decompLines: Decompress the Data Lines in a JCAMP-DX File

In readJDX: Import Data in the JCAMP-DX Format

Description

This function is used by the package, and can also be called by the user who wishes to study problematic lines in a file in a standalone manner. See the examples.

Usage

decompLines(VL, debug = 0)

Arguments

VL	Character. The variable list to be processed as a character vector. Depending upon the mode and the stage of processing: the lines may be named as "Line_1" etc a format code may be present as the first entry there may be other non-numeric lines that eventually get stripped off
debug	Integer. See readJDX for details.

Value

A list of numeric strings, the result of unpacking the compressed data. One list element is returned for each line. The numeric string is named with the ASDF compression mode.

Details

Each individual line passed here is converted to a list to make processing and naming the pieces easier.The individual entries are named according to their original ASDF compression code. Unless otherwise noted all functions called from here should act on a list of lines, via lapply. Note too that the X values are present, e.g. X, Y1, Y2 ... Yn.

Formats

AFFN is separated by any amount of white space so processing is straightforward, as exponents are handled automatically, and white space stripped off automatically, courtesy of R internals. It appears AFFN is never mixed with other formats. The other formats are collectively called ASDF in the standard.

Examples

testLines1 <- c(
  "482A885145L989378k853295J46714q39581j382088R41076k774051J365135l135709P53917",
  "472a903359j71857q18832K573831k615133L481852l395846L894844l478693M916433",
  "463B483240m513444O146172m826168N233079m522551M000252m097028L466111l460183",
  "454i0520L061628k524598K788931k509430L219286k511160K709095k122775J594246"
)
demo1 <- decompLines(testLines1, debug = 6)

testLines2 <- c(
  # EU AFFN:
  "1898,58486802541 -0,0170190036296844 -0,0170874372124672 -0,0171865783631802",
  "1917,23501403401 -0,0176097713410854 -0,0177919361740351 -0,0179808251559734",
  # AFFN with fixed field width/extra space:
  "           16383       2259260      -5242968      -7176216      -1616072",
  "           16379      10650432       4373926      -3660824       2136488"
)

demo2 <- decompLines(testLines2, debug = 6)

Example output

readJDX is tested with > 100 files before release.
However, there are still challenging files out in the wild.
If you have trouble importing a file, please file an issue at
github.com/bryanhanson/readJDX/issues




====================  Raw lines:

[1] "482A885145L989378k853295J46714q39581j382088R41076k774051J365135l135709P53917"
[2] "472a903359j71857q18832K573831k615133L481852l395846L894844l478693M916433"     
[3] "463B483240m513444O146172m826168N233079m522551M000252m097028L466111l460183"   
[4] "454i0520L061628k524598K788931k509430L219286k511160K709095k122775J594246"     



====================  Lines after preliminary processing:

$Line_1
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "482" "A885145" "L989378" "k853295"  "J46714"  "q39581" "j382088"  "R41076" 
      DIF       DIF       DIF       DIF 
"k774051" "J365135" "l135709"  "P53917" 

$Line_2
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "472" "a903359"  "j71857"  "q18832" "K573831" "k615133" "L481852" "l395846" 
      DIF       DIF       DIF 
"L894844" "l478693" "M916433" 

$Line_3
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "463" "B483240" "m513444" "O146172" "m826168" "N233079" "m522551" "M000252" 
      DIF       DIF       DIF 
"m097028" "L466111" "l460183" 

$Line_4
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "454"   "i0520" "L061628" "k524598" "K788931" "k509430" "L219286" "k511160" 
      DIF       DIF       DIF 
"K709095" "k122775" "J594246" 


Undoing DIF compression:

   Line_1 passed to deDIF:
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "482" "1885145" "L989378" "k853295"  "J46714"  "q39581" "j382088"  "R41076" 
      DIF       DIF       DIF       DIF 
"k774051" "J365135" "l135709"  "P53917" 

   Line_1 as processed by deDIF:
     NUM      SQZ      DIF      DIF      DIF      DIF      DIF      DIF 
     482  1885145  5874523  3021228  3167942  2328361   946273  1887349 
     DIF      DIF      DIF      DIF 
 -886702   478433 -2657276 -1903359 

Undoing DIF compression:

   Line_2 passed to deDIF:
       NUM        SQZ        DIF        DIF        DIF        DIF        DIF 
     "472" "-1903359"   "j71857"   "q18832"  "K573831"  "k615133"  "L481852" 
       DIF        DIF        DIF        DIF 
 "l395846"  "L894844"  "l478693"  "M916433" 

   Line_2 as processed by deDIF:
     NUM      SQZ      DIF      DIF      DIF      DIF      DIF      DIF 
     472 -1903359 -2075216 -2894048  -320217 -2935350   546502 -2849344 
     DIF      DIF      DIF 
 1045500 -2433193  2483240 

Undoing DIF compression:

   Line_3 passed to deDIF:
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "463" "2483240" "m513444" "O146172" "m826168" "N233079" "m522551" "M000252" 
      DIF       DIF       DIF 
"m097028" "L466111" "l460183" 

   Line_3 as processed by deDIF:
     NUM      SQZ      DIF      DIF      DIF      DIF      DIF      DIF 
     463  2483240 -2030204  4115968  -710200  4522879      328  4000580 
     DIF      DIF      DIF 
  -96448  3369663   -90520 

Undoing DIF compression:

   Line_4 passed to deDIF:
      NUM       SQZ       DIF       DIF       DIF       DIF       DIF       DIF 
    "454"  "-90520" "L061628" "k524598" "K788931" "k509430" "L219286" "k511160" 
      DIF       DIF       DIF 
"K709095" "k122775" "J594246" 

   Line_4 as processed by deDIF:
    NUM     SQZ     DIF     DIF     DIF     DIF     DIF     DIF     DIF     DIF 
    454  -90520 2971108  446510 3235441  726011 3945297 1434137 4143232 2020457 
    DIF 
3614703 

Carrying out Y value checks...

yValueCheck sees a literal DIF mode on Line_1 
yValueCheck is removing the last value, -1903359 from Line_1 

yValueCheck sees a literal DIF mode on Line_2 
yValueCheck is removing the last value, 2483240 from Line_2 

yValueCheck sees a literal DIF mode on Line_3 
yValueCheck is removing the last value, -90520 from Line_3 


yValueCheck: Line_4 does not appear to be a checkpoint line


...Y value checks completed



====================  Lines after full processing to numeric:

$Line_1
 [1]      482  1885145  5874523  3021228  3167942  2328361   946273  1887349
 [9]  -886702   478433 -2657276

$Line_2
 [1]      472 -1903359 -2075216 -2894048  -320217 -2935350   546502 -2849344
 [9]  1045500 -2433193

$Line_3
 [1]      463  2483240 -2030204  4115968  -710200  4522879      328  4000580
 [9]   -96448  3369663   -90520

$Line_4
 [1]     454 2971108  446510 3235441  726011 3945297 1434137 4143232 2020457
[10] 3614703




====================  Raw lines:

[1] "1898,58486802541 -0,0170190036296844 -0,0170874372124672 -0,0171865783631802"
[2] "1917,23501403401 -0,0176097713410854 -0,0177919361740351 -0,0179808251559734"
[3] "           16383       2259260      -5242968      -7176216      -1616072"    
[4] "           16379      10650432       4373926      -3660824       2136488"    



====================  Lines after preliminary processing:

$Line_1
                  NUM                   NUM                   NUM 
   "1898.58486802541" "-0.0170190036296844" "-0.0170874372124672" 
                  NUM 
"-0.0171865783631802" 

$Line_2
                  NUM                   NUM                   NUM 
   "1917.23501403401" "-0.0176097713410854" "-0.0177919361740351" 
                  NUM 
"-0.0179808251559734" 

$Line_3
       NUM        NUM        NUM        NUM        NUM 
   "16383"  "2259260" "-5242968" "-7176216" "-1616072" 

$Line_4
       NUM        NUM        NUM        NUM        NUM 
   "16379" "10650432"  "4373926" "-3660824"  "2136488" 




====================  Lines after full processing to numeric:

$Line_1
[1] 1898.58486803   -0.01701900   -0.01708744   -0.01718658

$Line_2
[1] 1917.23501403   -0.01760977   -0.01779194   -0.01798083

$Line_3
[1]    16383  2259260 -5242968 -7176216 -1616072

$Line_4
[1]    16379 10650432  4373926 -3660824  2136488

readJDX documentation built on Sept. 21, 2021, 1:07 a.m.