= User Manual Author's Task List =
Have at ...

= Category B =
shift probably requires Eric to write about. It basically shifts the center of a shape model to the center of its coordinate system, but there is not a lot of info anywhere about how to use it.

== Programs ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[autoregister]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[autoregisterP]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[bigmap]] ||TC ||TC ||KD JW ||JW ||YES * ||*FIXED* made SIGMAS.pgm picture look more organized. From JW - Need in add USED_PICS.TXT to this, and make the page for USED_PICS.TXT ||
||[[bigmapL]] ||TC ||TC ||KD ||KD ||YES * ||didn't change anything ||
||[[blemishes]] ||DL ||DL ||KD ||KD ||YES * || ||
||[[densify]] ||TC ||TC ||JW ||JW ||YES * ||*FIXED* Need a paragraph at the beginning that (in plain terms) says what densify does. Also, should define K before you use it. ||
||[[densifyA]] ||TC ||TC ||JW ||JW ||YES * ||*FIXED* Are there any substantial differences from densify?    Not really -TC ||
||[[duplicates]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[dynamics]] ||TC ||TC ||KD ||KD ||YES * ||didn't change anything ||
||[[Export_Import]] ||JW ||JW ||KD ||KD ||YES * ||didn't change anything ||
||[[find_nofit]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[find_nofitP]] ||KD ||KD ||JW ||JW ||YES * ||Change LMRK.OOT to <LMRK>.OOT and other similar changes ||
||[[find_nofitT]] ||KD ||KD ||JW ||JW ||YES * ||Change LMRK.OOT to <LMRK>.OOT and other similar changes ||
||[[geometry]] ||TC ||TC ||JW ||JW ||YES * ||*FIXED* Need more info on how to use the program. What are options 1, 2? Do you run one or other, or both at once? Which one of those is the example from? ||
||[[lithos]] ||JW ||JW ||DL ||DL ||YES * || ||
||[[lithosP]] ||JW ||JW ||DL ||DL ||YES * ||Unresolved queries:<<BR>>Z:Inspected code and commented on findings - still not sure of what use this option is. ||
||[[make_list]] ||JW ||JW ||TC ||TC ||YES * ||Consider revision of the first sentence of description, last part doesn't make sense. Provide example of what LIST.TXT looks like, not clear. ||
||[[make_lmrklistX]] ||DL ||DL ||KD ||KD ||YES * || ||
||[[make_scriptA]] ||DL ||DL ||KD JW ||KD JW ||YES * || ||
||[[make_scriptAP]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[make_scriptF]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[make_scriptP]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[make_scriptR]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[make_scriptT]] ||DL ||DL ||KD JW ||KD JW ||YES * || ||
||[[make_sumfiles]] ||KD ||KD ||JW ||JW ||YES * ||JW - Looks good to me, but I don't have experience with this program ||
||[[make_tilefile]] ||DL ||DL ||KD JW ||JW ||YES * || ||
||[[MAKE_TILES]] ||KD ||KD ||JW ||JW ||YES * ||See text for a comment. ||
||[[MAKE_TILESP]] ||KD ||KD ||JW ||JW ||YES * ||I changed the last line, also do you have to type that for every *.b file? ||
||[[map_coverage]] ||KD ||KD ||TC ||TC ||YES * ||Made a few minor grammatical alterations ||
||[[new_pole]]||DL|| || || || || ||
||[[omega]]||DL|| || || || || ||
||[[pole]] ||KD ||KD ||TC ||TC ||YES * ||Needs compiled by note ||
||[[process_fits]] ||KD ||KD ||DL ||DL ||YES * || ||
||process_img ||N/A ||N/A ||N/A ||N/A ||N/A ||Not required ||
||[[register]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[regres]] ||KD ||KD ||TC ||TC ||YES* ||Need to update PICTLISTR.TXT input file. Need to specify required files/directories to run. needs SUMFILES, NOMINALS, make_sumfiles.txt, etc ||
||[[rem_done]] ||KD ||KD ||TC ||TC ||YES * ||Few minor changes ||
||[[residuals]] ||KD ||KD ||TC || ||YES * ||What is the second user input? Bob says it is a 'linear residual limit' and the unit is km - but what does Bob mean? ||
||[[Script Makers Overview]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[shape_info]] ||KD ||KD ||TC ||TC ||YES * ||"Last bit of information is unknown" ..... :-/ ||
||[[shift]] ||EP ||EP ||JW ||JW ||YES * || ||
||[[spheremapsB]] ||JW ||JW ||TC ||TC ||YES * ||Consider revision of description based on Bob's abstract to add some detail and clear some ambiguity. Also page for MAPLIST.TXT is needed. ||


== Directories ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[BIGFILES]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[DATA]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[IMAGEFILES]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[LMKFILES]] ||TC ||TC ||JW ||JW ||YES * || ||
||[[MAPFILES]] ||TC ||TC ||JW ||JW ||YES * || ||
||[[NOMINALS]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[SHAPEFILES]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[SUMFILES]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[TESTFILES]] ||DL ||DL ||KD ||KD ||YES * || ||
||[[TESTFILES1]] ||DL ||DL ||KD ||KD ||YES * || ||
||UTILITIES ||N/A ||N/A ||N/A ||N/A ||N/A ||non-OSIRIS not required ||


== Key Input Files ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[BIGMAP.IN]] ||TC ||TC ||JW ||JW ||YES * || ||
||[[BIGLIST.TXT]] ||TC ||TC ||JW ||JW ||YES * || ||
||[[DYNAMICS.TXT]] ||TC ||TC ||KD ||KD ||YES * ||didn't change anything ||
||FONT.INC ||N/A ||N/A ||N/A ||N/A || ||can we delete this? ||
||[[IFRAME.TXT]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[INIT_LITHOS.TXT]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[LIMBLIST1.TXT]] ||JW ||JW ||TC ||TC ||YES || ||
||[[LMRKLIST.TXT]] ||DL ||DL ||JW ||JW ||YES * || ||
||[[LMRKLIST1.TXT]] ||JW ||JW ||TC ||TC ||YES * || ||
||[[LMRKLISTO.TXT]] ||JW ||JW ||TC ||TC ||YES * || ||
||[[LMRKLISTR.TXT]] ||JW ||JW ||KD ||KD ||YES * || ||
||[[LMRKLISTX.TXT]] ||DL ||DL ||KD ||KD ||YES * || ||
||[[make_sumfiles.in]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[make_sumfiles.txt]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[MAPLIST.TXT]] ||JW ||JW ||TC ||TC ||YES || ||
||[[PICTLISTR.TXT]] ||JW ||JW ||TC ||TC ||YES * || ||
||[[PICTLIST.TXT]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[PICTLISTS.TXT]] ||DL ||DL ||JW ||JW ||YES || ||
||[[PICTLISTX.TXT]] ||KD ||KD ||JW ||JW ||YES * || ||
||[[PICTLISTRX.TXT]] ||JW ||JW ||TC ||TC ||YES * || ||


== Key Output Files ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[check.txt]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[EMPTY.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[FLATLIST.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[INSIDE.TXT]] ||TC ||TC ||DL ||DL ||YES * || ||
||[[LIMINFO.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[LMKVECS.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[MAPCHK.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[MAPINFO.TXT]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[MAPRES.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[New_Limbs.in]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[NEW_LIST.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[no_update.txt]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[OVERLAPS.TXT]] ||JW ||JW ||TC ||TC ||YES * || ||
||[[PICINFO.TXT]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[PRUNE.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[RANGES_SOLVED.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[redo.txt]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[REMOVED.TXT]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[RESIDUALS.TXT]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[SHAPE.TXT]] ||KD ||KD ||TC ||TC ||YES * || ||
||[[SIGMAS.TXT]] ||TC ||TC ||DL ||DL ||YES * ||I checked the fortran, the column outputs are maximum and average standard deviation of weighted heights at each pixel/line location - comments added to Wiki ||
||[[SIGMA.TXT]] ||TC ||TC ||DL ||DL ||YES * ||I added details from [[SHAPE.TXT]] regarding line and column values. ||
||[[USED_MAPS.TXT]] ||TC ||TC ||DL ||DL ||YES * || ||
||[[USED_PICS.TXT]] ||TC ||TC ||DL ||DL ||YES * || ||
||[[veto.txt]] ||DL ||DL ||TC ||TC ||YES * || ||


== Support Files ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[make_script.in]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[make_scriptA.seed]] ||DL ||DL ||TC ||TC ||YES * || ||
||make_scriptAP.seed ||N/A ||N/A ||N/A ||N/A ||N/A ||make_scriptAP uses make_scriptA.seed ||
||[[make_scriptF.seed]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[make_scriptP.seed]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[make_scriptR.seed]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[make_scriptT.in]] ||DL ||DL ||TC ||TC ||YES * || ||
||[[make_scriptT.seed]] ||DL ||DL ||TC ||TC ||YES * || ||


== Lithos Menu Options ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||0. [[Find template]] || || || || ||YES * || ||
||1. [[Align landmarks]] || || || || ||YES * || ||
||2. [[Find heights]] || || || || ||YES * || ||
||O. [[Attach map to maps or limbs]] || || || || ||YES * || ||
||I. [[Input landmark]] || || || || ||YES * || ||
||U. [[Update landmark files]] || || || || ||YES * || ||
||C. [[Create new landmark]] || || || || ||YES * || ||
||R. [[Replicate or Rename landmark]] || || || || ||YES * || ||
||S. [[Change_scale_qsz_or_orientation]] || || || || ||YES * || ||
||G. [[Turn on rename]] || || || || ||YES * || ||
||N. [[Find normal]] || || || || ||YES * || ||
||V. [[Find_V_Z_or_PTG]] || || || || ||YES * || ||
||A. [[Reset albedo or slopes]] || || || || ||YES * || ||
||M. [[Get heights from shape model]] || || || || ||YES * || ||
||B. [[Get heights from surrounding map]] || || || || ||YES * || ||
||X. [[Turn on extract filter]] || || || || ||YES * || ||
||D. [[Delete or Disconnect landmark]] || || || || ||YES * || ||
||E. [[Eliminate pictures from landmark]] || || || || ||YES * || ||
||P. [[Picture status]] || || || || ||YES * || ||
||L. [[Turn off picture restriction]] || || || || ||YES * || ||
||F. [[Find maplets containing surface point]] || || || || ||YES * || ||
||Z. [[Use zoom display]] || || || || ||YES * || ||
||H. [[Hide screen output]] || || || || ||YES * || ||


== How Tos ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[stage1_description]] ||BM || || || || || ||
||[[stage2_description]] ||BM || || || || || ||
||[[stage3_description]] ||BM || || || || || ||
||[[stage4_description]] ||BM || || || || ||this one doesn't go in manual--save for later use. ||
||[[Block 1 - Setup Directory V0]]||BM || || || || || ||
||[[Block 2 - Ingest]] ||BM || || || || || ||
||[[Block 3 - Register]] ||BM || || || || || ||
||[[Block 4 - Autoregister]] ||BM || || || || || ||
||[[Block 5 - Iterate]] ||BM || || || || || ||
||[[Block 6A - Lat/Lon Tiling]]||BM || || || || || ||
||[[Block 6B - Bigmap Tiling]]||BM || || || || || ||
||[[Block 7 - Clean]] ||BM || || || || || ||



=== working how tos ===
||[[Basic Tiling - Achieving the Desired Maplet Overlap]] ||DL || || || || || ||
||Block 01-01 [[How to Test Directory Set-Up - ORIG V0]] ||DL ||BM || || || || ||
||Block 02-01 [[How to Ingest Images - Test Specific V0]] ||DL ||BM || || || || ||
||Block 03-01 [[How to Register Images - Batch V0]] ||DL ||BM || || || || ||
||Block 03-02 [[How to Autoregister Images - Batch V0]] ||DL ||BM || || || || ||
||Block 04-01 [[How to Iterate Landmarks V0]] ||DL ||BM || || || || ||
||Block 05-01 [[How to Tile - Bigmap V0]] ||DL ||BM || || || || ||


== Front Matter and Bibliography ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Complete and Handed Over to Bob ||Notes ||
||[[Scope]] || || || || || || pulled directly from the manual ||
||[[Introduction]] ||BM || || || || || modified to include everything that was in the manual ||
||[[spc_overview]] ||BM || || || || || modified to include everything that was in the manual  ||
||[[bibliography]] ||BM || || || || || pulled directly from the manual ||

== Outputting to print manual ==

||[[output_manual_directions]] || BM || || || || ||explains the steps for outputting to print manual ||
||[[ManualOutput]] || BM || || || || ||includes all the content set up for outputting to print manual ||
||[[TestPDFOutput]] ||BM || || || || ||used for outputting small pieces and tweaking the pdf inputs ||
||[[TestPDFOutput2]] ||BM || || || || ||used for testing output of the whole thing--has OLD includes in it ||

=== working files ===

||[[Title Page]] ||BM || || || || ||don't use: For pdf, it can generate based on inputs in overall file ||
||[[Copyright Page]] ||BM || || || || ||don't use: For pdf, this is also generated by inputs in overall file||
||[[What This Manual Includes]] ||BM || || || || ||don't use: early draft||
||[[How This Manual Is Organized]] ||BM || || || || ||don't use: early draft||
||[[Who This Manual Is Intended to Help]] ||BM || || || || ||don't use: early draft||
||[[How Standard Items Are Identified]] ||BM || || || || ||don't use: early draft||
||[[Table of Contents]] ||BM || || || || ||don't use: For pdf, this is generated during output. Can set how many levels of headings to pull, but probably only want one. ||


= Category D =
== Programs ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||coverage || || || || || ||
||[[coverage_p]] ||JW || || || ||No abstract in code. ||
||dumber || || || || || ||
||geometryx || || || || || ||
||harmonics || || || || || ||
||IMGLATLON || || || || || ||
||limber || || || || || ||
||map_coverage_p || || || || || ||
||ROUGHNESS || || || || || ||
||shape2maps || || || || || ||
||shape2mapsA || || || || || ||
||spheremapsA || || || || || ||
||triax || || || || || ||
||vecs2shape || || || || || ||


== IMAGER ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||display || || || || || ||
||imager_grid || || || || || ||
||imagar_MG || || || || || ||
||imager_MGF || || || || || ||
||make_font || || || || || ||
||SHOWMAP || || || || || ||
||view_map_rgb || || || || || ||
||view_map_stereo || || || || || ||
||view_shape || || || || || ||
||view_shapeA || || || || || ||
||view_shapeC || || || || || ||


== MAPMAKER ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||LIST_MMTILES || || || || || ||
||MAKE_MMTILES || || || || || ||
||MAPMAKER || || || || || ||


== RECOVERY ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||endless || || || || || ||
||GHOSTS || || || || || ||
||REFRESH_SUMFILES || || || || || ||


= No Category Listed =
== Programs ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||make_pictlist ||EVERYONE ASK KRIS! || || || || ||
||[[make_pictlistX]] ||KD ||KD ||JW ||JW || ||


== Key Input Files ==
||Page ||Started ||Completed ||Review Started ||Review Complete ||Notes ||
||GEOID.TXT || || || || || ||
||MGRAV.TXT || || || || || ||
||NEWFILES.TXT || || || || || ||
||SGRAV.TXT || || || || || ||
||SHAPEC.TXT || || || || || ||


== Other Comments ==