Stratigraphic correlation support (SCORS) User Guide
Peter Blum, 8 October 2016

Introduction

Stratigraphic correlation in the context of JOIDES Resolution shipboard operations refers to the construction of a core composite depth below sea floor (CCSF) depth scale for multiple adjacent holes, and a sampling splice composed of core intervals from multiple holes at a site. The CCSF depth scale overcomes many of the inadequacies of the original core depth below sea floor, method A (CSF-A) depth scale. The CSF-A scale is unique to each hole and derives from the length that the drill string advanced. In perfect layer cake stratigraphy, a stratigraphic feature has different CSF-A depths in each hole by up to a few meters because of ship heave (not compensated for in APC coring), tidal variations in sea level, and other sources of error. Furthermore, soft sediment cores regularly show core expansion due to stretching during coring, and elastic rebound and gas expansion upon recovery, resulting in "stratigraphic overlap", or >100% recovery. This means the bottom of an expanded core extends beyond the top of the next core at the CSF-A depth scale. In addition, we know from many multi-hole sites that in fact recovery gaps exist between cores as a result of the coring process, typically ranging from 0.5-2 m. To make things worse, the top of most cores is contaminated with material that fell from the borehole walls into the bottom of the hole and is stratigraphically useless (typically 10-40 cm). It is therefore impossible to recover a complete stratigraphy in a single hole and the most effective approach to achieve a continuous section is to develop a CCSF scale from multiple holes.
Shipboard stratigraphic correlation can be broken down into four (optionally, five) processes, each supported with specific software applications (Figure 1).
1: Download correlation data from the expedition (LIMS) database using the SCORS Downloader.
2: Correlate the downloaded data to create affine table and splice interval table (SIT) files. The affine table file results from depth-shifting cores relative to the CSF-A scale and is used to define a CCSF scale in LIMS. Because of core expansion, the CCSF depths are typically 10%–15% deeper than their CSF-A depths. The SIT results from defining core intervals that best represent the stratigraphy of a site when spliced together. This task is accomplished using the Correlator application or any other program of choice as long as the affine and SIT files are produced to LIMS specifications.
3: Upload affine table (and SIT) to the expedition (LIMS) database. LIMS internal computations store the cumulative offset of each core in the relevant database table and create a CCSF depth scale that can be applied to any data in LIMS.
4: (Optional) (A) Take the user-defined SIT file and use the top and bottom depth (CCSF) of each splice interval to compute core, section, offset, and CSF-A for a "corrected" SIT file (.CORR). Also create a difference report (.DIFF) if any of the aforementioned information is inconsistent between input and output files. This task is accomplished with the SpliceFileFixer program developed to correct and diagnose errors that originated in an earlier version of Correlator. This step is optional now that this aspect of Correlator has been fixed. (B) Upload the (corrected) SIT to the expedition (LIMS) database. LIMS internal computations store identities of the splice interval boundaries in the relevant tables so data can be retrieved by splice.
5:Use LIMS Reports to retrieve uploaded files and LIMS-computed data sets: (A) Lists of existing affine tables and splice interval tables, with links to uploaded user files, as well as the detailed, LIMS-computed affine and splice interval tables; (B) CCSF (alternate) depths for any data set; (C) data sets by selected splice.
Figure 1: Overview of SCORS tools and data flow, and the processes they are associated with. Blue shapes are JRSO supported user applications extracting and/or loading data from/to the LIMS database. Yellow shapes are data files. The green shape is the actual wiggle correlation tool, which may be a generic tool such as Excel, a custom tool such as Correlator, or any application users choose, and which interacts with the LIMS via files that must meet content and format specifications.
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Scientists preparing before the cruise on shore can:

• Download correlation data from shore database using the SCORS Downloader;
• Create affine and splice interval tables (SIT) using the Correlator app (or other program);
• Run the optional Splice File Fixer (SFF) to verify that the SIT information is correct.
• Explore the LORE reports for past expeditions' stratigraphic correlation data.

Users cannot upload affine and splice tables to the LIMS on shore because implementing the required "sandbox" is currently too costly. However, if the SFF yields no (significant) differences, the upload is guaranteed not to be a problem.

1. Download correlation data (SCORS Downloader)

Features of the SCORS Downloader application

With the SCORS Downloader, you can:

• Select any of the data types (components) in LIMS against CSF-A depth.
• For each data type, filter data to minimize effects of drilling, core handling, and measurement system issues on correlation:
• Eliminate outliers by specifying minimum and maximum values; this culls data points affected by extreme core disturbance or detector related issues.
• Eliminate data affected by the section edges by specifying a distance in cm applied to both top and bottom of section. Note: the distance applied to the bottom of the section is based on the section length last saved, which may vary from the section length at the time of measurement. Changes in section lengths as a result of the splitting process and/or continued core expansion are not uncommon but typically in the range of 1-2 cm).
• Optionally split the data file by instrument in cases where the same data type is collected on multiple instruments.
• Append a core's worth of data to the hole file to save significant data download time;
• Apply an external culling file that lists intervals identified as "bad data" by the science party, based on any information available;
• Save all selection and filtering parameters in a control file so they can be re-applied with the next download.

A Java Runtime application is provided with a user interface that allows the user to set all filter parameters, specify an external interval cull file, save everything to a control file, and download the files. The control file is JASON text file. If users decide that they prefer to edit that file directly and bypass some of the interface provided, IODP will not support any troubleshooting.

Software installation and setup

1. Download the Correlation Downloader application from JR-SO web site.

• 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/

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• Follow 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.

1. Log in with your credentials, if required, using Change user button.

• Ship: No login required, follow shipboard staff instructions.
• Shore: Moratorium credentials are required to access data within 1-year moratorium period.

Figure 1-1. SCORS Downloader user interface.

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

1. You can optionally Load a data control file if the SCORS Downloader generated the file in an earlier session. It contains all settings last saved by the user/owner of the file. Note: The file is not managed in LIMS; it is up to the user to keep it on a local drive.

• Use the Browse button to navigate your directory.
• Click the Load button to set the control file configurations.
• The data type and sample parameters tables are populated with the values from the control file.
• If previously saved parameters are fine, nothing else needs to be done. Proceed to 4. Apply external interval culling file area.

1. If changes to data type parameters need to be made, use the Select data type panel.

• Two windows/tabs are available, use the appropriate one to specify analysis/component to be downloaded:
• Quick select lists the data types typically used for stratigraphic correlation.
• Generic select allows user to select any data parameter available in the LIMS database – this should rarely be needed.
• Regardless of your parameter selection, each download will always update a Sections file in your specified download directory. This is a list of the sections corresponding to the sample range selected in the Select sample area (see below) with their length as well as top and bottom CSF-A depths. The Correlator (or equivalent) application can use this table to compute accurate splice interval boundaries (see next section).
• A special feature exists in the Quick select list: Drilling Disturbance Observations.
• This selection generates a table file with rows of sample identities (expedition, site, hole, core, type, section top offset, bottom offset) and CSF-A depths, every 0.5 cm for the interval corresponding to the samples selected in the Select sample area (see below). In addition, the table has two columns for Disturbance intensity and Disturbance flag, respectively, with the values subsampled every 0.5 cm from the two corresponding DESClogik parameters logged by core describers. These table values can then be plotted in Correlator and used to assess visually the effect of drilling disturbance on the core logging data.
• Select the data type (component) you want to add to the filter.
• Note: If the data type already exists in the settings display panel to the right, it must be removed using the Remove button before it can be added with new filter parameters. This is to avoid that multiple data files with different filters exist and are downloaded.
• While the data type (component) is selected, set the filter parameters:
• Consider the Split by instrument option.
• In a few cases, a data type (e.g., GRA density, magnetic susceptibility) may have been collected on multiple instruments (e.g., two core loggers). By default, one file is created for all data, assuming the data are comparable for all practical purposes. If you want to split the data into separate files per instrument, click this checkbox.
• Set the following optional filters as needed:
• Set minimum value in units reported for this parameter;
• Set maximum value in units reported for this parameter;
• Set section top trim as an interval (cm).
• Set section bottom trim as an interval (cm).
• Set "# of measurements" to be trimmed from top and bottom ends of section.
• Check "Exclude curated section end points" to eliminate measurements taken near the end caps, with irregular edge and useless results.
• Check "Exclude measurements past section curated length" to eliminate 'data overlaps' created when sections continue to 'grow' while being processed through the lab.
• Click Add button to add the parameter with its settings to the Settings panel.
• Note: If you want to change the filter settings for a data parameter, first select the row with the previous settings and use the Remove button, then configure and add the new settings.

1. If changes to expedition, site, hole, and/or core are needed, use the Select sample panel.

• Enter site, hole (and core) selection in the sample selector to the left.
• Click the Add button to add the selection to the Settings panel.
• Note 1: You can specify only one hole or one core at a time and add them to the Settings panel. Each row in the settings table will generate a file for each data parameter. You can add as many rows as needed.
• Note 2: If you want to change the site, hole, core settings, first select the row with the previous settings and use the Remove button to remove them from the configuration table, then configure and add the new filter settings.
• IMPORTANT: If you want to append the data for a core to an existing hole file (to avoid redundant downloading of same data), check the Append core data to hole check box.

1. In the Apply external interval culling file area, user has the option to select and apply a list of intervals for which the data shall be culled. The intervals may originate from any source of information in any of the labs, and are entered by assigned users via Excel or a text editor.

• About the file:
• Users keep the file on a local drive.
• The file layout has to follow the following column format: Site, Hole, Core, Coretype, Section, Top (cm), Bottom (cm), Comment(s).
• The format must be CSV.
• To apply the culling file:
• Click the Browse button, navigate your directory, and select the file. The file and its path will be saved in the data control file so updated versions can easily be used in iterative data downloads.
• Click the Apply check box if you want the interval data to be culled.
• Click the Remove button to remove the path the file if you want to browse to a different file.

1. Option: use Save control file button to save the latest changes.

• The message "unsaved changes" appears in red next to the button if filter parameters were changed but not saved to the control file.
• You don't need to save the parameters to the control file. The download will use whatever parameters are in the Settings display panels.
• You can keep multiple data control files on your local computer to choose from in future downloads.

1. Use Download correlation data button to download the data file(s).

• A directory browser window will open where you can set the location for the file to be stored.
• The download files are in CSV format.

2. Create affine table and splice interval table files

Process overview

Creating affine table and splice interval table files (the correlation files in short) is the essence of the affine-based stratigraphic correlation process, and the primary task of the stratigraphic correlation specialist (SCS) aboard the JR. Two sub-tasks must be completed in sequence:

1. Depth shifting of cores from multiple holes in a way that optimizes correlation of stratigraphic features across the holes.
2. Definition of splice intervals that result in the most complete stratigraphic representation possible.

The depth shifting and splicing tasks, which have been carried out on numerous paleoceanographic expeditions with the JR over the past 25 years, can be accomplished with various user-selected software tools. The following tools have been used in the past several years:

• Correlator, an application created specifically for that purpose by Lamont-Doherty Earth Observatory (LDEO) staff, based on the Splicer application used in the 1990s and until ~2006. Correlator is undergoing some significant upgrade development since late 2015 under a contract agreement between the JRSO and University of Minnesota, and is described below.
• Microsoft Excel, configured in each case by a SCS with multiple sheets for displaying the various correlation data types, shifting cores and creating the affine table, and splicing core intervals and creating the splice interval table.
• Other custom scripts and program configurations, Inc. Matlab, Igor Pro, etc., to accomplish the same.

Construction of the composite depth scale and the selection of splice intervals have a significantly subjective aspect. Scientific parties usually place a large degree of confidence into the shipboard SCS to accomplish these tasks to the satisfaction of the scientists, who use the splice for integrated subsampling and postcruise analysis of the cores. The basic rules, terminology and specifications provided here aim at providing a robust depth scale and splice support structure while at the same time strengthening correlation specialists' confidence in serving the science party and the science parties' confidence in the methods and the reliability of the results.
The affine-based correlation and splicing process by definition creates a stratigraphic section from a selection of core intervals and therefore leaves non-splice intervals in most cores from the holes participating in the CCSF depth scale. Stratigraphic features in the non-splice intervals of adjacent holes do not have the exact same depth than corresponding features in the splice at a cm-dm scale, even though they are at the same CCSF scale, because cores are stretched and squeezed during recovery, or because the stratigraphic architecture is not a perfect layer cake. Non-splice intervals can be mapped separately to the splice using a general depth mapping process. This process is currently being examined and defined to determine if IODP should implement SCORS infrastructure in the future to support it.

Depth shifting of cores and the affine table

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.

Splicing

After the cores of adjacent holes have been shifted into a CCSF depth scale, the SCS define intervals in the depth shifted cores that will constitute the splice for a site, representing the most continuous section and most complete stratigraphic representation possible with the recovered cores.

The splice tie-point concept (deprecated)

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:

• TIE - A correlative stratigraphic features in two cores from two different holes occurs at the same CCSF depths in both cores and is selected as a tie point (most common and preferred method);
• CORE - Tops and/or bottoms of cores are used to define the splice interval because ties do not exist. This is a typical scenario when the core was shifted using the ANCHOR, APPEND or SET method.
• TRUNC - In the absence of ties, parts of cores may be truncated (omitted from the splice interval) based on additional information such as drilling disturbance. This is a possible scenario when the core was shifted using the SET, APPEND, or rarely the ANCHOR method.
• Note: truncation is implicit if data from a disturbed core interval were culled during correlation data download (see "Download correlation data"), i.e., the SCS will not "see" that disturbed interval in the data.

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

Basic functions of Correlator

Correlator operates within a single window that can be toggled between the Data Manager view and the Display view (Fig. 2-1). To navigate between these views, use the top button on the floating toolbar, or use the View menu. The tool bar is always available unless turned off in the Preferences tab to the right of the window. The entire application window can be expanded as much as available monitor space permits.
Figure 2-1. The two main views in the Correlator main window.
A. Data Manager
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B. Display
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The Data Manager view has three functional tabs across the top:

• The Data List tab lists the files imported into Correlator and provides the main functions for managing the data in Correlator. The data list items are organized in a tree structure by site, data type, and hole.
• The Generic Data tab displays data from files being imported when such an import is triggered in the Data List tab.
• The Data File tab function is to display any data set listed in the Data List tab.

The Display view has task tabs located vertically on the right side of the window, mostly corresponding to buttons on the floating toolbar (Fig. 2-1B):

• Close: Closes Tab Information window
• Composite: Parameters and correlation plot for depth shifting.
• Splice Interval: Parameters and correlation plot to construct splices.
• Age Depth Model: not used/discussed here.
• Filter: Parameters for decimating, smoothing and/or culling data (creates Cull Table)
• Preferences: Display preferences

The graphics part of the Display view is separated into the depth shift (composite) and the splice sub-windows separated by a sliding middle bar. The bar can be dragged left or right for more room on either side (Fig. 2-1B).

• The splice sub-window can be removed by unchecking the Splice/Log Window box in the Preference tab.

Note that the selection of a particular tab does not constrain the actions user can take in the graphics part of the window. This means that user may have the splice tab selected but be depth shifting using the context menu.
Good or bad? For now just an observation.

Initial configurations

Set the path to your local data repository, the place where you download data from LIMS, so Correlator can update its data when new core data is appended. This directory indexes all files imported or created by Correlator. Go to:

• File>Data Repository Path

Import data that were downloaded from LIMS

• In the Data Manager view, click the Data List tab. The list is empty when you start out except for the Root item.
• You have to import each file separately for them to show up in the Data List.
• Right-click on the word Root on the top line item and select Add new data (the only option except deleting Root).
• A browser window opens that allows you to choose the data file for a given hole and data type.
• Data opens in Generic Data tab (Fig. 2-2)

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

• Make sure you select/highlight the item first, then right-click it to get the appropriate context menu.

This doesn't seem very intuitive for many users.

• The special data type items added to list, even if users don't import the data (Age Models, Downhole Log Data, Image Data, Stratigraphy), have their own import context menus and are not used/described here within the context of JR operations.

Table 2-6. Data List context menu items.

Load data for correlation

Whenever you have sufficient data imported and available in the Data List to start correlation, you need to load them for display and correlation.

• In the Data List, select, then right-click on a line item and select Load.
• You can load an individual file, a set of files for a data type, or all files for a site.
• Make sure that the files you want to load are enabled. When saved, affine and splice tables are enabled and will be applied to the loaded data.
• After loading the data, the Data Manager view turns into the Display view where the data is plotted and correlation and splicing functions are available.

Update Correlator data with added data from LIMS

During the typical JR work flow, correlators download the correlation data each time the data from a new core are available. The Correlation Downloader has features that all the download to be executed efficiently with pre-configured parameters and by appending core data to the hole data file (see chapter 1).
To update the Correlator internal database with these files:

• Select the highest practical item in the Data List, right click and select Update.
• No, you don't have to delete the data and re-import!
• Select the item again and select Upload.
• Yes, you do need to load them again.
• Make sure you also load the affine and splice tables again, if applicable.

Preferences

Before starting to work in the Display view it is worthwhile looking at the options in the Preferences tab (equivalent to using Go to Display Prefs button; Fig. 2-5). The options are largely self-explanatory and not described further at this time.
Figure 2-5. Display preference options.
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Filter data

If you haven't filtered the data a the time of download, or you would like to apply more filtering (masking) now to facilitate correlation:

• Select the Filter tab on the right or the Go to Filters button on the floating menu (Fig. 2-6).
• Set Filter Range option: if you loaded multiple data types, you can define here which ones the filter parameters shall apply to.
• It appears "All holes" is a misnomer and should read "All data types".
• If multiple data types were loaded, select the one the parameters shall be applied to.
• Decimate: to reduce excessively large data sets:
• Set the number to skip data points.
• Click the Apply button.
• Smooth: to reduce noise.
• In the Smooth window, leave Gaussian as the Type default
• Leave 9 for the Width default
• Set Display to SmoothedOnly
• Click the Apply button.
• Cull: get rid of outliers.
• If you want to cull, click the Use parameters Boolean, otherwise the Apply button will do nothing.

It is not clear why this Boolean is needed since user has to press the Apply button to activate the filters anyway.

• Enter # cm from each core top if warranted.

Why only top of core? I thought it used to be possible to cull intervals from section ends too. This should be easier now that a section summary is loaded.

• Data value: Set low pass and high pass values as needed for the data type. Apply to all cores or selected cores.
• Click the Apply button.

Figure 2-6. Filter options.
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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).

• TIE Shift Options
• Choice list 1: cores that shall be shifted.
• This core only
• This core and all below: This only shifts the cores "below" that are in the same hole, but not correlated cores from the other holes, thus invalidating all previously set ties below!

A change request is in the works to provide a third TIE option that shifts all correlated cores in all holes, sustaining all existing correlations.

• Choice list 2: Shift method
• To tie: shift is to user-defined tie (most common).
• To best correlation: user can let cross correlation function determine shift amount.
• By given amount (m): user can set shift depth interval.
• Clear tie button: allows user to clear a tie that has been defined but not yet applied.
• Apply shift button: applies the shift as defined.
• SET dialog: Set by growth rate or % button.
• Opens dialog….
• Undo Options
• Previous offset: The latest shift applied can be undone.

It would be helpful if multiple past shifts could be un-done.

• Offset of core above:
• Save Affine Table button.

Figure 2-7. Composite tab parameters.
Image Added
For the shift options user can also access context menus by right clicking on the red and green dot symbols (Fig. 2-7).

• Red dot options:
• Clear
• Green dot options:
• Adjust depth with this core only
• Adjust depth with this core and all below
• Undo to previous offset
• Undo to offset of core above
• Clear

To make a tie:

• Shift-left-click a characteristic reference point, creating a red dot (reference point). This core will not shift.
• Shift-left-click a matching point on the data from a different hole, creating a green dot. This core will shift. A copy of the data trace from the core with the green dot is overlain on the plot with the red dot.
• To move the floating trace over the reference trace for optimum correlation, drag the green line/dot up or down; alternatively toggle the line with the arrow keys.
• Click the Apply shift button.
• The core that had the green dot is moved relative to the red point (anchor) and changed to green (CCSF) to indicate the data has been depth adjusted. (Color cues for tracking depth scale changes can be changed in Preferences.)
• The amount of shift (m) is shown on the plot.
• To delete the last tie before it is applied, click the Clear Tie button.
• To delete all ties and start over:
• Select Clear all ties from the File menu; or
• Go to Data Manager, open the Saved Tables tree, and delete the affine and splice tables using right-click context menu.
• NOTE: Deleting the affine table will also remove your loaded data (rather than just undo the shifts) and you will have to load them again. After re-loading, you need to reset the Cull filters (the Smooth filter sticks).
• To save the depth shifts, do one of the following, which will save the affine and splice tables internally to Correlator:
• Click the Save Affine Table button on the Composite tab
• Click Save on the Tool Bar
• Switch to the Data Manager, which prompts you to save.

Construct the splice

For users of older versions of Correlator, note that the entire splicing functionality has been redone in 2015-2016 to (1) comply with the splice interval (as opposed to splice tie) concept, and (2) to use detailed section information imported along with the data types so top and bottom of splice intervals can be properly calculated. Splicing is now easier and more accurate and precise.
To create a splice:

• 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.

Image Added

• 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.

\[Oct 2016 discussion\] These problems could arguably be avoided if depth shifting and splicing were fully integrated in terms of accounting and graphics. Any core could be shifted at any time and any splice interval boundary could be defined at any time, and the resulting splice would be shown in the splice window in real time. Given the propose accounting of core correlations and the proposed "Shift all cores below in all holes" feature, splice interval boundaries could be shifted with the cores. Any core shift and any splice interval boundary shift would trigger an update in both affine and splice interval tables as well as the plots. At any time, what user sees is what user gets.

• 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.

Export Data

When ready to upload the affine and splice tables to the LIMS for general consumption by the science party, export data from the Data List window in the Data Manager.

• Select each affine/splice file item to be exported, right-click and select Export.
• If multiple affine or splice tables exist, the latest one will show as Enable (enabled) and earlier versions as Disable (disabled).
• You can export either status.
• The status matters for loading and working with an existing affine.
• You can change the status of tables via the context menu.
• Columns of tables exported from Correlator 2.1_rc2 are compliant with LIMS specification for all practical purposes (see Appendix 1 and Appendix 2). The exact column header spelling in the specifications is given to the right of the Correlator spelling.
• Affine table:

Correlator 2.1_rc2SiteLIMS
Site Site
Hole Hole
Core Core
Core TypeCore type
Depth CSF (m) Core top depth CSF-A (m)
Depth CCSF (m) Core top depth CCSF (m)
Cumulative Offset (m) Cumulative offset (m)
Differential Offset (m) Differential offset (m)
Growth Rate Growth rate
Shift Type Shift type
Data Used Data type used
Quality Comment Quality comment

• Splice interval table:

Correlator 2.1_rc2SiteLIMS
Site Site
Hole Hole
Core Core
Core TypeCore type
Top SectionTop section
Top Offset Top offset (cm)
Top Depth CSF-A Top depth CSF-A (m)
Top Depth CCSF-A Top depth CCSF (m)
Bottom SectionBottom section
Bottom Offset Bottom offset (cm)
Bottom Depth CSF-A Bottom depth CSF-A (m)
Bottom Depth CCSF-A Bottom depth CCSF (m)
Splice TypeSplice type
Data UsedData used
CommentQuality comment

3. Upload affine table

Getting ready

Before attempting upload of an affine file, ensure that it complies with the specified format (see previous section or examples from the LIMS database). The file must be CSV format and have the prescribed number and types of columns. The uploader will perform a limited number of tests and will reject non-compliant files.
To upload an affine file, or to manage already uploaded files and associated database entries (if authorized):

1. Access the SCORS Uploader and Manager application from

• Ship 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/ Look for the link of the same name.
• Note: SCORS Uploader was written for Firefox. It will show variations in behavior and display in other browsers: Chrome, Safari, Explorer, etc.

1. Select the Load affine tab from among the available tabs (Fig. 3-1):

• Load affine (will create a new CCSF depth scale)
• Load splice (requires associated affine to be loaded already)
• Manage (e.g., remove redundant affine/depth scales and splices)

Load affine

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

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.

• If the validation fails, you will get an error message that should be very explicit in terms of type and location of error. The most common errors encountered in initial uploads were:
• Scrambled character for negative sign, presumably generated by Excel that interpreted the value as a formula.
• Commas in the comment columns – these are not allowed in a CSV file.
• Commas only in the last row, which are not visible when viewing and editing the file in Excel, but easily so in a text editor.
• If the validation passes, a blinking message will appear: Affine validation in progress, please wait.
• During the validation, the field Name generated from content will be populated; it includes the sites(s) and hole(s) present in the file you loaded.
• The Current date (YYYYMMDD) field will also be populated.
• If validation fails, the message Validation failed, upload aborted, check the affine file format and content will appear. Click OK and check your file.
• If validation is successful, a new blinking message appears: Affine table file upload to asset manager in progress – please wait. Once this message disappears, you can proceed.

1. On the line Enter optional name extension (maximum 10 characters) you can add your initials, the time of day, or any other potentially useful information you want to appear in the CCSF scale name. The number of characters is limited to 10 to avoid overly lengthy file names. When leaving the field, the display labeled Final affine and depth scale name will display the complete standard name, including the expedition number you selected.
2. On the line Add new alternate scale or select existing affine/scale to replace, you can make an important decision:

• If you want to add a new affine and associated CCSF depth scale to the data base without replacing an existing one, keep the default Add a New Record in the choice list.
• If you want to replace an existing affine and associated CCSF depth scale, select the appropriate name from the choice list. The affine table and associated depth scale will be removed from the database. This action will reduce the accumulation of outdated information, user confusion, and the need for later cleanup in the database. However, consider that in some cases, it may be desirable to keep an older version (particularly if update is provided postcruise) because investigators may have been working with it.

1. Add any information useful to other correlation specialists or users of the depth scales in the Affine description field. The limit is 250 characters.
2. To complete the process, click the Upload Affine button.

• A blinking message will appear: Affine transfer and CCSF depth scale creation in progress
• The program will display a message when upload is successfully completed.

To confirm successful upload, go to the LIMS reports described below.

Delete affine table and CCSF scale

The Manager tab allows authorized users to delete redundant affine (and associated depth scales) and splices from the database. Unauthorized users cannot use this tab.
If user cancels an affine table by accident, user cannot re-instate them through the tools provided. However, a developer or database administrator can still recover the original upload files if needed (for a period of at least one year after).
To cancel an affine (and splice) (Fig. 3-2):

1. Select the affine you want to cancel and click the Cancel affine button.

• Note: If a splice has been associated with the affine at some point, the splice has to be canceled first. This is to ensure that "orphaned splices" do not exist in the database.

1. If applicable, select the splice you want to cancel and click the Cancel splice button.

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

LIMS internal computations

The uploaded affine files are stored and accessible in exactly the way they were uploaded. In addition, the affine tables are converted into Oracle database tables such that the cumulative offsets can be used to compute the alternate CCSF depths for samples and results. For any report available within the LIMS Reports framework, users can select the appropriate CCSF scale from the alternate depth choice list. At that point, the CCSF depths are reported for each observation or sample in the report, provided the associated core was included in the affine table to begin with.

4. Optional: Checking/fixing the splice interval file

Purpose and logic

The splice interval table (SIT) files generated by the Stratigraphic Correlation Specialist (SCS) using third party correlation applications of their choice (see section 2) may contain information that is inconsistent with the sample registry data in LIMS. Uploading inconsistent information to the LIMS would create unexpected results further downstream, particularly when LIMS retrieves data by splice, or when investigators use the splice table to sample cores. For example, we learned on Expedition 353, through the use of the new set of SCORS tools, that the Correlator application (http://www.corewall.org/downloads.html), under certain yet to be determined circumstances, returns CSF-A depths and/or section-offsets for the splice intervals that are not compatible with the CCSF depths picked by the user, according to the LIMS registry. Since the JR-SO cannot control what application the SCS use, and how those applications compute depths and section-offset identities, we created the SpliceFileFixer, which creates splice intervals that are consistent in terms of depth calculations and section-offsets.
We essentially assume that users trust their selection of core identity and CCSF depths for the splice intervals, but may not be certain about the computations of corresponding CSF-A depths and section-offsets. We can help with those.
Here is what the SCORS-QA application does:

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.

Read the discrepancy threshold value provided by the user (default: 1 cm; Fig. 4-1).
IF discrepancies in section-offset and CSF-A depths are larger than the threshold value they will be considered significant and will prompt a difference report, consisting of the OUTPUT line printed below the INPUT line.
If differences in section-offset and CSF-A depths are equal to or smaller than the threshold value they will be considered insignificant and are not reported.
Print the output file *.DIFF.
Print the DIFF report on the screen, in the application user interface, as well.

Getting ready

1. Before running the SpliceFileFixer, make sure the affine table was loaded to the LIMS (section 3) because the CCSF scale must have been created in the LIMS before a splice can be tested and corrected.
2. Ensure that the SIT complies with the specified format (see section 2). The file must be CSV format and have the prescribed number and types of columns.
3. Download and install the SCORS-QA (AKA SpliceFileFixer) JAVA application:

• Ship: http://ship.iodp.tamu.edu/tasapps/splicefilefixer/jnlp/splicefilefixer.jnlp
• Shore test: http://rtwebdv.iodp.tamu.edu/tasapps/splicefilefixer/jnlp/splicefilefixer.jnlp
• Shore production: http://web.iodp.tamu.edu/tasapps/splicefilefixer/jnlp/splicefilefixer.jnlp

Run SpliceFileFixer (Fig. 4-1)

Figure 4-1. SCORS-QA (SpliceFileFixer) user interface.

1. On the Select splice interval table input file line, click the Browse button and navigate to the input SIT file in your directory.
2. Click Open/Load in your navigator
3. On the Associate existing affine table (CCSF depth scale) line, select the scale corresponding to your SIT. If you don't see the scale corresponding to a recently uploaded affine table, click the Refresh Affine button.
4. If you want to change the threshold value for reporting differences between input and output offset and depth values, set it in the Differences will be reported if they are greater than line.
5. Click Validate Input File, and Generate Corrected File and Difference Report button.

• You will see a log of processing steps, with the final reading:
• "The splice interval table processing has ended or has completed."

5. Upload splice tables

Getting ready

1. Before attempting upload of a splice interval table file, ensure that it complies with the specified format (see section 2). The file must be CSV format and have the prescribed number and types of columns. The uploader will perform a limited number of tests and will reject non-compliant files.
2. The application is the same as the one used to upload the affine table file (see section 3).
3. Select the Load splice tab from the three tabs at your disposal (Fig. 3-1):

Load splice

To load a splice interval table (Figure 5-1):

1. Follow the same procedure as described for loading an affine. The following two steps are unique to loading a splice.
2. On the line Select affine for this splice, select the affine that applies to the splice you are uploading. Failure to select the correct affine will certainly produce unexpected results.
3. On the line Select optional splice tie point table file you can optionally browse to your splice tie point table (STPT), click the Load STPT button, which will load the file along with the splice interval table file. The STPT will not be used in splice calculations.

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

Delete existing affine and CCSF scales in LIMS

The Manager tab allows authorized users to delete redundant affine (and associated depth scales) and splices from the database.
If user cancels an affine or splice interval table by accident, user cannot re-instate them through the tools provided. However, a developer or database administrator can still recover the original upload files if needed (for a period of at least one year after).
To cancel a splice (Fig. 5-2):

1. Select the splice you want to cancel and click the Cancel splice button.
2. Consider if you want to cancel the associated affine/CCSF scale as well (in case it was updated). If so, select the affine you want to cancel and click the Cancel affine button.

Figure 5-2. SCORS Uploader user interface, Manager tab.
Image Added

LIMS internal computations

The uploaded splice files are stored and accessible in exactly the way they were uploaded. In addition, the splice interval tables are converted into Oracle database tables such that can be used to provide data by splice.
A splice was associated with an affine table at the time of upload and the corresponding CCSF scale is automatically set when user selects a splice from a choice list in the LIMS Report interface.

6. Reports

6.1. Access to reports

To get to all of the reports associated with stratigraphic correlation, go to URL:

• Ship: web.ship.iodp.tamu.edu/LORE/
• Shore: http://web.iodp.tamu.edu/LORE/
• Shore test: http://rtwebdv.iodp.tamu.edu/LORE/

User has typically one of three report needs that depend on the stratigraphic correlation processes:

1. Get correlation (affine, splice) tables: usually only the stratigraphic correlation specialists have a need for these reports (section 6.2).
2. Get data with CCSF depths: For sites where a CCSF depth scale was developed, most investigators usually want to use that scale for their stratigraphic work (section 6.3).
3. Get data by splice: Users who want to work with data for the splice only, this type of report is the most useful (section 6.4).

6.2. Correlation (affine and splice) table reports

Stratigraphic correlation data is reported in four types of reports (Fig. 6-1, lower left):

• List of affine tables
• Affine tables
• List of splice interval tables
• Splice interval tables

Figure 6-1. Screen capture of correlation reports options within the LIMS Reports framework.

List of affine tables report

This report lists the CCSF alternate depth scales available in LIMS, and the original affine table files that the scales are derived from, one per row (Fig. 6-2). Metadata for each scale are provided as well (see Table 6 for column descriptions). The list can be filtered by entering an expedition number.
To get a list of affine tables report (Fig. 6-2):

1. In the Select report panel, expand the Stratigraphic Correlation list and select List of affine tables report.
2. In the Hierarchy Search area, filter by Expedition(s), if so desired.
3. View data on screen using the View data button.
4. Option: download data in CSV format using the Download tabular data button.

Figure 6-2: List of affine tables report.

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):

1. In the Select report panel, expand Stratigraphic Correlation list and select Affine Tables report.
2. In the Additional Filters area, use the Alternate depth scale choice list to select the scale corresponding to the appropriate affine.

• You can reduce the choice list by selecting an expedition from the Expedition(s) filter in the Hierarchy Search area.

1. View data on screen using the View data button.
2. Option: download data in CSV format using the Download tabular data button.

Figure 6-3: Affine table report.

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

List of splice interval tables report

This report lists the splice interval tables available in LIMS, one per row, including metadata and links generated by the LIMS or added by the user at the time of file upload (Fig. 6-4; see Table 6-3 for description of columns). The list can be filtered by entering an expedition number.
To get a list of splice interval tables report (Fig. 6-4):

1. In the Select report panel, expand Stratigraphic Correlation list and select List of Splice Interval Tables report.
2. In the Hierarchy Search area, filter by Expedition(s), if so desired.
3. View data on screen using the View data button.
4. Option: download data in CSV format using the Download tabular data button.

Figure 6-4: List of splice interval tables report.

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

Splice interval tables report

This report provides the full splice interval table information, one interval per row (Fig. 6-5; see Table 6-4 for descriptions of columns). Sample identity information (i.e., hole, core, section, offset) is derived directly from user-uploaded files. However, the CSF-A and CCSF depths are computed in LIMS, based on latest sample registry data for hole and core. The original, unaltered splice interval table user file can also be downloaded.
To get an affine table report (Fig. 6-5):

1. In the Select report panel, expand Stratigraphic Correlation list and select Splice table report.
2. In the Splice Search area, use the choice list to select the appropriate splice.

• You can reduce the choice list by selecting an expedition from the Expedition(s) filter in the Hierarchy Search area.

1. View data on screen using the View data button.
2. Option: download data in CSV format using the Download tabular data button.

Figure 6-5: Splice table 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):

1. In the Select report area, select desired data type by expanding the category of interest.
2. In the Hierarchy Search area, filter Expedition(s), Site(s), Hole(s), Core(s), etc., as needed.
3. In the Additional Filters area, select the appropriate Alternate depth scale from the choice list.
4. View data on screen using the View data button. The alternate depths will be shown in the column nest to the CSF-A depths.
5. Option: download data in CSV format using the Download tabular data button.

Figure 6-6. Data report example with alternate depths shown in column #10.

6.3. Data by splice

One of the major goals of stratigraphic correlation is to generate "spliced data", or to retrieve "data by splice". To get data by splice (Fig. 6-7):

1. In the Select report area, select desired data type by expanding the category of interest.
2. In the Splice Search area, select the appropriate splice from choice list.

• You can filter the splice list by selecting an expedition in the Hierarchy Search area.

1. View data on screen using the View data button. The alternate depths will be shown in the column nest to the CSF-A depths.
2. Option: download data in CSV format using the Download tabular data button.

Figure 6-7. Data set extracted for user-selected splice.

Appendix 1: Specifications for affine tables

Appendix 2: Specifications for splice interval tables