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Today's Topics:
1. problem in write 3D array - allocation issue (Maicon Faria)
2. Re: problem in write 3D array - allocation issue (Calixte Denizet)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Sep 2012 16:59:59 -0300
From: Maicon Faria <maiconsaulfaria@gmail.com>
To: hdf-forum@hdfgroup.org
Subject: [Hdf-forum] problem in write 3D array - allocation issue
Message-ID:
<CAEbZ8ReGSfuHfGWB9=
7SxcB-4Vx79tN+ertDiUyejecjPEcb2A@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
I'm with a problem when I try to write 3D int array using HDF.
The problem happens when I use malloc to dynamically allocate the 3D int
array, the hdf5 file shows wrong numbers.
When I allocate 3D int arrays with: *int data[NX][NY][NZ]* all goes fine.
I try to print on screen all data with printf and I got correct answers.
I would appreciate some advices
Here is the source code:
*/* *
* * This example writes data to the HDF5 file.*
* * Data conversion is performed during write operation. *
* */*
* *
*#include<hdf5.h>*
*#include <stdio.h>*
*#include <stdlib.h>*
*
*
*#define FILE "SDS16.h5"*
*#define DATASETNAME "IntArray" *
*#define NX 5 /* dataset dimensions */*
*#define NY 5*
*#define NZ 5*
*#define RANK 3*
*
*
*int*** allocate3D(int l,int m,int n);*
*void deallocate3D(int*** arr3D,int l,int m);*
*
*
*
*
*int main (void)*
*{*
* hid_t file, dataset; /* file and dataset handles */*
* hid_t datatype, dataspace; /* handles */*
* hsize_t dimsf[3]; /* dataset dimensions */*
* herr_t status; *
* int i,j,k;*
*// int data[NX][NY][NZ];*
* int*** data; /* data to write */*
* *
*
*
* //Data and output buffer initialization. *
* data = allocate3D(NX,NY,NZ);*
*
*
* /**
* * Create a new file using H5F_ACC_TRUNC access,*
* * default file creation properties, and default file*
* * access properties.*
* */*
* file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);*
* /**
* * Describe the size of the array and create the data space for fixed*
* * size dataset. *
* */*
* dimsf[0] = NX;*
* dimsf[1] = NY;*
* dimsf[2] = NZ;*
* dataspace = H5Screate_simple(RANK, dimsf, NULL); *
* *
* //Define datatype for the data in the file. We will store little
endian INT numbers.*
* datatype = H5Tcopy(H5T_NATIVE_INT);*
* status = H5Tset_order(datatype, H5T_ORDER_LE);*
*
*
* /*Create a new dataset within the file using defined dataspace and*
* * datatype and default dataset creation properties.*/*
* *
* dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);*
* //Write the data to the dataset using default transfer properties.*
*
*
* *
* for (k = 0; k < NZ; k++) *
* {*
* for (j = 0; j < NY; j++) *
* {*
* for (i = 0; i < NX; i++)*
* {*
* data[i][j][k] = k;//campo[i*j*NX];*
* }*
* }*
* }*
* *
* *
* status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);*
* *
* deallocate3D(data,NX,NY);*
* *
* *
* //Close/release resources.*
* *
* H5Sclose(dataspace);*
* H5Tclose(datatype);*
* H5Dclose(dataset);*
* H5Fclose(file);*
* *
* return 0;*
*}*
*
*
*
*
*//allocate a 3D array*
*int ***allocate3D(int l,int m,int n)*
*{*
*int ***arr3D;*
*int i,j,k;*
*
*
*arr3D = (int***)malloc(l * sizeof(int **));*
*
*
*for(i=0;i<l;i++)*
*{*
* arr3D[i] = (int**)malloc(m * sizeof(int*));*
* for(j=0;j<m;j++)*
* {*
* arr3D[i][j] = (int*)malloc(n*sizeof(int));*
* }*
*}*
*
*
*return arr3D;*
*}*
*
*
*//deallocate a 3D array*
*void deallocate3D(int*** arr3D,int l,int m)*
*{*
* int i,j;*
*
*
* for(i=0;i<l;i++)*
* {*
* for(j=0;j<m;j++)*
* {*
* free(arr3D[i][j]);*
* }*
* free(arr3D[i]);*
* }*
* free(arr3D);*
*} *
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Message: 2
Date: Sat, 29 Sep 2012 17:30:12 +0200
From: Calixte Denizet <calixte.denizet@scilab-enterprises.com>
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] problem in write 3D array - allocation issue
Message-ID: <50671404.3020203@scilab-enterprises.com>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi,
you must allocate an int array with size NX*NY*NZ and to access the
element i,j,k, just use:
data[i + NX*j + NX*NY*k].
Best regards
Calixte
On 28/09/2012 21:59, Maicon Faria wrote:
> I'm with a problem when I try to write 3D int array using HDF.
> The problem happens when I use malloc to dynamically allocate the 3D
> int array, the hdf5 file shows wrong numbers.
> When I allocate 3D int arrays with: /int data[NX][NY][NZ]/ all goes
fine.
>
> I try to print on screen all data with printf and I got correct answers.
>
> I would appreciate some advices
>
> Here is the source code:
>
>
> //* /
> / * This example writes data to the HDF5 file./
> / * Data conversion is performed during write operation. /
> / *//
> //
> /#include<hdf5.h>/
> /#include <stdio.h>/
> /#include <stdlib.h>/
> /
> /
> /#define FILE "SDS16.h5"/
> /#define DATASETNAME "IntArray" /
> /#define NX 5 /* dataset dimensions *//
> /#define NY 5/
> /#define NZ 5/
> /#define RANK 3/
> /
> /
> /int*** allocate3D(int l,int m,int n);/
> /void deallocate3D(int*** arr3D,int l,int m);/
> /
> /
> /
> /
> /int main (void)/
> /{/
> / hid_t file, dataset; /* file and dataset handles *//
> / hid_t datatype, dataspace; /* handles *//
> / hsize_t dimsf[3]; /* dataset dimensions *//
> / herr_t status; /
> / int i,j,k;/
> /// int data[NX][NY][NZ];/
> / int*** data; /* data to write *//
> //
> /
> /
> / //Data and output buffer initialization. /
> / data = allocate3D(NX,NY,NZ);/
> /
> /
> / /*/
> / * Create a new file using H5F_ACC_TRUNC access,/
> / * default file creation properties, and default file/
> / * access properties./
> / *//
> / file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);/
> / /*/
> / * Describe the size of the array and create the data space for
> fixed/
> / * size dataset. /
> / *//
> / dimsf[0] = NX;/
> / dimsf[1] = NY;/
> / dimsf[2] = NZ;/
> / dataspace = H5Screate_simple(RANK, dimsf, NULL); /
> //
> / //Define datatype for the data in the file. We will store little
> endian INT numbers./
> / datatype = H5Tcopy(H5T_NATIVE_INT);/
> / status = H5Tset_order(datatype, H5T_ORDER_LE);/
> /
> /
> / /*Create a new dataset within the file using defined dataspace and/
> / * datatype and default dataset creation properties.*//
> //
> / dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
> H5P_DEFAULT);/
> / //Write the data to the dataset using default transfer properties./
> /
> /
> //
> / for (k = 0; k < NZ; k++) /
> / {/
> / for (j = 0; j < NY; j++) /
> /{/
> /for (i = 0; i < NX; i++)/
> / {/
> / data[i][j][k] = k;//campo[i*j*NX];/
> / }/
> /}/
> / }/
> //
> //
> / status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
> H5P_DEFAULT, data);/
> //
> / deallocate3D(data,NX,NY);/
> //
> //
> / //Close/release resources./
> //
> / H5Sclose(dataspace);/
> / H5Tclose(datatype);/
> / H5Dclose(dataset);/
> / H5Fclose(file);/
> //
> / return 0;/
> /}/
> /
> /
> /
> /
> ///allocate a 3D array/
> /int ***allocate3D(int l,int m,int n)/
> /{/
> /int ***arr3D;/
> /int i,j,k;/
> /
> /
> /arr3D = (int***)malloc(l * sizeof(int **));/
> /
> /
> /for(i=0;i<l;i++)/
> /{/
> / arr3D[i] = (int**)malloc(m * sizeof(int*));/
> / for(j=0;j<m;j++)/
> / {/
> / arr3D[i][j] = (int*)malloc(n*sizeof(int));/
> / }/
> /}/
> /
> /
> /return arr3D;/
> /}/
> /
> /
> ///deallocate a 3D array/
> /void deallocate3D(int*** arr3D,int l,int m)/
> /{/
> / int i,j;/
> /
> /
> / for(i=0;i<l;i++)/
> / {/
> / for(j=0;j<m;j++)/
> / {/
> / free(arr3D[i][j]);/
> / }/
> / free(arr3D[i]);/
> / }/
> / free(arr3D);/
> /} /
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
--
Calixte Denizet
Software Development Engineer
-----------------------------------------------------------
Scilab Enterprises
143bis rue Yves Le Coz - 78000 Versailles, France
http://www.scilab-enterprises.com
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