https://github.com/JuliaLang/julia
Tip revision: a865ca2777a883d4d67a77e71e5aa3ed59fe8f6d authored by Jeff Bezanson on 15 August 2014, 03:12:32 UTC
more scheme portability fixes
more scheme portability fixes
Tip revision: a865ca2
datafmt.jl
## file formats ##
module DataFmt
importall Base
import Base: _default_delims
export countlines, readdlm, readcsv, writedlm, writecsv
const invalid_dlm = char(0xfffffffe)
const offs_chunk_size = 5000
countlines(nameorfile) = countlines(nameorfile, '\n')
function countlines(filename::String, eol::Char)
open(filename) do io
countlines(io, eol)
end
end
function countlines(io::IO, eol::Char)
if !isascii(eol)
error("only ASCII line terminators are supported")
end
a = Array(Uint8, 8192)
nl = 0
preceded_by_eol = true
while !eof(io)
nb = readbytes!(io, a)
for i=1:nb
if a[i] == eol
preceded_by_eol = true
elseif preceded_by_eol
preceded_by_eol = false
nl+=1
end
end
end
nl
end
readdlm(input, T::Type; opts...) = readdlm(input, invalid_dlm, T, '\n'; opts...)
readdlm(input, dlm::Char, T::Type; opts...) = readdlm(input, dlm, T, '\n'; opts...)
readdlm(input; opts...) = readdlm(input, invalid_dlm, '\n'; opts...)
readdlm(input, dlm::Char; opts...) = readdlm(input, dlm, '\n'; opts...)
readdlm(input, dlm::Char, eol::Char; opts...) = readdlm_auto(input, dlm, Float64, eol, true; opts...)
readdlm(input, dlm::Char, T::Type, eol::Char; opts...) = readdlm_auto(input, dlm, T, eol, false; opts...)
function readdlm_auto(input, dlm::Char, T::Type, eol::Char, auto::Bool; opts...)
optsd = val_opts(opts)
use_mmap = get(optsd, :use_mmap, @windows ? false : true)
isa(input, String) && (fsz = filesize(input); input = use_mmap && (fsz > 0) && fsz < typemax(Int) ? as_mmap(input,fsz) : readall(input))
sinp = isa(input, Vector{Uint8}) ? ccall(:jl_array_to_string, ByteString, (Array{Uint8,1},), input) :
isa(input, IO) ? readall(input) :
input
readdlm_string(sinp, dlm, T, eol, auto, optsd)
end
function as_mmap(fname::String, fsz::Int64)
open(fname) do io
mmap_array(Uint8, (int(fsz),), io)
end
end
function ascii_if_possible(sbuff::String)
isa(sbuff, ASCIIString) && return sbuff
asci = true
d = sbuff.data
for idx in 1:length(d)
(d[idx] < 0x80) ? continue : (asci = false; break)
end
asci ? ASCIIString(sbuff.data) : sbuff
end
#
# Handlers act on events generated by the parser.
# Parser calls store_cell on the handler to pass events.
#
# DLMOffsets: Keep offsets (when result dimensions are not known)
# DLMStore: Store values directly into a result store (when result dimensions are known)
abstract DLMHandler
type DLMOffsets <: DLMHandler
oarr::Vector{Vector{Int}}
offidx::Int
thresh::Int
bufflen::Int
function DLMOffsets(sbuff::String)
offsets = Array(Array{Int,1}, 1)
offsets[1] = Array(Int, offs_chunk_size)
thresh = int(Base.Sys.total_memory() / sizeof(Int) / 5)
new(offsets, 1, thresh, length(sbuff.data))
end
end
function store_cell(dlmoffsets::DLMOffsets, row::Int, col::Int, quoted::Bool, startpos::Int, endpos::Int)
offidx = dlmoffsets.offidx
(offidx == 0) && return # offset collection stopped to avoid choking on memory
oarr = dlmoffsets.oarr
offsets = oarr[end]
if length(offsets) < offidx
offlen = offs_chunk_size * length(oarr)
if (offlen + offs_chunk_size) > dlmoffsets.thresh
est_tot = int(offlen * dlmoffsets.bufflen / endpos)
if (est_tot - offlen) > offs_chunk_size # allow another chunk
# abandon offset collection
dlmoffsets.oarr = Vector{Int}[]
dlmoffsets.offidx = 0
return
end
end
offsets = Array(Int, offs_chunk_size)
push!(oarr, offsets)
offidx = 1
end
offsets[offidx] = row
offsets[offidx+1] = col
offsets[offidx+2] = int(quoted)
offsets[offidx+3] = startpos
offsets[offidx+4] = endpos
dlmoffsets.offidx = offidx + 5
nothing
end
function result(dlmoffsets::DLMOffsets)
trimsz = (dlmoffsets.offidx-1)%offs_chunk_size
((trimsz > 0) || (dlmoffsets.offidx == 1)) && resize!(dlmoffsets.oarr[end], trimsz)
dlmoffsets.oarr
end
type DLMStore{T,S<:String} <: DLMHandler
hdr::Array{String, 2}
data::Array{T, 2}
nrows::Int
ncols::Int
lastrow::Int
lastcol::Int
hdr_offset::Int
sbuff::S
auto::Bool
eol::Char
tmp64::Array{Float64,1}
end
function DLMStore{T,S<:String}(::Type{T}, dims::NTuple{2,Integer}, has_header::Bool, sbuff::S, auto::Bool, eol::Char)
(nrows,ncols) = dims
((nrows == 0) || (ncols == 0)) && error("Empty input")
((nrows < 0) || (ncols < 0)) && error("Invalid dimensions")
hdr_offset = has_header ? 1 : 0
DLMStore{T,S}(fill(SubString(sbuff,1,0), 1, ncols), Array(T, nrows-hdr_offset, ncols), nrows, ncols, 1, 0, hdr_offset, sbuff, auto, eol, Array(Float64,1))
end
function store_cell{T,S<:String}(dlmstore::DLMStore{T,S}, row::Int, col::Int, quoted::Bool, startpos::Int, endpos::Int)
drow = row - dlmstore.hdr_offset
ncols = dlmstore.ncols
lastcol = dlmstore.lastcol
lastrow = dlmstore.lastrow
cells::Array{T,2} = dlmstore.data
sbuff::S = dlmstore.sbuff
tmp64 = dlmstore.tmp64
endpos = prevind(sbuff, nextind(sbuff,endpos))
(endpos > 0) && ('\n' == dlmstore.eol) && ('\r' == sbuff[endpos]) && (endpos = prevind(sbuff, endpos))
sval = quoted ? SubString(sbuff, startpos+1, endpos-1) : SubString(sbuff, startpos, endpos)
if drow > 0
# fill missing elements
while ((drow - lastrow) > 1) || ((drow > lastrow) && (lastcol < ncols))
(lastcol == ncols) && (lastcol = 0)
for cidx in (lastcol+1):ncols
if (T <: String) || (T == Any)
cells[lastrow,cidx] = SubString(sbuff, 1, 0)
elseif ((T <: Number) || (T <: Char)) && dlmstore.auto
throw(TypeError(:store_cell, "", Any, T))
else
error("missing value at row $lastrow column $cidx")
end
end
lastcol = ncols
lastrow += 1
end
# fill data
if quoted && ('"' in sval)
fail = colval(replace(sval, r"\"\"", "\""), cells, drow, col, tmp64)
else
fail = colval(sval, cells, drow, col, tmp64)
end
if fail
((T <: Number) && dlmstore.auto) ? throw(TypeError(:store_cell, "", Any, T)) : error("file entry \"$(sval)\" cannot be converted to $T")
end
dlmstore.lastrow = drow
dlmstore.lastcol = col
else
# fill header
colval((quoted && ('"' in sval)) ? replace(sval, r"\"\"", "\"") : sval, dlmstore.hdr, 1, col, tmp64)
end
nothing
end
function result{T}(dlmstore::DLMStore{T})
nrows = dlmstore.nrows - dlmstore.hdr_offset
ncols = dlmstore.ncols
lastcol = dlmstore.lastcol
lastrow = dlmstore.lastrow
cells = dlmstore.data
sbuff = dlmstore.sbuff
if (lastcol < ncols) || (lastrow < nrows)
while lastrow <= nrows
(lastcol == ncols) && (lastcol = 0; lastrow += 1)
for cidx in (lastcol+1):ncols
if (T <: String) || (T == Any)
cells[lastrow,cidx] = SubString(sbuff, 1, 0)
elseif ((T <: Number) || (T <: Char)) && dlmstore.auto
throw(TypeError(:store_cell, "", Any, T))
else
error("missing value at row $lastrow column $cidx")
end
end
lastcol = ncols
(lastrow == nrows) && break
end
dlmstore.lastrow = lastrow
dlmstore.lastcol = ncols
end
(dlmstore.hdr_offset > 0) ? (dlmstore.data, dlmstore.hdr) : dlmstore.data
end
function readdlm_string(sbuff::String, dlm::Char, T::Type, eol::Char, auto::Bool, optsd::Dict)
ign_empty = (dlm == invalid_dlm)
quotes = get(optsd, :quotes, true)
comments = get(optsd, :comments, true)
comment_char = get(optsd, :comment_char, '#')
dims = get(optsd, :dims, nothing)
has_header = get(optsd, :header, get(optsd, :has_header, false))
haskey(optsd, :has_header) && (optsd[:has_header] != has_header) && error("conflicting values for header and has_header")
skipstart = get(optsd, :skipstart, 0)
(skipstart >= 0) || error("invalid value for skipstart")
offset_handler = (dims == nothing) ? DLMOffsets(sbuff) : DLMStore(T, dims, has_header, sbuff, auto, eol)
for retry in 1:2
try
dims = dlm_parse(sbuff, eol, dlm, '"', comment_char, ign_empty, quotes, comments, skipstart, offset_handler)
break
catch ex
if isa(ex, TypeError) && (ex.func == :store_cell)
T = ex.expected
elseif get(optsd, :ignore_invalid_chars, false)
sbuff = ascii_if_possible(convert(typeof(sbuff), sbuff.data, ""))
else
rethrow(ex)
end
offset_handler = (dims == nothing) ? DLMOffsets(sbuff) : DLMStore(T, dims, has_header, sbuff, auto, eol)
end
end
isa(offset_handler, DLMStore) && (return result(offset_handler))
offsets = result(offset_handler)
!isempty(offsets) && (return dlm_fill(T, offsets, dims, has_header, sbuff, auto, eol))
optsd[:dims] = dims
return readdlm_string(sbuff, dlm, T, eol, auto, optsd)
end
const valid_opts = [:header, :has_header, :ignore_invalid_chars, :use_mmap, :quotes, :comments, :dims, :comment_char, :skipstart]
const valid_opt_types = [Bool, Bool, Bool, Bool, Bool, Bool, NTuple{2,Integer}, Char, Integer]
const deprecated_opts = [ :has_header => :header ]
function val_opts(opts)
d = Dict{Symbol,Union(Bool,NTuple{2,Integer},Char,Integer)}()
for (opt_name, opt_val) in opts
!in(opt_name, valid_opts) && error("unknown option $opt_name")
opt_typ = valid_opt_types[findfirst(valid_opts, opt_name)]
!isa(opt_val, opt_typ) && error("$opt_name should be of type $opt_typ")
d[opt_name] = opt_val
haskey(deprecated_opts, opt_name) && warn("$opt_name is deprecated, use $(deprecated_opts[opt_name]) instead")
end
d
end
function dlm_fill(T::DataType, offarr::Vector{Vector{Int}}, dims::NTuple{2,Integer}, has_header::Bool, sbuff::String, auto::Bool, eol::Char)
idx = 1
offidx = 1
offsets = offarr[1]
try
dh = DLMStore(T, dims, has_header, sbuff, auto, eol)
while idx <= length(offsets)
row = offsets[idx]
col = offsets[idx+1]
quoted = bool(offsets[idx+2])
startpos = offsets[idx+3]
endpos = offsets[idx+4]
((idx += 5) > offs_chunk_size) && (offidx < length(offarr)) && (idx = 1; offsets = offarr[offidx += 1])
store_cell(dh, row, col, quoted, startpos, endpos)
end
return result(dh)
catch ex
isa(ex, TypeError) && (ex.func == :store_cell) && (return dlm_fill(ex.expected, offarr, dims, has_header, sbuff, auto, eol))
rethrow(ex)
end
end
colval{T<:Bool, S<:String}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((sval=="true") && (cells[row,col]=true; return false); (sval=="false") && (cells[row,col]=false; return false); true)
colval{T<:Number, S<:String}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = (float64_isvalid(sval, tmp64) ? ((cells[row,col] = tmp64[1]); false) : true)
colval{T<:String, S<:String}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((cells[row,col] = sval); false)
colval{S<:String}(sval::S, cells::Array{Any,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((cells[row,col] = float64_isvalid(sval, tmp64) ? tmp64[1] : sval); false)
colval{T<:Char, S<:String}(sval::S, cells::Array{T,2}, row::Int, col::Int, tmp64::Array{Float64,1}) = ((length(sval) == 1) ? ((cells[row,col] = next(sval,1)[1]); false) : true)
colval{S<:String}(sval::S, cells::Array, row::Int, col::Int, tmp64::Array{Float64,1}) = true
dlm_parse(s::ASCIIString, eol::Char, dlm::Char, qchar::Char, cchar::Char, ign_adj_dlm::Bool, allow_quote::Bool, allow_comments::Bool, skipstart::Int, dh::DLMHandler) =
dlm_parse(s.data, uint8(eol), uint8(dlm), uint8(qchar), uint8(cchar), ign_adj_dlm, allow_quote, allow_comments, skipstart, dh)
function dlm_parse{T,D}(dbuff::T, eol::D, dlm::D, qchar::D, cchar::D, ign_adj_dlm::Bool, allow_quote::Bool, allow_comments::Bool, skipstart::Int, dh::DLMHandler)
all_ascii = (D <: Uint8) || (isascii(eol) && isascii(dlm) && (!allow_quote || isascii(qchar)) && (!allow_comments || isascii(cchar)))
(T <: UTF8String) && all_ascii && (return dlm_parse(dbuff.data, uint8(eol), uint8(dlm), uint8(qchar), uint8(cchar), ign_adj_dlm, allow_quote, allow_comments, skipstart, dh))
ncols = nrows = col = 0
is_default_dlm = (dlm == convert(D, invalid_dlm))
error_str = ""
# 0: begin field, 1: quoted field, 2: unquoted field, 3: second quote (could either be end of field or escape character), 4: comment, 5: skipstart
state = (skipstart > 0) ? 5 : 0
is_eol = is_dlm = is_cr = is_quote = is_comment = expct_col = false
idx = 1
try
slen = sizeof(dbuff)
col_start_idx = 1
was_cr = false
while idx <= slen
val,idx = next(dbuff, idx)
if (is_eol = (val == eol))
is_dlm = is_comment = is_cr = is_quote = false
elseif (is_dlm = (is_default_dlm ? in(val, _default_delims) : (val == dlm)))
is_comment = is_cr = is_quote = false
elseif (is_quote = (val == qchar))
is_comment = is_cr = false
elseif (is_comment = (val == cchar))
is_cr = false
else
is_cr = (eol == '\n') && (val == '\r')
end
if 2 == state # unquoted field
if is_dlm
state = 0
col += 1
store_cell(dh, nrows+1, col, false, col_start_idx, idx-2)
col_start_idx = idx
!ign_adj_dlm && (expct_col = true)
elseif is_eol
nrows += 1
col += 1
store_cell(dh, nrows, col, false, col_start_idx, idx - (was_cr ? 3 : 2))
col_start_idx = idx
ncols = max(ncols, col)
col = 0
state = 0
elseif (is_comment && allow_comments)
nrows += 1
col += 1
store_cell(dh, nrows, col, false, col_start_idx, idx - 2)
ncols = max(ncols, col)
col = 0
state = 4
end
elseif 1 == state # quoted field
is_quote && (state = 3)
elseif 4 == state # comment line
if is_eol
col_start_idx = idx
state = 0
end
elseif 0 == state # begin field
if is_quote
state = (allow_quote && !was_cr) ? 1 : 2
expct_col = false
elseif is_dlm
if !ign_adj_dlm
expct_col = true
col += 1
store_cell(dh, nrows+1, col, false, col_start_idx, idx-2)
end
col_start_idx = idx
elseif is_eol
nrows += 1
if expct_col
col += 1
store_cell(dh, nrows, col, false, col_start_idx, idx - (was_cr ? 3 : 2))
end
col_start_idx = idx
ncols = max(ncols, col)
col = 0
expct_col = false
elseif is_comment && allow_comments
if col > 0
nrows += 1
if expct_col
col += 1
store_cell(dh, nrows, col, false, col_start_idx, idx - 2)
end
ncols = max(ncols, col)
col = 0
end
expct_col = false
state = 4
elseif !is_cr
state = 2
expct_col = false
end
elseif 3 == state # second quote
if is_quote && !was_cr
state = 1
elseif is_dlm && !was_cr
state = 0
col += 1
store_cell(dh, nrows+1, col, true, col_start_idx, idx-2)
col_start_idx = idx
!ign_adj_dlm && (expct_col = true)
elseif is_eol
nrows += 1
col += 1
store_cell(dh, nrows, col, true, col_start_idx, idx - (was_cr ? 3 : 2))
col_start_idx = idx
ncols = max(ncols, col)
col = 0
state = 0
elseif is_comment && allow_comments && !was_cr
nrows += 1
col += 1
store_cell(dh, nrows, col, true, col_start_idx, idx - 2)
ncols = max(ncols, col)
col = 0
state = 4
elseif (is_cr && was_cr) || !is_cr
error_str = escape_string("unexpected character '$(char(val))' after quoted field at row $(nrows+1) column $(col+1)")
break
end
elseif 5 == state # skip start
if is_eol
col_start_idx = idx
skipstart -= 1
(0 == skipstart) && (state = 0)
end
end
was_cr = is_cr
end
if isempty(error_str)
if 1 == state # quoted field
error_str = "truncated column at row $(nrows+1) column $(col+1)"
elseif (2 == state) || (3 == state) || ((0 == state) && is_dlm) # unquoted field, second quote, or begin field with last character as delimiter
col += 1
nrows += 1
store_cell(dh, nrows, col, (3 == state), col_start_idx, idx-1)
ncols = max(ncols, col)
end
end
catch ex
if isa(ex, TypeError) && (ex.func == :store_cell)
rethrow(ex)
else
error("at row $(nrows+1), column $col : $ex)")
end
end
!isempty(error_str) && error(error_str)
return (nrows, ncols)
end
readcsv(io; opts...) = readdlm(io, ','; opts...)
readcsv(io, T::Type; opts...) = readdlm(io, ',', T; opts...)
# todo: keyword argument for # of digits to print
writedlm_cell(io::IO, elt::FloatingPoint, dlm, quotes) = print_shortest(io, elt)
function writedlm_cell{T}(io::IO, elt::String, dlm::T, quotes::Bool)
if quotes && !isempty(elt) && (('"' in elt) || ('\n' in elt) || ((T <: Char) ? (dlm in elt) : contains(elt, dlm)))
print(io, '"', replace(elt, r"\"", "\"\""), '"')
else
print(io, elt)
end
end
writedlm_cell(io::IO, elt, dlm, quotes) = print(io, elt)
function writedlm(io::IO, a::AbstractVecOrMat, dlm; opts...)
optsd = val_opts(opts)
quotes = get(optsd, :quotes, true)
pb = PipeBuffer()
nr = size(a,1)
nc = size(a,2)
for i = 1:nr
for j = 1:nc
writedlm_cell(pb, a[i,j], dlm, quotes)
j == nc ? write(pb,'\n') : print(pb,dlm)
end
(nb_available(pb) > (16*1024)) && write(io, takebuf_array(pb))
end
write(io, takebuf_array(pb))
nothing
end
writedlm{T}(io::IO, a::AbstractArray{T,0}, dlm; opts...) = writedlm(io, reshape(a,1), dlm; opts...)
function writedlm(io::IO, a::AbstractArray, dlm; opts...)
tail = size(a)[3:end]
function print_slice(idxs...)
writedlm(io, sub(a, 1:size(a,1), 1:size(a,2), idxs...), dlm; opts...)
if idxs != tail
print(io, "\n")
end
end
cartesianmap(print_slice, tail)
end
function writedlm(io::IO, itr, dlm; opts...)
optsd = val_opts(opts)
quotes = get(optsd, :quotes, true)
pb = PipeBuffer()
for row in itr
state = start(row)
while !done(row, state)
(x, state) = next(row, state)
writedlm_cell(pb, x, dlm, quotes)
done(row, state) ? write(pb,'\n') : print(pb,dlm)
end
(nb_available(pb) > (16*1024)) && write(io, takebuf_array(pb))
end
write(io, takebuf_array(pb))
nothing
end
function writedlm(fname::String, a, dlm; opts...)
open(fname, "w") do io
writedlm(io, a, dlm; opts...)
end
end
writedlm(io, a; opts...) = writedlm(io, a, '\t'; opts...)
writecsv(io, a; opts...) = writedlm(io, a, ','; opts...)
writemime(io::IO, ::MIME"text/csv", a::AbstractVecOrMat) = writedlm(io, a, ',')
writemime(io::IO, ::MIME"text/tab-separated-values", a::AbstractVecOrMat) = writedlm(io, a, '\t')
end # module DataFmt