Load and save DataFrames#

We do not cover all features of the packages. Please refer to their documentation to learn them.

Here we’ll load CSV.jl to read and write CSV files and Arrow.jl, JLSO.jl, and serialization, which allow us to work with a binary format and JSONTables.jl for JSON interaction. Finally we consider a custom JDF.jl format.

using DataFrames
using Arrow
using CSV
using Serialization
using JLSO
using JSONTables
using CodecZlib
using ZipFile
using JDF
using StatsPlots ## for charts
using Mmap ## for compression

Let’s create a simple DataFrame for testing purposes,

x = DataFrame(
    A=[true, false, true], B=[1, 2, missing],
    C=[missing, "b", "c"], D=['a', missing, 'c']
)
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc

and use eltypes to look at the columnwise types.

eltype.(eachcol(x))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, Char}

CSV.jl#

Let’s use CSV to save x to disk; make sure x1.csv does not conflict with some file in your working directory.

CSV.write("x1.csv", x)
"x1.csv"

Now we can see how it was saved by reading x.csv.

print(read("x1.csv", String))
A,B,C,D
true,1,,a
false,2,b,
true,,c,c

We can also load it back as a data frame

y = CSV.read("x1.csv", DataFrame)
3×4 DataFrame
RowABCD
BoolInt64?String1?String1?
1true1missinga
2false2bmissing
3truemissingcc

Note that when loading in a DataFrame from a CSV the column type for columns :C :D have changed to use special strings defined in the InlineStrings.jl package.

eltype.(eachcol(y))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, InlineStrings.String1}
 Union{Missing, InlineStrings.String1}

Serialization by JDF.jl and JLSO.jl#

Now we use serialization to save x.

There are two ways to perform serialization. The first way is to use the Serialization.serialize as below:

Note that in general, this process will not work if the reading and writing are done by different versions of Julia, or an instance of Julia with a different system image.

open("x.bin", "w") do io
    serialize(io, x)
end

Now we load back the saved file to y variable. Again y is identical to x. However, please beware that if you session does not have DataFrames.jl loaded, then it may not recognize the content as DataFrames.jl

y = open(deserialize, "x.bin")
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc
eltype.(eachcol(y))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, Char}

JDF.jl#

JDF.jl is a relatively new package designed to serialize DataFrames. You can save a DataFrame with the savejdf function. For more details about design assumptions and limitations of JDF.jl please check out xiaodaigh/JDF.jl.

JDF.save("x.jdf", x);

To load the saved JDF file, one can use the loadjdf function

x_loaded = JDF.load("x.jdf") |> DataFrame
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc

You can see that they are the same

isequal(x_loaded, x)
true

JDF.jl offers the ability to load only certain columns from disk to help with working with large files. set up a JDFFile which is a on disk representation of x backed by JDF.jl

x_ondisk = jdf"x.jdf"
JDF.JDFFile{String}("x.jdf")

We can see all the names of x without loading it into memory

names(x_ondisk)
4-element Vector{Symbol}:
 :A
 :B
 :C
 :D

The below is an example of how to load only columns :A and :D

xd = JDF.load(x_ondisk; cols=["A", "D"]) |> DataFrame
3×2 DataFrame
RowAD
BoolChar?
1truea
2falsemissing
3truec

JLSO.jl#

Another way to perform serialization is by using the JLSO.jl library:

JLSO.save("x.jlso", :data => x)

Now we can load back the file to y

y = JLSO.load("x.jlso")[:data]
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc
eltype.(eachcol(y))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, Char}

JSONTables.jl#

Often you might need to read and write data stored in JSON format. JSONTables.jl provides a way to process them in row-oriented or column-oriented layout. We present both options below.

open(io -> arraytable(io, x), "x1.json", "w")
106
open(io -> objecttable(io, x), "x2.json", "w")
76
print(read("x1.json", String))
[{"A":true,"B":1,"C":null,"D":"a"},{"A":false,"B":2,"C":"b","D":null},{"A":true,"B":null,"C":"c","D":"c"}]
print(read("x2.json", String))
{"A":[true,false,true],"B":[1,2,null],"C":[null,"b","c"],"D":["a",null,"c"]}
y1 = open(jsontable, "x1.json") |> DataFrame
3×4 DataFrame
RowABCD
BoolInt64?String?String?
1true1missinga
2false2bmissing
3truemissingcc
eltype.(eachcol(y1))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, String}
y2 = open(jsontable, "x2.json") |> DataFrame
3×4 DataFrame
RowABCD
BoolInt64?String?String?
1true1missinga
2false2bmissing
3truemissingcc
eltype.(eachcol(y2))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, String}

Arrow.jl#

Finally we use Apache Arrow format that allows, in particular, for data interchange with R or Python.

Arrow.write("x.arrow", x)
"x.arrow"
y = Arrow.Table("x.arrow") |> DataFrame
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc
eltype.(eachcol(y))
4-element Vector{Type}:
 Bool
 Union{Missing, Int64}
 Union{Missing, String}
 Union{Missing, Char}

Note that columns of y are immutable

try
    y.A[1] = false
catch e
    show(e)
end
ReadOnlyMemoryError()

This is because Arrow.Table uses memory mapping and thus uses a custom vector types:

y.A
3-element Arrow.BoolVector{Bool}:
 1
 0
 1
y.B
3-element Arrow.Primitive{Union{Missing, Int64}, Vector{Int64}}:
 1
 2
  missing

You can get standard Julia Base vectors by copying a data frame

y2 = copy(y)
3×4 DataFrame
RowABCD
BoolInt64?String?Char?
1true1missinga
2false2bmissing
3truemissingcc
y2.A
3-element Vector{Bool}:
 1
 0
 1
y2.B
3-element Vector{Union{Missing, Int64}}:
 1
 2
  missing

Basic benchmarking#

Next, we’ll create some files, so be careful that you don’t already have these files in your working directory! In particular, we’ll time how long it takes us to write a DataFrame with 1000 rows and 100000 columns.

bigdf = DataFrame(rand(Bool, 10^4, 1000), :auto)

bigdf[!, 1] = Int.(bigdf[!, 1])
bigdf[!, 2] = bigdf[!, 2] .+ 0.5
bigdf[!, 3] = string.(bigdf[!, 3], ", as string")

println("First run")
First run
println("CSV.jl")
csvwrite1 = @elapsed @time CSV.write("bigdf1.csv", bigdf)
println("Serialization")
serializewrite1 = @elapsed @time open(io -> serialize(io, bigdf), "bigdf.bin", "w")
println("JDF.jl")
jdfwrite1 = @elapsed @time JDF.save("bigdf.jdf", bigdf)
println("JLSO.jl")
jlsowrite1 = @elapsed @time JLSO.save("bigdf.jlso", :data => bigdf)
println("Arrow.jl")
arrowwrite1 = @elapsed @time Arrow.write("bigdf.arrow", bigdf)
println("JSONTables.jl arraytable")
jsontablesawrite1 = @elapsed @time open(io -> arraytable(io, bigdf), "bigdf1.json", "w")
println("JSONTables.jl objecttable")
jsontablesowrite1 = @elapsed @time open(io -> objecttable(io, bigdf), "bigdf2.json", "w")
println("Second run")
println("CSV.jl")
csvwrite2 = @elapsed @time CSV.write("bigdf1.csv", bigdf)
println("Serialization")
serializewrite2 = @elapsed @time open(io -> serialize(io, bigdf), "bigdf.bin", "w")
println("JDF.jl")
jdfwrite2 = @elapsed @time JDF.save("bigdf.jdf", bigdf)
println("JLSO.jl")
jlsowrite2 = @elapsed @time JLSO.save("bigdf.jlso", :data => bigdf)
println("Arrow.jl")
arrowwrite2 = @elapsed @time Arrow.write("bigdf.arrow", bigdf)
println("JSONTables.jl arraytable")
jsontablesawrite2 = @elapsed @time open(io -> arraytable(io, bigdf), "bigdf1.json", "w")
println("JSONTables.jl objecttable")
jsontablesowrite2 = @elapsed @time open(io -> objecttable(io, bigdf), "bigdf2.json", "w")
CSV.jl
  4.754439 seconds (44.69 M allocations: 1.127 GiB, 8.71% gc time, 64.78% compilation time)
Serialization
  0.185811 seconds (225.03 k allocations: 10.889 MiB, 31.49% compilation time)
JDF.jl
  0.139200 seconds (68.17 k allocations: 147.978 MiB, 19.55% gc time, 52.59% compilation time)
JLSO.jl
  1.039520 seconds (285.29 k allocations: 20.921 MiB, 6.88% compilation time)
Arrow.jl
  3.990405 seconds (5.45 M allocations: 276.260 MiB, 1.02% gc time, 97.10% compilation time)
JSONTables.jl arraytable
 11.973144 seconds (229.62 M allocations: 5.422 GiB, 17.09% gc time, 0.09% compilation time)
JSONTables.jl objecttable
  0.529385 seconds (95.82 k allocations: 309.045 MiB, 50.43% gc time, 16.25% compilation time)
Second run
CSV.jl
  1.493173 seconds (44.40 M allocations: 1.113 GiB, 8.79% gc time)
Serialization
  0.138710 seconds (15.01 k allocations: 401.070 KiB, 7.23% compilation time)
JDF.jl
  0.103308 seconds (35.13 k allocations: 146.246 MiB, 14.39% gc time)
JLSO.jl
  0.968727 seconds (33.10 k allocations: 7.951 MiB)
Arrow.jl
  0.099581 seconds (81.35 k allocations: 5.427 MiB)
JSONTables.jl arraytable
 11.833154 seconds (229.62 M allocations: 5.422 GiB, 15.36% gc time, 0.08% compilation time)
JSONTables.jl objecttable
  0.462064 seconds (20.71 k allocations: 305.233 MiB, 56.01% gc time, 2.19% compilation time)
0.462258087
groupedbar(
    repeat(["CSV.jl", "Serialization", "JDF.jl", "JLSO.jl", "Arrow.jl", "JSONTables.jl\nobjecttable"],
        inner=2),
    [csvwrite1, csvwrite2, serializewrite1, serializewrite1, jdfwrite1, jdfwrite2,
        jlsowrite1, jlsowrite2, arrowwrite1, arrowwrite2, jsontablesowrite2, jsontablesowrite2],
    group=repeat(["1st", "2nd"], outer=6),
    ylab="Second",
    title="Write Performance\nDataFrame: bigdf\nSize: $(size(bigdf))"
)
_images/5bd9d19bd11405b6d2a4982d511ee81629cedf6059ed0e6fbb801ff9a3d39a29.png
data_files = ["bigdf1.csv", "bigdf.bin", "bigdf.arrow", "bigdf1.json", "bigdf2.json"]
df = DataFrame(file=data_files, size=getfield.(stat.(data_files), :size))
append!(df, DataFrame(file="bigdf.jdf", size=reduce((x, y) -> x + y.size,
    stat.(joinpath.("bigdf.jdf", readdir("bigdf.jdf"))),
    init=0)))
sort!(df, :size)
6×2 DataFrame
Rowfilesize
StringInt64
1bigdf.arrow1742818
2bigdf.bin5201549
3bigdf.jdf5219601
4bigdf1.csv55084069
5bigdf2.json55088070
6bigdf1.json124029177
@df df plot(:file, :size / 1024^2, seriestype=:bar, title="Format File Size (MB)", label="Size", ylab="MB")
_images/d214e5026d4f2fd8c274482c84e421accf6c9d036516c90c3043c3f8f7cac33e.png
println("First run")
println("CSV.jl")
csvread1 = @elapsed @time CSV.read("bigdf1.csv", DataFrame)
println("Serialization")
serializeread1 = @elapsed @time open(deserialize, "bigdf.bin")
println("JDF.jl")
jdfread1 = @elapsed @time JDF.load("bigdf.jdf") |> DataFrame
println("JLSO.jl")
jlsoread1 = @elapsed @time JLSO.load("bigdf.jlso")
println("Arrow.jl")
arrowread1 = @elapsed @time df_tmp = Arrow.Table("bigdf.arrow") |> DataFrame
arrowread1copy = @elapsed @time copy(df_tmp)
println("JSONTables.jl arraytable")
jsontablesaread1 = @elapsed @time open(jsontable, "bigdf1.json")
println("JSONTables.jl objecttable")
jsontablesoread1 = @elapsed @time open(jsontable, "bigdf2.json")
println("Second run")
csvread2 = @elapsed @time CSV.read("bigdf1.csv", DataFrame)
println("Serialization")
serializeread2 = @elapsed @time open(deserialize, "bigdf.bin")
println("JDF.jl")
jdfread2 = @elapsed @time JDF.load("bigdf.jdf") |> DataFrame
println("JLSO.jl")
jlsoread2 = @elapsed @time JLSO.load("bigdf.jlso")
println("Arrow.jl")
arrowread2 = @elapsed @time df_tmp = Arrow.Table("bigdf.arrow") |> DataFrame
arrowread2copy = @elapsed @time copy(df_tmp)
println("JSONTables.jl arraytable")
jsontablesaread2 = @elapsed @time open(jsontable, "bigdf1.json")
println("JSONTables.jl objecttable")
jsontablesoread2 = @elapsed @time open(jsontable, "bigdf2.json");
First run
CSV.jl
  3.555968 seconds (4.29 M allocations: 227.794 MiB, 0.74% gc time, 123.88% compilation time)
Serialization
  0.436118 seconds (9.50 M allocations: 155.504 MiB, 8.33% gc time, 9.88% compilation time)
JDF.jl
  0.209458 seconds (158.15 k allocations: 157.899 MiB, 8.71% gc time, 84.55% compilation time)
JLSO.jl
  0.345232 seconds (9.52 M allocations: 158.183 MiB, 6.33% gc time, 8.86% compilation time)
Arrow.jl
  0.508166 seconds (549.91 k allocations: 26.400 MiB, 98.46% compilation time)
  0.049459 seconds (14.50 k allocations: 10.266 MiB)
JSONTables.jl arraytable
  6.263697 seconds (271.09 k allocations: 1.839 GiB, 10.43% gc time)
JSONTables.jl objecttable
  0.342288 seconds (7.44 k allocations: 403.808 MiB, 3.80% gc time, 0.02% compilation time)
Second run
  0.876441 seconds (631.49 k allocations: 43.592 MiB)
Serialization
  0.377509 seconds (9.48 M allocations: 154.596 MiB, 4.59% gc time)
JDF.jl
  0.368520 seconds (77.27 k allocations: 153.766 MiB, 86.12% gc time)
JLSO.jl
  0.331665 seconds (9.50 M allocations: 157.306 MiB, 4.20% gc time)
Arrow.jl
  0.006713 seconds (86.57 k allocations: 3.732 MiB)
  0.049687 seconds (14.50 k allocations: 10.266 MiB)
JSONTables.jl arraytable
  6.159747 seconds (271.09 k allocations: 1.839 GiB, 9.98% gc time)
JSONTables.jl objecttable
  0.328183 seconds (7.08 k allocations: 403.792 MiB, 0.99% gc time)

Exclude JSONTables due to much longer timing

groupedbar(
    repeat(["CSV.jl", "Serialization", "JDF.jl", "JLSO.jl", "Arrow.jl", "Arrow.jl\ncopy", ##"JSON\narraytable",
            "JSON\nobjecttable"], inner=2),
    [csvread1, csvread2, serializeread1, serializeread2, jdfread1, jdfread2, jlsoread1, jlsoread2,
        arrowread1, arrowread2, arrowread1 + arrowread1copy, arrowread2 + arrowread2copy,
        # jsontablesaread1, jsontablesaread2,
        jsontablesoread1, jsontablesoread2],
    group=repeat(["1st", "2nd"], outer=7),
    ylab="Second",
    title="Read Performance\nDataFrame: bigdf\nSize: $(size(bigdf))"
)
_images/9bf10199942486c152bb5e2c94e9bd83f0a59e70f602083ee0c63df4ba27f03c.png

Using gzip compression#

A common user requirement is to be able to load and save CSV that are compressed using gzip. Below we show how this can be accomplished using CodecZlib.jl. The same pattern is applicable to JSONTables.jl compression/decompression. Again make sure that you do not have file named df_compress_test.csv.gz in your working directory. We first generate a random data frame.

df = DataFrame(rand(1:10, 10, 1000), :auto)
10×1000 DataFrame
900 columns omitted
Rowx1x2x3x4x5x6x7x8x9x10x11x12x13x14x15x16x17x18x19x20x21x22x23x24x25x26x27x28x29x30x31x32x33x34x35x36x37x38x39x40x41x42x43x44x45x46x47x48x49x50x51x52x53x54x55x56x57x58x59x60x61x62x63x64x65x66x67x68x69x70x71x72x73x74x75x76x77x78x79x80x81x82x83x84x85x86x87x88x89x90x91x92x93x94x95x96x97x98x99x100
Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64
11054561028721446107187457759103810597236821068351710764316213482810869746104515872363321373127189725266255866
2810227598221634268345771910521616281074591545285105184112685825885744721662109621043888665711195101101862152
32452987694671051710910556379981091085384847687521341032109134469685172667786279710852583947434975239858105341
4233242102103102791099452865121010647101861536572510110732277926976271162109711025661328541367103104788464692710642
5104929237561057109168288285910288245104181810141044264610996101048510982510111172258891049388981087561924398369921
6925776748515961910510101086372355910521664327518681739616113827962639172141434371216259104521086102696172633
75310276876491714246538439593457911995112661593109491085851381131215210595851383158610488351047392351544717
89103310319581656101014410759699106102868632109761179447975191375103478910410428232821068871072571485510784723558510
94898935735105172867681987237610475781321988128108221012716102781964586191224589543731032154914541141835883
104582510275109618569597310109936253998235413854421348995164751113581111013106649786116711471891511326655597

GzipCompressorStream comes from CodecZlib

open("df_compress_test.csv.gz", "w") do io
    stream = GzipCompressorStream(io)
    CSV.write(stream, df)
    close(stream)
end
df2 = CSV.File(transcode(GzipDecompressor, Mmap.mmap("df_compress_test.csv.gz"))) |> DataFrame
10×1000 DataFrame
900 columns omitted
Rowx1x2x3x4x5x6x7x8x9x10x11x12x13x14x15x16x17x18x19x20x21x22x23x24x25x26x27x28x29x30x31x32x33x34x35x36x37x38x39x40x41x42x43x44x45x46x47x48x49x50x51x52x53x54x55x56x57x58x59x60x61x62x63x64x65x66x67x68x69x70x71x72x73x74x75x76x77x78x79x80x81x82x83x84x85x86x87x88x89x90x91x92x93x94x95x96x97x98x99x100
Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64Int64
11054561028721446107187457759103810597236821068351710764316213482810869746104515872363321373127189725266255866
2810227598221634268345771910521616281074591545285105184112685825885744721662109621043888665711195101101862152
32452987694671051710910556379981091085384847687521341032109134469685172667786279710852583947434975239858105341
4233242102103102791099452865121010647101861536572510110732277926976271162109711025661328541367103104788464692710642
5104929237561057109168288285910288245104181810141044264610996101048510982510111172258891049388981087561924398369921
6925776748515961910510101086372355910521664327518681739616113827962639172141434371216259104521086102696172633
75310276876491714246538439593457911995112661593109491085851381131215210595851383158610488351047392351544717
89103310319581656101014410759699106102868632109761179447975191375103478910410428232821068871072571485510784723558510
94898935735105172867681987237610475781321988128108221012716102781964586191224589543731032154914541141835883
104582510275109618569597310109936253998235413854421348995164751113581111013106649786116711471891511326655597
df == df2
true

Using zip files#

Sometimes you may have files compressed inside a zip file. In such a situation you may use ZipFile.jl in conjunction an an appropriate reader to read the files. Here we first create a ZIP file and then read back its contents into a DataFrame.

df1 = DataFrame(rand(1:10, 3, 4), :auto)
3×4 DataFrame
Rowx1x2x3x4
Int64Int64Int64Int64
141018
21888
32614
df2 = DataFrame(rand(1:10, 3, 4), :auto)
3×4 DataFrame
Rowx1x2x3x4
Int64Int64Int64Int64
15493
2101051
362610

And we show yet another way to write a DataFrame into a CSV file: Writing a CSV file into the zip file

w = ZipFile.Writer("x.zip")

f1 = ZipFile.addfile(w, "x1.csv")
write(f1, sprint(show, "text/csv", df1))

# write a second CSV file into zip file
f2 = ZipFile.addfile(w, "x2.csv", method=ZipFile.Deflate)
write(f2, sprint(show, "text/csv", df2))

close(w)

Now we read the compressed CSV file we have written:

z = ZipFile.Reader("x.zip");
# find the index index of file called x1.csv
index_xcsv = findfirst(x -> x.name == "x1.csv", z.files)
# to read the x1.csv file in the zip file
df1_2 = CSV.read(read(z.files[index_xcsv]), DataFrame)
3×4 DataFrame
Rowx1x2x3x4
Int64Int64Int64Int64
141018
21888
32614
df1_2 == df1
true
# find the index index of file called x2.csv
index_xcsv = findfirst(x -> x.name == "x2.csv", z.files)
# to read the x2.csv file in the zip file
df2_2 = CSV.read(read(z.files[index_xcsv]), DataFrame)
3×4 DataFrame
Rowx1x2x3x4
Int64Int64Int64Int64
15493
2101051
362610
df2_2 == df2
true

Note that once you read a given file from z object its stream is all used-up (reaching its end). Therefore to read it again you need to close the file object z and open it again. Also do not forget to close the zip file once you are done.

close(z)

Remove generated files

rm("x.arrow")
rm("x.bin")
rm("x.zip")
rm("x.jlso")
rm("x1.csv")
rm("x1.json")
rm("x2.json")
rm("x.jdf", recursive=true)
rm("bigdf.jdf", recursive=true)
rm("df_compress_test.csv.gz")
rm("bigdf1.json")
rm("bigdf1.csv")
rm("bigdf2.json")
rm("bigdf.jlso")
rm("bigdf.bin")
rm("bigdf.arrow")

This notebook was generated using Literate.jl.