1. About Correlator 4

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The Correlator application facilitates stratigraphic correlation of cores from multiple holes at a drill site. Its features support for

• depth shifting of cores based on high-resolution core logging data, including images, to construct a core composite depth below sea floor (CCSF) depth scale; and
• splicing of selected core intervals to construct the most complete stratigraphic representation possible at a site. 

On the JOIDES Resolution (JR), the Correlator 4 application documented here is used in conjunction with other applications within the stratigraphic correlation support (SCORS) ecosystem (Fig. 1-1), which are covered in a separate user guide guides (Table 1-1). 

Figure 1-1. Stratigraphic correlation support (SCORS) applications. See Table 1-1 for brief descriptions.

Image AddedImage Removed

Table 1-1. Stratigraphic correlation support (SCORS) application documentation

Software application	Task	Documentation
Correlator	Stratigraphic correlation of cores from multiple holes at a drill site, by depth shifting cores using high-resolution core logging data and constructing a core composite depth below sea floor (CCSF) depth scale, and by splicing selected core intervals to construct the most complete stratigraphy stratigraphic representation possible at a site.	scors_correlator_ug_4.0_2022
Correlation Downloader	Download core logging data from the LIMS database, with automatic addition of section summary data required by Correlator, options to filter the data as appropriate, and a feature to append new core data to hole files.	scors_lims_ug_20190321.docx
SCORS Uploader and Manager	Load affine tables and splice interval tables created by an external application (e.g., Correlator) to the LIMS database where the information can be reported and applied to all data in LIMS.
LORE Reports for Stratigraphic Correlation	Provide (A) lists of existing affine tables and splice interval tables, with links to uploaded user files; (B) detailed, LIMS-computed affine and splice interval tables; (C) CCSF (alternate) depths for any data set in the LIMS; and (D) data sets by selected splice.
IMG_REDUX	Batch-download all cropped section-half images from a hole via LORE, then batch-process the images with IMG-REDUX R script, which crops the peripheral ~1 cm from the images, then reduces the image to <200 kb, ready for import in Correlator.

Version 4.0 was released on 31 March 2022. It can be downloaded at

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5. Construct the splice

5.1. Splice concepts

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5.2. Create a basic splice

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5.3. Insert a core into an existing splice

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5.4. Shifting cores that are already part of a splice

Concept and rules

Ideally, depth shifting should be concluded before a splice is assembled. However, life is not ideal and you may want to shift a core after you have constructed a splice. Because splice intervals are defined by their CCSF depths, shifting their cores invalidates the splice interval boundaries. A core shift results in a gap, an overlap, or both in the splice, depending whether a chain of tied cores or a single core are shifted, and whether the core(s) are shifted up or down. Correlator will deal with each situation in a clearly defined manner and provide you with relevant information.

Splice intervals boundaries are specified relative to the CCSF depth scale defined by the core sifts. The reason we select a certain core interval as being a splice interval is based on our interpretation of core quality based on the proxy data used to correlate the cores. The interval is therefore intrinsically defined by the the core-section-offset-in-section identity. When we shift cores we want to preserve that intrinsic splice interval. Therefore:

• Rule 1: Splice intervals are shifted with the cores they are associated with.
  • This inevitably creates at least one gap or one overlap in splice intervals.
• Rule 2: Overlaps in splice intervals are automatically resolved by 'clipping' the redundant part of the interval that is shifting.
  • We can do that because both overlapping intervals were approved as suitable for the splice and which one to use is typically a toss-up. You can always move the spice interval boundary very easily if that is not your desired solution.
  • The core-section-offset identity of the clipped splice interval boundary is reverse-computed from the CCSF depth to the CSF-A depth, from where the offset (cm) from top of section is obtained.
• Rule 3: Gaps created by the shifting of splice intervals are left open and you need to go and close them.
  • We prefer not to do that automatically because the interval needed to close the gap has not explicitly been assigned to the splice.

Example

Here is an example of your options and the program's responses when you shift cores that are part of a splice.

Case 1: Shift chain down

'This core and all related cores below' down

• You define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m shallower than the REF tie point in A3. This means the SHIFT core will shift down (Fig. X).
• You select “This core and all related cores below”
• The program asks for confirmation of the action (Fig. X), and assuming you OK it:
  • Replaces the previous tie with the new tie and shifts core B3 with all related cores from all holes that are deeper than REF core A3 downwards by dz m, maintaining all ties below the new one.
  • Shifts all splice intervals from from the shifting cores downwards by dz.
  • Creates a gap of length dz between splice intervals A3 and B3 and extends the CCSF scale by dz m.
• You cover the splice gap with a segment from either core A3 or B3, or partially with segments from both cores - it is up to you to decide.

Fig. X. Dialog for repairing a splice gap 

Figure X. Dialog for non-existent core interval. 

• • This solution is not valid, interval boundary falls outside the core.
  • Click the OK button and you return to the four options.

• The third option on the menu allows users to cover the gap with a combination of extensions from both splice intervals using the normal interactive splicing interface.
• The final option cancels the shift and nothing happens to cores or splice intervals.

Case 2: Shift chain up

'This core and all related cores below' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m deeper than the REF tie point in A3. This means the SHIFT core will shift up (Fig. X).
• Select “This core and all related cores below” and click OK.
  • Results are analogous to those described in previous case.
• Because this action has shortened the CCSF scale, an overlap is created at the top of the splice interval representing the shifted cores. The overlap can be removed completely with a segment from either core A3 or B3, or partially with segments from both cores - it is up to you to decide. Correlator offers you the options in a pop-up window (Fig. X).

Figure X. Dialog for repairing a splice overlap. 

• • "This shift creates an overlap in the splice. How do you want to proceed?’
    • Clip the splice interval from core A3
    • Clip the splice interval from core B3
    • Leave the overlap and let me fix the splice manually
    • Cancel shift

• The first two options apply an “auto-fix”.  The calculated sample identity is validated and if the section-offset doesn’t actually exist in the same core, an error dialog is presented (Fig. X).

Figure X. Dialog for non-existent core interval.

• • This solution is not valid, interval boundary falls outside the core.
  • Click the OK button and you return to the four options.

• The third option on the menu allows users to remove the overlap with a combination of clipping parts from both splice intervals using the normal interactive splicing interface.
• The final option cancels the shift and nothing happens to cores or splice intervals.

Case 3: Shift single core down

'This core only' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m shallower than the REF tie point in A3. This means the SHIFT core will shift down (Fig. X).
• Select “This core only” and click OK:
  • Replaces the previous tie with the new tie and shifts core B3 downwards by dz m.
• Because this action has not changed the total length of the CCSF scale, a gap is created at the top of the core and an overlap is created at the bottom of the core. The gap and overlap can each be repaired in two ways (see the first two cases) and Correlator therefore simply reminds you to do so yourself using the normal splice interface, or cancel the shift (Fig. X):

Fig. X. Dialog for repairing a single core splice gap and overlap.

• • "This shift creates a gap and an overlap in the splice. The splice interval associated with this core is therefore deleted and you need to splice it in again".
  • Cancel shift

Case 4: Shift single core up

'This core only' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m deeper than the REF tie point in A3. This means the SHIFT core will shift up (Fig. X).
• Select “This core only” and click OK:
  • Replaces the previous tie with the new tie and shifts core B3 upwards by dz m.
• Because this action has not changed the total length of the CCSF scale, an overlap is created at the top of the core and a gap is created at the bottom of the core. The gap and overlap can each be repaired in two ways (see the first two cases) and Correlator therefore simply reminds you to do so yourself using the normal splice interface, or cancel the shift (Fig. X):

Fig. X. Dialog for repairing a single core splice gap and overlap.

• • "This shift creates a gap and an overlap in the splice. The splice interval associated with this core is therefore deleted and you need to splice it in again".
  • Cancel shift

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A splice is constructed by selecting cores from multiple holes that were stratigraphically aligned relative to a common core composite depth below seafloor (CCSF). The specification of the splice interval boundaries, where a core interval from one hole is spliced to a core interval from another hole, is a subjective matter. Ideally the splice interval boundaries are at positions where high-resolution stratigraphic features are at the same CCSF depth. This is the reason why the choice of splice interval boundaries should be on the correlation specialist’s mind when selecting TIE points in the depth shifting process.
Basic rules: 
•    A splice interval can only consist of one interval from one core.
•    A splice is always based on one specific affine table (and the CCSF depth scale derived from that affine). Correlator fully protect you from associating a splice table with an incompatible affine table. However, if you are loading an incompatible affine table with a splice table, Correlator will through an error, as shown later.

5.2. Create a basic splice

Before starting to splice, go to the Preferences control panel and make sure that
•    the Show Splice window partition check box is checked so plot area for the splice is enabled. 
•    The Independent Splice scroll bar check box is un-checked (unless you really fancy looking at different depth intervals in the two plot partitions).
Then switch to the Splice Interval tab to show the control panel for splicing on the right side of the plot window (Fig. 4-21).
Next, repeat the following for each core you want to include in the splice:
•    Drag core data traces from the depth shift window partition on the left to the splice window partition on the right side of the divider.
¿    The part of the trace covering a depth interval not yet covered by a previous core is added to the splice, in blue, resulting in a default splice where each interval extends to the bottom of the core.
•    To highlight the splice interval that was added, click on the splice trace (Fig. 4-21)
¿    The highlighted interval turns green.
¿    The trace of the entire core is added to the right in red for reference.
¿    The top and bottom boundaries of the splice interval appear with handle dots.
Figure 4-21. Core traces dragged into the splice partition turn blue. To highlight one, select it and the lower part that was spliced to the previous core turns green. At the same time, the entire core trace appears in red for reference.
 
•    The default splice boundaries are usually not the desired ones as they are exactly at the bottom of cores. 
¿    Try to drag any of the lower interval boundary dots down. It will turn red and say “Bottom of Core X”
•    To move the splice interval boundaries to the desired depth, drag or arrow the boundary button up (Fig. 4-22). 
¿    The resulting splice interval table in the control panel to the right shows the exact depth.
¿    Note how the labels on the plotted splice interval boundaries change to indicate the top and bottom of a core if you drag them far enough.
¿    This is where the user may want to align splice interval boundaries with the appropriate white TIE arrows in the depth shift window.
Figure 4-22. Drag the upper interval boundary up to desired splice depth. Compare with previous figure.
 
•    For each addition of a core to the splice, a record will be added to the Splice Intervals table on the control panel, which is a short form of the formal splice interval table that will ultimately be saved. The table has the following three columns (Fig. 4-22):
¿    Core: a combination of hole ID and core number.
¿    Top (m): splice interval top CCSF depth of the interval based on current affine.
¿    Bot (m): splice interval bottom CCSF depth of the interval based on current affine.
•    The interval selected in the display is selected in the table and vice versa.
•    Interval Comments: A text box where users can add a comment about the selected interval. The comment will be exported with the splice interval table.
•    Delete Interval <X> button: removes the selected splice interval.
NOTE: Correlator doesn’t care from which data type you drag a trace, it simply uses whatever trace you drag over. It normally makes sense to drag traces from only the same data type. In the end, any data type can be retrieved by splice.

5.3. Insert a core into an existing splice

You may have created a tentative splice using cores from holes A and B, and now that depth-shifted cores are available from hole C you would like to splice some of them in, or you simple decided on better interval from another core. If you try to drag a core over an existing  splice, Correlator simply won’t add it because no more than two overlapping core intervals can be in any one splice depth interval. You first need to create a gap, which requires you to split the splice.

To create a gap and insert a new core interval:

• Select a splice interval that overlaps in depth with the core you want to insert.
• Note the labels at the top and bottom splice interval boundaries, respectively, on the splice plot (Fig. 4-22):
• Tie D6 & A6
• Tie A6 & B6
• Also note the corresponding buttons in the control panel, which offer the user the option of splitting the splice either at the top or the bottom of the splice interval:
• Top: Split D6 & A6
• Bottom: Split A6 & B6
• Say you decide to Split D6 & A6, the following happens:
• the label in the plot changes to A6 bottom.
• the button changes to Bottom: Tie A6 & B6, which would allow you to revert the split.
• Now you can simply drag the new core D7 into the splice area, select the splice intervals, and adjust top and bottom boundaries. Alternatively, you can first move the A6 bottom up to create a visible gap and then drag the trace of core D7 into the splice area.

Figure 4-31. Create a gap to insert an interval from Core A3 into the splice.

Figure 4-32. Insert Core A3 into the gap.

5.4. Shifting cores that are already part of a splice

Concept and rules

Ideally, depth shifting should be concluded before a splice is assembled. However, life is not ideal and you may want to shift a core after you have constructed a splice. Because splice intervals are defined by their CCSF depths, shifting their cores invalidates the splice interval boundaries. A core shift results in a gap, an overlap, or both in the splice, depending whether a chain of tied cores or a single core are shifted, and whether the core(s) are shifted up or down. Correlator will deal with each situation in a clearly defined manner and provide you with relevant information.

Splice intervals boundaries are specified relative to the CCSF depth scale defined by the core sifts. The reason we select a certain core interval as being a splice interval is based on our interpretation of core quality based on the proxy data used to correlate the cores. The interval is therefore intrinsically defined by the the core-section-offset-in-section identity. When we shift cores we want to preserve that intrinsic splice interval. Therefore:

• Rule 1: Splice intervals are shifted with the cores they are associated with.
  • This inevitably creates at least one gap or one overlap in splice intervals.
• Rule 2: Overlaps in splice intervals are automatically resolved by 'clipping' the redundant part of the interval that is shifting.
  • We can do that because both overlapping intervals were approved as suitable for the splice and which one to use is typically a toss-up. You can always move the spice interval boundary very easily if that is not your desired solution.
  • The core-section-offset identity of the clipped splice interval boundary is reverse-computed from the CCSF depth to the CSF-A depth, from where the offset (cm) from top of section is obtained.
• Rule 3: Gaps created by the shifting of splice intervals are left open and you need to go and close them.
  • We prefer not to do that automatically because the interval needed to close the gap has not explicitly been assigned to the splice.

Example

Here is an example of your options and the program's responses when you shift cores that are part of a splice.

Case 1: Shift chain down

'This core and all related cores below' down

• You define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m shallower than the REF tie point in A3. This means the SHIFT core will shift down (Fig. X).
• You select “This core and all related cores below”
• The program asks for confirmation of the action (Fig. X), and assuming you OK it:
  • Replaces the previous tie with the new tie and shifts core B3 with all related cores from all holes that are deeper than REF core A3 downwards by dz m, maintaining all ties below the new one.
  • Shifts all splice intervals from from the shifting cores downwards by dz.
  • Creates a gap of length dz between splice intervals A3 and B3 and extends the CCSF scale by dz m.
• You cover the splice gap with a segment from either core A3 or B3, or partially with segments from both cores - it is up to you to decide.

Fig. X. Dialog for repairing a splice gap 

Figure X. Dialog for non-existent core interval. 

• • This solution is not valid, interval boundary falls outside the core.
  • Click the OK button and you return to the four options.

• The third option on the menu allows users to cover the gap with a combination of extensions from both splice intervals using the normal interactive splicing interface.
• The final option cancels the shift and nothing happens to cores or splice intervals.

Case 2: Shift chain up

'This core and all related cores below' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m deeper than the REF tie point in A3. This means the SHIFT core will shift up (Fig. X).
• Select “This core and all related cores below” and click OK.
  • Results are analogous to those described in previous case.
• Because this action has shortened the CCSF scale, an overlap is created at the top of the splice interval representing the shifted cores. The overlap can be removed completely with a segment from either core A3 or B3, or partially with segments from both cores - it is up to you to decide. Correlator offers you the options in a pop-up window (Fig. X).

Figure X. Dialog for repairing a splice overlap. 

• • "This shift creates an overlap in the splice. How do you want to proceed?’
    • Clip the splice interval from core A3
    • Clip the splice interval from core B3
    • Leave the overlap and let me fix the splice manually
    • Cancel shift

• The first two options apply an “auto-fix”.  The calculated sample identity is validated and if the section-offset doesn’t actually exist in the same core, an error dialog is presented (Fig. X).

Figure X. Dialog for non-existent core interval.

• • This solution is not valid, interval boundary falls outside the core.
  • Click the OK button and you return to the four options.

• The third option on the menu allows users to remove the overlap with a combination of clipping parts from both splice intervals using the normal interactive splicing interface.
• The final option cancels the shift and nothing happens to cores or splice intervals.

Case 3: Shift single core down

'This core only' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m shallower than the REF tie point in A3. This means the SHIFT core will shift down (Fig. X).
• Select “This core only” and click OK:
  • Replaces the previous tie with the new tie and shifts core B3 downwards by dz m.
• Because this action has not changed the total length of the CCSF scale, a gap is created at the top of the core and an overlap is created at the bottom of the core. The gap and overlap can each be repaired in two ways (see the first two cases) and Correlator therefore simply reminds you to do so yourself using the normal splice interface, or cancel the shift (Fig. X):

Fig. X. Dialog for repairing a single core splice gap and overlap.

• • "This shift creates a gap and an overlap in the splice. The splice interval associated with this core is therefore deleted and you need to splice it in again".
  • Cancel shift

Case 4: Shift single core up

'This core only' up

• Define a new tie from REF core A3 to SHIFT core B3 where the tie point in SHIFT core B3 is dz m deeper than the REF tie point in A3. This means the SHIFT core will shift up (Fig. X).
• Select “This core only” and click OK:
  • Replaces the previous tie with the new tie and shifts core B3 upwards by dz m.
• Because this action has not changed the total length of the CCSF scale, an overlap is created at the top of the core and a gap is created at the bottom of the core. The gap and overlap can each be repaired in two ways (see the first two cases) and Correlator therefore simply reminds you to do so yourself using the normal splice interface, or cancel the shift (Fig. X):

Fig. X. Dialog for repairing a single core splice gap and overlap.

• • "This shift creates a gap and an overlap in the splice. The splice interval associated with this core is therefore deleted and you need to splice it in again".
  • Cancel shift

5.5. Manage splice tables

Loading splice tables
The basic functions and dialogs to save, enable and disable, load, export and import, or delete splice tables works in principal the same way as for affine tables, described in the section Manage affine tables.
Two important exceptions exist for loading splices:
•    Splice tables remember the data type used for each splice interval when the splice is created and saved. If all data types used in a splice are not enabled in the Data Manager, loading that splice will fail with the message in Fig. 4-51.
•    Splices remember the core offsets at the time the splice is created and saved. This means a splice has always one compatible affine table and if you are trying to load an incompatible affine or splice you will get the warning in Fig. 4-52. Unfortunately, spices and affines are not  associated in Correlator and it is up to the user to keep track of who matches who. 
¿    However, Correlator does help you keep a quasi-association by using the same number in the file names of the affine and splice tables if you choose to Create New on the save dialog.
Figure 4-51. Message displayed when you are trying to load a splice and a data type used to make the splice is not enabled.
 

Figure 4-52. User is trying to load a splice that was saved/exported with a different offset for core B2 than the offset of core B2 in the currently enabled affine table.
 

Exporting and importing splice tables
If you export affine and splice tables, you give them a name, and Correlator adds extensions *. affine.csv and *.sit.csv, respectively. It is advisable that you assign names to these files that make sense as the files will ultimately be uploaded to, and available from the LIMS database. In particular, use a naming scheme that helps you and others recognize associated affine and splice tables. 
When you import an affine or splice table, be aware that Correlator will rename the files according to its internal rules.
•    It will ignore your name.
•    It will use the expedition, site and hole number information according to the data in your folder.
•    It will add the extension *.#.affine.table and *.#.sit.table, respectively, where # is an incremental number relative to the existing tables in the Data Manager. This is the way Correlator keeps track of things.
Select alternate splice feature
On the Splice Cores tab, you’ll find a button Select Alternate Splice. This feature allows you to view another, existing splice in the third (right-most) splice plotting track. You will probably have to expand your splice window width to see that column.
When you click the button, you get the dialog in Fig. 4-53. You can specify a data type and a splice.
•    Data Type: you can select any data type currently loaded and plotted in the Display. 
•    Splice: you can select one of splices listed in the Data Manager.
¿    CAVEAT: If you select a splice that is not compatible with you currently enabled affine table, you will get the Message in Fig. 4-52. This means this feature is mainly useful to display the current splice with a different data type than the one used to create the splice in the leftmost splice track.
Figure 4-52. Loading a different existing splice.
 

Alternatively, you can Go to Data Manager, open the Saved Tables tree, enable another splice and its associated affine table, and reload the tables.