Unverified Commit f5b435e7 authored by Jesse Mapel's avatar Jesse Mapel Committed by GitHub
Browse files

Topds4 (#4246) 



* Removed compile and deprication warnings. Fixes #4110

* temp add of to pds 4 test

* Initial topds4 app and cmake updates to include inja (#4207)

* Removed compile and deprication warnings. Fixes #4110

* temp add of to pds 4 test

* Inintal topds4 app and cmake updates to include inja

* Delete extra headers

* Fixed inja include

Co-authored-by: default avatarssides <ssides@usgs.gov>

* Added conda-forge inja

* add template file

* Adds PVL to JSON converters (#4212)

* Pvl to JSON conversion

* Renamed file

* Added repeated elements and examples

* Topds4 real parameters (#4223)

* now has some real parameters

* removed inja files

* Add full orex pds4 template (#4233)

* now has some real parameters

* removed inja files

* full orex xml

* add full orex template

* Added callbacks and tests (#4226)

* Adds Xml2Json capability to topds4 branch (#4228)

* Inintal topds4 app and cmake updates to include inja

* Delete extra headers

* Fixed inja include

* Added basic working XMLToJson functionality

* Updated to work with many nested levels of different amounts of repeated tags

* Add support for unsupported xml edge cases

* Add tests that work to test mutliple nested repeated values conversion

* cleanup

* Update to include no-text value cases to work in repeated-value cases

* Update test

* Break up tests

* Fix typoes in comments

* Normalized topds4 and added tests (#4234)

* Removed data source args and added app log

* Added simple tests for topds4

* Moved line

* Added more template elements and callback for file size (#4236)

* now has some real parameters

* removed inja files

* full orex xml

* add full orex template

* More template elements, and file size callback

* Added Extra data source parameters to topds4 (#4239)

* Added extra parameters

* Added duplicate warnings

* Fixed warning

* Add writing a cube out to topds4 (#4241)

* Basic cubeatt conversion

* Add more useful function signature

* Removed hardcoded path

* Update based on feedback

* Add better band test

* Updated to fix failing tests and remove old testfiles

* Add copy of topds4 templates to CMakeLists.txt (#4242)

* Fixed callbacks and doc updates (#4243)

* Fixed callbacks and doc updates

* added some extra docs

* Added original xml label and tests

* Update cubeattribute to include an option to supply CubeAttributeInput directly (#4244)

* Update cubeatt to add cubeattributeinput option. Also add tests for all function signatures available

* Remove unnecessary comments

* Update to use explicit array conversion.

* Remove commented out code

* Update CHANGELOG to include topds4 addition

* Delete osirisrex.xml.tpl

Removed temporary file

* Delete 20190612T090019S776_map_L0pan.xml.full

Remove temporary file

* Delete 20190612T090019S776_map_L0pan.xml.tpl

Remove temp file

* Added mis-deleted file (#4249)

* Update XmlToJson.cpp

* Update topds4.xml

* Update topds4.xml

* Update topds4.xml

* Add setting of virtual bands to topds4 and remove unneeded header file includes

Co-authored-by: default avatarssides <ssides@usgs.gov>
Co-authored-by: default avatarKristin Berry <kberry@usgs.gov>
parent aa02ab90

CHANGELOG.md

+2 −0
Original line number Diff line number Diff line
@@ -35,7 +35,9 @@ update the Unreleased link so that it compares against the latest release tag. 
- Added warning to ocams2isis about the model being out of date. [#4200](https://github.com/USGS-Astrogeology/ISIS3/issues/4200)

- Added documentation to lronaccal and lrowaccal to describe why there are negative DNs in I/F calibrated images. [#3860](https://github.com/USGS-Astrogeology/ISIS3/issues/3860)

- Update qview MeasureTool to add an option to calculate distances using RA/DEC and update qview to show DEC/RA rather than LAT/LON in lower-right corner [#3371](https://github.com/USGS-Astrogeology/ISIS3/issues/3371)

- Added a new application, topds4, which generates an output PDS4 XML label and a PDS4-compliant ISIS Cube from an input Cube, a PDS4 label template, and optionally additional input XML, PVL, or JSON data. The Inja templating engine is used to render the output PDS4 label from the label template. [#4246](https://github.com/USGS-Astrogeology/ISIS3/pull/4246)

- Updated spiceinit so that a user can specify a shape model and use the spice web service without any errors. [#1986](https://github.com/USGS-Astrogeology/ISIS3/issues/1986) 



### Fixed



- Fixed lrowaccal so required SPICE files are reported instead of continuing without them. [#4038](https://github.com/USGS-Astrogeology/ISIS3/issues/4038)

environment.yml

+1 −0
Original line number Diff line number Diff line
@@ -24,6 +24,7 @@ dependencies: 
  - gsl>=2.6

  - hdf5

  - icu

  - inja

  - jama

  - jpeg==9b

  - kakadu==1

environment_gcc4.yml

+1 −0
Original line number Diff line number Diff line
@@ -26,6 +26,7 @@ dependencies: 
  - gsl

  - hdf5

  - icu

  - inja

  - jama

  - jpeg==9b

  - kakadu==1

isis/CMakeLists.txt

+11 −1
Original line number Diff line number Diff line
@@ -80,7 +80,7 @@ option(JP2KFLAG "Whether or not to build using JPEG2000 support" OFF ) 
option(pybindings      "Turn on to build Python bindings"               OFF )



# if cmake install prefix is not set, and conda env is activated, use the

# conda env as the install directory

# conda env as the install directory.

if(DEFINED ENV{CONDA_PREFIX} AND CMAKE_INSTALL_PREFIX STREQUAL "/usr/local")

 set(CMAKE_INSTALL_PREFIX $ENV{CONDA_PREFIX})

endif()
@@ -293,6 +293,8 @@ find_package(Kakadu) 
find_package(Geos    3.5.0     REQUIRED)

find_package(Armadillo         REQUIRED)

find_package(Threads)

find_package(inja              REQUIRED)







# In this case, we specify the version numbers being searched for in the non-traditional installs.
@@ -347,6 +349,9 @@ foreach (_variableName ${_variableNames}) 
  endif()

endforeach()



# add target based linkages to ALLLIBS variable

list(APPEND ALLLIBS pantor::inja)



# Sometimes we add the same lib more than once (especially with LIBDIRS)

list(REMOVE_DUPLICATES ALLLIBDIRS)

list(REMOVE_DUPLICATES ALLLIBS)
@@ -496,6 +501,7 @@ file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/appdata/translations 
		    ${CMAKE_BINARY_DIR}/appdata/templates/jigsaw

		    ${CMAKE_BINARY_DIR}/appdata/templates/kernels

	            ${CMAKE_BINARY_DIR}/appdata/templates/labels

	            ${CMAKE_BINARY_DIR}/appdata/templates/topds4

	            ${CMAKE_BINARY_DIR}/appdata/templates/maps

		    ${CMAKE_BINARY_DIR}/appdata/templates/photometry

	            ${CMAKE_BINARY_DIR}/appdata/images/icons
@@ -614,6 +620,10 @@ add_custom_target(hidtmgen ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different 
  ${CMAKE_SOURCE_DIR}/appdata/templates/hidtmgen/* ${CMAKE_BINARY_DIR}/appdata/templates/hidtmgen/)

add_dependencies(isis hidtmgen)



add_custom_target(topds4 ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different

  ${CMAKE_SOURCE_DIR}/appdata/templates/topds4/* ${CMAKE_BINARY_DIR}/appdata/templates/topds4)

add_dependencies(isis topds4)



# Add a custom build target to clean out everything that gets added to the source

#  directory during the build process.

# - Only a few things are added in order to make the tests work properly so

isis/appdata/templates/topds4/osirisrex.xml.tpl

0 → 100644
+53 −0
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<?xml version="1.0" encoding="UTF-8"?>

<?xml-model href="https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1700.sch" schematypens="http://purl.oclc.org/dsdl/schematron" ?>

<?xml-model href="https://pds.nasa.gov/pds4/disp/v1/PDS4_DISP_1700.sch" schematypens="http://purl.oclc.org/dsdl/schematron" ?>

<?xml-model href="https://pds.nasa.gov/pds4/geom/v1/PDS4_GEOM_1700_1401.sch" schematypens="http://purl.oclc.org/dsdl/schematron" ?>

<?xml-model href="https://pds.nasa.gov/pds4/orex/v1/orex_ldd_OREX_1300.sch" schematypens="http://purl.oclc.org/dsdl/schematron" ?>

<Product_Observational

    xmlns="http://pds.nasa.gov/pds4/pds/v1"

    xmlns:pds="http://pds.nasa.gov/pds4/pds/v1"

    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

    xmlns:disp="http://pds.nasa.gov/pds4/disp/v1"

    xmlns:geom="http://pds.nasa.gov/pds4/geom/v1"

    xmlns:orex="http://pds.nasa.gov/pds4/mission/orex/v1"

    xsi:schemaLocation=

    "http://pds.nasa.gov/pds4/pds/v1 https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_1700.xsd

    http://pds.nasa.gov/pds4/disp/v1 https://pds.nasa.gov/pds4/disp/v1/PDS4_DISP_1700.xsd

    http://pds.nasa.gov/pds4/geom/v1 https://pds.nasa.gov/pds4/geom/v1/PDS4_GEOM_1700_1401.xsd

    http://pds.nasa.gov/pds4/mission/orex/v1 https://pds.nasa.gov/pds4/mission/orex/v1/PDS4_OREX_1300.xsd">

    <File_Area_Observational>

        <File>

            <file_name>filename</file_name>

            <creation_date_time>dateandtime</creation_date_time>

            <file_size unit="byte">filesize</file_size>

        </File>

        <Header>

            <offset unit="byte">headeroffset</offset>

            <object_length unit="byte">headerLength</object_length>

            <parsing_standard_id>fileType</parsing_standard_id>

        </Header>

        <Array_2D_Image>

            <local_identifier>Active Area</local_identifier>

            <offset unit="byte">imageOffsetBytes</offset>

            <axes>numAxes</axes>

            <axis_index_order>Last Index Fastest</axis_index_order>

            <description>OCAMS image 1024 by 1024 pixel active array.</description>

            <Element_Array>

                <data_type>bitType</data_type>

                <unit>DN</unit>

                <scaling_factor>1</scaling_factor>

                <value_offset>WHAT IS THIS</value_offset>

            </Element_Array>

            <Axis_Array>

                <axis_name>Line</axis_name>

                <elements>{{MainLabel.IsisCube.Core.Dimensions.Lines.Value}}</elements>

                <sequence_number>1</sequence_number>

            </Axis_Array>

            <Axis_Array>

                <axis_name>Sample</axis_name>

                <elements>{{MainLabel.IsisCube.Core.Dimensions.Samples.Value}}</elements>

                <sequence_number>2</sequence_number>

            </Axis_Array>

        </Array_2D_Image>

    </File_Area_Observational>

</Product_Observational>