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CCB > CCBSIGS > ShapeToolLibraryProgram > ShapeToolProgramProductStatusSummary > DualSurfaceWarpProjectDefinitionV1x0 > FluidWarpCorticalFlattening

Cortical Flattening Notes

Notes on the actions of script 07_Local_dual_med_flat_catchR.csh.

file / program descriptions

Sequence # Program Name Output File File Type Used By Notes
0 cp 64K_tri0_1oct.list Vertex List (?) rec131072_other_octants, COLORS_rec131072_other_octants 1 of 8 files, each is list of 16384 lines, each line has 3 integers,presumed to be face indices. Max integer value in set of all files is 65537.
0 cp 64K_tri0to8K.list Vertex List (?)   file with 16,384 lines, 3 col /line, max integer is: 22625. many integers appear more than once.
0 cp 64K_tri0to16K.list Vertex List (?)   file with 32,768 lines. Many integers appear more than once.
0 cp 64K_tri0to32K.list Vertex List (?)   file with 65,536 lines. Many integers appear more than once.
0 cp 64K_tri0to40K.list Vertex List (?)   file with 81,920 lines. Many integers appear more than once.
0 cp 64K_tri0to56K.list Vertex List (?)   file with 114,688 lines. Many integers appear more than once.
0 cp 64K_tri0to64K.list Vertex List (?)   file with 131,072 lines. Many integers appear more than once.
0 cp BIGflat.uvl a UVL   referring to : ordL.uif, ordR.uif, CordL?.uif, CordR?.uif, BIGCord.uif, BIGord.uif, BIGDECord.uif - probably a convenience to view the uif's.
0 cp COLORS_rec131072_other_octants IRIX Binary    
0 cp big64K_stream IRIX Binary    
0 cp real_64K_curve_find IRIX Binary    
0 cp rec131072_other_octants IRIX Binary    
0 cp pauls_AD64K_to_FULLvertex_list PERL script    
1   FULLvertex.list Vertex Coordinates rec131072_other_octants, COLORS_rec131072_other_octants a list of all coordinates in cortex obj, used in
1 pauls_AD64K_to_FULLvertex_list FULLvertex.list Vertex Coordinates   reads all .obj files in study directory and saves their 3-tuple coords into a single output file.
1 head , tail 64K_colors.txt   RGBA colors , ascii a list of 65538 face colors.
2 ? ord.uif RGBA Uif rec131072_other_octants, COLORS_rec131072_other_octants  
2 ? disord.uif RGBA Uif rec131072_other_octants, COLORS_rec131072_other_octants no source found, might not be used
2 rec131072_other_octants ${PIECE}oct_3D.ucf     ${PIECE} varies from1,...,8
2 reCOLORS_c131072_other_octants ${PIECE}oct_3D.ucf     ${PIECE} varies from1,...,8
Not Assigned real_64K_curve_find_in_BIGimage_or_reject DUAL_FLAT_ IRIX Binary   a) maps ucf to flat map space
b) rejects lines (fall off)
c) expects (hardwired) big image uif
d) may recompute the base 4 mappings
e) creates DUAL_(ucf) output, we dont' yet know
where to find the non DUAL flattened ucf.

Day One Speculations

"./rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > ${PIECE}oct_3D.ucf"

  • "0 2 3 4 5 6" is read and parsed, but not used. These must be integers.
  • "ord.uif" is written. This contains the an encoding of the obj's data in a two-dimensional data structure. For this call the vertex data is copied to the structure.
  • "disord.uif" is not read or written
  • "${PIECE}oct_3D.ucf" holds the data from the specified octant encoded to a ucf.

"./COLORS_rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > C${PIECE}oct_3D.ucf "

  • "0 2 3 4 5 6" is read and parsed, but not used. These must be integers.
  • "ord.uif" is written. This contains the an encoding of the obj's data in a two-dimensional data structure. For this call the vertex colors are copied to the structure.
  • "disord.uif" is not read or written
  • "64K_colors.txt" is required, though not mentioned in the command line statement
  • "C${PIECE}oct_3D.ucf" holds the data from the specified octant encoded to a ucf.

  • "DECord.uif" may encode the fractional part of the vertex coordinates

flatten script text, with inline annotations 



#! /bin/csh 

#NOTE: Change the directory where the subject is located. Change cases.

#NOTE: Must be run from the directory where subject cases live. Need 3 things in CORT directory...1)colored brain object 2)SHORTened RSP3 files for specific case and 3) Divided Lines (1, 5, 21; a & b) 

#When done, view with seg and load up by typing: seg -line 3 DUALflat.uvl FLAT_SHORTRSP3*.ucf OR seg -line 3 DUALflat.uvl DUALFLAT_SHORTRSP3*.ucf

#You will have two flattened images in DUALflat.uvl
#When loading FLAT*.ucf, use LsurrR_BIGCord to view flattened lines
#When loading DUALFLAT*.ucf, use RsurrL_BIGCord to view flattened lines

#foreach x ( `cat medial_anal.list`)
#foreach x ( `cat new_medial_anal.list`)
foreach x ( /cxfs/schizo/family_study/10396_/10396)

set STUDY = ${x:h}

echo ${STUDY}

cd ${STUDY}/Right_CORT

Sequence Number 0 


    echo "  Copying files..."
    cp /data/ad/d/thompson/Z_DAVES_STUFF_FROM_TMPNET/6NEW_CORTICAL_MESH_CODE/pauls_AD64K_to_FULLvertex_list .
    cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/rec131072_other_octants .
    cp /nethome/users/drex/models/64*list .
    cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/COLORS_rec131072_other_octants .
    cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/big64K_stream .
    cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/real_64K_curve_find .
    cp /nethome/users/thompson/HEM_FLAT/BIGflat.uvl .

##################################################################

    echo "  Running perl..."

Sequence # 1 


    ./pauls_AD64K_to_FULLvertex_list < {$STUDY}/Righ*CORT/*obj > FULLvertex.list

    echo "  Getting colors from object..."

    ## NOTE:  must use gnu version of tail as SGI sucks and decided in their
    ##        infinite wisdom to cut you off at 256K (since that is all their
    ##        "faster" buffered mode of tail can handle) -- drex 4/18/00
    head -n 196618 ${STUDY}/Righ*CORT/*obj | /usr/gnu/bin/tail -n 65538 | /usr/gnu/bin/tail -c +3 > 64K_colors.txt
    echo "  Unscrambling tiles to octant .ucfs..."

Sequence # 2 


    foreach PIECE ( 1 2 3 4 5 6 7 8 )
        echo "   $PIECE"

   ./rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > ${PIECE}oct_3D.ucf 
    end

    echo "  Starting texture descrambling to texture octant .ucfs..."

    foreach PIECE ( 1 2 3 4 5 6 7 8 ) 
   echo "   $PIECE"
   ./COLORS_rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > C${PIECE}oct_3D.ucf 
    end


######
    echo "  Making Right Hem. position map..."

    ./big64K_stream 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf > 1st_oct_set.ucf 
    cp ord.uif ordR.uif
    cp DECord.uif DECordR.uif


######
    echo "  Making Left Hem. position map..."

    ./big64K_stream 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf  7oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf > 2nd_oct_set.ucf
    cp ord.uif ordL.uif
    cp DECord.uif DECordL.uif


######
    echo "  Making Right Hem. texture map..."

    ./big64K_stream 1 2 3 4 5 6 C1oct_3D.ucf C2oct_3D.ucf C3oct_3D.ucf C4oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf > C1st_oct_set.ucf 
    cp ord.uif CordR.uif
    # caution,a DEC file is meaningless and actually makes things worse for a texture map.
    cp DECord.uif DECCordR.uif


######
    echo "  Making Left Hem. texture map..."

    ./big64K_stream 1 2 3 4 5 6 C6oct_3D.ucf C5oct_3D.ucf C8oct_3D.ucf  C7oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf > C2nd_oct_set.ucf
    cp ord.uif CordL.uif
    # caution,a DEC file is meaningless and actually makes things worse for a texture map.
    cp DECord.uif DECCordL.uif



###########
echo " This will paste the right parts of the ordL into the ordR, producing     BIGord" 

~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 CordL.uif CordR.uif BIGCord.uif
~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 ordL.uif ordR.uif BIGord.uif
~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 DECordL.uif DECordR.uif BIGDECord.uif

######
    echo "  Flattening Right. hem. curves into LsurrR (will skip to L if there are none)..."

    set wc_lines = `((ls SHORTRSP3_*R*.ucf > $$.tmp) >&! /dev/null); wc $$.tmp; /bin/rm -f $$.tmp`
    @ num_lines = ${wc_lines[1]}
# catch any that fall off in directories called LsurrR_FELL_OFF, RsurrL_FELL_OFF
if ( ! -e LsurrR_FELL_OFF ) mkdir LsurrR_FELL_OFF
if ( ! -e RsurrL_FELL_OFF ) mkdir RsurrL_FELL_OFF

    if ( ${num_lines} > 0 ) then
   foreach line ( SHORTRSP3_*R*.ucf )
       echo "   ${line}"
#test for medial data
#  ./real_64K_curve_find 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}
   
~thompson/HEM_FLAT/real_64K_curve_find_in_BIGimage_or_reject 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf  7oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}

      if ( -e $line:r.ucf_FELLOFF ) then
         echo "Found it"
         mv $line:r.ucf_FELLOFF LsurrR_FELL_OFF
         echo "Removing the fallen off FLAT line.."
         rm -f FLAT_{$line}
      endif
   end
    endif


######
    echo "  Flattening Left hem. curves into LsurrR...(will skip if there are none)..."
 
    set wc_lines = `((ls SHORTRSP3_*L*.ucf > $$.tmp) >&! /dev/null); wc $$.tmp; /bin/rm -f $$.tmp`
    @ num_lines = ${wc_lines[1]}
# catch any that fall off in directories called LsurrR_FELL_OFF, RsurrL_FELL_OFF
if ( ! -e LsurrR_FELL_OFF ) mkdir LsurrR_FELL_OFF
if ( ! -e RsurrL_FELL_OFF ) mkdir RsurrL_FELL_OFF

    if ( ${num_lines} > 0 ) then
   foreach line (SHORTRSP3_*L*.ucf )
       echo "   ${line}"
      # ./real_64K_curve_find 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf  7oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}

# now we catch the ones that fall off;
~thompson/HEM_FLAT/real_64K_curve_find_in_BIGimage_or_reject 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}
      if ( -e $line:r.ucf_FELLOFF ) then
         echo "Found it"
         mv $line:r.ucf_FELLOFF LsurrR_FELL_OFF
         echo "Removing the fallen off FLAT line.."
         rm -f FLAT_{$line}
      endif
   
   end
    endif
####################################################################################################################################
############# for DUAL flattening only - PT ###############
echo " This will paste the right parts of the ordR into the ordL (note new order), producing     BIGord" 
# old ones: - now have the UVL refer to the surr names
cp BIGCord.uif LsurrR_BIGCord.uif
cp BIGord.uif  LsurrR_BIGord.uif
cp BIGDECord.uif DECLsurrR_BIGord.uif

~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 CordR.uif CordL.uif BIGCord.uif
~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 ordR.uif ordL.uif BIGord.uif
~thompson/HEM_FLAT/paste_ordL_into_ordR 256 256 DECordR.uif DECordL.uif BIGDECord.uif

cp BIGCord.uif RsurrL_BIGCord.uif
cp BIGord.uif  RsurrL_BIGord.uif
cp BIGDECord.uif DECRsurrL_BIGord.uif

cp ~thompson/HEM_FLAT/DUALflat.uvl .
# note  BIGord.uif is hard coded so will now be the R surrounding the L ord. - 
# proceed with flattening into the new map - most medial will fall off this one? Note this will be
# blended with the other one somehow

######

#--------------------
    echo "  DUAL Flattening of Right. hem. curves, into RsurrL (will skip to L if there are none)..."

    set wc_lines = `((ls SHORTRSP3_*R*.ucf > $$.tmp) >&! /dev/null); wc $$.tmp; /bin/rm -f $$.tmp`
    @ num_lines = ${wc_lines[1]}
# catch any that fall off in directories called LsurrR_FELL_OFF, RsurrL_FELL_OFF
if ( ! -e LsurrR_FELL_OFF ) mkdir LsurrR_FELL_OFF
if ( ! -e RsurrL_FELL_OFF ) mkdir RsurrL_FELL_OFF

    if ( ${num_lines} > 0 ) then
   foreach line ( SHORTRSP3_*R*.ucf )
       echo "   ${line}"
#test for medial data
#  ./real_64K_curve_find 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}

~thompson/HEM_FLAT/real_64K_curve_find_in_BIGimage_or_reject 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf  7oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > DUALFLAT_${line}     

      if ( -e $line:r.ucf_FELLOFF ) then
         echo "Found it"
         mv $line:r.ucf_FELLOFF RsurrL_FELL_OFF
         echo "Removing the fallen off FLAT line.."
         rm -f DUALFLAT_{$line}
      endif
   end
    endif


######
    echo "  DUAL Flattening of Left hem. curves, into RsurrL...(will skip if there are none)..."
 
    set wc_lines = `((ls SHORTRSP3_*L*.ucf > $$.tmp) >&! /dev/null); wc $$.tmp; /bin/rm -f $$.tmp`
    @ num_lines = ${wc_lines[1]}
# catch any that fall off in directories called LsurrR_FELL_OFF, RsurrL_FELL_OFF
if ( ! -e LsurrR_FELL_OFF ) mkdir LsurrR_FELL_OFF
if ( ! -e RsurrL_FELL_OFF ) mkdir RsurrL_FELL_OFF

    if ( ${num_lines} > 0 ) then
   foreach line (SHORTRSP3_*L*.ucf )
       echo "   ${line}"
      # ./real_64K_curve_find 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf  7oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > FLAT_${line}

# now we catch the ones that fall off;
~thompson/HEM_FLAT/real_64K_curve_find_in_BIGimage_or_reject 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf ${line} 1oct_3D.ucf 1oct_3D.ucf > DUALFLAT_${line}

      if ( -e $line:r.ucf_FELLOFF ) then
         echo "Found it"
         mv $line:r.ucf_FELLOFF RsurrL_FELL_OFF
         echo "Removing the fallen off FLAT line.."
         rm -f DUALFLAT_{$line}
      endif
   
   end
    endif
end
#-----------------------------


    echo "  FINISHED - use seg to view results..."

 cd /cxfs/schizo/family_study/lists
 end

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Revised: r1.6 - 08 Apr 2008 - 19:42 - CraigSchwartz
 
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