Page History

...

• Ship (Don't try this on shore….!) http://web.ship.iodp.tamu.edu/apps/ Shore production http://web.iodp.tamu.edu/apps/ Shore test (only available to IODP staff) http://short.iodp.tamu.edu/apps/
• Anchor_GoBack_GoBackFollow your browser and operating system's instructions to install and launch the Java application.
• NOTE: Both Java and Apple safety protocols are being upgraded significantly almost every year. At some point we had to disable a default safety check in the Mac OS to be able to launch our latest Java apps. We are working to find out how to avoid that. In the meantime, IODP IT staff can help/advice with the work around.

...

Figure 1-1. SCORS Downloader user interface.

Image Added

Using the SCORS Downloader interface (Fig. 1-1):

...

Stratigraphic correlation specialists define a core composite depth below seafloor (CCSF) depth scale in the form of an affine table (example in Table 2-1; specifications in Appendix 1). Using different types of high-resolution data sets obtained from the cores recovered in multiple adjacent holes, each core is shifted to optimize alignment of stratigraphic features across the holes, assuming that the stratigraphy is a perfect "layer cake" across the holes. Even in cases where that assumption is true, in general not all stratigraphic features in two cores can be perfectly aligned because the cores are stretched and squeezed during the coring process. The SCS has to decide in which part of the core to establish the best alignment of features. As a rule of thumb, the alignment of features should be best where the SCS plans to establish a splice tie point, i.e., in the upper and lower parts of core intervals that will be used in the splice.
The affine table resulting from the shifting process is a list of all cores from the participating holes, each with a cumulative offset (m) relative to the default core depth below seafloor (CSF-A) depth scale, whereby:
CCSF_depth = CSF-A_depth + cumulative_offset
The cumulative offsets are usually positive (downhole direction), range from centimeters to tens of meters, and generally increase with depth.
Table 2-1. Affine table example, shown in spreadsheet view to facilitate view of content. The file must be in CSV text format for upload to the LIMS. Specifications for each column are given in Appendix 1.

Four methods are used to define core offsets and the applicable method can optionally be noted in the affine table (also see Table 2-2):

...

• ANCHOR - the top of one core from one of the participating holes is correlated to, or interpreted as, the seafloor reference. This is in general the only core not shifted relative to the CSF-A depth scale (zero offset).
• TIE - a core is shifted to align one or more stratigraphic features with those in a core from an adjacent hole that has (in general) already been shifted and is now considered the reference. If specific tie points are selected that link a specific stratigraphic feature between the two cores, the tie points have by definition the same CCSF-A depth. Any other stratigraphic feature may not have the exact same CCSF depth in the two cores because of physical squeezing and stretching of cores during drilling and recovery, or a stratigraphic architecture that is not a perfect layer cake.
• APPEND - features cannot be correlated between cores, and a core is shifted by appending the top of the cored interval to the bottom of the cored interval of the previous core in the same hole, as if no gap or overlap existed at the CSF-A scale. The appended core has the same cumulative offset as the previous core (zero differential offset).
• SET - features in a core cannot be tied to those in a core from an adjacent hole. A depth shift is applied based on some assumptions, most commonly the CCSF/CSF-A growth rate of the previous core in the same hole. This method is recommended over the APPEND option because it is more realistic, particularly in depth intervals where cores are expanding significantly.

Table 2-2. Shift types

In addition to the shift type, users can optionally indicate the data types used and the general quality of the depth shift for each core in the last two comment columns of the affine table (Table 2-1). Note that comments cannot contain commas because of the use of the CSV format, where commas are column delimiters. The SCORS Uploader will check and reject a correlation file if more commas exist than expected.
Short cores may not have had correlation data acquired, and data from cores disturbed or damaged by the drilling process may have been filtered during download with the SCORS Downloader. Those cores will not "appear" in the correlation data set and therefore not be used in the depth shifting process. Depending on the correlation tool used, they may not be present in the affine table unless manually added before uploading to the LIMS using the SCORS Uploader (see below). Correlation specialists need to be aware that if cores are not present in the affine upload file, they will not be included in the CCSF depth scale and therefore be missing in data reports. The uploader will check for the presence of all cores, and if one or more are missing, will prompt the user to add them to the affine table, or ignore them and be responsible for the consequences.
Core shifting and the affine table should be complete before splicing begins. If cumulative offsets of cores are adjusted after splice intervals for those cores have been defined, the splice intervals need to be revisited to ensure that no unintended gaps or overlaps persist in the splice.

...

The traditional process of defining the splice consists of using splice tie points, essentially tie lines that splice the bottoms of upper intervals with the tops of lower intervals at exactly the same CCSF depth. That process results in a splice tie point table (STPT) (Table 2-3), as published in many ODP and IODP Proceedings volumes. Although the STPT used to be the standard expression of a splice, it turned out to be inadequate when splices were discontinuous, i.e., all intervals could not be tied to one another because of coring gaps, drilling disturbance or inadequate data records. When scientists attempted to integrate the segments of a discontinuous splice (often referred to as "floating splices") to create a "complete but discontinuous splice" as the overall most useful stratigraphic framework for a site, they had to "fake" interval boundaries as ties in the STPT. Even in a continuous splice, the first and last interval could not be adequately defined in the STPT. This led to the computational routines in the IODP database to return unexpected and unpredictable results. Therefore, in the current implementation of SCORS, users can optionally upload their STPT files, but they are not used by the database internal computations.
Table 2-3. Example format of a splice tie-point table.

The splice interval concept

...

A more generic definition of a splice as a collection of splice intervals rather than tie points eliminates the restrictions of a STPT. Splice intervals are defined by the core (from a site and hole) that contains the interval, and the CCSF depths of the top and bottom boundary. This process results in the splice interval table (SIT) (example in Table 2-4; specifications in Appendix 2). Each splice interval is from one core only, however, more than one splice interval can theoretically be defined from the same core. The SIT has replaced the STPT as the correlation specialist's main deliverable, along with the affine table.
The SIT format also includes the section and offset for top and bottom boundaries, because those ultimately matter when investigators take sub-samples from the cores along the splice. We learned the hard way that a third application may not always compute section and offset correctly and therefore created the SCORS-QA applications to rectify that potential problem (see section 4).
Table 2-4. Splice interval table file example, given in spreadsheet view to facilitate view of content. The file must be in CSV format for upload to LIMS. Specifications for each column are given in Appendix 3.

Top and bottom of a splice interval can be determined in three ways:

...

This results in nine top-bottom combinations, or Splice interval types (Table 2-5), which can optionally be denoted in the SIT.
Table 2-5. Splice interval types.

Using the Correlator application

...

Figure 2-2. Data import opens in Generic Data window, where user may have to fill in the Data Type column by clicking on the header "Data Type" and selecting the appropriate item.

• Select appropriate items for the data columns.
• Mainly, you need to confirm or set the header of the first column if it is empty. Click on the header and select one of the listed data types.
• If a suitable data type is not available, create a data label using User define. (Fig. 2-3).
• In the case of User define, also click the Register box, which will add the name to the choice list. (Fig. 2-3).
• For the occasional column that has data and a question mark in the header, user typically needs to select Bottom Offset, or Depth.

...

Figure 2-3. Registering a data type not available in the Correlator choice list

• Click Import and the focus returns to the Data List tab where a data summary line is added.
• You may have to click on a parent item to expand the list (e.g., triangle in front of "Root" after importing the fist data file).
• The data are organized in a tree structure by site, data type, hole.
• Other lines without data are added such as Downhole Log Data, Image Data, etc., which is related to the original concept of Correlator as part of the Corewall suite (not relevant for JR operations).
• Keep right clicking in the Data List to add more data. See later for the other options that have now appeared in the context menu.
• Correlator also needs detailed section information so it can compute splice intervals correctly. Section files are automatically generated from LIMS with each Correlation Downloader download (a new, 2016 feature). To load a section file, right-click on Section Summary, then select Import Section Summary (Fig. 2-4).

...

ISSUE: Correlator currently only allows one section file to be uploaded. That means user has to concatenate the section files downloaded from LIMS for each hole (and simply name the resulting file "sections" or something). Then user has to delete the existing Section Summary before uploading the updated file.
A change request for Correlator to accept multiple section files is in the works.

Figure 2-4. In addition to the stratigraphic data, Correlator needs a section summary file.

Note that right clicking on highlighted Data List items brings up different context menus with several options (Table 2-6).

...

Table 2-6. Data List context menu items.

Load data for correlation

...

Figure 2-6. Filter options.

Shift Cores

To shift cores, you may want to select the Composite tab of the Display view to see the parameter sub-window. You can also get there using the Go to Composite button on the floating menu. If no data are displayed, switch to the Data Manager view and load a data type (see earlier section).
Note that you can shift cores even if you have not selected the Composite tab.
Several shift parameters are given in the parameter panel to the right (Fig. 2-7).

...

• Choose the Splice Interval tab in Display view, or use the Go to Splice button on the floating menu.
• This will show the parameter sub-window for splicing on the right (Fig. 2-8).
• Drag core data traces from the depth shift sub-window on the left to the splice window on the right side of the divider.
• Click on a core trace to make the splice interval top and bottom lines appear with handle dots and drag or toggle them to the desired splice interval boundary depths.
• The resulting splice interval table in the parameter window to the right shows the exact depth.

...

\[Oct 2016 discussion\] Dragging the core data traces over to the splice window seems redundant. Why not allow splice interval definition in the depth shift window and then display the resulting splice in the splice window?

...

\[Oct 2016 request\] Users would like the option of displaying section boundaries as this (a) helps identify core disturbance effects associated with section boundaries, and (b) helps users avoid setting splice interval boundaries very near section boundaries.

...

• A short form of the splice interval table, updated in real time as user defines intervals:
• Core: a combination of hole ID and core number.
• Top (m): interval top CCSF depth of the interval based on current affine.
• Bot (m): interval bottom CCSF depth of the interval based on current affine.

\[Oct 2016 discussion\] Having the short form of the splice interval table displayed in the parameter window is great; however, why not display the full SIT (as specified for export), as well as the affine table, preferentially as a floating window? Those tables are currently viewable as CSV text files (not as nice as in columnar form) by going to the Data Manager and using ~5 click actions.

• Interval Comments box: user can add a comment about the interval selection for the interval selected in the table – the comment will be exported with the splice interval table.
• Delete Interval @# button: removes the interval selected in the table.
• Tie Options: If two cores dragged into the splice area overlap (say A2 and B2), one or two of the following buttons become enabled:
• Top: Split A2 & B2 toggles with Tie A2 & B2 , with the notation on the splice interval top changing accordingly between Tie: A2 & B2 and B2 Top, respectively.
• Bottom: No Action if bottom of B2 interval dos not overlap with another core data trace, otherwise it works the same as Top.

\[Oct 2016 discussion\] It is not immediately clear what the buttons are trying to accomplish for the user; apparently, the buttons simply change the nomenclature for the same thing, namely a splice interval boundary. Perhaps this feature is

• Select Alternate Splice button opens a dialog where user can select one of multiple splices if multiple splices were previously created:
• CAUTION: "alternate" splice does not mean that this is a "secondary splice" that only uses intervals NOT used in the "primary" splice! It's just another splice.
• Data Type: User can select the data type for which to display the splice.
• Splice: user can select one among multiple splices.
• Save Splice… button brings up a dialog with the following options:
• Create New If you do this, you will see in the Data Manager window that the previous splice is automatically disabled.
• Update Existing is the typical choice.
• Cancel

Changing the affine during the splicing process

While on the Splice Interval tab, the depth shift display area on the left is still active and lets user define a shift using.

• If user clicks the Apply Shift button, a warning dialog appears:
• "Warning: This affine shift affects cores included in the current splice. These cores will be removed from the splice. Do you want to continue?" (No, Yes). (Fig. 2-8).
• If user chooses "Yes", the affected cores are removed from the splice sub-window.
• User then simply has to drag the affected core trace(s) back into the splice area and again define the top and bottom of the adjusted splice interval.
• If user chooses "No" and then cancels the shift TIE (e.g., via context menu), nothing changes.
• If user has at some point created an alternate splice, the cores with compromised splice interval boundaries are not removed from that splice. Only if and when user switches to that alternate splice using the Alternate Splice button will they find a surprise:
• "Error: Core B2: Applied affine shift (9.243) does not match shift in Splice Table (7.918), can't load splice."
• In any case, user should make sure the depth shifting is complete before spending the time selecting splice interval boundaries.

...

• .

As a result of completing issue C001 from September 2015, Correlator now has the precise information needed to draw section boundaries.
Figure 2-8. Display view with Splice Interval tab selected.
Image Added
Features in the parameter panel to the right (Fig. 2-8):

• A short form of the splice interval table, updated in real time as user defines intervals:
• Core: a combination of hole ID and core number.
• Top (m): interval top CCSF depth of the interval based on current affine.
• Bot (m): interval bottom CCSF depth of the interval based on current affine.

• Interval Comments box: user can add a comment about the interval selection for the interval selected in the table – the comment will be exported with the splice interval table.
• Delete Interval @# button: removes the interval selected in the table.
• Tie Options: If two cores dragged into the splice area overlap (say A2 and B2), one or two of the following buttons become enabled:
• Top: Split A2 & B2 toggles with Tie A2 & B2 , with the notation on the splice interval top changing accordingly between Tie: A2 & B2 and B2 Top, respectively.
• Bottom: No Action if bottom of B2 interval dos not overlap with another core data trace, otherwise it works the same as Top.

• Select Alternate Splice button opens a dialog where user can select one of multiple splices if multiple splices were previously created:
• CAUTION: "alternate" splice does not mean that this is a "secondary splice" that only uses intervals NOT used in the "primary" splice! It's just another splice.
• Data Type: User can select the data type for which to display the splice.
• Splice: user can select one among multiple splices.
• Save Splice… button brings up a dialog with the following options:
• Create New If you do this, you will see in the Data Manager window that the previous splice is automatically disabled.
• Update Existing is the typical choice.
• Cancel

Changing the affine during the splicing process

While on the Splice Interval tab, the depth shift display area on the left is still active and lets user define a shift using.

• If user clicks the Apply Shift button, a warning dialog appears:
• "Warning: This affine shift affects cores included in the current splice. These cores will be removed from the splice. Do you want to continue?" (No, Yes). (Fig. 2-8).
• If user chooses "Yes", the affected cores are removed from the splice sub-window.
• User then simply has to drag the affected core trace(s) back into the splice area and again define the top and bottom of the adjusted splice interval.
• If user chooses "No" and then cancels the shift TIE (e.g., via context menu), nothing changes.
• If user has at some point created an alternate splice, the cores with compromised splice interval boundaries are not removed from that splice. Only if and when user switches to that alternate splice using the Alternate Splice button will they find a surprise:
• "Error: Core B2: Applied affine shift (9.243) does not match shift in Splice Table (7.918), can't load splice."
• In any case, user should make sure the depth shifting is complete before spending the time selecting splice interval boundaries.

To delete a splice:

• Go to the Data Manager
• Right-click on the line item
• Select Delete.
• After user acknowledges the warning, the splice is deleted and all loaded data are cleared from the Display view. User has to re-load the data.

...

To load an affine table (Fig. 3-1):
Figure 3-1. SCORS Uploader user interface, Load affine tab.

1. On the Select affine table file line, click the Choose File button and navigate to the file in your directory.
2. Click Open/Load in your navigator
3. On the Select expedition that created the affine line, select the expedition (project) from the choice list. It will appear in the affine name.
4. Click Validate Affine button.

...

Figure 3-2. SCORS Uploader user interface, Manager tab.

LIMS internal computations

...

1. Create a corrected SIT file that has the same name as the input file plus the extension *.CORR. For each INPUT line, an OUTPUT line with corrected section-offset and CSF-A depths is computed and printed to the output CSV file. This output splice file will be suitable for upload to the LIMS. The following is the approximate sequence of tests and computations performed.

Create a copy of the input file where floating point values for offset and depth values are rounded to 1 mm precision fixed values. This should avoid issues with very small floating-point number differences in depth comparison tests. \[ONLY IF TRULY NEEDED\].
For each splice interval (INPUT line) in the input file:
Get all the sections for the given core. Each section record in LIMS has a stored CSF-A as well as CCSF depth (based on loaded affine table) for both top and bottom of section and the array of these four values per section will be used here.
Proceed with the following steps separately for top and bottom of the splice interval, respectively. 
Find the section that contains the given CCSF depth.
If the CCSF for the given core is smaller than the smallest section top depth, return message "ABOVECORE" in the output file. This will fail splice file upload and user needs to address the issue somehow.
If the CCSF for the given core is greater than the largest section bottom depth, return message "BELOWCORE" in the output file. This will fail splice file upload and user needs to address the issue somehow.
If two section IDs are returned because the CCSF corresponds exactly to the bottom of a section and the top of the subsequent section, select the section with the smaller section number.
For the section determined to be the correct one, compute
offset = CCSF(given) - CCSF(section_top).
Then compute CSF-A = CSF-A(section_top) + offset
Print the half-line to the output file. Repeat with the bottom of interval if this was the top.
Proceed with the next splice interval.
End.

1. Create a difference report file that has the same name as the input SIT file plus the extension *.DIFF. This will allow the user to review potential issues quickly and take action if needed. A corresponding screen view is also created.

...

Figure 5-1. SCORS Uploader user interface, Load splice tab.

Delete existing affine and CCSF scales in LIMS

...

Table 6-1. Description of List of affine tables report columns.

Affine tables report

This report provides the full affine table information, one core per row (Fig. 6-3; see Table 6-2 for descriptions of columns). Sample identity information (i.e., hole and core) and the cumulative offset for each core resulting from depth shifting, are derived directly from user-uploaded files. However, the CSF-A and CCSF depths as well as differential offset and growth rate are computed in LIMS, based on latest sample registry data for hole and core. The original, unaltered affine table user file can also be downloaded.
To get an affine table report (Fig. 6-3):

...

Table 6-2. Description of Affine tables report columns.

List of splice interval tables report

...

Table 6-3. Description of List of splice interval tables report columns.

Splice interval tables report

...

Table 6-4. Description of Splice interval tables report columns.

6.3. Alternate depths

This report feature provides CCSF alternate depth for any sample and data point in any data report that uses depth (CSF-A) as the primary independent variable. User must select the appropriate alternate scale for a report.
To retrieve CCSF depths with data (Fig. 6-6):

...

Appendix 1: Specifications for affine tables

Appendix 2: Specifications for splice interval tables