Tucson format

From Cybis Wiki
Revision as of 19:08, 9 July 2009 by Lars-Ake (Talk | contribs)
Jump to: navigation, search

Tucson format or decadal format or rwl format is one of the most common formats for storing ring width data. It is the standard format for ITRDB. It is a text file format. Different extensions are used, such as .rwl, .crn, .tuc and .dec. (.crn is used for derivate chronologies). The name comes from the city of Tucson in Arizona.

Contents

Basics of the Tucson format for ring width data

A Tucson file usually consists of three lines of meta data followed by an undefined number of data lines. Ring width data is written as integers either in units of 0.01 mm or in units of 0.001 mm A data line consist of the core identity (max 8 alphanumeric characters, i.e. letters or digits), the year of the oldest measurement of the line (4 digits) followed by ring width data, up to ten rings per line. Except for the first and last lines of each core, there are always measurements for one full decade per line.

After the youngest ring there is a stop marker as an extra value. The stop marker depends on the resolution used:

  • When using 0.01 mm as the unit of measure, the stop marker is "999"
  • When using 0.001 mm as the unit of measure, the stop marker is "-9999"

I.e. the stop marker is used to show not only the end of the series but also the units of measurement used (0.01 mm or 0.001 mm)!

The missing data mark is actually not defined, though usually the mark "-999" is used within 0.01 mm files, and "0" in 0.001 mm files.


Note 1: The consequence of using the value 999 as a stop marker is that a measurement of 9.99 mm, in 0.01 mm units, has to be changed into 9.98 mm (written value=998) or 10.00 mm (1000)! To avoid fooling any other software, it is probably best never to write the value "999" as measurement data also for files with 0.001 mm units!
Note 2: If 5 digits are needed for the year number, i.e. a core older than -999, the identity cannot be more than 7 alphanumeric characters.
Note 3: An ITRDB specification of the Tucson format is found here: [1] though that specification cannot be fully trusted. E.g. it currently (2009-07-09) specifies the missing data mark to be 999, which value in reality is used as the stop marker.

PMkr12b 1781   120    87    69   122   108    85   125   114    77
PMkr12b 1790   134   131   114    97   117    49    69   100   123    89
PMkr12b 1800   137    89  -999    79    44    38    62    99    68    26
PMkr12b 1810    27    43    51    57    36   999

An example of a sample saved in 0.01 mm units, which covers the timespan AD 1781-1814, with a missing ring for AD 1802 (-999). The width of AD 1781 (the first year) annual ring is 1.20 mm and for 1782 AD 0.87 mm.

PMkr12b 1781  1200   870   690  1220  1080   850  1250  1140   770
PMkr12b 1790  1340  1310  1140   970  1170   490   690  1000  1230   890
PMkr12b 1800  1370   890     0   790   440   380   620   990   680   260
PMkr12b 1810   270   430   510   570   360 -9999

The same sample written in 0.001 mm units. Note the missing data mark which is here "0".

Examples

The Tucson format standard is sometimes interpreted in ways that will make the programming a bit hard. The following examples are taken from files in ITRDB but also from other sources.

Examples of variants of the decadal file format
6682    1980   143   231   154   145   150   201   130   156   245   137
6682    1990   141   202   120    96   999
NM002   1632    90    92    91   174    84    45   185   111
NM002   1640   116    72    91    49    85   146   125   126   136   131

The usual ending and start of samples (0.01 mm units resolution)


SH387C  1170    14    16    14    19    22    22    26    16    23    23
SH387C  1180    17    11    14    12   999     0     0     0     0     0
SH387D  1078    48    48
SH387D  1080    50    42    46    62    49    53    41    28    17    31

An example from brit9.rwl[1] where the positions after the end mark are filled out with "0"


Q 9730   990    72    98   112   124   107   132   137   145   114    80

This snappet from brit045.rwl[2] looks very much normal, but ends with two Asciichar(13) characters which will not be trimmed away by the VB Trim function.


WRU9    1190   190   192   218   213   204   259   206   150   178   149
WRU9    1200   198   232   151   199   175   196  9990  9990  9990  9990
WRU13   1075  9990  9990  9990  9990  9990   342   426   240   213   217

A snappet from brit5.rwl.[3] It both ends and start a sample with 9990 markers.


MWK964  1970    16    11    22    25     9    13    26    24    23    16        
MWK964  1980   999                                                              
MWK965   509    62     0     0     0     0     0     0     0     0     0        
MWK965   510    47    45    25    19    33    24    32    51    24    22        
...
MWK401 -3550    26    21    19    20    28    21    13    11    -0    11  

Example from ca535.rwl[4] where zeroes are filled into positions which are not in use and this with a -0 instead of 0 or -999 for missing rings.


606 13  1570    24    31    30    25    26    24    27    27    33    30
606 13  1580    20   999
606 13  1586    20    19    19    18
606 13  1590    27    20    20    25    22    22    23    23    10    15

Example from fran009.rwl.[5] I.e. two segments with a small gap of missing rings in between is written in the same way as two separate samples though here with the same identity.

Note, that there exist also .rwl files of the type above but with several other samples written between the segments. See e.g. Itrdb germ011.rwl where the identity 371241 starts the collection with a segment, then many other members follow and at last still a segment of 371241 ends the collection.

In CDendro these segments are handled as separate samples though they have the same identity within the .rwl file. The identity problem is then solved by giving them a temporary identity like "616 13:1" and "616 13:2"


OMA0851A1623   232   126   216   213   157   258   263     .     .     .
OMA0851A1630   246   182   174   187   240   175   169   173   149   150
...
OMA0851A1810    29    33    30    31    30    41    38    32    52    65
OMA0851A1820    47    57    55    40   999     .     .     .     .     .
OMA0851B1623   216   142   209   181   207   273   265     .     .     .
OMA0851B1630   189   172   162   153   155   145   147   150   157   155
OMA0851B1640   166   138   132   105    99   107   129    69    78    86
OMA0851B1650   140   156    60    47    35    75    26    41    50    37
...
OMA0851B1840    14    15    15    12    12    11    13    10    11    11
OMA0851B1850     6     8   999     .     .     .     .     .     .     .
OMA0852A1692   140   161   151   144    97   122   149   160     .     .
OMA0852A1700   222   237   251   153   185   191   234   293   189   159
OMA0852A1710   213   182   174   213   114   136   143   129   170   130
...

Example from the Finnish Tree ring data bank of Saima With this layout each "unused position" is marked with a dot (.).

Tab- or Space-characters as field delimiters

There are Tucson alike files with a tab-character as a delimiter between the fields.
Also space characters occur, especially when a Tucson file has been read in from a printed document or a .pdf file

CDendro interpretation

Using comments

When various dendrochronology programs are described as e.g. Cofecha and Arstan, it is often noted that lines that cannot be interpreted as ring width data lines are considered as comments. That feature is used by CDendro. Comments may then be bound both to the .rwl file (the sample collection) itself and to individual members (samples) of the collection.

SN     1 Saltsjobaden                                        PISY
SN     2 SWEDEN       Scots pine               5917N1818E          1696 2005
SN     3 Lars-Ake Larsson
SN      #### Samples taken from living or fallen trees except the group SNKBxx, which are poles of an old pier
SN      #### (Kolbryggan) in the bay Palnasviken, which have been standing in clay for a 110 years.
SN      #### The sample SNSU01 is taken from the Skutudden cottage.
SN001A  1923   341   374   369   298   500   382   396
SN001A  1930   332   297   421   250   290   288   317   320   256   215
SN001A  1940   111   183   229   183   159   157   163   134   105   111
SN001A  1950    81    62    89   138   164   180   138   157   170   130
SN001A  1960   108   184   137   148   124   164    80    98   105    67
SN001A  1970    57    89   126   101   114   100    83    76    71    57
SN001A  1980   114    87    79    85    56    49    61    79    81    70
SN001A  1990    99   139   132   161   132   118   999
SN001A  #### You may store comments for a sample too
SN001A  #### and it may extend over several lines.
SN001B  1923   329   375   319   299   435   366   384
SN001B  1930   287   258   392   280   251   293   296   278   200   181
SN001B  1940   114   154   224   160   138   106   127   126    97    96
SN001B  1950    68    65    83   114   168   176    91   163   189   146

Example of .rwl file with comments created with CDendro

The CDendro .rwc format for specifying the proportion of Latewood

In CooRecorder there are provisions for measuring latewood and earlywood. As a .rwl file cannot contain both latewood and earlywood, CDendro has a .rwc format which is almost the same as the .rwl format, though the latewood is specified as a sequence of permillage values at the end of the normal ring width lines:

SN     1 Saltsjobaden                                        PISY
SN     2 SWEDEN       Scots pine               5917N1818E          1733 2003
SN     3 Lars-Ake Larsson
SN001A  1923   341   374   369   298   500   382   396                   #   79  131   63  179  143  288  139
SN001A  1930   332   297   421   250   290   288   317   320   256   215 #  245  190  300   76  201  267  288  326  281  230
SN001A  1940   111   183   229   183   159   157   163   134   105   111 #  101  160  210  214  151  243  173   49  123  139
SN001A  1950    81    62    89   138   164   180   138   157   170   130 #   55   47  100  189  283   25  167  293  350   26
SN001A  1960   108   184   137   148   124   164    80    98   105    67 #  392  377  195  209   99  280  108  187  195  108
SN001A  1970    57    89   126   101   114   100    83    76    71    57 #  247  315  209  105  331  152   98  248  263  301
SN001A  1980   114    87    79    85    56    49    61    79    81    70 #  412  199  253   77  203  190  146  215  391  206
SN001A  1990    99   139   132   161   132   118   999                   #  518  345  278  369  229  163
SN001B  1923   329   375   319   299   435   366   384                   #   99  122   73  135  146  223  139
SN001B  1930   287   258   392   280   251   293   296   278   200   181 #  239  126  150  126  232  178  183  326  363  228

The ring width value of 1923 is 3.41 mm with the latewood being 0.079*3.41=0.27 mm.


Meta data

Meta data that is collect from e.g. a Heidelberg file can be written by CDendro to a .rwl file:

...
1AD0046A1500    54    64    64    67    64    54    61    71    78    81
1AD0046A1510    84    94   105    84   108   108   115    88   135   108
1AD0046A1520   111    98   121    94   138   118   111    94   108   105
1AD0046A1530   999
1AD0046A#### Location=Stockholm;  Species=PISY;  TreeNo=0;
1AD0046A#### CoreNo=0;  Project=123;

Naming standard

See CDendro naming standard

Limitations of the Tucson format

  • The amount of meta data is limited to what is specified for the three first lines of a .rwl file. Then we should also be aware that the syntax of that meta data is not very specified, i.e. in practice it will be almost free text.
  • If meta data is stored as comments with a special syntax, then we have to recognize that there is no common specification for how that meta data should be named and specified.
  • There is no specification on how Latewood and Earlywood should be stored within the same .rwl file.
  • There is no specification on e.g. a naming standard to allow for keeping radii from the same stem together, though see also CDendro naming standard

Notes

  1. ITRDB: brit9.rwl info
  2. ITRDB: brit045.rwl info
  3. ITRDB: brit5.rwl info
  4. ITRDB: ca535.rwl info
  5. ITRDB: fran009.rwl info
Personal tools