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Class wrapping the GDAL VSIVirtualHandle API for binary file I/O

Source: R/vsifile.R
VSIFile-class.Rd

VSIFile provides bindings to the GDAL VSIVirtualHandle API. Encapsulates a VSIVirtualHandle (https://gdal.org/api/cpl_cpp.html#_CPPv416VSIVirtualHandle). This API abstracts binary file I/O across "regular" file systems, URLs, cloud storage services, Zip/GZip/7z/RAR, and in-memory files. It provides analogs of several Standard C file I/O functions, allowing virtualization of disk I/O so that non-file data sources can be made to appear as files.

Arguments

filename

Character string containing the filename to open. It may be a file in a regular local filesystem, or a filename with a GDAL /vsiPREFIX/ (see https://gdal.org/user/virtual_file_systems.html).

access

Character string containing the access requested (i.e., "r", "r+", "w", "w+). Defaults to "r". Binary access is always implied and the "b" does not need to be included in access.

AccessExplanationIf file exists
"r"open file for readingread from start
"r+"open file for read/writeread from start
"w"create file for writingdestroy contents
"w+"create file for read/writedestroy contents
options

Optional character vector of NAME=VALUE pairs specifying filesystem-dependent options (GDAL >= 3.3, see Details).

Value

An object of class VSIFile which contains a pointer to a VSIVirtualHandle, and methods that operate on the file as described in Details. VSIFile is a C++ class exposed directly to R (via RCPP_EXPOSED_CLASS). Methods of the class are accessed using the $ operator.

Note

File offsets are given as R numeric (i.e., double type), optionally carrying the bit64::integer64 class attribute. They are returned as numeric with the integer64 class attribute attached. The integer64 type is signed, so the maximum file offset supported by this interface is 9223372036854775807 (the value of bit64::lim.integer64()[2]).

Some virtual file systems allow only sequential write, so no seeks or read operations are then allowed (e.g., AWS S3 files with /vsis3/). Starting with GDAL 3.2, a configuration option can be set with:

set_config_option("CPL_VSIL_USE_TEMP_FILE_FOR_RANDOM_WRITE", "YES")

in which case random-write access is possible (involves the creation of a temporary local file, whose location is controlled by the CPL_TMPDIR configuration option). In this case, setting access to "w+" may be needed for writing with seek and read operations (if creating a new file, otherwise, "r+" to open an existing file), while "w" access would allow sequential write only.

Usage (see Details)


## Constructors
vf <- new(VSIFile, filename)
# specifying access:
vf <- new(VSIFile, filename, access)
# specifying access and options (both required):
vf <- new(VSIFile, filename, access, options)

## Methods
vf$seek(offset, origin)
vf$tell()
vf$rewind()
vf$read(nbytes)
vf$write(object)
vf$eof()
vf$truncate(new_size)
vf$flush()
vf$ingest(max_size)

vf$close()
vf$open()
vf$get_filename()
vf$get_access()
vf$set_access(access)

Details

Constructors

new(VSIFile, filename)
Returns an object of class VSIFile, or an error is raised if a file handle cannot be obtained.

new(VSIFile, filename, access)
Alternate constructor for passing access as a character string (e.g., "r", "r+", "w", "w+"). Returns an object of class VSIFile with an open file handle, or an error is raised if a file handle cannot be obtained.

new(VSIFile, filename, access, options)
Alternate constructor for passing access as a character string, and options as a character vector of "NAME=VALUE" pairs (all arguments required, GDAL >= 3.3 required for options support).

The options argument is highly file system dependent. Supported options as of GDAL 3.9 include:

  • MIME headers such as Content-Type and Content-Encoding are supported for the /vsis3/, /vsigs/, /vsiaz/, /vsiadls/ file systems.

  • DISABLE_READDIR_ON_OPEN=YES/NO (GDAL >= 3.6) for /vsicurl/ and other network-based file systems. By default, directory file listing is done, unless YES is specified.

  • WRITE_THROUGH=YES (GDAL >= 3.8) for Windows regular files to set the FILE_FLAG_WRITE_THROUGH flag to the CreateFile() function. In that mode, the data are written to the system cache but are flushed to disk without delay.

Methods

$seek(offset, origin)
Seek to a requested offset in the file. offset is given as a positive numeric scalar, optionally as bit64::integer64 type. origin is given as a character string, one of SEEK_SET, SEEK_CUR or SEEK_END. Package global constants are defined for convenience, so these can be passed unquoted. Note that offset is an unsigned type, so SEEK_CUR can only be used for positive seek. If negative seek is needed, use:

vf$seek(vf$tell() + negative_offset, SEEK_SET)

Returns 0 on success or -1 on failure.

$tell()
Returns the current file read/write offset in bytes from the beginning of the file. The return value is a numeric scalar carrying the integer64 class attribute.

$rewind()
Rewind the file pointer to the beginning of the file. This is equivalent to vf$seek(0, SEEK_SET). No return value, called for that side effect.

$read(nbytes)
Read nbytes bytes from the file at the current offset. Returns a vector of R raw type, or NULL if the operation fails.

$write(object)
Write bytes to the file at the current offset. object is a raw vector. Returns the number of bytes successfully written, as numeric scalar carrying the integer64 class attribute. See also base R charToRaw() / rawToChar(), convert to or from raw vectors, and readBin() / writeBin() which read binary data from or write binary data to a raw vector.

$eof()
Test for end of file. Returns TRUE if an end-of-file condition occurred during the previous read operation. The end-of-file flag is cleared by a successful call to $seek().

$truncate(new_size)
Truncate/expand the file to the specified new_size, given as a positive numeric scalar, optionally as bit64::integer64 type. Returns 0 on success.

$flush()
Flush pending writes to disk. For files in write or update mode and on file system types where it is applicable, all pending output on the file is flushed to the physical disk. On Windows regular files, this method does nothing, unless the VSI_FLUSH=YES configuration option is set (and only when the file has not been opened with the WRITE_THROUGH option). Returns 0 on success or -1 on error.

$ingest(max_size)
Ingest a file into memory. Read the whole content of the file into a raw vector. max_size is the maximum size of file allowed, given as a numeric scalar, optionally as bit64::integer64 type. If no limit, set to a negative value. Returns a raw vector, or NULL if the operation fails.

$close()
Closes the file. The file should always be closed when I/O has been completed. Returns 0 on success or -1 on error.

$open()
This method can be used to re-open the file after it has been closed, using the same filename, and same options if any are set. The file will be opened using access as currently set. The $set_access() method can be called to change the requested access while the file is closed. No return value. An error is raised if a file handle cannot be obtained.

$get_filename()
Returns a character string containing the filename associated with this VSIFile object (the filename originally used to create the object).

$get_access()
Returns a character string containing the access as currently set on this VSIFile object.

$set_access(access)
Sets the requested read/write access on this VSIFile object, given as a character string (i.e., "r", "r+", "w", "w+"). The access can be changed only while the VSIFile object is closed, and will apply when it is re-opened with a call to $open(). Returns 0 on success or -1 on error.

See also

GDAL Virtual File Systems (compressed, network hosted, etc...):
/vsimem, /vsizip, /vsitar, /vsicurl, ...
https://gdal.org/user/virtual_file_systems.html

vsi_copy_file(), vsi_read_dir(), vsi_stat(), vsi_unlink()

Examples

# The examples make use of the FARSITE LCP format specification at:
# https://gdal.org/drivers/raster/lcp.html
# An LCP file is a raw format with a 7,316-byte header. The format
# specification gives byte offets and data types for fields in the header.

lcp_file <- system.file("extdata/storm_lake.lcp", package="gdalraster")

# identify a FARSITE v.4 LCP file
# function to check if the first three fields have valid data
# input is the first twelve raw bytes in the file
is_lcp <- function(bytes) {
  values <- readBin(bytes, "integer", n = 3)
  if ((values[1] == 20 || values[1] == 21) &&
      (values[2] == 20 || values[2] == 21) &&
      (values[3] >= -90 && values[3] <= 90)) {

    return(TRUE)
  } else {
    return(FALSE)
  }
}

vf <- new(VSIFile, lcp_file)
vf$read(12) |> is_lcp()
#> [1] TRUE

vf$tell()
#> integer64
#> [1] 12

# read the whole file into memory
bytes <- vf$ingest(-1)
vf$close()
#> [1] 0

# write to a VSI in-memory file
mem_file <- "/vsimem/storml_copy.lcp"
vf <- new(VSIFile, mem_file, "w")
vf$write(bytes)
#> integer64
#> [1] 252132

vf$tell()
#> integer64
#> [1] 252132
vf$rewind()
vf$tell()
#> integer64
#> [1] 0

vf$seek(0, SEEK_END)
#> [1] 0
(vf$tell() == vsi_stat(lcp_file, "size"))  # TRUE
#> [1] TRUE

vf$rewind()
vf$read(12) |> is_lcp()
#> [1] TRUE

# read/write an integer field
# write invalid data for the Latitude field and then set back
# save the original first
vf$seek(8, SEEK_SET)
#> [1] 0
lat_orig <- vf$read(4)
readBin(lat_orig, "integer")  # 46
#> [1] 46
# latitude -99 out of range
vf$seek(8, SEEK_SET)
#> [1] 0
writeBin(-99L, raw()) |> vf$write()
#> integer64
#> [1] 4
vf$rewind()
vf$read(12) |> is_lcp()  # FALSE
#> [1] FALSE
vf$seek(8, SEEK_SET)
#> [1] 0
vf$read(4) |> readBin("integer")  # -99
#> [1] -99
# set back to original
vf$seek(8, SEEK_SET)
#> [1] 0
vf$write(lat_orig)
#> integer64
#> [1] 4
vf$rewind()
vf$read(12) |> is_lcp()  # TRUE
#> [1] TRUE

# read a vector of doubles - xmax, xmin, ymax, ymin
# 327766.1, 323476.1, 5105082.0, 5101872.0
vf$seek(4172, SEEK_SET)
#> [1] 0
vf$read(32) |> readBin("double", n = 4)
#> [1]  327766.1  323476.1 5105082.0 5101872.0

# read a short int, the canopy cover units
vf$seek(4232, SEEK_SET)
#> [1] 0
vf$read(2) |> readBin("integer", size = 2)  # 1 = "percent"
#> [1] 1

# read the Description field
vf$seek(6804, SEEK_SET)
#> [1] 0
bytes <- vf$read(512)
rawToChar(bytes)
#> [1] "LCP file created by GDAL."

# edit the Description
desc <- paste(rawToChar(bytes),
              "Storm Lake AOI,",
              "Beaverhead-Deerlodge National Forest, Montana.")

vf$seek(6804, SEEK_SET)
#> [1] 0
charToRaw(desc) |> vf$write()
#> integer64
#> [1] 88
vf$close()
#> [1] 0

# verify the file as a raster dataset
ds <- new(GDALRaster, mem_file)
ds$info()
#> Driver: LCP/FARSITE v.4 Landscape File (.lcp)
#> Files: /vsimem/storml_copy.lcp
#> Size is 143, 107
#> Origin = (323476.071970863151364,5105081.983031376264989)
#> Pixel Size = (30.000000000000000,-30.000000000000000)
#> Metadata:
#>   DESCRIPTION=LCP file created by GDAL. Storm Lake AOI, Beaverhead-Deerlodge National Forest, Montana.
#>   LATITUDE=46
#>   LINEAR_UNIT=Meters
#> Corner Coordinates:
#> Upper Left  (  323476.072, 5105081.983) 
#> Lower Left  (  323476.072, 5101871.983) 
#> Upper Right (  327766.072, 5105081.983) 
#> Lower Right (  327766.072, 5101871.983) 
#> Center      (  325621.072, 5103476.983) 
#> Band 1 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Elevation
#>   Metadata:
#>     ELEVATION_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     ELEVATION_MAX=3046
#>     ELEVATION_MIN=-9999
#>     ELEVATION_NUM_CLASSES=-1
#>     ELEVATION_UNIT=0
#>     ELEVATION_UNIT_NAME=Meters
#> Band 2 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Slope
#>   Metadata:
#>     SLOPE_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     SLOPE_MAX=54
#>     SLOPE_MIN=-9999
#>     SLOPE_NUM_CLASSES=53
#>     SLOPE_UNIT=0
#>     SLOPE_UNIT_NAME=Degrees
#> Band 3 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Aspect
#>   Metadata:
#>     ASPECT_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     ASPECT_MAX=359
#>     ASPECT_MIN=-9999
#>     ASPECT_NUM_CLASSES=-1
#>     ASPECT_UNIT=2
#>     ASPECT_UNIT_NAME=Azimuth degrees
#> Band 4 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Fuel models
#>   Metadata:
#>     FUEL_MODEL_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     FUEL_MODEL_MAX=183
#>     FUEL_MODEL_MIN=-9999
#>     FUEL_MODEL_NUM_CLASSES=12
#>     FUEL_MODEL_OPTION=0
#>     FUEL_MODEL_OPTION_DESC=no custom models AND no conversion file needed
#>     FUEL_MODEL_VALUES=0,98,99,101,102,121,122,123,142,162,165,181,183
#> Band 5 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Canopy cover
#>   Metadata:
#>     CANOPY_COV_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     CANOPY_COV_MAX=75
#>     CANOPY_COV_MIN=-9999
#>     CANOPY_COV_NUM_CLASSES=8
#>     CANOPY_COV_UNIT=1
#>     CANOPY_COV_UNIT_NAME=Percent
#> Band 6 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Canopy height
#>   Metadata:
#>     CANOPY_HT_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     CANOPY_HT_MAX=390
#>     CANOPY_HT_MIN=-9999
#>     CANOPY_HT_NUM_CLASSES=8
#>     CANOPY_HT_UNIT=3
#>     CANOPY_HT_UNIT_NAME=Meters x 10
#> Band 7 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Canopy base height
#>   Metadata:
#>     CBH_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     CBH_MAX=100
#>     CBH_MIN=-9999
#>     CBH_NUM_CLASSES=22
#>     CBH_UNIT=3
#>     CBH_UNIT_NAME=Meters x 10
#> Band 8 Block=143x1 Type=Int16, ColorInterp=Undefined
#>   Description = Canopy bulk density
#>   Metadata:
#>     CBD_FILE=/netapp/sharedwebfs1/shared/landfire/public/temp_q8dTbIJ4w6Qi36Omkzk0/LCP_LF2022_FBFM40_220_CONUS/temp/merged_modified.tif
#>     CBD_MAX=34
#>     CBD_MIN=-9999
#>     CBD_NUM_CLASSES=15
#>     CBD_UNIT=3
#>     CBD_UNIT_NAME=kg/m^3 x 100

# retrieve Description from the metadata
# band = 0 for dataset-level metadata, domain = "" for default domain
ds$getMetadata(band = 0, domain = "")
#> [1] "DESCRIPTION=LCP file created by GDAL. Storm Lake AOI, Beaverhead-Deerlodge National Forest, Montana."
#> [2] "LATITUDE=46"                                                                                         
#> [3] "LINEAR_UNIT=Meters"                                                                                  
ds$getMetadataItem(band = 0, mdi_name = "DESCRIPTION", domain = "")
#> [1] "LCP file created by GDAL. Storm Lake AOI, Beaverhead-Deerlodge National Forest, Montana."

ds$close()