8.0.4 LTS Release Prep

.zenodo.json

@@ -336,6 +336,10 @@
     {
       "name": "Miller-Ribelin, Elizabeth"
     },
+    {
+      "affiliation": "Japan Aerospace Exploration Agency, Institute of Space and Astronautical Science",
+      "name": "Murakami, Shin-ya",
+      "orcid": "0000-0002-7137-4849"
     {
       "affiliation": "United States Geological Survey, Astro Geology Science Center",
       "name": "Nelson, Gavin"
@@ -437,6 +441,10 @@
     {
       "name": "Sucharski, Tracie"
     },
+    {
+      "affiliation": "University of Arizona, Lunar and Planetary Laboratory",
+      "name": "Sutton, Sarah S."
+    },
     {
       "name": "Takir, Driss"
     },

CHANGELOG.md

@@ -35,11 +35,43 @@ release.
 
 ## [Unreleased]
 
+## [8.0.4] - 2024-11-27
+
+### Added
+- Added HRSC support in socetlinescankeywords [#5465](https://github.com/DOI-USGS/ISIS3/issues/5465)
+
+### Changed
+- Skypt has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5443](https://github.com/USGS-Astrogeology/ISIS3/issues/5443)
+- Noseam has been refactored to be callable; old Makefile test has been removed and replaced by a gtest. Issue: [#5599](https://github.com/USGS-Astrogeology/ISIS3/issues/5599)
+- Explode has been refactored to be callable; old Makefile test has been removed and replaced by a gtest. Issue: [#5557](https://github.com/USGS-Astrogeology/ISIS3/issues/5557)
+- Isisminer has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5516](https://github.com/USGS-Astrogeology/ISIS3/issues/5516)
+- Algebra has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5594](https://github.com/USGS-Astrogeology/ISIS3/issues/5594)
+- Photrim has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5581](https://github.com/USGS-Astrogeology/ISIS3/issues/5581)
+- Bandtrim has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5571](https://github.com/USGS-Astrogeology/ISIS3/issues/5571)
+- Modified kaguyasp2isis to work with new (detached) data [#5436](https://github.com/DOI-USGS/ISIS3/issues/5436)
+- Added jigsaw error message for csminit'd images without csm parameters[#5486](https://github.com/DOI-USGS/ISIS3/issues/5486)
+
+### Fixed
+- Fixed a bug in noproj.cpp which left a persisent lbl file after running noproj. [#5577](https://github.com/DOI-USGS/ISIS3/issues/5577)
+- Fixed a bug in PolygonTools in which the program exited before attempting to fix an invalid Polygon [#5520](https://github.com/DOI-USGS/ISIS3/issues/5520)
+- Fixed a bug in QVIEW where images would double load if loaded from the commandline [#5505](https://github.com/DOI-USGS/ISIS3/pull/5505)
+- Fixed CSMSerialNumber.trn typo [#5485](https://github.com/DOI-USGS/ISIS3/issues/5485)
+- Fixed CSMSerialNumber.trn to be PVL compliant [#5484](https://github.com/DOI-USGS/ISIS3/issues/5484)
+- Fixed hrsc2isis to support level 3 hrsc images [#5497](https://github.com/DOI-USGS/ISIS3/issues/5497)
+- Fixed gllssi2isis to support V1.1 data [#5396](https://github.com/DOI-USGS/ISIS3/issues/5396)
+- Fixed noseam bug where a debugging output statement was inadvertently left in noseam.cpp. Issue: [5660](https://github.com/DOI-USGS/ISIS3/issues/5660)
+- Fixed jigsaw bugs in which RADIUS is handled incorrectly in the jigsaw gui and in the bundleout.txt file. Slightly modified the FunctionalTestJigsawBundleXYZ ctest accordingly. Issue: [5642](https://github.com/DOI-USGS/ISIS3/issues/5642)
+- Fixed a bug in kaguyasp2isis that doesn't work for data with a detached label. [#5568](https://github.com/DOI-USGS/ISIS3/pull/5568)
+- Fixed FunctionalTestCamstatsDefaultParameters test by increasing the runtime speed [#5459](https://github.com/DOI-USGS/ISIS3/issues/5459)
+- Fixed PHOTOMET not accepting backplanes [#5281](https://github.com/DOI-USGS/ISIS3/issues/5281)
+- Fixed dstripe parallel test failing by converting tests to gtests [#5613](https://github.com/DOI-USGS/ISIS3/issues/5613)
+
 ## [8.0.3] - 2023-04-18
 
 ### Changed
 - Disabled option to use web=true when running spiceinit with HRSC images. [#5223](https://github.com/DOI-USGS/ISIS3/issues/5223)
 - Changed the default spiceinit url to https://astrogeology.usgs.gov/apis/ale/v0.9.1/spiceserver/ and added deprecation warning for use of https://services.isis.astrogeology.usgs.gov/cgi-bin/spiceinit.cgi url. [#5327](https://github.com/USGS-Astrogeology/ISIS3/issues/5327)
+- Skypt has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5443](https://github.com/USGS-Astrogeology/ISIS3/issues/5443)
 
 ### Fixed
 - Fixed a bug in which capital E was problematic for OSX / Ubuntu [#5466](https://github.com/DOI-USGS/ISIS3/pull/5466)

code.json

@@ -43,6 +43,43 @@
     "date": {
       "metadataLastUpdated": "2023-02-27"
     }
+  }, {
+    "name": "ISIS3",
+    "organization": "U.S. Geological Survey",
+    "description": "GitHub code repository for the Integrated Software for Imagers and Spectrometers (ISIS)",
+    "version": "8.0.4",
+    "status": "Production",
+    "permissions": {
+      "usageType": "openSource",
+      "licenses": [
+        {
+          "name": "Public Domain, CC0-1.0",
+          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.4/LICENSE.md"
+        }
+      ]
+    },
+    "homepageURL": "https://isis.astrogeology.usgs.gov",
+    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.0.4/isis-8.0.4.zip",
+    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.4/DISCLAIMER.md",
+    "repositoryURL": "https://code.usgs.gov/astrogeology/isis.git",
+    "vcs": "git",
+    "laborHours": 0,
+    "tags": [
+      "Planetary",
+      "Remote Sensing",
+      "Photogrammetry",
+      "Data Processing"
+    ],
+    "languages": [
+      "C++"
+    ],
+    "contact": {
+      "name": "Christine Kim",
+      "email": "[email protected]"
+    },
+    "date": {
+      "metadataLastUpdated": "2024-11-27"
+    }
   }, {
     "name": "ISIS3",
     "organization": "U.S. Geological Survey",

environment.yml

@@ -3,10 +3,10 @@ channels:
   - defaults
 
 dependencies:
-  - ale=0.9.1
+  - ale =0.10.0,<1
   - armadillo
-  - boost=1.72
-  - boost-cpp=1.72
+  - boost >=1.78.0,<1.79
+  - boost-cpp >=1.78.0,<1.79
   - blas
   - usgs-astrogeology::bullet
   - bz2file
@@ -32,9 +32,9 @@ dependencies:
   - jpeg
   - usgs-astrogeology::kakadu==1
   - krb5
-  - libopencv>=4.5.2
+  - libopencv >=4.7,<4.8
   - libpng>=1.6.34
-  - libprotobuf<3.20
+  - libprotobuf
   - libtiff>=4.0
   - libxml2
   - make
@@ -47,16 +47,17 @@ dependencies:
   - nn
   - opencv>=4.5.2
   - openssl>=1.1.1k
-  - pcl >= 1.10.0
-  - protobuf<3.20
-  - python>=3.7.11
+  - pcl >=1.13,<1.14
+  - protobuf
+  - python >=3.10
+  - python_abi >=3.10
   - pytest
   - rclone
   - qhull
-  - qt>=5.9.6,<5.15.0
-  - qwt
-  - sqlite
-  - suitesparse
+  - qt-main >=5.15.8, <5.16
+  - qwt <6.3.0
+  - sqlite >=3.46.0,<3.47
+  - suitesparse<7.7.0
   - superlu
   - swig
   - texlive-core

isis/CMakeLists.txt

@@ -34,7 +34,7 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "8.0.3")
+set(VERSION            "8.0.4")
 string(REPLACE "." ";" VERSION_LIST ${VERSION})
 list(GET VERSION_LIST 0 VERSION_MAJOR)
 list(GET VERSION_LIST 1 VERSION_MINOR)

isis/appdata/serialnumbers/CsmSerialNumber.trn

@@ -1,6 +1,6 @@
 Group = Keyword1
-  Auto
-  InputKey       = CSMPlatformId
+  Auto           = 1
+  InputKey       = CSMPlatformID
   InputGroup     = "IsisCube,CsmInfo"
   InputPosition  = (IsisCube, CsmInfo)
   OutputName     = Keyword1
@@ -9,7 +9,7 @@ Group = Keyword1
 End_Group
 
 Group = Keyword2
-  Auto
+  Auto           = 1
   InputKey       = CSMInstrumentId
   InputGroup     = "IsisCube,CsmInfo"
   InputPosition  = (IsisCube, CsmInfo)
@@ -19,7 +19,7 @@ Group = Keyword2
 End_Group
 
 Group = Keyword3
-  Auto
+  Auto           = 1
   InputKey       = ReferenceTime
   InputGroup     = "IsisCube,CsmInfo"
   InputPosition  = (IsisCube, CsmInfo)

isis/cmake/FindPCL.cmake

@@ -7,7 +7,7 @@
 
 find_path(PCL_INCLUDE_DIR
   NAME pcl_base.h
-  PATH_SUFFIXES "pcl-1.8/pcl" "pcl-1.9/pcl" "pcl-1.11/pcl" "pcl-1.13/pcl" 
+  PATH_SUFFIXES "pcl-1.8/pcl" "pcl-1.9/pcl" "pcl-1.11/pcl" "pcl-1.12/pcl" "pcl-1.13/pcl" "pcl-1.14/pcl"
 )
 
 find_library(PCL_COMMON_LIBRARY NAMES pcl_common)

isis/src/base/apps/algebra/algebra.cpp

@@ -0,0 +1,178 @@
+/** This is free and unencumbered software released into the public domain.
+
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
+#include "algebra.h"
+
+#include "Cube.h"
+#include "FileName.h"
+#include "ProcessByLine.h"
+#include "SpecialPixel.h"
+
+namespace Isis {
+
+  /*
+   * Algebra
+   *
+   * This program performs simple algebra on either one or two
+   * cubes. The two cubes may be added, subtracted, multiplied or divided.
+   * 
+   * The following equations are used:
+   *     UNARY:      out = (A * from1) + C
+   *     ADD:        out = ((from1 - D) * A) + ((from2 - E) * B) + C
+   *     SUBTRACT:   out = ((from1 - D) * A) - ((from2 - E) * B) + C
+   *     MULTIPLY:   out = ((from1 - D) * A) * ((from2 - E) * B) + C
+   *     DIVIDE:     out = ((from1 - D) * A) / ((from2 - E) * B) + C   
+   *
+   * The FROM2 cube must have either one band or the same number of bands
+   * as the FROM cube. If the FROM2 cube has one band, then the algebraic
+   * formula will be applied to all bands in FROM using that single band
+   * in FROM2. If FROM2 is a multi-band cube, the algebra will be performed
+   * between corresponding bands from FROM and FROM2.
+   * 
+   * @param ui UserInterface object containing parameters
+   */
+   void algebra(UserInterface &ui) {
+    Cube* icube1 = new Cube();
+    icube1->open(ui.GetCubeName("FROM"));
+
+    Cube* icube2 = nullptr;
+     if(ui.WasEntered("FROM2")) {
+       icube2 = new Cube();
+       icube2->open(ui.GetCubeName("FROM2"));
+     }
+
+    algebra(icube1, ui, icube2);
+  }
+
+
+  /*
+   * Algebra
+   *
+   * This program performs simple algebra on either one or two
+   * cubes. The two cubes may be added, subtracted, multiplied or divided.
+   * 
+   * The following equations are used:
+   *     UNARY:      out = (A * from1) + C
+   *     ADD:        out = ((from1 - D) * A) + ((from2 - E) * B) + C
+   *     SUBTRACT:   out = ((from1 - D) * A) - ((from2 - E) * B) + C
+   *     MULTIPLY:   out = ((from1 - D) * A) * ((from2 - E) * B) + C
+   *     DIVIDE:     out = ((from1 - D) * A) / ((from2 - E) * B) + C   
+   *
+   * The FROM2 cube must have either one band or the same number of bands
+   * as the FROM cube. If the FROM2 cube has one band, then the algebraic
+   * formula will be applied to all bands in FROM using that single band
+   * in FROM2. If FROM2 is a multi-band cube, the algebra will be performed
+   * between corresponding bands from FROM and FROM2.
+   *
+   * @param icube1 Cube* input cube1
+   * @param ui UserInterface object containing parameters
+   * @param icube2 Cube* input cube2; optional second input cube
+   */
+  void algebra(Cube* icube1, UserInterface &ui, Cube* icube2) {
+
+    // Processing by line
+    ProcessByLine p;
+
+    // Set input cubes and attributes into ProcessByLine p
+    CubeAttributeInput inatts1 = ui.GetInputAttribute("FROM");
+    CubeAttributeInput inatts2;
+    p.SetInputCube(icube1->fileName(), inatts1);
+    if(icube2 != nullptr) {
+      inatts2 = ui.GetInputAttribute("FROM2");
+      p.SetInputCube(icube2->fileName(), inatts2);
+    }
+
+    // Set output cube and attributes into ProcessByLine p
+    QString outCubeFname = ui.GetCubeName("TO");
+    CubeAttributeOutput &outatts = ui.GetOutputAttribute("TO");
+    p.SetOutputCube(outCubeFname, outatts);
+
+    // Get the coefficients
+    double Isisa = ui.GetDouble("A");
+    double Isisb = ui.GetDouble("B");
+    double Isisc = ui.GetDouble("C");
+    double Isisd = ui.GetDouble("D");
+    double Isise = ui.GetDouble("E");
+
+    QString op = ui.GetString("OPERATOR");
+
+    //*****************************************
+    // Lambda functions to perform operations *
+    //*****************************************
+
+    // operatorProcess for add, subtract, multiply, divide
+    auto operatorProcess = [&](std::vector<Buffer *> &in, std::vector<Buffer *> &out)->void {
+      Buffer &inp1 = *in[0];
+      Buffer &inp2 = *in[1];
+      Buffer &outp = *out[0];
+
+      // Loop for each pixel in the line
+      // Special pixel propagation:
+      //   1) special pixels in inp1 propagate to output cube unchanged
+      //   2) if inp1 is not special and inp2 is, the output pixel is set to Null
+      for(int i = 0; i < inp1.size(); i++) {
+        if(IsSpecial(inp1[i])) {
+          outp[i] = inp1[i];
+        }
+        else if(IsSpecial(inp2[i])) {
+          outp[i] = NULL8;
+        }
+        else {
+          double operand1 = (inp1[i] - Isisd) * Isisa;
+          double operand2 = (inp2[i] - Isise) * Isisb;
+          if(op == "ADD") {
+            outp[i] = (operand1 + operand2) + Isisc;
+          }
+          if(op == "SUBTRACT") {
+            outp[i] = (operand1 - operand2) + Isisc;
+          }
+          if(op == "MULTIPLY") {
+            outp[i] = (operand1 * operand2) + Isisc;
+          }
+          if(op == "DIVIDE") {
+            if((inp2[i] - Isise) * Isisb  == 0.0) {
+              outp[i] = NULL8;
+            }
+            else {
+              outp[i] = (operand1 / operand2) + Isisc;
+            }
+          }
+        }
+      }
+    };
+
+    // Unary process
+    auto unaryProcess = [&](Buffer &in, Buffer &out)->void {
+      // Loop for each pixel in the line.
+      // Special pixels propagate directly to output
+      for(int i = 0; i < in.size(); i++) {
+        if(IsSpecial(in[i])) {
+          out[i] = in[i];
+        }
+        else {
+          out[i] = in[i] * Isisa + Isisc;
+        }
+      }
+    };
+
+    //*****************************************
+    // End Lambda functions                   *
+    //*****************************************
+
+    // Start processing based on the operator
+    if(op == "UNARY") {
+      p.ProcessCube(unaryProcess);
+    }
+    else {
+      p.ProcessCubes(operatorProcess); // add, subtract, multiply, divide
+    }
+
+    p.EndProcess();
+  }
+}
+