Isis::UnsignedByte);
     min = 0.0;
     max = 255.0;
-    checkRange(ui, min, max);
-    setRangeAndPixels(ui, p, min, max, BOTH);
+    pixType = BOTH;
   }
   else if(ui.GetString("BITTYPE") == "S16BIT") {
     p.SetOutputType(Isis::SignedWord);
     min = -32768.0;
     max = 32767.0;
-    checkRange(ui, min, max);
-    setRangeAndPixels(ui, p, min, max, NEG);
+    pixType = NEG;
   }
   else if(ui.GetString("BITTYPE") == "U16BIT") {
     p.SetOutputType(Isis::UnsignedWord);
     min = 0.0;
     max = 65535.0;
-    checkRange(ui, min, max);
-    setRangeAndPixels(ui, p, min, max, BOTH);
+    pixType = BOTH;
   }
   else if(ui.GetString("BITTYPE") == "32BIT") {
     p.SetOutputType(Isis::Real);
+    pixType = NONE;
+  }
+
+  if (ui.GetString("STRETCH") != "NONE" || ui.GetString("BITTYPE") != "32BIT") {
     checkRange(ui, min, max);
-    setRangeAndPixels(ui, p, min, max, NONE);
   }
+  setRangeAndPixels(ui, p, min, max, pixType);
 
   // Set the output endianness
   if(ui.GetString("ENDIAN") == "MSB")
@@ -117,7 +120,7 @@ void IsisMain() {
 // Validates provided range
 void checkRange(UserInterface &ui, double &min, double &max) {
   Isis::Histogram *hist = p_cube->histogram(0);
-  
+
   if(ui.WasEntered("OMIN")) {
     if(ui.GetDouble("OMIN") < min) {
       QString message = "OMIN [" + toString(min) + "] is too small for the provided BITTYPE [";
@@ -136,7 +139,7 @@ void checkRange(UserInterface &ui, double &min, double &max) {
       min = ui.GetDouble("MINIMUM");
     }
   }
-    
+
   if(ui.WasEntered("OMAX")) {
     if(ui.GetDouble("OMAX") > max) {
       QString message = "OMAX [" + toString(max) + "] is too large for the provided BITTYPE [";