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F il e Ex ch an ge A ns we rs N ew sg ro up L in k Ex ch an ge B lo gs T ren dy C od y C on te st Ma th Wo rks .c om

by Stuart Kozola

Large Data in MATLAB: A SeismicData Processing Case Study

01 Mar 2011

These are the files used in the webinar on Feb. 23, 2011.

SegYFileReader

Download Zip

Code covered by the BSD License

Highlights from

Large Data in MATLAB: ASeismic Data ProcessingCase Study

Large Data in MATLAB: A C...

Seismic Migration Example...

fm2d(v,model,nz,dz,nx,dx,...

fm2d_gpu(v,model,nz,dz,nx...

ibm2ieee

Name: ibm2ieee

migrate(travelTime,shot,d...

Migrate a shot record for a given

travel time between shot (source)

and

plotProgress(X,Y,Z,curren...

check to see if figure exists

ray2d(V,Shot,dx)

2D ray-tracing

ricker(f,n,dt,t0,t1)

RICKER creates an causal ricker

wavelet signal

rtm2d(v,data,nz,dz,nx,dx,...

rtm2d_gpu(v,data,nz,dz,nx...

seismic(n)

seismic(n) creates a colormap,

ranging from dark blue via white to

dark red.

shot2RecTime(travelTime,i...

shotRecordLocator(shotNum...

Number of traces per shot record

Seg2FileReader

Seg2FileReader SEG2 file reader

class.

SegYFileReader

SegYFileReader SEG Y file reader

class.

SegyMemmap

SeismicFileReader

SeismicFileReader Seismic file

reader class.

travelTimeMemmap

migrateExample.m

Seismic Migration with a 20 GB Arraybuild.m

saltModelMigrationRTM.m

Seismic Migration Example

setup.m

View all files

classdef SegYFileReader < SeismicFileReader%SegYFileReader SEG Y file reader class.%% SegYFileReader is a SeismicFileReader class that provides basic% functionality for reading a SEG Y formatted file. This class can read% SEG Y Version 0/1 files.%% SegYFileReader properties:

% FileDescriptor SEG2 file identifier label (must = 3A55h)% FileName name of the seismic binary file% FilePath path of the file% FileFormat file format description% FileHeader Header information from the seismic file% MachineFormat Binary file format, big/little endian% NumberOfTraces Number of traces in the file% TraceDescription Trace information from the seismic file%% See also SEISMICFILEREADER, SEG2FILEREADER

properties (SetAccess = protected)TapeLabel = '';

end % public properties

methodsfunction obj = SegYFileReader(fileName,procHeader,procTraceHeader,endian)

% Constructor for Seg2FileReaderif ~exist('fileName','var')

% creat an empty clasefileName = '';procHeader = false;

end

if ~exist('procHeader','var')% read in the headerprocHeader = true;

end

if ~exist('procTraceHeader','var')% read in the headerprocTraceHeader = true;

end

if ~exist('endian','var')endian = 'ieeebe'; % SEGY Rev 1.0 should be big endianend

obj = obj@SeismicFileReader(fileName);obj.MachineFormat = endian;

if procHeaderreadFileHeader(obj);

end

if procHeader && procTraceHeaderreadTraceHeader(obj);

endend

function fh = readFileHeader(obj)%READFILEHEADER reads SEG Y header information
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= ,% 3200 bytes textual header, the 400 byte binary header, and option 3200% byte textual headers.%% Example: TODO%% See also SEGYFILEREADER, READTAPEHEADER, READTAPEDATA

% read in the optional header if present% Is there a optional file header?fmt = {'uchar',{128,'TapeLabel'}};fh = readFileHeader@SeismicFileReader(obj,fmt);tapeHeader = char(fh.TapeLabel');

% if SYX.X is present, this file contains an optional headerif strcmpi('SY',tapeHeader(5:6))obj.TapeLabel.StorageUnitSeqNumber = tapeHeader(1:4);obj.TapeLabel.SEGYRevision = tapeHeader(5:9);obj.TapeLabel.StorageUnitStructure = tapeHeader(10:15);obj.TapeLabel.BindingEdition = tapeHeader(16:19);obj.TapeLabel.MaxBlockSize = tapeHeader(20:29);obj.TapeLabel.ProducerOrganizationCode = tapeHeader(30:39);obj.TapeLabel.CreationDate = tapeHeader(40:50);obj.TapeLabel.SerialNumber = tapeHeader(51:62);obj.TapeLabel.Reserved = tapeHeader(63:68);obj.TapeLabel.StorageSetIdentifier = tapeHeader(69:128);

elseobj.TapeLabel = 'None';

end

% if present, set the offset to account for itif isstruct(obj.TapeLabel)

offset = 128;else

offset = 0;end

% read in the 3200 byte required headerfmt = {'uchar',{3200,'TextHeader'}};fh = readFileHeader@SeismicFileReader(obj,fmt,offset);obj.FileHeader.TextualHeader = char(fh.TextHeader');

% read in the 400 Byte binary headeroffset = offset + 3200;fmt = {'int32',{'JobID','LineNumber','ReelNumber'};

'int16',{'DataTracePerEnsemble',...'AuxillaryTracePerEnsemble',...'SamplingTimeInMicroSec',...'OrigninalSamplingTime',...'NumberOfSamples','OriginalNumberOfSamples',...'SampleFormatCode','EnsembleFold',...'TraceSorting','VerticalSumCode',...'SweepFreqencyStart','SweepFrequencyEnd',...'SweepLength','SweepType','SweepChannel',...'SweepTaperLengthStart',...'SweepTaperLengthEnd','TaperType',...'CorrelatedTraces','BinaryGain',...'AmplitudeRecovery','MeasurementSystem',...'ImpulsePolarity','VibratoryPolarity'};

'int16',{120,'Unassigned1'};'int16',{'RevisionNumber','FixedLengthTraceFlag',...

'NumberOfExtendedTextualHeaders'};'int16',{94,'Unassigned2'}};

fh = readFileHeader@SeismicFileReader(obj,fmt,offset);obj.FileHeader.BinaryHeader = fh;

% Verify SEG Y supported revisionv = obj.FileHeader.BinaryHeader.RevisionNumber;if v > 257

error('SegYFileReader:UnsupportedVersion',...'Version number found in file is %2.2f. Supported versions are up tonum2str(v/10));

elseobj.FileFormat = ['SEG Y Version ',num2str(v/10)];

end

% Set number of tracesobj.NumberOfTraces = obj.FileHeader.BinaryHeader.DataTracePerEnsemble;

offset = offset+400;

% Read Extended 3200 byte textual headers if presentfor i = 1:obj.FileHeader.BinaryHeader.NumberOfExtendedTextualHeaders;

' ' ' '


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= , ,fh = readFileHeader@SeismicFileReader(obj,fmt,offset);obj.FileHeader.ExtendedTextualHeader(i) = char(fh.TextHeader');offset =offset+3200;

end

% Validate input selectionsswitch obj.FileHeader.BinaryHeader.SampleFormatCode

case 1 % 4byte IBM floatingpointobj.FileHeader.TraceFormat = 'uint';mult = 4;

case 2 % 4byte two's complement integerobj.FileHeader.TraceFormat = 'int32';

mult = 4;case 3 % 2byte two's complement integerobj.FileHeader.TraceFormat = 'int16';mult = 2;

case 4 % 4byte fixed point with gain (obsolete)obj.FileHeader.TraceFormat = 'int32';mult = 4;

case 5 % 4byte IEEE floatingpointobj.FileHeader.TraceFormat = 'float32';mult = 4;

case 8 % 1byte two's complement integerobj.FileHeader.TraceFormat = 'int8';mult = 1;

otherwisewarning('Couldn''t determine data format, assuming float 32');obj.FileHeader.TraceFormat = 'float32';mult = 4;

end

% Store trace offset pointersfmt = {'int16',{1,'NumberOfSamples'}};fh = readFileHeader@SeismicFileReader(obj,fmt,offset+114);traceSize = fh.NumberOfSamples*mult + 240;mxTraces = ceil((obj.FileSize offset)/traceSize);obj.FileHeader.TracePointers = zeros(mxTraces,1);obj.FileHeader.TracePointers(1) = offset;% check to see if all traces are of equal sizeif obj.FileHeader.BinaryHeader.FixedLengthTraceFlag == 1

% all are the same size so build pointersi = 1:(mxTraces+1);obj.FileHeader.TracePointers = [(i1)*traceSize + offset]';obj.NumberOfTraces = mxTraces;

else % traces could be different sizesi = 1;

while (offset


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,'int16',{'ElevationOrDepthScalar','CoordinateScalar'};'int32',{'SourceX','SourceY','GroupX','GroupY'};'int16',{'CoordinateUnits','WeatheringVelocity',...

'SubweatheringVelocity',...'SourceUpholeTime_ms','GroupUpholeTime_ms',...'SourceStaticCorrection_ms',...'GroupStaticCorrection_ms',...'TotalStaticApplied_ms',...'ALagTime_ms','BLagTime_ms',...'RecordingDelay_ms',...'MuteTimeStart_ms','MuteTimeEnd_ms',...'NumberOfSamples',...'SampleInterval_ms',...

'GainType','GainConstant_dB',...'InitialGain_dB','Correlated',...'SweepFrequencyStart_Hz',...'SweepFrequencyEnd_Hz',...'SweepLength_ms','SweepType',...'SweepTaperLengthStart_ms',...'SweepTaperLengthEnd_ms',...'TaperType','AliasFilter_Hz',...'AliasSlope_dBperOctave',...'NotchFilterFrequency_Hz',...'NotchFilterSlope_dBperOctave',...'LowCutFrequency_Hz',...'HighCutFrequency_Hz',...'LowCutSlope_dBperOctave',...'HighCutSlope_dBperOctave',...'Year','Day','Hour','Minute','Second',...'TimeBasisCode','WeightingFactor',...'GeophoneGroupNumberRoll1',...

'GeophoneGroupNumberFirstTraceOriginalRecord',...'GeophoneGroupNumberLastTraceOriginalRecord',...'GapSize','OverTravel'};

'int32',{'EnsembleX','EnsembleY','InLineNumber3D',...'CrossLineNumber3D','ShotPointNumber'};

'int16',{'ShotPointScalar','TraceMeasurementUnit'};'int32',{1,'TransductionConstantMantissa'};'int16',{'TransductionConstantExponent',...

'TranductionUnits','TraceIdentifier',...'TimeScalar','SourceTypeOrientation'};

'bit48',{1,'SourceEnergyDirection'};'int32',{1,'SourceMeasurementMantissa'};'int16',{'SourceMeasurementExponent',...

'SourceMeasurementUnit'};'int16',{4,'Unassigned'}};

for t = 1:length(traceNumber)offset = obj.FileHeader.TracePointers(traceNumber(t));f = readTraceHeader@SeismicFileReader(obj,fmt,offset);th(t) = f;

end

if nargout == 0 % add to object if no output requestedobj.TraceDescription = th;

endend % readTraceHeader

function [td,th] = readTraceData(obj,traceNumber,td)if nargin == 1 || isempty(traceNumber)

traceNumber = 1:obj.NumberOfTraces;end

% get 1st trace size to determine initial array sizeth = readTraceHeader(obj,1);

r = th.NumberOfSamples;c = length(traceNumber);

% create as distributed array if requestedif nargin > 2 && license('test','distrib_computing_toolbox')

td = distributed.nan(r,c);else

trytd = nan(r,c);

catche = lasterror;

if strcmpi(e.identifier,'MATLAB:nomem')% test maximum array sizeu = memory;str = ['\n\tCould not allocate an array of ',...

num2str(r*c*8),'bytes. Available memory is: \n',...u.MaxPossibleArrayBytes,...'\tTry declaring as a distributed array:\n\t\t',...

' '


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= rea race a a o , race um ers, s r u e ;e.message = sprintf([e.message,str]);

endrethrow(e)

end

end

for t = 1:length(traceNumber)% read the trace header informationth(t) = readTraceHeader(obj,traceNumber(t));

% need to account for variable length data (NaNs)n = th(t).NumberOfSamples;

% since r is sized by the first data set, it should never% be smaller than this, we only need to test for the case% where it is greater

%if th(t).NumberOfSamples > r% th(end:end+n,:) = NaN;%end

% get trace data and fill preallocated arrayfmtCode = obj.FileHeader.TraceFormat;fmt = {fmtCode, th(1).NumberOfSamples};offset = obj.FileHeader.TracePointers(traceNumber(t)) + ...

240; % offset for trace binary header% account for ibm floating pointif obj.FileHeader.BinaryHeader.SampleFormatCode == 1

td(:,t) = ibm2ieee(readTraceData@SeismicFileReader(obj,fmt,offset));else

td(:,t) = readTraceData@SeismicFileReader(obj,fmt,offset);

endend % for loop

end % readTraceData

function txt = parseTextBlock(obj,textBlock)% parse out text block datatxt = [];

% extract keywords[keys,idx] = regexp(textBlock, '[AZ_]\w*', 'match','start');% check validity[~,idx] = obj.validKeys(keys,idx);

% remove 1st two bytes (offsets) in file from keywords% and last offset bytestextBlock([idx2, idx1,end1:end]) = [];

% extract keywords with new index locations

[keys,idx] = regexp(textBlock, '[AZ_]\w*', 'match','end');% check validity[keys,idx] = obj.validKeys(keys,idx);

for i = 1:length(idx)if i < length(idx)

str = textBlock((idx(i)+1):(idx(i+1)length(keys{i+1})));else

str = textBlock((idx(i)+1):end);end% check if it is a date or time stringif isempty(strfind(str,':')) && isempty(strfind(str,'\'))

tmpStr = str2num(str);else

tmpStr = deblank(strtrim(str));endif isempty(tmpStr)

% If only whitespaces don't add

if ~isempty(strtok(str,char(0)))txt.(keys{i}) = deblank(strtrim(str));

endelse

txt.(keys{i}) = tmpStr;end

end % forend % parseTextBlock

function varargout = subsref(obj,s)if numel(obj) > 1

if length(s) > 1obj = obj(s(1).subs{:});varargout{1} = subsref(obj,s(2:end));

elsevarargout{1} = obj(s.subs{:});

endelse

' '


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s rcmp s 1 . ype,if length(s) > 1

error('SeismicFileReader:InvalidIndexing','This index operation iendif strcmpi(s.subs{2},':')

ind = [];else

ind = s.subs{2};endtmp = readTraceData(obj,ind);varargout{1} = tmp(s.subs{1},:);

elseif strcmp(s.type,'.')varargout{1} = obj.(s.subs);

end

endend % subsref

end % methods

methods (Static)

function [keys,idx] = validKeys(keys,idx)% check valid keysvalidKey = {'ACQUISITION_DATE',... % file header

'ACQUISITION_TIME',...'CLIENT',...'COMPANY',...'GENERAL_CONSTANT',...'INSTRUMENT',...'JOB_ID',...'OBSERVER',...'PROCESSING_TIME',...'TRACE_SORT',...

'UNITS',...'NOTE',...

'ALIAS_FILTER',... % trace header'AMPLITUDE_RECOVERY',...'BAND_REJECT_FILTER',...'CDP_NUMBER',...'CDP_TRACE',...'CHANNEL_NUMBER',...'DATUM',...'DELAY',...'DESCALING_FACTOR',...'DIGITAL_BAND_REJECT_FILTER',...'DIGITAL_HIGHT_CUT_FILTER',...'DIGITAL_LOW_CUT_FILTER',...'END_OF_GROUP',...'FIXED_GAIN',...'HIGH_CUT_FILTER',...

'LINE_ID'...'LOW_CUT_FILTER',...'NOTCH_FREQUENCY',...'POLARITY',...'RAW_RECORD',...'RECEIVER',...'RECEIVER_GEOMETERY',...'RECEIVER_LOCATION',...'RECEIVER_SPECS',...'RECEIVER_STATION_NUMBER',...'SAMPLE_INTERVAL',...'SHOT_SEQUENCE_NUMBER',...'SKEW',...

'SOURCE',...'SOURCE_GEOMETRY',...'SOURCE_LOCATION',...'SOURCE_STATION_NUMBER',...'STACK',...

'STATIC_CORRECTIONS',...'TRACE_TYPE',...'UNIT',...% nonspec keywords below'ACQUISITION_SECOND_FRACTION'};

lidx = ismember(keys,validKey);keys = keys(lidx);idx = idx(lidx);

end % validKeys

end % Static methods

end % Seg2FileReader Class


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