Marcical update to be fully congruent with calibration method #5004

ladoramkershner · 2022-07-17T19:40:17Z

One small functional update to make sure we are fully implimenting the MARCI calibration method outlined here. Specifically step 3 is being implemented in this PR.

Description

In the MARCI calibration documentation output by the MRO mission team, after the flat file is taken through normalization and flattening there should be a check applied. If the flat file value is below 0.25 the equation in the follow step (step 4) should be set to zero. This was not reflected in the code.

All other changes are syntax improvements.

Related Issue

Related to issue #4619

Motivation and Context

Our MARCI calibration was not fully congruent to what the mission teams outlined for calibration of MARCI images.

How Has This Been Tested?

Output from running tests locally

The following tests did not run:
	1732 - TempTestingFiles.FunctionalTestJitterfitDefault (Disabled)
	1763 - TempTestingFiles.UnitTestImageImporterTestJpeg (Disabled)

The following tests FAILED:
	128 - isis_unit_test_JP2Importer (Failed)
	811 - deltack_app_test_directOffTarget (Failed)
	905 - cassini_module_test_vims (Failed)
	951 - hayabusa_module_test_fullframe (Failed)
	952 - hayabusa_module_test_subframe (Failed)
	984 - lronaccal_app_test_nacl-full (Failed)
	985 - lronaccal_app_test_nacl-summed (Failed)
	986 - lronaccal_app_test_nacr-full (Failed)
	987 - lronaccal_app_test_nacr-summed (Failed)
	1042 - mex_unit_test_MexHrscSrcCamera (Failed)
	1109 - mro_module_test_hirise (Failed)
	1110 - near_module_test_msi (Failed)
	1759 - TempTestingFiles.FunctionalTestStd2isisJp2 (Failed)
	1765 - TempTestingFiles.UnitTestImageImporterStd2IsisJp2 (Failed)
	1912 - IsisTruthCube.FunctionalTestsIsis2StdJpeg2KGray (Failed)
	1913 - IsisTruthCube.FunctionalTestsIsis2StdJpeg2KU16 (Failed)
	1914 - IsisTruthCube.FunctionalTestsIsis2StdJpeg2KS16 (Failed)
	1924 - SmallARGBCube.FunctionalTestsIsis2StdJpeg2KRGB (Failed)
	1925 - SmallARGBCube.FunctionalTestsIsis2StdJpeg2KARGB (Failed)
	1997 - LronaccalDefault.FunctionalTestsLronaccal (Failed)
	1998 - LronaccalNear.FunctionalTestsLronaccal (Failed)
	1999 - LronaccalPair.FunctionalTestsLronaccal (Failed)

Screenshots (if appropriate):

Types of changes

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Documentation change (update to the documentation; no code change)
Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

I have read and agree to abide by the Code of Conduct
I have read the CONTRIBUTING document.
My change requires a change to the documentation.
I have updated the documentation accordingly.
I have added tests to cover my changes.
All new and existing tests passed.
I have added myself to the .zenodo.json document.
I have added any user impacting changes to the CHANGELOG.md document.

Licensing

This project is mostly composed of free and unencumbered software released into the public domain, and we are unlikely to accept contributions that are not also released into the public domain. Somewhere near the top of each file should have these words:

This work is free and unencumbered software released into the public domain. In jurisdictions that recognize copyright laws, the author or authors of this software dedicate any and all copyright interest in the software to the public domain.

I dedicate any and all copyright interest in this software to the public domain. I make this dedication for the benefit of the public at large and to the detriment of my heirs and successors. I intend this dedication to be an overt act of relinquishment in perpetuity of all present and future rights to this software under copyright law.

ladoramkershner · 2022-07-17T19:41:04Z

The tests that are failing are unrelated to the changes created in this PR. I am not sure if these test failures are expected however.

ladoramkershner · 2022-07-17T19:41:58Z

isis/src/mro/apps/marcical/marcical.cpp

-    filterNameToFilterIndex.insert(pair<QString, int>("NIR",      5));
-    filterNameToFilterIndex.insert(pair<QString, int>("SHORT_UV", 6));
-    filterNameToFilterIndex.insert(pair<QString, int>("LONG_UV",  7));
+    map<QString, int> filterNameToFilterNumber;


The filter index used in this code is zero based, so renamed for accuracy.

ladoramkershner · 2022-07-17T19:42:34Z

isis/src/mro/apps/marcical/marcical.cpp

@@ -347,21 +337,14 @@ namespace Isis {
    PvlKeyword &colOff = icube.label()->findGroup("Instrument", Pvl::Traverse)["ColorOffset"];
    int colorOffset = toInt(colOff[0]);

-    for (int filter = 0; filter < numFilters; filter++) {
+    for (int i = 0; i < numFilters; i++) {


filter variable is set previously, it did not seem to be resetting the larger variable, but changed for readability

ladoramkershner · 2022-07-17T19:43:19Z

isis/src/mro/apps/marcical/marcical.cpp

+          if ((*fcubeMgrs[fcubeIndex])[i] < 0.25) {
+            ocubeMgr[i] = 0;
+          }
+          else {
+            ocubeMgr[i] = stretch.Map(icubeMgr[i]) / (*fcubeMgrs[fcubeIndex])[i];
+          }


This is the portion of the calibration logic missing from our implementation

See step 3 of https://pds-imaging.jpl.nasa.gov/data/mro/mars_reconnaissance_orbiter/marci/mrom_1343/calib/marcical.txt

ladoramkershner · 2022-07-17T19:43:56Z

isis/src/mro/apps/marcical/marcical.cpp

@@ -524,6 +512,11 @@ namespace Isis {
      icubeMgr++;
      ocubeMgr++;

+      // checks if we have reached the end before setting higher band
+      if (ocubeMgr.end()) {


Prevents non-existent band from being set in the last chunk of code in the loop.

jessemapel

Make sure you add an entry to the changelog and to the marcical.xml file.

jessemapel · 2022-07-18T17:54:08Z

CHANGELOG.md

@@ -34,6 +34,7 @@ release.
 -->

 ## [Unreleased]
+- Update marcical to include step 3 of the mission team's MARCI calibration process described [here](https://pds-imaging.jpl.nasa.gov/data/mro/mars_reconnaissance_orbiter/marci/mrom_1343/calib/marcical.txt). [#5004](https://github.com/USGS-Astrogeology/ISIS3/pull/5004)


Put this under an appropriate header

Can do! I will move the other entries while I am at it!

jessemapel

Looks good to go in

jessemapel · 2022-07-19T16:15:56Z

@ladoramkershner Go ahead and merge then when you're ready to add the new data

jessemapel · 2022-07-19T16:16:20Z

@ladoramkershner Go ahead and merge then when you're ready to add the new data

ladoramkershner commented Jul 17, 2022

View reviewed changes

jessemapel reviewed Jul 18, 2022

View reviewed changes

ladoramkershner changed the title ~~Small clean up of single use variables and convoluted logic~~ Marcical update to be fully congruent with calibration method Jul 18, 2022

ladoramkershner force-pushed the marci branch 2 times, most recently from c2db8c6 to 73b00cb Compare July 18, 2022 17:08

jessemapel reviewed Jul 18, 2022

View reviewed changes

ladoramkershner added 4 commits July 19, 2022 08:45

Small clean up of single use variables and convoluted logic

59f7757

Update CHANGELOG

f364dda

update history in xml

a8e46b9

update CHNGLG and tests

d8567ba

ladoramkershner force-pushed the marci branch from 444f885 to d8567ba Compare July 19, 2022 15:48

jessemapel approved these changes Jul 19, 2022

View reviewed changes

ladoramkershner merged commit ad3d02c into DOI-USGS:dev Jul 19, 2022

jessemapel mentioned this pull request Jul 21, 2022

Clean up for 7.0.1 #4994

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Marcical update to be fully congruent with calibration method #5004

Marcical update to be fully congruent with calibration method #5004

ladoramkershner commented Jul 17, 2022

ladoramkershner commented Jul 17, 2022

ladoramkershner Jul 17, 2022

ladoramkershner Jul 17, 2022

ladoramkershner Jul 17, 2022

ladoramkershner Jul 17, 2022

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jessemapel Jul 18, 2022

ladoramkershner Jul 19, 2022 •

edited

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jessemapel commented Jul 19, 2022

jessemapel commented Jul 19, 2022

Marcical update to be fully congruent with calibration method #5004

Marcical update to be fully congruent with calibration method #5004

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ladoramkershner commented Jul 17, 2022

Description

Related Issue

Motivation and Context

How Has This Been Tested?

Screenshots (if appropriate):

Types of changes

Checklist:

Licensing

ladoramkershner commented Jul 17, 2022

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ladoramkershner Jul 19, 2022 • edited Loading

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jessemapel commented Jul 19, 2022

jessemapel commented Jul 19, 2022

ladoramkershner Jul 19, 2022 •

edited

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