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irisFetch.m
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classdef irisFetch
% IRISFETCH allows seamless access to data stored within the IRIS-DMC via FDSN services
%
% irisFetch Methods:
%
% irisFetch waveform retrieval Methods:
% Traces - retrieve sac-equivalent waveforms with channel metadata
%
% irisFetch FDSN station webservice Methods:
% Channels - retrieve metadata as an array of channels
% Stations - retrieve metadata as an array of stations
% Networks - retrieve metadata as an array of networks
%
% irisFetch FDSN event webservice Methods:
% Events - retrieve events parameters (such as origins and magnitudes) from a catalog
%
% irisFetch miscelleneous Methods:
% Resp - retrive RESP formatted response data from the irisws-resp service
% version - display the current version number
% connectToJar - attempt to connect to the required IRIS-WS JAR file
% runExamples - displays and runs some sample queries to the web service.
%
% irisFetch requires version 2.0 or greater of the IRIS Web Services Library java jar
% for more details, click on 'connectToJar' above.
%
% For additional guidance, type help <method>, use irisFetch.runExamples, or check out
% the online manual http://www.iris.edu/dms/nodes/dmc/software/downloads/irisFetch.m/.
%
%see also JAVAADDPATH
% Celso Reyes, Rich Karstens
% IRIS-DMC
% JUNE 2013
%{
*******************************************************************************
* Copyright (c) 2013 IRIS DMC supported by the National Science Foundation.
*
* This file is part of Iris Matlab Fetch (irisFetch).
*
* irisFetch is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* irisFetch is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* A copy of the GNU Lesser General Public License is available at
* <http://www.gnu.org/licenses/>.
******************************************************************************
%}
properties (Constant = true)
VERSION = '2.0.1'; % irisFetch version number
DATE_FORMATTER = 'yyyy-mm-dd HH:MM:SS.FFF'; %default data format, in ms
MIN_JAR_VERSION = '2.0.2'; % minimum version of IRIS-WS jar required for compatibility
VALID_QUALITIES = {'D','R','Q','M','B'}; % list of Qualities accepted by Traces
DEFAULT_QUALITY = 'B'; % default Quality for Traces
FETCHER_LIST = {'Traces','Stations','Events','Resp'}; % list of functions that fetch
forceDataAsDouble = true; %require that traces are returned as doubles regardless of original format
end %constant properties
properties (Constant = true, Hidden = true)
MS_IN_DAY = 86400000; % milliseconds in day
BASE_DATENUM = 719529; % Matlab startdate=0000-Jan-1 vs java's startdate=1970-Jan-1
SURROGATE_JAR = 'http://www.iris.edu/files/IRIS-WS/2/IRIS-WS-2.0-latest.jar';
M2J_MAP = containers.Map (...
{'java.util.Date',...
'java.lang.Double',...
'java.lang.Long',...
'java.lang.Integer',...
'java.lang.String',...
'boolean'},...
{@(x) java.util.Date(((datenum(x)-irisFetch.BASE_DATENUM) * irisFetch.MS_IN_DAY) + .5), ...%@(x) irisFetch.mdate2jdate(x) ,...
@(x) java.lang.Double(x),...
@(x) java.lang.Long(x),...
@(x) java.lang.Integer(x),...
@(x) x,...
@(x) x}...
); %details for MATLAB to JAVA conversions
appName = ['MATLAB:irisFetch/' irisFetch.VERSION]; %used as useragent of queries
recursionAssert = false; %check for recursions while parsing java into structs
end %hidden constant properties
methods(Static)
function v = version()
v = irisFetch.VERSION;
end
function ts = Traces(network, station, location, channel, startDate, endDate, varargin )
%irisFetch.Traces retrieves sac-equivalent waveform with channel metadata
% tr = irisFetch.Traces(network, station, location, channel, startDate, endDate)
% will use channel and date criteria to retrieve one or more seismic traces,
% which are stored as structures containing typical SAC-equivalent metadata.
%
% startDate and endDate must be formatted thusly:
% 'YYYY-MM-DD hh:mm:ss' or 'YYYY-MM-DD hh:mm:ss.sss'
%
% network, station, location, and channel all accept comma separated lists, as
% well as '*' and '?' wildcards.
%
% tr = irisFetch.Traces(..., quality) allows you to specify the data's quality,
% such as 'B' (which stands for "best"). This SEED quality code defines how data overlaps
% are processed by the dataselect service.
%
% tr = irisFetch.Traces(..., 'includePZ') will also retrieve poles and zeroes.
% These are the same poles/zeros as found from http://service.iris.edu/irisws/sacpz/1/
%
% tr = irisFetch.Traces(..., 'verbose') provides additional debugging information
%
% tr = irisFetch.Traces(..., usernameAndPassword ) allows authorized users to
% access restricted data. usernameAndPassword must be a cell containing the
% username and password.
% Sample:
% unamepwd = {'nobody@iris.edu', 'anonymous'}
%
% tr = irisFetch.Traces(..., urlbase) will allow traces to be read from an
% alternate data center. url base is only the first part of the web address. For
% example, the IRIS datacenter would be 'http://service.iris.edu/'. These
% settings are "sticky", so that all calls for waveform data or station metadata
% will go to that datacenter until a new one is specified.
%
% ABOUT THE RETURNED TRACE
% The returned trace(s) will be a 1xN array of structs. Each struct contains
% fields with information pertaining to that specific trace, such as channel
% information, start & end times, units, etc.
%
% If the requested data does not exist, then an empty (1x0) trace struct will be
% returned. If the original data contains data gaps, then each continuous data
% segment will be returned as its own trace.
%
% COMMON MANIPULATIONS:
%
% See a text representation of the start date to millisecond accuracy, from a trace tr:
% datestr(tr.startTime, 'yyyy-mm-dd HH:MM:SS.FFF')
%
% Scale the data, so that resulting values are in sensitivityUnits.
% tr.data = tr.data ./ tr.sensitivity; % this example works only for single trace
%
% EXAMPLES:
% Get 4 hours of data (timeseries + metdata) from a station:
% tr = irisFetch.Traces('IU','ANMO','10','BHZ','2010-02-27 06:30:00','2010-02-27 10:30:00')
%
% Get 3 channels (via wildcards), including response, for a 4-hour time period:
% ts = irisFetch.Traces('IU','ANMO','10','BH?','2010-02-27 06:30:00','2010-02-27 10:30:00','includePZ')
%
%
% Get data from all channels from a comma-separated list of stations:
% ts = irisFetch.Traces('IU','ANMO,ANTO,YSS','00','*','2010-02-27 06:30:00','2010-02-27 10:30:00')
%
% SEE ALSO datestr
if ~exist('extensions.fetch.TraceData','class')
irisFetch.connectToJar()
end
import edu.iris.dmc.*
% import edu.iris.dmc.*
% these variables are shared among all the nested functions
getsacpz = false;
verbosity = false;
authorize = false;
quality = irisFetch.DEFAULT_QUALITY;
username = '';
userpwd = '';
newbase = '';
safeLocation = @(x) strrep(x,' ','-');
extractAdditionalArguments(varargin);
startDateStr = irisFetch.makeDateStr(startDate);
endDateStr = irisFetch.makeDateStr(endDate);
location = safeLocation(location);
tracedata = edu.iris.dmc.extensions.fetch.TraceData();
tracedata.setAppName(irisFetch.appName);
tracedata.setVerbosity(verbosity);
if ~isempty(newbase); tracedata.setBASE_URL(newbase);end;
getTheTraces();
return
% ---------------------------------------------------------------
% END TRACES: MAIN
% ===============================================================
function extractAdditionalArguments(argList)
% extracts getsacpz, verbosity, authorize, quality, username, and userpwd
% Parameters are handled "intelligently" so that [paramname, paramval] pairs
% aren't necessry
for n=1:numel(argList)
param = argList{n};
switch class(param)
case 'cell'
assert(numel(param)==2 && all(cellfun(@ischar, param)),...
'A cell parameter is assumed to contain credentials. eg. {''nobody@iris.edu'',''anonymous''}.');
[username, userpwd] = deal(param{:});
authorize = true;
case 'char'
switch upper(param)
case irisFetch.VALID_QUALITIES
quality = param;
case {'INCLUDEPZ'}
getsacpz = true;
case {'VERBOSE'}
verbosity = true;
otherwise
if length(param)>7 && strcmpi(param(1:7),'http://')
% set the bases
newbase = param;
else
error('IRISFETCH:Trace:unrecognizedParameter',...
'The text you included as an optional parameter did not parse to either a qualitytype (D,R,Q,M,B) or ''INCLUDEPZ'' or ''VERBOSE''');
end
end
%case 'logical' DEPRECATED
% verbosity = param; % old usage, deprecated.
otherwise
error('IRISFETCH:Trace:unrecognizedParameter',...
'The optional parameter wasn''t recognized. %s', class(param));
end
end
if verbosity
disp({'spz:',getsacpz,'vb:',verbosity,'auth:',authorize,'qual:',quality,'un&pw:',username,userpwd});
end
end % extractAdditionalArguments
function getTheTraces()
try
if authorize
if verbosity
fprintf('traces = tracedata.fetchTraces("%s", "%s", "%s", "%s", "%s", "%s", ''%s'', %d, "%s", "%s")\n',...
network, station, location, channel, startDateStr, endDateStr, quality, getsacpz, username, char(userpwd - userpwd + 42));
end
traces = tracedata.fetchTraces(network, station, location, channel, ...
startDateStr, endDateStr, quality, getsacpz, username, userpwd);
else
if verbosity
fprintf('traces = tracedata.fetchTraces("%s", "%s", "%s", "%s", "%s", "%s", ''%s'', %d)\n',...
network, station, location, channel, startDateStr, endDateStr, quality, getsacpz);
end
traces = tracedata.fetchTraces(network, station, location, channel, ...
startDateStr, endDateStr, quality, getsacpz);
end
catch je
switch je.identifier
case 'MATLAB:Java:GenericException'
if any(strfind(je.message,'URLNotFoundException'));
error('IRISFETCH:Trace:URLNotFoundException',...
'Trace found no requested data and returned the following error:\n%s',...
je.message);
end
otherwise
fprintf('Exception occured in IRIS Web Services Library: %s\n', je.message);
end
rethrow(je)
end
ts = irisFetch.convertTraces(traces);
clear traces
end %function getTheTraces
end % Traces
function [channelStructure, urlParams] = Channels(detailLevel, varargin)
%irisFetch.Channels retrieves station metadata from IRIS-DMC as an array of channels
% s = irisFetch.Channels(DETAIL,NETWORK,STATION,LOCATION,CHANNEL) retrieves
% station metadata from the IRIS-DMC into an array of channels. DETAIL is one of
% 'CHANNEL', or 'RESPONSE' and should be explicitly declared. DETAIL defaults to 'CHANNEL'
% Network, station, location, and channel parameters are passed directly to the
% java library, so both comma-separated lists and wildcards (? and *) are accepted.
%
% All five parameters are required for all queries, but may be wildcarded by
% using '' for their values.
%
% [s, myParams] = irisFetch.Channels( ... ) also returns the URL parameters that
% were used to make the query.
%
% irisFetch.Channels(..., 'BASEURL',alternateURL) specifies an alternate base URL
% to query. By default queries go to: http://service.iris.edu/fdsnws/station/1/
%
% s = irisFetch.Channels( ... , paramName, value [, ...]]) allows any number of
% parameter-value pairs to be included in the selection criteria. Valid
% parameter names are listed in help for irisFetch.Networks
%
% Example: to retrieve channel-level BHZ metadata from any station named ANMO:
% s = irisFetch.Channels('channel','*','ANMO','*','BHZ')
%
% Note: This function effectively deprecates irisFetch.flattenToChannel
%
%See also Networks, Stations
if isempty(detailLevel)
detailLevel = 'CHANNEL';
end
assert(ismember(upper(detailLevel),{'CHANNEL','RESPONSE'}),...
'To retrieve channels, the detailLevel must be either ''CHANNEL'' or ''RESPONSE''');
[channelStructure, urlParams] = irisFetch.Networks(detailLevel, varargin{:});
if ~isempty(channelStructure)
channelStructure = irisFetch.flattenToChannel(channelStructure);
end
end
function [stationStructure, urlParams] = Stations(detailLevel, varargin)
%irisFetch.Stations retrieves station metadata from IRIS-DMC as an array of stations
% s = irisFetch.Stations(DETAIL,NETWORK,STATION,LOCATION,CHANNEL) retrieves
% station metadata from the IRIS-DMC into an array of stations. DETAIL is one
% of 'STATION','CHANNEL', or 'RESPONSE' and should be explicitly declared.
% DETAIL defaults to 'STATION'
%
% Network, station, location, and channel parameters are passed directly to the
% java library, so both comma-separated lists and wildcards (? and *) are accepted.
%
% All five parameters are required for all queries, but may be wildcarded by
% using '' for their values.
%
% [s, myParams] = irisFetch.Stations( ... ) also returns the URL parameters that
% were used to make the query.
%
% irisFetch.Stations(..., 'BASEURL',alternateURL) specifies an alternate base URL
% to query. By default queries go to: http://service.iris.edu/fdsnws/station/1/
%
% s = irisFetch.Stations( ... , paramName, value [, ...]]) allows any number of
% parameter-value pairs to be included in the selection criteria. Valid
% parameter names are listed in help for irisFetch.Networks
%
% Example: to retrieve channel-level metadata, stored in an array of stations:
% s = irisFetch.Stations('channel','IU','A*','*','BHZ')
%
% Note: This function effectively deprecates the irisFetch.flattenToStation
%
%See also Networks, Channels
if isempty(detailLevel)
detailLevel = 'STATION';
end
assert(ismember(upper(detailLevel),{'STATION','CHANNEL','RESPONSE'}),...
'To retrieve stations, the detailLevel must be either ''STATION'', ''CHANNEL'', or ''RESPONSE''');
[stationStructure, urlParams] = irisFetch.Networks(detailLevel,varargin{:});
if ~isempty(stationStructure)
stationStructure = irisFetch.flattenToStation(stationStructure);
end
end
function [networkStructure, urlParams] = Networks(detailLevel, network, station, location, channel, varargin)
%irisFetch.Stations retrieves station metadata from IRIS-DMC as an array of networks
% s = irisFetch.Networks(DETAIL,NETWORK,STATION,LOCATION,CHANNEL), retrieves
% station metadata into an array of networks. These parameters are required for
% all queries, but may be wildcarded by using '' for their values. Network,
% station, location, and channel parameters are passed directly to the java
% library, so both comma-separated lists and wildcards (? and *) are accepted.
% Detail is one of 'NETWORK','STATION','CHANNEL', or 'RESPONSE' and should be
% explicitly declared. Defaults to 'NETWORK'
%
% [s, myParams] = irisFetch.Networks( ... ) also returns the URL parameters that
% were used to make the query.
%
% irisFetch.Networks(..., 'BASEURL',alternateURL) specifies an alternate base URL
% to query. By default queries go to: http://service.iris.edu/fdsnws/station/1/
%
% s = irisFetch.Networks( ... , paramName, value [, ...]]) allows any number of
% parameter-value pairs to be included in the selection criteria. See the list
% below.
%
% Valid parameters are listed below. For detailed descriptions of their effect
% and use, consult the station webservice webpage, available at:
% http://service.iris.edu/fdsnws/station/1/
%
% PARAMETER LIST (for IRIS-WS-2.0.0.jar)
% The following take time values, of the format 'yyyy-mm-dd HH:MM:SS'
% 'StartTime', 'EndTime', 'StartBefore', 'EndBefore'
% 'StartAfter', 'EndAfter' 'UpdatedAfter'
%
% The following take values in degrees and work together to define a search box
% 'MinimumLatitude', 'MaximumLatitude', 'MinimumLongitude','MaximumLongitude'
%
% These params take values in degrees to define a search disk / annular region
% 'Latitude', 'Longitude', 'MinimumRadius','MaximumRadius'
%
% Other params, that accept true or false (no quotes)
% 'IncludeAvailability','MatchTimeSeries', 'IncludeRestricted'
%
% CONVENIENCE PARAMETERS
% 'boxcoordinates' : [minLat, maxLat, minLon, maxLon]
% % use NaN as a wildcard
% 'radialcoordinates' : 1x4 double :
% [Lat, Lon, MaxRadius, MinRadius]
% % MinRadius is optional
%
% To retrieve similar information, but organize as an array of either channels
% or stations, use irisFetch.Channels or irisFetch.Stations respectively.
%
%SEE ALSO Channels, Stations
import edu.iris.dmc.*
outputLevel = '';
service = []; % will be a java service object
crit = []; % will be a java criteria object
j_networks = []; % will be the returned java networks
%if ~exist('edu.iris.dmc.criteria.StationCriteria','class')
if ~exist('criteria.StationCriteria','class')
irisFetch.connectToJar()
end
if isempty(detailLevel)
detailLevel = 'NETWORK';
end
verifyArguments(nargin);
setOutputLevel();
connectToStationService();
setCriteria();
fetchTheStations();
networkStructure=irisFetch.parser_for_IRIS_WS_2_0_0(j_networks);
if nargout == 2
urlParams = crit.toUrlParams;
end
return
% -------------------------------------------------------------
% END STATIONS: MAIN
% =============================================================
function verifyArguments(nArgs)
if nArgs==1 && strcmpi(detailLevel,'help')
disp('HELP request recognized, but not implemented');
return
elseif nArgs < 5
error('not enough arguments.%d',nArgs);
end
end %verifyArguments
function setOutputLevel()
try
outputLevel = edu.iris.dmc.criteria.OutputLevel.(upper(detailLevel));
% outputLevel = edu.iris.dmc.criteria.OutputLevel.(upper(detailLevel));
catch je
switch je.identifier
case 'MATLAB:undefinedVarOrClass'
error('IRISFETCH:NoIrisWSJarInstalled',...
['The necessary IRIS-WS java library was not recognized or found. ',...
'Please ensure it is on your javaclasspath']);
case 'MATLAB:subscripting:classHasNoPropertyOrMethod'
error('IRISFETCH:invalidOutputLevel',...
'The selected outputLevel [''%s''] was not recognized.',...
upper(detailLevel));
otherwise
rethrow(je);
end
end
end % setOutputLevel
function connectToStationService()
serviceManager = edu.iris.dmc.service.ServiceUtil.getInstance();
serviceManager.setAppName(['MATLAB:irisFetch/' irisFetch.version()])
setBaseUrlFromParameterList();
removeParameter('BASEURL');
return
% - - - - - - - - - - - - - - -
function setBaseUrlFromParameterList()
baseUrl = getParameter('BASEURL');
if ~isempty(baseUrl)
service = serviceManager.getStationService(baseUrl);
else
service = serviceManager.getStationService();
end % setBaseUrlFromParameterList
end
end %connectToStationService()
function removeParameter(s)
[UNUSED_VARIABLE, idx] = getParameter(s); %#ok<ASGLU>
varargin(idx * 2 -1 : idx* 2) = [];
end
function [p, i] = getParameter(s)
i = find(strcmpi(parameterNames(),s),1,'first');
p = parameterValues();
p = p(i);
end
function pn = parameterNames()
pn = varargin(1:2:end);
end
function pv = parameterValues()
pv = varargin(2:2:end);
end
function setCriteria()
crit = edu.iris.dmc.criteria.StationCriteria;
%crit = edu.iris.dmc.criteria.StationCriteria;
%----------------------------------------------------------
% Deal with the Station/Network/Channel/Location parameters
% These are treated separately, as they're "add" & not "set"
% Each may handle multiple strings (as a cell array)
%----------------------------------------------------------
crit = irisFetch.addCriteria(crit, network, 'addNetwork');
crit = irisFetch.addCriteria(crit, station, 'addStation');
crit = irisFetch.addCriteria(crit, location,'addLocation');
crit = irisFetch.addCriteria(crit, channel, 'addChannel');
crit = irisFetch.setCriteria(crit, varargin);
end %setCriteria
function fetchTheStations()
try
j_networks = service.fetch(crit, outputLevel);
catch je
if strfind(je.message,'ServiceNotSupportedException')
error('IRISFETCH:ServiceNotSupportedByLibrary',...
'The IRIS-WS java library version doesn''t support the requested station service version');
elseif strfind(je.message,'NoDataFoundException')
warning('IRISFETCH:NoDataFoundException','No data was found that matched your criteria');
j_networks = [];
else
rethrow(je)
end
end %catch
end %fetchTheStations
end %Networks
function [events, urlParams] = Events(varargin)
%irisFetch.Events retrieves event data from the IRIS-DMC
% ev = irisFetch.Events(param, value [, ...]) retrieves event data from the
% IRIS-DMC database as a matlab structure. An arbitrary number of
% parameter-value pairs may be specified in order to narrow down the search
% results.
%
% [ev, myParams] = irisFetch.Events( ... ) also returns the URL parameters that
% were used to make the query.
%
% irisFetch.Events(..., 'BASEURL',alternateURL) specifies an alternate base URL
% to query. By default queries go to: http://service.iris.edu/fdsnws/event/1/
%
% Usable parameters are listed below. For detailed descriptions of their effect
% and use, consult the webservice webpage for events, available at:
%
% http://service.iris.edu/fdsnws/event/1/
%
% Examples:
%
% Retrieve event parameters regarding earthquakes of a specific size and location:
% ev = irisFetch.Events('MinimumMagnitude',6.0,...
% 'minimumLatitude',45,'maximumLatitude', 60,...
% 'minimumLongitude', -150,'maximumLongitude', -90)
%
%PARAMETER LIST (for IRIS-WS-2.0.0.jar)
% contributor, endTime, eventId, fetchLimit, latitude, longitude, magnitudeType,
% maximumDepth, maximumLatitude, maximumLongitude, maximumMagnitude,
% minimumDepth, minimumLatitude, minimumLongitude, minimumMagnitude,
% minimumRadius, maximumRadius, offset, startTime updatedAfter
%
%CONVENIENCE PARAMETERS
% 'boxcoordinates' : [minLat, maxLat, minLon, maxLon] % use NaN as a wildcard
% 'radialcoordinates' : [Lat, Lon, MaxRadius, MinRadius] % MinRadius is optional
%
%NOTE: Any parameter-value pair that is not listed here will be passed along to
% the Event Service. this is to accomodate other datacenters that may have
% specialized request parameters.
import edu.iris.dmc.*
% import edu.iris.dmc.*
%if ~exist('edu.iris.dmc.criteria.EventCriteria','class')
if ~exist('criteria.EventCriteria','class')
irisFetch.connectToJar()
end
%serviceManager = ws.service.ServiceUtil.getInstance();
serviceManager = edu.iris.dmc.service.ServiceUtil.getInstance();
serviceManager.setAppName(['MATLAB:irisFetch/' irisFetch.version()]);
indexOffsetOfBASEURL=find(strcmpi(varargin(1:2:end),'BASEURL'),1,'first') * 2;
if ~isempty(indexOffsetOfBASEURL)
baseURL = varargin{indexOffsetOfBASEURL};
end
if exist('baseURL','var')
varargin(indexOffsetOfBASEURL-1:indexOffsetOfBASEURL) = [];
service = serviceManager.getEventService(baseURL);
else
service = serviceManager.getEventService();
end
%crit = ws.criteria.EventCriteria;
crit = criteria.EventCriteria;
crit = irisFetch.setCriteria(crit, varargin);
if nargout == 2
urlParams = crit.toUrlParams;
end
disp('fetching...')
try
j_events = service.fetch(crit);
catch er
if any(strfind(er.message,'NoDataFoundException')) || any(strfind(er.message,'No Content'))
warning('IRISFETCH:NoDataFoundException','No data was found that matched your criteria');
events=[];
return
end
rethrow(er);
end
fprintf('\n\n%d events found *************\n\n',j_events.size);
disp('parsing into MATLAB structures')
events=irisFetch.parser_for_IRIS_WS_2_0_0(j_events);
% v2.0 uses Preferred, while original code uses "Primary"
end
function connectToJar(isSilent)
%irisFetch.connectToJar connects to the jar for this MATLAB session
% irisFetch.connectToJar() searches the javaclasspath for the
% IRIS-WS jar file. If it does not exist, then it will try to access the latest
% jar over the internet. If it cannot connect, it will error.
%
% irisFetch requires version 2.0.2 or greater of the IRIS Web Services Library java jar,
% available from:
%
% http://www.iris.edu/files/IRIS-WS/2/
%
% This jar file must be added to your MATLAB path, which may be done
% in a variety of ways. One common way is to include a javaaddpath
% statement in the startup.m file. For more details, consult MATLAB's
% documentation for 'Bringing Java Classes and Methods into MATLAB
% Workspace'.
%
% SEE ALSO javaaddpath
assert(usejava('jvm'),'IRISFETCH:jvmNotRunning','irisFetch requires Java to run.');
isSilent = nargin>0 && strcmpi(isSilent,'silent');
if exist('edu.iris.dmc.extensions.fetch.TraceData','class');
return
end
if ~isSilent
disp('please add the latest IRIS-WS.jar file to your javaclasspath.');
fprintf('Available here: %s\n',irisFetch.SURROGATE_JAR);
disp('ex. javaaddpath(''/usr/local/somewhere/IRIS-WS.jar'');');
end
javaaddpath(irisFetch.SURROGATE_JAR);
if ~exist('edu.iris.dmc.extensions.fetch.TraceData','class');
error('irisFetch:noDefaultJar',...
'Unable to access the default jar. Please download and add the latest IRIS-WS-JAR to your javaclasspath.');
end
end
function [respstructures, urlparams] = Resp(network, station, location, channel, starttime, endtime)
% retrieve the RESP information into a character string.
% net, sta, loc, and cha are all required.
% channels and locations may be wildcarded using either ? or *
% starttime and endtime options may be ignored by using [] instead of a time.
import edu.iris.dmc.*
% crit = edu.iris.dmc.criteria.RespCriteria();
crit = criteria.RespCriteria();
crit.setNetwork(network);
crit.setStation(station);
crit.setLocation(location);
crit.setChannel(channel);
if ~isempty(starttime)
crit.setStartTime(irisFetch.mdate2jdate(starttime));
end
if ~isempty(endtime)
crit.setEndTime(irisFetch.mdate2jdate(endtime));
end
urlparams = char(crit.toUrlParams());
serviceManager = edu.iris.dmc.service.ServiceUtil.getInstance();
baseUrl = 'http://service.iris.edu/irisws/resp/1/';
serviceManager.setAppName(['MATLAB:irisFetch/' irisFetch.version()]);
service = serviceManager.getRespService(baseUrl);
respstructures= char(service.fetch(crit));
end
function runExamples()
delay=1; % seconds
codeToExecute={
'% Retrieve 1 hr of all ''HZ'' channels from all locations at station ANMO for net IU'
'traces = irisFetch.Traces(''IU'',''ANMO'',''*'',''?HZ'',''2010-02-27 06:30:00'',''2010-02-27 07:30:00'')'
'% Notice that multiple traces were retrieved, look at the first trace.'
'tr = traces(1)'
'% -------- plot the data from the first trace, and then label the plot ------'
'sampletimes=linspace(tr.startTime,tr.endTime,tr.sampleCount); %calculate the time of each sample'
'whos(''sampletimes'')'
'plot(sampletimes,tr.data);'
'legendDetails = sprintf(''%s-%s-%s'', tr.network, tr.station, tr.location, tr.channel)'
'legend(legendDetails);'
'title(''Simple plot'');'
'datetick;'
' '
'% next, get some station data (same data, at different levels of detail'
'n = irisFetch.Networks(''Response'',''IU'',''ANMO'','''',''BHZ'')';
's = irisFetch.Stations(''Response'',''IU'',''ANMO'','''',''BHZ'')';
'c = irisFetch.Channels(''Response'',''IU'',''ANMO'','''',''BHZ'')';
' '
'% retrieve station data using other search parameters'
'arcticNetworkList = irisFetch.Networks(''Station'','''','''','''','''',''minimumlatitude'',66.3)';
'netNames = {arcticNetworkList.NetworkCode}'
' '
'% retrieve event data'
' ev = irisFetch.Events(''minimummagnitude'',8.0)'
' ev(1)'
' ev = irisFetch.Events(''starttime'',''2010-02-27'',''endtime'',''2010-02-28 12:00:00'',''catalog'',''ISC'',''includeallorigins'',true,''includeallmagnitudes'',true)'
' '
'% retrieve the RESP formatted response for a station'
'irisFetch.Resp(''IU'',''ANMO'',''00'',''BHZ'',now,now)'
};
for n=1:numel(codeToExecute)
disp(codeToExecute{n});
eval(codeToExecute{n});
pause(delay);
end
clear traces tr n s c ev
end %fn runExamples
end % static methods
methods(Static, Hidden=true)
function channelList = flattenToChannel(networkTree)
%irisFetch.flattenToChannel flattens the structure returned by irisFetch.Networks
% flatStruct = irisFetch.flattenToChannel(networkTree) takes the hierarchy
% returned by irisFetch.Networks, and returns a 1xN array of channels (channel
% epochs, technically).
%
% flatStruct is an array containing ALL channel epochs.
assert(isa(networkTree,'struct'),'Cannot Flatten a non-structure');
%eliminate stations that have no channels
for n=1:numel(networkTree)
hasNoChannel = arrayfun(@(x) isempty(x.Channels),networkTree(n).Stations);
networkTree(n).Stations(hasNoChannel) = []; % networkTree(n).Stations(~hasNoChannel);
end
%eliminate networks that have no stations
networksWithoutStations = arrayfun(@(x) isempty(x.Stations),networkTree);
networkTree(networksWithoutStations) = [];
if isempty(networkTree);
warning('IRISFETCH:flattenToChannel:noValidChannels','No channels found, returning an empty array');
return
end
for n=1:numel(networkTree)
nc = networkTree(n).NetworkCode;
nd = networkTree(n).Description;
[networkTree(n).Stations.NetworkCode] = deal(nc);
[networkTree(n).Stations.NetworkDescription] = deal(nd);
for m = 1 : numel(networkTree(n).Stations)
sc = networkTree(n).Stations(m).StationCode;
sd = networkTree(n).Stations(m).Description;
sn = networkTree(n).Stations(m).Site;
[networkTree(n).Stations(m).Channels.NetworkCode] = deal(nc);
[networkTree(n).Stations(m).Channels.NetworkDescription] = deal(nd);
[networkTree(n).Stations(m).Channels.StationCode] = deal(sc);
[networkTree(n).Stations(m).Channels.StationDescription] = deal(sd);
[networkTree(n).Stations(m).Channels.Site] = deal(sn);
% write the long StationName again to the main level.
[networkTree(n).Stations(m).Channels.StationName] = deal(sn.Name);
end
end
tmp = [networkTree.Stations];
channelList=[tmp.Channels];
clear tmp
% now, reorder to make it visually coherent.
descriptorstuff={'NetworkCode';'StationCode';'LocationCode';'ChannelCode';'NetworkDescription';'StationName';'Site'};
positionalstuff={'Latitude';'Longitude';'Elevation';'Depth';'Azimuth';'Dip'};
otherstuff={'SampleRate';'SampleRateRatio';'StartDate';'EndDate'};
fieldsattop=[descriptorstuff; positionalstuff; otherstuff];
fn = fieldnames(channelList);
fieldsattop = fieldsattop(ismember(fieldsattop,fn)); %ensure fields exist
for n=1:numel(fieldsattop);
fn(strcmp(fn,fieldsattop(n))) = [];
end
neworder = [fieldsattop; fn];
channelList = orderfields(channelList, neworder);
end
function stationList = flattenToStation(networkTree)
%irisFetch.flattenToStation flattens the structure returned by irisFetch.Stations
%
%USAGE
% flatStruct = irisFetch.flattenToStation(networkTree)
%
%This takes the hierarchy returned by irisFetch.Stations, and
%returns a 1xN array of stations (station epochs, technically).
assert(isa(networkTree,'struct'),'Cannot Flatten a non-structure');
emptyNetworks = arrayfun(@(x) isempty(x.Stations),networkTree);
for n=1:numel(networkTree)
nc = networkTree(n).NetworkCode;
nd = networkTree(n).Description;
[networkTree(n).Stations.NetworkCode] = deal(nc);
[networkTree(n).Stations.NetworkDescription] = deal(nd);
end
stationList = [networkTree(~emptyNetworks).Stations];
for m=1:numel(stationList)
stationList(m).StationName = stationList(m).Site.Name;
end
% now, reorder to make it visually coherent.
descriptorstuff={'NetworkCode';'StationCode';'NetworkDescription';'StationName';'Site'};
positionalstuff={'Latitude';'Longitude';'Elevation'};
otherstuff={'StartDate';'EndDate'};
fieldsattop=[descriptorstuff; positionalstuff; otherstuff];
if ~isstruct(stationList)
warning('IRISFETCH:flattenToStation:noValidStations','No stations found, returning an empty array');
return
end
fn = fieldnames(stationList);
fieldsattop = fieldsattop(ismember(fieldsattop,fn)); %ensure fields exist
for n=1:numel(fieldsattop);
fn(strcmp(fn,fieldsattop(n))) = [];
end
neworder = [fieldsattop; fn];
stationList = orderfields(stationList, neworder);
end
function [js, je] = testResp(starttime, endtime)
n=now;
testThis('IU','ANMO','00','BHZ',[],[]);
testThis('IU','ANMO','00','*',[],[]);
testThis('IU','ANMO','*','BHZ',[],[]);
testThis('IU','ANMO','00','BHZ',[],now-1);
testThis('IU','ANMO','00','BHZ',n-600,[]);
testThis('IU','ANMO','00','BHZ',n,n-1);
testThis('IU','ANMO','?0','BHZ',n,n-1);
testThis('IU','ANMO','00','B?Z',n,n-1);
testThis('IU','ANMO','00','BHZ','9/20/2012','9/20/2012 03:00:00');
%testThis('IU','*','00','BHZ',[],[]); %should fail
%testThis('*','ANMO','00','BHZ',[],[]); % should fail
if exist('starttime','var') && ~isempty(starttime)
js = showTimeInDetail(starttime);
end
disp(' ');
if exist('endtime','var') && ~isempty(endtime)
je = showTimeInDetail(endtime);
end
function testThis(varargin)
try
[r, url] = irisFetch.Resp(varargin{:});
whos r
disp(['url: ', url]);
parampairs={
'network' ,varargin{1}, 'station' ,varargin{2}, 'location' ,varargin{3}, 'channel' ,varargin{4}
};
disp(paramPairs)
if ~isempty(varargin{5})
st = datestr(varargin{5},31);
st(11)='T';
parampairs = [parampairs, {'starttime',st}];
end
if ~isempty(varargin{6})
ed = datestr(varargin{6},31);
ed(11)='T';
parampairs = [parampairs, {'endtime',ed}];
end
[s,code]=urlread('http://service.iris.edu/irisws/resp/1/query','get', parampairs); %#ok<NASGU>
assert(strcmp(r,s));
catch myerror
warning('RESPTEST:failure',myerror.identifier);
end
end
function javadateTime = showTimeInDetail(t)
dv = datevec(t);
dv(6) = ceil(dv(6) * 1000) / 1000;
t = datenum(dv);
s = dv(6);
% t must be either a date number or a string.
javadateTime = irisFetch.mdate2jdate(t);
matlabTimeString = datestr(t,irisFetch.DATE_FORMATTER);
%crit = edu.iris.dmc.criteria.RespCriteria();
crit = criteria.RespCriteria();
crit.setEndTime(javadateTime);
reconvertedMatlabTime = ...
datestr(irisFetch.jdate2mdate(javadateTime),irisFetch.DATE_FORMATTER);
%urlString = char(criteria.toUrlParams().get(0));
urlString = crit.toUrlParams().get(0).toCharArray()';
if ~(all(reconvertedMatlabTime == matlabTimeString));
disp(s-fix(s));
if datenum(reconvertedMatlabTime) > datenum(t)
fprintf('^ ');
else
fprintf('v ');
end
fprintf('InputTime: %s ; jDateTime: %s ; millis: %d\nReConvert: %s\nURL: %s\n',...
matlabTimeString, ...
javadateTime.toGMTString.toCharArray()', ...
rem(javadateTime.getTime(),1000),...
reconvertedMatlabTime,...
urlString);
end
end %fn showTimeInDetail
end %fn testResp
end %static hidden methods
methods(Static, Access=protected)
function myDateStr = makeDateStr(dateInput)
myDateStr = datestr(dateInput, irisFetch.DATE_FORMATTER);
end
function d = jArrayList2complex(jArrayList)
% for use on ArrayList objects containing things with getReal() and getImaginary()
% edu.iris.dmc.sacpz.model.Pole
% edu.iris.dmc.sacpz.model.Zero
% edu.iris.dmc.station.model.ComplexNumber
if jArrayList.size()<1
assert(0==1,'Never should reach this');
d = zeros(0,1); % optimized
else
jArray = jArrayList.toArray;
dr = zeros(numel(jArray),1);
di = zeros(numel(jArray),1);
for n = 1 : jArrayList.size()%:-1: 1
dr(n,1) = jArray(n).getReal().doubleValue;
di(n,1) = jArray(n).getImaginary().doubleValue;
end
d = complex(dr,di);
end
end
function mts = convertTraces(traces)
%irisFetch.convertTraces converts traces from java to a matlab structure
% mts = convertTraces(traces) where TRACES a java trace class. If the input
% traces are empty, then a 1x0 structure is returned.
blankSacPZ = struct('units','','constant',[],'poles',[],'zeros',[]);
blankTrace = struct('network','','station','','location',''...
,'channel','','quality','',...
'latitude',0,'longitude',0,'elevation',0,'depth',0,...
'azimuth',0,'dip',0,...
'sensitivity',0,'sensitivityFrequency',0,...
'instrument','','sensitivityUnits','UNK',...
'data',[],'sampleCount',0,'sampleRate',nan,...
'startTime',0,'endTime',0,'sacpz',blankSacPZ);
mts=blankTrace;
if isempty(traces)
mts(1) = []; % keep the structure, but force it to be 1x0 trace
end
for i = 1:length(traces)
mt=blankTrace;
mt.network = char(traces(i).getNetwork());
mt.station = char(traces(i).getStation());
mt.location = char(traces(i).getLocation());
mt.channel = char(traces(i).getChannel());
mt.quality = char(traces(i).getQuality());
mt.latitude = traces(i).getLatitude();
mt.longitude = traces(i).getLongitude();
mt.elevation = traces(i).getElevation();
mt.depth = traces(i).getDepth();
mt.azimuth = traces(i).getAzimuth();
mt.dip = traces(i).getDip();
mt.sensitivity = traces(i).getSensitivity();
mt.sensitivityFrequency = traces(i).getSensitivityFrequency();
mt.instrument = char(traces(i).getInstrument());