Check if the input of sample1d & filter1d have attributes and reprodu…

…ce them on output if yes. (#1686)

* Test/demo file for the whittaker smoothing function.

* When passing -R=G only set -I if -I was not explicitly set.

* Do not reset opt_T if it's not empty.

* Fix bugs in days=float. Let list accept a country name.

* Add a yeardecimal method to do real > DateTime

* A couple of cleanings.

* Check if the input of sample1d & filter1d have attributes and reproduce them on output if yes.

src/common_options.jl

@@ -170,7 +170,7 @@ function parse_R(d::Dict, cmd::String; O::Bool=false, del::Bool=true, RIr::Bool=
 	if (RIr)
 		if (isa(val, GItype))
 			opt_I = parse_I(d, "", [:I :inc :increment :spacing], "I", true)
-			(opt_I == "") && (cmd *= " -I" * arg2str(val.inc))::String
+			(opt_I == "") ? (cmd *= " -I" * arg2str(val.inc))::String : (cmd *= opt_I)
 			opt_r = parse_r(d, "")[2]
 			(opt_r == "") && (cmd *= " -r" * ((val.registration == 0) ? "g" : "p"))
 		else				# Here we must parse the -I and -r separately.

src/filter1d.jl

@@ -63,6 +63,11 @@ function filter1d_helper(cmd0::String, arg1; kwargs...)
 		cmd = add_opt(d, cmd, "F", [:F :filter :filter_type], (type="1", width="", highpass="_"))
 	end
 
-	(isvector(arg1)) && (arg1 = cat_1_arg(arg1))	# Accept vectors (GMT should do that too)
-	common_grd(d, cmd0, cmd, "filter1d ", arg1)		# Finish build cmd and run it
+	(isvector(arg1)) && (arg1 = cat_1_arg(arg1))		# Accept vectors (GMT should do that too)
+	r = common_grd(d, cmd0, cmd, "filter1d ", arg1)		# Finish build cmd and run it
+	if (isa(arg1, GDtype))								# Keep the attribs if they existed in arg1
+		isa(arg1, GMTdataset) && !isempty(arg1.attrib) && (r.attrib = arg1.attrib)
+		isa(arg1, Vector) && !isempty(arg1[1].attrib) && [r[k].attrib = arg1[1].attrib for k = 1:length(arg1)]
+	end
+	return r
 end

src/gmt_main.jl

@@ -1700,9 +1700,9 @@ info(C::GMTcpt) = show(C)
 Base.:show(io::IO, mime::MIME"image/png", wp::WrapperPluto) = write(io, read(wp.fname))
 
 # ---------- For Tables -----------------------------------------------------------------------------
-Base.:names(D::GDtype) = isa(D, Vector) ? D[1].colnames : D.colnames
-#Base.:names(D::GMTdataset) = D.colnames
-#Base.:names(D::Vector{<:GMTdataset}) = D[1].colnames
+#Base.:names(D::GDtype) = isa(D, Vector) ? D[1].colnames : D.colnames
+Base.:names(D::GMTdataset) = D.colnames
+Base.:names(D::Vector{<:GMTdataset}) = D[1].colnames
 
 # ---------- For fck stop printing UInts in hexadecinal ---------------------------------------------
 #Base.show(io::IO, x::T) where {T<:Union{UInt, UInt128, UInt64, UInt32, UInt16, UInt8}} = Base.print(io, x)

src/gmtreadwrite.jl

@@ -88,7 +88,7 @@ function gmtread(_fname::String; kwargs...)
 		elseif ((opt_T = guess_T_from_ext(fname)) == " -Tg")  fname *= "=gd"
 		end
 	else
-		opt_T = add_opt(d, "", "Ti", [:img :image])
+		(opt_T == "") && (opt_T = add_opt(d, "", "Ti", [:img :image]))
 	end
 
 	if (opt_T == "")  opt_T = add_opt(d, "", "Td", [:data :dataset :table])  end
@@ -425,8 +425,9 @@ function file_has_time!(fname::String, D::GDtype, corder::Vector{Int}=Int[], opt
 		isone ? (D.colnames = String[]) : [D[k].colnames = String[] for k = 1:lastindex(D)]
 		@warn("Failed to parse file '$fname' for file_has_time!(). Error was:\n $err")
 	end
-	isone ? (length(D.colnames) < n_cols && (D.colnames = String[])) : (length(D[1].colnames) < n_cols && (D[1].colnames = String[]))
 	close(fid)
+	isone ? (length(D.colnames) < n_cols && (D.colnames = String[])) : (length(D[1].colnames) < n_cols && (D[1].colnames = String[]))
+	!isone && !isempty(D[1].attrib) && [D[k].attrib = D[1].attrib for k = 2:lastindex(D)]	# All segs must have same attrib (?)
 	return nothing
 end
 

src/maregrams.jl

@@ -21,7 +21,8 @@ a valid one, we still return the data for that station. Example:
    This is an alternative way of selecting a station instead of using `code` or `name` that require knowing them.
 
 ### Kwargs
-- `list::Bool`: If true, returns a GMTdataset with the list all available stations and their codes and coords.
+- `list`: If equal to `true`, returns a GMTdataset with the list all available stations and their codes and coords.
+   If it is a string, search all entries that contain that string. _e.g.,_ `list=Canada` returns all stations in Canada.
 - `code`: Station code (See the output of `list`)
 - `name`: In alternative to `code` give the station name (See the output of `list`)
 - `days`: Number of days to be downloaded. It can be a decimal number.
@@ -39,8 +40,14 @@ D = maregrams(code="lgos", days=4, starttime="2025-02-01")
 viz(D, title="Tide Gauge at Lagos (Portugal)")
 ```	
 """
-function maregrams(; list::Bool=false, code="", name="", days=2, starttime::String="", printurl::Bool=false)::GMTdataset
-	(list == true) && return gmtread(TESTSDIR * "/assets/maregs_online.csv")
+function maregrams(; list=false, code="", name="", days=2, starttime::String="", printurl::Bool=false)::GMTdataset{Float64, 2}
+	if (list != 0)			# Either list all stations or search those that contains a "list" string
+		Dl = gmtread(TESTSDIR * "/assets/maregs_online.csv")
+		list == 1 && return Dl
+		inds = findall(contains.(Dl.text,list))
+		isempty(inds) && (println("'$list' was not found in stations list."); return GMTdataset())
+		return mat2ds(Dl, (inds,:))
+	end
 	@assert days > 0  "Number of days must be > 0."
 	_code::String = string(code)		# To let 'code' be a symbol as well
 	d = read_maregrams()
@@ -52,7 +59,9 @@ function maregrams(; list::Bool=false, code="", name="", days=2, starttime::Stri
 	# The shit here is that the site wants the endtime instead of starttime, sowe must do the maths to get it right.
 	(starttime != "") &&
 		try DateTime(starttime) catch; error("The start time '$starttime' is not a valid date.") end 
-	endtime = (starttime == "") ? DateTime(now()) : DateTime(starttime) + Dates.Day(days)
+	M = ((daydec = getdecimal(days)) != 0) ? round(Int, daydec*24*60) : 0
+	(daydec != 0) && (days = trunc(Int, days))
+	endtime = (starttime == "") ? DateTime(now()) : DateTime(starttime) + Dates.Day(days) + Dates.Minute(M)
 	endtime > DateTime(now()) && (days -= round((endtime - DateTime(now())).value / (24*3600000), digits=6); endtime = DateTime(now()))
 	url = "http://www.ioc-sealevelmonitoring.org/bgraph.php?code=$_code&output=asc&period=$days&endtime=$endtime"
 	printurl && println(url[1:(54+length(_code))])		# Station's URL

src/sample1d.jl

@@ -3,8 +3,6 @@
 
 Resample 1-D table data using splines
 
-See full GMT (not the `GMT.jl` one) docs at [`sample1d`]($(GMTdoc)sample1d.html)
-
 Parameters
 ----------
 
@@ -101,6 +99,7 @@ function sample1d_helper(cmd0::String, arg1; kwargs...)
 	if isa(arg1, GDtype)
 		colnames = isa(arg1, GMTdataset) ? arg1.colnames : arg1[1].colnames
 		have_cumdist && append!(colnames, ["cumdist"])
+		!isempty(arg1.attrib) && (r.attrib = arg1.attrib)	# Keep the attribs
 	else		# Input was eith a matrix or a file name
 		nc = isa(r, GMTdataset) ? size(r, 2) : size(r[1], 2)
 		colnames = [@sprintf("Z%d", k) for k = 1:nc]

src/utils.jl

@@ -1,7 +1,7 @@
 # Collect generic utility functions in this file
 
 """ Return the decimal part of a float number `x`"""
-getdecimal(x::AbstractFloat) = x - trunc(Int, x)
+getdecimal(x::Number) = x - trunc(Int, x)
 
 """ Return an ierator over data skipping non-finite values"""
 skipnan(itr) = Iterators.filter(el->isfinite(el), itr)
@@ -353,7 +353,8 @@ date2doy(date::String) = dayofyear(Date(date))
 """
     yeardecimal(date)
 
-Convert a Date or DateTime or a string representation of them to decimal years.
+Convert a Date or DateTime or a string representation of them to decimal years, or vice-versa.
+That is, convert from decimal year to DateTime.
 
 ### Example
     yeardecimal(now())
@@ -375,6 +376,14 @@ function yeardecimal(dtm::Union{DateTime, Vector{DateTime}})
 	Y .+ frac
 end
 
+# This function is from DateFormats.jl
+function yeardecimal(years::Real)		# Covert from decimal years to DateTime
+	years_whole = floor(Int, years)
+	year_ms = DateTime(years_whole + 1) - DateTime(years_whole) |> Dates.value
+	period_ms = year_ms * (years - years_whole)
+	return DateTime(years_whole) + Millisecond(round(Int64, period_ms))
+end
+
 # --------------------------------------------------------------------------------------------------
 function peaks(; N=49, grid::Bool=true, pixreg::Bool=false)
 	x,y = meshgrid(range(-3,stop=3,length=N))

src/utils_types.jl

@@ -138,9 +138,7 @@ function mat2ds(mat::Vector{<:AbstractMatrix}; hdr=String[], kwargs...)
 	d = KW(kwargs)
 	mat2ds(mat, hdr, d)
 end
-#function mat2ds(mat::Vector{<:AbstractMatrix}; hdr=String[], kwargs...)
 function mat2ds(mat::Vector{<:AbstractMatrix}, hdr::Vector{String}, d::Dict)
-	#d = KW(kwargs)
 	D = Vector{GMTdataset{eltype(mat[1]), 2}}(undef, length(mat))
 	pen   = find_in_dict(d, [:pen])[1]
 	color = find_in_dict(d, [:lc :linecolor :color])[1]
@@ -201,7 +199,8 @@ the georeference info as well as `attrib` and `colnames`.
 mat2ds(mat::Array{T,N}, ref::GMTdataset) where {T,N} = mat2ds(mat; ref=ref)
 
 # ---------------------------------------------------------------------------------------------------
-function mat2ds(mat::Array{T,N}, txt::Union{String,Vector{String}}=String[]; hdr::Union{String,VecOrMat{String}}=String[], geom=0, kwargs...)::GDtype where {T,N}
+function mat2ds(mat::Array{T,N}, txt::Union{String,Vector{String}}=String[];
+                hdr::Union{String,VecOrMat{String}}=String[], geom=0, kwargs...)::GDtype where {T,N}
 	d = KW(kwargs)
 	_mat2ds(mat, txt, isa(hdr, String) ? [hdr] : vec(hdr), Int(geom), d)
 end
@@ -612,7 +611,6 @@ function ds2ds(D::GMTdataset; is3D::Bool=false, kwargs...)::Vector{<:GMTdataset}
 	d = KW(kwargs)
 	ds2ds(D, is3D, d)
 end
-#function ds2ds(D::GMTdataset; is3D::Bool=false, kwargs...)::Vector{<:GMTdataset}
 function ds2ds(D::GMTdataset, is3D::Bool, d::Dict)::Vector{<:GMTdataset}
 	# Take one DS and split it into an array of DS's, one for each row and optionally add -G<fill>
 	# Alternativelly, if [:multi :multicol] options lieve in 'd', split 'D' by columns: [1,2], [1,3], [1,4], ...

test/test_maregrams.jl

@@ -2,6 +2,6 @@
 
 	println("	MAREGRAMS")
 
-	maregrams(list=true);
+	maregrams(list="Portugal");
 	maregrams(-25, 36);
 end