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Tucson format - Cybis Wiki

Tucson format

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'''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 [[extension]]s 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]].
+
'''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 [[extension]]s are used, such as .rwl, .crn, .tuc and .dec. (.crn is used for derivate chronologies with not exactly the same syntax). The name comes from the city of [[Tucson]] in [[Arizona]].
  
 
==Basics of the Tucson format for ring width data==
 
==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.  
 
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
+
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
 
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.  
 
of the line (4 digits) followed by ring width data, up to ten rings per line.  
Line 14: Line 14:
 
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)!
 
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.
+
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. See also Note 4 below!
  
<br/>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
+
<br/><b>Note 1:</b> 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!
 
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!
<br/>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.
+
<br/><b>Note 2:</b> 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.
<br/>Note 3: An ITRDB specification of the Tucson format is found here: [http://www.ncdc.noaa.gov/paleo/treeinfo.html] though that specification cannot be
+
<br/><b>Note 3:</b> An ITRDB specification of the Tucson format is available <ref>ITRDB's specification of the tucson format: http://www.ncdc.noaa.gov/paleo/treeinfo.html</ref>, 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.
 
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.
 +
<br/><b>Note 4:</b> It seems that Cofecha is handling these two marks differently: When Cofecha runs over a -999 value, then the series is broken into two series by this mark.
 +
While a "0" value seems to be handled as an "absent" value which is just omitted from correlations. CDendro from version 8.2 will have a setting to make
 +
missing values marked as "0" also in .rwl files having 0.01 mm measurement units.
 +
You can attain the same effect of unbroken series by changing the Decadal measurement unit to 0.001 mm in CDendro and again write out your series to a .rwl file
 +
before submitting it to Cofecha.
 +
 
<PRE>
 
<PRE>
 
PMkr12b 1781  120    87    69  122  108    85  125  114    77
 
PMkr12b 1781  120    87    69  122  108    85  125  114    77
Line 37: Line 43:
 
''The same sample written in 0.001 mm units. Note the missing data mark which is here "0".''
 
''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:
 
 
<pre>
 
<pre>
 
6682    1980  143  231  154  145  150  201  130  156  245  137
 
6682    1980  143  231  154  145  150  201  130  156  245  137
Line 48: Line 51:
 
''The usual ending and start of samples (0.01 mm units resolution)''
 
''The usual ending and start of samples (0.01 mm units resolution)''
  
 +
==Unexpected 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.
  
 
<pre>
 
<pre>
Line 59: Line 64:
 
<pre>
 
<pre>
 
Q 9730  990    72    98  112  124  107  132  137  145  114    80</pre>
 
Q 9730  990    72    98  112  124  107  132  137  145  114    80</pre>
''This snappet from brit045.rwl<ref>{{itrdb|brit045|europe}}</ref> looks very much normal, but ends with two Asciichar(13) characters which will not be trimmed away by the VB Trim function.''
+
''This snappet from brit045.rwl<ref>{{itrdb|brit045|europe}}</ref> looks very much normal, but ends with two Asciichar(13) characters which will not be trimmed away by the Visual Basic Trim function.''
  
  
Line 77: Line 82:
 
...
 
...
 
MWK401 -3550    26    21    19    20    28    21    13    11    -0    11  </pre>
 
MWK401 -3550    26    21    19    20    28    21    13    11    -0    11  </pre>
''Example from ca535.rwl<ref>{{itrdb|ca535|northamerica/usa}}</ref> where zeroes are filled into positions which are not in use and this with a -0 instead of 0 or -999 for missing rings.''
+
''Example from ca535.rwl<ref>{{itrdb|ca535|northamerica/usa}}</ref> where zeroes are filled into positions which are not in use and this with a -0 instead of 0 or -999 for missing rings. Each row also ends with a number of extra white spaces''
 +
 
 +
<pre>
 +
BG8    1920  324  693  690  700  1130  847  980  1143  680  566
 +
BG8    1930  548  671  907  1197  902  1169  969  862  1051  1125
 +
BG8    1940  549  361  496  767  782  168    38    -7    -7    -7
 +
BG8    1950  102  119    31    94  110    79  118  240  245  251</pre>
 +
''Example where "-7" has been used to indicate a missing ring.
 +
<br/>A comment from a CDendro user: <i>"To give an example of when negative values are used with a particular meaning, it is possible to fill in missing data in ARSTAN. The relevant setting fills in missing data if the data points are denoted with a negative number (excluding -9999). Data points with zero values do not get filled in."</i>
  
  
Line 90: Line 103:
 
See e.g. [ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/measurements/europe/germ011.rwl 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.
 
See e.g. [ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/measurements/europe/germ011.rwl 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"
+
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 "606 13:1" and "606 13:2"
 +
 
 +
 
 +
<pre>
 +
638003  1450  148  101  114    93    81    96  100    95    79    57
 +
638003  1460    78  119    78    86    89    64    89    89  101    99
 +
638003  1470    94  192  172  143    81  103    91  100  122  999
 +
638003    0    0    0    0    0    0    0    0    0    0    0
 +
638003    10    0    0    0    0    0    0    0    0    0    0
 +
638003    20    0    0    0    0    0    0    0    0    0    0
 +
638003    30    0    0    0    0    0    0    0    0    0    0
 +
</pre>
 +
''Example from swit177w.rwl. <ref>{{itrdb|swit177w|europe}}</ref> This is currently detected as a "jump in years" error by CDendro.
 +
Then CDendro supposed that the 999 meant a missing ring, though we could as well say that if a 999 is followed by a not anticipated
 +
year number, then that data section should be handled as a new member (a new sample) even when the member identity is not changed.
  
  
Line 111: Line 138:
 
...
 
...
 
</pre>
 
</pre>
''Example from the [http://sokl.joensuu.fi/saima/homepage3/lemola/ab/kinsys/lemoltu_.txt Finnish Tree ring data bank of Saima]
+
''Example from the [http://lustiag.pp.fi/Saima/homepage3/lemola/ab/kinsys/lemoltu_.txt Finnish Tree ring data bank of Saima]
 
''With this layout each "unused position" is marked with a dot (.).
 
''With this layout each "unused position" is marked with a dot (.).
 +
 +
 +
<pre>
 +
109540  1690    48    45    45    39    39    33    33    36    33    33
 +
109540  1700    36    30    33    27    36    39    36    39    36    39
 +
109540  1710    39    33    33    30    33    30  22.5  22.5  25.5  25.5
 +
109540  1720  25.5  31.5  34.5    30  37.5    45    39  37.5  40.5    36
 +
109540  1730    30  31.5  31.5  34.5    30    30  34.5  34.5    33    36
 +
109540  1740  31.5    30  25.5    27    30    30    24    30  999
 +
109550  1521  138  129  114    99    99  189  120  114  111
 +
109550  1530  111  105    99  102  105    96    90  102    81    93</pre>
 +
''A snappet from germ21.rwl.<ref>{{itrdb|germ21|europe}}</ref> This is the only case we have found with decimal values (like "22.5").
 +
<br>Note: The germ21.rwl file contains another severe error (a missing line of data) that makes it unreadable to CDendro.''
 +
 +
 +
<pre>
 +
cc321201  0    0  3934  2736  2620  4184  4334  4438  4790  4968  5330 wb     
 +
cc321201  10  5008  1796  4786  3940  2762  1870  1804  1912  1588  1874 wb     
 +
cc321201  20  2634  1840  1994  2120  3334  1252  1206  1362  4186  1938 wb     
 +
cc321201  30  2090  530  1594  2492  1686  2064  518  2854  1426  1652 wb     
 +
cc321201  40  774  1080  1130  1248 -9999                              wb     
 +
cc321202  0    0  5022  4404  5402  4176  5676  2666  6004  5212  4262 wb     
 +
cc321202  10  2206  2928  1894  2458  4806  2846  2880  2354  2318  2550 wb     
 +
cc321202  20  2028  2178  2054  2230  2492  1756  1892  2730  1948  1922 wb     
 +
cc321202  30  1334  2016  1386  2154  1708  4396  1336  1742  502  2868 wb     
 +
cc321202  40 -9999                                                      wb      </pre>
 +
''From measurements performed on a Velmex machine and saved as time series in a decadal format
 +
<br>(The " wb" word at end of each line made CDendro versions before 8.1.2 reject the data.)
 +
 +
 +
;Tucson data created from old Catras files
 +
<PRE>
 +
S00400791970  231  122  124  128  101  118  117  127  120  142
 +
S00400791980  106  117  124  144  122  117  117    99  131  115
 +
S00400791990  121    90 -9999  999
 +
S00400891828 -9999  325
 +
S00400891830  318  211  228  236  227  345  300  350  298  287
 +
S00400891840  222  208  262  259  221  216  255  327  309  255
 +
....
 +
S00400891970  185  172  211  200  143  208  203  208  185  206
 +
S00400891980  183  240  191  221  194  197  156  156  200  198
 +
S00400891990  219  211 -9999  999
 +
S00400991772 -9999 -9999 -9999 -9999  162  103  133  131
 +
S00400991780  101  141  237  233  207  132  121  222  198  206
 +
S00400991790  226  271  387  384  273  309  273  224  269  313
 +
S00400991800  230  246  290  233  274  199  145  162  180  213
 +
</PRE>
 +
''Example created by [[Convert5]] from files available in [[.cat]]-format in the [[ITRDB]], [ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/updates/contributions/christensen_denmark_oak/sverige/ christensen_denmark_oak/sverige/] (When CDendro opens such Catras files, all -9999 data is automatically removed.)
 +
 +
 +
;Tab- or Space-characters as field delimiters
 +
There are Tucson alike files with a tab-character as a delimiter between the fields.
 +
<br/>Also one or more space characters occur as a field delimiter, especially when a Tucson file has been read in from a printed document or a .pdf file
  
 
==CDendro interpretation==
 
==CDendro interpretation==
Line 166: Line 246:
  
 
===Meta data===
 
===Meta data===
Meta data that is collect from e.g. a Heidelberg file can be written by CDendro to a .rwl file:
+
Meta data that is collected from e.g. a Heidelberg file can be written by CDendro to a .rwl file:
 
<PRE>
 
<PRE>
 
...
 
...
Line 183: Line 263:
 
*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.  
 
*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.
 
*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 how [[Latewood]] and [[Earlywood]] should be stored within the same .rwl file. Within the ITRDB Latewood and Earlywood data is saved in separate .rwl files.
 
*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]]
 
*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]]
 +
 +
==The Tucson chronology .crn format==
 +
Citation from http://www.ncdc.noaa.gov/paleo/treeinfo.html
 +
<pre>
 +
Processed Data Files (Site Chronologies, File Extension .CRN)
 +
 +
These are the standardized tree-growth indices from a stand of trees, representing the mean growth observed for each year
 +
over the entire stand. Site chronologies are used in climate analysis. Data are stored as 3 or 4-digit numbers, with a value
 +
of 1000 representing mean growth, a minimum value of 0 (no growth), and no defined maximum. There is only one time series per
 +
file, in contrast to the raw data files. Missing value code is 9990. Site information is stored in the first 3 records of the file.
 +
 +
Format for chronology header records:
 +
 +
Record #1: 1-6 Site ID, 10-61 Site Name, 62-65 Species Code, optional ID#'s
 +
Record #2: 1-6 Site ID, 10-22 State/Country, 23-30 Species, 41-45 Elevation, 48-57 Lat-Long, 68-76 1st & last Year
 +
Note: lat-lons are in degrees and minutes, ddmm or dddmm
 +
Record #3: 1-6 Site ID, 10-72 Lead Investigator, 73-80 comp. date
 +
 +
Chronology Data, Records 4-??
 +
 +
Site ID# column 1-6
 +
Decade column 7-10
 +
Index Value-Sample Number* pairs of values, columns 11-80, 10(I4+I3)
 +
TRL ID#(optional) column 82-88
 +
 +
*Index Values, columns 11-14,18-21,25-28,32-35,etc
 +
# of samples used in calculating chronology, columns 15-17,22-24,29-31,36-38,etc.
 +
Example:1450 670 171018 17 897 18...
 +
Here, 670 is the ring-width index value for the year 1450, with a sample size of 17;
 +
1018 is the ring-width index value for the year 1451, with a sample size of 17;
 +
897 is the ring-width index value for the year 1452, with a sample size of 18
 +
 +
 +
Chronology Statistics, Last Record, Optional:
 +
Site ID# column 1-6
 +
Number of Years column 8-10
 +
First Order Autocorrelation column 13-16
 +
Standard Deviation column 19-22
 +
Mean Sensitivity column 25-28
 +
Mean Index Value column 29-35
 +
Sum of Indices column 37-44
 +
Sum of Squares of Indices column 46-53
 +
Max# of series column 62-63
 +
</pre>
 +
<b>Example:</b>
 +
<pre>
 +
ANEBY  1 Anebymossen                                        PISY             
 +
ANEBY  2 Sweden      Scots Pine        295M  5751 01438    __    1846 1996   
 +
ANEBY  3 Hans Linderholm                                                       
 +
ANEBYS18469990  09990  09990  09990  09990  09990  0 798  11495  1 779  1 976  1
 +
ANEBYS1850 869  1 984  11116  1 881  2 936  2 843  2 394  2 613  21538  21406  2
 +
ANEBYS18601466  2 967  21468  3 735  3 701  31041  3 776  31116  31271  3 804  3
 +
ANEBYS18701270  3 821  31034  4 772  4 818  41011  41067  41052  41073  61195  6
 +
ANEBYS18801523  71086  8 926  8 771  9 986  9 950  9 992  9 807  9 908  91041  9
 +
ANEBYS18901169  9 920  91274  91259  91074 10 974 101198 101208 111371 121022 12
 +
ANEBYS1900 774 121071 12 755 12 851 12 721 12 730 12 814 12 758 12 642 12 727 12
 +
ANEBYS19101101 12 987 13 830 14 731 141001 141022 14 991 14 701 14 992 141047 14
 +
ANEBYS1920 973 141158 141149 141212 14 960 16 978 17 992 17 957 17 660 17 498 17
 +
ANEBYS1930 539 17 679 17 774 17 903 171183 171261 171490 171603 181441 181407 19
 +
ANEBYS19401087 191163 191048 20 981 20 900 201398 201485 201044 21 900 211003 21
 +
ANEBYS1950 974 21 962 21 836 21 975 21 881 21 891 21 822 21 967 211093 21 905 21
 +
ANEBYS1960 702 21 843 21 803 21 829 21 901 21 900 21 908 211256 211256 211122 21
 +
ANEBYS1970 846 21 852 211198 211274 211026 211320 211507 211178 211384 211313 21
 +
ANEBYS19801232 211075 21 861 21 977 21 984 21 945 21 956 21 922 21 779 21 819 21
 +
ANEBYS1990 703 21 889 21 774 21 892 21 939 211097 21 820 219990  09990  09990  0
 +
</pre>
 +
''Example from swed314.crn<ref>[[ITRDB]]: [ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/europe/swed314a.crn swed314.crn]</ref> showing the structure of a chronology file.''
 +
 +
===CDendro interpretation===
 +
CDendro allows for storing extra comments in the header not only of ordinary .rwl files but also in .crn files.
 +
Example:
 +
<pre>
 +
NORRW  1 Norrland wood                                      PISY
 +
NORRW  2 Sweden      Scots pine              6300N1800E          1513 1874
 +
NORRW  3 Lars-Ake Larsson
 +
#Based on
 +
#A. samples from boards (outside wooden panel) of the Sandviken house, Vastanvik, Namdo.
 +
#B. a sample from a board in an old barn at Langholmen, Runmaro, an island east of Stockholm.
 +
#C. a house built in 1907 in Saltsjobaden (Palnasv 1)
 +
#The wood obviously seems to be imported from long way north of the Stockholm area.
 +
#CDENDRO_DC This chronology is intended for crossdating purpose only!  Standardization: NegExpDetrend SumByStem=Yes
 +
NorTrd15139990  09990  09990  01544  11752  11690  11225  11713  11345  11239  1
 +
NorTrd1520 823  11235  11489  11208  1 834  11265  11050  11416  11923  12001  1
 +
NorTrd15301797  12041  12305  12632  13319  13204  12575  13262  12438  12525  1
 +
NorTrd15401932  12727  12650  11674  21748  21832  21842  21856  21438  21350  2
 +
NorTrd15501305  21713  21395  21572  21233  21572  21531  21439  21546  31482  3
 +
......
 +
</pre>
 +
 +
==See also==
 +
See also [[:Category:Dendro data format|Dendro data format]]
  
 
==Notes==
 
==Notes==
 
<references/>
 
<references/>
 +
 +
[[Category: Dendro data format]]

Latest revision as of 12:25, 11 January 2017

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