Operating Manual for DigitSeis.v.1.3
Thomas Lee
Department of Earth and Planetary Sciences, Harvard University
February 2018

This manual is provided to complement the DigitSeis.v.1.3 package for digitizationof analog seismograms available on the website of the Harvard Seismology Group.

For more general information on the Harvard Seismology Group, please visit:
http://www.seismology.harvard.edu/index.html.

For any questions, comments, or bug reports, please contact Marisa Reilly,
Administrative Assistant, Harvard Seismology Group at reilly@eps.harvard.edu

The development of DigitSeis was partially supported by the United States
Geological Survey Earthquake Hazard Program through the following grants:
G14AP00016
G16AP00021
G17AP00007
G18AP00018
and by the Miller Institute for Basic Sciences at the University of California,
Berkeley.

DigitSeis uses two functions that were not written by the authors nor are built-infunctions that come with MATLAB. We have permissions from the authors toinclude the functions in the DigitSeis package, and they can be obtained fromsources below.
rgb2hsv fast.m This function was written by Dr. Alexander Ihlow (Technische
Universitt Ilmenau), and is available from http://www.mathworks.com/
matlabcentral/fileexchange/15985-fast-rgb2hsv/content/rgb2hsv fast.m
writesac.m This function was written by Dr. David Yang (Los Alamos National
Laboratory). We obtained the latest version of this function from the author, but it
can also be found in the SAC distribution.
http://ds.iris.edu/ds/nodes/dmc/forms/sac/

Copyright statement for this function:
Copyright, 19, The Board of Governors of the Los Alamos National Security, LLC.
This software was produced under a U. S. Government contract(DE-AC52-06NA25396) by Los Alamos National Laboratory, which is operated by
the Los Alamos National Security, LLC for the U. S. Department of Energy. The
U. S. Government is licensed to use, reproduce, and distribute this software.
Permission is granted to the public to copy and use this software without charge,
provided that this Notice and any statement of authorship are reproduced on all
copies. Neither the Government nor the LANS makes any warranty, express or
implied, or assumes any liability or responsibility for the use of this software.

2

Contents
1 Introduction
1.1 Uses for DigitSeis . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Overview of the Digitization Process . . . . . . . . . . . . . . . . . .

66
7

2 Installation of DigitSeis
2.1 Mac OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.1 Installing . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.2 Running DigitSeis . . . . . . . . . . . . . . . . . . . . . . . . .
2.1.3 Uninstalling . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.1 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.2 Running DigitSeis . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.3 Uninstalling . . . . . . . . . . . . . . . . . . . . . . . . . . . .

9
9
9
11
11
11
12
12
12

3 Loading of Images
14
3.1 Opening DigitSeis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.1.1 Loading an Image . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.1.2 Loading an Analysis . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Image Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.2.1 Cropping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.2.2 Timemark Length . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.2.3 Timemark Offset . . . . . . . . . . . . . . . . . . . . . . . . . 20
4 Object Classification
21
4.1 End-Goal for Object Classification . . . . . . . . . . . . . . . . . . . 21
4.2 Point Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.2.1 Pixel Removal Tools . . . . . . . . . . . . . . . . . . . . . . . 23
4.2.2 Object Modification Tools . . . . . . . . . . . . . . . . . . . . 26
4.2.3 Classification Modification Tools . . . . . . . . . . . . . . . . 27
1

4.3
4.4

4.2.4 Checking Classification . . . . . . . . . . . . . . . . . . . . . .
Region Modification . . . . . . . . . . . . . . . . . . . . . . . . . . .
Missing Tools in Edit Classification . . . . . . . . . . . . . . . . . . .

28
30
35

5 Trace Identification
36
5.1 Automated Trace Identification . . . . . . . . . . . . . . . . . . . . . 36
6 Digitization and Correction of Traces38
6.1 Automated Digitization . . . . . . . . . . . . . . . . . . . . . . . . . 38
6.2 Correcting Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
6.2.1 Selecting Area for Correction . . . . . . . . . . . . . . . . . . 40
6.2.2 Modifying Base Image . . . . . . . . . . . . . . . . . . . . . . 41
6.2.3 Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
6.2.4 Digitization and Application . . . . . . . . . . . . . . . . . . . 44
6.3 Missing Tools in Correct Trace . . . . . . . . . . . . . . . . . . . . . . 46
7 Timing
47
7.1 Calculation of Time Anchors . . . . . . . . . . . . . . . . . . . . . . . 47
7.2 Assigning of Absolute Timing . . . . . . . . . . . . . . . . . . . . . . 48
8 Saving Results
52
8.1 Saving an Analysis as a .mat . . . . . . . . . . . . . . . . . . . . . . . 52
8.2 Saving a Timeseries as .SACs . . . . . . . . . . . . . . . . . . . . . . 53
A Toolbars
55
A.1 Main DigitSeis Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . 56
A.2 Left Sidebar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.3 Edit Classification Toolbar . . . . . . . . . . . . . . . . . . . . . . . . 58
A.4 Correct Trace Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . 59
B Increased Controls
60
B.1 Edit Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
B.2 Identify Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
B.3 Digitize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
B.4 Correct Trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
B.5 Calculate Timing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
B.6 Extract SAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

2

C Dealing with Crossed Traces
75
C.1 Classification of Crossed Traces . . . . . . . . . . . . . . . . . . . . . 76
C.2 Correction of Digitized Crossed Traces . . . . . . . . . . . . . . . . . 79
C.3 Point-Fitting Option . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

3

List of Figures
1.1

Flow of Information Through DigitSeis . . . . . . . . . . . . . . . . .

8

2.1Open DigitSeis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

10

3.1
3.2
3.3
3.4
3.5
3.6

Select Load Option Window . . . . . . . . . . . . . . . . . . . . . . .
Polarity Change Window . . . . . . . . . . . . . . . . . . . . . . . . .
DigitSeis Main Window . . . . . . . . . . . . . . . . . . . . . . . . .
Cropping Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Measuring Timemark Length . . . . . . . . . . . . . . . . . . . . . .
Set Timemark Offset . . . . . . . . . . . . . . . . . . . . . . . . . . .

14
15
16
17
19
20

4.1 Classification Screen . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Edit Classification Toolar . . . . . . . . . . . . . . . . . . . . . . . .
4.3 Pixel Removal Tools . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.4 Case for Pixel or Region Removal . . . . . . . . . . . . . . . . . . . .
4.5 Object Modification Tools . . . . . . . . . . . . . . . . . . . . . . . .
4.6 Combining Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.7 Classification Modification Tools . . . . . . . . . . . . . . . . . . . . .
4.8 Classification Modification Tools . . . . . . . . . . . . . . . . . . . . .
4.9 Identifying Timemarks to check Classification . . . . . . . . . . . . .
4.10 Example of Where Regional Modification can be Applied . . . . . . .
4.11 Selection of Area for Regional Modification . . . . . . . . . . . . . . .
4.12 Lowering Brightness Threshold . . . . . . . . . . . . . . . . . . . . .
4.13 Point-Specific Modification within the Regional Modification Window

22
23
23
25
26
27
27
28
29
30
31
32
34

5.1
5.2

Trace Identification Waitbar . . . . . . . . . . . . . . . . . . . . . . .
Estimated Trace Zero-Lines . . . . . . . . . . . . . . . . . . . . . . .

37
37

6.1
6.2

Automated Digitization Process . . . . . . . . . . . . . . . . . . . . .
Example of Trace Needing Correction . . . . . . . . . . . . . . . . . .

39
40

4

6.3
6.4
6.5
6.6
6.7
6.8
6.9

Selecting Area for Correction . . . . . . . . . . . . . . . . . . . . . .
Correct Trace Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . .
Original and Masked Image . . . . . . . . . . . . . . . . . . . . . . .
Isolated Image Data . . . . . . . . . . . . . . . . . . . . . . . . . . .
Classifying Corrected Region . . . . . . . . . . . . . . . . . . . . . . .
Corrected Region with Digital Trace Overlay . . . . . . . . . . . . . .
Comparison of Automated and Corrected Digitizations . . . . . . . .

41
41
42
43
44
45
45

7.1
7.2
7.3

Calculation of Standalone Timing . . . . . . . . . . . . . . . . . . . .
Setting Absolute Time for a Timemark . . . . . . . . . . . . . . . . .
Propagated Absolute Time . . . . . . . . . . . . . . . . . . . . . . . .

48
49
50

8.1

SAC Extraction Window . . . . . . . . . . . . . . . . . . . . . . . . .

54

A.1
A.2
A.3
A.4

Main DigitSeis Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . .
Left Sidebar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Edit Classification Toolbar . . . . . . . . . . . . . . . . . . . . . . . .
Correct Trace Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . .

56
57
58
59

B.1
B.2
B.3
B.4
B.5
B.6
B.7

Edit Classification ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . . .
Trace Identification ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . .
Adjust Traces Window . . . . . . . . . . . . . . . . . . . . . . . . . .
Digitize ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Correct Trace ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . . . . .
Timing ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Extract SAC ‘+’ Menu . . . . . . . . . . . . . . . . . . . . . . . . . .

61
63
65
67
69
71
73

C.1 Example of Crossed Traces . . . . . . . . . . . . . . . . . . . . . . . .
C.2 Classified Crossed Traces . . . . . . . . . . . . . . . . . . . . . . . . .
C.3 Separating Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.4 Overlapping Object . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.5 Defining Overlapping Region . . . . . . . . . . . . . . . . . . . . . . .
C.6 Combining Overlapping Segments . . . . . . . . . . . . . . . . . . . .
C.7 Digitized Crossed Traces . . . . . . . . . . . . . . . . . . . . . . . . .
C.8 Isolation and Classification of Crossing Trace . . . . . . . . . . . . . .
C.9 Digitization and Application of Crossing Trace . . . . . . . . . . . . .
C.10 Base Image with Point Fit . . . . . . . . . . . . . . . . . . . . . . . .
C.11 Point Fit Generated Object . . . . . . . . . . . . . . . . . . . . . . .
C.12 Digitization of Point Fit . . . . . . . . . . . . . . . . . . . . . . . . .

75
76
77
78
78
79
79
80
81
82
83
84

5

Chapter 1
Introduction
1.1

Uses for DigitSeis

DigitSeis is an image processing tool that will fit a digital line to the traces shownon analog seismograms in both time and location spaces. It takes a high-resolution
digital scan of an analog seismogram1 and then allows the user to create a digital
copy of the information presented, which can then be extracted as time series in
the .SAC format allowing for old analog data to be treated like modern digital timeseries. This opens up a veritable wealth of data which was previously both relatively
inaccessible and had little use with regard to modern techniques.
DigitSeis is MATLAB based software2 , which, where possible, uses automated imageprocessing algorithms to extract data, however, it still requires human input andsupervision for the purposes of correction and monitoring (and hence, this operating
manual).
Please note that DigitSeis is optimized for use with seismograms that were generated without a pen (e.g., photographic type-records). The behavior of DigitSeis is
not well constrained or tested for pen-generated seismograms due to the curvature
introduced by the swinging armature. However, work is being done to add the capability to process these images to future releases of DigitSeis. Similarly, DigitSeis was
also built around seimograms that have timemarks. In this version, changes have
1

These images should be single scans of the whole seismogram, that is, multiple small scans
stitched together may not work2
While MATLAB based, DigitSeis is provided in a standalone format where a MATLAB installation is not necessary (Chapter 2

6been implemented to allow records without timemarks to be processed, but these are
not as efficient, optimized, and well tested as the options for records with timemarks,
and consequently, results may not be as accurate.

1.2

Overview of the Digitization Process

The Digitization process can be separated into the following sequence of steps:• In the Loading step, the image read from the scanned analog seismogram into
DigitSeis3 . This step should also involve the cropping the image to remove
spaces around traces, along with inputting a few parameters specific to eachindividual seismogram.
• In the Classification step, the image is divided into “objects” which are classified to be timemarks, traces, and noise. The user can use a multitude of tools
to tweak and correct the automated classification calculation.
• In the Trace Identification step, the program will use the classified information in order to determine the best-guess for trace-zero lines (i.e., positions
where the amplitude is zero). Again, if these need to be adjusted, this can bedone so manually by the user.
• In the Digitization step, the user simply presses the Digitize button, and therest is fully automated. Here the program actually fits digital waveforms to
the lines on the image.
• In the Trace Correction step, the user can correct any issues present in theautomated digitization using an area-specific tool combining the classificationand digitization steps.
• In the Timing step, the program interpolates between timemarks in order tocalculate an associated time for every point in the analysis. The user must
input the absolute time for the program to reference the rest of the points
from.
• In the Saving step, the user can finally extract the digital timeseries from theanalysis as SAC files.
These steps are illustrated in the chart presented on the following page.
3

DigitSeis works with all image formats supported by the MATLAB function imread,the list of which can be found https://www.mathworks.com/help/matlab/import export/
supported-file-formats.html

7

Figure 1.1: This chart illustrates the chronological sequence of actions which theuser must take (represented by triangles) in DigitSeis along with the changing typesof information (represented by boxes) being passed from one step to another. Thismanual is organized in a similar chronological manner to follow this process.
8

Chapter 2
Installation of DigitSeis
DigitSeis is available at http://www.seismology.harvard.edu/research/DigitSeis.html.
It is provided as a standalone package for both Mac OS X and Windows not requiring
an installation of MATLAB1 .

2.1

Mac OS X

2.1.1

Installing

The DigitSeis download will be a .zip file containing the software and all necessary
dependents. To install the program, the user needs only to unzip the file2 which will
create the folder DigitSeis. Within this folder, the user will find another folder calledresources3 , a README.txt file with instructions for installation4 , and two clickto-run shell scripts RunInstaller.sh and RunDigitSeis.sh. To install the proper
MATLAB runtimes (dependencies for DigitSeis), right-click5 RunInstaller.sh andselect Open. This will bring up a warning box saying “install” is from an unknown developer. Are you sure you want to open it? (Figure 2.1). Select1

If the user wants the MATLAB source codes, please contact the Harvard Seismology Group(contact information is provided at the beginning of this document).
2
DigitSeis.zip
3This folder should not have to be touched except in the special case outlined in the
README.txt file found in the DigitSeis folder.
4
For a standard installation, this section should be sufficient, however the user should see the
README.txt for information on how to permanently set the proper environmental variables fortheir system to bypass the program launcher.
5Note that if a mouse is not being used, right-clicking can be achieved by clicking while holding
down the Control key, or using two fingers on a trackpad.

9

open.6 Doing so will open a terminal window that will display some output ofthe progress7 and that can be closed once [process completed] is displayed (thisshould be the final output)8 . This completes the installation process. As a final noteon installation, please keep in mind that in order for DigitSeis to operate properly,
the user must have permission to read and write to the folder where the program isinstalled, and where the images are being read in from.

Figure 2.1: The system warning box that will show up the first time the user tries torun either of the provided scripts. If the user double-clicks instead of right-clicking
and selecting open, the Open option will not be available in this warning box.
6

This only need be done the first time the script is run.
this output is not particularly important, and no user interaction is required.
8
Note that the user may modify their Terminal preferences to make the window close automatically by changing their settings under Terminal > Preferences > Profiles > Shell > Whenthe shell exits:.
710

2.1.2

Running DigitSeis

To launch DigitSeis, the user double-clicks the RunDigitSeis.sh launcher script9 .
This will once again open a terminal window10 (output otherwise displayed on the
MATLAB Command Line will now be displayed here) and will launch the app to
the DigitSeis Select Load Option Window from which an image or a saved analysis
can be loaded.11
To close DigitSeis, the user should simply use the x button in the top left to closethe main DigitSeis window as would be done for any window in Mac OS X. Notethat if the user has not saved the analysis Section 8.1 in the last five minutes, awarning box will appear asking the user if they really want to quit. If the user wants
to go back, they just need to use the Cancel button, and they will be returned tothe main DigitSeis window.

2.1.3

Uninstalling

To uninstall the standalone version of DigitSeis, the user just needs to delete theDigitSeis folder. All dependencies for DigitSeis are contained in this folder12 andthis can be considered a clean uninstall.

2.2

Windows

As a caveat, please note that DigitSeis was developed for, compiled for, and primarily
tested on the Mac OS X operating system13 . A Windows version is available, but
it has not been extensively tested14 . There are differences in appearance, and there
are known cosmetic issues such as text in messages being cut off and buttons having
9

If this is the first time the RunDigitSeis.sh script is being run, it must be opened with aright-click in the same way as the RunInstaller.sh script as was detailed in Section 2.1 andillustrated in Figure 2.1.
10This window can be closed when the user quits DigitSeis, or the preferences mentioned in theabove footnote may be modified to make it close automatically.
11
This launcher script can be bypassed by permanently setting environmental variables (the script
RunDigitSeis.sh temporarily sets them on each launch to work across most machines and setups)
as described in the README.txt.
12
This is not the case if the user has set environmental variables and moved the MATLAB runtime
folder as detailed in the README.txt.
13
This manual and the images within, also represent an OS X environment.
14
It has been confirmed that the software is usable and analyses can be processed, however thetesting was limited to a half-dozen analyses.

11some overlap. Please note that this software remains primarily a Mac OS X software,and that as a result, support for the Windows version may be limited.

2.2.1

Installation

The installation of the DigitSeis software for a Windows operating system begins withthe user downloading the file InstallDigitSeis.exe from http://www.seismology.
harvard.edu/research/DigitSeis.html. The user then must run this script, and an
installer “wizard” will guide the user through the steps of the installation15 . The
user may select where the program folder is installed, and further, may specify the
option for a desktop shortcut to be created. Please note that this installation requires
an internet connection in order for the software to download the necessary open-use
MATLAB runtimes. Please keep in mind that as a result of these downloaded files,
the final application size for DigitSeis will be around 2.2 GB. As a final note on
installation, please keep in mind that in order for DigitSeis to operate properly, theuser must have permission to read and write to the folder where the program isinstalled, and where the images are being read in from.

2.2.2

Running DigitSeis

The program may then be run like any other (including through the desktop shortcut
if one was created), by clicking on the application. There is a known issue with theWindows version wherein the program may get stuck on the “Please Wait” window
while saving analyses. If this occurs, please close the “Please Wait” window andthen attempt to close the main DigitSeis window. If the analysis has not been savedin the last five minutes, the program will ask if you would really like to quit, select“Cancel” and then attempt to save again. If the window closes, the analysis has beensaved in the last five minutes, and the user should reopen DigitSeis as they normally
would.

2.2.3

Uninstalling

Should the user wish to uninstall DigitSeis, they need to run the uninstaller script
which is created when the program is first installed. This script can be found in
15

Note that dependent upon your machine and version of Windows, a user confirmation window
asking for permission to make changes will appear, please select in the affirmative to continue theinstallation.

12the following directory (starting from the directory in which the runtimes were originally installed): uninstall/bin/win64/. In this directory the user should find an
uninstaller in the form of an executable.

13

Chapter 3
Loading of Images
3.1

Opening DigitSeis

When the user first opens DigitSeis, the following window will be presented:

Figure 3.1: The Select Load Option window will be the first thing the user will see
after opening DigitSeis.

3.1.1

Loading an Image

If the Open an Image option is selected, the user is prompted to select the image
which the program should load1 . A window will pop up saying that the image isloading, and the path to the selected image will be displayed. The user will then be
further prompted to select whether or not the polarity change should be consideredin the following window:
1

To follow along with this manual, the user should select the Z-component of the long-period(LP) record for February 13, 1938 through February 14, 1938 available at http://www.seismology.
harvard.edu/HRV/1938.html#0214

14

Figure 3.2: Here the user can opt whether or not the polarity of the loaded image
should be flipped, the choice should result in light traces over a dark background.
DigitSeis is built to work with images that have light-colored traces over a dark
background. Therefore, if this already describes the image that is being loaded, theuser should select the No button, whereas if the image has dark traces over a lightbackground2 then the user should select the Yes button to flip the polarity of theimage. In this step, color images are also converted into grayscale through use of oneof the HSV channels3 .

3.1.2

Loading an Analysis

The user can also select the Load Existing Analysis button from the initial load
window in order to retrieve a previous analysis and pick up from where they leftoff. The process for saving this type of .mat analysis for loading with this option iscovered in Section 8.1. For the purpose of the rest of this manual, the assumption
will be made that a new image was loaded.
2e.g., light colored photographic paper with dark lines generated by exposure to light by thegalvanometer.
3
For detailed discussion of this process, see Bogiatzis & Ishii, 2016.

15

3.2

Image Preparation

Once the image loads, the user will be presented with the main DigitSeis window
which looks like this:Figure 3.3: Shown is the DigitSeis main window, note the loaded image (1), thetoolbar (2), and the left sidebar (3).

This is the main working window for DigitSeis. As the processing of the analysis
works toward completion, the user will work down the left sidebar (Figure 3.3)
starting from the top. The associated buttons for each step will not be available
until the previous step has been completed, that is, one cannot skip straight fromClassification to Timing. That this order of operations is followed is crucial to thebuilding up of the analysis in a way that will produce usable data. Therefore, as theuser progresses through the process, some buttons will also become available (e.g.,
Identify Traces) and the user will have to make corrections to data generated in thesesteps with other tools. That being said, it is of utmost importance to make sure a
step is completed satisfactorily before moving along in the analysis, and also that the16analysis is saved as a .mat file4 at several points throughout the analysis. Keeping
all this in mind, this manual now begins with the first step of processing.

3.2.1

Cropping

Most seismograms have a lot of space without any data (or in any case, without
data which is pertinent to the digitization). For example, in the image loaded into
the program shown in Figure 3.3, we can see that there is not only unused space
where no traces are present, but also a completely different component which canbe cropped out5 . This cropping is done by selecting the Crop Image tool (second
from left on the toolbar) which will draw a box that the user can then drag thecorners and edges of to surround the area to be preserved. To crop this area, simply
double-click somewhere on the screen. This is illustrated below in Figure 3.4.

Figure 3.4: At left is the image with a box drawn by the crop tool, and at right is
the resultant cropped image showing only the traces of the vertical component.
4

See Section 8.1 for more information on how to save the analysis as a .mat file and the timeseries as .SAC files.
5
Here we are interested in the upper recording, which is the vertical component of the seismogram, the simultaneously recorded lower portion shows the horizontal component (East-West),
that is, there are essentially two different seismograms shown here, and only the top one is being
considered for the purposes of this manual.

173.2.2

Timemark Length

In the next step where the program goes through an automated classification process,one crucial piece of information is the length of the timemarks. This parameter canvary from seismogram to seismogram6 , and so the user must measure and input thisfor each new image. Timemarks should all be roughly the same length along thehorizontal axis, so only a few need to be measured so long as they generally agree.
To do this, use the Zoom Image, Pan Image and Show Whole Image toolson the far right of the toolbar to zoom into a timemark. The user should then use
Measure Timemark Length tool (fifth from left in the toolbar)7 which allows theuser to construct a line in any orientation, and returns the length in pixels of thedrawn line along the horizontal axis. When the user has measured a few timemarks
and determined a suitable length representative of the majority of the timemarks,
this average value should then be inputted into the first box at the top of the left
sidebar labelled Pixels/Timemark. This process is shown below in Figure 3.5.
6

In the case where there are no timemarks, the user should input a negative value into the
Pixels/Timemark box. The negative indicates to DigitSeis that there are no timemarks present,
and it will instead calculate just trace and noise objects using the absolute value of the input as
the cutoff.
7
For more information on the different tools in the toolbar, see Appendix A: Toolbars.

18

Figure 3.5: Here the arrows indicate the three steps of measuring a timemark, (1)clicking the Measure Timemark Length button in the toolbar, (2) drawing a line
along the length of the timemark, and (3) inputting this value into the left sidebar.

193.2.3

Timemark Offset

The other important information that must be set before proceeding is the directionof timemark offset. This simply requires the user to visually inspect the seismogramand determine whether the timemarks are offset from the traces in an upward or
downward direction. This information is then passed to DigitSeis simply by setting
the Timemarks Up/Down button in the toolbar (fourth from left) to match theoffset seen in the seismogram. This is a simple toggle button, and switches back andforth between upward and downwards offset each time it is pressed8 .

Figure 3.6: Here we can see on visual inspection that the timemarks are offset below
the trace (this is easily seen by looking at the topmost trace), shown in bottom rightis the Timemarks Up/Down button set accordingly.

8

The way this button is set will not matter in the case where there are no timemarks.

20

Chapter 4
Object Classification

4.1

End-Goal for Object Classification

During the Classification process, DigitSeis automatically converts the image to abinary format1 and creates objects based upon pixels that are connected. These objects are then classified into three categories: Traces, Timemarks, and Noise. Trace
objects are those much longer than the timemark length threshold2 , Timemarks arethose objects whose length is around the timemark length threshold, and Noise objects are those whose length are below the timemark length threshold.
After clicking the Edit Classification button, the user will be presented with a
wait-screen while the program computes the automatic classification described above.
Once this process is finished, the modification window for the classified objects will
open and display the results of the automatic calculations (Figure 4.1). Here, thetrace objects will be displayed in white, the timemarks in blue, and noise in red3 .
1This is why the traces must be light on a dark background.
This threshold is based on the timemark length input in the Pixels/Timemark box as described in Section 3.2.2
3These are default colors and can be modified along with other parameters in the Edit Classification step, for more information see Appendix B.1
221Figure 4.1: Shown here is the window where the user can modify the objects andtheir classifications.

Before proceeding to the next step, the user must now go through the classificationand make sure that all objects are classified properly4 . That is, to make sure all
extemporaneous objects (written notes, stains on the paper, etc...) are removed, that
all timemarks are classified as so, and that all traces are classified as so. There is asuite of tools which give the user the ability to modify objects and their classifications,and they can be divided into the two categories which are detailed in the remaining
part of this chapter.
4

Note that in the top right of the Edit Classification window there is a red button and box withthe default value of 85. The 85 indicates the threshold which indicates how bright a pixel needs to
be to be an “object” pixel. This value can be changed (higher for more “object pixels” and lower forless “object” pixels )and the red button clicked to recalculate the classification if the classification
calculated with the default value of 85 is poor.

22

4.2

Point Modification

The first way which we can modify the classification is by targeting individual objects,
for example, a single object, or part of an object. There are several tools which we
can use to do this, and these will be covered in this section while moving across theEdit Classification toolbar (Figure 4.2) generally from left to right.

Figure 4.2: The Edit Classification Toolbar

The first icon from the left, is to save the analysis at the current point you are at5and the second button from left is the regional modification tool covered in Section
4.3. Therefore, we begin with:

4.2.1

Pixel Removal Tools

Figure 4.3: Shown boxed are the Line Removal (Left) and Region Removal(Right) tools.

The tools shown above are important for two main tasks. The first of these is theremoval of extemporaneous information, mainly noise and written notes which thefitting-algorithm need not “see”. The second is for use in separating timemarks andtraces which are connected and therefore classified as a single object (or isolating
trace or timemark objects from noise objects). To use the Line Removal tool, theuser simply clicks the associated button, and then holds the mouse button down
while drawing a line along which pixels will be removed. This tool is best usedfor very small modifications and for object separation cases where the objects to
5

See Section 8.1 for more information on saving analysis.

23

be separated must be very close together even after separation. In the case of theRegion Removal tool, the usage is similar to that of the Line Removal tool. The
button is clicked, and the user holds down the mouse button while drawing a shape.
After the mouse button is released, the endpoints of this shape will be connected tocreate a closed polygon. Pixels residing within this closed polygon will be removed.
Both of these tools can be used multiple times until another tool is selected (e.g., thetool remains active until another option is selected, or the button is clicked again).
It is also worth noting here, that all noise objects can be deleted using the button
directly to the right of the brightness threshold box. In cases where there are manysmall noise objects, this can speed up processing considerably.

24

Figure 4.4: In the above case, there are written hour notes that need to be removed,along with the written date. However, in the case of the written date, care must be
taken to separate the notes where they touch both a timemark and a trace object.
The image shown below is an example of what this should look like after cleanup(note that the notes could have been separated and marked as noise objects, however
removing objects is more memory-efficient).

25

4.2.2

Object Modification Tools

Figure 4.5: Shown boxed are the Combine Objects (Left) and Overlapping Objects (Right) tools.

These two tools allow for the user to modify what a “single” object is. The Combine
Objects tool allows the user to select several objects which will then be combined
and reclassified into a single object. To utilize this tool, the user first clicks the associated button and will be presented with a set of yellow crosshairs. These crosshairs
are then used to click the objects which the user would like to combine (these selected objects should turn yellow). To exit the tool and finalize the combination,
the user simply right-clicks or presses the ENTER key and the crosshairs should
disappear.6 The main advantages of combining objects are that it allows users toreclassify objects (e.g., using the tools described in Section 4.2.3) with one click
as opposed to several (note, however, that these objects are line-independent in thesense that objects belonging to separate traces or non-adjacent objects should not
be combined), and also that objects that are too far away from the zero position canbe properly grouped. This tool is demonstrated in Figure 4.6.
The second tool in this category is the Overlapping Objects Tool. This tool
allows the user to select7 and object and then modify it’s properties either adding
or removing “object” pixels with tools similar to the Region Removal tool whereareas to either add or subtract pixels are drawn. This is mainly used for processing
traces who cross over one another (e.g., where pixels overlap) and more informationon this process can be found in Appendix C.1.
6
7Note that the selection must be finalized for it to take effect.
This is done in the same fashion as that for Combine Objects.

26

Figure 4.6: Shown here three separate trace objects (right side of the second line)
which it would be advantageous to classify as one. This is done using the Combine
Objects tool, and the selection of all three to combine is shown at right. To finalize
their combination into one object, the user would right-click or press ENTER toleave the tool.

4.2.3

Classification Modification Tools

Figure 4.7: Shown boxed are the Classify as Noise (Left), Classify as Timemark(Middle) and Classify as Trace (Right) tools.

This grouping of three tools allows the user to change the classification of any object.
The color of the circle in the button corresponds to the type of object, with red used
to reclassify objects as noise, blue to reclassify as a timemark, and white to reclassify
as a trace object. To use these tools, simply toggle the button and a pair of yellow
crosshairs will appear in the classification window. These crosshairs are then used
to target objects and reclassify them simply by clicking on them. To leave thetool, the user should right-click or press ENTER and the crosshairs will disappear.
For example, in the image presented in Figure 4.4, the user could also separate thewritten notes and then reclassify as noise, however, it is often more efficient to simply
delete noise objects rather than reclassify them since he program stores all objects
27

(including noise objects). However, note that objects which have been classified asnoise will be masked in the Correct Trace step, and this may be advantageous in acase where the data is very noisy.

4.2.4

Checking Classification

Figure 4.8: Shown boxed is the Identify Timemarks tool used to check for inclusionof all true timemarks and location of extemporaneous timemarks.

Oftentimes, it can be difficult to be sure whether the all objects have been properlyclassified. To this end, the Identify Timemarks tool has been provided to allow
the user to quickly scan over the classification and be able to tell if there are either too many or not enough timemarks. To turn this feature on, simply click the
button highlighted above once. Once this is done, all objects which are classified
as timemarks will have a yellow box drawn around them. The user can now scanacross the whole classification and if the “grid” formed by the timemarks (Figure4.9) seems to be missing a node, it is likely that there is an object there that should
be classified as a timemark but is not. Conversely, if there is a yellow box that does
not match up with the timemark “grid” it is likely that there is an object there thathas been incorrectly classified as timemark. To escape this viewing mode, the user
just clicks the button again.

28

Figure 4.9: Shown here is a screencapture depicting the yellow “grid” formed by
the highlighted timemarks, note how it is easy to identify areas where timemarks
should be (e.g., bottom right) and where they should not be (e.g., along the top of
the classification).

29

4.3

Region Modification

Figure 4.10: In the above image, there are data missing that were not calculated into
the original classification. To work with this part of the image the user should recalculate the classification for this specific region using the Regional Modification
tool.

Sometimes, there are cases where areas of a classification (as opposed to single objects) need correction or where there are missing data (Figure 4.10). It is often
less labor intensive to take care of these areas by recalculating the classification for aselected region8 then by using the point-specific methods and tools described above.
To do this, the user needs to use the Region Modification tool, whose icon issecond from left in the Edit Classification toolbar.
After selecting this tool, the user will need to drag a box around the region forwhich they would like the classification recalculated, and double click anywhere on
the screen in order to finalize and select this region9 . After this is done, the Analyze
Small Image Patch window will pop up with the recalculated classification for theselected region.
8

This is done in a method similar to how the original whole-image classification was done, but
only taking into consideration the brightness of the pixels in the selected region.
9
The box can be resized until the user double-clicks.

30

Figure 4.11: Shown at top is the box used to select the region from Figure 4.10
where there are missing/incomplete objects. Shown below is the Analyze Small
Image Patch window which displays the new classification for this particular area.

31

It can be seen that there has been some data recovered in the recalculated region,
however, it still misses some of the data. To remedy this, the brightness threshold
above which pixels are defined as being objects can be modified. This can be doneby modifying the number in the box in the top right of the window and pressing the
red button to the left of the box. The default value in this box is 8510 , but the user
can increase the data pixels by lowering this number (Figure 4.12).

Figure 4.12: When comparing the above image with that of Figure 4.11, lowering
the brightness threshold to 80 brought out nearly all of the data that were “missing.”
10This means that the brightest 15% of pixels are considered object pixels.

32

Once all the data exist as objects11 , the user can make further changes using thesame point-specific modification tools which were described in the previous section(note that these tools are also present in the Analyze Small Patch Window). In thecase shown in Figure 4.13, after lowering the brightness threshold enough to haveall data present, there were timemarks which had to be separated.
The user should also note the presence of a few new tools in the Analyze Small
Image Patch window. The first tool from left in the toolbar is the Cycle Mask
button which switches between, the masked (modified) image and original image.
This button is used when viewing the underlying image, which can be done with theeighth button from left. This is the Show Classification button which switches
the view between the classified objects and the underlying image. If the user desires
to bring part of the original image back to the masked version, they should use thesecond button from left (Region Recovery tool) which allows them to draw polygon whose interior will be recovered.
When the selected region has been processed satisfactorily, the Apply button canbe used to export these changes back into the main classification. By combining
this method with those described in Section 4.2, the user should go through theclassification until they have deemed it satisfactory. Users should keep in mind thatthe classification stage is the most time-intensive and important step in the analysis
process and so one should not hesitate to take their time with this stage. When
the whole classification is completed, the Edit Classification window can be closed,
returning the user to the main DigitSeis window.
11

It is worth noting that this is actually a small earthquake logged into the station records.

33

Figure 4.13: After the brightness threshold reduction demonstrated previously, theuser now separates timemarks from trace in the Analyze Small Image Patch window
in a manner identical to that detailed in 4.2.

While the steps and tools described in this chapter are perfectly sufficient for handling
most analyses, there are other tools which allow the user further control over what
the computer is doing during the automatic classification calculation. These controls
are detailed in Appendix B.1. Also, read Appendix C: Dealing With Crossed
Traces for information and tips on how to handle classification of objects that overlap
many other objects.

34

4.4

Missing Tools in Edit Classification

The Edit Classification step is the most complex of the process and as a result,
there is a lot going on. To keep the program from becoming confused, sub-windows
must be closed, and processes completed before the user is allowed to do anythingelse. Therefore, if tools become unavailable during the Edit Classification step,
the user should check for the following situations (in the given order):• The small region classification window is still open.
• The overlap analysis window is still open.
• The object selection or combine object process has not completed.
• Processing is slow (e.g., after removing a region) and after the process is completed, the tools become available. In this case, the user might want to restart
the program/computer.

35

Chapter 5
Trace Identification
5.1

Automated Trace Identification

Once the classification stage of the analysis has been satisfactorily completed, thenext step is to have the program estimate the zero-lines of the traces based on thepositioning of the objects defined previously. These trace-zero lines are importantas they are the basis for the digitization that occurs in the next step1 . To begin
the process, the user simply needs to click the Identify Traces button on the left
sidebar2 . The program will display a waitbar showing the progress (Figure 5.1),
and when it is complete will display the estimated zero-lines as dotted lines overlaid
on the image (Figure 5.2).
In Figure 5.2 note how the dotted lines line up right on top of the traces which
they represent. This is the ideal case. In some cases where there is more curvature
to the traces3 , the trace-zero lines may be slightly off at the ends. However, if there
are either too many trace-zero lines, too few trace-zero lines, or simply lines offset
to an unacceptable degree, the user must manually modify the trace-zero lines. See
Appendix B.2 for information on how to manually set the trace-zero lines.
1

The zero line provides the backbone from which the algorithm looks to either side to findobjects that belong to this particular line. This zero-line will also determine the amplitude of the
waveforms and will provide a basis for time calculation in a analyses without timemarks.
2
Recall that as the user works through the analysis, they will proceed down the left sidbar
3
The trace-zero line is assumed to be a quadratic polynomial function.

36

Figure 5.1: The waitbar showing progress on trace identification. The user shouldbe patient as this may take a few minutes.

Figure 5.2: Shown above are the estimated trace zero-lines calculated by the program.

37

Chapter 6
Digitization and Correction ofTracesAt this point in the analysis, all the classification work can now be turned into
something more tangible in the way of actual digital lines representing the data on
the image. Once again, there are two stages to this part of the analysis. First
the program takes the classification information and trace zero-lines provided in theprevious steps and does its best to fit digital lines to the image. After this, the user
can go and make any corrections that may be necessary.

6.1

Automated Digitization

To begin the automated portion of the digitization process, the user needs only toclick the Digitize button1 below the Identify Traces button in the left sidebar,
doing so will initiate the automatic digitization process2 . As the work progresses,
each line that has been digitized will have its digital trace overlaid on the image andtrace-zero line in a blue color. Once all of these traces have populated, the process
is finished. If this is not the first time the traces are being digitized, then a table
will appear after the Digitize button is pressed that will prompt the user to selectwhich traces to re-digitize3
1

The user should again note the presence of a + button which allows for increased controls
covered in Appendix B.3.
2
The program also attempts to vertically offset the timemark objects to merge smoothly withthe trace objects in this step
3
There is a button on the bottom of this table that allows the user to simply select all traces
for re-digitization.

38

Figure 6.1: Shown above is the automated digitization algorithm of the program
progressing its way through the image and overlaying digital traces.

6.2

Correcting Traces

Once the automated portion of the digitization process has finished, it is up to
the user to carefully go over the seismogram to make sure that the program has
successfully captured all the data visible on the image. If the seismogram is “easy” inthe sense of having no crossed traces and not being particularly noisy, the automateddigitization often captures all data present. However in many cases, the user must
make small tweaks to correct the automatic digitization (Figure 6.2)4 . Oftentimes,
these can be found by checking the Find Gaps button at bottom of the left sidebar,
which will draw yellow boxes around gaps in the digitized traces.
4

The keen reader will recall that this issue was actually corrected as an example in Section 4.3,
however, this will once again serve as an example of another way traces are corrected.

39

Figure 6.2: Note in the above trace how the digital trace clearly does not capture all
the data present in the image.

6.2.1

Selecting Area for Correction

To select the area to be corrected, the user needs to click the Correct Trace button.
This will bring up a set of yellow crosshairs5 which the user should use to select apoint on the trace-zero line for the trace they would like to correct6 . Once this point
has been selected, the crosshairs will disappear and a box with movable borders will
be drawn, the user can drag these borders until the region which they would like tocorrect is fully within the box7 . Double clicking this box will open up the Correct
5This may take a few seconds. Note also, that while the crosshairs are loading, tools will be
unavailable and continue to be as such until an item has been selected. As a result, if the Correct
Trace button is selected unintentionally, the user must still select an item to correct and then close
the resultant sub-window in order to regain access to tools.
6
Trace Correction is a trace-specific procedure, and can only deal with one trace or parts of one
trace at a time.
7
With regard to Trace Correction being trace-specific, this box can contain more than one trace,
however any data not belonging to the trace that was initially selected will need to be deleted. This
sort of operation will be necessary in cases where corrections are being made on traces that cross40

Trace window8 where the user will repeat a regionally specific version of the process
which has been used so far on the whole trace: editing the base image, classifying
objects, and digitizing.

Figure 6.3: Shown here is the area that should be corrected within the bounds ofthe box.

6.2.2

Modifying Base Image

Figure 6.4: Shown above is the toolbar of the Correct Trace window. Most of thesetools should look familiar to the user.
over one another (dealing with crossed traces is covered in Appendix C: Dealing with Crossed
Traces).
8
The user should look at the name of the window for confirmation that they are indeed correcting
the intended trace.

41

The first thing that the user will need to do is to modify the base image to isolate the data of interest. There are several tools available to the user to allow this.
In the fifth and sixth positions from left, note the familiar Line Removal and Region Removal tools from Chapter 4. New tools in the third and fourth positions
from left9 are the Cycle Mask tool and the Region Recovery tool, respectively.
The Cycle Mask allows the user to cycle between the masked image (that modified
by removal of certain areas) and the original image (Figure 6.5). The Region Recovery tool is the opposite of the Region Removal tool, as it allows the user toselect a region where data will be recovered from the original image and reinserted
back into the masked image, this is especially useful for when too much of an area
is removed. The user should use these tools to isolate the data of interest as shownin Figure 6.6.

Figure 6.5: Shown above at left is the masked image (the dark regions are what
DigitSeis knows to be parts of other traces or noise), at right is the original image.
The user can switch between these two views using the Cycle Mask tool.
9

The first two tools are used for an alternative spline fitting method for digitizing traces. Thismethod is covered in Appendix C: Dealing With Crossed Traces.

42Figure 6.6: Shown here is the masked image after connected segments were separated
and missing regions recovered.

6.2.3

Classification

Once the image has been cleaned, the user can reclassify the objects present in theselected region. To do this, the Calculate and Show Classification button (ninth
from left, and to the left of the three familiar Classification Modification tools).
Selecting this option will take the user into an Edit Classification-style screen where
the classification of objects can be changed using the Classification Modification
tools covered in Section 4.2.3. Note that areas and lines can still be removed in thisclassification view if objects are touching, also note the presence of the Overlapping
Objects tool which is used in the same way as was described in Section 4.2.2. It isalso sometimes necessary for the user to modify the brightness threshold as describedin the latter half of Section 4.3 (this box and red button are once again present in
the top right corner of the window).

43

Figure 6.7: Shown here is the correctly classified selected region, the process usedhere is nearly identical to that described in Chapter 4.

6.2.4

Digitization and Application

The final step before the selected region can be merged back into the main analysis
is to re-digitize the trace. To do this, select the Digitize button in the Edit Trace
toolbar (Figure 6.4) (thirteenth from right, and marked with a “D”). Clicking thisbutton will digitize the objects the user has classified and overlay the calculated digital trace onto the objects10 . The user can also use the Set Vertical Offset button(to the right of the Digitize button), in order to tell DigitSeis how much it should
vertically offset the timemarks to merge smoothly with the rest of the trace the Gradient Minimization button will reset the offset back to the default, otherwise thenumerical offset can be changed manually until the user is satisfied.
To merge this corrected region back into the main analysis, the user selects either
the Apply Skip NaN button or Apply Include NaN button, both located in thebottom left of the window. Both will merge the correction and main analysis, but
the user must select whether to include NaN values (resulting in gaps in the digital
trace) or ignore NaN values (previously digitized traces in these positions will bepreserved).
10

If this overlay is not what the user expects, then the user must go back and re-modify the image
and classified objects until the desired result is achieved.

44

Figure 6.8: Shown above is the digital trace overlay calculated with the Digitize
tool, the digital trace now captures all the data present and can be remerged withthe main analysis. Because there is no gap in the trace, the two Apply ... options
have the the same result.

Figure 6.9: Here, the corrected digital trace from Figure 6.8 has been mergedback into the main analysis (Above Right) and compared to the original automateddigitization (Above Left).

45

6.3

Missing Tools in Correct Trace

Much like the Edit Classification step, there is a lot happening during the Correct
Trace step, and as a result, there are cases where tools may not be available in the
expected fashion or time. Once the Correct Trace button is clicked, all of the
pushbuttons on the left sidebar become disabled until the Correct Trace routine
is completed. Therefore, if these buttons are unclickable, the user should try thefollowing remedies that commonly cause this to happen.
• Wait a few seconds to see if the yellow crosshairs appear on the screen. Ifthey appear, then the Correct Trace routine has been begun. If this wasunintentional, simply select a trace, double-click on the region selection box,
and then close the resultant Correct Trace sub-window.
• Check to see if there is a box somewhere in the main DigitSeis window. This
indicates that the Correct Trace routine has begun, and a trace has been
selected. Once again, if this was unintentional, simply double-click the box
to open the Correct Trace sub-window and close it to complete the Correct
Trace routine.
• Check to make sure there is a not a Correct Trace window open (note that
this may be behind the current main DigitSeis window). Close this window tocomplete the Correct Trace routine, and the tools should once again become
available.

46

Chapter 7
TimingAt this point, digital waveforms have been generated and corrected to be accurate
reproductions of the data displayed on the analog seismogram. However, that leaves
one crucial component still missing, the timing1 . To generate digital time series, eachdata point must have a time assigned to it. To begin the timing process, the program
must first calculate time anchor locations for the trace by using the timemarks andends of the traces. These anchor locations then have absolute time assigned to them.
The steps the user must take to do this are described in the following section. Before
proceeding, note again that while DigitSeis has the capability to process records withno timemarks, these features are not yet optimized and may not produce results withthe same accuracy as is seen on records with timemarks.

7.1

Calculation of Time Anchors

The timing anchor calculation is an automated process. The user needs to initiate
this process by clicking the Calculate Timing button2 . This will open a waitbar
showing the progress of the calculation. As the calculation progresses, the main
DigitSeis window will be populated with time anchors appearing as yellow “timebars”
within traces3 and as red “timebars” at the ends of each trace.. When this is finished,
the waitbar will close and the Calculate Timing button will change to an un1

At this point in the analysis, the digitized traces are expressed in terms of x and y coordinates
as opposed to being expressed as a time and amplitude.
2
If the Calculate Timing button is unavailable, check to make sure that all windows associatedwith the Correct Trace step have been closed.
3
These correspond to the identified timemarks and will not appear in analyses which do nothave timemarks47

clickable Update Time button.

Figure 7.1: As the time anchors are calculated, the waitbar will progress and “timebars” will populate in yellow and red.

After the time anchors have been populated, the user should go through the analysis
and make sure that the yellow “timebars” correspond properly to timemarks and red“timebars” correspond to the ends of the lines. If these locations are inaccurate, theuser can move the “timebars” to reset the anchors. This is important as these willdefine the accuracy of the absolute timing4 .

7.2

Assigning of Absolute Timing

Once the time anchors are satisfactorily placed, the user must tell DigitSeis whattime to assign to the anchors. This is done by right-clicking one or more of the
4

Note that at this time there is no way to add a yellow “timebar”, but moving a red one off ofthe end of the trace will cause a new yellow “timebar” to appear.

48

“timebars” and setting the absolute time to which it corresponds. Doing this willthen allow DigitSeis to extrapolate from that one absolute point to the rest of theseismogram. The written notes5 can often be helpful for knowing what timemarks
correspond to what absolute times. In the case of an analysis without timemarks,
two of the red “timebars” at the ends of traces should be set6 .

Figure 7.2: Shown above left is the right clicking of the 15:00 hour mark (this isindicated by the written notes) and shown at right is the inputting of this time into
the Set Reference Time box.

Once the time for a timebar has been set, the time will be displayed next to the
timebar in red. Once the minimum number of times are set7 , the Update Time
5

While these may have been deleted from the classification, they should still be present on theoriginal image which everything is overlaid atop.
6
Recall that these types of analyses did not have yellow “timebars” calculated, that is, the only
time anchors are at the ends of traces.
7
Analyses with timemarks only need one timebar or any color to be set, analyses without
timemarks require two red timebars to be set (movable yellow timebars will propagate after Update
Time is clicked.

49

button will go from grayed-out and un-clickable to red and clickable. This button
should now be used to assign absolute timing from the reference point(s) to therest of the seismogram. When clicked, the absolute time will be displayed every 15
minutes in the analysis as is shown in Figure 7.3.

Figure 7.3: Shown here is the absolute time extrapolated from the reference point(s)to the rest of the analysis with 15-minute markers in yellow. Note that the timebar
for the original reference point is brighter and bolder. Also note that the 15-minutemarks align vertically.

Once again, it is important that the user checks over the work of the program tomake sure that the absolute time has been calculated properly. This can be done bymaking sure that the 15-minute marks all line up vertically8 . If this is not the case,the user needs to define another reference time point someplace on the problematic
8

That is, that each trace is an integer multiple of 15 minutes, which should be the case because
traces are typically one-hour long, therefore, 15-minute marks should all be in the same positions
and should form columns (these may have some shift, but not large jumps).

50

trace and Update Time again. If need be, this can be done (though this should
seldom be necessary) for every trace to get all of the 15-minute marks to line upproperly.

51

Chapter 8
Saving Results
There are two very different ways that data can be saved from DigitSeis. One is used
to save the analysis so that the user can leave and come back later to pick up where
they left off or make a correction. The second is used to extract the finalized data
in SAC format for use like any other modern time series. These two methods arecovered in this order in the following two sections.

8.1

Saving an Analysis as a .mat

This section has been referenced a few times previously in this manual, and with goodreason. Saving analyses as .mat files is the way the user can save work in the DigitSeis
and return to where they were if they are not yet at the point where .SAC files can beextracted. For that matter, even after .SAC files can be extracted it is often prudent
to save the completed analysis as a .mat file so that it can be reopened with DigitSeis
and used to generate the .SAC files again should anything happen to the original
copies. That being said, executing this type of save is extremely straightforward. In
both the DigitSeis main window and the Edit Classification window, the first iconfrom left in the toolbar is a blue save icon. The user need only click this icon andtell DigitSeis where the .mat file should be saved. A window asking the user to wait
while the save is in progress will pop up and disappear when the save is complete.
There are several times where it is recommended that the analysis is saved in caseof mishap further down the line. These are as follows:• After the image has been loaded and cropped• After classification has been completed (for more complicated and in depth
seismograms, it may be a good idea to save several times throughout the clas52

sification process)• After traces have been digitized• After traces have been corrected (again, if this is a complicated analysis requiring many corrections, several saves throughout this stage would be sensible)• After timing has been completed
Note that if the save icon is inactive there are several possibilities for why this might
be the case. These are as follows:• The analysis is currently being saved. Please wait a few seconds until theprocessing is complete.
• The trace selection function in Correct Trace has been initiated. Complete
the Correct Trace routine (Section 6, esp. Section 6.3).
• The identify trace function is in process. Let the process complete.
• The digitization function is in process. Let the process complete.
• The time calculation function is in process. Let the process complete.
As a final note on .mat files generated by DigitSeis, it is worth mentioning that
this version of DigitSeis is completely back-ward compatible in the sense that files
generated by earlier versions will open without any problem. However, note that files
saved in DigitSeis.v.1.3 will not be compatible with earlier versions of the software.

8.2

Saving a Timeseries as .SACs

When the classification, digitization, and timing are all complete, all the components
of a complete and modern digital time series are there. Now, all that must be done
is to get this timeseries out of DigitSeis and into a form usable for modern analysis
techniques. To do this, the user just needs to utilize the Extract SAC button at
the bottom of the left sidebar1 . This button will bring up another window asking forstation information that is included in the .SAC files (Figure 8.1). After these arefilled out, all that needs to be done is click the Generate SAC Files button andselect the location for DigitSeis to write the .SAC files in.
1

Now that the timeseries is finished and ready for extraction, note that we’ve worked our way
to the bottom of the left sidebar!

53

Figure 8.1: The window where the user can input station information for inclusionin the SACs.

54

Appendix A
Toolbars
In this appendix, explanations are provided for the tools in the various toolbars usedthroughout the digitization process.
Explanations will be brief, however for the most important tools, references to themain body of this manual will be provided telling the user where to look to find more
information on their use.
This appendix is not a quick-start guide and should mainly be used as a reference torefresh the memory on what tools do what. It is highly recommended that the user
read through the main body of this manual in its entirety as it will provide the best
walkthrough of how to use DigitSeis.

55

A.1

Main DigitSeis Toolbar

Figure A.1: The Main DigitSeis Toolbar

From left to right, the tools in the Main DigitSeis Toolbar are as follows:• The Save icon allows the user to save the analysis as a .mat file (Section 8.1)
• The Crop tool allows the user to select area to crop (Section 3.2.1)• The Undo button allows the last action to be undone (when clickable)• The Timemarks Up/Down toggle lets the user define the direction whichtimemarks are offset in (Section 3.2.3)• The Measure Timemark Length tool allows the user to measure horizontal
length of objects (Section 3.2.2)• The Curved Offsets tool allows the user to define and correct curvature frompen-style seismograms1• The Show Point Time tool allows the user to click anywhere on a trace
and see what the absolute time that has been assigned to that point (becomes
available after traces have been timed)• The Zoom buttons allow the user to both zoom into and out from the image
in the main DigitSeis window• The Pan button allows the user to move the image in the main DigitSeis
window by dragging• The Show Whole Image button allows the user to snap back to the wholeseismogram view
1This feature would be used in the case of seismograms generated with an armature (hence thecurvature) and reflects functionality that has not yet been fully developed.

56

A.2

Left Sidebar
The Left Sidebar is the main “control panel” for DigitSeis.
As theuser progresses through the analysis ofa seismogram, they will also progress
downwards along the length of theLeft Sidebar.
In fact, the chapters of this manual are essentially organized in the same order as the different options present on the Left Sidebar.
This chronological order is as important
for this document as it is for DigitSeis itself, and this is why certain options in the Sidebar will populate onlyat certain times or after certain actions have been taken.
In this case,
all the options have been enabled forbetter viewing.
However, in practicethere will not be a time when all options are enabled as is illustrated atleft.

Figure A.2: The Left Sidebar

What is most important to note about
the left sidebar aside from its directionality is the presence of the + buttons on most of the options.
Thesebuttons will open menus that will give
additional controls over the steps they
are paired with.
These menus andtheir options can be considered “Advanced Features” and provide controls
sometimes necessary for more complicated analyses, these are covered in detail in Appendix B: Increased Controls.
57

A.3

Edit Classification Toolbar

Figure A.3: The Edit Classification Toolbar

The Edit Classification toolbar is slightly different from the Main DigitSeis toolbar
with some Classification-specific tools. The tools from left-to-right are as follows:• The Save icon allows the user to save the analysis as a .mat file (Section 8.1)
• The Regional Modification tool allows the user to select an area over which
to recalculate and make changes to the classification (Section 4.3)
• The Line Removal tool allows the user to draw a line along which object
pixels will be removed (Section 4.2.2)• The Region Removal tool allows the user to draw a polygon inside which
object pixels will be removed (Section 4.2.1)• The Combine Objects tool will allow the user to select multiple objects tocombine as one (Section 4.2.2)• The Overlapping Objects tool allows the user to add or remove pixels, anddefine pixels that belong to multiple objects (Section 4.2.2 and Appendix
C.1)• The Undo button allows the user to undo the last action taken• The three Classify as ... tools allows the user to select an object to reclassify
as either noise, timemarks, or traces (Section 4.2.3)• The Identify Timemarks tool will draw yellow boxes around all timemark
objects (Section 4.2.4)• The Zoom, Pan, and Show Whole Image buttons have the same function
as those in the Main DigitSeis Toolbar (Appendix A.1)
58

A.4

Correct Trace Toolbar

Figure A.4: The Correct Trace Toolbar
Icons in this toolbar from left to right are:
• The Spline Fitting option allows the user to place points over the image andfit a curve through them (Appendix C.3)
• The Spline Object Generation tool generates objects from the splines fit
with the Spline Fitting tool (Appendix C.3)
• The Cycle Mask toggle allows the user to go between the masked and original
image (Section 6.2.2)• The Region Recovery tool allows the user to draw an area in the masked
image to recover the original image in (6.2.2)• The Region/Line Removal, Overlapping Objects, and Undo tools havethe same function as in the Edit Classification toolbar (Appendix A.3)
• The Calculate and Show Classification button will calculate a classificationfrom the modified image and switches between the view between the masked
image and classified objects (Section 6.2.3)• The three Classify As ... tools have the same function as in Edit Classification(Appendix A.3)
• The Digitize button will calculate the digital line (Section 6.2.4)• The Set Vertical Offset tool allows the user to manually define the timemark
offset distance or find the vertical offset resulting in the smoothest transition
from trace to timemark (Section 6.2.4)• The Zoom, Pan, and Show Whole Image buttons have the same function
as those in the Main DigitSeis Toolbar (Appendix A.1)

59

Appendix B
Increased Controls
In this appendix, the menus allowing for increased controls over different parameters
DigitSeis uses (accessible via the + button to the left of the different major steps inthe left sidebar) are covered. These parameters have been optimized and many simple seismograms should be processable without needing to use any of these controls.
This simple and straightforward type of digitization is detailed in the main body ofthis manual.
However, there are cases where these parameters will need to be modified in order to successfully digitize more complicated or difficult seismograms. That being
said, it is highly recommended that the user be very comfortable with the standard
digitization process (i.e., that described in Chapter 1 to Chapter 8) before moving
to these more difficult analyses.
Finally, as a word of warning, it is best to modify no more than a few parametersat a time1 , this way, the direct result of changing this parameter can be observed.
Also note that all of the increased controls menus have Save buttons in the bottom
right. These will save the parameters as they are shown as the new defaults for every
subsequent analysis 2 . That being said, it would be prudent to make notes of what
the default values are before making program-wide changes with the Save button.
As a final caution, there are a few parameters which are included in these menus but
should generally not be modified. These will be marked with a: h1This is especially true if this is the first time the user is modifying these parameters!
Simply changing the parameters and not using the Save button will keep these changes analysisspecific with the changed parameters only being used when this analysis is opened.
2

60

B.1

Edit Classification

Figure B.1: + Menu for Edit Classification

61

In the + menu for the Edit Classification stage, the user can change several parameters relevant to the automatic calculation of classification3 .
In the uppermost group of three boxes, the Image threshold (%)4 controls thecutoff level for which pixels are defined to be “objects”. For example, with the current setting of 85, the brightest 15% of pixels will be considered “object” pixels. The
Threshold Range(h) parameter is a “wiggle room” factor modifying the Image
threshold (%) parameter. The Minimum number of pixels parameter controls
the number of object-pixels that must be grouped to be defined as an object5 .
The Classification Colour Scheme box allows the user to set what colors trace,
timemark, and noise objects appear in.
The Small Classification Window Setup grouping of parameters allows the user
to set the bounds for the size of the Regional Modification (Section 4.3) and Overlap Traces (Section 4.2.3) sub-windows6 .
When calculating the automatic classification, DigitSeis divides the image into small
patches and calculates the objects for each independently. The image x divisionand image y division parameters control how the image is divided into the patches.
Finally the timemark length perturbation for classification(h) parameter isa “wiggle room” factor which modifies the pixels/timemark parameter set in Section 3.2.2.
3This is touched on in Section 4.1.
This parameter can also be easily modified in the Edit Classification window, as well as the
Modify Region window with value shown at the top right corner of the windows.
5
Take caution if lowering this parameter, as it may lead to a very large number of objects being
created which will eat up memory and slow down the program.
6
These can be manually changed after they pop-up, but the user may desire that the window
always pop up in a certain place and be a certain size to begin with.
4

62

B.2

Identify Traces

Figure B.2: + Menu for Trace Identification

63

The first and only parameter in this + menu is the number of vertical strips tobe considered box whose default value is 15. This controls the number of segments
or strips that the program looks at when estimating trace zero lines. For seismograms
that result in trace-zero lines that span two different traces, this number needs to beraised.
There are three different modes for estimating the trace zero lines, and the modecan be selected in the Trace Identification Method(h) box. The default trace
method7 looks at the objects classified as trace objects and then fits trace-zero lines
to their locations. The trace mask method considers trace object pixels to be theonly valid pixels of the original image and ignores the rest. The image mode is theleast accurate and looks only at the image itself without taking any of the classification data into account.
The Adjust Traces button will only populate after the Trace Identification algorithm has been run8 , and can be used to manually adjust the number of traces,
and their locations.
7This has consistently been the most accurate method in testing, and there are very few cases
where this would not be the case, so long as the trace objects have been properly defined in the
Edit Classification step.
8
This is done by pressing the associated left sidebar button back in the Main DigitSeis Window.

64Figure B.3: Shown above at left is the + menu brought up by clicking the button
to the left of the Identify Traces button. Clicking the Adjust Traces button inthis menu will bring up the spreadsheet-type display shown above at right. Here theuser can add, delete, or move trace-zero lines.

Pressing the Adjust Traces button will bring up a spreadsheet (Figure 5.3) withthe trace-zero lines organized in rows. To move individual traces, the user can modify
the First y-pixel, First x-pixel, and Last x-pixel parameters. To remove a trace,
the user should simply uncheck the box under the Active column corresponding tothat trace and click the Apply button. To add a trace the user should use the +button in the bottom right corner. Clicking this button will take the user back to
the main DigitSeis window where they will have to click the starting position for
the trace they are adding. This will bring up a circle that the user can drag to thepoint they would like to define as the start position of the new trace. Once the start
position is finalized, double clicking anywhere will confirm this selection and a new65zero-line will be added. Finally, in the case where all trace zero-lines seem to beoffset either too far above or below the traces they correspond to the user can move
all traces by a given offset using the ˆ button to the left of the + button. This
option asks the user for a vertical offset in pixels to move all trace zero lines by9 .
The Apply button can be used at anytime to update trace-zero lines to reflect thechanges made. Once the user is satisfied with the changes, they simply close thewindow.
9Note that y values increase downward, so a positive value will lower the lines.

66

B.3

Digitize

Figure B.4: + Menu for Digitize

67

The Digitize + menu hosts parameters that allow the user to control how far ofan area to either side10 of the trace zero lines the Digitization algorithm looks forobjects in. These are the boxes in the top left of the window.
Below these parameter boxes are the Check Traces and Check STD tools. These
allow the user to highlight a given trace number11 . If no trace number is specified,pressing either button will cycle through all the traces (this is especially helpful forchecking that traces are in the right order).
In cases where traces are not in the correct order, they can be added, deleted, orreassigned using the grouping of three buttons found just below the Check Traces
and Check STD buttons. Again, the box next to the Delete Trace button is used
to specify a trace by number.12
The user can also uncheck the box at bottom of the window if they would liketo see a pie-chart progress display as traces digitize instead of the current traces (ifany) being removed and new ones drawn as they are calculated.
10

In this case “either side” is meant to mean above and below rather than to the left and rightof.
11This number corresponds to that of the trace numbers that were assigned and labelled in theTrace Identification step, and should be input into the box next to the Check ... button.
12Note that if there are many problems with traces and their order, it is often easier to re-run thedigitization, or even go back and re-identify traces. If it is the case that the traces are not being
identified properly, there may be issues with the Classification.

68

B.4

Correct Trace

Figure B.5: + Menu for Correct Trace

69

The first parameter in the Correct Trace + menu is similar to the Image threshold(%) parameter in the Edit Classification + menu (Appendix B.1), just applied tothe classification calculation done in the Correct Trace window13 .
The next two groupings are to control the intial size of the Box for Trace Selection
and the Correct Trace Window Selection. The Box for Trace Selection is
the starting size of the box that the user uses to select the area they would like tocorrect as is described in Section 6.2.1 and shown in Figure 6.3. The bounds here
are measured in pixels relative to where the user clicked on the trace. The Correct
Trace Window Selection refers to the separate window which is brought up after
selecting the region to correct. The bounds here are in normalized units and thesesettings are analogous to the Small Classification Window Setup group of parameters in the + menu for Edit Classification (Appendix B.1).
The next drop-down menu titled Interpolation Scheme refers to the method usedby the point fitting tool (Appendix C.3 and Appendix A.4) to connect the points(linear or spline)14 .
The HRV Hour Mark Identification tool will identify and highlight the doubletimemarks used as hour markers in the early HRV (Harvard Seismic Station) records15 .
It then recalculates the digitized trace around the second of the double-timemarks,
this corrects slightly different vertical offsets between the hour marks.
If the check box marked “full image when switching to classification” is checked,
the program will snap back to the whole area being corrected (any zoom will be lost)when toggling between the underlying image and the classified objects in the Correct
Trace Window.
In rare cases, DigitSeis may become very slow during trace correction. If this is
the case, the Reset Window will save where the user currently is, and then closeand reopen the program clearing the memory logs of unneeded data.
13

Note, again that there is a also a way to change this parameter within the Correct Trace window
in the form of the box and red button at top right.
14
Linear interpolation may be needed for traces that have very rapid motion creating linear“zig-zag” traces.
15
This is fairly specific to HRV records, but can probably be used on most seismograms that use
the “double timemark” to mark the hour.

70

B.5

Calculate Timing

Figure B.6: + Menu for Timing71

In the Calculate Timing + menu, the user can reset the default reference time in the
Reference Time group of parameters16 . The user can also reset the increment at
which the absolute time is displayed using the time display increment parameter.
The default value of 15 for this parameter, gives the “15-minute marks” describedin Section 7.2 and shown in Figure 7.3.
While the parameters described above are mostly for convenience and appearance,
the next group of three checkboxes is very important for timing accuracy and can beseismogram-dependent17 . The first of these is the time on left setting, which will
put the beginning of the absolute minute on the left-side of the time-mark18 . The
ignore timemark parameter will calculate time based solely on the reference times
provided and their corresponding trace length19 . The third checkbox labelled use
trace gap to time will treat gaps in traces as timemarks, and this option should
be used if the timemarks in the seismogram being digitized are gaps in the trace (asopposed to offset segments).
The Segment Trace button allows the user to deal with time discontinuities withina trace, and will allow the user to time multiple portions of the same trace independently of one another. This is done by right-clicking on one of the purple verticalbars generated in the main DigitSeis window and selecting Segment Trace, thetool is exited by right-clicking anywhere. Where the trace was segmented, marks thedivisions between what are now essentially separate timings. The Reset Time Infobutton allows the user to remove all current timing data and recalculate the timingfrom scratch, something that is often helpful when mistakes in setting reference times
lead to messy timing extrapolations.
Finally, the last parameter box marked factor for vertical time bar length willcontrol how the timebars appear.
16

The default reference time is the date initially displayed in the Set Reference Time box
shown in Figure 7.2.
17
Some of the information that would affect these settings may have to be sourced from theoriginal station logs.
18
The default for this parameter, and the convention at the HRV station is for the minute tobegin on right side of the timemark.
19
This method is much less accurate than using timemarks for reference, and should only be
used in cases where there are no timemarks present or those timemarks have been deemed to beunreliable.

72

B.6

Extract SAC

Figure B.7: + Menu for Extract SAC

73

The Extract SAC + menu allows the user to control the sampling of and timecorrection applied to the SAC files. This is done using the SAC Interpolation
parameters and the Time Correction (s)20 parameter. The SAC files are generated with the Interpolation Sampling rate specified here by the user. Note that theuser can also uncheck the time to nearest second(h) box, however, this is notrecommended.
The user can also deal with complicated or non-linear trace-zero lines with the tools
in the Additional Zero Line Correction to apply a higher-order polynomial fit
to the trace-zero-line calculation. However, note that this higher-order polynomial
fit is not used for time assignment when there are no timemarks (for those withtimemarks, the trace trace-zero curve has limited implications).
The third grouping of parameters (Station/Record Information) sets the default values for information that gets input into the SAC headers. Note that theseparameters just set the initial values that can then be changed in the Extract SAC
window as shown in Figure 8.1. Note also, that if the user desires a blank Extract
SAC window, then the Station/Record Information defaults can be set as empty
and saved.

20This particular parameter does not save for all subsequent analyses and is instead analysis
specific

74

Appendix C
Dealing with Crossed Traces
The main body of this manual1 deals with how to do a “simple” digitization withwell-separated timemarks2 and more importantly, no crossed traces. Crossed traces
occur when the amplitude of a trace (for example, if an earthquake were to occur)
exceeds the spacing between them, this causes the traces to “cross” over one anotheras shown in Figure C.1. This part of the manual provides some hints and methods
for dealing with this type of problem. Note however, that these are methodologies
found useful and efficient by the author, not necessarily the most efficient and usefulway. That being said, the user should approach this as a starting point from which
they can modify as they see fit to develop their own strategies for dealing with thesemore complicated analyses.

Figure C.1: This seismogram depicts the arrival of a teleseismic event whose amplitude is greater than the spacing between traces, leading to a “crossed trace” situation.
1

Chapter 1 through Chapter 8.
At times, the timemarks are offset but not fully separated from the trace. They are therefore
classified as being part of the trace and must be manually separated in the Edit Classification step.
2

75

C.1

Classification of Crossed Traces

Figure C.2: In the above image, two main problems can be observed (1) there areseveral crossed traces (2) because the crossing trace is “stretched” it is not as visible,
and some data appears to be missing.
When a situation as shown in Figure C.2 is left as-is, there will be a problem when
traces-zero lines are calculated, and consequently, also when the analysis is digitized.
The problem here is that due to the crossing trace having amplitude that causes it tooverlap with other crossed traces3 , they are classified as one object. This large object
spanning multiple traces creates problems for both the trace-zero line calculation andthe digitization algorithm, since both function by assigning each object to a single
trace.
3

From this point forward the trace whose large amplitude causes it to overlap with other traces
will be referred to as the “crossing trace”, while the traces which the “crossing trace” overlaps will
be referred to as the “crossed traces”.

76Consequently, the general solution to a crossed trace situation is to separate thecrossed traces from the crossing trace so each can be an individual object which will
be properly assigned to the trace-zero line that it belongs to. The way that the author
prefers to do this4 is to separate out all of the crossed traces as coherent objects inthe classification stage and leaving the crossing trace cut up to be recovered in the
Correct Trace stage. The way this would be classified is illustrated in Figure C.3.
This approach also avoids the potential for objets belonging to the crossing trace tobe identified as part of one of the crossed traces.

Figure C.3: Separation of crossed traces by cutting the crossing trace.

Note that from this stage, the user could proceed to the trace zero-line calculation anddigitization, and then can recover the crossing trace using the Correct Trace function(the method that will be detailed in this appendix). Alternatively, at this point, theuser could also define pixels belonging to multiple objects using the Overlapping
Trace Tool, and combine these with their respective traces using the Combine
Objects Tool. For example, see Figure C.5.
4Note again, that this appendix should serve as an example of one way in which this can be done.
DigitSeis is an extremely versatile program which, once proficient, a user can utilize in numerous
ways to take care of such complicated situations.

77

Figure C.4: Shown here is an object that is really two separate objects with significant
overlapping portions.

Figure C.5: Using the Retrieve Original Image tool (second from left), the overlapping region has been defined here and as a result has turned pink, and the surrounding objects reclassified.

78

Figure C.6: The pink overlapping region can be assigned to multiple objects, andso the three components each of both the top and bottom trace (including the overlapping region which is common to both) are combined with the Combine Object
tool and the modification applied.

C.2

Correction of Digitized Crossed Traces

Figure C.7: Shown here is the result of digitizing the classified crossed trace situation
shown in Figure C.3. Note how the crossed traces are intact and properly digitized,
while the crossing trace needs correction.

79

After the traces have been digitized, it can be seen that the crossed traces look
to be intact and properly digitized. However, because it was left in a cut-up statein the Edit Classification stage, the crossing trace is not properly digitized5 . Thiscan be remedied by using the Correct Trace tool to re-classify and redigitize thecrossing trace. As described in Chapter 6, and shown here in Figure C.8, the trace
of interest (in this case, the crossing trace) is isolated by removing the other sectionsof the base image and then classified. This new classification is then digitized andreapplied to the original image, resulting in having correct digital traces for both thecrossing and crossed traces (Figure C.8).

Figure C.8: In the upper part of the image, the un-isolated trace can be seen in thebase image, and in the lower part, the crossing trace has been isolated and classified.
5This is easily seen since there are several gaps where there are no digitized traces (blue lines)
over the trace. The gaps can be emphasized by using the Find Gaps tool (Section 6.2).

80

Figure C.9: The new classification is then used to recalculate the digital lines for the
trace as shown in the upper portion of the image. These new digital lines are thenmerged back into the main analysis to give the correct classification (lower portion).

C.3

Point-Fitting Option

At several points throughout this manual, the Point Fitting option in the Correct Trace window has been mentioned. This tool provides a way to create objects
without having to deal with removing regions from and generally modifying the baseimage. This is especially helpful in cases where the traces on the base image may bevery light, or where there are enough crossings that it would be easier to fit a curveto the crossing trace than isolate it from many crossed traces.
To use this tool, simply click it in the Correct Trace Toolbar (Appendix A.4)
and then select points along the trace which you would like to create an object for6 .
Right-click when the points have been picked, and a red line will be fit to the points
that were selected7 . The points are movable by clicking and dragging, and should be
adjusted until the red line overlays the trace with reasonable precision. An exampleof this process is shown in Figure C.10. If the trace is rapidly undulating, thespline interpolation may be too smooth to reproduce the line. In this case, change
the interpolation scheme to linear (Appendix B.4).
6

A set of yellow crosshairs will appear when you are in this point picking mode
The end points from this first picking of points will represent the endpoints of this object.
Points added between these end points will be incorporated into that object. If a new object isdesired, add points outside of these original endpoints. If the objects are overlapping, create thesecond object and then move the endpoint after the object has been defined.
781

Figure C.10: Shown above is the base image with the point selection in blue and thefitted curve in red.

82

Figure C.11: Shown here is the object generated by creating object pixels aroundthe fitted line shown in Figure C.10.

Once the user is satisfied with the line8 that has been fitted, the Point Object
Generation tool9 should be used to generate objects from the lines which havebeen fitted (Figure C.11). These should be classified in the normal way and shouldfrom this point forward be treated the same as if they were objects that had beencreated by brightness analysis of the original image10 , and can be simply digitized(Figure C.12) and merged back with the main analysis.
8

Or lines, in the case of multiple objects.
To the right side of the Point Fitting tool in the Correct Trace Toolbar (Appendix A.4).
10
That is, the standard method that has been used throughout this manual.
983

Figure C.12: Shown here is the digitization of the object shown in Figure C.11.

84

85