Commit 061140cb authored by Moses Milazzo's avatar Moses Milazzo
Browse files

Improved smear correction and updated documentation. 



git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/trunk@6024 41f8697f-d340-4b68-9986-7bafba869bb8
parent 2a245286

isis/src/docsys/build/doctoc.xml

+1 −611
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8" standalone="yes"?><tableofcontents><document>

<title>References</title>

<brief>ISIS References/Citations and Preferred Acknowledgement</brief>

<description>

      Acknowledgement, Citations, and References for the ISIS software package.

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/References/References.html</source>

</file>

</files>

</document>

<document>

<title>Environment and Preference Setup</title>

<brief>Setting up the UNIX environment and customizing ISIS preferences</brief>

<description>Setting up the UNIX environment to run ISIS and customizing the operation of ISIS</description>

<category>

<categoryItem>administration</categoryItem>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>intermediate</target>

<target>administrator</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/EnvironmentAndPreferencesSetup/EnvironmentAndPreferencesSetup.html</source>

</file>

</files>

</document>

<document>

<title>User Rights Notice</title>

<brief>Licensing, copyright, distribution, and warranty information</brief>

<description>

      User Rights Notice

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/UserRights/UserRights.html</source>

</file>

</files>

</document>

<document>

<title>ISIS 2 Technical Documentation</title>

<brief>Links to ISIS 2 Technical Documents</brief>

<description>List of links to ISIS 2 documents covering technical topics, such as administration, release notes, and installation.</description>

<category>

<categoryItem>hidden</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>isis2</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Isis2TechnicalDocs/index.html</source>

</file>

</files>

</document>

<document>

<title>Glossary</title>

<brief>

      ISIS and Image Processing Terms and Definitions

    </brief>

<description>

      This article acts as a collection of common definitions used frequently in

      ISIS and general image processing.

    </description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Glossary/Glossary.html</source>

</file>

</files>

</document>

<document>

<title>Disclaimers</title>

<brief>Standard legalese regarding usage, trademarks, and privacy</brief>

<description>

      This section contain standard USGS comments regarding software

      accuracy, use of trademarks and tradenames and other general

      disclaimers.

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Disclaimers/Disclaimers.html</source>

</file>

</files>

</document>

<document>

<title>Label Dictionary</title>

<brief>Reference to the objects and groups in ISIS cube labels</brief>

<description>

        This document is a reference to the various objects and groups, which can be found in ISIS labels.

        The definition of each object/group, the parameter meanings, and an example will be given.

    </description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/LabelDictionary/LabelDictionary.html</source>

</file>

</files>

</document>

<document>

<title>Error Handling Facility</title>

<brief>Guide to the various aspects of the Error Handling Facility</brief>

<description>General overview of the Error Handling Facility, what form error messages take, how error messages differ between the command line and GUI, and Tips For Programmers.</description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/ErrorHandlingFacility/ErrorHandlingFacility.html</source>

</file>

</files>

</document>

<document>

<title>Command Line Usage</title>

<brief>

    Invoking ISIS programs from the UNIX command line

    </brief>

<description>

      How to run ISIS on the UNIX Command Line.

      Required reading before using the software in any scripting language.

    </description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/CommandLine/CommandLine.html</source>

</file>

</files>

</document>

<document>

<title>ISIS 2 User Documentation</title>

<brief>Links to ISIS 2 User Documents</brief>

<description>List of links to documents covering general topics for users of ISIS 2.1</description>

<category>

<categoryItem>hidden</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>isis2</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Isis2UserDocs/index.html</source>

</file>

</files>

</document>

<document>

<title>ISIS Application Examples How-to</title>

<brief>Guide to writing the examples section of ISIS Application XML</brief>

<description>Guide to writing application examples in the ISIS Application XML. All examples added to the official ISIS

                        application documentation will be automatically added to the application documentation pages. This guide

                        describes the examples section of the ISIS Application XML, provides instructions on how to add sample

                        files to an example, and gives general guidance for writing examples for ISIS.</description>

<category>

<categoryItem>xml</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/HowToApplicationExamples/index.html</source>

</file>

</files>

</document>

<document>

<title>Conversion from ISIS 2 to ISIS 3</title>

<brief>Reasons and considerations to upgrade from ISIS 2 to ISIS 3</brief>

<description>The reasons, considerations, and major design changes related to the upgrade from ISIS 2 to ISIS 3</description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Conversion/Conversion.html</source>

</file>

</files>

</document>

<document>

<title>Session Logs</title>

<brief>Guide to understanding, controlling, and reading Session Logs</brief>

<description>Guide to understanding, controlling, and reading Session Logs, a mechanism for users to keep track of work that they have done</description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/SessionLogs/SessionLogs.html</source>

</file>

</files>

</document>

<document>

<title>Programmer Guide</title>

<brief>Guide to Programming the ISIS software package</brief>

<description>Guide for the Programmers using ISIS software libraries, writing libraries and applications, working in the team development area, and writing XML files.</description>

<category>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>guide</categoryItem>

<categoryItem>api</categoryItem>

</category>

<audience>

<target>programmer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/ProgrammerGuide/ProgrammerGuide.html</source>

</file>

</files>

</document>

<document>

<title>Backward Compatibility Policy</title>

<brief>Policy for ISIS backward compatibility for users</brief>

<description>

     Backward Compatibility Policy for user applications to help ensure

     processing scripts developed outside of the USGS are easier to maintain.

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/BackwardCompatibility/BackwardCompatibility.html</source>

</file>

</files>

</document>

<document>

<title>System Architecture</title>

<brief>An in-depth "get started" tour of ISIS, including history, mechanics, and basic use.</brief>

<description>Take an in-depth "get started" tour of ISIS, from the software's history to an overview of the newest features. Learn the basics of working in the ISIS software environment.</description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>user</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/SystemArchitecture/SystemArchitecture.html</source>

</file>

</files>

</document>

<document>

<title>Preference Dictionary</title>

<brief>

    Complete reference to all user preference settings

    </brief>

<description>

      Complete reference to all user preference settings

    </description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/PreferenceDictionary/PreferenceDictionary.html</source>

</file>

</files>

</document>

<document>

<title>Credits</title>

<brief>Contributors to the ISIS software package</brief>

<description>

      A summary of USGS and non-USGS contributors to the ISIS

      software package

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Credits/Credits.html</source>

</file>

</files>

</document>

<document>

<title>History</title>

<brief>History of USGS Astrogeology image processing software</brief>

<description>

      This is a history of the evolution of the USGS Astrogeology image 

      processing software from 1971 to 2013.

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/IsisHistory/IsisHistory.html</source>

</file>

</files>

</document>

<document>

<title>ISIS Application and Category Test How-to</title>

<brief>Guide to writing an application and category tests </brief>

<description>Guide to writing application and category tests using make. This guide describes

      step by step the process of writing a test for an application or category.  The guide

      also gives general guidance on errors and common mistakes in writing a test.

    </description>

<category>

<categoryItem>xml</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/HowToApplicationCategoryTest/index.html</source>

</file>

</files>

</document>

<document>

<title>Pattern Matching</title>

<brief>

      A discussion of pattern matching techniques used in ISIS, designed to help

      users construct automatic registration templates.

    </brief>

<description>

      This article describes the pattern matching techniques used for automatic

      registration in ISIS.  The information is designed to give users an idea

      of how they can alter their automatic registration templates to improve

      their results from applications such as "pointreg" and "coreg".  This

      should also give programmers a better understanding of how AutoReg works.

    </description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>advanced</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/PatternMatch/PatternMatch.html</source>

</file>

</files>

</document>

<document>

<title>Installing ISIS</title>

<brief>Downloading and installing ISIS 3</brief>

<description>

      This document describes how to download and install a

      binary version of ISIS.

    </description>

<category>

<categoryItem>technicaldoc</categoryItem>

</category>

<audience>

<target>administrator</target>

</audience>

<files>

<file hidden="" primary="true">

<type>HTML</type>

<source>../documents/InstallGuide/index.html</source>

</file>

</files>

</document>

<document>

<title>ISIS 2 Tutorials</title>

<brief>Links to ISIS 2 tutorials, procedures, and how-to's</brief>

<description>List of links to ISIS 2 tutorials, procedures, and how-to's.</description>

<category>

<categoryItem>hidden</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>isis2</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Isis2Tutorials/index.html</source>

</file>

</files>

</document>

<document>

<title>Overview</title>

<brief>Summary of ISIS</brief>

<description>

      This document summarizes ISIS and support for planetary space missions.

    </description>

<category>

<categoryItem>about</categoryItem>

</category>

<audience>

<target>all</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/Overview/Overview.html</source>

</file>

</files>

</document>

<document>

<title>Style Guide</title>

<brief>

      Object source code styles and conventions

    </brief>

<description>

      This document describes Object naming conventions,

      documenting source code for automatic documentation generation,

      and formatting documentation.

    </description>

<category>

<categoryItem>api</categoryItem>

<categoryItem>guide</categoryItem>

<categoryItem>technicaldoc</categoryItem>

</category>

<audience>

<target>programmer</target>

</audience>

<files>

<file hidden="" primary="true">

<type>HTML</type>

<subtitle>Introduction</subtitle>

<source>../documents/DocStyle/intro.html</source>

</file>

<file hidden="" primary="">

<type>HTML</type>

<subtitle>Mandatory Commands</subtitle>

<source>../documents/DocStyle/mandatoryCommands.html</source>

</file>

<file hidden="" primary="">

<type>HTML</type>

<subtitle>Useful Commands</subtitle>

<source>../documents/DocStyle/usefulCommands.html</source>

</file>

<file hidden="" primary="">

<type>HTML</type>

<subtitle>Example Header</subtitle>

<source>../documents/DocStyle/exampleHeader.html</source>

</file>

<file hidden="" primary="">

<type>HTML</type>

<subtitle>Example Implementation</subtitle>

<source>../documents/DocStyle/exampleImplementation.html</source>

</file>

<file hidden="" primary="">

<type>HTML</type>

<subtitle>HTML Quick Reference</subtitle>

<source>../documents/DocStyle/HTMLQuickRef.html</source>

</file>

</files>

</document>

<document>

<title>ISIS 3 Coding Standards and Style Guide</title>

<brief>Coding standards for ISIS 3 developers (effective February 1, 2012).</brief>

<description>

      This document will describe the coding standards for maintaining 

      ISIS 3 source code.  It was created to ensure that the 

      ISIS 3 package is programmed for consistency, readability and ease

      of future maintenance. This document does not attempt to address every

      possible issue. However, the guidelines that have been outlined should not

      be deviated from, except under special situations.

    </description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/CodingStandards/CodingStandards.html</source>

</file>

</files>

</document>

<document>

<title>Logical Cube Format Guide</title>

<brief>Guide to core ISIS labels and a conceptual file structure for a cube</brief>

<description>

    This basic guide focuses on core ISIS labels and a conceptual file structure for a cube

    </description>

<category>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/LogicalCubeFormatGuide/LogicalCubeFormatGuide.html</source>

</file>

</files>

</document>

<document>

<title>Error Dictionary</title>

<brief>Reference of error messages, their meanings, and resolving errors</brief>

<description>Reference of error messages, their meanings, and resolving errors</description>

<category>

<categoryItem>reference</categoryItem>

</category>

<audience>

<target>intermediate</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/ErrorDictionary/ErrorDictionary.html</source>

</file>

</files>

</document>

<document>

<title>ISIS Documents How-to</title>

<brief>Guide to writing documents using ISIS Documentation XML</brief>

<description>Guide to adding documents to the ISIS documentation tree. All documents added to the official ISIS

                        documentation will be automatically linked on the ISIS web pages and distributed with ISIS. This guide

                        describes the formats documents may be in, what types of documents may be added, and how to

                        write the ISIS Documentation XML metadata file that is used automatically add a document to the ISIS

                        system.</description>

<category>

<categoryItem>xml</categoryItem>

<categoryItem>technicaldoc</categoryItem>

<categoryItem>guide</categoryItem>

</category>

<audience>

<target>developer</target>

</audience>

<files>

<file hidden="" primary="">

<type>HTML</type>

<source>../documents/HowToGeneralDocumentation/index.html</source>

</file>

</files>

</document>

</tableofcontents>
 
 No newline at end of file
 
<?xml version="1.0" encoding="UTF-8" standalone="yes"?><tableofcontents></tableofcontents>
 
 No newline at end of file

isis/src/messenger/apps/mdiscal/mdiscal.cpp

+11 −6
Original line number Diff line number Diff line
@@ -98,7 +98,7 @@ void IsisMain() { 
  PvlGroup& inst = icube->group("Instrument");

  isNarrowAngleCamera = ((QString)inst["InstrumentId"] == "MDIS-NAC");

  exposureDuration = inst["ExposureDuration"] ;

  exposureDuration /= 1000.0;  //  Convert ms to sec

  exposureDuration /= 1000.0;



  // Determine dark columns

  int fpuBin = inst["FpuBinningMode"];
@@ -521,13 +521,17 @@ void Calibrate(vector<Buffer *>& in, vector<Buffer *>& out) { 
  Buffer& imageIn   = *in[0];

  Buffer& flatField = *in[1];

  Buffer& imageOut  = *out[0];

  double t2 = smearComponent / imageIn.SampleDimension();

  //exposureDuration is in seconds, but we need to work in ms.

  double exposureTime = exposureDuration * 1000.0;



  if (imageIn.Line() == 1) {

    prevLineData.resize(imageIn.SampleDimension());

    smearData.resize(imageIn.SampleDimension());

    double added = 16.0*t2/exposureTime;



    for (unsigned int i = 0; i < prevLineData.size(); i++) {

      prevLineData[i] = 0.0;

      prevLineData[i] = added;

      smearData[i] = 0.0;

    }

  }
@@ -582,10 +586,8 @@ void Calibrate(vector<Buffer *>& in, vector<Buffer *>& out) { 
      }



      // Step 3: Readout Smear Correction (ms -> seconds)

      double t2 = smearComponent / imageIn.SampleDimension() / 1000.0;



      if (exposureDuration > 0.0 && imageIn.Line() > 1) {

        smearData[i] += t2 / exposureDuration * prevLineData[i];

      if (exposureTime > 0.0) {

        smearData[i] += t2 / exposureTime * prevLineData[i];

        imageOut[i] -= smearData[i];

      }
@@ -595,6 +597,9 @@ void Calibrate(vector<Buffer *>& in, vector<Buffer *>& out) { 
      imageOut[i] /= flatField[i]; // divide by flat field



      // Step 5: Absolute coefficient

      // Using exposureDuration (in seconds). This gives ~ the same results

      // as the previous version of mdiscal did. Using exposureTime gives

      // a factor of 1000 smaller value, as one would expect. 

      if (exposureDuration > 0.0) {

        imageOut[i] = imageOut[i] / exposureDuration * abs_coef;

      }

isis/src/messenger/apps/mdiscal/mdiscal.xml

+75 −42

File changed.

Preview size limit exceeded, changes collapsed.