Introduction

NCLIP

This help file introduces the NCLIP application.
Mail comments here.

Release Notes

Release Notes


Version 1.1

A bug fix version of the original beta release, work in progress. All of the fixed bugs at http://sqlcore.geo.umn.edu/CoreVault/bugs/ are in this release.

Here are the fixed bugs. 

ID  	 Sev  	 Pri  	 OS  	 Assignee  	 Status  	 Resolution  	 Summary
31 [SEC] 	nor 	P1 	All 	billkamp@gmail.com 	RESO 	FIXE 	Compositing mis-identifies the hole, needs highlighting o...
42 [SEC] 	nor 	P1 	All 	billkamp@gmail.com 	RESO 	FIXE 	Help files may not be archived correctly.
45 [SEC] 	nor 	P1 	All 	billkamp@gmail.com 	RESO 	FIXE 	Does the XML file allow movement between OS's
49 [SEC] 	blo 	P1 	All 	billkamp@gmail.com 	RESO 	FIXE 	Compsite does not collapse
52 	nor 	P1 	All 	billkamp@gmail.com 	RESO 	FIXE 	Bad depths show in the splice window when clicking in a gap.
55 [SEC] 	nor 	P1 	Mac 	billkamp@gmail.com 	RESO 	FIXE 	The splicer preview window is small on a virgin session.
57 	nor 	P1 	All 	kamp@iagp.net 	RESO 	FIXE 	Crash on Undo Grab
9 [SEC] 	nor 	P2 	All 	billkamp@gmail.com 	RESO 	FIXE 	Allow clipping of parts of sections
18 [SEC] 	nor 	P2 	All 	billkamp@gmail.com 	RESO 	FIXE 	Shorten log annotations
30 [SEC] 	nor 	P2 	All 	billkamp@gmail.com 	RESO 	FIXE 	Composite may disappear when there is no overlap.
44 [SEC] 	nor 	P3 	All 	sean@ldeo.columbia.edu 	RESO 	FIXE 	New Sagan Features
51 	nor 	P3 	All 	billkamp@gmail.com 	RESO 	FIXE 	Splicer Summary window is blank
58 	nor 	P3 	All 	billkamp@gmail.com 	RESO 	FIXE 	Crashes after deleting a track

for more details, consult the website.


Version 1.002

A bug fix version of the original beta release.


What is New in this Release

    

  1. You can now set the default location of your xml and data files using the 
NCLIP_DATA environment variable. Set that varibale to where your data is located.

  2. We have a data map round trip in NclGridFromText. This means
we can store and retrive the data map used for a data set at will. 
We still need to hook it up to the file manager so the use can access it.

  3. We cleaned up the locations and directories that are stored in the system.
See Locations/Directories for
more information.




What to Test


    

  1. The ability to find help files and locations from a blank xml def session, using
the NCLIP_DATA environment variable.




Bugs Fixed


368 Fix the help upload to web site
from the RSync script to put help in the help and not 
the help/help directory. It is not in mvWinMm1 9/19/06
367 Update all the menu snapshots in the help.




Version 1.001

A bug fix version of the original beta release.


What is New in this Release

    

  1. Fixed typoos in help files.




What to Test


    

  1. 




Bugs Fixed







Version 1.0

We declare victory! Version 1.0 is the beta release, out for testing!


The big new feature is Splice Round Trip. You can build a spliced log,
export it, and read it back in as a new log. 

The next feature to be added is one that is not in Splicer.
Import Splice, that is re-building 
a splice from a new set of data, e.g. using the magnetic log splices to 
automatically build a new spliced density log from the density data.
This latter one is close, but my vacation in Alaska took a priority.

What is New in this Release


    

  1. All menus now have contextual help.

  2. The splice information box now gives complete information.

  3. The interval measurements are now from the top of the section instead
of the top of the core.

  4. Fixed more vertical and horizontal bugs. 

  5. The menus now have more mnemonic names.

  6. The well log annotation was simplified.

  7. If you try to add a second session file to an existing session,
we added an "Are you sure box" that explains the consequences.

  8. Many of the pop-up boxes now have a "More Information" option that 
link to the appropriate help page. 

  9. Added the current bug list to the help file. If you are having issues, with NCLIP that is,
please see if that bug is listed. If not, send an e-mail to kamp@iagp.net.




What to Test


    

  1. Splice round Trip: Build a spliced track, and export it. Then reload it as a new well log.

  2. Recheck the compositing, in case I broke it.

  3. Prufreed the help files.

  4. Do all menus have active help?




Bugs Fixed


361 Change Toggle Dots to Hide/Display Data Points 8/4/06
359 When you Save the Affine table, and then start over,
either with a Ctrl-n (New Session) or quit the program and restart,
and then load the original data, and then import the affine table,
you cannot set a reference point. 
Fixed: I moved the SetTitle("") from init to the NclFrame constructor.
before it was setting the title to "" when starting a new session, and
the ref point is only installed when the title is Composite. 8/4/06
362 Drop the S:, H: and T: from the annotation. 8/4/06
360 Change "Set Gravity" to "Vary Splice Window Size/Vary Composite Window Size"
We now call it the Grow/Shrink control. 8/4/06
351 Add a warning for multiple sessions. Added a whole bunch of 
caveats to NclFrame::SessionAdd. 8/4/06
143 the ties occur in the Composite Window when more than one section
 is moved into it. depends on 198 8/4/06
364 Add Import Composite Track in legacy and xml mode. Just do it from the output composite. 8/4/06
347 Add Export Composite Track in legacy and xml mode. 8/4/06
366 The splice window start cut is not refreshing. 8/4/06
348 Write the InputSplices for xml and txt. 8/4/06
349 Change the int depths on the splice output to top of section instead
of top of core. Output it in centimeters. 8/4/06




Version 0.991



What is New in this Release


    

  1. We continue polishing in preparation for a beta release.

  2. Removed all deferred menus.

  3. Fixed vertical and horizontal bugs.

  4. Added an FAQ

  5. Added lot's of help.




What to Test


    

  1. Are all visible menus active?

  2. Is splice round trip working?

  3. Do all menus have active help?




Bugs Fixed


355 Show hide session file fails if the data was loaded from a different directory. 8/2/06
356 If in horizontal mode, when adding a vertical session file, we display 
vertically, but still have horizontal windows. Fixed in 
NclFrame::ShowHideSplicer 8/3/06
357 Save does not save to the last opened session file. but Save As remembers
the right location. In NclSession::Close, I was changing to the default
dir if the save name was the default file name. Removed that. 8/3/06
353 We need to walk through all menus and menu items and decide if  
they (A) should be there (B) If so, are they named correctly or  
clearly (C)  Have you explain what some of them do in general??
Can use help->What's This to show the help for each menu. All
menu's now have help. 8/3/06
352 I save an affine table, then try  
to work with it -- and can't interact with anything until I start new  
session or erase old session file? I suspect this is a corrupt or old
xml session file. The pick is based on the canvas name, which
may be blank if using an old XML file. See if your default session file
has " " near the top. If instead it
has   things will not work. You can view the 
session file using "View->Show/Refresh the Session File." Added this 
to the FAQ. 8/3/06
354 Need to simplify track labels.... something like Site 926  Hole A  
would be fine.... If it had data type, so much the better...
Simplified. 8/3/0
350 When you switch between horizontal and vertical and then hide  
splicer window and then bring it back, it comes back  
horizontal ...see attached image. fixed. 8/3/06





Version 0.99



What is New in this Release


    

  1. We cleaned up the visual cues for when we are in composite and splice mode.

  2. We added a View->View Log, 
and a View->View Session file method.

  3. We fixed a bunch of bugs in the cross correlation.

  4. We added an View->Auto Raise method to show all windows if they were hidden.
The windows are also moved onto your screen if they are off screen.
(The latter is needed when a session file on a large screen is used
on a small screen machine.) This is also implemented as 
a ShortCut Key F2

  5.  Some of the legacy affine data has incomplete information,
such as odpDepth, which is inferred from the log. Since
we will trade affine data between logs, we added
a means to recover that missing information in NclTrack::Normalize.

  6.    Pressing a middle mouse button between two tracks in any mode will 
bring up a cross correlation between those two tracks. 
See Checking Your Fit

  7. The splice GUI is now complete. See Splice How To   and
Splice Mode for more information.

  8. We now output text and xml versions of the splices. See
Export the Splice Table as XML and Export the Splice Table as Text for more details.

  9. The help files are expanded and more cross indexed. Also, the code documentation will link to 
the help files.

  10. We will input the Splices in version 0.991.

  11. We will export a composited track in traditional format in 0.991. (You can export it now
in XML.)




What to Test


    

  1. Try out the Fetch URL.

  2.  Load susfix_0926a.dat, susfix_0926b.dat, susfix_0926c.dat

  3.  Import an affine table to get the correct depths, e.g. sample.926.affine.table.

  4. Grab some cores to the splice window.

  5. Make some splices.

  6.  Undo some splices.

  7.  Try out the F2 shortcut.

  8. Pressing a middle mouse button between two tracks in any mode will 
bring up a cross correlation between those two tracks. Try it.

  9. Export the splices as xml and text.

  10. Import of splices is 0.991, next week.




Bugs Fixed


------------------------------0.99--------------------
319 If you F4 the cross plot window, and then restart composite, it crashes. 7/15/04
330 The warning of failure to save a session file appears more than once.
9/13/06
323 Remove the Ref annotation, not just the <--Ref when restoring a session. 6/15/06
325 You need a positive length in the corr window for the Xcore to 
show in composite. We now bring up a warning box. 9/13/06
326 Add a log line for the start and end of composite and splice mode,
to help solve 325.  6/15/06
327 When 2 composites are far apart, you only get an xCorr when they 
are near their start point, not when they are near each other.
It seems the composite is based on the delta move from the ref and the 
move point, and not on the absolute depth. 6/15/06
332 Complete the ViewLog method in frame. 6/15/06
333 Make all windows show at least partly on the screen.  6/15/06
334 Add an "AutoArrange" menu to the View menu for 333. 6/15/06
335 Save the composite splice state and resotre it from the session file. 6/15/06
312 If you F4 the affine or splice summary window, and then reopen it,
you get a crash. 7/15/06
342 The affine preview window position is not remembered. 7/17/06
338 Make the expert mode the default. No.
343 Stagger the annotations on the track label. 7/17/06
341 The start and stop of the composite and splice mode should
reflect the current splice, composite state. 7/17/06
337 Check the loading of a legacy affine table. It fails on the MT95.dat  
stuff without a complaint. 7/18/06
345 If a value in the summary window is NCL_UNDEF, show the string Undefined and not the number. We decided to not show it. 7/18/06
339 Import of an affine table should fail with warning when in the splice mode.
Nope, it is OK. We can realign when we want. 7/18/06
346 Change the default tic mark to 1 and annotation to 5. 7/1/9/06
344 Splicing variable is not following the middle mouse button. 7/18/06
340 Add the splice type of cross corr as an option on the composite mode, 
e.g. shift-middle mouse button. 7/19/06
331 When you have a 0 length window in the Splice mode, the color cue
is for a non-zero length window. Instead, it uses the last non-0 length.
7/19/06
331 When you have a 0 length window in the Splice mode, the 
xcorr does not change, and you do not get a warning.
We now put up a warning box and stop the splicing if the window
length is 0. 7/19/06
328 Make sure that the Window Length of XCor is positive when loading it from
XML. Superseded by 331.
324 When you have a leftover ref point from the splice mode or the xml restore,
and you start the composite mode, the composite process is ignored, you 
grab the whole core. Fixed by 288. 7/19/06
317 When switching to Composite mode, remove the left and right cuts. 7/19/06
310 Have the splicer html input put up in NclSpliceFrame, not the affine html
window. 7/15/06
336 On a Mac, opening the legacy splice file only allows txt extensions,
not dat or other extensions.7/21/06
272 Add a Get Inventory button in NCLIP. 7/15/06
308 What is the ODP Id used in the Splice Window and the Composite window? y/21/06
320 If the window is zero length, and xcorr in splice crashes it. 7/20/06
321 If you are in composite, the xcorr colors do not match. 7/21/06
322 Set up the XCorr in Splice Mode to work in both windows. 7/21/06
329 The xcorr color on the composite mode is not over-riding a moved track 
color of green. 7/21/06



Version 0.98



What is New in this Release


    

  1. Splicing is starting to work. You can now grab cores, and move them to the
splice window, and then choose a sliding splice depth and 
watch the cross correlation between the composite and grabbed track. 
(Splicing a second and later grab into the composite is next on the list.)

  2.  See Splice for how to splice.

  3. We have beefed up the fetch URL menu. You now have a 
host of options.

    

  4. The Fetch URL help item tells the meaning of these items. You can 
now automatically discover, and/or download all of the data entries 
by leg, or hole, or whatever. The default menu downloads all logs for Leg199.

  5. At some places we have F1 key help. Let me know if you are interested in this.

  6. In all cross correlations, while moving the window, the portions that 
are cross correlated are highlighted in a different color. 




What to Test


    

  1. Try out the Fetch URL.

  2. Grab some cores to the splice window.

  3. Try out the cross correlation window in the splice window. See
Splice for instructions.

  4. Please give me some feedback on the XCorr window in the splice process.

  5. I changed the annotation of the composite XCorr window. Please provide 
feedback.




Bugs Fixed


298  When span core for xcorr is checked, it seems to be only for a section.
No, it is for the whole window. The drag is for the length of the 
window when span core is checked. 6/30/06
299 Add to help what the numbers in the xcorr window mean. 6/30/06
300 Hide the composite window when opening the splice window, and vice versa.
6/30/06
---------------------------------
288 The ref point is posted on a restart, but it is not chosen, i.e. a right click on a log
does not stat the xcorr. 7/4/06
--------------------------
302 The Ref point is inverted (x and y swapped) when restored from session.
Supplanted by 307. 7/5/06
304 In splice, grab core only grabs the top core.		 7/5/06
305 After a cut the active track deactivates. It should not. 7/5/06
306 You must first activate a track should say In order to do a grab, ....,
and the title should not read "No reference point" 7/5/06
318 When starting a session, we now do vertical and horizontal correctly. 7/11/06
313 The floater should reflect the actual window. 7/11/06
314 Is there is a way to highlight the floater in the xcorr window, but floats.  7/11/06
316 We should link the annotation to a window position, a x and/or y of the track. 7/11/06
311 F1 in the composite mode brings up the splice help window. 7/12/06
301 When dragging a core with span core unchecked, only pull along the 
correlation window. 7/12/06
309 When picking a reference point in the Splicer mode, make the reference
track the active track. 7/12/06





Version 0.97



What is New in this Release


    

  1. We updated much of the help.

  2. We now have unlimited Undo's in the compositing process.

  3. We put up an HTML window showing the current state of affine transformations.

  4. The cross correlation window is now accurate.

  5. The Composite Window menu is re-designed.

  6. The process menu now has contextual help.

  7. The menus are now stateful, i.e. change to reflect the current state of variables.

  8. All cross correlation parameters are now user definable, and are persistent, that is
saved from session to session.

  9.  You can restrict the cross correlation to a window or to a core.

  10.  You can apply a shift to a single core or from that core on down.

  11. We have annotation on the cross correlation window. 

  12. Sometime this weekend, we will add the splice window. 




What to Test


    

  1. Try out various cross correlation parameters.

  2. Try out the undo shift and/or add some shifts and watch the Affine Preview Window reflect those changes.

  3. Verify that the depth shifts apply to core or well bottom, as prescribed in the Composite Window Menus.

  4. I had to punt on the ODP depth, delta depth, and composite depth of affines. Here is what
I did: The accumulated depth offsets are added to the ODP depth to make the composite
depth. Hope that is right.




Bugs Fixed

We have spent a lot of time fixing bugs. I think the composite process is now feature complete, and 
on to splice.

291 The axis is appearing now. This was only when Annotate =1, not when it was 0. 6/28/06

289 Reload of data set needs to be tested. done. 6/28/06

285 Typo: in the track deactivate is spelled wrong. In the on track should be one track. 6/28/06

284 The help files should say in the window the file that should be picked. I did it for 
all FullFileName calls. 6/28/06

293 Put confirmations on the Delete Active Track, and the New Session tasks.  6/28/06

290 Setting an active track highlights the axis, not the track. This is only true if annotate = 1. 6/28/06

277 Make the xcorr windows exactly the same. Use GetTopBottomCore when making a reference point
i.e. on middle mouse down. 6/28/06

173 The save session as box should default to the name of the opened data file with XML Attached. We use session.xml instead, since there can be multiple tracks. 6/16/06

295 We draw only the points in the window, and connect the missing points at the border,
distorting out of window lines. This is only in the vertical mode.
I was clipping on data, something I did not need to do. When I removed 
data < sDTop.y || data > sDBottom.y  || it was fixed. 6/28/06

294 Maybe add a novice mode to eliminate confirmations. 6/28/06

279 The m_width and m_height are switching when we save and retrieve the session xml. 6/28/06

296 When a shift is completed, the active track only highlights above the shift, 
probably because the shifted color is not using the highlight pen. 6/29/06

292 Make the Undo apply to the active track. NclCanvas::UndoLastShift 6/29/06

258 In following up on 3 above, is there a way to show the horizontal  
scale of values somehow (assuming you are working vertically) for a  
track(s), similar to the vertical stuff. 6/29/06

252 there is an extra offset in the x-corr window. fix it by using 
the same window for both logs. The width of the window should be a user input. 6/29/06

261 On affine table input, 
look for sub-leg, mbsf, and mcb by counting the number of  
elements in a line. If they are there, use them, otherwise don't. 
Started. See NclAffine::ReadLegacyAffine.
I did composite, mcb as the second drop off, and mbsf as the third. 6/29/06

225 We would like some un-do commands.  We can undo all composites. We 
will do the same for splice. 6/29/06

243 The default load is vertical, even if the present session is horizontal.
Correlation is used by both  processes (modes) with various options. 6/29/06







Version 0.96



What is New in this Release


    

  1. We updated much of the help.

  2. We added a Composite Window Menu that will allow more interaction in 
the composite process.

    

  3. We hooked up all features to the window, except for the Correlation Customization.

  4. We can now move a single core, or the whole well below the active core (well bottom).

  5. You can move a core or well bottom by a numerical value.

  6. There is a "last move" undo.

  7. The help files can now be printed as a manual: NCLIP/help/FullHelpManual.html.

  8. The Clip Help manuals are now monolithic: NCLIP/oldHelp/FullClipHelp.html.

  9. Using the above, we now have a printed manual.

  10. The Process menu has been streamlined. 

    

  11. We have a list of keyboard shortcuts in the help file.

  12. We now have four QuickStart entries:Tutorial, ShortcutKeys,Composite HowTo, and Splice HowTo.

  13. You can now complete a composite, and construct a spliced log. The splicer table output 
will be completed next week.

  14. My 30" monitor is working! :-)




What to Test


    

  1. Please check the Composite Window Menu entries. See Composite Window Help
for details.

  2.  Try out the splice methods, described in the Splice How To in the Quick Start section.

  3. Verify that the depth shifts apply to core or well bottom, as prescribed in the Composite Window Menus.




Bugs Fixed

We fixed several bugs having to do with compositing and splicing, but the main emphasis
was on new features.


Version 0.95



What is new in this release


    

  1.  There is now contextual help for the File and Track menus. 
It is activated and turned off using the 
Help->Toggle ContextualHelp. 
    

    

     When activated, choosing a menu item will bring 
up its help file.

  2. The affine output menus are now under the File menu.

  3. The plots are connected across section breaks, and not 
on core breaks.

  4. The affine output is now for all tracks in the composite window.

  5. Affine input and output works. Export you composite
changes as XML or text, and read them back in. There
also is now a Remove Affine Corrections menu, so you
can start fresh. 

  6. The logs are now colored correctly.

  7. Multiple files are lexicographical sorted when loading.

  8. Adjusted cores are now colored yellow green, and unadjusted are yellow.

  9.  You can change the colors of more things, see the 
Graph menu.




What to Test


    

  1. Try a compositing session, i.e. pick a reference point, using the middle mouse button.

  2. Right click on a second track.

  3. Slide the track, seeing the x-corr line up.
(Warning there is still a bug in the x-corr origin. See "User
Feedback Needed" below. 

  4.  Accept the composite.

  5. In this release, you do not need to activate a track.

  6.  Choose Export Affine of type txt or XML.
    

    
You will then be asked for a file name.

    In this release, the output affine file should have all tracks data stored.



User Feedback Needed


    

  1. Is the format for the multiple track affine output correct?

  2.  Is the default name used to save the affine table OK? 
Since we are saving more than one track, we use the site and leg 
names, but not the hole names.



Bugs Fixed



262 Make the affine output match Sean's specs. 6/13/06

274 Add a real depth column to the mdo in canvas, follow mdoDepthCol. It is 
called mdoOrigDepthCol. 6/13/06

275 Make the affine write out and read in on the session xml. 6/13/06

282 Make the reference point red 6/16/06

283 make the moving point green 6/16/06

280 We are not reading in all of the Affines in xml. We are only reading the first one. Should we combine them into 1 affine object? Yes. 6/14/06

263 Sort the affine to depth. 6/13/06

266 Make unadjusted tracks yellow, adjusted green. 6/16/06

267 Move the save file menus to under the file menu. 6/10/06b

166 "splice to tie" to complete the splice on the composite. 

(On the composite there is also an overlay like in the plot window.)

264 When a core is adjusted, change its color. 6/15/05

268 Multiple files should load with the top file picked first.
Done, changed in NclFileManager::OpenTextFile. 6/16/06.

246   there's 2 things going on:
A)The old software called it compositing --- you call it aligning  
(output is "affine table" relationship of the cores relative to one  
another)
B) "        "     "     calls the next part splicing ---you call it  
compositing (grabbing of cores) and clipping  (tying the splice  
together) and (Output is creation of "splice table" which lists which  
cores make up splice and at what depth they are "clipped...tied  
together" Renamed. 6/16/06

277 If loading an affine from the session, adjust the depth versus real depth of the mdo.
Not needed, since 276 will do it. 6/15/06

276 If loading an affine from an affine file, adjust the depth versus real depth of the mdo.
done. 6/16/06

281 Load multiple data sets in lexicographically order. done. 6/16/06

278 Model the affine text output on the affine xml output. 6/16/06


Version 0.94


What to Test


    

  1. Try a compositing session, i.e. pick a reference point, using the middle mouse button.

  2. Right click on a second track.

  3. Slide the track, seeing the x-corr line up.
(Warning there is still a bug in the x-corr origin. See "User
Feedback Needed" below. 

  4.  Accept the composite.

  5. Cmd-Left click on a track to choose that track.

  6.  Choose Export Affine of type txt or XML.

You will then be asked for a file name.



User Feedback Needed

We need feedback on:

    

  1. Do we need to output affine in both the composite and splice
window? It is only composite for now.

  2. Where do we usually store affine files?

  3.  Are affine files always associated with one track only?

  4.  Do we need to mix well types in an affine file?

  5.  I assume that given a track, we can read an affine file
on top of it. Do we need to match the affine file and the track,
or can we use an affine file from say a magnetic log on a density log?

  6.  Did I get the format of the affine file right?



What is new in this release


    

  1.  The NclAffine object, which manages the reading and writing 
of affine files. This object can support both read and write
of text and XML affine tables.

  2.  Hook up the write methods for the affine transformations.
(Read of affine is not done yet.) 

  3. Index based help. (Next release, we should have contextual help.)
    


  4.  The clip documentation as a separate help file.

  5.  Several bug fixes. 

  6. We have added a copy of the old NCLIP help as the OldHelp file, which you can see when you type Cmd-h, h, or choose the Help->Help Contents.

  7. We have added a comprehensive help framework as Help file, which you can see when you type Cmd-h, h, or choose the Help->Help Contents.


For a complete source code documentation, see http://www.iagp.net/NCLIP/Docs/html/index.html


Version 0.93


In this version we allow compositing of data. 
See the How to Composite section for details.








NClip FAQ


    

  1. 
I save an affine table, then try  
to work with it -- and can't interact with anything until I start new  
session or erase old session file? 

    This is probably a corrupt or old
xml session file. The action associated
with 
the reference pick is based on the 
composite canvas name, which
may be blank if using an old XML file. See if your default session file
has 

    <NclCanvas name="compositeCanvas"> 
    near the top. If instead it
has
     
 <NclCanvas name=""> 

    or worse yet if the "NclCanvas name" label is missing,

    things will not work. You can view the 
session file using "View->Show/Refresh the Session File." Added this 
to the FAQ. 8/3/06







Quick Start



Quick Start

Here are some documents that will help you get quickly started 
using NCLIP.






Tutorial



NCLIP User Manual


How to Open a Data Set
First start with a new . 
Choose the 
load text file menu.
 
Choose your 
data set:

Choose your 
columns:



You can have several rows for non-data items, one or more rows for column 
headings, and various columns for the data. You should not usually have to 
change anything. Then add this track to the window. 


Menus, Keyboard Shortcuts, and Mouse Moves

If you do not see all of the windows, use the F2 key to 
raise them all and put them on the screen. See
Auto Raise for more information.

Menus
Once the data are loaded, there are several things you can do with 
the mouse and key board. 

Process->Align->How to Align
You can align a set of tracks by 
picking it using your middle mouse button to set a reference point. After that, 
you can right click the corresponding point or feature on the track to be 
aligned. Continue holding the right mouse down, and move it up and down, 
watching the correlation window. 
When that window peaks, you have a match. 

You must immediately register your match by pressing the enter key.
If 
you want to abort the match, immediately hit the delete key. 

You can save your work at any time by saving the current session. Then, by 
restoring your session at a later time, you can resume. 

Process->Composite->How Manage Composites
You may start an 
alignment process by First completing the alignment process.
You then choose 
which core's to move to the composite canvas by cmd (or control) right clicking 
that core. 
Then that core will move to the right window. will choose the 
last cut point, which will then be moved to the composite. 
You can save your 
work at any time by saving the current session. Then, by restoring your session 
at a later time, you can resume. 
See Session
Save as Default for details.

Process -> How to Clip->How to Clip
The clipping process occurs 
after the composite process. After you initiate the clipping process, you need 
to set a cut point by choosing it with the middle mouse button.
Then 
choose the next core that will fill in after that cut point. 
Continue clip 
and fill until you are done. 
You can save your work at any time by saving 
the current session. Then, by restoring your session at a later time, you can 
resume. 

Control Key Summary
A summary of the control keys used. 


  
  

    Title
    Key
    Description

  

    Load Graphic File Key
    Ctrl-g 
    Deferred 

  

    Load XML File Key
    Ctrl-x 
    Deferred State files, and user preferences are stored as session XML. 
      See Session 

  

    Load Binary File Key
    Ctrl-b 
    Load a binary data file into the system. Deferre 

  

    Open/Add Key
    Ctrl-o 
    Open a session XML file, adding it to this sessi 

  

    Save Key
    Ctrl-s 
    Save the current session as in-place XML. 

  

    Save As Key
    Ctrl-a 
    Save the current session in a new XML file. 

  

    Save As Default Key
    Ctrl-d 
    Save this session as the default session that will automatically 
      open when you start a session. If you just want to save your user defaults, 
      choose Session->New Session, then use Ctrl-d.

  

    New Session Key
    Ctrl-n 
    Wipe out the current session, leaving only your user 
preferences.

  

    Change Session Type Key
    Ctrl-i 
    Make this application Splicer or Sagan.

  

    Show Composite Vertically Key
    Ctrl-v 
    Show the current logs vertically.

  

    Show Composite Horizontally Key
    Ctrl-h 
    Show the current logs horizontally.

  

    Hide Composite Key
    Ctrl-u 
    Show/Hide the composite window.

  

    Live update Key
    Ctrl-L 
    Update both windows together.

  

    Set composite position Key
    Ctrl-P 
    Change the 

  

    Set min size Key
    Ctrl-M 
    Set the minimum size of a window.


Mouse Keys: Here are the various mouse actions. 


  
  

    Left Mouse
    Show the current coordinates of the active track. Used when tracks 
      overlap.

  

    Cmd Left Mouse or Middle Mouse
    Make a track active. (Items such a Change Track Color are applied to 
      the active track.

  

    Right Mouse
    Extract the chosen section to this track. Cmd Right Mouse: Extract the 
      chosen section to the other track.


Keyboard Shortcuts
I use ctrl for PC. The Mac version is the cmd 
key. 

Scaling



  
  

    AutoScale
    Shift-a

  

    Specific Scale
    Shift-s

  

    Saving

  

    Save in Place
    Ctrl-s

  

    Save As
    Ctrl-s

  

    Save this session as the default session
    Ctrl-d


Session
 

Graphics
 

Openging and Closing
 

Track Manipulation
 

View
 

Help
 



Bill Kamp 






Shortcut Keys


Function Keys




Show Help
F1
Show the general help for this window



Raise All
F2
Raise all windows, and move them on the screen if they are off screen.



Refresh
F5
Redraw all graphics windows




At the present time, the function keys work on the 
main Composite/Splice window only.


Control Keys


Control Keys


Load Text Data File Key
Ctrl-t 
Define how to parse a text file, and then load it into the system.


Load Graphic File Key

Ctrl-g 
Load a graphic file into the system. Deferred.




Load Text Data File Key
Ctrl-t 
Define how to parse a text file, and then load it into the system.


Load Graphic File Key

Ctrl-g 
Load a graphic file into the system. Deferred.


Load XML File Key
Ctrl-x 
Load an data XML log into the system. Deferred. 


State files, and user preferences are stored as session XML.


Load Binary File Key
Ctrl-b 


Load a binary data file into the system. Deferred.
Open/Add Key
Ctrl-o 


Open a session XML file, adding it to this session.
Save Key
Ctrl-s 


Save the current session as in-place XML.
Save As Key
Ctrl-a 


Save the current session in a new XML file.
Save As Default Key
Ctrl-d 


Saving this session as the default session means you will
return to this state when you start a session
If you just want to save your user defaults, choose Session->New Session, 
set your defaults, do not open any data, and 
then use Ctrl-d. In this way your next session will have the same defaults.


What's This
Ctrl-w 
Start/Stop the What's This? help on click.


New Session Key
Ctrl-n 
Wipe out the current session, leaving only your user preferences.


Change Session Type Key
Ctrl-i 
Make this application Splicer or Sagan.


Show Splicer Vertically Key
Ctrl-v 
Show the current logs vertically.


Show Splicer Horizontally Key
Ctrl-h 
Show the current logs horizontally.


Hide Splicer Key
Ctrl-u 
Show/Hide the composite window.


Live update Key
Ctrl-L 
Update both windows together.


Set composite position Key
Ctrl-P 
Change the 


Set min size Key
Ctrl-M 
Set the minimum size of a window.





Here is a list of the shortcut keys:






Mouse Keys: Composite Mode

 Here are the various mouse actions.



MovementDescription


Left Mouse
 Show the current coordinates of the currently active track.

Cmd Left Mouse
 Make a track active. (Items such a Change Track Color
are applied to the active track.) If you press delete key, the active track 
will be deleted. A moved track is just one core long.

Right Mouse
If there is no reference point, Make a copy of the core, and follow your mouse. 

If there is a reference point, pick up the core, and start the 
compositing session.



Middle Mouse
Set a reference point. 


Also, if you hold down the middle mouse, and move up and down between two tracks, 
the Cross  Correlation window shows the cross correlation between those two tracks. 
This is a great way to confirm the efficacy of your composite.






Mouse Keys: Splicer Mode

 Here are the various mouse actions.



MovementDescription


Left Mouse
 Show the current coordinates of the currently active track.

Cmd Left Mouse
 Make a track active. (Items such a Change Track Color
are applied to the active track.) If you press delete key, the active track 
will be deleted. A moved track is just one core long.


Shift Left Mouse
 Make a Start Cut Point. If the "Selection" radio button is checked in the Splice Window
this will set the "Start Cut" point for the grab.


Right Mouse
If there is no reference point, Make a copy of the core, and follow your mouse. 


If there is a reference point, pick up the core, and start the 
compositing session.



Shift Right Mouse
 Make a End Cut Point. If the "Selection" radio button is checked in the Splice Window
this will set the "End Cut" point for the grab. Then the grab will be from the Start Cut to the End Cut.



Middle Mouse
If you hold down the middle mouse, and move up and down between two tracks, 
the Cross  Correlation window shows the cross correlation between those two tracks. 
When you release the middle mouse button, it will ask you if that is the splice you want.
Answer Yes or No, as you wish. 




I urge you to explore the menus for other options.




Composite How-To


Composite How-To

You can align a set of tracks by picking a reference point on a reference track
using your middle mouse button to set a reference point.


After that, you can right click the corresponding
point or feature on the track to be aligned. 
Continue holding the right mouse down, and move it up 
and down, watching the correlation window.
When that window peaks, you have a match.


You must immediately register your match 
by pressing the enter key.
If you want to abort the match, immediately hit
the delete key.


You can save your work at any time by saving the current session.
Then, by restoring your session at a later time, you can resume.


For more detail, see 
Compositing: Step by Step




Splice How To

Splice How-To
This is a short How-To. For a longer
version, see Splice Mode

You may start a splice by  
first completing the composite alignment process.

Then choose "Start Splice from the Process menu."

Move a whole core

You choose which core's to move to the splice canvas by

    

  1. Middle mouse clicking that core.

  2.  Pressing the "Grab" button on this menu: 

     will move the 
core to the splice window.



Move part of a core

Moving part of a core is a five step process.

    

  1. Select the "Selection" button in the Grab window.

  2. Activate the track you want a part of with a middle mouse click.

  3. Shift-left-mouse click on the starting point of the cut.

  4. Shift-right-mouse click on the ending point of the cut.

  5.  Pressing the "Grab" button on this menu: 

     will move the 
core to the splice window.




If this is the first grab you are moving, it will automatically
be loaded into the composite track. For second and subsequent grabs,
we will load the grab into the grab track.

The grab track must be empty for a move to be completed. If it is not
empty, a new grab will bring up an error box.

You can empty a grab track in one of three ways:

    

  1. Click on .

  2. Complete a splice by pressing the middle mouse button, 
and dragging it to the desired splice point, and releasing the middle
mouse button. 

  3. Preforming a Cmd-Left Click on the grab track, and then pressing the delete button. 





You can save your work at any time by saving the current session.
Then, by restoring your session at a later time, you can resume.


Completing a Splice

Once you have at least one core in the composite track, and one and only
one core in the grab track, you can complete the splice:

    

  1. Press the middle mouse button on a point where the grab and composite tracks overlap.

  2.  While holding the mouse button done, drag it up and down (or left or right 
in the horizontal case) while watching the Cross Correlation window.

  3. When the cross correlation peaks, you have a good splice point. Release the middle
mouse button.

    When you are down, simple release the middle mouse button. 
You will then be asked if you want to complete this splice.


    
If you answer yes, the portion of the grab track below the splice point is put into the corresponding portion of the composite track. (This will overwrite the bottom portion of the composite track.) 






Checking Your Fit

You can use the cross correlation at any time:
Pressing a middle mouse button between two tracks in any mode will bring up a cross correlation between those two tracks. 
(Note however, that when you release the middle mouse button, you will have set a new
Reference Point.

While holding down the middle mouse button, slide it back an forth, and you will 
see





 Where the changed color reflects the width of the Cross Correlation Window.

The resulting dynamic cross correlation will be presented in the 


Cross Plot Window





Directories/Locations

We sometimes refer to directories as locations.

Since this application relies heavily on XML, and the location
of the data, we define two locations in terms of 
environment variables. We then use those environment variables to 
locate the files.

This table describes the two environment variables we use:



Variable Name>Description


NCLIP_DATA_DIRThe location of this user's data directory.


NCLIP_APP_DIRThe location of the executable.




Both of the above variables are fully qualified names.
For example:


Note that we do NOT use a trailing directory separator.

NCLIP_APP_DIR must set as a global environment variable at the time of installation.
If not, you may be constantly asked "Where are the help files?".

NCLIP_DATA_DIR is set as a user's environment variable which can vary between users. 
If it is not set, we pick a reasonable value.

These are one time setups, and must be remembered between sessions.

How to permanently set the Locations

Since the environment variables should be remembered from session to session, you will 
need to set them in the following ways.



Linux/Unix

First determine the type of shell you are using:

env | grep SHELL

You then should see something like:

SHELL=/bin/bash

In general you will need to edit your shell's startup file. Check the man page of
your shell to find that. For bash it is .profile in you home directory. For tcsh 
it is .tcshrc, and for csh it is .cshrc. 
Usually your program or application is on your desktop. However, this is not a requirement. NCLIP_APP_DIR can point anywhere. It should 
in all cases point to the location of the NCLIP executable. 


Bash Users

Edit your .profile file adding these lines:


export NCLIP_DATA_DIR=~/data

export NCLIP_APP_DIR=~/Desktop/NCLIP

Logout, and then log back in. 
Type env to verify that the NCLIP variables are now set. 


Your data will will now be in your home sub-directory data and your
program will be accessed through the home sub-directory Desktop/NCLIP.


Csh or tcshrc Users

Edit your .cshrc or .tcshrc file adding these lines:


setenv NCLIP_DATA_DIR ~/data

setenv NCLIP_APP_DIR ~/Desktop/NCLIP

Logout, and then log back in. 
Type env to verify that the NCLIP variables are now set. 


Your data will then be in your home sub-directory data and your
program should be in the home sub-directory Desktop/NCLIP.



Macintosh OSX

You can set environment variables quite easily from a Terminal session, or set them up in your shell's start up files. This works fine for UNIX-ey programs. It also works if you launch 
NCLIP from the command line. However, for Mac GUI programs, which don't see variables set in these ways you will need to make an XML file in a pre-determined location. To set up variables that are truly global, and can be accessed from command line and GUI alike, you want to set up an environment.plist file.


Inside the ~/.MacOSX directory (create it if it doesn't already exist), create a file called environment.plist. This is a plain old Mac OS X Property List. Create an environment.plist file that looks like this:



<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
        <key>NCLIP_DATA_DIR</key>
        <string>/Users/YourAccount/YourDataDirectory</string>
        <key>NCLIP_APP_DIR</key>
        <string>/Users/YourAccount/Desktop/NClipMac</string>
</dict>
</plist><HR>






For each environment variable you want to set, just add another  and  pair. The Property List Editor (found at /Developer/Applications/Utilities/Property List Editor.app; requires Developer Tools) can help with the creation and maintenance of this file.


When you log into your system the next time, the environment variables defined in this way will be available to all programs.


Here's an Apple Tech Note on this subject: 
http://developer.apple.com/qa/qa2001/qa1067.html 


Your data will then be in your home sub-directory YourDataDirectory and your
program should be in the home sub-directory Desktop/NClipMac.


The changes will not take effect until you logoff your machine, and then log back in.

After you have logged back in, test the changes by examining


env | grep NCLIP


and seeing if NCLIP_DATA_DIR and NCLIP_APP_DIR are set.



PC

Select Start->Control Panel->System.
Choose the Advanced tab.  
You then should see:
System Properties Window

Choose the Environment Variables button. You will
then see 
Environment Variables Window

You can add the variables to either the user (top window) or to the system (bottom window).
Normally the data path is a user variable, and the application path is 
a system variable. Let's add the data path. Click on the top New button:
Fill in your variable name and value:





Similarly, click on the bottom New button, and add your application
location variable:



When you are done, you should see something like:






How Files are Found


The following table describes the locations used by NCLIP. All directory
changes are made relative to either NCLIP_DATA_DIR or NCLIP_APP_DIR.
In this way, XML files can be moved across platforms. 


Warning: A common error is for the user to not have a HOME or a NCLIP_DATA
environment variable defined. 

In that case, the system will use the application directory for a data directory.

In this case, any sample default session in the application directory will
be loaded without comment. 

So make sure your NCLIP_DATA environment variable is set!

You must have write permission to this directory.


After your first save, the system will remember the new data set location.
(Remember to use the Save As Default Session menu to save those locations for your next session.)





LocationDefaultStored in Default Xml file?Comments



XML$NCLIP_DATA_DIR environment variable, and lacking that, your
HOME environment variable, and lacking that the
location of the executableNoSince we want to move XML 
files between machines, this value is not stored in that file:
It can change when moved to another machine. This is also by default the 
starting point for the location of data files.


DataSame as XML aboveYesWhen you open a data
set, and then if you save your session using 
the Save as Default menu, 
the system will remember the new data location when you restart. 

This may cause problems on a new system (you may not have the default data directory
listed in the xml file), but only the first time you open a new data set.
Application$NCLIP_APP_DIRNoThis is an immutable value.



Help PathThe location of this applications help, usually $NCLIP_APP_DIR/help.Yes
This is the help file location for NCLIP.

In some cases, we cannot find the separate help file. In those cases, we
ask you to locate it by hand, and then save it automatically in the default session file.



Old Help PathUsually $NCLIP_APP_DIR/oldHelpYes
This is the help file for the old application Clip.

In some cases, we cannot find the separate help file. In those cases, we
ask you to locate it by hand, and then save it automatically in the default session file.



Data Maps$NCLIP_DATA_DIR/DataMap
No, but this subdirectory is created at this location if does not exist.
This location contains the XML files that contain the 
data maps used to parse your data sets.

If we do not find it, we will ask you to locate it.

When you share data formats with others, you will place their data maps in this 
subdirectory.








Using these directory maps, users can trade XML files, data files, and data maps across 
machines.


You can view your locations at any time using the Help->Show Locations menu. A typical set of locations is:








Bug List

The most current ToDo list is now in BugZilla at
http://sqlcore.geo.umn.edu/CoreVault/bugs/.

Here is the obsolete list. 


The Splicer window is blank during the splicing process. 


In splice, shift right and shift left mouse only grabs a core, not the whole 
selection.




$Id: FullHelpManual.html,v 1.37 2007/02/24 23:51:18 kamp Exp $

Items To Do for NCLIP


106 Add a cross plot capability to the mdo/track information. (Use a dot plot) 
It is a 2D of shift and window width around the tie point.
108 Delimiter and Quote boxes might be able to have a drop down menu with 
the most common possibilities there (Andy) Or use predictive text 
(autocomplete) on the typed text.
109 Move the number of lines in preview closer to the preview window, 
on the same line as the refresh button (Andy)
115 When registering a file type, allow the option of using a Suffix,
using the (partial) header, and/or the number of columns. 
116 Regarding the file types, show the candidates that fit 
one or more of the above.
127 PDF output? or Screen dump, at least a screen dump of the whole log.
141 Allow people to Clip (pardon the pun), off parts of a section, e.g. 
the top of the section. depends on 198
144 Add a status box that summarizes the culling ala the mac version. 
145 and use a cull table to make the culls. 
146 Add the composite versus depth plot as in the view menu on Clip on the Mac.
153 The refresh on parser only changes the colors in the first 5 rows.
154 Put color codes in the text of the parser to explain.
156 When changing the delimiter on the parser, the refresh only does one row. 
Make it do all of the rows.
157 "Register File" should be map format with a name that can be called up 
from a drop down menu.
161 Make a white slash on the composite (splice?) when there was a splice
between say A1 and B1, i.e. the transition in the composite from A1 to
B1 is marked by a white slash.
See the Mac version for details.
255 How about something like this? I'm not sure what the appropriate 
order is for the items in the right column, but I think putting smaller 
input fields to the right of the header will be cleaner, and separating 
the preview related things from the data parsing things I think also 
makes things cleaner. I also pulled out the NumLimes / Number of Lines 
since I don't think 'Number' is necessary.
257 so can you scale individual track(s) , esp. different when different
data types.
271 On the text parser use a1 as well as a for the leg, site, etc. 
Use the 1218 data set as an example.
273 Why when loading 1218 and using 4,1, A, D is only 
part of the plot showing?
286 Default should not be black on the mac.
287 Mac logfile is storing on the desktop. 
297 Mac: clicking on 'about' on the apple menu seems to go nowhere 
but leaves the NCLIP Menu highlighted
303 Line up the text for the start and end cut with the dot.
307 When bringing the annotation back from XML, the scale is dependent on the 
active track, which can change. Put another way, the annotation is not 
tied to a track. 
315 Can we type in labels.
358 Warn if loading a second copy of the same well/hole.
363 If there is no type on a track, note that on loading, and expose
a "Add Track Type to Active Track" menu when a typeless track is activated.
365 When adding a second and fourth grab the previous one disappears if 
there is no overlap, and if the tie is on the bottom core.
370 When you grab cores, it mis-identifies the core grabbed.
At least the hole anyways - in the splicer window.
371  We should scale only one track if there is an active track.
372 Emulate a three button mouse.
373 Have a y-data scale pop up when scaling.
374 check negative y-data scale. 
375 The wget does not work on the mac, but it works on pc and linux.
376 The wget should have a janus option, that lists the legs  at
http://www.ldeo.columbia.edu/BRG/ and then uses the leg at 
http://www.ldeo.columbia.edu/BRG/online2/Leg199/ and then calls 
http://www.ldeo.columbia.edu/cgi-bin/brg-cgi-bin/Zipit.cgi
377 Save the data map in the global XML.
379 Make install scripts for mac, linux, and xp that set up the environment
variables.
384 When a new data map dir is made on the mac, we do not have write and read
permission to it.
385 On the mac version, the log is in the application, not the data directory.
388 Make sure all of the htm files for all of the htd fiels in help are in cvs.
389  

Deferred
2 NclFileManager.cpp Not all XML formats are supported.
5 NclFileManager.cpp Fill in the body of NclFileManager::OpenBinaryFile
15 NclGridFromTextCtrl.cpp:	 Register the file type. 
17 NclFileManager.h: Not all graphic file formats are supported.
18 NclFileManager.h: We have an open binary file, but 
I do not know what a binary file is.
21 NclGridFromText.h: GuessDelimiter is not yet active.
24 NclGridFromText.h: We use wxTextFile::GuessType and 
ignore the eol parameter. We should override instead.
72 Add a plot for graphics (gif, bmp) file.
86 When we choose 2 Mdo's in ChooseMdo, only the first is plotted.
102 Have a way to turn on separate MDO's in a track.
118 Enable Mdo::StoreDataValue ( long data, size_t *location, size_t dir ) 
119 Enable Mdo::StoreDataValue ( float data, size_t *location, size_t dir )
120 Enable Mdo::StoreDataValue ( H_BYTE data, size_t *location, size_t dir ) 
158 Examine the first few bytes of the file to guess the format. 
159 Store in the format definition, the identifier in the first few bytes.
165 Regarding 164, there is an optional constraint on movement.
167 Add a tutorial mode and menu: Each box will have a "Don't 
show this again" and the menu can unset or set all of the tutorial boxes.
168 Make the tutorial pop-ups be writable HTML help.
169 Add check boxes on the top of the text parser for the roles of columns.
170 Add check boxes on the side for the roles of the rows. (Ignore,
Column Header, data).
178 Separate the user defaults from the data set defaults.
182 Save the scroll positions in the personal preferences and in the session.
211 If we check to see if all fields are loaded in 
NclGridFromText::AddCurrentFilesDataToMdo, we can stop parsing the 
line, speeding it up by a factor of 2;
226 We should be able to delete more than one track at a time.
(We need to split the concept of the active track and the scale track.) 
235 Allow pick of core, section, or whole track, so we can move tracks.
237 Don't shrink the screen size to the screen. On multiple monitors
we want to restore the large screen. Low priority.
238 Make "Shrink to screen" a shortcut, just like autoscale is.
259 Is there a way just to keep a label field at the top of the track so  
that its not affected by scrolling??

Items Completed
1 NclFileManager.cpp Not all Graphic file formats are supported. 17 11/10/05
3 NclFileManager.cpp:  Cancel does not make a graceful exit. 
Maybe a conditional at the modal exit, or a call back from destroy. 
Fixed, 12/15/05
4 NclFileManager.cpp This is where we need to close the preview window, using EndModal? 11/3/05
6 NclGridFromText.cpp Make the number of rows in the preview grid match the number of rows of data. 34 11/10/05.
7 NclGridFromText.cpp We use wxTextFile::GuessType and ignore the eol parameter. We should override instead. 24 11/10/05
8 NclGridFromText.cpp GuessDelimiter is not yet active. 21 11/10/05
9 NclGridFromText.cpp:	 We need to clear the previewGrid before starting AddDataToPreviewGrid. 32 11/10/50.
10 NclGridFromText.cpp:   We ignore the quote when parsing a line. 22 11/10/05
11 NclGridFromText.cpp:   The line parser accumulates the columns rather than starting over. 11/7/05
12 NclGridFromTextCtrl.cpp We set the file name of the text parser, and show it here for now. 11/7/05
13 NclGridFromTextCtrl.cpp Experimenting with the placement of the preview window. 34 11/10/05
14 NclGridFromTextCtrl.cpp:			 Find a way to make the preview grid sizing automatic. 34 11/10/05
16 NclGridFromTextCtrl.cpp Make the refresh grid fit the window. 34 11/10/05
19 NclFrame.h: This is the first version of the frame. More to come. NA 11/10/05
20 NclFrame.h: The frame needs to manage file opening, with the text file type first. 11/10/05
22 NclGridFromText.h: We do not use the user provided quote. 
Use the ReadMe file as a test. "NCLIP Project" should be in one field.
12/19/05
23 NclGridFromText.h: The delimiter is ignored. Fixed. 12/12/05
25 NclGridFromTextCtrl.h: Open the preview window from this object. 11/10/05
26 NclGridFromTextCtrl.h: Fill out RegisterFileType. See 15. 12/19/05
27 NclGridFromTextCtrl.h: Make the preview window refresh when the delimiters are changed. 11/10/05
28 NclSession.h: So far, the file manager is only stubbed out. 11/10/05
29 NclGridFromTextCtrl.cpp The Preview window does not open to the right size. Maybe hardcode it? Solved by 34. 11/10/05
30 NclGridFromTextCtrl.cpp Putting too long of a trailer will get rid of the preview window. 34 11/10/05
31 NclGridFromTextCtrl.cpp Put in too many header lines, and the preview window covers the buttons. 34 11/10/05
32 NclGridFromTextCtrl.cpp We need to get rid of extra rows when you enter a large number of header lines, and then reduce them. Used NclGridFromText::ShrinkPreviewGridRows in NclGridFromText::BuildPreviewGrid. 11/10/05
33 NclGridFromTextCtrl.cpp When the preview window is too long, e.g.the number of header lines is large, the frame overwrites the buttons.  I used Best Fitting Size instead of AutoSize. 11/10/05
34 NclGridFromTextCtrl.cpp When the preview window is too long, e.g.the number of header lines is large, the frame does not shrink when the header is made smaller. I used Best Fitting Size instead of AutoSize. 11/10/05
35 NclGridFromTextCtrl.cpp Scroll bars only appear on the grid after the second refresh. 
12/20/05
36 The first row first column of the preview is obscured by either 
the phrase "Header" or the phrase "Data". Fixed. To put it back
(for debugging) define _SHOW_GRID_HEADINGS. 12/19/05
37 The grid data object disappears when we destroy NclGridFromText.
I work around that now by storing a copy of the Mdo before I destroy it.
12/19/05.
38 The copy Mdo we make is not deleted, and so we have a memory leak. 
Fixed, see 40. 12/5
39 When we click on Graph this Data, we should only load the 
the selected columns into the MDO. 12/26/05
40 GetXmlArray has a fixed leak. Put that fix into GetXmlAttributes array. 12/5
41 The items listed in 40 use frame and mdo stuff. So,they should be 
in those classes instead. 12/19/05
42 GetXmlValue may have a memory leak similar to 41. I fixed it. 12/6
43 Put an hour glass up when loading a grid into the graphics. 
Used ::wxEndBusyCursor 12/19/05.
44 although MdoTest is free from leaks, NCLIP has a small leak even when we
do not load a grid. I used _CrtSetBreakAlloc(2075) to break at the alloc
for that leak, since the debug printout from 
  _CrtSetDbgFlag ( _CRTDBG_ALLOC_MEM_DF | _CRTDBG_LEAK_CHECK_DF ); 
said {2075} meaning the leak was from the 2075th call to malloc.
The leak was head (alloc'ed at line 39 of NclMdoList) was 
not freed at the end of the object. This took about 4 hours to find. 12/13
45 NCLIP crashes when we load a grid. Maybe I don't wait long enough?
Fixed by using calling RegisterMdo in a different place. 12/16/05
46 When we cancel loading a grid, NclGridFromText crashes the program.
Fixed by using calling RegisterMdo in a different place. 12/16/05
47 Instrument NclGridFromTextCtrl to log it.
Fixed by using calling RegisterMdo in a different place. 12/16/05
48 NclGridFromText is not being destroyed. That is the current mem leak.
Fixed by using calling RegisterMdo in a different place. 12/16/05
49 The file open and close in GridText is screwed up. It causes an abend.
Make the file open sticky. Done, wrote routine NclGridFromText::FileOpen
12/16/05
50 I think the leak is from a wxString close when we leave AddDataToMdo in 
NclGridFromText, in the unlock of fileName. Did we destroy the file ptr?
We probably need to have only one open and close per instantiation.
Nope, see 51. 12/16/05
51 AddDataToMdo, when called from Clean tries to overwrite it's memory.
Fixed by using calling RegisterMdo in a different place. 12/16/05
52 We execute InsertMdo from RegisterMdo from Clean, l321 of NclGridFromTxt
whether we cancel the loading or not. Supplanted by 54. 12/16/05.
53 In TextCtrl, Refresh after reset causes it to  crash at 
L l199 text::SetNolHeader. textPrser is NULL at that point.
We removed the init from OnResetClick in TextCtrl. 12/16/05
54 We need to register the Mdo by copying it before destroying any 
objects when the "Add Data to This Frame" is pressed in TextCtrl.
(This is the ID_OK logic path.)
This should fix 52 as well. 12/16/05
55 I fixed a memory leak in CopyMdo: I was copying the headers 
contiguousDirections array to the new mdo, instead of copying its values.
12/16/05
56 Move GetXmlArray and GetXmlAttributes to Mdo, since it uses mdo methods.
I was mis-informed, it used a list that I called mdoList, but had nothing
to do with Mdo's. I changed the name to elementList.
57 I can't resize the grid window to see more rows. 12/19/05
58 If a line has no breaks, we are not parsing it.  12/19/05
59 Add a number of preview lines box to the NclGrid. 12/19/05
60 Plot the Mdo's in the MdoList in NclFrame. 2/10/06
61 Make the axis dimension of an Mdo the meta track. I now use a depth axis in the first column. 2/10/06
62 Add drawing function to each tracks Mdo. Done, but buggy. 2/10/06 Supplanted by 90.
63 Make sure every track has an Mdo, or a NULL. Done. 2/10/06
64 Add a "Plot" menu with an AddData for m_left and M-right. 2/4/06
65 Have the Depth Axis scroll box in Ctrl change the value in Txt 
without a refresh. See #69. 2/10/06
66 Debug that the DepthAxis is indeed in column 0 of the Mdo. 2/10/06
67 The count in the tracks does not come back as > 0 2/6/06
68 NclGridFromText::AddCurrentFilesDataToMdo adds an empty depth axis
that screws up the scaling. 2/10/06
69 When the depth axis is changed, do not require a refresh to make it effective.
I added StoreMenuValues to TextCtrl, and called it right after the OK 
button was pressed. 2/10/06
70 Add the column names to col10.dat. 2/9/06
71 Add a sort on data in the text list. Not needed. Supplanted by 81.
73 Add annotation to the track for the well log segment. 4/3/06
74 Add autoscaling menus. I use a zoom in and out now. 2/10/06
75 Add pick on a track. 3/17/06
76 Add a splice to the composite track. 3/17/06
80 Activate the save and retrieve on the Xml Session. (The
objects have it, but the menus need to hook up to that.) 3/15/06
81 Adjust the drawing for breaks: A break in the depth scale should
allow for a disconnected graph. 4/6/06
82 Add a zoom in and out. 2/10/06
83 You need getmax to work on a column. Otherwise the scale will include the depth column. 2/10/06
84 Do we want to scale individual Mdo data columns, or just the track as a whole?
(We currently in NclCanvas::OnDraw scale on column 1, since column 0 is the depth column.) Track as a whole. 3/31/06
85 The plotting scale should take into account the number of tracks. 2/10/06
87 Add a Clear Graphics menu. 2/10/06
88 In the frame, rename the previewCanvas to the compositeCanvas 2/11/06
89 Pick up pieces from the displayCanvas and put them on the compositeCanves. 3/24/06
90 Add graphic context information to the Track Object. 3/19/06
91 Add the zero axis to the track's display. Make the default center 
on the 1/2 way between the max and the min of the data, not on zero. 
3/20/06
92 Add annotation and ticks to the track's display. 4/3/06
94 Replace Right Window gives fault in NclReplace. Cannot reproduce, need
more detail. 3/17/06
95 Change "Right window" to "Composite window"
96 Add Help About. 2/11/06
97 Add a spacing parameter between the tracks. 3/14/06
100 Have a "Go to Bottom" on the GrdtTxt window for very long files.
101 Test the grd input to see if it can handle some very long files.
93 Add a spacing parameter to the columns in the track's display. 3/15/06
98 Don't plot the first point of the mdo. why Not? Overruled by 81. 3/29/06
99 The Mdo's are being plotted relative to the scaling of 0 between their max's and min's, not zero relative to the first MDO. supplanted by 84. 3/26/06
103 Install and MDO algebra: Correlation, stack, add, multiply, divide, 
affine transformation, AGC, clip. (Clip, especially near the edge of a core.)
104 Insert Andy's comments: 
ftp://ftp.evl.uic.edu/pub/INcoming/andy/nclip-tweak.tiff Superseded
by 106-110 4/15/06
105 Add a Line Thickener and/or bring the plot in front. 3/13/06
107 Make the plot scale off of zero as needed to center the plot. 3/23/06
110 I'm also wondering if 'NumLines' is too programmer-ish. Maybe just 
'Num Lines' or even just 'Lines' (Andy) 3/23/06
111 Make the zero axis movable. Supplanted by 91, 3/26/06
112 Make the default view show all data in 4-5 standard deviations of the
zero axis. Set the number of SD's in a menu. Take from the average in a window.
Supplanted by 84 etal. 3/26/06.
113 Clip the drawing of the outliers to the far right of the track. 3/31/06
114 Isolate the track drawing in NclCanvas::OnDraw to a track draw function, 
thus using the track's graphic context., 3/17/06
117 Make an outlier's menu that specifies the way we clip. See #112. supplanted by 84 et.al. 3/26/06
121 In NclTrack::Addtrack, we use the first MDO loaded to initialize the metaTrack. We need instead to allow a smart meta track. No longer needed, 3/25/06
122 We need to change the coordinate system to algebraic for the horizontal case.done, 3/17/06
123 Make the graphic context turn points on and off. done, 3/21/06
124 Make the colors on the composite match the tracks.done, 3/21/06
125 Put the titles in the correct spot on the vertical. 4/5/06
126 Put up a warning when there is an atof error in the parser.
4/19/06
128 Rename "Choose Mdo to Plot" to "Choose data set to plot" 3/27/06
129 The "don't draw Line when depth is not increasing" in OnDraw is broken. 
See #81 4/15/06
130 Visual feedback when in splice or Sagan Mode 4/6/06
131 The feedback in #130 can be a subtle change in the background. 4/6/06
132 Or for 130 use a different icon and window name. 4/6/06
133 When there is no XML def session, say that, and don't say "We can't parse the file" 4/5/06
134 When moving a cut move all of that 1.5 meter section to the composite 
window, and 
then in the composite window use the ties to set which part of each section 
is used at that depth. (This is in Splicer, not in Sagan.) Depends on 198
3/23/06
136 If there is no session file, save one upon exit. 4/5/06
138 Annotation is in meters. 4/5/06
139 Show the boundary of a section using the annotation. depends on 198
4/21/06
140 We lost the "Wait Cursor" when saving a session file. use a thermometer.  3/31/06
147 the Open session looks like a save session, i.e. it has a "Save" instead of an "Open" button. 3/27/06
148 Add an "Un-Activate" menu item. Just choose an active track to 
deactivate it. 4/21/06
149  If there was no session file, there is no "Save As name" 4/3/06 
150 Set all tracks to the same scale. 3/31/06
151 Change "Num Lines in Header" to "Number of Lines to Skip" 3/23/06
152 Depth Axis Column should use letters. 4/15/06
160 Assume a three button mouse. OK. 3/25/06
162 Make the "Activate" only highlight the center axis, not the data plotted. 4/6/06
163 Add a Scale menu to rescale the data. 3/31/06
174 Do not toggle vertical and horizontal. Make it and absolute change. 
Otherwise, a screwed up XML file may show horizontal in a vertical window, 
and vice versa. 4/6/06
175 We do not save the defaultScale in Frame in XML. 3/31/06
176 Ncl2DTransformation is not putting the right screen size onto the xml. 3/31/06
177 When first loading a text file in Linux, you have to scale the
file before it appears. Auto Scale 4/15/06
179 On the mac version there are two windows menu. Rename ours. 4/13/06
180 On the mac version, the zoom does not work. May involve #181. 4/13/06
181 On the Mac version, the scale does not remember DepthScale and 
DataScale between loads. See #180. Also, this may be because of the 
elimination of the Unsized method in NclBase::XmlTagIt for unsigned long.
4/16/06
183 Scales are not set to sensible values when you open without a default session file.
Fixed by #185.
184 The Ncl2DTransformation Orientation can be different than the canvas
when starting from scratch. Fixed by #185. 5/4/06
185 I need to open the Scale menu right after opening a session to get
the horizontal and vertical to work. I think the scale is loaded
right from xml. The depth scale are inverted in the control. 
We added depth scale and data scale explicitly to the XML, whereas
before we were (incorrectly) calculating it. 4/5/06.
186 There are too many indents when saving a session just after opening 
a session.
4/19/06
191 Put an annotation buffer on the top of the drawing, to show 
the name of the hole. 4/15/06
192 When loading a file from scratch, the scales are not right. Added AutoScale. 4/7/06
193 Set trackOffset on opening. 4/7/06
194 Set Scales on opening. Added AutoScale 4/7/06.
195 Add trackOffset to the scaling menu, and remove it from the pulldown menu. 4/11/06
196 Use FLT_MAX in the get min and max of the mdo. 4/13/06
197 The default track spread is set to 0 when a text file is added. 4/7/06
198 Store the section information in a section table, and use it for 
annotation and plot breaks. Yea! 4/21/06
199 Save as default save in the env variable dir HOME, but opens in the 
exe's home dir. I added the dirname so the user is aware.
200 NclSession has an Xml output, but needs an Xml input. 4/13/06
203 When NCLIP does find the Default Session file, the window is
positioned at 0,0, and this makes the title  bar in accessible. 04/13/06
204 When starting without an xml file, we get the horizontal graphing
with a vertical window after loading text data.
4/19/06
205 The location of the default file is in the directory $HOME, not in
the exe's directory. Maybe that is OK.
4/19/06
206 When starting with no session file, there is a memory leak.
4/19/06
207 In a fresh start, Save As Default is in the application directory,
but on startup, we read the file in the $HOME directory.
4/19/06
208 On startup, the mirror on display and composite canvases does not match.
4/19/06
209 The SaveAs does not save to any but the default file. 4/22/06
210 We don't seem to remember horizontal versus vertical after 208 
was installed. I made the horizontal/vertical case an if else,
so one and only one gets set. (Before, I had the first overriding the second.)
4/20/06
214 There are 2 control-t's in the menu system: One for Splicer/Sagan
and the other for load-text. 3/23/06
215 activeTrack is being re-set in both display and composite. 3/23/06

187 Make break in the drawing when the section changes. See 135. 4/27/06
224 On the mac, changing to Sagan on a new session, and loading 
causes a crash. I no longer change the menu color. I 
change the foreground color as a Splicer/Sagan cue. 4/27/06
230 Changing from horizontal to vertical to horizontal on the PC changes the
window size. It becomes square. Fixed in Horizontal and Vertical locals
in NclFrame. Also added SetBarlocation in NclSplitter. 4/27/06
223 The track spread does not change with the zoom 4/26/06
229 If the zoom factor is changed on the PC, the zoom stops working.
It only works on the first zoom if there is an integer value. 4/27/06
228 Change the title orientation when changing vertical and horizontal.
4/27/06
222 Allow the axis and directory link to turn on and off.
I did this by changing the diagnoticsLevel to an integer.
If it is > 1 we show the axis and file info.
If it is > 4, we show the log entries.
4/27/06
218 Make the default background black, and the lettering white. 4/27/06
227 Make the delete key delete an active track. 4/27/06
216 Composting is shifting of the cores relative to each other.  4/27/06
212 Too many refreshes on the move of mTrack. 4/27/06
213 The method NclTrack::FollowMe does not do enough to drive the 
plot to the right place, unless #212 is interfering. Do #212 first.
4/27/06
201 Do not call it NCLIP.app because it is not a .app system. 
Basically a .app is a directory and it does not seem to be that your's
is.  It looks like it's just a file.  So I would call it just NCLIP.
4/27/06
202 You need to run this command so that people can just double click
on your executable and have it be able to find your xerces dylib:
install_name_tool -change /usr/local/lib/libxerces-c.27.dylib @executable_path/libxerces-c.27.dylib NCLIP
4/27/06

219 Color changes are visual clues for moving: yellow for moving, green for moved.
So, make a color palette to show choose all of the colors. 5/3/06
164 Middle button sets the reference point for a tie, and then holding
the right button on the other track will pick up that section and (a)
move it, and (b) put it on top of the reference track.  Depends on 198
5/4/06
220 Pick more than one file of the same format when loading. 5/6/06
245 Show only core annotation. 5/6/06
244 Zoom of more than 1 overlaps the core. 5/6/06
217 Pick a reference point on track A, and then grab a similar 
point on track B,
and slide it past the rp of track A to show the autocor, which has a 20 meter
window. 5/4/06
171 Make a move method in the gui. Use it during the tie. 5/3/06
172 Make a copy/move method. Use it during the depth correction phase
in the display canvas. 5/3/06
234 Make the splice on the right a non-floater with no track spread, 
so we can build the log. Supplanted by Collapse/Expand composite. 5/1/06
239 The dll for the pc version is not included in the zip. Fix mvPcMm1 5/6/06
240 The PC needs the dll MSVCR71.dll as well. Why? Check the compilation type. 
5/6/06
241  Same as 235 for MsVCp71.dll Also that is not in the index of the 
binaries web page. 5/6/06
242 Separate the track spacing, making it a 0 on the right track. 5/6/06
254 The pop up autocor covers the current window. 5/17/06
247 Combine make the first process compositing 5/15/06
248 Make the latter 2 Splicing 5/15/06
253 The refresh window when compositing does not always cover the 
whole clip. 5/19/06
250 Change the windows names: Left: composite, Right: Splicer 5/20/06
251 make the C3 be hole-name3 5/20/06
221 Show the hole number on the graph. 5/20/06
142 Pop up an auto coor window when doing the ties and composites. 5/2/06
231 When there is a moving track, do make a new one until the old
one is deleted. Otherwise, you cannot pick up and put down during xcor
5/20/06
232 We need to normalize the cross-correlation with sum of the squares 
of the data. 5/20/06
135 Use the display window for lining up the logs before moving a section to 
the splicer window. (Splicer, not Sagan) Depends on 198 5/20/06
188 Build an affine table that holds the start and end of a section 
and of a core,
and holds the type of the core. 6/1/06
77 Add help files, that are built on a base, and edited and added to 
by the user. 6/1/06
137 Save the grid associated with an mdo, and use it in the output of the 
affine table. 6/02/06
190 Regarding 188, use it to post the section number. 6/2/06
189 Put the current annotation from #188 into the status box.
We put in cross plot info instead. 6/7/06
236 Output right hand splices as the affine table. 6/6/06
249 Output of Compositing is affine table. 6/1/06
256  Cores  should appear as continuous. 6/7/06
270 Change load binary file to load with known format 6/8/06
260 The help files in the Mac version seem to come from a strange location.
Make sure they come from the sibling directory of the application. 
I added a "find dialog" if the files are not found. 6/8/06
79 Activate contextual help. 6/13/06
262 Make the affine output match Sean's specs. 6/13/06
274 Add a real depth column to the mdo in canvas, follow mdoDepthCol. It is 
called mdoOrigDepthCol. 6/13/06
275 Make the affine write out and read in on the session xml. 6/13/06
282 Make the reference point red 6/16/06
283 make the moving point green 6/16/06
280 We are not reading in all of the Affines in xml. We are only reading the first one. Should we combine them into 1 affine object? Yes. 6/14/06
263 Sort the affine to depth. 6/13/06
265 Store the original depth and the changed depth in separate columns of the
mdo. 6/12/06
266 Make unadjusted tracks yellow, adjusted green. 6/16/06
267 Move the save file menus to under the file menu. 6/10/06b
166 "splice to tie" to complete the splice on the composite. 
(On the composite there is also an overlay like in the plot window.)
264 When a core is adjusted, change its color. 6/15/05
268 Multiple files should load with the top file picked first.
Done, changed in NclFileManager::OpenTextFile. 6/16/06.
246   there's 2 things going on:
A)The old software called it compositing --- you call it aligning  
(output is "affine table" relationship of the cores relative to one  
another)
B) "        "     "     calls the next part splicing ---you call it  
compositing (grabbing of cores) and clipping  (tying the splice  
together) and (Output is creation of "splice table" which lists which  
cores make up splice and at what depth they are "clipped...tied  
together" Renamed. 6/16/06
277 If loading an affine from the session, adjust the depth versus real depth of the mdo.
Not needed, since 276 will do it. 6/15/06
276 If loading an affine from an affine file, adjust the depth versus real depth of the mdo.
done. 6/16/06
281 Load multiple data sets in lexicographical order. done. 6/16/06
278 Model the affine text output on the affine xml output. 6/16/06
291 The axis is appearing now. This was only when Annotate =1, not when it was 0. 6/28/06
289 Reload of data set needs to be tested. done. 6/28/06
285 Typo: in the track deactivate is spelled wrong. In the on track should be one track. 6/28/06
284 The help files should say in the window the file that should be picked. I did it for 
all FullFileName calls. 6/28/06
293 Put confirmations on the Delete Active Track, and the New Session tasks.  6/28/06
290 Setting an active track highlights the axis, not the track. This is only true if annotate = 1. 6/28/06
277 Make the xcor windows exactly the same. Use GetTopBottomCore when making a reference point
i.e. on middle mouse down. 6/28/06
173 The save session as box should default to the name of the opened data file with Xml Attached. We use session.xml instead, since there can be multiple tracks. 6/16/06
-----------------------------0.97-----------------------------
295 We draw only the points in the window, and connect the missing points at the border,
distorting out of window lines. This is only in the vertical mode.
I was clipping on data, something I did not need to do. When I removed 
data < sDTop.y || data > sDBottom.y  || it was fixed. 6/28/06
294 Maybe add a novice mode to eliminate confirmations. 6/28/06
279 The m_width and m_height are switching when we save and retrieve the session xml. 6/28/06
296 When a shift is completed, the active track only highlights above the shift, 
probably because the shifted color is not using the highlight pen. 6/29/06
292 Make the Undo apply to the active track. NclCanvas::UndoLastShift 6/29/06
258 In following up on 3 above, is there a way to show the horizontal  
scale of values somehow (assuming you are working vertically) for a  
track(s), similar to the vertical stuff. 6/29/06
252 there is an extra offset in the x-coor window. fix it by using 
the same window for both logs. The width of the window should be a user input. 6/29/06
261 On affine table input, 
look for sub-leg, mbsf, and mcb by counting the number of  
elements in a line. If they are there, use them, otherwise don't. 
Started. See NclAffine::ReadLegacyAffine.
I did composite, mcb as the second dropoff, and mbsf as the third. 6/29/06
225 We would like some un-do commands.  We can undo all composites. We 
will do the same for splice. 6/29/06
243 The default load is vertical, even if the present session is horizontal.
Correlation is used by both  processes (modes) with various options. 6/29/06
-------------------------------0.97a-----------------------------
298  When span core for xcorr is checked, it seems to be only for a section.
No, it is for the whole window. The drag is for the length of the 
window when span core is checked. 6/30/06
299 Add to help what the numbers in the xcorr window mean. 6/30/06
300 Hide the composite window when opening the splice window, and vice versa.
6/30/06
---------------------------------
288 The ref point is posted on a restart, but it is not chosen, i.e. a right click on a log
does not stat the xcorr. 7/4/06
--------------------------
302 The Ref point is inverted (x and y swapped) when restored from session.
Supplanted by 307. 7/5/06
304 In splice, grab core only grabs the top core.		 7/5/06
305 After a cut the active track deactivates. It should not. 7/5/06
306 You must first activate a track should say In order to do a grab, ....,
and the title should not read "No reference point" 7/5/06
318 When starting a session, we now do vertical and horizontal correctly. 7/11/06
313 The floater should reflect the actual window. 7/11/06
314 Is there is a way to highlight the floater in the xcorr window, but floats.  7/11/06
316 We should link the annotation to a window position, a x and/or y of the track. 7/11/06
311 F1 in the composite mode brings up the splice help window. 7/12/06
301 When dragging a core with span core unchecked, only pull along the 
correlation window. 7/12/06
309 When picking a reference point in the Splicer mode, make the reference
track the active track. 7/12/06
------------------------------0.99--------------------
319 If you F4 the cross plot window, and then restart composite, it crashes. 7/15/04
330 The warning of failure to save a session file appears more than once.
9/13/06
323 Remove the Ref annotation, not just the <--Ref when restoring a session. 6/15/06
325 You need a positive length in the corr window for the Xcore to 
show in composite. We now bring up a warning box. 9/13/06
326 Add a log line for the start and end of composite and spclie mode,
to help solve 325.  6/15/06
327 When 2 composites are far apart, you only get an xCorr when they 
are near their start point, not when they are near each other.
It seems the composite is based on the delta move from the ref and the 
move point, and not on the absolute depth. 6/15/06
332 Complete the ViewLog method in frame. 6/15/06
333 Make all windows show at least partly on the screen.  6/15/06
334 Add an "AutoArrange" menu to the View menu for 333. 6/15/06
335 Save the composite splice state and resotre it from the session file. 6/15/06
312 If you F4 the affine or splice summary window, and then reopen it,
you get a crash. 7/15/06
342 The affine preview window position is not remembered. 7/17/06
338 Make the expert mode the default. No.
343 Stagger the annotations on the track label. 7/17/06
341 The start and stop of the composite and splice mode should
reflect the current splice, composite state. 7/17/06
337 Check the loading of a lagacy affine table. It fails on the MT95.dat sus 
stuff without a complaint. 7/18/06
345 If a value in the summary window is NCL_UNDEF, show the string Undefined and not the number. We decided to not show it. 7/18/06
339 Import of an affine table should fail with warning when in the splice mode.
Nope, it is OK. We can realign when we want. 7/18/06
346 Change the default tic mark to 1 and annotation to 5. 7/1/9/06
344 Splicing variable is not following the middle mouse button. 7/18/06
340 Add the splice type of cross corr as an option on the composite mode, 
e.g. shift-middle mouse button. 7/19/06
331 When you have a 0 length window in the Splice mode, the color cue
is for a non-zero length window. Instead, it uses the last non-0 length.
7/19/06
331 When you have a 0 length window in the Splice mode, the 
xcorr does not change, and you do not get a warning.
We now put up a warning box and stop the splicing if the window
length is 0. 7/19/06
328 Make sure that the Window Length of XCor is positive when loading it from
XML. Superceded by 331.
324 When you have a leftover ref point from the splice mode or the xml restore,
and you start the composite mode, the composite process is ignored, you 
grab the whole core. Fixed by 288. 7/19/06
317 When switching to Composite mode, remove the left and right cuts. 7/19/06
310 Have the splicer html input put up in NclSpliceFrame, not the affine html
window. 7/15/06
336 On a Mac, opening the lagacy splice file only allows txt extensions,
not dat or other extensions.7/21/06
272 Add a Get Inventory button in NCLIP. 7/15/06
308 What is the ODP Id used in the Splice Window and the Composite window? y/21/06
320 If the window is zero length, and xcorr in splice crashes it. 7/20/06
321 If you are in composite, the xcorr colors do not match. 7/21/06
322 Set up the XCorr in Splice Mode to work in both windows. 7/21/06
329 The xcorr color on the composite mode is not over-riding a moved track 
color of green. 7/21/06
---------------------------0.991---------------------
355 Show hide session file fails if the data was loaded from a different directory. 8/2/06
356 If in horizontal mode, when adding a vertical session file, we display 
vertically, but still have horizontal windows. Fixed in 
NclFrame::ShowHideSplicer 8/3/06
357 Save does not save to the last opened session file. but Save As remembers
the right location. In NclSession::Close, I was changing to the default
dir if the save name was the default file name. Removed that. 8/3/06
353 We need to walk through all menus and menu items and decide if  
they (A) should be there (B) If so, are they named correctly or  
clearly (C)  Have you explain what some of them do in general??
Can use help->What's This to show the help for each menu. All
menu's now have help. 8/3/06
352 I save an affine table, then try  
to work with it -- and can't interact with anything until I start new  
session or erase old session file? I suspect this is a corrupt or old
xml session file. The pick is based on the canvas name, which
may be blank if using an old XML file. See if your default session file
has " <NclCanvas name="compositeCanvas">" near the top. If instead it
has  <NclCanvas name=""> things will not work. You can view the 
session file using "View->Show/Refresh the Session File." Added this 
to the FAQ. 8/3/06
354 Need to simplify track labels.... something like Site 926  Hole A  
would be fine.... If it had data type, so much the better...
Simplified. 8/3/0
350 When you switch between horizontal and vertical and then hide  
splicer window and then bring it back, it comes back  
horizontal ...see attached image. fixed. 8/3/06
----------------------------1.0-----------------------------------
361 Change Toggle Dots to Hide/Display Data Points 8/4/06
359 When you Save the Affine table, and then start over,
either wiht a ctrl-n (New Session) or quit the program and restart,
and then load the original data, and then import the affine table,
you cannot set a reference point. 
Fixed: I moved the SetTitle("") from init to the NclFrame constructor.
before it was settng the title to "" when starting a new session, and
the ref point is only installed when the title is Composite. 8/4/06
362 Drop the S:, H: and T: from the annotation. 8/4/06
360 Change "Set Gravity" to "Vary Splice Window Size/Vary Composite Window Size"
We now call it the Grow/Shrink control. 8/4/06
351 Add a warning for multiple sessions. Added a whole bunch of 
caveats to NclFrame::SessionAdd. 8/4/06
143 the ties occur in the Composite Window when more than one section
 is moved into it. depends on 198 8/4/06
364 Add Import Composite Track in legacy and xml mode. Just do it from the output composite. 8/4/06
347 Add Export Composite Track in legacy and xml mode. 8/4/06
366 The splice window start cut is not refreashing. 8/4/06
348 Write the InputSplices for xml and txt. 8/4/06
349 Change the intx depths on the splice output to top of section instead
of top of core. Output it in cenimeters. 8/4/06
-------------------Version 1.002 -----------------------
368 Fix the help upload to web site
from the RSync script to put help in the help and not 
the help/help directory. It is not in mvWinMm1 9/19/06
378 The default application location varies by system, and is not 
related to the location of the application, e.g. on Mac it is /usr/local/share.
So we need to add an environment variable called NCLIP_APP_DIR that will
locate the application, and hence the help files in a system independent 
way.
269 Save the text parser state. 
380 Alt-Q should work in all windows.
381 Save the help window position in the help file.
382 On refresh also bring up the help window.
367 Update all the menu snapshots in the help.
369 There is not splice preview window on the mac-non-intel. We have
modified the f2 key to fix this? It might have been off window.
Hit f2 to bring it back.
383 We now have a set of global keys: F2 to raise and show all windows, 
F5 to refresh, and alt-q and alt-Q to quit. All global keys work in all active 
windows, except for the help and the affine preview windows.
386 On the mac, the help file does not show from the composite menu. There is 
a help button, use that.
387 ON the mac, chosing Quit from the application menu only closes that window.
Now the quit on each window is wired to the quit on the main frame.






File Formats

There are two file formats documented here:





Affine File Format








Affine Table General Information:


The AFFINE TABLE contains the depth offset values which are
used to build a composite depth section using multiple-hole
core data. 


The AFFINE TABLE depth offsets are determined using the
tie/correlation/depth-shift features of the 
Splice COMPOSITE tool
under the PROCESS menu item. The depth offset values are
determined when cores are depth-shifted to match core data
from adjacent holes. 


The AFFINE TABLE should be saved frequently as the
compositing progresses. The file is written as simple ASCII
text - these data can be downloaded and pasted directly into
the Initial Reports volumes.


The Affine table format is as follows:


leg, sub_leg, site, hole, core, coretype, section, ODP
depth, meters below seafloor (mbsf),  depth offset (x.xx m),
Y/N (Y=core has been correlated and depth-shifted),  meters
composite depth (x.xx mcd).

Some items may be missing. In the XML version that is not an issue. 
In the text version, we must account for missing items in this order:



OrderNameDescription



 If there are 10 or fewer columns
 SubLeg
 The name of the SubLeg used. If there are only 10 columns, we
assume the sub-leg is missing.





 If there are 9 or fewer columns
 ODP Depth
 If there are 9 or fewer columns, we assume the ODP depth is missing. It 
can be inferred from the  core number.





 If there are 8 or fewer columns
 Composite Depth
 If there are 8 or fewer columns, we assume the Composite Depth
if missing. It can be inferred ODP depth and the Depth Offset.






Note that we always need the core number and the depth offset.

Here is the same affine table in several formats. Note that in this case, 
the sub-leg field is missing. NCLIP shows the HTML version, and can both import and export the 
XML and Text versions. 



Text Version



154		926	A	10	H	4	87.27	0.90	0	88.17
154		926	A	16	H	6	148.12	1.18	0	150.19
154		926	B	1	H	1	7.89	1.53	0	9.42
154		926	B	2	H	6	18.94	1.70	0	22.17
154		926	B	3	H	4	28.52	2.33	0	34.07
154		926	B	7	H	3	65.47	1.20	0	72.22
154		926	B	11	H	2	103.17	0.70	0	110.62
154		926	B	15	H	5	148.84	3.15	0	159.44
154		926	C	4	H	1	31.04	0.15	0	31.19
154		926	C	9	H	4	83.82	1.38	0	85.34





HTML Version


Here is an html version of the affine table, as seen in the preview window:




LegSub-LegSiteHole
CoreCore TypeSection
ODP DepthDepth OffsetmbComposite Depth




154926A
10H4
87.270.90088.17




154926A
16H6
148.121.180150.19








LegSub-LegSiteHole
CoreCore TypeSection
ODP DepthDepth OffsetmbComposite Depth




154926B
1H1
7.891.5309.42




154926B
2H6
18.941.70022.17




154926B
3H4
28.522.33034.07




154926B
7H3
65.471.20072.22




154926B
11H2
103.170.700110.62




154926B
15H5
148.843.150159.44








LegSub-LegSiteHole
CoreCore TypeSection
ODP DepthDepth OffsetmbComposite Depth




154926C
4H1
31.040.15031.19




154926C
9H4
83.821.38085.34






_____  



XML Version



<AffineTable>
  <NclAffine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>10</core>
      <coreType>H</coreType>
      <section>4</section>
      <odpDepth>87.267700</odpDepth>
      <depthOffset>0.900028</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>88.167725</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>16</core>
      <coreType>H</coreType>
      <section>6</section>
      <odpDepth>148.119583</odpDepth>
      <depthOffset>1.175036</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>150.194641</compositeDepth>
    </AffLine>
  </NclAffine>
  <NclAffine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>1</core>
      <coreType>H</coreType>
      <section>1</section>
      <odpDepth>7.890242</odpDepth>
      <depthOffset>1.525047</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>9.415289</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>2</core>
      <coreType>H</coreType>
      <section>6</section>
      <odpDepth>18.940584</odpDepth>
      <depthOffset>1.700053</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>22.165684</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>3</core>
      <coreType>H</coreType>
      <section>4</section>
      <odpDepth>28.515881</odpDepth>
      <depthOffset>2.325072</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>34.066051</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>7</core>
      <coreType>H</coreType>
      <section>3</section>
      <odpDepth>65.467026</odpDepth>
      <depthOffset>1.200037</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>72.217232</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>11</core>
      <coreType>H</coreType>
      <section>2</section>
      <odpDepth>103.168198</odpDepth>
      <depthOffset>0.700022</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>110.618431</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>B</hole>
      <core>15</core>
      <coreType>H</coreType>
      <section>5</section>
      <odpDepth>148.844620</odpDepth>
      <depthOffset>3.150098</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>159.444946</compositeDepth>
    </AffLine>
  </NclAffine>
  <NclAffine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>4</core>
      <coreType>H</coreType>
      <section>1</section>
      <odpDepth>31.040960</odpDepth>
      <depthOffset>0.150005</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>31.190966</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>9</core>
      <coreType>H</coreType>
      <section>4</section>
      <odpDepth>83.817596</odpDepth>
      <depthOffset>1.375043</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>85.342644</compositeDepth>
    </AffLine>
  </NclAffine>
</AffineTable>




updated 4 July, 2006





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author








Splice File Format



The user can choose to save the tie points which define how
a particular spliced data record was constructed. 


The user types the name of the SPLICER TABLE  (e.g.
SiteXXXX.splicer.table) in the "Save Splicer Table"  dialog
box.


The SPLICER TABLE consists of rows of paired tiepoints which
define the splices used to build a spliced data record. The
file is written in a tab-delimited format. 


The SPLICER TABLE can be read during a subsequent Splicer
session to reload a previously-generated spliced data
record. The SPLICER TABLE can be applied to generate a
spliced data record from any dataset from a given Site which
had been previously composited. 



SPLICER TABLE



In the example shown below, the splice begins at 926B, Core 1 (0 cm) and continues
in 926B until section 1H-4 (19.5 cm). A splice is then made to Hole 926C 1H-2 (51.5 cm)
and data is read in that hole until sample 926C-1H-6 (135.5 cm). 



File format (Tab-delimited, all on one line):
Site	Hole	Core	Type	Sect.	Int1	Int2	mbsf	mcd		"tie to"
Site	Hole	Core	Type	Sect.	Int1	Int2	mbsf	mcd

926     B       1       H       4       19.50   19.50   4.70    4.70    tie to	
926     C       1       H       2       51.50   51.50   2.52    4.71
926     C       1       H       6       135.50  135.50  9.36    11.55   tie to
926     A       2       H       4       64.70   64.70   9.15    11.58
926     A       2       H       5       59.50   59.50   10.60   13.03   tie to
926     B       2       H       4       1.70    1.70    11.52   13.08
926     B       2       H       6       37.50   37.50   14.88   16.44   tie to
926     C       2       H       2       135.50  135.50  12.86   16.45
926     C       2       H       7       60.50   60.50   19.60   23.19
.
.
.


where,

    

  •   Site = Site Number
    • 

  •   Hole = Hole Letter
    • 

  •   Core = Core Number
    • 

  •   Type = Core Type
    • 

  •   Sect = Section Number
    • 

  •   Int1 = Top of the tie interval.
    • 

  •   Int2 = Bottom of the tie interval
    • 

  • 
MBSF = drilled depth of core top, meters below seafloor
    • 

  • 
MCD = depth-shifted composite depth of core top, meters composite depth
    • 



Here is a sample from an actual file. Note that the words "tie to" are 
actually only "tie" in the file.

926	B	1	H	4	25.6	25.6	4.76	4.76	tie	926	C	1	H	2	57.5	57.5	2.58	4.76
926	C	1	H	5	102.5	102.5	7.53	9.71	tie	926	A	2	H	3	38.0	38.0	7.38	9.71
926	A	2	H	5	99.5	99.5	10.99	13.32	tie	926	B	2	H	4	36.2	36.2	11.87	13.32
926	B	2	H	5	115.5	115.5	14.15	15.60	tie	926	C	2	H	2	60.5	60.5	12.11	15.60
926	C	2	H	5	129.5	129.5	17.30	20.79	tie	926	B	3	H	2	27.2	27.2	18.28	20.79
926	B	3	H	5	85.5	85.5	23.35	25.86	tie	926	C	3	H	2	99.5	99.5	22.00	25.86
926	C	3	H	6	72.5	72.5	27.73	31.59	tie	926	B	4	H	2	65.0	65.0	28.16	31.59
926	B	4	H	5	84.6	84.6	32.85	36.28	tie	926	C	4	H	3	26.0	26.0	32.27	36.28
926	C	4	H	5	90.5	90.5	35.90	39.91	tie	926	A	5	H	3	61.0	61.0	36.12	39.91
926	A	5	H	4	74.2	74.2	37.74	41.53	tie	926	B	5	H	2	84.7	84.7	37.85	41.53
926	B	5	H	5	139.6	139.6	42.90	46.58	tie	926	C	5	H	3	146.0	146.0	42.96	46.58






Modes

There are two modes:

    

  1. Splicer 

  2. Sagan


One and only one of these must be active to do any work 
in a session.

The Sagan Mode is deferred.




Splicer Modes


Splicer

This puts NCLIP into the mode of the old "Splicer" application.

Once you are in the Splicer Program, there are two 
modes from which you must choose.
One and only  one of these modes must be active to complete any work
in your session.

    

  1. Composite Mode

  2. Splice Mode






About Splicer



AboutSplicer Help





About Splicer ...


Splicer was developed by Peter deMenocal, Ann Esmay, and
Suzanne O'Hara at Lamont-Doherty Earth Observatory,
Palisades, New York.


Inquiries: peter@ldeo.columbia.edu


This is Motif Version 2.1. (june 10, 1999, Peter deMenocal, L-DEO)


--


Splicer is an interactive workstation software product for
graphically displaying and depth-shifting multiple-hole core
physical property and age-control data for constructing complete,
composite stratigraphic records and timeseries. 


--


The program serves three main functions:


COMPOSITING - Optimal intercorrelation and depth-shifting of
multiple-hole core data and development of the Composite
Depth Scale.


SPLICING - Construction of complete, spliced sequences from
multiple-hole data using the Composite Depth Scale.


AGE MODEL AND TIMESERIES DEVELOPMENT - The program also reads 
biostratigraphic and magnetostratigraphic age control data
which can be displayed, depth-shifted, and applied to generate
continuous time-series records from the spliced data records.


--


Here is a general overview of how Splicer works:


1) Multisensor Track core data (GRAPE density, magnetic
susceptibility, natural gamma activity, P-wave velocity,
color reflectance) are read for any number of offset holes
using the "OPEN..." menu item (under FILE). The user
specifies data culling, smoothing, and decimating options.
These data are plotted in the left-hand window as a series
of channels, each channel represents the data from a given
hole. Data from each core are presented as a single
continuous trace; core numbers are shown at the lower left
of each core. 


2) Up to five different types of age control data
(Nannofossil, foraminifera,radiolaria, and diatom
biostratigraphy, and paleomagnetic reversal boundaries) can
be read using the "OPEN/STRATIGRAPHY FILE..." menu item
(under FILE). These data are plotted as a series of
color-coded bars adjacent to the core data for each hole.
There is a simple tab-delimited (Excel) format for
stratigraphic files.



3) The user then selects the "COMPOSITE" menu item (under
PROCESS) to begin  linearly depth-shifting the core data
from adjacent holes to intercorrelate all core data to a
common (composite) depth scale. Using the COMPOSITE tool,
the user selects tie points between holes based on visually
correlative features. When a tie is made the program
calculates the cross-correlation between the two records at
the tie point and suggests an optimized tie point based on
the best cross-correlation between the two cores. The user
can then depth-shift this core (and all the others below it
in that hole..) relative to the other cores. All user
activity is stored in a REPORT FILE which keeps a
time-stamped log of correlation and splicing activity for
poserity purposes. The correlation proceeds downward
stratigraphically on a core-by-core basis. 


  The resulting depth scale is referred to as the COMPOSITE
DEPTH SCALE and depth values are in meters composite depth
(mcd). The depth offsets required to construct the composite
depth scale is stored in a file called an AFFINE TABLE. The
AFFINE TABLE contains the depth adjustment values which must
be applied to the depths of each core from each hole to
(re)build the composite depth scale. These offset values can
be applied to the biostratigraphic and magnetic polarity
data and saved as separate files. 


4) Once all data have been depth shifted to the composite
depth scale then individual core segments can be selected
and spliced together in the right-hand window to build a
continuous, complete record. One begins splicing by
selecting the SPLICE -> CONSTRAINED menu item (under
PROCESS). (CONSTAINED means that the resulting splice
preserves the composite depth scale established in the
left-hand window; this is the preferred way to build a
spliced composite record. UNCONSTRAINED means that the user
can make a splice which differs slightly from the composite
depth scale). 


  The SPLICE pop-up window allows the user to select the
first core to begin splicing: The user clicks on any core
with the center mouse button, hits the GRAB CORE button, and
the core is redrawn in the left column of the right-hand
panel. The user then selects a second core - the one which
will be spliced below the first core - and it is drawn on
the right column of the right window. The user then clicks
any place where the two cores overlap (with the center mouse
button) and the cross-correlation between the two cores at
that point of overlap is shown. The user can drag (mouse
button depressed) over the interval to find the best point
to define the splice. 


  The program indicates a good splice position by flashing
"This is a good splice" when the cross-correlation is
centered and the difference between the tie point data
values is less than 10% of the splice value. If the tiepoint
is satisfactory then the user hits the SPLICE TO TIE button
and the program splices the two core records at that point
(trims the bottom off the left core and trims the top off
the right core). The results can be stored in a SPLICE TABLE
which defines the ODP identifier, mbsf, and mcd tiepoint
data to rebuild the spliced record. 


-----


updated: 15 February, 1997


Back to Index





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Composite Mode


Composite


Overview

This is the mode used when adjusting the depths in tracks to 
match each other. 

    

  1.  Open multiple tracks, using the 
Text Parser

  2. Try a compositing session, i.e. pick a reference point, using the middle mouse button.

  3. Right click on a second track.

  4. Slide the track, seeing the x-coor line up.
(Warning there is still a bug in the x-coor origin. See "User
Feedback Needed" below. 

  5.  Accept the composite.

  6.  Choose Export Affine of type txt or XML.
    

    
You will then be asked for a file name.

    The output affine file should have all tracks data stored.


     See Composting, Step by Step for more details.


June 13, 2006









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author











Compositing: Step by Step


Compositing: Step by Step



The COMPOSITE tool (under the 
PROCESSES 
menu) is used to

depth-shift core data in one hole relative to core data in

other holes. 


The COMPOSITE tool allows users to optimally intercorrelate
core data from multiple holes so that all stratigraphic
features recovered at a given site are aligned with the same
features at other sites, producing a new depth scale which is 
formally termed the Composite Depth Scale, with depth units 
of mcd (meters composite depth).


The COMPOSITE tool is used in the following manner:

    

  1.  Find two features in adjacent holes which are visually
correlative, representing the same stratigraphic level.

    

  2.  Define one core as being stratigraphically "fixed"
whereas the other core will "move" relative to the "fixed"
core.

    

  3.  Use the center mouse button to place a RED point on the
"fixed" core feature (RED=stop). Use the right mouse button
to place a GREEN point on the "moving" core feature
(GREEN=go). The mbsf of the reference and
the moving points are shown in the status box. Note that the mouse pointer
does not need to be on the actual feature, just near where the feature
occurs in that hole.

    

  4.  A tieline is drawn between the two tiepoints and the
program determines the cross-correlation between the two
cores at the tieline and for a range of depths away from the
tieline. The program determines the average sample interval
of the datasets, interpolates these data to a constant
average sample interval, then computes the correlation
between the two cores for a definable data window (default =
+/- 2 meters; user-definable) centered at the tieline, and
for a series of leads/lags (the "moving" core moves relative
to the "fixed" core) above and below this tieline (default =
1 meter;user-definable).  

    

  5.  If the two features are precisely correlated then the
cross-correlation function is centered; the yellow line
defining the position of the maximum cross-correlation will
be at the zero lead/lag position. More commonly, the tieline
is slightly misplaced and the yellow line will be offset
from the zero lead/lag position. (when the pointer is in the
correlation plotting window the right mouse button can be
depressed and dragged to reveal the statistical results).


    

  6. When you release the mouse button, you are asked "Keep this composite?" If
you answer "Yes",
the core of the moving point, and all cores below it are shifted down.

    

  7.  (Deferred): Splicer allows the user to shift cores based on the
calculated optimal (highest) correlation - a more efficient
way to intercorrelate multiple-hole core data. The user need
only click the "ADJUST DEPTH" button to shift the core to
its best position relative to the selected correlation
feature. 

    

  8. The shifted core will then change color (indicating that the
core has been correlated and depth-shifted; default = yellow
to blue) and shift to its new depth. The (user-definable)
default settings will always shift a core (and all those
below it) to the depth where the best cross-correlation
occurs. The user can chose to shift only a single core, or
shift it using the specified tieline or by a definable
depth-adjustment.

    


The user can change the correlation window and the 
width of the lead/lag window to test the robustness
of a given correlation or to focus on a difficult
correlation. To do this, change the window widths and lead
lag widths to the desired values.


__ 


June 15, 2006





Affine Table Description


AffineOpen Help





Open Affine Table:


The AFFINE TABLE contains the depth offsets which must be
applied to the ODP drilling depths (e.g. meters below
seafloor, mbsf) to (re)build the composite depth scale.
Values are determined using the tie/correlate/and
depth-shift features of the COMPOSITE tool.


The AFFINE TABLE can be saved iteratively as the compositing
progresses. As each core is depth-shifted to correlate with
other depth-shifted cores, the AFFINE TABLE is internally
updated with the depth offset value applied to each core and
a binary (Y/N) switch value to indicate if the core has been
depth-shifted (=Y).


When the AFFINE TABLE is opened, a verbose 
Affine Preview Window is
also opened from the same directory as the AFFINE TABLE. 
This Affine Preview Window contains all
information regarding the type of data which was read, what
processing was done, and ODP ID and correlation information
about the details of each composite and splice action on the
current and equivalent (same site) previous dataset by the
user. 


A preexisting AFFINE TABLE can be read when core data are
read-in initially to restore a previously-constructed
composite depth scale. This is done by pressing the "READ
AFFINE TABLE" button under OPEN DATA... menu item (under
FILE). The previously-saved AFFINE TABLE (e.g.
Sitexxxx.aff.out) is located and then selected by the user.


After core data have been read (and culled, smoothed,
decimated as desired), the program applies the depth offset
values contained in the AFFINE TABLE to the primary (ODP)
core depth values. The core data are then plotted in the
left-hand window in user-selected colors indicating whether
the core has been shifted (composite depth default = light
blue) or not (default = yellow). 


See the AFFINE TABLE article for format information.


_____  


updated: 30 April, 1996





Send comments to the 

author






Saving Affine Tables



AffineSave Help




Save Affine Table:


The AFFINE TABLE contains the depth offsets which must be
applied to the ODP drilling depths (e.g. meters below
seafloor, mbsf) to (re)build the composite depth scale.
Depth-shift values are determined using the
tie/correlate/and depth-shift features of the COMPOSITE tool
(under PROCESS). 


The AFFINE TABLE can be saved iteratively as the compositing
is progressing. As each core is depth-shifted to correlate
with other depth-shifted cores, the AFFINE TABLE is
internally updated with the depth offset value applied to
each core and a binary (Y/N) switch value to indicate if the
core has been depth-shifted (=Y).


The AFFINE TABLE can be saved at any time and it is
recommended that it be saved often. The AFFINE TABLE
documents the depth offsets which have been applied to all
cores within all holes of a given site; a logical naming
convention (e.g Sitexxxx.aff.out) is recommended. When
saved, it records the depth offsets which are needed to
build the composite depth scale which is plotted in the
left-hand window of the main screen and a binary (Y/N)
switch value to indicate if the core has been depth-shifted.



When the AFFINE TABLE is saved, a verbose REPORT FILE
(Sitexxx.aff.out.rpt) is also saved automatically to the
same location as the AFFINE TABLE. This REPORT FILE contains
information regarding the type of data which was read, what
processing was done, and ODP ID and correlation information
about the details of each composite and splice action on the
current and equivalent (same site) previous dataset by the
user. 


See the AFFINE TABLE --> General Information regarding
AFFINE TABLE file formats.


______  


updated: 30 April, 1996




Send comments to the

author





Age Depth Description



AgeDepth Help






Age-Depth window


Splicer allows users to read in biostratigraphic
and/or paleomagnetic age control data, and to
plot and depth-shift these data during the 
compositing and splicing processes. These age
control data can also be used to interactively 
develop an age model for the Site and to apply
this age model to the Spliced data record
to develop/plot/output a complete, continuous 
spliced time series.


The Age-Depth window is arranged so that 
biostratigraphic and or paleomagnetic age-depth 
control information are plotted in the right
window. The user can select or deselect which 
kinds of age control data are plotted by clicking
on the stratigraphic data type (e.g. "nannofossils").


The stratigraphic data can be plotted as either MCD 
depth vs. Age or MBSF depth vs. age by selecting the 
appropriate button beneath the plotting window. The
stratigraphic datums are plotted as vertical bars,
representing the depth ranges for each datum. 


_____


Updated 1 Nov., 1996



Constructing an Age Model


The user can define an age model (age, depth 
control) for a given spliced data record using 
the "Construct Age Model" button in the Age
Modeling window. 


The Age Modeling window is arranged so that 
biostratigraphic and or paleomagnetic age-depth 
control information are plotted in the right
window. The user can select or deselect which 
kinds of age control data are plotted by clicking
on the stratigraphic data type (e.g. "nannofossils").


The stratigraphic data can be plotted as either MCD 
depth vs. Age or MBSF depth vs. age by selecting the 
appropriate button beneath the plotting window. The
stratigraphic datums are plotted as vertical bars,
representing the depth ranges for each datum. 


To construct an age model, click on a selected datum
label with the CENTER mouse button (not the actual 
point which is beneath it). The age-depth datum is 
then added to a list on the left side of the window. 
A line is drawn from the 0-0 age-depth position to this
datum. The user can then add to the age model by 
selecting another datum. The user can also explore the 
Age-Depth plot locations by depressing the LEFT mouse 
button and viewing the stratigraphic information in 
the dialog box below. 


User-defined age-depth control points can be entered 
into the age model datum list by typing in the
"depth" and "age" dialog boxes and clicking the 
"Add hand pick..." button. 


Age control points can be removed by clicking on the
datum label in the list and then clicking the "Remove 
datum..." button directly below. This removes the 
datum from the list and updates the age-depth plot and
the Splice time series plot (if opened). 


Tuning to time series
_____


Updated 1 Nov., 1996






Send comments to the

author








Splice Mode









There are two ways to construct a spliced data record

using Splicer:

    

  1. Splice--> CONSTRAINED Tool for building spliced data

records. Preserves the Composite Depth Scale (mcd) position

of every core. This is the preferred tool for building 

spliced data records. 

  2. 
SPLICE --> UNCONSTRAINED: (Deferred) Tool for building spliced data

records. Permits the splice depth scale to differ from the

Composite Depth Scale. Useful in difficult recovery or

disturbed core situations.

      



      Constrained
      

      
The SPLICE --> CONSTRAINED tool is used to build a complete

spliced record after the multiple-hole core data have been

depth-shifted and stratigraphically aligned. "CONSTRAINED"

means that the spliced record will ALWAYS preserve the

composite depth scale which is displayed in the left-hand

Composite panel. This is the preferred tool for building

spliced data records.  

      
This SPLICE Splice Window
manages the core selection and splicing.
This process occurs in two stages:

        

      1. Grabbing

      2. Splicing

      



      Grabbing
      
With the center mouse button, set a 
Reference Point,
      

      
using the middle mouse button, on the core you want to grab. 


      Then Press the 
      Grab Button 
      to move
the selected core to the splicer window.


      If it is the first core to be moved, it will now be the first
core of the .

the core is redrawn in the left column of the right-hand

panel. 
      

      
The user then selects a second core - again by first setting a 
Reference Point,
at a point where the new core

overlaps with and can be spliced below the first core.
Then by pressing the 
      Grab Button, 

      you can move 
that core to the Grab Track.

      Splicing Your Grab
      
Once you have completed your grab, you will now have 
two tracks on the screen, the 
Composite Track and
the Grab Track.


      Next press and hold the middle mouse button somewhere in the
overlap of the two tracks. 


      While holding down the middle mouse button you will see a tie line:

      ,
and a cross plot
      


      that is changing as you move the mouse.

      Slide the mouse back and forth
until you have a well defined cross-correlation in the 
Cross Correaltion Window.


      When you are done, simple release the middle mouse button. 
You will then be asked if you want to complete this splice.


      If you answer yes, the portion of the grab track below the
splice point is put into the corresponding portion of the 
composite track. (This will overwrite  the bottom portion of the 
composite track.)



      You will also now see a Splice Preview Window,


      
that shows you the result of your splice. 

      Undo a Splice
      
Don't like this splice? You can undo it by using the 
      
Undo Last Splice

       button. 



      Unconstrained (Deferred)
      

The SPLICE --> UNCONSTRAINED tool is used to build a

complete spliced record after the multiple-hole core data

have been depth-shifted and stratigraphically aligned.

"UNCONSTRAINED" means that the spliced record will NOT

NECESSARILY preserve the composite depth scale which is

displayed in the left-hand Composite panel. This tool is

useful in difficult recovery or disturbed core situations.

      
This SPLICE pop-up window also allows the user to select the

first core to begin splicing: The user clicks on any core

with the center mouse button, hits the GRAB CORE button, and

the core is redrawn in the left column of the right-hand

panel. The user then selects a second core - the one which

overlaps with and can be spliced below the first core - and

it is drawn on the right column of the right window.

      
The user then uses the center mouse button to place a red

dot on a correlative feature on the  left-most core in the

Splice panel. Using the right mouse button, the user defines

the position of that same feature in the rightmost core in

the splice panel. A splice tieline is drawn (not necessarily

a perfectly horizontal tieline). Examining the

cross-correlation plot, the user can either drag the

appropriate mouse button over the core data, or use the

up/down arrows to find the best splice tiepoint between the 

two cores. 

      
When the tiepoint is satisfactory the user then hits the

SPLICE TO TIE button and the program splices the two core

records at that point (trims the bottom off the left core

and trims the top off the right core). 

      
The results can be stored in a SPLICE TABLE which defines

the ODP identifier, mbsf, and mcd tiepoint data to rebuild

the spliced record. 

      
NOTE: Because the splice is not constrained to be horizontal 

the spliced depth scale can differ appreciably from the

Composite depth scale (mcd). 

      


____

      
updated: July 21, 2006


      



      


      
Send comments to the  
      

author




      





      Grab Track
      
The grab track is the segment most recently moved from the composite window. 
You will use it to splice new information into the composite track.

      You can have only one source track in the splice window at a time. 




      Composite Track
      
The Composite Track is the track that holds the Composite Well that you are building.

      You start the composite track with your first Grab




      Sagan
      

      Sagan
      
The application is instrumented for Sagan, but it does not yet have a gui.




      Active Track
      

      Active Track or Section
      
The NCLIP system uses the concept of Active Track throughout the system.
Many actions need to be applied to a specific track, and we use Active Track
to apply those actions.

      Activating a Track
      
To activate a track, simply hold down the command key, and use a left-mouse click to activate the track.
The track will then appear in bold.
      
(If the Diagnostic Level is greater than 0, the center axis of the track will be highlighted instead.)

      De-Activating a Track
      
To de-activate a track, choose De-Activate Active Tracks from the 
Track menu.




      Reference Point
      
The reference point is the point lat chosen with the middle mouse button. It is marked by a "Ref" in the window.

It is used in both the 
Composite 
and the 
Splice 
modes.

      In the splice mode, setting a reference point will also 

activate that track. 




      Start and End Cut
      

      

      How to Select a Start and End Cut
      
At some points in the program, you will want to select a start and end cut,
that is specify a section of the track. Here is how to do that:

      

        

      1. First, while holding down the shift key, select the start cut
by pressing the left mouse button.
You will then see an annotation, "<--start cut". 

      2. Next, while holding the shift key down, press the right
mouse button where you want the cut to end. 

      

      You then have a selection. 

      If you want to change either cut point, simple repeat steps one and/or two.

      Note: Start and End cuts are usually made on the active track.




      Menus
      


      Use the following sections to explore the various menus 
of NCLIP.




      File
      

      A description of the File Menu
      

      

      





      Load Text File
      

      Load Text File
      
Loads a tab, space, and/or comma delimited file into the system.




      Fetch URL
      

      Fetch URL
      

      Given a User provided URL, the URL is fetched to local cache.
For more information, see 
Set Fetch Parameters
and
wget arguments.




      Export an Affine Table as XML
      

      Export an Affine Table as XML
      
Export all of the tracks in the 
Composite window into a single XML file.
See About Affine for more information.

      Here is an example:

      <AffineTable>
  <NclAffine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>1</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>0.090000</odpDepth>
      <depthOffset>0.000000</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>0.090000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>2</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>4.090000</odpDepth>
      <depthOffset>2.330000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>6.420000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>3</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>13.600000</odpDepth>
      <depthOffset>1.490000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>15.090000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>4</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>23.090000</odpDepth>
      <depthOffset>2.840000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>25.930000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>5</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>32.590000</odpDepth>
      <depthOffset>3.790000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>36.380001</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>6</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>3.230000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>7</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>5.760000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>8</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>6.040000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>9</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>7.340000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>10</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>9.080000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>11</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>10.230000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>12</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>10.480000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>13</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>9.980000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>14</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>12.030000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>15</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>13.380000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>16</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>14.580000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>17</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>15.030000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>18</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>16.530001</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>19</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>17.879999</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>20</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>19.879999</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>21</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>19.879999</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>22</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>19.879999</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>23</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>19.879999</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>A</hole>
      <core>24</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>19.879999</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
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    <AffLine>
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      <depthOffset>10.690000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>13</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>11.190000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>14</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>13.090000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>15</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>14.090000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>16</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>15.040000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>17</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>15.790000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>18</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>16.340000</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>19</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>16.790001</depthOffset>
      <correaltion>1</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>20</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>16.790001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>21</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>22</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>23</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>24</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>25</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
    <AffLine>
      <leg>154</leg>
      <subLeg></subLeg>
      <site>926</site>
      <hole>C</hole>
      <core>26</core>
      <coreType>H</coreType>
      <section>-1</section>
      <odpDepth>-340282346638528860000000000000000000000.000000</odpDepth>
      <depthOffset>18.190001</depthOffset>
      <correaltion>0</correaltion>
      <compositeDepth>-340282346638528860000000000000000000000.000000</compositeDepth>
    </AffLine>
  </NclAffine>
</AffineTable>



      

      




      Export an Affine Table as Text
      

      Export an Affine Table as Text
      
Export all of the tracks in the 
Composite window into a single tab delimited text file.
See About Affine for more information.

      Here is an example:
      154		926	A	1	H	-1	0.09	0.00	0	0.09
154		926	A	2	H	-1	4.09	2.33	1	6.42
154		926	A	3	H	-1	13.60	1.49	1	15.09
154		926	A	4	H	-1	23.09	2.84	1	25.93
154		926	A	5	H	-1	32.59	3.79	1	36.38
154		926	B	1	H	-1	0.09	0.00	0	0.09
154		926	B	2	H	-1	7.09	1.45	1	8.54
154		926	B	3	H	-1	16.59	2.51	1	19.10
154		926	B	4	H	-1	26.09	3.43	1	29.52
154		926	C	1	H	-1	0.60	2.18	1	2.78
154		926	C	2	H	-1	10.10	3.49	1	13.59
154		926	C	3	H	-1	19.59	3.86	1	23.45
154		926	C	4	H	-1	29.09	4.01	1	33.10

      

      




      Import Affine Table
      

      Import an Affine Table
      
This item will import an affine table as either (legacy) text or
as xml. It will then apply the affine transformations to 
any applicable tracks.

      You will be presented with a file selection menu:

      

      Please note that the default file types are Xml, Txt, and Text. 
However, you can load any file type you want. 

      Any file type that is not XML is treated as text.

      An affine shift is applied to all tracks, in 
both the 
Compsite
and the 
Splice windows. It is applied to all 
tracks that have matching
leg,  site, hole, and coretype. The matching of coretype will be optional.




      Export the Splice Table as XML
      

Export all of the splices in the 
Splice window into a single XML file.
See About Splice Mode for more information.

      Here is a sample output:

      

      <SpliceTable>
  <NclSplice>
    <AffLine>
      <siteL>154-926</siteL>
      <holeL>A</holeL>
      <coreL>1</coreL>
      <typeL>H</typeL>
      <sectionL>2</sectionL>
      <int1L>2.610000</int1L>
      <int2L>2.610000</int2L>
      <mbsfL>2.700000</mbsfL>
      <mcdL>2.700000</mcdL>
      <siteR></siteR>
      <holeR>B</holeR>
      <coreR>1</coreR>
      <typeR>H</typeR>
      <sectionR>2</sectionR>
      <int1R>2.610000</int1R>
      <int2R>2.610000</int2R>
      <mbsfR>2.700000</mbsfR>
      <mcdR>2.700000</mcdR>
    </AffLine>
    <AffLine>
      <siteL>154-926</siteL>
      <holeL>B</holeL>
      <coreL>1</coreL>
      <typeL>H</typeL>
      <sectionL>5</sectionL>
      <int1L>6.510000</int1L>
      <int2L>6.510000</int2L>
      <mbsfL>6.600000</mbsfL>
      <mcdL>6.600000</mcdL>
      <siteR></siteR>
      <holeR>A</holeR>
      <coreR>2</coreR>
      <typeR>H</typeR>
      <sectionR>1</sectionR>
      <int1R>0.110000</int1R>
      <int2R>0.110000</int2R>
      <mbsfR>4.200000</mbsfR>
      <mcdR>6.530000</mcdR>
    </AffLine>
    <AffLine>
      <siteL>154-926</siteL>
      <holeL>A</holeL>
      <coreL>2</coreL>
      <typeL>H</typeL>
      <sectionL>7</sectionL>
      <int1L>8.900001</int1L>
      <int2L>8.900001</int2L>
      <mbsfL>13.100000</mbsfL>
      <mcdL>15.430000</mcdL>
      <siteR></siteR>
      <holeR>A</holeR>
      <coreR>3</coreR>
      <typeR>H</typeR>
      <sectionR>1</sectionR>
      <int1R>0.389999</int1R>
      <int2R>0.389999</int2R>
      <mbsfR>13.990000</mbsfR>
      <mcdR>15.480000</mcdR>
    </AffLine>
    <AffLine>
      <siteL>154-926</siteL>
      <holeL>A</holeL>
      <coreL>3</coreL>
      <typeL>H</typeL>
      <sectionL>6</sectionL>
      <int1L>8.200001</int1L>
      <int2L>8.200001</int2L>
      <mbsfL>22.190001</mbsfL>
      <mcdL>23.680000</mcdL>
      <siteR></siteR>
      <holeR>C</holeR>
      <coreR>3</coreR>
      <typeR>H</typeR>
      <sectionR>1</sectionR>
      <int1R>0.209999</int1R>
      <int2R>0.209999</int2R>
      <mbsfR>19.799999</mbsfR>
      <mcdR>23.660000</mcdR>
    </AffLine>
  </NclSplice>
</SpliceTable>


      




      Export the Splice Table as Text
      

Export all of the splices in the
Splice window into a single text (txt) file.
See About Splice Mode for more information.

      Here is what it looks like:

      154-926	A	1	H	2	2.610000	2.610000	2.700000	2.700000	tie	B	1	H	2	2.610000	2.610000	2.700000	2.700000	
154-926	B	1	H	5	6.510000	6.510000	6.600000	6.600000	tie	A	2	H	1	0.110000	0.110000	4.200000	6.530000	
154-926	A	2	H	7	8.900001	8.900001	13.100000	15.430000	tie	A	3	H	1	0.389999	0.389999	13.990000	15.480000	
154-926	A	3	H	6	8.200001	8.200001	22.190001	23.680000	tie	C	3	H	1	0.209999	0.209999	19.799999	23.660000

      




      Export the Splice Track as XML
      

Export the track built in the 
Splice window into a single XML file.
See About Splice Mode for more information.

      Here is a sample output:

      

      <SplicedTrack>
  <NclTrack name="SplicedTrack">
    <mdoSpacing>0</mdoSpacing>
    <floater>0</floater>
    <mN>
      <x>0.090000</x>
      <y>141.000000</y>
    </mN>
    <mO>
      <x>13.950000</x>
      <y>99.500000</y>
    </mO>
    <mX>
      <x>27.990000</x>
      <y>340.000000</y>
    </mX>
    <vN>
      <x>0</x>
      <y>0</y>
    </vN>
    <vO>
      <x>99</x>
      <y>557</y>
    </vO>
    <vX>
      <x>199</x>
      <y>1115</y>
    </vX>
    <vCenter>
      <x>185</x>
      <y>593</y>
    </vCenter>
    <dataAverage>
      <x>14.040000</x>
      <y>240.500000</y>
    </dataAverage>
    <trackName>SplicedTrack</trackName>
    <scaleData>0.178475</scaleData>
    <scaleDepth>0.140201</scaleDepth>
    <testDistance>
      <x>0.000000</x>
      <y>0.000000</y>
    </testDistance>
    <trackBackground>
      <red>0</red>
      <green>0</green>
      <blue>0</blue>
    </trackBackground>
    <movedTrackColor>
      <red>0</red>
      <green>255</green>
      <blue>0</blue>
    </movedTrackColor>
    <trackColor>
      <red>240</red>
      <green>240</green>
      <blue>0</blue>
    </trackColor>
    <dx>10000.000000</dx>
    <dy>10000.000000</dy>
    <dxy>10000.000000</dxy>
    <annotationName>blank</annotationName>
    <mdoDepthCol>0</mdoDepthCol>
    <mdoDataCol>1</mdoDataCol>
    <mdoCoreCol>2</mdoCoreCol>
    <mdoSectionCol>3</mdoSectionCol>
    <mdoConnectCol>4</mdoConnectCol>
    <mdoCullCol>5</mdoCullCol>
    <mdoOrigDepthCol>6</mdoOrigDepthCol>
    <trackFont>
      <FaceName>MS Shell Dlg 2</FaceName>
      <Family>70</Family>
      <PointSize>8</PointSize>
      <Style>90</Style>
      <UnderLined>0</UnderLined>
      <Weight>90</Weight>
    </trackFont>
    <vN>
      <x>0</x>
      <y>0</y>
    </vN>
    <vO>
      <x>99</x>
      <y>557</y>
    </vO>
    <vX>
      <x>199</x>
      <y>1115</y>
    </vX>
    <mO>
      <x>13.950000</x>
      <y>99.500000</y>
    </mO>
    <legName>154</legName>
    <holeName>B</holeName>
    <siteName>926</siteName>
    <typeName>H</typeName>
    <Ncl2DTransformation>
      <sDepth>0.025022</sDepth>
      <sData>1.000000</sData>
      <oDepth>0.000000</oDepth>
      <trackOffset>50</trackOffset>
      <oData>50.000000</oData>
      <screenMin>
        <x>0</x>
        <y>0</y>
      </screenMin>
      <screenMax>
        <x>199</x>
        <y>1115</y>
      </screenMax>
      <dataMin>
        <x>0.090000</x>
        <y>141.000000</y>
      </dataMin>
      <dataMax>
        <x>27.990000</x>
        <y>340.000000</y>
      </dataMax>
      <depthScale>10.000000</depthScale>
      <dataScale>1.000000</dataScale>
      <myOrientation>0</myOrientation>
      <mOffset>
        <x>36</x>
        <y>36</y>
      </mOffset>
    </Ncl2DTransformation>
    <Mdo>
      <MdoHeader>
        <SerialNumber>38</SerialNumber>
        <length>4</length>
        <title> used in this track </title>
        <dataLength>2464</dataLength>
        <dimension>2</dimension>
        <storageWordLength>4</storageWordLength>
        <totalLength>2468</totalLength>
        <maxValue>278.000000</maxValue>
        <minValue>-42201683186052844000000000000000000000.000000</minValue>
        <maxAbs>42201683186052844000000000000000000000.000000</maxAbs>
        <fileName></fileName>
        <xmlImportFileName></xmlImportFileName>
        <xmlExportFileName></xmlExportFileName>
        <origMinValue>-42201683186052844000000000000000000000.000000</origMinValue>
        <origMaxValue>278.000000</origMaxValue>
        <dateTime>889486848</dateTime>
        <counts_vector>
                  <counts_value>88</counts_value>
                  <counts_value>7</counts_value>
        </counts_vector>
        <sampleRates_vector>
                  <sampleRates_value>1.000000</sampleRates_value>
                  <sampleRates_value>1.000000</sampleRates_value>
        </sampleRates_vector>
        <annotationStart_vector>
                  <annotationStart_value>0.000000</annotationStart_value>
                  <annotationStart_value>0.000000</annotationStart_value>
        </annotationStart_vector>
        <annotationEnd_vector>
                  <annotationEnd_value>0.000000</annotationEnd_value>
                  <annotationEnd_value>0.000000</annotationEnd_value>
        </annotationEnd_vector>
        <annotationLabels_vector>
                <annotationLabels_value></annotationLabels_value>
                <annotationLabels_value></annotationLabels_value>
        </annotationLabels_vector>
        <contiguousDirection_vector>
                  <contiguousDirection_value>0</contiguousDirection_value>
                  <contiguousDirection_value>0</contiguousDirection_value>
        </contiguousDirection_vector>
      </MdoHeader>
      <MdoData>
        <value location="0,0">0.090000</value>
        <value location="1,0">5.550000</value>
        <value location="2,0">5.640000</value>
        <value location="3,0">5.750000</value>
        <value location="4,0">5.850000</value>
        <value location="5,0">5.950000</value>
        <value location="6,0">6.050000</value>
        <value location="7,0">6.140000</value>
        <value location="8,0">6.250000</value>
        <value location="9,0">6.350000</value>
        <value location="10,0">6.450000</value>
        <value location="11,0">6.550000</value>
        <value location="12,0">6.650000</value>
        <value location="13,0">6.840000</value>
        <value location="14,0">6.950000</value>
        <value location="15,0">7.050000</value>
        <value location="16,0">7.140000</value>
        <value location="17,0">7.240000</value>
        <value location="18,0">7.350000</value>
        <value location="19,0">7.450000</value>
        <value location="20,0">7.550000</value>
        <value location="21,0">7.650000</value>
        <value location="22,0">7.750000</value>
        <value location="23,0">7.850000</value>
        <value location="24,0">7.950000</value>
        <value location="25,0">8.050000</value>
        <value location="26,0">8.150000</value>
        <value location="27,0">8.350000</value>
        <value location="28,0">8.450000</value>
        <value location="29,0">8.550000</value>
        <value location="30,0">8.639999</value>
        <value location="31,0">8.740000</value>
        <value location="32,0">8.850000</value>
 ..........
        <value location="68,6">11.400000</value>
        <value location="69,6">11.600000</value>
        <value location="70,6">11.690000</value>
        <value location="71,6">11.800000</value>
        <value location="72,6">11.900000</value>
        <value location="73,6">12.000000</value>
        <value location="74,6">12.100000</value>
        <value location="75,6">12.200000</value>
        <value location="76,6">12.300000</value>
        <value location="77,6">12.400000</value>
        <value location="78,6">12.490000</value>
        <value location="79,6">12.600000</value>
        <value location="80,6">12.700000</value>
        <value location="81,6">12.800000</value>
        <value location="82,6">12.900000</value>
        <value location="83,6">13.100000</value>
        <value location="84,6">13.190000</value>
        <value location="85,6">13.300000</value>
        <value location="86,6">13.400000</value>
        <value location="87,6">-42201683186052844000000000000000000000.000000</value>
      </MdoData>
    </Mdo>
    <NclAffine>
    </NclAffine>
  </NclTrack>
</SplicedTrack>

      







      Export the Splice Track as Text
      

Export the track built in the 
Splice window into a single text (txt) file.
See About Splice Mode for more information.

      Here is what it looks like:

      Leg	Site	Hole	Core	Type	Section	Depth	Data
154	926	A	1	H	1	0.090000	186.000000
154	926	A	1	H	1	0.190000	231.000000
154	926	A	1	H	1	0.290000	216.000000
154	926	A	1	H	1	0.400000	267.000000
154	926	A	1	H	1	0.500000	291.000000
154	926	A	1	H	1	0.600000	304.000000
154	926	A	1	H	1	0.700000	291.000000
154	926	A	1	H	1	0.800000	340.000000
154	926	A	1	H	1	0.900000	292.000000
154	926	A	1	H	1	1.000000	267.000000
154	926	A	1	H	1	1.100000	242.000000
154	926	A	1	H	1	1.200000	244.000000
..........
154	926	A	3	H	5	22.619999	191.000000
154	926	A	3	H	6	22.820000	241.000000
154	926	A	3	H	6	22.920000	260.000000
154	926	A	3	H	6	23.020000	218.000000
154	926	A	3	H	6	23.119999	209.000000
154	926	A	3	H	6	23.219999	272.000000
154	926	A	3	H	6	23.320000	250.000000
154	926	A	3	H	6	23.420000	244.000000
154	926	A	3	H	6	23.520000	236.000000
154	926	A	3	H	6	23.619999	194.000000
154	926	A	3	H	6	23.719999	225.000000
154	926	A	3	H	6	23.820000	254.000000
154	926	A	3	H	6	23.920000	214.000000
154	926	A	1	H	0	196.000000	3.000000


      




      Exit
      

Exit and close all windows. The shortcut for this item is Cmd-Q.




      Graph
      


      Explore the various Graph Menu options:

      




      Graph Set Scale
      



      Use this menu to set how the tracks are scaled.


      The tracks are plotted as depth versus data. The depth axis is vertical in 
the vertical mode, and horizontal in the horizontal mode.


      The minimum and maximum values determine how much data is in the 
scroll window, not in the visible window. 



      The Data Scale determines how much data is in the visible window. In this 
example, the depth ranges over 27 meters. Since we have 40 pixels
per meter, and a typical window is 800 pixels, we will see 20 meters 
of the data at one time.



      The "Meters / Tic Mark" and "Meters / Annotation" determine how
often there is a tic mark, and a numerical depth mark, respectively.



      The "Track Spacing (Pixels)" is the number of nominal pixels between 
tracks. A higher value means more track spacing.



      The "Apply" button will apply the current values and leave the 
scale box visible.



      The "Reload Current Values" button will restore the values to the
state that existed before the scale window was opened. 



      The "OK" button will dismiss this window, and apply the scale shown in 
this window.



      The "Cancel" button will close this window, leaving the scales that 
are in effect unchanged. (If you had hit an "Apply" before a "Cancel", the
scales applied will remain in effect.)





      Graph Zoom In
      
The Zoom In menu will zoom in on the tracks by the factor
that is set in the 
Change Zoom Factor menu.

      This is effected by multiplying the Pixels Per Meter and Pixels
per Data Unit factors by the Zoom Factor.




      Graph Zoom Out
      
The Zoom Out menu will zoom out on the tracks by the factor
that is set in the 
Change Zoom Factor menu.


      This is effected by dividing the Pixels Per Meter and Pixels
per Data Unit factors by the Zoom Factor.




      Graph Change Zoom Factor
      



      This is the Zoom factor used in the 
Zoom In
and
Zoom Out menus.




      Graph Auto Scale
      
This will set the same scale on all tracks in such a way
that the data will all be visible in a scrolling window. Use this when you 
have 
zoomed  in 
or 
zoomed out 
too much.





      Show/Hide Data Points
      
This entry will show/hide the dots used to signify a data point.


      Without Dots a plot looks like:

      

      and with dots, it looks like:

      




      Change Background Color
      
This item will bring up a canvas selection menu: 

      


      Chose one or both of the canvas' and then you will 
see a color choice menu:

      

      After choosing and closing, your 
backgrounds will be in the new color.




      Change Text Color
      
This item will bring up a canvas selection menu: 

      


      Chose one or both of the canvas' and then you will 
see a color choice menu:

      

      After choosing and closing, your 
annotatino text will be in the new color.




      Track
      

      A description of the Track Menu
      

      
Active tracks are used for purposes of scaling, setting refernce
points, deleting tracks, etc. 


      For instance, if you want to delete a track, you can 
activate it by cmd-left mouse click on the track. It will then
be displayed in bold. 
Then, using this menu will delete that track.
Tracks can be active in both the
Compsite
and the 
Splice
windows. 
      
Thus, more than one track may be deleted using this menu.

      





      Change Track Color
      

      Change Track Color
      
This menu item will change the color of the 
currently active track.

      If there is no active track, you will see this menu:
      


      When this happens, please choose an 
      
active track before proceeding.




      Delete Active Track(s)
      

      Delete Active Track
      
To clear a track, simply activate it, and then press the delete key.




      Remove All Affines
      

      Remove All Affines
      
Remove all affine translations in all the tracks of all the windows. 
You can then restore selected affine translations
using  
Import an Affine Table.




      Remove An Affine
      

      Remove An Affine
      
Remove the affine translation
of the active track.
You can then restore selected affine translations
using  
Import an Affine Table.




      Track Deactivate
      
Active Tracks are used for purposes of scaling, setting reference
points, deleting tracks, etc. 


      For instance, if you want to delete a track, you can 
activate it by cmd-left mouse click on the track. It will then
be displayed in bold. 
Then, using this menu will delete that track.
Tracks can be active in both the 
Compsite
and the 
Splice
windows. 

Thus, more than one track may be deleted using this menu.




      Processes
      



      
This chooses which process is used:

      Compsite

      or
      


      Splice.

      There is also an option to collapse the 
splices in to a single track. We may eliminate 
this third option in the final version.

      Collapse/Expand the splices.






      Collapse Expand
      
Use this menu:

      

      to collapse all of the splices in the right window 
into a single track. 

      We may not include this option in the final version. It is up for 
a vote!

      The idea is that we can split the splices into separate tracks for 
viewing, and alternatively combine them into a single track for 
viewing.




      Session
      


      
This menu manages the various aspects of this session.

      




      Session Open Add
      

Add a session file to this session, adding tracks as necessary.

      Warning: If there are already tracks in the current session,
this menu item will add yet more tracks to the session. It will not
replace pre-existing tracks. To do the latter, first start a 
New Session, and then add tracks as you wish.

      You can also selectivly delete tracks by 

        

      1. Activating a Track, and then

      2. Deleting a track.

      




      Session Save
      

Save this session in place.




      Session Save As
      

Save this session to a new session file that you will name.




      Session Save As Default
      

The default session file is saved in the directory specified by your HOME 
environment variable. . 
The file is stored on your desktop on Mac, your "My Documents" folder in Windows,
and your ~ directory in Unix. The file name is NclDefaultSessionFile.xml. 

      When NCLIP is opened, we automatically load your default session file.

      To save your current session as a default, either use the Session->Save as Default menu, or type a 
"control-d". Then the next time you open the system,
the default file will be loaded.

      To save your parameters, but not your data as the 
default, do these steps:

        

      1. Set up your session with a data set.

      2. Delete the data from the session.

      3. Save this blank session as the default.

      
In this way, your future sessions will have 
information such as scales, colors, etc. as the 
default. 

      If you have just started a new session file, and have not yet saved it, 
you are in a "No Session File State." Your session file is created when you save it, 
either as a default file or as a named file. 




      New Session
      

If you want to wipe out all of this session's data, and start over, this menu is for you.


      If you have just started a new session file, and have not yet saved it, 
you are in a "No Session File State." Your session file is created when you save it, 
either as a default file or as a named file. 




      Session Show/Hide FP Errors
      


      Show Floating Point Errors?
      
When parsing text files, sometimes data is not in the right place. Parsing "foo" as a number
can cause an error. Sometimes this is OK, and sometimes not. This menu will either
allow those errors to be shown during parsing, or it will hide those errors. 




      Set Novice/Expert Mode
      

This menu presents itself in one of two ways:

        

      1. Set Novice Mode
        
Clicking this will put you into the novice mode, increasing the number of confirmation boxes.
        

      2. Set Expert Mode
        
Clicking this will put you into the expert mode, reducing the number of confirmation boxes. 
        

      




      Change Session Type
      



      This will change your session between a 
Splicer
and a 
Sagan
session.




      View
      


      This menu controls how the windows are shown. 

      





      Show Splice Vertically
      
Show the windows in a vertical mode.




      Show Splice Horizontally
      
Show the windows in a horizontal mode.




      Hide Splicer Window
      
Use this menu
when you are just compositing, and do not want the splicer window takign up real estate.




      Live Update
      
Disable live update on slow systems. It causes the system to refresh the 
window less often.




      ShowDataAxis
      
Show/Hide the data axis on each track.

      The shorcut to this menu is alt-v,alt-d.




      Set Composite Position
      
The Set Composite Position menu item will 
allow you to enter the number of pixels used in the composite window.

      You can also simply click and drag the Composite/Spclier window
bar.




      Set Min Size
      
Set the minimum size, in pixels, of both the 
composite
and 
splice
windows.




      Window To Vary
      
If the variation factor is set to 0, the splice window grows and shrinks with the main window.

      If the variation factor is 1, the composite window grows and shrinks with the main window.

      If the variation factor is 0.5, both windows grow and shrink equally.




      View Log
      
This menu item will open a read only text window that will show the log.

      If the window already exists, it will be refreshed, and scrolled 
to the bottom.

      
The log file window looks like this:

      


      




      View Session File
      
This item will show the default session file as a text file.    

      If the window already exists, it will be refreshed, and scrolled 
to the bottom. It looks like this:
      


      You can select and copy from this window as needed.

      




      Auto Raise
      
Raise all windows, and move them on the screen if they are off screen.
      
This method can also be invoked using the F2 function key. 
      
See Shortcut Keys for more information.




      ShowTheXCoorWindow
      
Show the cross correlation window.




      Hide the x-corr window
      
Hide the cross correlation window.




      Help
      

      Help Menu
      
The Help Menu has these entries:

      


      
Help Contents shows the contents of this help file.
      
Help Tutorial displays the Users Manual.
      
Release Notes displays the Users Manual.
      
Start/Stop What's This? turns the contextual help
on and off.
      
Show Shortcut Keys and Mouse Actions displays the Users Manual.
      
Composite HowTo explains how to manage the composite process.
      
Splice HowTo explains how to manage the splice process.
      
Set Diagnostic Level Set the diagnositc level higher to get more diagnostic information.
      
Show Locations displays the current 
locations of the various directories we use.
      
About NCLIP displays NCLIP version information.
      





      Contextual Help
      

      Contextual Help
      


      
This menu toggles the contextual help:
When on, contextual help will bring up a menu's help instead of executing that menu.
When off, the menus are active, and the help is not automatically shown.




      Diagnostic Level
      


      

      
Raise this number to get more diagnostics.
      
Lower it to get fewer diagnostics.
      
Set it to 0 to eliminate the diagnostics.
      


      If you set the diagnostic level greater than 0, a 0 data axis will be drawn on the track.

      If you set it greater than 3, the coordinates of your pick will be displayed. 


      In general, a non-zero diagnostic will print out more information if there is an error. 


      See also Session->Show Floating Point Errors  for more information. 






      Show Locations
      
This application has several locations where it looks for information. They are described in the section Directories/Locatoins.

      When this menu is used, you will see something like:

      


      





      Start Whats This?
      

      Use this menu item to toggle the "Whats This".

      When "Whats This?" is on, there will be a "?" icon, and choosing a menu will not activate that menu. It will instead bring up the help for that menu. 

      When "Whats This?" is on, you will see:

      

      When "Whats This?" is off, the menus will behave normally.
If "Whats This?" is off, you will see:

       in the menu





      Windows
      
We described the various windows used in the application.





      Composite Window
      

      Composite Window
      


      
This window is used to control and track the compositing process.

      


      

      

      The top section shows the currently active tie points.


      

      
The second section shows the correlation parameters. The only items you can change are


      Correlation Window Length: The number of meters you want the correlation window to cover.

      

      

      The third section is a series of radio buttons that select various parameters of 
the cross correlation.

        

      1. Restrict the Xcorr Window to a Single Core:

          

        • Keep Xcorr in Core: Even if your specified window would cross a core boundary, we 
stop the window at the core boundary. This could cause a slight corruption of the 
cross correlation since the reference and the moving windows may be of different length.
(Although, with our normalization method, as described in 
Cross Correlation Window, such corruption is slight.)

        • Let Xcorr Window Span Cores: The Xcorr window can cross a core boundary. This too can corrupt
the cross correlation in that there may be a gap across the core boundary.

         
It would be best to keep your cross correlation windows away from core boundaries.

      2. Shift is for:

          

        • This core and all below: The chosen shift will affect the current moving core, and all cores below 
it.

        • This core only: The chosen shift will change the position of this core only. 

          If you have picked a reference point, and you 
have not used the right mouse to move a section yet,
you are in a reference state.

          If you have picked a reference point, and you have
moved a section, you are in a tie state.

          In either case, if the "This core and all below" button is checked, your move will be for, um, this core and all cores below
this core.

          Caution
          Using this option may corrupt the Affine Table.

        

      3. Correlation Locking:

          

        • Lock to the best correlation: This is a deferred option.

        • To Tie: If the "This core only" button is checked, your move will only affect this core.

          (For more information, see 
Compositing: Step by Step.)

        

      

      

      

      
The manual shift button will shift the core at the reference point by the given number 
of meters. There is also an undo button for the manual shift.

      
The Undo Button, 

      

      
will undo either the last shift you have "Core Only" active.
It will undo the last tie shift if you have "This Core and All Below" active. 
      


      
This button will undo the last shift of the active track, and then update the
Affine Preview Window


      

      
This section has three buttons:

        

      1. DISMISS: Which will close this window. To reopen it, choose a process from the 
Process Menu.

      2. Defaults: Set this menu's user parameters to their (original) default values.

      3. Help: Show (um) this help file.

      




      Cross Correlation Window
      


      

      Composite
      
Here is an example cross correlation in the composite mode:
      

      
This window displays the cross correlation of the section surrounding the 
reference point 
as the moving point and its window is sliding past it. 
The difference of depth between the moving point and the reference
point is displayed in the main window status box. When you see a well
defined peak, you have a good match. 


      X Axis
      
The numbers along the x-axis are the depth points in the reference window.
In this example, that window is 5 meters wide, and the reference point is at 
31.9, and the window runs from 29.4 to 34.4. 
the window. 


      Y Axis
      
The numbers along the y axis are the magnitude of the cross correlation.
      
The y axis only runs to -0.3 since values lower than that are of little interest. 


      

      Splicing
      
The cross correlation in the splicing mode is slightly different. 
Instead of a reference and moving point, we have two cores that, hopefully,
are at corresponding depths. The upper or left core is the composite core,
and the lower or right core is the splice. Here is a typical view during
the splice cross correaltion:

      

      We initiated this session with a middle mouse down action, and while
holding that mouse down, sliding the mouse back and forth. When 
you get a well defined peak, as here:

      
you have a good place to put your splice. 

      The Cross Correlation Formula
      
When we cross correlate, we pre-process the data by normalizing each array of data. 
That is, we

        

      1. Remove the mean of each array, thus making their data centered around 0.

      2. We normalize by the geometric average of the energy of 
the two arrays used in the calculation. 

      
In this way, the best result will always be a peak of 1. 

      

      The Little Red Bar
      
The little red bar that moves as you move your track marks the point of peak 
correlation.

      

      General Thoughts About Cross Correlation
      
There are five variables for a cross correlation:

        

      1.  Array One's origin. 

      2. Array Two's origin

      3. Array Ones Window

      4. Array Two's Window

      5. The shift between the array one origin and the array two origin.

      
In the       Composite Mode we have:


        

      1.  Array One's origin at the reference point. 

      2. Array Two's origin at the moving point

      3. Array Ones Window is set in the Composite Window

      4. Array Two's Window is the same as Array One's.

      5. The shift between the array one origin and the array two origins is the 
offset between the initial position of you moving point and the 
current position of your moving point.

      
So, in this mode, moving the mouse changes the offset between the reference and the 
moving point.

      
In the Splice Mode we have


        

      1.  Array One's origin is the depth the mouse is at on the composite track. 

      2. Array Two's origin is the depth the mouse is at on the splice (grab) track.

      3. Array Ones Window is set in the Splice Window

      4. Array Two's Window is set in the Splice Window

      5. The shift between the array one origin and the array two origin is 0.

      
So, in this mode, moving the mouse changes the origins of the cross correlation data window. 






      Affine Preview Window
      

      Affine Preview Window
      

      

      This window is used to show a dynamic picture of the current affine file, if you were to export
it at this time. (The file may be exported using the export options on the 
File Menu.
      
Each hole has its own section. For an explanation of the columns, see
About Affine.
      
If the Diagnostic Level is set to a level higher than 0,
the Affine Preview window will also show the original file's data set name.
      
Here is an example:


      




      Set Fetch Parameters
      



      
Use this menu to set the parameters used to fetch data from a URL.

      (A URL is a uniform resource locater, such as http://www.iagp.net or ftp://sqlcore.umn.geo.umn.edu, 
or file:///C:/dl/odp/index.html).
      

We are assuming that you have wget installed on your system.
(Linux and Mac's have this installed by default. NCLIP provides a 
Win32 version of wget with the PC distribution.) Wget 1.10 or higher works best.
You can learn more about wget at 
http://www.gnu.org/software/wget/

      
When your data is downloaded, the files are in a local
directory structure that copies the one on the web site.
For example, if I download leg199 to my c:\dl\odp directory, the 
data are under www.ldeo.columbia.edu in that directory.

      If you have a local copy of a data set in that directory tree,
all links of other pages in the tree will point to that local copy. 
If you do not have a local copy, the links in all of the pages
in that tree will point to the remote copy of the data. In 
this way, you can download only well logs, but still automatically
access the images when needed.

      
The first line is where you provide a URL. We provide a sample:

      http://www.ldeo.columbia.edu/BRG/online2/Leg199/
      
If you want all of the data for Leg199 (be careful) on your 
machine, use a type of fetch of URL, and a depth of Recursive. 


      If you want only a list of the files of leg199 on your machine,
press the 
button, and you will see 
change to 
. Then we will only download the files of type 
html or htm from the system. These files are usually index files,
and so will tell you what files are on the system.


      If you only want one file, press the 
button, and it will change to . In this 
case, your URL should be a complete file name.


      Use the  button to change the place where your 
files are downloaded.


      If you only want files of a specific type, e.g. *.dat files to 
get all well logs, enter the desired file extension in the "File Type"
box.


      For you savvy wget users, you can use the "Additional Arguments" box
to add other wget arguments. There is a list of valid wget arguments listed
here.





      Wget Arguments
      


      



      

wget --help
GNU Wget 1.10.2, a non-interactive network retriever.
Usage: wget [OPTION]... [URL]...

Mandatory arguments to long options are mandatory for short options too.

Startup:
  -V,  --version           display the version of Wget and exit.
  -h,  --help              print this help.
  -b,  --background        go to background after startup.
  -e,  --execute=COMMAND   execute a `.wgetrc'-style command.

Logging and input file:
  -o,  --output-file=FILE    log messages to FILE.
  -a,  --append-output=FILE  append messages to FILE.
  -d,  --debug               print lots of debugging information.
  -q,  --quiet               quiet (no output).
  -v,  --verbose             be verbose (this is the default).
  -nv, --no-verbose          turn off verboseness, without being quiet.
  -i,  --input-file=FILE     download URLs found in FILE.
  -F,  --force-html          treat input file as HTML.
  -B,  --base=URL            prepends URL to relative links in -F -i file.

Download:
  -t,  --tries=NUMBER            set number of retries to NUMBER (0 unlimits).
       --retry-connrefused       retry even if connection is refused.
  -O,  --output-document=FILE    write documents to FILE.
  -nc, --no-clobber              skip downloads that would download to
                                 existing files.
  -c,  --continue                resume getting a partially-downloaded file.
       --progress=TYPE           select progress gauge type.
  -N,  --timestamping            don't re-retrieve files unless newer than
                                 local.
  -S,  --server-response         print server response.
       --spider                  don't download anything.
  -T,  --timeout=SECONDS         set all timeout values to SECONDS.
       --dns-timeout=SECS        set the DNS lookup timeout to SECS.
       --connect-timeout=SECS    set the connect timeout to SECS.
       --read-timeout=SECS       set the read timeout to SECS.
  -w,  --wait=SECONDS            wait SECONDS between retrievals.
       --waitretry=SECONDS       wait 1..SECONDS between retries of a retrieval.
       --random-wait             wait from 0...2*WAIT secs between retrievals.
  -Y,  --proxy                   explicitly turn on proxy.
       --no-proxy                explicitly turn off proxy.
  -Q,  --quota=NUMBER            set retrieval quota to NUMBER.
       --bind-address=ADDRESS    bind to ADDRESS (hostname or IP) on local host.
       --limit-rate=RATE         limit download rate to RATE.
       --no-dns-cache            disable caching DNS lookups.
       --restrict-file-names=OS  restrict chars in file names to ones OS allows.
       --user=USER               set both ftp and http user to USER.
       --password=PASS           set both ftp and http password to PASS.

Directories:
  -nd, --no-directories           don't create directories.
  -x,  --force-directories        force creation of directories.
  -nH, --no-host-directories      don't create host directories.
       --protocol-directories     use protocol name in directories.
  -P,  --directory-prefix=PREFIX  save files to PREFIX/...
       --cut-dirs=NUMBER          ignore NUMBER remote directory components.

HTTP options:
       --http-user=USER        set http user to USER.
       --http-password=PASS    set http password to PASS.
       --no-cache              disallow server-cached data.
  -E,  --html-extension        save HTML documents with `.html' extension.
       --ignore-length         ignore `Content-Length' header field.
       --header=STRING         insert STRING among the headers.
       --proxy-user=USER       set USER as proxy username.
       --proxy-password=PASS   set PASS as proxy password.
       --referer=URL           include `Referer: URL' header in HTTP request.
       --save-headers          save the HTTP headers to file.
  -U,  --user-agent=AGENT      identify as AGENT instead of Wget/VERSION.
       --no-http-keep-alive    disable HTTP keep-alive (persistent connections).
       --no-cookies            don't use cookies.
       --load-cookies=FILE     load cookies from FILE before session.
       --save-cookies=FILE     save cookies to FILE after session.
       --keep-session-cookies  load and save session (non-permanent) cookies.
       --post-data=STRING      use the POST method; send STRING as the data.
       --post-file=FILE        use the POST method; send contents of FILE.

HTTPS (SSL/TLS) options:
       --secure-protocol=PR     choose secure protocol, one of auto, SSLv2,
                                SSLv3, and TLSv1.
       --no-check-certificate   don't validate the server's certificate.
       --certificate=FILE       client certificate file.
       --certificate-type=TYPE  client certificate type, PEM or DER.
       --private-key=FILE       private key file.
       --private-key-type=TYPE  private key type, PEM or DER.
       --ca-certificate=FILE    file with the bundle of CA's.
       --ca-directory=DIR       directory where hash list of CA's is stored.
       --random-file=FILE       file with random data for seeding the SSL PRNG.
       --egd-file=FILE          file naming the EGD socket with random data.

FTP options:
       --ftp-user=USER         set ftp user to USER.
       --ftp-password=PASS     set ftp password to PASS.
       --no-remove-listing     don't remove `.listing' files.
       --no-glob               turn off FTP file name globbing.
       --no-passive-ftp        disable the "passive" transfer mode.
       --retr-symlinks         when recursing, get linked-to files (not dir).
       --preserve-permissions  preserve remote file permissions.

Recursive download:
  -r,  --recursive          specify recursive download.
  -l,  --level=NUMBER       maximum recursion depth (inf or 0 for infinite).
       --delete-after       delete files locally after downloading them.
  -k,  --convert-links      make links in downloaded HTML point to local files.
  -K,  --backup-converted   before converting file X, back up as X.orig.
  -m,  --mirror             shortcut for -N -r -l inf --no-remove-listing.
  -p,  --page-requisites    get all images, etc. needed to display HTML page.
       --strict-comments    turn on strict (SGML) handling of HTML comments.

Recursive accept/reject:
  -A,  --accept=LIST               comma-separated list of accepted extensions.
  -R,  --reject=LIST               comma-separated list of rejected extensions.
  -D,  --domains=LIST              comma-separated list of accepted domains.
       --exclude-domains=LIST      comma-separated list of rejected domains.
       --follow-ftp                follow FTP links from HTML documents.
       --follow-tags=LIST          comma-separated list of followed HTML tags.
       --ignore-tags=LIST          comma-separated list of ignored HTML tags.
  -H,  --span-hosts                go to foreign hosts when recursive.
  -L,  --relative                  follow relative links only.
  -I,  --include-directories=LIST  list of allowed directories.
  -X,  --exclude-directories=LIST  list of excluded directories.
  -np, --no-parent                 don't ascend to the parent directory.

Mail bug reports and suggestions to <bug-wget@gnu.org>.


      






      Splice Window
      

      
The Splice window is used to control the Splice process. 
      
Help on each component:

      





      Grab
      


      
In the 
Splice Mode
this button will grab the core or selection from the current track.
In the splice mode, you can set the current track either by 
clicking with the middle mouse button, and thus setting a 
reference point,
or by cmd-left moust click, setting an 
active track. 

      If the core button is selected, we will grab the core from around the 
startCut point you have selected.

      If the selection button is selected, we will grab all of the track
from the startCut point to the endCut point you have selected.

      For information marking a cut, seeStart and End Cut





      Constrained
      


      

The SPLICE --> CONSTRAINED tool is used to build a complete

spliced record after the multiple-hole core data have been

depth-shifted and stratigraphically aligned. "CONSTRAINED"

means that the spliced record will ALWAYS preserve the

composite depth scale which is displayed in the left-hand

Composite panel. This is the preferred tool for building

spliced data records. 





      Undo Last Splice
      


      As you build splices into the composite, you may want to undo one or more
of the previous splices. Use this button for that purpose.





      Undo Last Grab
      


      bcha	 into the composite, you may want to undo one or more
of the previous cuts. For instance, you made a cut and  do not like it.
Use this button for that purpose.





      Deferred
      
This section contains documents that have not yet been implementd.

      Patience is a virtue!





      Load Graphic File
      

      Load Graphic File
      

      Load a graphic file into a track. 

      This is a deferred implementation.




      Load XML File
      

      Open Xml File Menu
      
This menu opens an Xml data file for input.

      This is a deferred implemenation.




      Load Known Format
      

      Load Known Format
      

      Load a text file of a memorized format. You can memeorize a formate in one of two ways:


    1. Using the parser menu option "Register File", or

    2. Importing someone else's Format xml file to the sub-directory
"format". 


      This is a deferred implemenation.