geopsy_20051026(2)

Contents• Next• Top of page•

Geopsy Manual: Contents1. Introduction• 2. Installation• 3. Tutorials•

3.1. Creating a database♦ 3.2. Refraction survey♦ 3.3. H/V measurements♦ 3.4. Noise array measurements♦

4. Database• 4.1. Load signal files♦ 4.2. Create, Open, Close and Save♦ 4.3. Groups of signals♦ 4.4. Preferences♦ 4.5. File structure♦

5. Signal viewers• 5.1. Table♦ 5.2. Graphic♦ 5.3. Map♦

6. Basic signal processing• 6.1. DC Removal♦ 6.2. Filters♦ 6.3. Automatic Gain Control♦ 6.4. Fast Fourier Transform♦ 6.5. Tapering signals♦ 6.6. Cutting signals♦ 6.7. Merging signals♦ 6.8. Subtracting signals♦ 6.9. Rotate components♦

7. Specific processing tools• 7.1. H/V♦ 7.2. Damping♦ 7.3. Frequency−wavenumber for 2D arrays♦ 7.4. Frequency−wavenumber for 1D arrays♦ 7.5. Spatial auto−correlation for 2D arrays♦ 7.6. Particle motion♦ 7.7. Refraction♦

8. Writing scripts• 9. Developers•

9.1. Reading file formats♦ 9.2. Exporting file formats♦ 9.3. Specific processing tools♦

Geopsy licenses• References•

Geopsy manual: content

Geopsy Manual: Contents 1

Contents• Previous• Next• Up• Top of page• Database• Viewers• Processing• Scripting•

1. IntroductionThis manual documents how to use Geopsy as well as the tools developed for ambient vibration processing. Itcorresponds to version 2.0.0.


1. Introduction 2


1. Introduction 3

Figure 1: Main frame of Geopsy. On the left, the File and Group navigation bars. On the right, the three kindsof viewers: table, graphic and map.

Geopsy is a graphical user interface for organising, viewing, and processing geophysical signals. These threeaspects are detailed hereafter and they are illustrated in figure 1 by a screen capture. Geopsy is also a databaseused to gather all information about recorded signals. External command line or GUI programs can access thisdatabase, enjoying the optimised core library designed for very long signals (hours of recording or tens ofmillions of samples).

Though extensions to other scientific or engineering fields are potentially possible, this software has beenprimarily designed for seismology and seismic prospecting. It is available under all common platforms(Linux, Mac OS X, and Windows) and released for free under the GNU Public License. Please refer theinstallation section for details.

Database

Various common signal file formats can be loaded. These formats are automatically recognised to simplify theaccess to the measured signals. Reading the original file format is usually better than using conversion toolswhere data losses are likely to occurs (e.g. correction factors).

There is virtually no limit to the number of signals that can be loaded at the same time. Once loaded, thesignals can be grouped in ordered lists (groups) and supplementary information can be added to each trace(signal name, X Y Z coordinates, picks, ...). These data cannot be stored in all types of file headers due to theheterogeneities of the signal file formats.

For this reason, a database is generated to gather in an independent and handy way all information. A databaseis stored under a .sdb file that lists all signal files corresponding to a particular project or site. Hence, thesignals are not duplicated when creating a database, keeping links to the original signal files and saving diskspace. One interest of databases is to reload all signal files of a project with a simple click. Each database isaffected a directory containing the .sdb file plus other secondary files.

New files are automatically added to the database when a trace is modified (Processing) and saved inside thedatabase directory with a quick access format (binary). The original signals are still present in the database.

Viewers

They are three ways of viewing the signals in Geopsy: Table, Graphic and Map. Each viewer is a floatingwindow in the main Geopsy frame that contains a sub list of signals currently loaded (with or without adatabase created). According to each viewer, it is possible make a selection of signals and to create anotherviewer containing only the selected signals (drag and drop mechanism).

The table shows textual information about each signal (one per row). The number of columns and the datadisplayed is entirely configurable. Each field can be directly edited. For long signals (millions of samples), itis handy to select signals with a table because only the header information is loaded into memory, the wholetraces are not loaded from files. The contents of tables can be exported and imported to ASCII files.

The graphic shows the signal themselves with a time scale. Various options are available for plotting traces(e.g. variable black area, normalisation, colour scale, ...). All signals are stored as time series. However, theycan be plotted as frequency spectra after Fourier transforms. A zooming facility has been implemented to easedata inspection. Signals cannot be selected inside a graphic viewer, they are all selected by default.


Database 4

The map shows a 2D map of the signal coordinates. Scales of axis are automatically adjusted to fit thecoordinate range. Selection of signals can be performed directly with mouse picks.

Processing

Geopsy proposes two kinds of signal processing tools:

Basic processing (menu "Waveform"): filters, Fourier transform, taper, cut , DC removal, merge,subtract, multiply, ... These transformations directly affect the signals and the results are automaticallyupdated on the screen. Reverting to the original is always possible. On saving a database, themodified signals are saved with a raw binary format (best I/O performances) into the database'sdirectory. Both the original and the modified signals remain accessible in the database.

1.

Advanced processing (menu "Tools"): these are tools developed for special purposes. A plug−inmechanism allows you to add new tools without upgrading the main Geopsy frame. Originally, theavailable tools were dedicated to the analysis of ambient vibrations. The development of newspecialised tools are pretty welcome (developers).

2.

Scripting

In certain cases, the graphical user interface may not be useful especially for repetitive tasks. Thanks to QtScript for Application (QSA from Trolltech), it has been possible to propose a versatile scripting language toexecute any of the functions available with mouse clicks. These scripts can be launched from the commandline allowing its inclusion into complex bash scripts, for instance.

The available functions within a script currently do not cover the whole functionalities of Geopsy. The usersare particularly encouraged to give their feedback on this topic to accelerate the development on the mostpopular tools ().


Viewers 5

http://doc.trolltech.com/qsa-1.2/language.html

Contents• Previous• Next• Up•

2. InstallationThe next beta release is installed from distribution packages. This step is still under development. Developer:CVS basic commands and registration at www.geopsy.org


2. Installation 6


3. TutorialsThe following tutorials are documented in this chapter:

3.1. Creating a database• 3.2. Refraction survey• 3.3. H/V measurements• 3.4. Noise array measurements•

Tutorials 3.3 and 3.4 are both built around a demo database which is build with the tutorial 3.1. You can skipthe database construction by downloading the finalised database. When opening it for the first time, you willprobably receive a warning complaining about a missing signal file. Click "No" and specify the path to therequired file (usually in "geopsy_tutorials/raw_signals"). Save the database at least once to save the modifiedpaths.


3. Tutorials 7

Contents• Previous• Next• Up• Top of page• 1. Download the signals• 2. Unpack the archive• 3. Launch geopsy• 4. Load the demo signals• 5. Create a table of signals• 6. Modify the list of visible fields• 7. Extract the component• 8. Construct the station names• 9. Set station coordinates• 10. Creating the database on disk• 11. Creating groups• 12. Saving changes•

3.1 Creating a databaseThis tutorial helps you constructing the demo database used in tutorials 3.3 and 3.4. It is divided into thefollowing steps:

1. Download the signals• 2. Unpack the archive• 3. Launch geopsy• 4. Load the demo signals• 5. Create a table of signals• 6. Modify the list of visible fields• 7. Extract the component• 8. Construct the station names• 9. Set station coordinates• 10. Creating the database on disk• 11. Creating groups• 12. Saving changes•

1. Download the signals

Download the raw signals: database−step0.tar.gz. These signals were generated with HISADA code (Hisada1994 and 1995) within the framework of the SESAME European Research project (Bonnefoy 2004,SESAME). The reference model used to generate these signals is detailed in Wathelet 2005 (Modeldescription).

2. Unpack the archive

Open a terminal and execute the following commands (note: "mwathele@Canucks:~$" is my bash prompt).Keep this terminal open until the end of this tutorial. Under Windows, double−click on the downloadedarchive, and copy directory "geopsy_tutorials" to another location (e.g. "My documents").


3.1 Creating a database 8

http://sesame-fp5.obs.ujf-grenoble.fr/index.htm

http://marc.geopsy.org/thesis/node104.html

http://marc.geopsy.org/thesis/node104.html

Unpacking the raw signals and the list of station coordinatesmwathele@Canucks:~$ tar xvfz database−step0.tar.gz...

3. Launch geopsy

For Linux or Mac users, it is interesting to start geopsy from the terminal at least once to be familiar with theoutput messages or warnings. Otherwise, go to the platform specific menu to start new applications: KDE orGnome menus, 'Startup' for Windows,... The exact name of the shortcut depends upon your installationparameters.

Starting Geopsy's main framemwathele@Canucks:~$ geopsy&

Check your configuration, specified in the installation manual, if geopsy fails to start. If it is the first time youexecute geopsy, you should see a splash screen and a first dialog box entitled "Preferences". At this stage,click on "OK" to accept the default settings.

4. Load the demo signals

Click on menu "File" and select "Load signal" item, or alternatively hit CTRL+l, or click on "Load Files" icon

from the tool bar ( ). Change the current directory to "geopsy_tutorials/raw_signals". Select all files from"demo_01A.1.sac" to "demo_10A.3.sac" (with mouse and SHIT key). Click on "Load" to proceed with theloading of files. If you get a dialog box asking for the format, make sure to select "Automatic recognition" andto unckeck "Show this dialog next time" before clicking on "OK". After a short delay (waiting for the progressbar at the bottom right to increase up to 100%), the loaded signal should appear on the left in the Files/Groupslist. If not, please refer to the specialised sections or use the search engine of this documentation.

Note: at this stage, the signals are loaded into memory. For the purpose of this tutorial, the components, thestation names, and the coordinates of the stations have been cleared from the SAC headers. Adjusting thesefields is a common task for signals acquired on stations that do not record the information correctly. Duringthe next step, you will learn how to set these fields in a rational way.

5. Create a table of signals

Select "All signals" in the "Files" list. Drag and drop this item to the "Table" icon from the tool bar ( ). Todrag and drop signals, press the left mouse button on the selected signals move the pointer to the desireddestination, and release the right mouse button. Possible destinations are:

a table ( );•

a graphic ( );•

a map ( );• any existing viewer already opened in the main frame.•

The three first destinations will create new viewers with the selected signals. The last destination will add theselected signals to the existing viewer. A table should appear with header information of all loaded signals, asshown in figure 1.


2. Unpack the archive 9

Figure 1: Table containing all loaded signals, empty headers.

The headers contain only the basic signal information: sampling frequency and number of samples. Otherfields (such as the component) have been set to default values for all signals.

6. Modify the list of visible fields

Click on menu "View" and select "Set data fields" item. A dialog box as shown in figure 2 lets you modify theinformation displayed in the current table.


5. Create a table of signals 10

Figure 2: Dialog box that lets you modify the information displayed in tables.

In the left column, you have the names of the internal variables. On the right, you have the associated title inthe table. Replace one the useless fields (in this tutorial, e.g. "ID"), by the name of the file ("FILE_NAME").Make sure (for the next steps) that the fields "NAME", "COMPONENT", "REC_X", "REC_Y", and "REC_Z"are in the list. Click on "OK" to apply the changes to the current table. The complete names of each signalshould appear in the table.

7. Extract the component

The component is extracted from the signal file names. The components were stored in the file name structurewith a number from 1 to 3, meaning Vertical, North, and East, respectively. Click on menu "Edit" and select"Set headers" item. A dialog box as shown in figure 3 lets you modify the header information by the means ofa series of user defined equations.

Figure 3: Dialog box that lets you modify header information of each signal contained in the current viewer.


6. Modify the list of visible fields 11

The white area containing the formulas is empty when you open this dialog box. Modify the fields at the topto construct the equation:

Equation to extract the component indexes from the file namesname = file name right 5

Click on "Add" to add this equation to the main list.

Alternatively, you can download the file getcomp.formulas to add the equation. Make sure that the list ofequations is empty before loading the file. Click on "Load" and select the downloaded file.

Figure 4: Dialog box that lets you sort the signal in a viewer.

Click on "OK" to apply the equation to the signals of the current table. Sort the signals by "name" to group thesame components together. Click on menu "Edit" and select "Sort" item. A dialog box as shown in figure 4lets you re−order signals in the current viewer according a series of user−defined criteria. Select a "Signalname" in the bottom list, click on "Add". If the list of criteria was not empty, first remove all items by clickingon "Remove". The position within the list is important, the first item is the main sort key. Click on "OK" tore−order the signals in the current table.

Select all the signals with the name equal to "2.sac". Drag and drop these signals to the table icon ( ). Clickon menu "Edit" and select "Set headers" item to modify the "COMPONENT" field for the signals of thenewly created table. Enter the following equation or load the file setnorth.formulas:

Equation to set component as Northcomponent = & North

Once the components are changed, close the current table and go back to the first table containing all thesignals. The same job must be done for "3.sac" (corresponding to East components). Enter the followingequation or load the file seteast.formulas:

Equation to set component as Eastcomponent = & East

The content of the main table is not refreshed after any changes performed in another table. To check theresult, close the main table and create a new one as described here above.


7. Extract the component 12

8. Construct the station names

Click on menu "Edit" and select "Set headers" item to modify the "NAME" field of all signals. Enter thefollowing equation or load the file setnames.formulas:

Equations to set the station namesname = & Rname &= file name right 9name = name left 4

9. Set station coordinates

Click on menu "Edit" and select "Set receivers" item to set the receiver coordinates. A dialog box will displaythe list station names with the coordinates X, Y, and Z. Click on "Load" to load the coordinate filereceivers.coord. This operation adds new rows in the station list. The added station names should be identicalto the existing names to overwrite the current coordinates. By clicking on "OK", the coordinates of the signalsare modified. To check them, a map of the station can be viewed be dragging "All signals" to the map icon

( ). The result should look like in figure 5.


8. Construct the station names 13

Figure 5: Station map

10. Creating the database on disk

Click on menu "File" and select "Create database" item. You will be prompted for a database name. Adirectory will be created and information will be saved inside this new directory. Creating a database allowsyou to create groups of signals as described in the next step.


9. Set station coordinates 14

11. Creating groups

Make sure that the map created in step 9 is currently active. Right click in middle of the map to display thecontext menu and select "Edit" item or alternatively hit CTRL+SHIFT+e. If no "Edit" item is present in thecontext menu it is likely that you right click at the wrong place. Four distinct areas are present on such XYgraph: X axis, Y axis, bottom left corner and the graph's content. A "editing ..." message should appear on theplot. By pressing mouse left button and moving the pointer, you create virtual rectangles. All stationscoordinates falling inside this rectangle are selected. To unselect all, construct a rectangle with no stationinside. To add new selected station press SHIFT while pressing the mouse.

Three station array can be constructed from the ensemble of stations:

One small circle with stations: R01A to R10A;• Three triangle rotated by 120°: R10A, R03A, R06A, R09A, R01B to R08B;• One big circle: R10A, and all stations on the big circle.•

Select the stations of one array. The stations must appear in red. Hit CTRL+SHIFT+e to end the editing mode.Drag and drop the content of the graph to the table icon to create a new table. Click on menu "Edit" and select"New group" item. Enter a name for the group of signals (e.g. "array_A"). Close the table, and activate themap again. Go back to editing mode by hitting CTRL+SHIFT+e again. Unselect all stations and select anotherarray. Other arrays should be named "Array_B" and "Array_C".

For conventional array analysis, the vertical component is often used without the North and East components.Special groups of signals with only the Vertical components can be created for each array, for instance,"Array_A Vertical", "Array_B Vertical" and "Array_C Vertical".

Right click on group "Array_A" in the "Groups" list on the left. Select the "Table" item to create a tablecontaining only this group. Select "Sort" from menu "Edit". "Insert" sort key "Component" to re−order signals

by components. Select only the signals with a Vertical component and drag it to the graphic icon ( ). Clickon menu "Edit" and select "New group" item. Enter a name for the group of signals (e.g. "array_A Vertical").Close all windows and redo the same task for arrays B and C.

12. Saving changes

Click on menu "File" and select "Save database" item. The groups and any modification to the signals aresaved on the disk.


11. Creating groups 15

Contents• Previous• Next• Up• Top of page•

3.2 Refraction surveyThis tutorial helps you interpreting refraction experiments. Currently this feature is in development state. Afirst version has been developed with na_viewer but must revised to be integrated into Dinver.


3.2 Refraction survey 16


3.3 H/V measurementsThis tutorial helps you interpreting single station measurements of ambient vibration with the H/V spectralmethod. TODO


3.3 H/V measurements 17


3.4 Noise array measurementsThis tutorial helps you interpreting multiple station measurements of ambient vibration with the FK and theSPAC methods. TODO


3.4 Noise array measurements 18

Contents• Previous• Next• Up• Top of page• A bit of theory• Why creating a database?•

4. DatabaseThis chapter explains how to work with a Geopsy Database. Creating a database on the disk is not amandatory step. You can use Geopsy to view and to process signals on single file basis. However, you wouldmiss a number of interesting features such as grouping of signals and automatic storage of modified signals.

This chapter contains the following sections:

4.1. Load signal files• 4.2. Create, Open, Close and Save• 4.3. Groups of signals• 4.4. Preferences• 4.5. File structure•

A bit of theory: the internal database structure

Geopsy Database is not build on an existing database engine such as MySQL. The database is only made of alist of signals. A signal is a vector of numbers (double floating point real numbers, 64 bits) documented by acollection of information fields, typically the information extracted from file headers.

Information fields of a signal

Field name Type Description

COMPONENT string Name of the component, it must be one of the followingkeywords: Vertical, North or East

COUNT2VOLT double

The conversion factor between 'counts' and 'volts'. 'counts'are divided by this factor to obtain 'volts'. This value is readfrom the majority of signal files. By default this value is 1.0.When the factor is equal to unity, the amplitude scale of thesignal is automatically considered as counts, else as volts.This parameter is read−only. Conversions to acceleration,velocity or displacements are currently not handled. Furtherimprovements of the database will probably include thisfeature with a secondary table containing the responses ofcommon sensors.

DELTAT double

It is the sampling period expressed in period. Thisproperty, as well as SAMPFREQUENCY, can bemodified. However, make sure that it correspondsexactly to the true recording frequency sampling rate.


4. Database 19

DUPLICATE_RAYS_AVERAGEn double

This parameter is useful for travel time tomography analysis.n varies from 1 to 10. For phase picking (see PICKn), atravel time from source to receiver should be equivalent to atravel time from receiver to source observed on anothersignal. Couples of PICKn are identified by a uniqueDUPLICATE_RAYS_ID. The average and the standarddeviation for each couple is calculated inDUPLICATE_RAYS_AVERAGEn andDUPLICATE_RAYS_STDERRn, respectively. Thisparameter is read−only.

DUPLICATE_RAYS_ID integer

This parameter is useful for travel−time tomographyanalysis. Identifies uniquely a couple of signals with thesame ray path, where sources and receivers are justswapped. This parameter is read−only.

DUPLICATE_RAYS_STDERRn doubleThis parameter is useful for travel time tomography analysis.n varies from 1 to 10. SeeDUPLICATE_RAYS_AVERAGEn for details.

DURATION double

Time elapsed between the first and the last sample of thesignal (in seconds). This parameter is not saved in thestructure but calculated from DELTAT and NSAMPLES.This parameter is read−only.

END_TIME double

Time elapsed between the first and the last sample of thesignal (in seconds). This parameter is not saved in thestructure but calculated from DURATION and T0. Thisparameter is read−only.

FILE_NAME string The complete name of the signal file to which the signalbelongs, including its path. This parameter is read−only.

FILE_NUMBER integerThe number affected to the signal file to which the signalbelongs. This number depends upon the order of loadingfiles into the database. This parameter is read−only.

ID integer Unique number to reference the signal, used by groups.This value is read−only.

ISORIGINALFILE string

Contains "Original" if the signal samples have not beenaffected by any signal processing. Otherwise, the field isblank. See saving a database for details. This value isread−only.

MAXAMPLITUDE double

It is the maximum amplitude reached by the signal for thewhole DURATION. The units depends upon the value ofCOUNT2VOLTS. Contrary to the other fields, calculatingthis value requires the signal samples to be loaded intomemory. Hence using this field may slow down Geopsy. Weadvise using it only if necessary. This value is read−only.

NAME string Arbitrary name to identify the signal, usually it is set to thename of the recording station.


A bit of theory: the internal database structure 20

NSAMPLES integerThe number of samples in the signal. This value isread−only. You can change the length of a signal bycutting it.

NUMBER_IN_FILE integerA signal file may contain various signals. This parameteris this index of this signal in its file. This parameter isread−only.

PICKn double

It is a time value that can be modified by the user, either byediting the field or by picking phases (with the mouse) on agraphic representation of the signal. n varies from 1 to 10.This parameter is useful for travel time tomography analysis,to define time limits of a taper or of a signal cut, or for anyprocessing that requires phase picking. Additionally, thesevalues are frequently used as temporary storage for headerassignations.

PICK_IDn integer

For each PICKn, an integer value can be affected. Currently,no processing tool is using these parameters. However, itmay be useful for GRM methods (refraction method toimplement?) where a layer number must be affect to eachPICKn.

REC_X,Y,Z double The coordinates of the receiver where the signal wasrecorded (Cartesian system expressed in metres).

SAMPFREQUENCY double

It is the sampling frequency expressed in Hz. Thisparameter is not saved in the structure but calculatedfrom DELTAT. You can modified it, DELTAT ischanged accordingly.

SIGNALPTR addressThe memory address of the block containing the signalinformation. This parameter is read−only and reserved fordebug purpose.

SRC_X,Y,Z double

The coordinates of the source for which the signal wasrecorded (Cartesian system expressed in metres). Thesefields are relevant to records where the source is clearlyidentified. It is generally useful for refraction and travel timetomography analysis.

T0 double

The delay (in seconds) between the time reference andthe first sample of the signal. It can be either positive ornegative. Various formats are accepted: "ss.ss[...]ss s","ss.ss[...]ss", or "hh:mm:ss.ss...ss". For all formats, a '−'sign can be added as a prefix.

TIME_REF string It is the time reference with the format "DD/MM/YYYYhh:mm:ss". All signals recorded synchronously must havethe same time reference. The T0 takes the distinct start−uptimes into account with an arbitrary precision in the timescale (time reference is limited to seconds). A good practiceis to set the time reference to the day of acquisition and at


A bit of theory: the internal database structure 21

midnight (19/05/2005 00:00:00). All T0 are then the numberof seconds since the beginning of the day. The visualisationmodules can handle such time to convert it into "hh:mm:ss"which corresponds to the true time of measurement.

TYPE char

It is a single character that records the current type ofsignal: 'w' for waveforms, 's' for frequency spectra, and't' for arrival time without signal. The type is read−only,you cannot modify it directly. Conversion from 'w' to 's'and vice−versa is done after a Fourier transform.

Notes: "double" means double floating point real numbers coded on 64 bits, "integer" means a positive ornegative integer, "string" means any string of characters, and "char" is a single character. The fields marked inbold represent the most important parameters that must be correctly defined to allow a visualisation of thesignal.

When a new signal file is loaded into the database, a new memory structure is allocated for the signal and thefields listed above are filled in from the information contained in the file header. The information extractedfrom the file header depends upon the file format (see Load signal files).

The signal samples are never directly read on opening a file which greatly speeds up the signal handling forthe user comfort. According to the user actions (e.g. visualisation of traces), it might be necessary to load thesamples into memory. In Geopsy core engine (library geopsycore), a special mechanism has been developedto cache the signal vectors (keep signals in memory as long as possible until no space is left, then purgerationally according to space needed). From the user point of view, it might be noticed that the first time asignal is visualised, it may be slower than for any later access.

Any subset of the total ensemble of signals can be created. The information is never duplicated because subsetare defined by pointers to the original signal structures. The subsets are visualised through tables, graphics andmaps detailed in other sections.

Why creating a database on disk?

The various signal file formats available in seismology and geophysical prospecting generally include aheader which contain heterogeneous information. There was a need to store in a uniform format basicinformation useful for the data processing implemented in Geopsy (e.g. picks of events, source and receivercoordinates, ...).

Some signal file formats can store various signals in a single file, others not. Signal processing, such as arraycomputations, may be applied to only a part of a file or to signals located in various files. There was a need forgrouping signals independently of the original file organisation. Exporting signals of interest to a temporaryfile before processing is not a satisfactory way of doing things because it duplicates the data on disk and thereis a risk of altering information from the file conversion. Furthermore, confusion is likely to occur betweentrue original signals and pre−processed signals (e.g. filtering, DC removal, ...).

Geopsy proposes an alternative with the concept of groups. A group is a list of signal ID (identificationnumber). A name is given to each group which explains its content. The ID are automatically affected to eachsignal when loading files into Geopsy. Hence, the affectation depends upon the order of loading files. Thedatabase concept ensures that all files are loaded in the same order each time the signals are accessed, andconsequently, that each ID effectively corresponds to a unique and well defined signal.


Why creating a database on disk? 22

External signal processing tools (e.g. command line softwares like Cap) can access a geopsy database toretrieve the signals of interest. The ensemble of signals is generally referenced by the name of a grouppreviously created in Geopsy's main frame. The command line tools have access to the signal samples with nocare about the original file format. The geopsy core engine handles all file access and memory allocations toease the development of processing tools based on signals.

Each time a command line tool is started with access to a Geopsy database all the header information isloaded into memory. This step is only based on the database's internal files. There is no access to the originalfile which ensures a very quick start−up of any database even if it contains a lot of signals (thousands). Firstversions of Geopsy required reading of file headers which is sometimes long (e.g. GSE format with multiplesignals in a file).

The file structure of a Geopsy database is described in section File structure.


Why creating a database on disk? 23

Contents• Previous• Next• Up• Top of page• How to load a file?• Selecting the file format• Automatic recognition• Database signals• Binary SEG2• Seismic Unix• Arrival times• RD3 RAMAC• NiSismo• SAC• Radan GSSI• GSE• CityShark• ASCII Multi column• SESAME SAF• Sismalp• Wave PCM• Formats not supported• Removing a file•

4.1 Load signal filesThis section explains how to load signal files into Geopsy and which file format are currently supported.

How to load a file?


4.1 Load signal files 24

Figure 1: "Files" list after loading several signal files.

Click on menu "File" and select "Load signal" item, or alternatively hit CTRL+l or the "Load signals" icon inthe tool bar. You get the open file dialog box where you can select one or more files to open. Use the SHIFTand CTRL keys to create custom selections. Click on "Load" to proceed with the loading of files. All theloaded files appear in the file list as shown in figure 1. This list contains all currently loaded files. File pathsare prefixed with base name of the file. According to the current preferences, the signals may be directlydisplayed in a table or in a graphic, or you can get the file format dialog box as shown in section Selecting thefile format.

If the list does not appear, it is likely that it has been hidden by previous use of Geopsy. Select "Files andgroups" in menu "Windows" to show the list. The list can be moved to any part of the screen by pressing themouse in its title bar and dragging it to the desired position. In the vicinity of the left and the right border ofthe main frame, the list is automatically docked to the main frame, otherwise it has a free position and size.Moving the mouse the edges of the list, the shape of the cursor is changed to a double arrow, any press anddrag of the mouse will resize the list. The same behaviour occurs at the limit between the "Files" and"Groups" lists.

Selecting the file format


How to load a file? 25

Figure 2: Preferences for file format selection.

Figure 3: Manual selection of file format.

In most situation, the automatic format determination does a good job. If you want to specify manually theformat, you have to edit the preferences. Click on menu "File" and select "Preferences" item, or alternativelyhit CTRL+p. In the preference dialog box, click on the "Loading files" tab. You get the screen shown in figure2.

Select "Always ask for file format" to manually specify the file format for all loaded file. If "Use this format"is selected, the format specified on the right is always used. "Automatic recognition" is the default andprobably the best option.

Before loading each file, you are asked to specify the file format with the dialog box shown in figure 3. If allthe selected files have the same format, you can uncheck the checkbox "Show this dialog next time". Choosethe right format in the list. Once the list is displayed after a mouse click on it, you can hit initial letters toquickly scroll to the right format. Selecting a wrong format is generally reported, but, in some situations, itmay read erroneous information without reporting error.

Automatic recognition

The table here below gives the criteria used to recognise the file formats. The conditions are processed inorder from the first to the last row. At the first match, the format is considered to be recognised.


Selecting the file format 26

Conditions for recognising file formats

Conditions File formats

file extension is ".su"SU big endian. Currently, no automatic detection of the byte order has beenimplemented for SU format. For SU little endian, the manual file formatselection is necessary.

file extension is ".rd3" RAMAC/RD3 format for RAMAC Ground Penetrating Radar

file extension is ".dzt" Radan format for GSSI Ground Penetrating Radar

file extension is ".ndx" or".sis"

Sismalp format, a ".sis" or ".ndx" (and vice−versa) must also exists in thesame directory.

file extension is ".wav" Wave PCM sound file, just for fun to analyse your favourite music albums.

First line contains"Arrival_times_file" Arrival times format

First 16 bits are 0x 55 3A Binary SEG2 file

First 32 bits are 0x 66 5F 9C6E NiSismo file format ???

First 4 characters are"WID2"

GSE2 format, test by default for multiple signals in the file. This option maytake some time for long signals. If there are only one signal per file, selectmanually "GSE2 Single Signal".

First line begins with"Original file name" City shark 2 file. No distinction between format 1 and 2, both are accepted.

First 10 bytes begins with"DBSignals" Geopsy database signals.

First line begins with"SESAME ASCII dataformat (saf) v. 1"

SESAME ASCII File format

First 4 characters are "RIFF" Wave PCM sound file, just for fun to analyse your favourite music albums.

First field (TAB or SPC) is anumber ASCII file, one column per signal.

NVHDR==6, IFTYPE=1 andLEVEN is true SAC format. The big and little endian are automatically recognised.

else Error message, unknown format.

Database signals

It is the format used by Geopsy to automatically save modified signals. Usually you never import originalsignals written under this format. This new format has been introduced in Geopsy because it is the closer tointernal memory vectors, hence I/O access are optimised.

Geopsy database signal format


Automatic recognition 27

http://www.cwp.mines.edu/cwpcodes/

http://www.malags.com

http://www.geophysical.com/index.htm

http://sismalp.obs.ujf-grenoble.fr/sismalp.html

http://sesame-fp5.obs.ujf-grenoble.fr/index.htm

http://www.llnl.gov/sac/

Offset (bytes) Size (bytes) Description

0 10 Recognition tag: "DBSignals"

10 4 Version, current is 1

14 4 Offset to first signal in file (bytes)

18 4 Number of signals in file (n)

22 4*n Number of samples in each signal (nsamp[i], 0<=i<n)

22+4*n 8*n Conversion factor for each signal

22+12*n nsamp[i] For each signal (0<=i<n), the samples coded on 64 bits floating pointnumbers.

Binary SEG2

This file format is described in ...???(text of the norm). It is the usual format acquired with Geometricsinstruments.

Seismic Unix

Arrival times

RD3 RAMAC

NiSismo

SAC

Radan GSSI

GSE

CityShark

ASCII Multi column

SESAME SAF

Sismalp


Database signals 28

Wave PCM

Formats not supported

SEG−Y and other instrument specific formats should be implemented as soon as possible.

Removing a file

To remove a file from the database or from the "Files" list, select "Remove" from the context menu in "Files"list. Multiple and complex selections (SHIFT and CTRL) can be used to remove several files at the same time.If the removed files are original files, the signal file is unaffected, only the information stored in the databaseis irreversibly lost. In the other case (modified files), the signal is removed from the database directory and theinformation about these signals is also lost.


Wave PCM 29

Contents• Previous• Next• Up• Top of page• Creating a database• Opening a database• Closing a database• Saving a database•

4.2 Create, Open, Close and Save databaseThis section explains how to create, to open, to close and to save a Geopsy database. The concept of a Geopsydatabase has been presented in section Database.

Creating a database on disk

First load the original signal files as described in section Load signal files to create the database in memory.Click on menu "File" and select "Create database". You will be prompted for a directory name and path withthe common file dialog box. The name of the directory is the name of the database. On clicking on "Save",Geopsy will create the directory and it will store all files as described in section File structure.

If some signals were modified with any processing tools (Basic signal processing), the corresponding files aresaved in the same way as Saving a database.

Opening an existing database

This operation requires that no signals are loaded in the current database. Click on menu "File" and select

"Open database". Alternatively, you can click on the "Open database" icon from the tool bar ( ). The openfile dialog box lets you select the appropriate database (".sdb" files). On clicking on "Open", the files areloaded into memory as well as the groups previously defined.

The ".sdb" file contains the absolute file paths of all original files to open. If the location of these files changes(directories or files renamed), a warning will be issued as shown in figure 1.

Figure 1: Warning issued when signal files cannot be found.

If you want to skip the file not found, just hit "Yes". Be careful that on the next "Save database" the file willbe permanently removed from the database (not removed from the disk). If the file still exists but has been


4.2 Create, Open, Close and Save database 30

moved to another location, hit "No". You will be prompted to enter the new path to this file with the classicalopen file dialog box. A path translator is automatically constructed to avoid repetitive warnings. You must hit"Save database" once to store the new paths into the ".sdb" file. "Cancel" just stops the database opening, allother signal files are skipped.

Closing a database

Right click in "Files" list, the context menu shown in figure 2 will appear. Select "Clear all". You will beprompted for closing all active viewers. This is normal because viewers have references to signals that will beremoved by this action. If header information or signals were modified, you will be asked to save the databasefirst.

Figure 2: Context menu of "Files" list.

If no named database was opened, but signal files were loaded individually, this operation clears all signalsfrom memory but without offering the option to save changes.

Saving a database on disk

This operation requires that a database has been created or opened. Click on menu "File" and select "Save


Opening an existing database 31

database". Alternatively, you can click on the "Save database" icon from the tool bar ( ). The changesbrought to the header information and any new signals added to the database are saved in the ".sdb" file. Theoriginal signal files are left untouched.

If the samples of some signals were modified by any processing tools (Basic signal processing), the signalsare saved in a Geopsy Database binary format in the database directory. The name is identical to the originalfile plus "_n" where n is chosen to avoid any overwriting of exiting files. The newly generated files are addedto the database as usual files. A flag (ISORIGINALFILE) allows the user to distinguish between original andmodified signals.


Saving a database on disk 32

Contents• Previous• Next• Up• Top of page• Selecting signals• Sorting signals• Creating a new group• Viewing groups• Renaming a group• Modifying a group• Deleting groups•

4.3 Groups of signalsThis section explains how to create and to use groups of signals. Groups of signals can be created only withinthe framework of a database. When files are loaded individually this operation is not permitted. The reasonsfor using groups are explained here. Groups are simply lists of signals referenced by their unique signal ID.The original order of signals at the group creation is always preserved. This section presents also the "dragand drop" mechanism used to associate signals.

Groups are saved in the database directory under files named ".group". These are binary files with the list ofsignal IDs. The list of groups is stored in the file ".grouplist". Only one exists per database. The files aremodified or created only when the database is saved (see 4.2. Create, Open, Close and Save).

Selecting signals

As detailed in section Signal viewers, they are three ways of viewing signals: tables, graphics and maps. Eachviewer is associated with a sub set of signals. Here, we use the "table" viewer to explain the "drag and drop"mechanism. The specificities of the "drag and drop" for each viewer are explained in section Signal viewers.

You can select the signals on a file basis with the "Files" list, or on a group basis with the "Groups" list. Inboth cases, press SHIFT or CTRL key to create complex selections. "All files" and "All groups" represent allsignals (except the temporary signals, see Basic signal processing) and the union of all groups, respectively.Press the mouse left button on the selection and move the pointer towards a viewer icon in the tool bar (e.g.

the table icon is ). Release the mouse button, a table will be created containing the selected signals.

In a table, you can select various signals with SHIFT and CTRL keys. Press the mouse left button on aselected row and move the pointer again to the table icon. A new table is created with the restricted selection.A signal may appear several times in a single viewer. You can drop signals into an existing table, the newsignals will be added at the end.

Sorting signals

To select signals, it may be interesting to sort the list of signals. For instance, if you want to select all thesignals measured on the vertical component, first create a table with all signals. Sort the signals by componentand select the block of signals with the vertical component.


4.3 Groups of signals 33

Figure 1: Dialog box that lets you sort the signal in a viewer.

Sorting can be done in the active viewer by selecting item "Sort" in menu "Edit". The "Edit" menu alwaysapply to all signals of the active viewer. A dialog box as shown in figure 1 will be displayed.

The selected keys are listed in the two−column table (Key and Order). Available keys are listed in the combobox at the bottom. Check or uncheck the "Descending order" checkbox as necessary and click on "Add"button to add a key to the sort. To use "Delete" or "Insert", you must select one row of the table. "Insert" willinsert the new key right before the selected key. Hit "Delete" several times to remove all keys. After clickingon "OK", the list of keys are stored and the signals of the active viewer are sorted.

Though multiple keys of the same kind are possible, it is totally useless. Moreover, using multiple keys has aneffect only when there are equal values in the first keys.

Creating a new group

There must be an active viewer. If it is not the case, create one as described in the preceding sections. Selectitem "New group" from menu "Edit". A simple dialog box lets you enter a name for the group. All types ofnames are accepted (blanks, accents, ...). If the name of the group already exists in the database, you will beprompted to overwrite the existing one. The new group is added to the "Groups" list. The ".group" filecontaining the list of IDs is directly written to the disk. However, the ".grouplist" file will be effectivelywritten on the disk once the database is saved.

Viewing groups

Groups are manipulated in the same way as files with the drag and drop mechanism described here above.

Renaming a group

Select only one group (not the first one "All groups"). Click on the right mouse button. In the context menuselect "Rename". Type the new name in the simple dialog box and hit "OK". The ".group" file correspondingto the group is directly renamed, but the ".grouplist" file is not affected. Do not forget to save the database to


Sorting signals 34

avoid any loss of the ID list belonging to this group. This situation may be repaired by renaming manually the".group" file to its original name.

Modifying a group

Create a viewer (e.g. a table) with the group. Modify its content (sorting, adding new signals, ...). Select "Newgroup" in menu "Edit" and enter the name of the existing group. The original group will be overwritten.Saving the database in this case is not necessary but strongly advised to avoid confusions with the otheractions.

Deleting groups

Select one of more groups and choose "Remove" from the context menu (after a right click in the "Groups"list"). ".group" files are directly removed from the database directory, hence this action cannot be cancelled.Saving the database is mandatory if you do not want to pollute the "Groups" list with empty defunct groups.


Renaming a group 35

Contents• Previous• Next• Up• Top of page• Preferences dialog box• Loading files• Memory• Table• Tools• H/V• Directory paths• Storage of settings•

4.4 PreferencesThis section explains how to configure geopsy. Various settings can be adjusted within the graphical userinterface. This section also explains how to deal with directory paths that are automatically saved during yourwork. For advanced users, the way the options are saved and how to change them are detailed.

Preferences dialog box

The preference dialog box is automatically displayed at startup when geopsy is installed on a new machine.The defaults option values are usually valid for a majority of users. However, in certain circumstances or ifyou want to optimise your work with geopsy, it may be interesting to change these options. Select item"Preferences" from menu "File" (under Mac this item is under the Apple menu). The preference dialog box,shown in figure 1 to 5, contains several independent tabs explained here after.

Loading files


4.4 Preferences 36

Figure 1: Tab for changing the "Loading files" options.

These options apply to the loading of new files into the database (item "Load file" from menu "File").

File format

There are two exclusive options: either ask for the file format interactively or always use a given file format."Automatic recognition" does not specify any special format but lets the automatic format recognitionalgorithm select the right formats of files. The rules for selecting formats are presented in section Automaticrecognition. The default and mostly used option is the one presented in figure 1.

Time reference

The definition of the time reference is given in Database section. Either you can set the time referenceinteractively for each file ("Always ask ...") or you can skip this step. If not set interactively, the timereference is automatically deduced from the information contained in header files. However, not all fileformats have this kind of information available. The recording startup time, read until the seconds, isconsidered as the time reference. The remaining milliseconds are added to T0.


Loading files 37

For signals recorded simultaneously but with distinct startup times (e.g. the time needed to manually start therecordings of stations synchronised by GPS), the time reference must identical for all stations. Hence, it ismandatory to force the time or eventually the date to a common reference. If all the signals were started thesame day, you can use the default, shown in figure 1. The reference is set at midnight, and T0 is the number ofseconds since midnight (including milli or micro seconds). If synchronous signals are distributed over severaldays, it is mandatory to force the date as well. Thus, you must edit this preference before loading the files forthe first time.

Changing the time reference afterwards, once the signals are loaded, is possible but not strongly advised.Actually, when loading the files, T0 are automatically calculated from the true time of measurement and fromthe deduced or forced reference time. When editing the time reference in the database, T0 are left unchangedand it may lead to errors in signal synchronisations. We would recommend to edit the time reference only in atable containing all synchronous signals.

Viewing signals after loading

For some applications, especially if no database is created (single files mode), it may be appreciated to displaya table or a graphic of the signals directly after loading the files. You can choose to open a table or a graphic,or both. A single window summarising all files or one window per file may be created. This action can beperformed only if less a certain number of files are opened together. To suppress all viewers after loadingfiles, uncheck the checkbox "Do it only if less than".

Signal names

Names of signals are most of the time set to the name of station specified in file headers. If you do not want toextract this name and to leave the names as blank, uncheck the option "Use station names ...". For someinterpretation tools, such as H/V, if the signal names are blank the signals are referenced by their file names.

In some cases (e.g. when loading files from CityShark 2), it may be interesting to automatically name thesignals R001, R002,... For all file formats except CityShark, the index is the index of signal inside the file. ForCityShark format with more than 3 channels, it is assumed that three−component sensors are used.

Memory


Time reference 38

Figure 2: Tab for changing the "Memory" options.

Geopsy is built upon a powerful mechanism for allocating memory for signal vectors. With this system, it ispossible to view many signals over long periods at the same time. The program almost never ends withmemory full errors, as a specific internal swap system ensures that the memory usage is limited. The size ofthis maximum is specified here. This is not a static memory allocation, hence, most of the time this amount ofmemory space is never used. However, for some computations, huge amounts of memory may be necessary(e.g. SPAC for long signals) and signals are efficiently swapped to the disk (either to the system temporarydirectory or to the database directory if the current user has write permissions).

The default value is 256 Mbytes which allows reasonable computations to be executed without swapping.However, to avoid swap and to speed up computations, it is better to exploit all resources of your computer.The best performances are obtained when the maximum memory size is a bit lower than the true physicalmemory size. In the case presented in figure 2, the true physical memory is 1 GBytes. Setting somethinggreater than the physical memory is possible (if your operating system supports swap memory) but inefficient.Experience has proved that the system swap is less efficient that geopsy internal swap (the priority of memoryblocks are set by the running process as a function of the future usage of the memory, not the case for systemswap).


Memory 39

Table

Figure 3: Tab for changing the "Table" options.

This tab specify the information to display in all new tables. Each data field correspond to one column in thetables. In the left column ("Data field"), the names of the internal variables chosen for display are listed.These internal variables are described here. On the right column ("Title"), the associated titles in the tables arelisted. A default title is defined for all variable. You can change it to your convenience.

New data fields can be added by clicking on "Add". It will be added at the end of the list. If one item in thelist is selected, a new data field can be inserted ("Insert") before the current data field or it can be deleted("Remove"). The "Default" button reset to the original default configuration.

Currently, there is no system to save/restore typical or user defined configurations. However, if you areworking under Linux, you can save and restore table configuration by editing the setting file in your homedirectory. On other platforms, like Windows, you have to edit the registry with "regedt32"(CURRENT_USER/Softwares/geopsy). Make sure that there is no running Geopsy. Open the file"$HOME/.qt/geopsyrc" with your favourite editor (vi, kwrite, nedit,...). Search for "[TableFields]", you willprobably find two lines like these ones:


Table 40

ids=0ê10ê59ê55ê1ê58ê62ê2ê3ê57ê4ê5ê6ê7ê8ê9ê11êtitles=IDêNameêComponentêTime referenceêSignal startêSignal [...]

To save the current configuration, copy these lines to another text file for backup. Modify the configurationwith the Preferences dialog box. To restore the old settings, close all instances of geopsy, open the setting fileagain and replace the lines "ids=..." and "titles=..." by the lines you saved. The reason for closing geopsybefore writing to the setting file is that the file is updated by geopsy on closing and it may overwrite yourchanges.

Tools

Figure 4: Tab for changing the "Tools" options.

This tab helps you configuring the "Tools" menu. "Tools" menu lets you start specific processing toolsdeveloped as plug−ins. Plug−ins are dynamic libraries containing executable code that can be added to geopsywithout recompiling the core program. The available tools that are listed in "Tools" menu are managed in thistab. The "Tools" menu is replicated in the context menu displayed when clicking on the mouse right button inthe "Files" and "Groups" lists.


Tools 41

To add a new tool, you first have to download and to install the corresponding library on your computer. Thelocation of the library in the file hierarchy is arbitrary. Click on "Add tool", you will be prompted to select thefile (and its path) of the library (extension is ".so", ".dylib", and ".dll" for Linux, Mac OS X, and Windows,respectively). The library name will be added at the end of the list. If the library can be opened and if itcontains the correct interface functions to dialog with geopsy core, a green light is displayed on the left. If thelight is orange, it means that the library can be loaded but no correct dialog can be establish with geopsy core.Either, this library is using an old version of the geopsy plug−in interface or you are trying to add a librarythat is not a geopsy plug−in. In the first case, update geopsy or try to find the right version of the tool. If thelight is red, there is problem loading the library (access permissions, disk error, ...).

To remove a tool, select it and click on "Remove". You can re−arrange the tools by selecting one and bymoving upwards or downwards ("Up" or "Down" arrows). You can also add separators (horizontal lines inmenus) to better separate categories of tools. Any change to the tool list will be effective for next geopsystartup.

H/V

Figure 5: Tab for changing the "H/V" options.

This tab is present only if you add the "H/V" tool (see preceding section). It lets you configure the graphicaloutputs. The "H/V" tool produces basically two kinds of graphical outputs: H/V spectra and component


H/V 42

spectra. You can select both, only one of them or none of them. These graphical outputs contains XY plotswith various layers (see scifigs documentation for details). For each plot, you can select which layer you wantto see. These options are detailed in the H/V tools specific section.

Directory paths

Each time you select a file to open or to save, geopsy automatically stores the path of the selected file. Thenext time you will open or save the same type of file, the dialog box will start on this directory avoidingfastidious clicks to move from your home or your "My Documents" directory to your working directory.Furthermore, every visited directory for this type of files is stored in the combobox at the top of the dialog box(figure 6). You can them quickly jump to a frequently used directory.

Figure 6: Quickly jumping to frequently used directories in the file dialog box.

Within the context shown in figure 6, if the current project you are working on is located in"/data/belgium_march02/baviere", all paths to load or save files (database, signals, formulas, ...) will beginwith "/data/belgium_march02/baviere". If you want to switch to another project located, for instance, in"/data/M2/", you can modify the stored paths in a single click by using projectpath utility.


Directory paths 43

http://www.geopsy.org/scifigs/index.html

http://marc.geopsy.org/softwares/projectpath.html

Figure 7: projectpath interface to change current directories.

projectpath is an external program usually distributed with geopsy. Follow the instructions here to downloadand install it if not available on your machine. Once installed, start the software with a double−click or bylaunching the command "projectpath&" from a terminal. You will see a window like the one shown in figure7. Add paths to the list of projects by clicking on "New path". When you click on "Set current", all root pathsdisplayed in this list are searched in your stored paths and they are replaced by the selected path ("/data/M2"in the example of figure 7).

Furthermore, if you are using exactly the same directory structure for all your projects (e.g. "db/" for geopsydatabase, "fk/" for results of FK processing, "map/" for all localisations stuffs, ...), projectpath will changeonly the root of the stored paths. In our example, if "/data/belgium_march02/baviere/db" was stored as thecurrent directory for loading databases, and if "/data/M2/db" exists, the current path for opening newdatabases is changed to "/data/M2/db". If "/data/M2/db" does not exist, the current path is changed to"/data/M2/".

Storage of settings

The default values appearing in dialog boxes displayed by geopsy are always equal to the preceding values setby the user for these items. These values are stored in the same file (for Linux users) as fields of tables,"$HOME/.qt/geopsyrc", under the label "[DialogOptions]". If you want to remove all user settings and returnto the original default, close all instances of geopsy and remove all entries under "[DialogOptions]".Removing the file "$HOME/.qt/geopsyrc" has the same effect but also resets other stored settings. UnderWindows, the same reset can be done by removing key entries in the registry (with regedt32, key"CURRENT_USER/Softwares/geopsy").


Storage of settings 44

http://marc.geopsy.org/softwares/projectpath.html

Contents• Previous• Next• Up• Top of page• ".sdb" file• ".grouplist" file• ".group" files• ".sig" files• "_n" files•

4.5. File structureThis section details how a database described in section Database is saved on a file system (e.g. disks, usbflash cards, ...). The database is saved a defined directory containing three kinds of basic files: ".sdb",".group", and ".grouplist". Other files are also saved in this directory: modified signals (seeISORIGINALFILE) and temporary swap files.

In the following, the database name is supposed to be "db". Hence the directory containing the database is"db/" and the ".sdb" file is "db/db.sdb".

".sdb" file

This is a text file containing one value per line, with the following syntax.

Syntax of lines for the ".sdb" fileKEYWORD=VALUE

KEYWORD is case sensitive and it cannot contain any '=' sign. Blanks are not accepted before theKEYWORD and around the '=' sign. The VALUE on the right can contain any characters including blanks.

The order of KEYWORDs is strict. The first line of the file is the version of the format. Currently, version is2. The file contains a list of signals grouped by file. The general structure is:

General structure of ".sdb" fileversion 2FILE=/absolute/file/path/and/file/name/of/first/signal/fileFORMAT=7ISORIGINALFILE=1ID=1 ... specific information about first signal

ID=2 ... specific information about second signal

...ID=n ... specific information about signal n

FILE=/absolute/file/path/and/file/name/of/second/signal/fileFORMAT=8ISORIGINALFILE=1ID=n+1 ... specific information about first signal


4.5. File structure 45

ID=n+2 ... specific information about second signal

...

The information about each signal contains the following keywords (the order is strict):

Information about each signalID=1NAME=R01ACOMPONENT=0T0=0TIME REF=01/01/2003 00:00:00DELTA T=0.00875TYPE=0PICK 1=102.688PICK 2=298.102PICK 3=0PICK 4=0PICK 5=0PICK 6=0PICK 7=0PICK 8=0PICK 9=0PICK 10=0PICK ID 1=1PICK ID 2=0PICK ID 3=0PICK ID 4=0PICK ID 5=0PICK ID 6=0PICK ID 7=0PICK ID 8=0PICK ID 9=0PICK ID 10=0RECEIVER=1988 2002 0SOURCE=0 0 0

The number of signals in each file specified in "db.sdb" must be equal to the real number of signals stored inthe signal file. On opening a database, the signal files are not checked. Though a database may be createdoutside geopsy, this method is not advised and may lead to unstable behaviours. However, the original filesare never modified and the ".sdb" is written only when choosing "Save database" from menu "File", hencethere is absolutely no risk to corrupt the original information.

".grouplist" file

There is only one ".grouplist" file per database. It contains the list of groups referenced by their names. Eachcharacters is coded on 16 bits which forbid its modification with any text editor. Under Linux, you canvisualise this file with bvi or with kwrite (set encoding to UTF16). The binary format depends upon the exportformat of QStringList. The first 32 bits is the number of groups. Then, each name is stored with a first 32 bitsfor the string length and the characters coded on 16 bits.

".group" files

This is a binary file that contains the list signal IDs belonging to the group. The format is very simple: a list ofintegers (32 bits). The base name of these files is the group's name. Under Linux, you can visualise this filewith bvi.


".sdb" file 46

http://bvi.sourceforge.net/

http://doc.trolltech.com/3.3/qstringlist.html

http://bvi.sourceforge.net/

".sig" files

When geopsy is running low on memory space, it may be forced to swap signal vectors to the disk. If thecurrent user have sufficient permissions in the database directory, temporary files are written in this directory.When no instance of geopsy is running, none of these files must exist. In case of crash, it may be possible thatsome of these file were not correctly cleared. You can remove all of them without any consequences assumingthat no database is currently running.

"_n" files

When saving a database, the modified signals are automatically saved to the database directory. These fileshave the same names as their original files with a suffix "_n", n being a unique number. Do not remove thesefiles manually. You can remove these files by removing their entries in the database.


".sig" files 47

Contents• Previous• Next• Up• Top of page• File export• Waveform• Tools• "Edit" menu• Sorting signals• Editing headers• Editing receivers• Creating new groups•

5. ViewersAny subset of the total ensemble of opened signals can be created with the "drag and drop" mechanismexplained in section Selecting signals. The subsets are visualised through tables, graphics and maps detailed inthis chapter:

5.1. Table• 5.2. Graphic• 5.3. Map•

The various actions that can be performed with a subset of signals (either a table, a graphic or a map) aredescribed here after.

File export

Select item "Export" from menu "File". You will be prompted to select the file format. Various formats arecurrently proposed:

SEG2• SAC: little or big endian• SU: little or big endian• ASCII: one or multi columns• Surf: surface−wave inversion from R. Herrmann• SAF: Sesame ASCII file format• WAV: PCM sound file, to create sound from seismic signals (generally requires a strong modificationof the sampling frequency: 44 kHz for usual music records).

•

Not all these formats support multiple signals in a single file. If those case you will be prompted to select anexport directory or to enter the names manually.

Waveform

Basic signal processing can be performed on all the signals of the active viewer. These processing aregathered in menu "Waveform". For details, refers to chapter Basic signal processing.


5. Viewers 48

Tools

Tools are developed as plug−ins and provide specific signal processing (menu "Tools"). As for basic signalprocessing, the selected tool is applied to the signals of the active viewer. For details, refers to chapterSpecific processing tools.

"Edit" menu

All menu items in "Edit" menu apply to all signals contained in the active viewer.

Sorting signals

This feature is explained in section Sorting signals.

Editing headers

This feature helps you modify the header information by the means of generic formulas.

Editing receivers

This feature helps you modify the coordinates of receivers. The signal names are considered as names ofstations to which corresponds only one unique set of coordinates.

Creating new groups

This feature is explained in section Creating a new group.


Tools 49

Contents• Previous• Next• Up• Top of page• Signal selection• Cell editing• Export• Import•

5.1. TableBasically, a table allows you to view and to edit the header information about signals. Each row represents asignal and each column is an information field. The order and the list of displayed fields is specified by thetable preferences for all newly created table. You can also change the displayed information for the activetable only by selecting item "Set data fields" from menu "View". Columns and rows can be resized (pressmouse at the limit between two columns or cells). However, automatic resizing is usually correct.

Signal selection

Signals are selected with the mouse left button. If the SHIFT key is also pressed the selection is extended fromthe current row to the selected row. If the CTRL key is pressed at the same time as the mouse left button, theselected row is added to the selection and become the current row. The current row contains the active cell.

Pressing the mouse left button on any selected row and moving the pointer initialise the drag and dropmechanism marked by a modified mouse cursor. A circle crossed by a line means that the signals cannot bedropped at this place. When it changes to a plus sign, the mouse left button can be released to drop the signals

to the destination (an existing viewer or the icons of viewers: , , ).

Cell editing

To edit the contents of a cell, double−click on it and modify the value. The signal internal structure isautomatically modified. However, if other tables are opened and if they also contains the modified signal, thechanges are not updated automatically. To update them, select one of them and choose "Refresh now" frommenu "View", or alternatively type CTRL+r.

You can edit any cells, but some of them are linked to read−only fields (e.g. NSAMPLES, the number ofsamples). Error messages are displayed in those cases and the edition has no consequences.

Export

Copy and paste action are not possible like in common tabular softwares. However, it is possible to export theinformation contained in a table to a text file (column separated by TABs) which can be in turn loaded in anyusually tabular software. The file can be edited and imported in the table to apply the changes. The samerestrictions as when editing read−only cells individually apply.

To export a table, select "Export" from menu "File". A combobox lets you select the export format. Select thelast one ("Table"). The re−sampling parameter is ignored. Enter the file name to export. A default extension


5.1. Table 50

(".txt") is provided for compatibility with usual tabular software. Comment are marked with '%' at thebeginning of lines. Not all fields attached to a signal are exported but only the fields displayed in the activetable. The list of fields is given by field IDs separated by TABs (not to be confused with signals IDs) in thefirst uncommented line.

Example of a file exported from a table% This file contains all the variables that were listed in Geopsy's Table% You can edit this file as you want. The names of columns appear here only% for readability. All columns must be separated by only one tabulation.% Lines starting with "%" are always ignored when importing. The first line% starting without "%" must contains the ID of each variable. Those IDs are% listed below: (variables marked with * could not be changed by the user)% ID_VAR_ID* = 0% ID_VAR_T0 = 1% ID_VAR_DELTAT* = 2% ID_VAR_NSAMPLE* = 3% ID_VAR_REC_X = 4% ID_VAR_REC_Y = 5% ID_VAR_REC_Z = 6% ID_VAR_SRC_X = 7% ID_VAR_SRC_Y = 8% ID_VAR_SRC_Z = 9% ID_VAR_NAME = 10% ID_VAR_TYPE* = 11% ID_VAR_PICK1 = 12% ID_VAR_PICK2 = 13% ID_VAR_PICK3 = 14% ID_VAR_PICK4 = 15% ID_VAR_PICK5 = 16% ID_VAR_PICK6 = 17% ID_VAR_PICK7 = 18% ID_VAR_PICK8 = 19% ID_VAR_PICK9 = 20% ID_VAR_PICK10 = 21% ID_VAR_PICK_ID1 = 22% ID_VAR_PICK_ID2 = 23% ID_VAR_PICK_ID3 = 24% ID_VAR_PICK_ID4 = 25% ID_VAR_PICK_ID5 = 26% ID_VAR_PICK_ID6 = 27% ID_VAR_PICK_ID7 = 28% ID_VAR_PICK_ID8 = 29% ID_VAR_PICK_ID9 = 30% ID_VAR_PICK_ID10 = 31% ID_VAR_FILE_NUMBER* = 32% ID_VAR_NUMBER_IN_FILE* = 33% ID_VAR_DUPLICATE_RAYS_ID* = 34% ID_VAR_DUPLICATE_RAYS_AVERAGE1* = 35% ID_VAR_DUPLICATE_RAYS_AVERAGE2* = 36% ID_VAR_DUPLICATE_RAYS_AVERAGE3* = 37% ID_VAR_DUPLICATE_RAYS_AVERAGE4* = 38% ID_VAR_DUPLICATE_RAYS_AVERAGE5* = 39% ID_VAR_DUPLICATE_RAYS_AVERAGE6* = 40% ID_VAR_DUPLICATE_RAYS_AVERAGE7* = 41% ID_VAR_DUPLICATE_RAYS_AVERAGE8* = 42% ID_VAR_DUPLICATE_RAYS_AVERAGE9* = 43% ID_VAR_DUPLICATE_RAYS_AVERAGE10* = 44% ID_VAR_DUPLICATE_RAYS_STDERR1* = 45% ID_VAR_DUPLICATE_RAYS_STDERR2* = 46% ID_VAR_DUPLICATE_RAYS_STDERR3* = 47% ID_VAR_DUPLICATE_RAYS_STDERR4* = 48


Export 51

% ID_VAR_DUPLICATE_RAYS_STDERR5* = 49% ID_VAR_DUPLICATE_RAYS_STDERR6* = 50% ID_VAR_DUPLICATE_RAYS_STDERR7* = 51% ID_VAR_DUPLICATE_RAYS_STDERR8* = 52% ID_VAR_DUPLICATE_RAYS_STDERR9* = 53% ID_VAR_DUPLICATE_RAYS_STDERR10* = 54% ID_VAR_TIME_DATUM = 55% ID_VAR_FILE_NAME = 56% ID_VAR_DURATION = 57% ID_VAR_END_TIME = 58% ID_VAR_COMPONENT = 59% ID_VAR_MAXAMPLITUDE = 60% ID_VAR_ISORIGINALFILE = 61% ID_VAR_SAMPFREQUENCY = 62% ID_VAR_SIGNALPTR = 63%%−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−%Variables:%ID Name Component Time reference Signal start Signal end Sampling frequency dt N samples Duration Rec x Rec y Rec z Type 0 10 59 55 1 58 62 2 3 57 4 5 6 11 %−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−− 2 R01A North 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1988.00 2002.00 0.00 w 3 R01A East 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1988.00 2002.00 0.00 w 5 R01B North 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1976.00 2005.00 0.00 w 6 R01B East 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1976.00 2005.00 0.00 w

...

62 R09C North 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1958.00 1976.00 0.00 w 63 R09C East 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 1958.00 1976.00 0.00 w 65 R10A North 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 2000.00 2000.00 0.00 w 66 R10A East 01/01/2003 00:00:00 0.0000 s 00:06:45.3875 114.286 0.00875 46330 00:06:45.3875 2000.00 2000.00 0.00 w

Import

Select "Import table" from menu "File". The first uncommented line must contains the list of fields to modifyspecified with IDs separated by TABs (see Export). The first signal of the active table is modified accordingto the second uncommented line of the imported file. The second signal with the third uncommented line andso on until reaching either the last signal or the last line of the file.

To avoid errors when importing files, it is better to leave the exported table active while modifying theexported file and to re−import the modified file with the same active table, to be sure that the order and thenumber of signals is exactly the same. In this case, never remove lines from the exported file. To limit thenumber of potential errors, you can remove all columns except the ones you really want to change. Thismethod for modifying the fields of a table must be used with care and should be used only when there is noother choice.


Import 52

Contents• Previous• Next• Up• Top of page• SignalDisplay Layer: signal properties• SignalDisplay Layer: picking• Y axis: zoom blocked• Signal selection• Time or frequency spectra•

5.2. GraphicA graphic is an XY plot where one or more signals are represented as a function of time or frequency. Whenonly one signal is represented, the Y scale is the signal amplitude (count or volts). When various signals areshown (see figure 1), the Y scale ranges from 0.5 to n+0.5 where n is the number of signals. The axis label aregenerally replaced by the names of signals suffixed by the signal's component. The baseline (reference linewith a null amplitude) of each signal is located at y=1, 2,..., n. The signals are drawn around their baseline.The maximum amplitude around this baseline is adjusted by the normalisation parameters described hereafter.

Figure 1: Graphic viewer, definition of areas: red = graphic's background,yellow = Y axis, green = X axis, and blue = graphic's content.

The graphic viewer makes use of a general XY plot object from the scifigs library. More information about itcan be found in the scifigs documentation. scifigs offers highly configurable XY plots which can be saved andrestored easily. Usually, figures are exported to bitmap formats like jpeg or png, or as postscripts or pdf. Inthis case, any modification of the aspect (fonts, scales, ticks, ranges, ...) require the original program to bere−run. One of the reason for changing the aspect would be to provide a figure on two kinds of supports: aprinted book and a slide presentation for instance. With scifigs, you can save the aspects and the data withtheir real scales (files ".mkup" and ".layer", respectively). figue, is an external program released with scifigslibrary, that allows you to construct complex figures from these files grabbed here and there from programs


5.2. Graphic 53

http://www.geopsy.org/scifig/userdoc/index.html

linked with scifigs (like geopsy).

A graphic is divided into four distinct areas.

Red: graphic's background (context menu (a));• Yellow: Y axis (context menu (c));• Green: X axis (context menu (c));• Blue: graphic's content (context menu (b)).•

Figure 2: Context menus for graphic: (a) graphic's background,(b) graphic's content, and (c) axis.

The graphic's contents is itself divided in layers. Various types of layer have been developed to plot curves,points, grids, ... Signals are plotted in a special type of layer developed especially for geopsy. Only theparameters linked to this layer are discussed here.

In each area, a particular context menu (mouse right button, figure 2) is available to control the object. In eacharea, a double−click is equivalent to "Properties" in menus in figure 2. CTRL+m is equivalent to a right clickin the graphic's background (red zone). This feature is useful when the background is not visible, i.e. whenaxis are hidden.

The make−up is the set of parameters that describe the aspect of the graphic, modified by the means of"Properties" in each specific area. You can save the current set or restore an existing one ("Save make−up" or"Restore make−up", figure 2(a)). In a similar way, the data contained in the visible layers of the graphic'scontents can be saved to or restore from a file ".layer" (figure 2(b)). Note that ".layer" files needcomplementary files named ".layer.bin" which contained binary data. Do not separate these files whenmoving or copying to other locations.

Note: the export of the layer developed for signals as ".layer" is currently not implemented. To avoid spaceconsumption on disk, the complete geopsy core should be used in figue, which is more complex than otherstandard layers. A bitmap layer might be an alternative. However, you are free to import other types of layersin graphic viewer for comparison purposes (e.g. a segmented line representing travel−times estimatedelsewhere). Currently, to export the signals to a figure, adjust the axis to their final sizes, set a resolutioncompatible with your final medium (e.g. 300 or 600 dpi for a laser printer, 72 to 100 dpi for screen or webpublication) and export the graphic as bitmap (png or jpeg).


5.2. Graphic 54

SignalDisplay Layer: signal properties

You can change the appearance of the signal layer by selecting "Properties" from the context menu of thegraphic's contents, or double−click in the graphic's contents (blue area in figure 1). Switch to tab "Signals", adialog box like the one shown in figure 3 will let you edit the current properties.

Figure 3: Signal properties.

On the left, "Type" box lets you select the features you want for plotting signals.

"Colours": the amplitude of the signals is represented with a colour scale. This mode of representationhas some constraint: the sampling frequency of all signals must be the same and the differences of T0must a multiple of the sampling period. This mode is generally reserved for reflection data (radar orseismic).

•

"Wiggle": if selected, an oscillating line is drawn• "Variable area": the positive (this option should be replaced by negative or positive) areas arecoloured in black.

•

The right part contained the normalisation parameters:

"Normalise by": in a first step, maxima are calculated on each signal by one of the proposedmethods:

"max of all traces": a unique maximum is the maximum of the maxima found on each trace.♦ "max of each trace": the maxima are the maxima found on each trace. The normalisationvaries from one trace to another.

♦

"visible max of all traces": a unique maximum is the maximum of the maxima found on thecurrently visible part of each trace.

♦

"visible max of each trace": the maxima are the maxima found on the currently visible part ofeach trace. The normalisation varies from one trace to another.

♦

"specified value": an arbitrary value can be specified.♦

•


SignalDisplay Layer: signal properties 55

"Clip": in a second step, a clip value is calculated (as a function of the maximum or the maxima if"percentage" is selected). If "each trace" is selected in the normalisation, the clip value may changefrom one trace to another.

"no": the clip value is the maximum or the maxima, no visualisation clip effect.♦ "value": an arbitrary value can be fixed.♦ "percentage": the clip value is set as a percentage of the maximum or the maxima.♦

•

"Overlap": in a third step, the time dependent offsets from the signal baseline are calculated. Theseoffsets are equal to the half of the overlap value (no division by 2 for frequency spectra) if theamplitude of the signal is equal to the maximum of the considered signal (case of "each trace"normalisation). An overlap of 1 ensures that the signals will never overlap.

•

The procedure remains valid when only one signal is plotted, except that "max of each" or "max of all" haveno effects. An example of signals normalised by "visible max of each trace", clipped at 25%, and with anoverlap of 4 is given in figure 3.

Figure 3: Signal normalisation, clipping and overlapping.

The y of the baselines may also be calculated according to the receiver positions ("Use receiver coordinates").An horizontal line is automatically adjusted to the receiver X,Y coordinates with a least square method. Thereceivers coordinates are then projected on to this line to calculate distances along this line. The scale of the Yaxis is the distance along this line.

For colour representation of signals, the values of the colour palette can be adjusted by clicking on "Defaultvalues for colour palette". The normalisation and the clipping settings are taken into account.

The display settings are saved in file "$HOME/.qt/geopsyrc" under the rubric "DialogOptions", entries"Signalgcprop/*" (for Linux users). For Windows users, this information is located in the registry (regedt32).The settings are automatically saved when the properties of the graphic's contents are edited. The savedsettings are restored only each time a new graphic viewer is created.


SignalDisplay Layer: signal properties 56

SignalDisplay Layer: picking

Picks are time markers that you can use to identify particular times (e.g. Vp arrivals for refraction, time limitsfor signal processing such as a time domain taper). There are 10 distinct time picks you can use. You canchange select the visible time picks as well as their colours with the tab "Pick" in the graphic's contentsproperties (figure 4). These parameters are saved and restored in the same way as other settings.

Figure 4: Signal picks, visibility and colours.

You can modify picks in a table by editing the corresponding fields. However, it is usually edited in a graphicviewer with mouse clicks. As shown in figure 2(b), select menu "Pick" from the graphic's contents menu. Youwill be prompted to select one of the ten picks to edit.

In certain circumstances, it may be useful to magnify the signal around the picks, select "Magnifier window"to display a signal signal viewer with a zoomed time scale. It is a usual graphic viewer, with a vertical line tomark the current position of the mouse (created with ParallelBands layer, hence you can hide it if you want).All the common properties of a graphic viewer may be changed, for instance to enlarge the time interval or tofix the Y scale. The X interval is kept constant as the mouse moves.

The active trace is highlighted in red and the current pick number is displayed in the bottom right corner. If"Picking disabled" is displayed, it is likely that you are in "Zooming" or "Editing" mode (displayed in bottomleft corner). In this case, the clicks will not have any effects. First you have to quit this mode by hittingCTRL+SHIFT+z or by selecting "Zoom" in the context menu (figure 2(b)). Once "Setting pick n" isdisplayed, any click on the mouse left button will modify the value of the current pick. Use the "Up" and"Down" arrows to change the active signal, "Left" and "Right" arrows to switch to other picks. If hitting thosekeys has no effect, check that the main graphic viewer is active, if not click in its title bar (this is frequentlythe case when a magnifier is used).


SignalDisplay Layer: picking 57

Y axis: zoom blocked

By default, the minimum and the maximum visible limits of the Y axis are fixed. You cannot change themwith the zoom (figure 2(b)). You can still change them by editing the axis properties (min and max). Theblocked zoom lets zoom in the signals with a rectangle which Y limits are ignored. Only the X interval (thetime or the frequency) is taken into account. You can unlock this feature by unchecking the option "Zoomblocked" in tab "General" of the Y axis properties dialog box. This feature may be manually set for X axis butit is less useful.

Signal selection

Contrary to tables, it is not possible to select particular signals in a graphic viewer. The drag and dropmechanism works in a similar way but all the signals are considered rather than a selection. Graphic viewersalso accept drops of signals that are added at the end.

Time or frequency spectra

If the signals to plot are all of the same TYPE, the X scale is adjusted automatically (time or frequency). Itmay append that the signals are not of the same type, in this case, the X title is set as "Time or Frequency".Usually, the orders of magnitude of the X axis for time and frequency are quite different, hence the plot ispartially unreadable. To recover signals, either as time series or frequency, select either "FFT/Time" or"FFT/Frequency" from menu "Waveform". If the signals are zoomed in (marked by scroll bars along X and Yaxis), and if you transform time series into spectra and vice−versa, it is likely that the current zoom rectanglewill not be adequate for the new X scale. Thus, it is better to unzoom (or CTRL+−), until the scroll barsdisappear, before or after a FFT transformation.


Y axis: zoom blocked 58

Contents• Previous• Next• Up• Top of page• Map scale• Signal selection•

5.3. MapA map is a two−dimensional representation of the receiver coordinates in the XY plane. Like the graphicviewer, it makes use of a general XY plot object from the scifigs library. More information about it can befound in the scifigs documentation. The area of a map is partitioned in the same way as a graphic viewer. Themain layer is a XYNamePlot which means that signals (or stations) are represented by configurable symbols(shape, size, colour, ...) and by their names the relative positions of which can be adjusted (top, left, right,bottom, distance). To create plots suitable for publication, you can save the layer to a ".layer" file, edit thestructured text file to customise your presentation (see scifigs documentation), and restore the modified layerinto figue.

Map scale

Scales of maps are intrinsic properties of XY plot objects (see scifigs documentation for details). Some tipsare given here.

Both X and Y axis have by default the same scale. The scale is automatically adjusted so that all the receivercoordinates of the signals contained in the viewer remain visible. Resizing the viewer has no effect on thescale, it changes only the axis minimum and maximum values. To change the scale, edit the axis propertiesdouble−click or context menus, "Properties"), tab "Geometry". Modify the scale (e.g. 400, for 1cm = 4m).Make sure the scales are the same for X and Y axis to avoid distortions. Alternatively, you can resize the mapviewer (this saves the size to the user settings). Then create a new viewer with the drag and drop mechanism(or redo the what you did to create the present one):

Select all signals (see hereafter);• Leave the editing mode;•

Press the mouse left button and move the pointer to the map icon ( );• Release the mouse button.•


5.3. Map 59




Figure 1: Selection of signals on map viewer.Four coordinates are selected.

Signal selection

Apart from the visualisation, maps offer the advantage over tables that you can select station according totheir localisations. In the graphic's contents, click on the mouse right button to activate the context menu,select "Edit". The object switch to the editing mode marked by "Editing ..." in red in the lower left corner (seefigure 1). When you press and move the mouse in this mode, a dotted rectangle is displayed. When releasingthe mouse, all coordinates that fall within this rectangle are selected (marked as bold and red), others areunselected. To add selected signals (without unselecting signals outside the rectangle), press SHIFT whenreleasing the mouse. To leave the the "Editing" mode hit CTRL+SHIFT+e or select "Edit" again. If severalsignals have the same coordinates they are indistinctively selected together.

The drag and drop mechanism is deactivated when the "Zooming" or the "Editing" mode is switched on. Tomove the selected signals to another viewer, first leave these modes and drag and drop as usual.


Map scale 60

Contents• Previous• Next• Up• Top of page• Modified signals• Temporary signals•

6. Basic signal processingThis chapter explains how to transform signals with a set of basic processing. They all apply to the activesignal viewer.

This chapter contains the following sections:

6.1. DC Removal• 6.2. Frequency filters• 6.3. Automatic Gain Control• 6.4. Fast Fourier Transform• 6.5. Tapering signals• 6.6. Cutting signals• 6.7. Merging signals• 6.8. Subtracting signals• 6.9. Rotate components•

Some of these processing either modify existing signals or create new temporary signals. Each processing isperformed in a specific domain (e.g. time of frequency). If the signals of the active viewer are not in the rigthdomain, they are internally converted with the Fast Fourier Transform before processing. The initial domain isrestored after processing.

Modified signals

On opening a database, all signals (either orignal or not) belong to one unique file. The amplitude vectors arestored on disks and a copy is made into memory on request (e.g. calculating MAXAMPLITUDE in a table,viewing signals in a graphic). When a process modifies the signal (e.g. a filter), only the amplitude vector inmemory is affected. The original file remains unchanged. The signal is marked as modified.

For those signals, it is possible to erase the changes and to reload the amplitude vector stored in the disk file.Select "Revert to saved" from menu "Waveform". The signal is then marked as untouched.

On closing a database, if there are still marked signals, a warning will be issued to remind you to save thechanges. When the database is saved, the modified signals are saved in the database directory with a binaryformat. Those signals become individual new signals in the database (not specifically linked to the originalsignals). They are just stored in a file name closed to the original file name (decorated by "_n", n beingunique).


6. Basic signal processing 61

Temporary signals

Some processing create new temporary signals (e.g. cut). These signals have no storage on the disk to revertfrom. They are totally lost, without warning, on closing database, nor they are saved when you save adatabase. Temporary signals are easily recognized in a table which displays the FILE_NAME. The file nameis set to "### Temporary signal ###".

If you want to check if there are temporary signals in your opened database, Drag "All signals" from "Files"list to a table. Look at the FILE_NAME field.

To export those files to a disk file, create a viewer with them gathered and select "Export ..." for menu "File".Select the appropriate format in the list. If you want to include them permanently in the database, "SAC"format is a good choice. Load the generated file(s) into the database and save the database. Note: the exportedfiles must not be in a temporary location, create them in a permanent directory (e.g. the database directory).


Temporary signals 62


6.1. DC removalTime Domain

Figure 1: needed parameters for Suppress DC.

A value can be subtracted from the signal amplitudes (e.g. to remove constant shifts of signals). On selecting"Suppress DC" from menu "Waveform", a dialog box like the one displayed in figure 1 is shown.

If "Mean value" is selected, the value to be subtracted is the arithmetic average of the amplitude signalcalculated over the whole signal duration. If "value" is selected, the value entered in the field is subtractedfrom all samples. It might either positive of negative.


6.1. DC removal 63

Contents• Previous• Next• Up• Top of page• Butterworth• Spectral amplitude taper•

6.2. Frequency filters

Figure 1: frequency filter paramters.

Four types of filters are available:

Low pass: remove all frequency components above a frequency threshold (F2);• High pass: remove all frequency components below a frequency threshold (F1);• Band pass: remove all frequency components outside an interval [ F1, F2 ] ;• Band reject: remove all frequency components inside an interval [ F1, F2 ] .•

Two methods for filtering signals are implemented in geopsy.

Butterworth

Time Domain

Butterworth: this is a causal filter of adjustable order. The lowest order is the best (shortest) in the timedomain, and the higher orders being better in the frequency domain. More information about such filters canbe found for instance at sepwww.stanford.edu. Causality is an option of the filter. Causal filters are outphasingand vice−versa.

Spectral amplitude taper

Frequency Domain


6.2. Frequency filters 64

Figure 2: filter function in frequency domain.

This filter does not alter the phase of the signals but it is not causal. The width of the transition is specified inthe parameters (number between 0 and 1). A cosine function is used in the transition ranges.

The transition range is defined from the width and the corner frequencies F1 and F2. In figure 2, the spectrumof a delta−like function (uniform spectum) as been taken as an example. The spectum is filtered with the fourtypes of filters. The light coloured lines around the main one are located at Fi*(1−width) and Fi*(1+width), ibeing 1 (red) or 2 (blue).

The specified frequencies are the limits above or below which the energy of the filtered signals is null. Forinstance, in the case of a band reject filter calculated between 0.5 and 3 Hz, there will absolutely no energybetween 0.5 and 3 Hz.


Spectral amplitude taper 65


6.3. Automatic Gain ControlTime Domain


6.3. Automatic Gain Control 66


6.4. Fast Fourier TransformTime to Frequency Domains (and vice versa)

Figure 1: Fast Fourier Transform menu.

All Fourier Transforms in geopsy are based on the algorithms developed by Matteo Frigo and Steven G.Johnson (MIT) and encapsulated in FFTW library. Called the "Fastest Fourier Transform in the West", itaccepts arbitrary input size for signals. On the contrary, the classical Fast Fourier Transform required the sizeto be a power of 2. Various papers are found in the litterature about FFTW the references of which are givenat www.fftw.org.

Changing from Time Domain to Frequency Domain is not considered as a modification of the signalamplitudes, but it only alters the header information (TYPE). Hence, the transformed signals are never savedas spectra. Theoretically, successive transformations do not modify the original signal. However, dueprecision limits, the signal may be slightly modified. If you suspect errors of this kind, select "Revert tosaved" in "Waveform" menu to get the original signal back.

about menu..., axis (ref to graphic)


6.4. Fast Fourier Transform 67

http://web.mit.edu

http://www.fftw.org

http://www.fftw.org