updated function names for profile processing

Author: mthielma

src/ProfileProcessing.jl

@@ -2,8 +2,8 @@
 # this is ProfileProcessing.jl
 # It contains functions and type definitions to gather selected data for given profiles
 
-export ProfileData, extract_ProfileData, create_ProfileData, GMG_Dataset, load_dataset_file, combine_vol_data
-export extract_ProfileData!, read_picked_profiles
+export ProfileData, extract_profile_data, create_ProfileData, GMG_Dataset, load_dataset_file, combine_vol_data
+export extract_profile_data!, read_picked_profiles
 import Base: show
 
 """
@@ -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
@@ -349,17 +348,17 @@ end
 
 
 """
-    extract_ProfileData!(Profile::ProfileData,VolData::GeoData, SurfData::NamedTuple, PointData::NamedTuple; DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50)
+    extract_profile_data!(Profile::ProfileData,VolData::GeoData, SurfData::NamedTuple, PointData::NamedTuple; DimsVolCross=(100,100),Depth_extent=nothing,DimsSurfCross=(100,),section_width=50)
 
 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)
+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)
 
     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
@@ -384,11 +383,11 @@ end
 
 # this is mostly for backwards compatibility
 """
-    extract_ProfileData(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
+    extract_profile_data(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
 
 This is a convenience function (mostly for backwards compatibility with the MATLAB GUI) that loads the data from file & projects it onto a profile
 """
-function extract_ProfileData(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
+function extract_profile_data(ProfileCoordFile::String,ProfileNumber::Int64,DataSetFile::String; DimsVolCross=(100,100),DepthVol=nothing,DimsSurfCross=(100,),WidthPointProfile=50km)
 
     # read profile
     profile_list = read_picked_profiles(ProfileCoordFile)
@@ -409,7 +408,7 @@ function extract_ProfileData(ProfileCoordFile::String,ProfileNumber::Int64,DataS
     VolData_combined = combine_vol_data(VolData)
 
     # project data onto profile:
-    extract_ProfileData!(profile, VolData_combined, SurfData, PointData,
+    extract_profile_data!(profile, VolData_combined, SurfData, PointData,
                         DimsVolCross=DimsVolCross, DimsSurfCross=DimsSurfCross,
                         Depth_extent=DepthVol, section_width=WidthPointProfile)
 
@@ -421,7 +420,7 @@ end
 
 # Boris: I don't know exactly in which format you have your current files;
 ### wrapper function to extract data for a single profile
-function extract_ProfileData(ProfileCoordFile,ProfileNumber,DataSetName,DataSetFile,DataSetType,DimsVolCross,DepthVol,DimsSurfCross,WidthPointProfile)
+function extract_profile_data(ProfileCoordFile,ProfileNumber,DataSetName,DataSetFile,DataSetType,DimsVolCross,DepthVol,DimsSurfCross,WidthPointProfile)
 
     # start and end points are saved in a text file
     profile_data = readdlm(ProfileCoordFile,skipstart=1,',')
@@ -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
@@ -480,7 +479,7 @@ function create_ProfileData(file_profiles,file_datasets;Depth_extent=(-300,0),Di
     for iprofile = 1:length(ProfileNumber)
 
         # 2. process the profiles
-        ExtractedData = extract_ProfileData(file_profiles,ProfileNumber[iprofile],DataSetName,DataSetFile,DataSetType,DimsVolCross,Depth_extent,DimsSurfCross,WidthPointProfile)
+        ExtractedData = extract_profile_data(file_profiles,ProfileNumber[iprofile],DataSetName,DataSetFile,DataSetType,DimsVolCross,Depth_extent,DimsSurfCross,WidthPointProfile)
 
         # 3. save data as JLD2
         fn = "Profile"*string(ProfileNumber[iprofile])

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

@@ -61,46 +61,46 @@ 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 the main profile extraction routines:
-extract_ProfileData!(prof1, VolData_combined1, Data.Surface, Data.Point)
-extract_ProfileData!(prof2, VolData_combined1, Data.Surface, Data.Point)
-extract_ProfileData!(prof3, VolData_combined1, Data.Surface, Data.Point)
-extract_ProfileData!(prof4, VolData_combined1, Data.Surface, Data.Point)
+extract_profile_data!(prof1, VolData_combined1, Data.Surface, Data.Point)
+extract_profile_data!(prof2, VolData_combined1, Data.Surface, Data.Point)
+extract_profile_data!(prof3, VolData_combined1, Data.Surface, Data.Point)
+extract_profile_data!(prof4, VolData_combined1, Data.Surface, Data.Point)
 
-extract_ProfileData!(prof1, VolData_combined2, Data.Surface, Data.Point)
-extract_ProfileData!(prof2, VolData_combined2, Data.Surface, Data.Point)
-extract_ProfileData!(prof3, VolData_combined2, Data.Surface, Data.Point)
-extract_ProfileData!(prof4, VolData_combined2, Data.Surface, Data.Point)
+extract_profile_data!(prof1, VolData_combined2, Data.Surface, Data.Point)
+extract_profile_data!(prof2, VolData_combined2, Data.Surface, Data.Point)
+extract_profile_data!(prof3, VolData_combined2, Data.Surface, Data.Point)
+extract_profile_data!(prof4, VolData_combined2, Data.Surface, Data.Point)
 
-extract_ProfileData!(prof1, VolData_combined3, Data.Surface, Data.Point)
-extract_ProfileData!(prof2, VolData_combined3, Data.Surface, Data.Point)
-extract_ProfileData!(prof3, VolData_combined3, Data.Surface, Data.Point)
-extract_ProfileData!(prof4, VolData_combined3, Data.Surface, Data.Point)
+extract_profile_data!(prof1, VolData_combined3, Data.Surface, Data.Point)
+extract_profile_data!(prof2, VolData_combined3, Data.Surface, Data.Point)
+extract_profile_data!(prof3, VolData_combined3, Data.Surface, Data.Point)
+extract_profile_data!(prof4, VolData_combined3, Data.Surface, Data.Point)
 
 
 # Test that it works if only EQ's are provided:
 prof4 = ProfileData(depth = -20)
-extract_ProfileData!(prof4, nothing, NamedTuple(), Data.Point)
+extract_profile_data!(prof4, nothing, NamedTuple(), Data.Point)
 @test isnothing(prof4.VolData)
 @test isempty(prof4.SurfData)
 @test length(prof4.PointData[1].depth) == 3280
@@ -121,6 +121,6 @@ Depth_extent=nothing
 DimsSurfCross=(100,)
 section_width=50km
 
-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)
+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)
 
 @test length(profile_backwards_compat.PointData[1].lon) == 440