npyio

npyio provides read/write access to numpy data files.

Installation

Is done via go get:

$> go get github.com/sbinet/npyio

Documentation

Is available on godoc

npyio-ls

npyio-ls is a command using github.com/sbinet/npyio (located under github.com/sbinet/npyio/cmd/npyio-ls) to display the content of a (list of) NumPy data file(s).

$> npyio-ls testdata/data_float64_2x3_?order.npy 
================================================================================
file: testdata/data_float64_2x3_corder.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<f8, Fortran:false, Shape:[2 3]}}
data = [0 1 2 3 4 5]

================================================================================
file: testdata/data_float64_2x3_forder.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<f8, Fortran:true, Shape:[2 3]}}
data = [0 1 2 3 4 5]

$> npyio-ls testdata/data_float64_2x3x4_corder.npy 
================================================================================
file: testdata/data_float64_2x3x4_corder.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<f8, Fortran:false, Shape:[2 3 4]}}
data = [0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23]

npyio-ls automatically detects .npz archive files and inspects them too:

$> npyio-ls testdata/data_float64_corder.npz 
================================================================================
file: testdata/data_float64_corder.npz
entry: arr1.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<f8, Fortran:false, Shape:[6 1]}}
data = [0 1 2 3 4 5]

entry: arr0.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<f8, Fortran:false, Shape:[2 3]}}
data = [0 1 2 3 4 5]

Example

Reading a .npy file

Consider a .npy file created with the following python code:

>>> import numpy as np
>>> arr = np.arange(6, dtype="float64").reshape(2,3)
>>> f = open("data.npy", "w")
>>> np.save(f, arr)
>>> f.close()

The (float64) data array can be loaded into a (float64) mat.Matrix by the following code:

package main

import (
	"fmt"
	"log"
	"os"

	"github.com/sbinet/npyio"
	"gonum.org/v1/gonum/mat"
)

func main() {
	f, err := os.Open(os.Args[1])
	if err != nil {
		log.Fatal(err)
	}
	defer f.Close()

	r, err := npyio.NewReader(f)
	if err != nil {
		log.Fatal(err)
	}

	fmt.Printf("npy-header: %v\n", r.Header)
	shape := r.Header.Descr.Shape
	raw := make([]float64, shape[0]*shape[1])

	err = r.Read(&raw)
	if err != nil {
		log.Fatal(err)
	}

	m := mat.NewDense(shape[0], shape[1], raw)
	fmt.Printf("data = %v\n", mat.Formatted(m, mat.Prefix("       ")))
}

$> my-binary data.npy
npy-header: Header{Major:1, Minor:0, Descr:{Type:<i8, Fortran:false, Shape:[2 3]}}
data = ⎡0  1  2⎤
       ⎣3  4  5⎦

Reading a .npy file with npyio.Read

Alternatively, one can use the convenience function npyio.Read:

package main

import (
	"fmt"
	"log"
	"os"

	"github.com/sbinet/npyio"
)

func main() {
	f, err := os.Open(os.Args[1])
	if err != nil {
		log.Fatal(err)
	}
	defer f.Close()

	var m []float64
	err = npyio.Read(f, &m)
	if err != nil {
		log.Fatal(err)
	}

	fmt.Printf("data = %v\n", m)
}

$> my-binary ./data.npy
data = [0 1 2 3 4 5]

Writing a .npy file with npyio.Write

package main

import (
	"log"
	"os"

	"github.com/sbinet/npyio"
)

func main() {
	f, err := os.Create("data.npy")
	if err != nil {
		log.Fatal(err)
	}
	defer f.Close()

	m := []float64{0, 1, 2, 3, 4, 5}
	err = npyio.Write(f, m)
	if err != nil {
		log.Fatalf("error writing to file: %v\n", err)
	}

	err = f.Close()
	if err != nil {
		log.Fatalf("error closing file: %v\n", err)
	}
}

loading a .npz or npy file

package main

import (
    "log"
    "os"
    "fmt"

    "github.com/sbinet/npyio"
    "gonum.org/v1/gonum/mat"
)

func main() {
    f, err := os.Open(os.Args[1])
    if err != nil {
        log.Fatal(err)
    }
    defer f.Close()
    npzData,npyData,err:= npyio.Load(f)
    if err != nil {
        log.Fatal(err)
    }
    if npyData!=nil {
        //npy file
        fmt.Printf("data = %v\n", npyData.Value)
        return
    }
    for fileName, data := range npzData {
        fmt.Printf("file = %s ", fileName)
        fmt.Printf("data = %v\n", data.Value)
    }
}

saving data to .npz file

package main

import (
    "log"
    "os"
    "fmt"

    "github.com/sbinet/npyio"
    "gonum.org/v1/gonum/mat"
)

func main() {
    f, err := os.Open(os.Args[1])
    if err != nil {
        log.Fatal(err)
    }
    defer f.Close()
    data := make(map[string]interface{})
    data["a"] = []float64{1,2,3,4,5,6}
    data["b"] = []float32{3,4,5,6,7}
    data["c"] = mat.NewDense(3,2,[]float64{1,3,5,7,9,11})
    err = npyio.SaveNPZ(f,data)
    if err != nil {
        log.Fatal(err)
    }
}