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15.16 Editing the Contents of an HDF File: hdfed

15.16.1 General Description

The hdfed utility allows experienced HDF users to manipulate the elements of an HDF file. These manipulations include

It is designed primarily for users who need to know about HDF files at the level of individual data elements. It is not designed to provide a comprehensive high-level view of the contents of an HDF file -- other tools and utilities should be used for that purpose. To use hdfed one should be familiar with the components of an HDF file covered in the HDF Specifications manual.

The hdfed utility is loosely modeled on ed, the UNIX line editor. When hdfed is invoked, it prompts the user for commands, as does ed. Also, basic command syntax and description information is available to the user through hdfed. The most common hdfed commands are used to control the position in the HDF file and the format of the information provided.

The initial view of the file under hdfed consists of a set of tag/reference number pairs. Although hdfed allows modification of tags and reference numbers within strict constraints, it will not allow the user to arbitrarily modify binary data in the file.

The following terms and concepts must be understood in order to use hdfed correctly and will be used in the following discussion about hdfed.

Once an HDF file has been opened by hdfed, the following operations can be performed on the data file, among others:

15.16.2 Command-line Syntax

The syntax of hdfed is

hdfed [-nobackup][-batch] filename
If a file named filename exists, it is opened and a backup is made of the file. Files may also be opened from within the editor.

The option flags are described in Table 15L.

TABLE 15L
-nobackup

Specifies that no backup file is to be made. If this option is omitted, a backup file is automatically created.

-batch

Specifies that input to hdfed is to be input via a stream of hdfed commands, rather than interactively.

hdfed Option Flags

The -batch flag is useful when a group of commonly-used commands are included in a UNIX shell script. The following is an example of such a script, using the C-shell, that lists information about the groups in a specified HDF file.

#!/bin/csh -f
set file=$1
shift
hdfed -batch $file -nobackup << EOF
info -all group $*
close
quit
EOF
echo ""
To receive usage information, as well as a quick list of the hdfed commands, type the command

hdfed -help
While in hdfed, the standard command prompt is displayed.

hdfed>
Many hdfed commands have qualifiers, or flags. For example, the command info may be followed by the -all, -long, -group, or -label flags.

All of the commands and flags can be abbreviated to the extent that their abbreviations are unique. For example, -he is ambiguous as it could stand for either the -hexadecimal or the -help flags, but -hel is not ambiguous.

TABLE 15M - The hdfed Command Set

Name
Description
help Displays general hdfed help information.

open Opens an HDF file.

close Closes an HDF file.

revert Reverts to the original HDF file.

next Goes to the next object or group that satisfies the predicate.

prev Goes to the previous object or group that satisfies the predicate.

info Displays information about the current data object.

dump Displays information about the current data object in non-default formats. (i.e., binary, ASCII, etc.). The default is octal.

display Displays a raster image using ICR.

put Writes the current data element in a non-HDF file with the specified filename in binary format.

putr8 Writes the current RIS8 group into a non-HDF file with the specified filename.

getr8 Reads a RIS8 group from a non-HDF file with the specified filename.

delete Deletes an object or group.

write Writes an object or group to an HDF file.

annotate Annotates an object.

if Conditional statement.

select Loop for each object.

alias Defines an alias or display the alias list.

unalias Deletes an alias.

wait Prints a message and wait for a carriage return.

To obtain information about the usage of any hdfed command, type the following at the hdfed prompt.

any-hdfed-command -help
Note that usage information cannot be obtained by typing only the command, with no flags. There are other hdfed commands, such as delete, that do not require an argument, so watch out for this kind of error.

There is a subset of hdfed commands where predicates, items, and comparators are used. Items are used to denote an HDF object type and can be any of the following identifiers; tag, ref, image_size, or label. A comparator is an expression used to compare an item with a user-defined value, and can be any of the following:
=

equal

!=

not equal

<

less than

<=

less than or equal

>

greater than

>=

greater than or equal

User-defined values can be either a number (with or without a decimal point) or a string of characters delimited by double-quotes. Predicates consist of items, comparators and user-defined values and are of the syntax:

item comparator-value 
Or they may consist of the identifier group, as in the next group command. Some examples of predicates are:



next group
next (same as "next group" as "group" is the default identifier)
next tag = 720
next ref = 2
next image_size < 1000
next label = "abc"
The following is a more inclusive description of the hdfed commands.

The help command

Syntax:	help
Flags: 	None
Description: Prints a help screen describing the basic purpose and functionality of the hdfed utility.
Usage Example:

hdfed> help
hdfed allows sophisticated HDF users the ability to manipulate the
elements in an HDF file. These manipulations include selecting groups
...
The open command

Syntax:	open [-nobackup] filename
Flags: 	-nobackup	The specified file name is not backed up.
Description: Opens the specified HDF file.
Usage Example:

	hdfed> open -help
	open <file> [-nobackup]
	-nobackup 	Don't make a backup for this file.
	hdfed> 
	hdfed> open h1
	hdfed>
The info command

Syntax:	info [-all] [-long] [-group] [-label]
Flags: 	-all		Displays information for all of the objects in the current file.
	-long		Displays the long form of the information.
	-group		Organizes the information into groups.
	-label		Shows any labels.
Description: Displays information for a data object. The listing for special elements will contain a special tag value (in Item 13 below it's 18347, which corresponds to DFTAG_VS) and the text "Unknown Tag".
Usage Example:

hdfed> info -all -label -long
(1)	Version Descriptor	: (Tag 30)
	Ref: 1, Offset: 202, Length	:92 (bytes)
(2)	Scientific Data	: (Tag 702)
	Ref: 2, Offset: 294, Length 	: 200 (bytes)
(3)	Number type	: (Tag 106)
	Ref: 2, Offset: 494, Length	: 4 (bytes)
(4)	SciData description	: (Tag 701)
	Ref: 2, Offset: 498, Length	: 2 (bytes)
(5)	SciData max/min	: (Tag 707)
	Ref: 2, Offset: 520, Length	: 4 (bytes)
*(6)	Numeric Data Group	: (Tag 720)
	Ref: 2, Offset: 524, Length	: 12 (bytes)
	Label: Experiment #1
(7)	Data Id Label	: (Tag 104)
	Ref: 3, Offset: 536, Length	: 17 (bytes)
(8)	Scientific Data	: (Tag 702)
	Ref: 4, Offset: 553, Length	: 400 (bytes)
(9)	Number type	: (Tag 106)
	Ref: 4, Offset: 953, Length	: 4 (bytes)
(10)	SciData description	: (Tag 701)
	Ref: 4, Offset:957, Length	: 22 (bytes)
(11)	Numeric Data Group	: (Tag 720)
	Ref: 4, Offset: 979, Length	: 8 (bytes)
	Label: Experiment #2
(12)	Data Id Label	: (Tag 104)
	Ref: 5, Offset: 987, Length	: 17 (bytes)
(13)	Unknown Tag	: (Tag 18347)
	Ref: 8, Offset: 0, Length	: 40(bytes
hdfed>
hdfed> info -group -all
**Group 1:
	Numeric Data Group	: (Tag 720) Ref 2
	Scientific Data	: (Tag 702) Ref 2
	SciData description 	: (Tag 701) Ref 2
	SciData max/min 	: (Tag 707) Ref 2
**Group 2:
	Numeric Data Group	: (Tag 720) Ref 4
	Scientific Data 	: (Tag 702) Ref 4
	SciData description 	: (Tag 701) Ref 4
**These do not belong to any group:
	Version Descriptor	: (Tag 30) Ref 1
	Number Type 	: (Tag 106) Ref 2
	Data Id Label	: (Tag 104) Ref 3
	Number Type 	: (Tag 106) Ref 4
	Data Id Label	: (Tag 104) Ref 5
hdfed>
The prev command

Syntax:	prev predicate-list
Flags: 	None.
Description: Moves to the next object that satisfies the predicate list.
Usage Example:

hdfed> info -all
	(1)	Version Descriptor	: (Tag 30) Ref 1
	(2)	Scientific Data	: (Tag 702) Ref 2
	(3)	Number type 	: (Tag 106) Ref 2
	(4) 	SciData description	: (Tag 701) Ref 2
	(5)	SciData max/min 	: (Tag 707) Ref 2
	*(6)	Numeric Data Group 	: (Tag 720) Ref 2
	(7)	Data Id Label	: (Tag 104) Ref 3
	(8)	Scientific Data	: (Tag 702) Ref 4
	(9)	Number type 	: (Tag 106) Ref 4
	(10)	SciData description	: (Tag 701) Ref 4
	(11) 	Numeric Data Group	: (Tag 720) Ref 4
	(12) 	Data Id Label	: (Tag 104) Ref 5
hdfed>
hdfed> ! The '*' in the first column marks the current
hdfed> ! position.
hdfed> ! The 'next' and 'prev' commands work with predicates.
hdfed> ! If I want to move to the max/min element,
hdfed> ! I can use the 'tag=' predicate.
hdfed>
hdfed> prev tag=707
hdfed> info
	(5) 	SciData max/min (SciData) 	: (Tag 707) Ref:2
hdfed>
The next command

Syntax:	next predicate-list
Flags: 	None.
Description: Moves to the next object that satisfies the predicate.
Usage Example:

hdfed> ! Move in the file using next and prev
hdfed> ! The move direction depends on the relative positions.
hdfed> ! so it is often necessary to do an 'info -all' first.
hdfed> info -all
	(1)	Version Descriptor	: (Tag 30) Ref 1
	(2)	Scientific Data 	: (Tag 702) Ref 2
	(3)	Number type 	: (Tag 106) Ref 2
	(4) 	SciData description 	: (Tag 701) Ref 2
	*(5)	SciData max/min 	: (Tag 707) Ref 2
	(6)	Numeric Data Group 	: (Tag 720) Ref 2
	(7)	Data Id Label	: (Tag 104) Ref 3
	(8)	Scientific Data 	: (Tag 702) Ref 4
	(9)	Number type 	: (Tag 106) Ref 4
	(10)	SciData description	: (Tag 701) Ref 4
	(11)	Numeric Data Group	: (Tag 720) Ref 4
	(12)	Data Id Label 	: (Tag 104) Ref 5
hdfed>
hdfed> ! This predicate persists for the next and prev
hdfed> ! commands. That means if I now type another 'next'
hdfed> ! command, it will look for a tag that equals 707.
hdfed> 
hdfed> next
Reached end of file. Not moved.
hdfed> info
	(5)	 SciData max.min (SciData)	: (Tag 707) Ref: 2
hdfed>
hdfed> next group
hdfed> next group
hdfed> info
	(11)	Numeric Data Group 	: (Tag 720) Ref 4
hdfed>
The dump command

Syntax:	dump [-offset offset] [-length length] [-decimal|-short|-byte|-octal|-hexadecimal|-float|-double|-ascii]
Flags:	-offset		Starting offset
	-length		Length of the object to dump.
	-decimal	Decimal format (32-bit integers)
	-short		Decimal format (16-bit integers)
	-byte		Decimal format (8-bit integers)
	-octal		Octal format (the default)
	-hexadecimal	Hexadecimal format
	-float		Single-precision floating-point format (32-bit floats)
	-double		Double-precision floating-point format (16-bit floats)
	-ascii		ASCII format
Description: Displays the contents of the current object in the specified format.
Usage Example:

hdfed> ! to see the binary representation of this element
hdfed> 
hdfed> dump
0: 257400004 257200004
hdfed> 
hdfed> dump -short
hdfed>
0:	702 	4	701	4
hdfed>
The delete command

Syntax:	delete
Flags:	None.
Description: Deletes the current object or group.
Usage Example:

hdfed> ! deleting groups
hdfed>
hdfed> ! If an element is required by other group it is alone.
hdfed> ! However, this is not perfect as the method by which group
hdfed> ! membership is determined can be pretty ad hoc.
hdfed>
hdfed> delete
hdfed> ! This deletes the Scientific Data Group
hdfed> info -all
	(1) 	Version Descriptor	: (Tag 30) Ref 1
	(2) 	Scientific Data	: (Tag 702) Ref 2
	(3) 	Number type	: (Tag 106) Ref 2
	(4) 	SciData description 	: (Tag 701) Ref 2
	(5) 	SciData max/min	: (Tag 707) Ref 2
	(6) 	Numeric Data Group 	: (Tag 720) Ref 2
	(7) 	Data Id Label 	: (Tag 104) Ref 3
	(8) 	Number type 	: (Tag 106) Ref 4
	(9) 	Data Id Label 	: (Tag 104) Ref 5
hdfed>
hdfed> ! Notice that the Numeric Data Group with reference
hdfed> ! number 4 is missing, and now there are only 9
hdfed> ! objects in the file.
hdfed>
The annotate command

Syntax:	annotate [-label] [-descriptor] [-editor editor]
Flags:	-label		Edit a label (the default)
	-descriptor	Edit a descriptor.
	-editor		Use an editor. (Default is the editor referred to by the EDITOR environment variable.
Description: Edits an annotation.
Usage Example:

hdfed>
hdfed> ! Annotations are labels and descriptors
hdfed> 
hdfed> prev -group
hdfed> info -label
	(6)	Numeric Data Group	: (Tag 720) Ref 2
		Label: Experiment #1
hdfed> annotate -editor /usr/ucb/ex
"/tmp/he5091.1" 1 line, 14 characters
:p
Experiment #1
:s/$/	<more stuff>/
Experiment #1	<more stuff>
:wq
"/tmp/he5091.1" 1 line 27 characters
hdfed> info -label
	(6) 	Numeric Data Group	: (Tag 720) Ref 2
		Label: Experiment #1 <more stuff>
hdfed>
The write command

Syntax:	write [-attachto tag-reference-number] filename
Flags:	-attachto	Which element the annotation will be attached to. (only for writing annotations)
Description: Writes an element or group into another HDF file.
Usage Example:

hdfed> 
hdfed> ! Write object or group to another HDF file.
hdfed>
hdfed> write test
hdfed>
hdfed> ! Let's take a look at the file 'test'
hdfed> close; open test; info -all
	(1)	Version Descriptor	(Tag 30) Ref 1
	(2) 	Scientific Data	(Tag 702) Ref 2
	(3)	Number type 	(Tag 106) Ref 2
	(4)	SciData description	(Tag 701) Ref 2
	(5) 	SciData max/min	(Tag 707) Ref 2
	*(6)	Numeric Data Group 	(Tag 720) Ref 2
hdfed>
hdfed> close;
hdfed>
The display command

Syntax:	display [-position x-position y-position] [-expansion expansion] [-large]
Flags:	-position	Image position on console screen
	-expansion	Image expansion factor
	-large		Make image as large as possible
Description: Displays image on screen. 
Usage Example:

hdfed> ! We will open a file with some RIS8 images.
hdfed>
hdfed> open denm,HDF
hdfed> display
hdfed>
hdfed> ! The 'display' command displays the current RIS8
hdfed> ! group image via ICR. I.e. if you are using NCSA Telnet
hdfed> ! on a Mac II, this would display the images from denm.HDF
hdfed> ! on your screen.
hdfed> ! NOTE: not guaranteed to work otherwise.
hdfed>
The putr8 command

Syntax:	putr8 [-image image_filename palette _ilename -verbose]
Flags:	-image 		Image file name template (Default is "img#.@.%")
	-palette	Palette file name template (Default is "pal#")
	-verbose	To give output of steps taken.
Description: Writes a RIS8 group into raw image and palette files.
Usage Example:

hdfed> ! putr8 puts an RIS8 group into raw files
hdfed>
hdfed> putr8 -image my_image.#.@.% -palette testPalettes# -verbose
Writing to file: my_image8.10.10
Writing to file: my_palette
hdfed>
The close command

Syntax:	close [-keep]
Flags:	-keep		The backup file is not deleted.
Description: Closes the HDF file opened by the last open command.
Usage Example:

hdfed> close
hdfed>
The select command

Syntax:	select predicate_list command_list
Flags:	None.
Description: Step through all the elements in the HDF file that satisfies the predicates, and execute the command list.
Usage Example:

hdfed> ! To step through a file and, for example, putr8 on all 
hdfed> ! RIS8 groups we can use the select command.
hdfed>
hdfed> select tag=306
>> putr8 -image testImages# -palette testPalettes# -verbose
>> end
Writing to file: testImages8
Writing to file: testPalettes8
Writing to file: test Images14
Writing to file: testPalettes14
Writing to file: testImages21
Writing to file: testPalettes21
hdfed>
hdfed> ! The 'select' and 'if' commands take the same 
hdfed> ! predicates as 'next' and 'pref'. There are also
hdfed> ! the predicates 'succeed" and "fail" that test the 
hdfed> ! return status of the 'last' command.
hdfed>
The put command

Syntax:	put [-file filename] [-verbose]
Flags:	-file		Output file name (Default is "elt#.@")
	-verbose	Output diagnostic information.
Description: Writes the raw binary image of the current object to a file.
Usage Example:

hdfed> ! The 'put' command writes an element into a binary file.
hdfed> ! This is a dumb routine and does not know about the 
hdfed> ! formats of an element.
hdfed>
hdfed> put -file binary#
hdfed> put -file myBinary -verbose
Writing to file: myBinary
hdfed>
The revert comma nd

Syntax:	revert
Flags:	None.
Description: Discards all changes made in the current hdfed session.
Usage Example:

hdfed> revert
hdfed>
The getr8 command

Syntax:	getr8 image-file-name [x-dimension y-dimension] [-palette palette-file-name] [-raster|-rle|-imcomp]
Flags:	-palette	Palette will be read from a binary file.
	-raster		No compression will be performed during the write. (the default)
	-rle		Run-length compression will be performed during the write.
	-imcomp		IMCOMP compression will be performed during the write.
Description: Reads a RIS8 group from binary files.
The if conditional

Syntax:	if predicate-list command-list end
Flags:	None.
Description: Executes commands in a loop if predicates are satisfied for each element processed.
The select loop command

Syntax:	select predicate-list command-list end
Flags:	None.
Description: Executes the list of commands for each element that satisfies the predicates.
The wait command

Syntax:	wait message
Flags:	None.
Description: Prints a message, then waits for a carriage return to be typed.


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HDF User's Guide - 05/19/99, NCSA HDF Development Group.