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:
Choose the Environment Variables button. You will
then see
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.
| Location | Default | Stored 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 executable | No | Since 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. |
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.
| Data | Same as XML above | Yes | When 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. |
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.)
| Application | $NCLIP_APP_DIR | No | This is an immutable value. |
| Help Path | The 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 Path | Usually $NCLIP_APP_DIR/oldHelp | Yes |
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:
| Order | Name | Description |
|---|
| 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:
| Leg | Sub-Leg | Site | Hole |
Core | Core Type | Section |
ODP Depth | Depth Offset | mb | Composite Depth |
| 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 |
| Leg | Sub-Leg | Site | Hole |
Core | Core Type | Section |
ODP Depth | Depth Offset | mb | Composite Depth |
| 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 |
| Leg | Sub-Leg | Site | Hole |
Core | Core Type | Section |
ODP Depth | Depth Offset | mb | Composite Depth |
| 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 |
_____
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
Send comments to the
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:
- Splicer
- 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.
- Composite Mode
- 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
Send comments to the
author
Composite Mode
Composite
Overview
This is the mode used when adjusting the depths in tracks to
match each other.
- Open multiple tracks, using the
Text Parser
- Try a compositing session, i.e. pick a reference point, using the middle mouse button.
- Right click on a second track.
- 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.
- Accept the composite.
- 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
Send comments to the
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:
- Find two features in adjacent holes which are visually
correlative, representing the same stratigraphic level.
- Define one core as being stratigraphically "fixed"
whereas the other core will "move" relative to the "fixed"
core.
- 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.
- 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).
- 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).
- 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.
- (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.
- 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. Th
You will then be asked for a file name.
.
