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
  4.353533 seconds (44.69 M allocations: 1.127 GiB, 3.58% gc time, 68.03% compilation time)
Serialization
  0.183549 seconds (225.03 k allocations: 10.915 MiB, 31.33% compilation time)
JDF.jl
  0.406490 seconds (68.17 k allocations: 147.974 MiB, 71.33% gc time, 13.83% compilation time)
JLSO.jl
  1.066876 seconds (285.29 k allocations: 20.920 MiB, 6.59% compilation time)
Arrow.jl
  3.994454 seconds (5.44 M allocations: 276.181 MiB, 0.93% gc time, 97.64% compilation time)
JSONTables.jl arraytable
 11.474020 seconds (229.62 M allocations: 5.422 GiB, 15.78% gc time, 0.08% compilation time)
JSONTables.jl objecttable
  0.526300 seconds (95.82 k allocations: 309.046 MiB, 50.23% gc time, 15.23% compilation time)
Second run
CSV.jl
  1.471065 seconds (44.40 M allocations: 1.113 GiB, 8.79% gc time)
Serialization
  0.147182 seconds (15.01 k allocations: 401.070 KiB, 6.70% compilation time)
JDF.jl
  0.098852 seconds (35.13 k allocations: 146.243 MiB, 12.92% gc time)
JLSO.jl
  0.969784 seconds (33.10 k allocations: 7.949 MiB, 0.18% gc time)
Arrow.jl
  0.099803 seconds (81.35 k allocations: 5.427 MiB)
JSONTables.jl arraytable
 11.784715 seconds (229.62 M allocations: 5.422 GiB, 15.59% gc time, 0.08% compilation time)
JSONTables.jl objecttable
  0.237829 seconds (20.71 k allocations: 305.232 MiB, 9.21% gc time, 4.84% compilation time)
0.237994466
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/49a0eefcb56dc21933894eecfd78d1bb05deafaa7357803a1d698a6cc1fb2391.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.arrow1742842
2bigdf.bin5198341
3bigdf.jdf5221546
4bigdf1.csv55086460
5bigdf2.json55090461
6bigdf1.json124031568
@df df plot(:file, :size / 1024^2, seriestype=:bar, title="Format File Size (MB)", label="Size", ylab="MB")
_images/0c6c7bd25b6506ea66119818707324dd8fad7d9a7b2417a3344b7083f7185d8d.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
  3.646664 seconds (4.28 M allocations: 227.519 MiB, 0.79% gc time, 124.86% compilation time)
Serialization
  0.412577 seconds (9.50 M allocations: 155.504 MiB, 9.76% gc time, 10.48% compilation time)
JDF.jl
  0.228015 seconds (158.14 k allocations: 157.892 MiB, 9.57% gc time, 94.61% compilation time)
JLSO.jl
  0.359031 seconds (9.52 M allocations: 158.179 MiB, 5.90% gc time, 8.99% compilation time)
Arrow.jl
  0.522957 seconds (549.90 k allocations: 26.355 MiB, 98.48% compilation time)
  0.049789 seconds (14.50 k allocations: 10.266 MiB)
JSONTables.jl arraytable
  6.284399 seconds (271.09 k allocations: 1.839 GiB, 10.74% gc time)
JSONTables.jl objecttable
  0.342706 seconds (7.44 k allocations: 403.812 MiB, 3.24% gc time, 0.02% compilation time)
Second run
  0.980560 seconds (631.43 k allocations: 43.591 MiB)
Serialization
  0.346492 seconds (9.48 M allocations: 154.596 MiB, 6.57% gc time)
JDF.jl
  0.055103 seconds (77.27 k allocations: 153.763 MiB, 12.46% gc time)
JLSO.jl
  0.323772 seconds (9.50 M allocations: 157.307 MiB, 2.75% gc time)
Arrow.jl
  0.006769 seconds (86.57 k allocations: 3.732 MiB)
  0.055049 seconds (14.50 k allocations: 10.266 MiB, 9.34% gc time)
JSONTables.jl arraytable
  6.249196 seconds (271.09 k allocations: 1.839 GiB, 10.66% gc time)
JSONTables.jl objecttable
  0.329991 seconds (7.08 k allocations: 403.796 MiB, 1.29% 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/e89d201684ac4d048a34a509b9b693070ebb0c56a8c86d0774a388b5cb9c42ef.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
1310888386910851058519153683221021018835297984838448851079884686857279957846537789381051010891534103964149466105
29318196510522226810493332110103365865164181053555410758887687879176565110910993881721102753467310765124110107482
31010646106288108771410108785310417101099877596887234811813188673382256310972645987993105661061016104106255898771111
451026721039617538479371978231055107664125335595642432107793462479497379261078599676105262254477331374284813
51394161095159321586381071013101374293846784669710451031021046101581177106137148247334181726910147910410669101056687
6226743535877341656412410124822109610485104615587237995676478491109369101616161064493101012104333487891023291163
78363118221910639561011011537110986512768868106941051296467191731043101372542661263737493171219259761210558481
864221035926108225765372108174591010135751864110910918912635485388214251042415143521192191110429751072395961491
9761019611110491944475591043101667465103510543582443655889310811049221103105194572101593433268869939539224295924
106110351551012594883910110893101041184887883291286163342155967818911094714451097997491052911076435710587499857710

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
1310888386910851058519153683221021018835297984838448851079884686857279957846537789381051010891534103964149466105
29318196510522226810493332110103365865164181053555410758887687879176565110910993881721102753467310765124110107482
31010646106288108771410108785310417101099877596887234811813188673382256310972645987993105661061016104106255898771111
451026721039617538479371978231055107664125335595642432107793462479497379261078599676105262254477331374284813
51394161095159321586381071013101374293846784669710451031021046101581177106137148247334181726910147910410669101056687
6226743535877341656412410124822109610485104615587237995676478491109369101616161064493101012104333487891023291163
78363118221910639561011011537110986512768868106941051296467191731043101372542661263737493171219259761210558481
864221035926108225765372108174591010135751864110910918912635485388214251042415143521192191110429751072395961491
9761019611110491944475591043101667465103510543582443655889310811049221103105194572101593433268869939539224295924
106110351551012594883910110893101041184887883291286163342155967818911094714451097997491052911076435710587499857710
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
18655
21624
31551
df2 = DataFrame(rand(1:10, 3, 4), :auto)
3×4 DataFrame
Rowx1x2x3x4
Int64Int64Int64Int64
12977
28738
32345

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
18655
21624
31551
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
12977
28738
32345
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.