Merge pull request #106 from JuliaGeodynamics/mt_fix_function_names

updated function names for profile processing

Author: mthielma

.gitignore

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

src/ProfileProcessing.jl

@@ -251,11 +251,11 @@ end
 
 
 """
-    CreateProfileVolume!(Profile::ProfileData, VolData::AbstractGeneralGrid; DimsVolCross::NTuple=(100,100), Depth_extent=nothing)
+    create_profile_volume!(Profile::ProfileData, VolData::AbstractGeneralGrid; DimsVolCross::NTuple=(100,100), Depth_extent=nothing)
 
 Creates a cross-section through a volumetric 3D dataset `VolData` with the data supplied in `Profile`. `Depth_extent` can be the minimum & maximum depth for vertical profiles
 """
-function CreateProfileVolume!(Profile::ProfileData, VolData::AbstractGeneralGrid; DimsVolCross::NTuple=(100,100), Depth_extent=nothing)
+function create_profile_volume!(Profile::ProfileData, VolData::AbstractGeneralGrid; DimsVolCross::NTuple=(100,100), Depth_extent=nothing)
 
     if Profile.vertical
         # take a vertical cross section
@@ -276,7 +276,7 @@ end
 
 
 ### internal function to process surface data - contrary to the volume data, we here have to save lon/lat/depth pairs for every surface data set, so we create a NamedTuple of GeoData data sets
-function CreateProfileSurface!(Profile::ProfileData, DataSet::NamedTuple; DimsSurfCross=(100,))
+function create_profile_surface!(Profile::ProfileData, DataSet::NamedTuple; DimsSurfCross=(100,))
     num_datasets = length(DataSet)
 
     tmp = NamedTuple()             # initialize empty one
@@ -309,9 +309,8 @@ function CreateProfileSurface!(Profile::ProfileData, DataSet::NamedTuple; DimsSu
 end
 
 
-
 ### function to process point data - contrary to the volume data, we here have to save lon/lat/depth pairs for every point data set
-function CreateProfilePoint!(Profile::ProfileData, DataSet::NamedTuple; section_width=50km)
+function create_profile_point!(Profile::ProfileData, DataSet::NamedTuple; section_width=50km)
     num_datasets = length(DataSet)
 
     tmp = NamedTuple()             # initialize empty one
@@ -356,10 +355,10 @@ Extracts data along a vertical or horizontal profile
 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)
 
     if !isnothing(VolData)
-        CreateProfileVolume!(Profile, VolData; DimsVolCross=DimsVolCross, Depth_extent=Depth_extent)
+        create_profile_volume!(Profile, VolData; DimsVolCross=DimsVolCross, Depth_extent=Depth_extent)
     end
-    CreateProfileSurface!(Profile, SurfData, DimsSurfCross=DimsSurfCross)
-    CreateProfilePoint!(Profile, PointData, section_width=section_width)
+    create_profile_surface!(Profile, SurfData, DimsSurfCross=DimsSurfCross)
+    create_profile_point!(Profile, PointData, section_width=section_width)
 
     return nothing
 end
@@ -446,13 +445,13 @@ function extract_ProfileData(ProfileCoordFile,ProfileNumber,DataSetName,DataSetF
     ind_point  = findall( x -> x .== "Point", DataSetType)
 
     # extract volume data
-    CreateProfileVolume!(Profile,DataSetName[ind_vol],DataSetFile[ind_vol],DimsVolCross,DepthVol)
+    create_profile_volume!(Profile,DataSetName[ind_vol],DataSetFile[ind_vol],DimsVolCross,DepthVol)
 
     # extract surface data
-    CreateProfileSurface!(Profile,DataSetName[ind_surf],DataSetFile[ind_surf],DimsSurfCross)
+    create_profile_surface!(Profile,DataSetName[ind_surf],DataSetFile[ind_surf],DimsSurfCross)
 
     # extract point data
-    CreateProfilePoint!(Profile,DataSetName[ind_point],DataSetFile[ind_point],WidthPointProfile)
+    create_profile_point!(Profile,DataSetName[ind_point],DataSetFile[ind_point],WidthPointProfile)
 
     return Profile
 end

src/utils.jl

@@ -124,7 +124,7 @@ GeoData
 """
 function cross_section_volume(V::AbstractGeneralGrid; dims=(100,100), Interpolate=false, Depth_level=nothing, Lat_level=nothing, Lon_level=nothing, Start=nothing, End=nothing, Depth_extent=nothing )
 
-    DataSetType = CheckDataSet(V);
+    DataSetType = check_data_set(V);
 
     if DataSetType != 3
         error("cross_section_volume: the input data set has to be a volume!")
@@ -253,7 +253,7 @@ GeoData
 """
 function cross_section_surface(S::AbstractGeneralGrid; dims=(100,), Interpolate=true, Depth_level=nothing, Lat_level=nothing, Lon_level=nothing, Start=nothing, End=nothing )
 
-    DataSetType = CheckDataSet(S);
+    DataSetType = check_data_set(S);
     if DataSetType != 2
         error("cross_section_surface: the input data set has to be a surface!")
     end
@@ -337,7 +337,7 @@ Creates a projection of separate points (saved as a GeoData object) onto a chose
 """
 function cross_section_points(P::GeoData; Depth_level=nothing, Lat_level=nothing, Lon_level=nothing, Start=nothing, End=nothing, section_width = 10km)
 
-    DataSetType = CheckDataSet(P);
+    DataSetType = check_data_set(P);
     if DataSetType != 1
         error("cross_section_points: the input data set has to be a pointwise data set!")
     end
@@ -529,7 +529,7 @@ GeoData
 """
 function cross_section(DataSet::AbstractGeneralGrid; dims=(100,100), Interpolate=false, Depth_level=nothing, Lat_level=nothing, Lon_level=nothing, Start=nothing, End=nothing, Depth_extent=nothing, section_width=50km)
 
-    DataSetType = CheckDataSet(DataSet); # check which kind of data set we are dealing with
+    DataSetType = check_data_set(DataSet); # check which kind of data set we are dealing with
 
     if DataSetType==1 # points
         DataProfile = cross_section_points(DataSet; Depth_level, Lat_level, Lon_level, Start, End, section_width)
@@ -814,7 +814,7 @@ function extract_subvolume(V::CartData;
             X_cross[i,j,1] = x_val
         end
 
-        Data_extract = InterpolateDataFields_CrossSection(V, X, Y, Z, X_cross);
+        Data_extract = interpolate_data_fields_cross_section(V, X, Y, Z, X_cross);
 
     else
         # Don't interpolate
@@ -838,11 +838,11 @@ end
 
 
 """
-    InterpolateDataFields_CrossSection(V::CartData, X,Y,Z,Xcross)
+    interpolate_data_fields_cross_section(V::CartData, X,Y,Z,Xcross)
 
 Interpolates data fields along a cross-section defined by `Xcross` and `Z`
 """
-function InterpolateDataFields_CrossSection(V::CartData, X,Y,Z, X_cross)
+function interpolate_data_fields_cross_section(V::CartData, X,Y,Z, X_cross)
 
     Data_extract = CartData(X,Y,Z, (FlatCrossSection=X_cross,))
 
@@ -895,7 +895,7 @@ function CheckBounds(Data::AbstractArray, Data_Cross)
 end
 
 # CHECKS FOR VOLUME, SURFACE OR POINTS
-function CheckDataSet(DataSet::GeoData)
+function check_data_set(DataSet::GeoData)
     if length(size(DataSet.lon)) == 1 # scattered points
         return 1
     else
@@ -907,7 +907,7 @@ function CheckDataSet(DataSet::GeoData)
     end
 end
 
-function CheckDataSet(DataSet::CartData)
+function check_data_set(DataSet::CartData)
     if length(size(DataSet.x)) == 1 # scattered points
         return 1
     else

test/test_ProfileProcessing.jl

@@ -61,22 +61,22 @@ prof3 = ProfileData(start_lonlat=(5,45), end_lonlat=(5,49))
 prof4 = ProfileData(depth = -20)
 
 # test internal routines to intersect profile with volumetric data:
-GeophysicalModelGenerator.CreateProfileVolume!(prof1, VolData_combined1)
+GeophysicalModelGenerator.create_profile_volume!(prof1, VolData_combined1)
 @test prof1.VolData.fields.Hua2017_Vp[30,40] ≈ 9.141520976523731
 
-GeophysicalModelGenerator.CreateProfileVolume!(prof2, VolData_combined1)
+GeophysicalModelGenerator.create_profile_volume!(prof2, VolData_combined1)
 @test prof2.VolData.fields.Hua2017_Vp[30,40] ≈ 8.177263544536272
 
-GeophysicalModelGenerator.CreateProfileVolume!(prof1, VolData_combined1,  Depth_extent=(-300, -100))
+GeophysicalModelGenerator.create_profile_volume!(prof1, VolData_combined1,  Depth_extent=(-300, -100))
 @test extrema(prof1.VolData.depth.val) == (-300.0, -100.0)
 
 # Intersect surface data:
-GeophysicalModelGenerator.CreateProfileSurface!(prof1,Data.Surface)
+GeophysicalModelGenerator.create_profile_surface!(prof1,Data.Surface)
 @test prof1.SurfData[1].fields.MohoDepth[80] ≈ -37.58791461075397km
 
 # ditto with EQ data:
-GeophysicalModelGenerator.CreateProfilePoint!(prof1,Data.Point, section_width=5km)
-GeophysicalModelGenerator.CreateProfilePoint!(prof4,Data.Point, section_width=10km)
+GeophysicalModelGenerator.create_profile_point!(prof1,Data.Point, section_width=5km)
+GeophysicalModelGenerator.create_profile_point!(prof4,Data.Point, section_width=10km)
 @test  length(prof1.PointData[1].lon) == 13
 @test  length(prof4.PointData[1].lon) == 445
 

test/test_data_import.jl

@@ -81,7 +81,9 @@ data_Image          =   screenshot_to_UTMData(filename,Corner_LowerLeft, Corner_
 
 # test the import of xml files from ISC
 # the search criteria are set in a way that only one event should be found
-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")
-Data_ISC = getlonlatdepthmag_QuakeML("ISCTest.xml");
+# as the download fails quite frequently, the XML file has been added to the repository
+# for completeness, the download link is kept here
+# 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")
+Data_ISC = getlonlatdepthmag_QuakeML("test_files/ISCTest.xml");
 @test Value(Data_ISC.depth[1])==-13.0km
 @test Data_ISC.fields.Magnitude[1]==5.8

test/test_files/ISCTest.xml

@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<q:quakeml xmlns:q="http://quakeml.org/xmlns/quakeml/1.2" xmlns="http://quakeml.org/xmlns/bed/1.2">
+  <eventParameters publicID="smi:ISCEHB/bulletin">
+    <creationInfo>
+      <agencyID>ISC</agencyID>
+      <creationTime>2024-03-19T09:56:26</creationTime>
+    </creationInfo>
+    <description>ISC-EHB Bulletin</description>
+    <event publicID="smi:ISCEHB/evid=610803926">
+      <preferredOriginID>smi:ISCEHB/origid=608918847</preferredOriginID>
+      <description>
+        <text>Sicily</text>
+        <type>Flinn-Engdahl region</type>
+      </description>
+      <type>earthquake</type>
+      <typeCertainty>known</typeCertainty>
+      <creationInfo>
+        <agencyID>ISC-EHB</agencyID>
+        <author>ISC-EHB</author>
+      </creationInfo>
+      <origin publicID="smi:ISCEHB/origid=608918847">
+        <time>
+          <value>2002-09-06T01:21:29.08Z</value>
+        </time>
+        <latitude>
+          <value>38.3200</value>
+        </latitude>
+        <longitude>
+          <value>13.7240</value>
+        </longitude>
+        <depth>
+          <value>13000.0</value>
+        </depth>
+        <depthType>operator assigned</depthType>
+        <quality>
+          <usedPhaseCount>769</usedPhaseCount>
+          <associatedStationCount>743</associatedStationCount>
+          <standardError>0.9500</standardError>
+        </quality>
+        <creationInfo>
+          <author>ISC-EHB</author>
+          <agencyID>ISC-EHB</agencyID>
+        </creationInfo>
+        <evaluationMode>manual</evaluationMode>
+        <evaluationStatus>reviewed</evaluationStatus>
+        <originUncertainty>
+          <preferredDescription>uncertainty ellipse</preferredDescription>
+          <minHorizontalUncertainty>1700</minHorizontalUncertainty>
+          <maxHorizontalUncertainty>2600</maxHorizontalUncertainty>
+          <azimuthMaxHorizontalUncertainty>20.0</azimuthMaxHorizontalUncertainty>
+        </originUncertainty>
+      </origin>
+      <magnitude publicID="smi:ISCEHB/magid=5498826">
+        <mag>
+          <value>5.80</value>
+        </mag>
+        <type>mb</type>
+        <originID>smi:ISCEHB/origid=608918847</originID>
+        <stationCount>118</stationCount>
+        <creationInfo>
+          <author>ISC</author>
+        </creationInfo>
+      </magnitude>
+      <magnitude publicID="smi:ISCEHB/magid=5498827">
+        <mag>
+          <value>5.50</value>
+        </mag>
+        <type>MS</type>
+        <originID>smi:ISCEHB/origid=608918847</originID>
+        <stationCount>123</stationCount>
+        <creationInfo>
+          <author>ISC</author>
+        </creationInfo>
+      </magnitude>
+      <magnitude publicID="smi:ISCEHB/magid=3622904">
+        <mag>
+          <value>5.93</value>
+        </mag>
+        <type>MW</type>
+        <originID>smi:ISCEHB/origid=608918847</originID>
+        <stationCount>27</stationCount>
+        <creationInfo>
+          <author>HRVD</author>
+        </creationInfo>
+      </magnitude>
+      <preferredMagnitudeID>smi:ISCEHB/magid=5498827</preferredMagnitudeID>
+    </event>
+  </eventParameters>
+</q:quakeml>