Skip to main content

performance tuning - Speeding up Import and Export in CSV format


I am handling large numerical data in Mathematica. In smaller problems everything worked fine using Export and Import with the parameter csv and nothing more.


Now I am facing a much larger data volume and plain Export and Import is way too slow for CSV format.


What I want to do: First, exporting a numerical list of approximately $1400 \cdot 260$. Then I perform some calculations outside of mathematica and finally I import a csv file back using Import.



In this question I read how to improve the speed of Export with CSV.


I tried


Export["data.csv", 
ExportString[Transpose[temp], "CSV", "FieldSeparators" -> ", "],
"Table"];

for a toy-example of dimension $9 \cdot 6$. This could be


temp = RandomReal[{0, 1000}, {9, 6}];

The problem is that I got additional blank lines in my CSV file. How can I avoid those blank lines? I did not have them using plain Export.



Second part of the question: can I use a similar approach to speed up Import for CSV files?


I work in English locale in Windows 7 and Mathematica 8. My data should be comma-separated.


The result of the above looks like this:


155.9418457227914,427.72566448956945,462.4370455183139,434.230107096781,377.73423736605037,457.7044624877774,229.5721937681028,453.6973831247924,827.5146478718962

656.9573702857699,975.1048399942904,716.715190156526,67.07781324817643,168.78248854317894,863.1953962590844,997.7580107302701,427.94798294100747,565.2955778916687

192.3648037459477,435.0418975785194,126.17228368369842,772.0737083559297,453.73573640921836,957.9178360741387,920.4158275934401,234.75353158374764,162.82606110943834

841.7132070637356,799.1268178998612,931.2448706410551,950.7753472229233,114.01596316796622,145.0771999411104,287.47149951303663,786.9008107323455,99.09420650484662


116.9916885502289,715.7594598282562,970.6252946068753,654.1742185278038,262.3778046629968,200.13980161337577,347.24862854841354,314.5612015073982,241.11046402342163

203.65015448763597,952.1236458849723,578.2673369638862,527.2990305555661,655.1228742370724,318.81372163827496,311.2738362265584,315.97629887850667,514.7676854642548

EDIT: A small example of the data that I want to import (2nd step) can be found here. The true problem size is here.



Answer



Here's a much faster, purely Mathematica way than using Import to import your data:


UPDATE


As Leonid mentioned the previous code doesn't exactly replicate Import. The truth is I was only trying to retrieve the numerical part. Here's an updated version that tries to replicate the output from Import.



readYourCSV2[file_String?FileExistsQ, n_Integer] := Module[{str = OpenRead[file], data}, 
data = ReadList[str, Table[Record, {n}], RecordSeparators -> {",", "\n"}];
Close[str];
ReleaseHold[ToExpression[data, InputForm, Hold] /. {Plus[Times[x_, E | e], y_] :> x * 10 ^ y}]
]

Here, n is the number of columns.


UPDATE 2


Now for the Export, here's a fast, again, purely Mathematica way to export in CSV format.


writeYourCSV[file_String, list_List?MatrixQ] := 

With[{str = OpenWrite[file, PageWidth -> Infinity], len = Length[ list[[1]] ]},
Scan[Write[str, Sequence @@ (Flatten[Table[{FortranForm[ #[[i]] ], OutputForm[","]},
{i, len - 1}]]) ~ Join ~ { FortranForm[ #[[len]] ] }] &, list]; Close[str];
]

This takes less than 10 seconds to write your large data back to CSV format:


writeYourCSV["testcsv.csv", databig] // AbsoluteTiming


{9.921969, Null}




Comments

Popular posts from this blog

plotting - How to draw lines between specified dots on ListPlot?

I would like to create a plot where I have unconnected dots and some connected. So far, I have figured out how to draw the dots. My code is the following: ListPlot[{{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4,13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full] I have thought using ListLinePlot command, but I don't know how to specify to the command to draw only selected lines between the dots. Do have any suggestions/hints on how to do that? Thank you. Answer One possibility would be to use Epilog with Line : ListPlot[ {{1, 1}, {2, 2}, {3, 3}, {4, 4}, {1, 4}, {2, 5}, {3, 6}, {4, 7}, {1, 7}, {2, 8}, {3, 9}, {4, 10}, {1, 10}, {2, 11}, {3, 12}, {4, 13}, {2.5, 7}}, Ticks -> {{1, 2, 3, 4}, None}, AxesStyle -> Thin, TicksStyle -> Directive[Black, Bold, 12], Mesh -> Full, Epilog -> { Line[ ...

dynamic - How can I make a clickable ArrayPlot that returns input?

I would like to create a dynamic ArrayPlot so that the rectangles, when clicked, provide the input. Can I use ArrayPlot for this? Or is there something else I should have to use? Answer ArrayPlot is much more than just a simple array like Grid : it represents a ranged 2D dataset, and its visualization can be finetuned by options like DataReversed and DataRange . These features make it quite complicated to reproduce the same layout and order with Grid . Here I offer AnnotatedArrayPlot which comes in handy when your dataset is more than just a flat 2D array. The dynamic interface allows highlighting individual cells and possibly interacting with them. AnnotatedArrayPlot works the same way as ArrayPlot and accepts the same options plus Enabled , HighlightCoordinates , HighlightStyle and HighlightElementFunction . data = {{Missing["HasSomeMoreData"], GrayLevel[ 1], {RGBColor[0, 1, 1], RGBColor[0, 0, 1], GrayLevel[1]}, RGBColor[0, 1, 0]}, {GrayLevel[0], GrayLevel...

list manipulation - Selecting multiple columns from a matrix?

Sample data: data = { {{2013, 1, 1}, 24.13, 167.67, 231.82}, {{2013, 1, 2}, 32.15, 170.92, 225.99}, {{2013, 1, 3}, 35.43, 172.68, 221.67}, {{2013, 1, 4}, 36.73, 173.05, 218.32}, {{2013, 1, 5}, 58.19, 165.96, 197.05}, {{2013, 1, 6}, 69.99, 163.50, 187.52}, {{2013, 1, 7}, 71.37, 154.21, 175.58}, {{2013, 1, 8}, 72.51, 149.66, 163.25}}; I want a DateListPlot with three graphs, so for a matrix formed by columns 1 and 2, one for columns 1 and 3, and 1 for columns 1 and 4. At the moment I'm using this code: data2 = Transpose[{data[[All, 1]], data[[All, 2]]}]; data3 = Transpose[{data[[All, 1]], data[[All, 3]]}]; data4 = Transpose[{data[[All, 1]], data[[All, 4]]}]; DateListPlot[{data2, data3, data4}, Joined -> True, Filling -> {3 -> {1}}] but I have a hunch that this can be done more efficiently. I don't like the Transpose s in particular. Any ideas? edit (for extra credit) What if I need to multiply the second column by 2, which in my solution is simp...