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mthielmamthielma
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address comments
- updated gitignore - changed extract_profile_data back to extract_ProfileData - adapted tests
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5 files changed

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-25
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‎.gitignore‎

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@@ -22,3 +22,4 @@ tutorial/test.tiff
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*.jld2
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*.tiff
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*.nc
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!/test/test_files/ISCTest.xml

‎src/ProfileProcessing.jl‎

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@@ -2,8 +2,8 @@
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# this is ProfileProcessing.jl
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# It contains functions and type definitions to gather selected data for given profiles
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5-
export ProfileData, extract_profile_data, create_ProfileData, GMG_Dataset, load_dataset_file, combine_vol_data
6-
export extract_profile_data!, read_picked_profiles
5+
export ProfileData, extract_ProfileData, create_ProfileData, GMG_Dataset, load_dataset_file, combine_vol_data
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export extract_ProfileData!, read_picked_profiles
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import Base: show
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"""
@@ -348,11 +348,11 @@ end
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"""
351-
extract_profile_data!(Profile::ProfileData,VolData::GeoData, SurfData::NamedTuple, PointData::NamedTuple; DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50)
351+
extract_ProfileData!(Profile::ProfileData,VolData::GeoData, SurfData::NamedTuple, PointData::NamedTuple; DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50)
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Extracts data along a vertical or horizontal profile
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"""
355-
function extract_profile_data!(Profile::ProfileData,VolData::Union{Nothing,GeoData}=nothing, SurfData::NamedTuple=NamedTuple(), PointData::NamedTuple=NamedTuple(); DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50km)
355+
function extract_ProfileData!(Profile::ProfileData,VolData::Union{Nothing,GeoData}=nothing, SurfData::NamedTuple=NamedTuple(), PointData::NamedTuple=NamedTuple(); DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50km)
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if !isnothing(VolData)
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create_profile_volume!(Profile, VolData; DimsVolCross=DimsVolCross, Depth_extent=Depth_extent)
@@ -383,11 +383,11 @@ end
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# this is mostly for backwards compatibility
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"""
386-
extract_profile_data(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
386+
extract_ProfileData(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
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This is a convenience function (mostly for backwards compatibility with the MATLAB GUI) that loads the data from file & projects it onto a profile
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"""
390-
function extract_profile_data(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
390+
function extract_ProfileData(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
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# read profile
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profile_list = read_picked_profiles(ProfileCoordFile)
@@ -408,7 +408,7 @@ function extract_profile_data(ProfileCoordFile::String,ProfileNumber::Int64,Data
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VolData_combined = combine_vol_data(VolData)
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410410
# project data onto profile:
411-
extract_profile_data!(profile, VolData_combined, SurfData, PointData,
411+
extract_ProfileData!(profile, VolData_combined, SurfData, PointData,
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DimsVolCross=DimsVolCross, DimsSurfCross=DimsSurfCross,
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Depth_extent=DepthVol, section_width=WidthPointProfile)
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@@ -420,7 +420,7 @@ end
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# Boris: I don't know exactly in which format you have your current files;
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### wrapper function to extract data for a single profile
423-
function extract_profile_data(ProfileCoordFile,ProfileNumber,DataSetName,DataSetFile,DataSetType,DimsVolCross,DepthVol,DimsSurfCross,WidthPointProfile)
423+
function extract_ProfileData(ProfileCoordFile,ProfileNumber,DataSetName,DataSetFile,DataSetType,DimsVolCross,DepthVol,DimsSurfCross,WidthPointProfile)
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# start and end points are saved in a text file
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profile_data = readdlm(ProfileCoordFile,skipstart=1,',')
@@ -479,7 +479,7 @@ function create_ProfileData(file_profiles,file_datasets;Depth_extent=(-300,0),Di
479479
for iprofile = 1:length(ProfileNumber)
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# 2. process the profiles
482-
ExtractedData = extract_profile_data(file_profiles,ProfileNumber[iprofile],DataSetName,DataSetFile,DataSetType,DimsVolCross,Depth_extent,DimsSurfCross,WidthPointProfile)
482+
ExtractedData = extract_ProfileData(file_profiles,ProfileNumber[iprofile],DataSetName,DataSetFile,DataSetType,DimsVolCross,Depth_extent,DimsSurfCross,WidthPointProfile)
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# 3. save data as JLD2
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fn = "Profile"*string(ProfileNumber[iprofile])

‎test/test_ProfileProcessing.jl‎

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@@ -82,25 +82,25 @@ GeophysicalModelGenerator.create_profile_point!(prof4,Data.Point, section_width=
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# Test the main profile extraction routines:
85-
extract_profile_data!(prof1, VolData_combined1, Data.Surface, Data.Point)
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extract_profile_data!(prof2, VolData_combined1, Data.Surface, Data.Point)
87-
extract_profile_data!(prof3, VolData_combined1, Data.Surface, Data.Point)
88-
extract_profile_data!(prof4, VolData_combined1, Data.Surface, Data.Point)
85+
extract_ProfileData!(prof1, VolData_combined1, Data.Surface, Data.Point)
86+
extract_ProfileData!(prof2, VolData_combined1, Data.Surface, Data.Point)
87+
extract_ProfileData!(prof3, VolData_combined1, Data.Surface, Data.Point)
88+
extract_ProfileData!(prof4, VolData_combined1, Data.Surface, Data.Point)
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90-
extract_profile_data!(prof1, VolData_combined2, Data.Surface, Data.Point)
91-
extract_profile_data!(prof2, VolData_combined2, Data.Surface, Data.Point)
92-
extract_profile_data!(prof3, VolData_combined2, Data.Surface, Data.Point)
93-
extract_profile_data!(prof4, VolData_combined2, Data.Surface, Data.Point)
90+
extract_ProfileData!(prof1, VolData_combined2, Data.Surface, Data.Point)
91+
extract_ProfileData!(prof2, VolData_combined2, Data.Surface, Data.Point)
92+
extract_ProfileData!(prof3, VolData_combined2, Data.Surface, Data.Point)
93+
extract_ProfileData!(prof4, VolData_combined2, Data.Surface, Data.Point)
9494

95-
extract_profile_data!(prof1, VolData_combined3, Data.Surface, Data.Point)
96-
extract_profile_data!(prof2, VolData_combined3, Data.Surface, Data.Point)
97-
extract_profile_data!(prof3, VolData_combined3, Data.Surface, Data.Point)
98-
extract_profile_data!(prof4, VolData_combined3, Data.Surface, Data.Point)
95+
extract_ProfileData!(prof1, VolData_combined3, Data.Surface, Data.Point)
96+
extract_ProfileData!(prof2, VolData_combined3, Data.Surface, Data.Point)
97+
extract_ProfileData!(prof3, VolData_combined3, Data.Surface, Data.Point)
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extract_ProfileData!(prof4, VolData_combined3, Data.Surface, Data.Point)
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# Test that it works if only EQ's are provided:
102102
prof4 = ProfileData(depth = -20)
103-
extract_profile_data!(prof4, nothing, NamedTuple(), Data.Point)
103+
extract_ProfileData!(prof4, nothing, NamedTuple(), Data.Point)
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@test isnothing(prof4.VolData)
105105
@test isempty(prof4.SurfData)
106106
@test length(prof4.PointData[1].depth) == 3280
@@ -121,6 +121,6 @@ Depth_extent=nothing
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DimsSurfCross=(100,)
122122
section_width=50km
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124-
profile_backwards_compat = extract_profile_data("test_files/PickedProfiles.txt",1,"test_files/AlpineData_remote.txt",DimsVolCross=DimsVolCross,DepthVol=Depth_extent,DimsSurfCross=DimsSurfCross,WidthPointProfile=section_width)
124+
profile_backwards_compat = extract_ProfileData("test_files/PickedProfiles.txt",1,"test_files/AlpineData_remote.txt",DimsVolCross=DimsVolCross,DepthVol=Depth_extent,DimsSurfCross=DimsSurfCross,WidthPointProfile=section_width)
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126126
@test length(profile_backwards_compat.PointData[1].lon) == 440

‎test/test_data_import.jl‎

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@@ -81,7 +81,9 @@ data_Image = screenshot_to_UTMData(filename,Corner_LowerLeft, Corner_
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# test the import of xml files from ISC
8383
# the search criteria are set in a way that only one event should be found
84-
download_data("http://www.isc.ac.uk/cgi-bin/web-db-run?request=COLLECTED&req_agcy=ISC-EHB&out_format=QuakeML&ctr_lat=&ctr_lon=&radius=&max_dist_units=deg&searchshape=RECT&top_lat=49&bot_lat=37&left_lon=4&right_lon=20&srn=&grn=&start_year=2000&start_month=1&start_day=01&start_time=00%3A00%3A00&end_year=2005&end_month=12&end_day=31&end_time=00%3A00%3A00&min_dep=&max_dep=&min_mag=5.8&max_mag=&req_mag_type=Any&req_mag_agcy=Any&min_def=&max_def=&include_magnitudes=on&include_links=on&include_headers=on&include_comments=on&table_owner=iscehb","ISCTest.xml")
85-
Data_ISC = getlonlatdepthmag_QuakeML("ISCTest.xml");
84+
# as the download fails quite frequently, the XML file has been added to the repository
85+
# for completeness, the download link is kept here
86+
# download_data("http://www.isc.ac.uk/cgi-bin/web-db-run?request=COLLECTED&req_agcy=ISC-EHB&out_format=QuakeML&ctr_lat=&ctr_lon=&radius=&max_dist_units=deg&searchshape=RECT&top_lat=49&bot_lat=37&left_lon=4&right_lon=20&srn=&grn=&start_year=2000&start_month=1&start_day=01&start_time=00%3A00%3A00&end_year=2005&end_month=12&end_day=31&end_time=00%3A00%3A00&min_dep=&max_dep=&min_mag=5.8&max_mag=&req_mag_type=Any&req_mag_agcy=Any&min_def=&max_def=&include_magnitudes=on&include_links=on&include_headers=on&include_comments=on&table_owner=iscehb","ISCTest.xml")
87+
Data_ISC = getlonlatdepthmag_QuakeML("test_files/ISCTest.xml");
8688
@test Value(Data_ISC.depth[1])==-13.0km
8789
@test Data_ISC.fields.Magnitude[1]==5.8

‎test/test_files/ISCTest.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<q:quakeml xmlns:q="http://quakeml.org/xmlns/quakeml/1.2" xmlns="http://quakeml.org/xmlns/bed/1.2">
4+
<eventParameters publicID="smi:ISCEHB/bulletin">
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<creationInfo>
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<agencyID>ISC</agencyID>
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<creationTime>2024-03-19T09:56:26</creationTime>
8+
</creationInfo>
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<description>ISC-EHB Bulletin</description>
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<event publicID="smi:ISCEHB/evid=610803926">
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<preferredOriginID>smi:ISCEHB/origid=608918847</preferredOriginID>
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<description>
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<text>Sicily</text>
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<type>Flinn-Engdahl region</type>
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</description>
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<type>earthquake</type>
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<typeCertainty>known</typeCertainty>
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<creationInfo>
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<agencyID>ISC-EHB</agencyID>
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<author>ISC-EHB</author>
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</creationInfo>
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<origin publicID="smi:ISCEHB/origid=608918847">
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<time>
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<value>2002-09-06T01:21:29.08Z</value>
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</time>
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<latitude>
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<value>38.3200</value>
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</latitude>
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<longitude>
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<value>13.7240</value>
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</longitude>
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<depth>
33+
<value>13000.0</value>
34+
</depth>
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<depthType>operator assigned</depthType>
36+
<quality>
37+
<usedPhaseCount>769</usedPhaseCount>
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<associatedStationCount>743</associatedStationCount>
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<standardError>0.9500</standardError>
40+
</quality>
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<creationInfo>
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<author>ISC-EHB</author>
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<agencyID>ISC-EHB</agencyID>
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</creationInfo>
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<evaluationMode>manual</evaluationMode>
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<evaluationStatus>reviewed</evaluationStatus>
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<originUncertainty>
48+
<preferredDescription>uncertainty ellipse</preferredDescription>
49+
<minHorizontalUncertainty>1700</minHorizontalUncertainty>
50+
<maxHorizontalUncertainty>2600</maxHorizontalUncertainty>
51+
<azimuthMaxHorizontalUncertainty>20.0</azimuthMaxHorizontalUncertainty>
52+
</originUncertainty>
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</origin>
54+
<magnitude publicID="smi:ISCEHB/magid=5498826">
55+
<mag>
56+
<value>5.80</value>
57+
</mag>
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<type>mb</type>
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<originID>smi:ISCEHB/origid=608918847</originID>
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<stationCount>118</stationCount>
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<creationInfo>
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<author>ISC</author>
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</creationInfo>
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</magnitude>
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<magnitude publicID="smi:ISCEHB/magid=5498827">
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<mag>
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<value>5.50</value>
68+
</mag>
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<type>MS</type>
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<originID>smi:ISCEHB/origid=608918847</originID>
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<stationCount>123</stationCount>
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<creationInfo>
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<author>ISC</author>
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</creationInfo>
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</magnitude>
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<magnitude publicID="smi:ISCEHB/magid=3622904">
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<mag>
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<value>5.93</value>
79+
</mag>
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<type>MW</type>
81+
<originID>smi:ISCEHB/origid=608918847</originID>
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<stationCount>27</stationCount>
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<creationInfo>
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<author>HRVD</author>
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</creationInfo>
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</magnitude>
87+
<preferredMagnitudeID>smi:ISCEHB/magid=5498827</preferredMagnitudeID>
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</event>
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</eventParameters>
90+
</q:quakeml>

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