H5D: HDF5 Dataset Interface
In rhdf5: R Interface to HDF5
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
These functions create and manipulate dataset objects, and set and retrieve their constant or persistent properties.
Usage
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H5Dcreate (h5loc, name, dtype_id, h5space, lcpl=NULL, dcpl=NULL, dapl=NULL)
H5Dopen (h5loc, name, dapl=NULL)
H5Dclose (h5dataset)
H5Dget_space (h5dataset)
H5Dget_type (h5dataset)
H5Dget_create_plist (h5dataset)
H5Dget_storage_size (h5dataset)
H5Dread (h5dataset, h5spaceFile = NULL, h5spaceMem = NULL,
buf = NULL, compoundAsDataFrame = TRUE,
bit64conversion, drop = FALSE)
H5Dwrite (h5dataset, buf, h5spaceMem = NULL, h5spaceFile = NULL)
H5Dset_extent (h5dataset, size)
Arguments
h5loc
An object of class H5IdComponent representing a H5 location identifier (file or group). See H5Fcreate, H5Fopen, H5Gcreate, H5Gopen to create an object of this kind.
name
Name of the dataset (character).
dtype_id
A character name of a datatype. See h5const("H5T") for possible datatypes. Can also be an integer representing an HDF5 datatype.
h5space
An object of class H5IdComponent representing a H5 dataspace. See H5Dget_space, H5Screate_simple, H5Screate to create an object of this kind.
h5dataset
An object of class H5IdComponent representing a H5 dataset. See H5Dcreate, H5Dopen to create an object of this kind.
h5spaceFile,h5spaceMem
An object of class H5IdComponent representing a H5 dataspace. See H5Dget_space, H5Screate_simple, H5Screate to create an object of this kind. The dimensions of the dataset in the file and in memory. The dimensions in file and in memory are interpreted in an R-like manner. The first dimension is the fastest changing dimension. When reading the file with a C-program (e.g. HDFView) the order of dimensions will invert, because in C the fastest changing dimension is the last one.
buf
Reading and writing buffer containing the data to written/read. When using the buffer for reading, the buffer size has to fit the size of the memory space h5spaceMem. No extra memory will be allocated for the data. A pointer to the same data is returned.
compoundAsDataFrame
If true, a compound datatype will be coerced to a data.frame. This is not possible, if the dataset is multi-dimensional. Otherwise the compound datatype will be returned as a list. Nested compound data types will be returned as a nested list.
bit64conversion
Defines, how 64-bit integers are converted. Internally, R does not support 64-bit integers. All integers in R are 32-bit integers. By setting bit64conversion='int', a coercing to 32-bit integers is enforced, with the risc of data loss, but with the insurance that numbers are represented as integers. bit64conversion='double' coerces the 64-bit integers to floating point numbers. doubles can represent integers with up to 54-bits, but they are not represented as integer values anymore. For larger numbers there is again a data loss. bit64conversion='bit64' is recommended way of coercing. It represents the 64-bit integers as objects of class 'integer64' as defined in the package 'bit64'. Make sure that you have installed 'bit64'. The datatype 'integer64' is not part of base R, but defined in an external package. This can produce unexpected behaviour when working with the data.
drop
(logical) If TRUE, the HDF5 object is read as a vector with NULL dim attributes.
size
An integer vector with the new dimension of the dataset. Calling this function is only valid for chunked datasets.
lcpl
An object of class H5IdComponent representing a H5 link creation property list. See H5Pcreate, H5Pcopy to create an object of this kind.
dcpl
An object of class H5IdComponent representing a H5 dataset creation property list. See H5Pcreate, H5Pcopy to create an object of this kind.
dapl
An object of class H5IdComponent representing a H5 dataset access property list. See H5Pcreate, H5Pcopy to create an object of this kind.
Details
Interface to the HDF5 C-library libhdf5. See https://portal.hdfgroup.org/display/HDF5/Datasets for further details.
Value
H5Dcreate and H5Dopen return an object of class H5IdComponent represinting a H5 dataset identifier.
H5Dget_space returns an object of class H5IdComponent representing a H5 dataspace identifier.
H5Dread returns an array with the read data.
The other functions return the standard return value from their respective C-functions.
Author(s)
Bernd Fischer
References
https://portal.hdfgroup.org/display/HDF5
See Also
rhdf5
Examples
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# write a dataset
fid <- H5Fcreate("ex_H5D.h5")
fid
sid <- H5Screate_simple(c(10,5,3))
sid
did <- H5Dcreate(fid, "A", "H5T_STD_I32LE", sid)
did
H5Dwrite(did, 1L:150L, h5spaceMem = sid, h5spaceFile = sid)
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# read a dataset
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
B <- H5Dread(did)
B
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# write a subarray
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
H5Sselect_index(sid, list(1:3,2:4,2))
sidmem <- H5Screate_simple(c(3,3,1))
sidmem
A = array(-801:-809,dim=c(3,3,1))
H5Dwrite(did, A, h5spaceMem = sidmem, h5spaceFile = sid)
H5Dread(did)
H5Sclose(sid)
H5Dclose(did)
H5Sclose(sidmem)
H5Fclose(fid)
Example output
HDF5 FILE
name /
filename
[1] name otype dclass dim
<0 rows> (or 0-length row.names)
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 FILE
name /
filename
name otype dclass dim
0 A H5I_DATASET INTEGER 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
[3,] 3 13 23 33 43
[4,] 4 14 24 34 44
[5,] 5 15 25 35 45
[6,] 6 16 26 36 46
[7,] 7 17 27 37 47
[8,] 8 18 28 38 48
[9,] 9 19 29 39 49
[10,] 10 20 30 40 50
, , 2
[,1] [,2] [,3] [,4] [,5]
[1,] 51 61 71 81 91
[2,] 52 62 72 82 92
[3,] 53 63 73 83 93
[4,] 54 64 74 84 94
[5,] 55 65 75 85 95
[6,] 56 66 76 86 96
[7,] 57 67 77 87 97
[8,] 58 68 78 88 98
[9,] 59 69 79 89 99
[10,] 60 70 80 90 100
, , 3
[,1] [,2] [,3] [,4] [,5]
[1,] 101 111 121 131 141
[2,] 102 112 122 132 142
[3,] 103 113 123 133 143
[4,] 104 114 124 134 144
[5,] 105 115 125 135 145
[6,] 106 116 126 136 146
[7,] 107 117 127 137 147
[8,] 108 118 128 138 148
[9,] 109 119 129 139 149
[10,] 110 120 130 140 150
HDF5 FILE
name /
filename
name otype dclass dim
0 A H5I_DATASET INTEGER 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 3 x 3 x 1
maxsize 3 x 3 x 1
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
[3,] 3 13 23 33 43
[4,] 4 14 24 34 44
[5,] 5 15 25 35 45
[6,] 6 16 26 36 46
[7,] 7 17 27 37 47
[8,] 8 18 28 38 48
[9,] 9 19 29 39 49
[10,] 10 20 30 40 50
, , 2
[,1] [,2] [,3] [,4] [,5]
[1,] 51 -801 -804 -807 91
[2,] 52 -802 -805 -808 92
[3,] 53 -803 -806 -809 93
[4,] 54 64 74 84 94
[5,] 55 65 75 85 95
[6,] 56 66 76 86 96
[7,] 57 67 77 87 97
[8,] 58 68 78 88 98
[9,] 59 69 79 89 99
[10,] 60 70 80 90 100
, , 3
[,1] [,2] [,3] [,4] [,5]
[1,] 101 111 121 131 141
[2,] 102 112 122 132 142
[3,] 103 113 123 133 143
[4,] 104 114 124 134 144
[5,] 105 115 125 135 145
[6,] 106 116 126 136 146
[7,] 107 117 127 137 147
[8,] 108 118 128 138 148
[9,] 109 119 129 139 149
[10,] 110 120 130 140 150
rhdf5 documentation built on Nov. 8, 2020, 6:56 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
These functions create and manipulate dataset objects, and set and retrieve their constant or persistent properties.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 | H5Dcreate (h5loc, name, dtype_id, h5space, lcpl=NULL, dcpl=NULL, dapl=NULL)
H5Dopen (h5loc, name, dapl=NULL)
H5Dclose (h5dataset)
H5Dget_space (h5dataset)
H5Dget_type (h5dataset)
H5Dget_create_plist (h5dataset)
H5Dget_storage_size (h5dataset)
H5Dread (h5dataset, h5spaceFile = NULL, h5spaceMem = NULL,
buf = NULL, compoundAsDataFrame = TRUE,
bit64conversion, drop = FALSE)
H5Dwrite (h5dataset, buf, h5spaceMem = NULL, h5spaceFile = NULL)
H5Dset_extent (h5dataset, size)
|
Arguments
h5loc |
An object of class |
name |
Name of the dataset (character). |
dtype_id |
A character name of a datatype. See |
h5space |
An object of class |
h5dataset |
An object of class |
h5spaceFile,h5spaceMem |
An object of class |
buf |
Reading and writing buffer containing the data to written/read. When using the buffer for reading, the buffer size has to fit the size of the memory space |
compoundAsDataFrame |
If true, a compound datatype will be coerced to a data.frame. This is not possible, if the dataset is multi-dimensional. Otherwise the compound datatype will be returned as a list. Nested compound data types will be returned as a nested list. |
bit64conversion |
Defines, how 64-bit integers are converted. Internally, R does not support 64-bit integers. All integers in R are 32-bit integers. By setting bit64conversion='int', a coercing to 32-bit integers is enforced, with the risc of data loss, but with the insurance that numbers are represented as integers. bit64conversion='double' coerces the 64-bit integers to floating point numbers. doubles can represent integers with up to 54-bits, but they are not represented as integer values anymore. For larger numbers there is again a data loss. bit64conversion='bit64' is recommended way of coercing. It represents the 64-bit integers as objects of class 'integer64' as defined in the package 'bit64'. Make sure that you have installed 'bit64'. The datatype 'integer64' is not part of base R, but defined in an external package. This can produce unexpected behaviour when working with the data. |
drop |
(logical) If TRUE, the HDF5 object is read as a vector with NULL dim attributes. |
size |
An integer vector with the new dimension of the dataset. Calling this function is only valid for chunked datasets. |
lcpl |
An object of class |
dcpl |
An object of class |
dapl |
An object of class |
Details
Interface to the HDF5 C-library libhdf5. See https://portal.hdfgroup.org/display/HDF5/Datasets for further details.
Value
H5Dcreate and H5Dopen return an object of class H5IdComponent represinting a H5 dataset identifier.
H5Dget_space returns an object of class H5IdComponent representing a H5 dataspace identifier.
H5Dread returns an array with the read data.
The other functions return the standard return value from their respective C-functions.
Author(s)
Bernd Fischer
References
https://portal.hdfgroup.org/display/HDF5
See Also
rhdf5
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | # write a dataset
fid <- H5Fcreate("ex_H5D.h5")
fid
sid <- H5Screate_simple(c(10,5,3))
sid
did <- H5Dcreate(fid, "A", "H5T_STD_I32LE", sid)
did
H5Dwrite(did, 1L:150L, h5spaceMem = sid, h5spaceFile = sid)
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# read a dataset
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
B <- H5Dread(did)
B
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# write a subarray
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
H5Sselect_index(sid, list(1:3,2:4,2))
sidmem <- H5Screate_simple(c(3,3,1))
sidmem
A = array(-801:-809,dim=c(3,3,1))
H5Dwrite(did, A, h5spaceMem = sidmem, h5spaceFile = sid)
H5Dread(did)
H5Sclose(sid)
H5Dclose(did)
H5Sclose(sidmem)
H5Fclose(fid)
|
Example output
HDF5 FILE
name /
filename
[1] name otype dclass dim
<0 rows> (or 0-length row.names)
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 FILE
name /
filename
name otype dclass dim
0 A H5I_DATASET INTEGER 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
[3,] 3 13 23 33 43
[4,] 4 14 24 34 44
[5,] 5 15 25 35 45
[6,] 6 16 26 36 46
[7,] 7 17 27 37 47
[8,] 8 18 28 38 48
[9,] 9 19 29 39 49
[10,] 10 20 30 40 50
, , 2
[,1] [,2] [,3] [,4] [,5]
[1,] 51 61 71 81 91
[2,] 52 62 72 82 92
[3,] 53 63 73 83 93
[4,] 54 64 74 84 94
[5,] 55 65 75 85 95
[6,] 56 66 76 86 96
[7,] 57 67 77 87 97
[8,] 58 68 78 88 98
[9,] 59 69 79 89 99
[10,] 60 70 80 90 100
, , 3
[,1] [,2] [,3] [,4] [,5]
[1,] 101 111 121 131 141
[2,] 102 112 122 132 142
[3,] 103 113 123 133 143
[4,] 104 114 124 134 144
[5,] 105 115 125 135 145
[6,] 106 116 126 136 146
[7,] 107 117 127 137 147
[8,] 108 118 128 138 148
[9,] 109 119 129 139 149
[10,] 110 120 130 140 150
HDF5 FILE
name /
filename
name otype dclass dim
0 A H5I_DATASET INTEGER 10 x 5 x 3
HDF5 DATASET
name /A
filename
type H5T_STD_I32LE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 10 x 5 x 3
maxsize 10 x 5 x 3
HDF5 DATASPACE
rank 3
size 3 x 3 x 1
maxsize 3 x 3 x 1
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1 11 21 31 41
[2,] 2 12 22 32 42
[3,] 3 13 23 33 43
[4,] 4 14 24 34 44
[5,] 5 15 25 35 45
[6,] 6 16 26 36 46
[7,] 7 17 27 37 47
[8,] 8 18 28 38 48
[9,] 9 19 29 39 49
[10,] 10 20 30 40 50
, , 2
[,1] [,2] [,3] [,4] [,5]
[1,] 51 -801 -804 -807 91
[2,] 52 -802 -805 -808 92
[3,] 53 -803 -806 -809 93
[4,] 54 64 74 84 94
[5,] 55 65 75 85 95
[6,] 56 66 76 86 96
[7,] 57 67 77 87 97
[8,] 58 68 78 88 98
[9,] 59 69 79 89 99
[10,] 60 70 80 90 100
, , 3
[,1] [,2] [,3] [,4] [,5]
[1,] 101 111 121 131 141
[2,] 102 112 122 132 142
[3,] 103 113 123 133 143
[4,] 104 114 124 134 144
[5,] 105 115 125 135 145
[6,] 106 116 126 136 146
[7,] 107 117 127 137 147
[8,] 108 118 128 138 148
[9,] 109 119 129 139 149
[10,] 110 120 130 140 150
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