NetcdfFile (NetCDF-Java CDM API v5.0.0)

java.lang.Object
- ucar.nc2.NetcdfFile

All Implemented Interfaces:

Closeable, AutoCloseable, ucar.nc2.util.cache.FileCacheable

Direct Known Subclasses:

NetcdfDataset, NetcdfFileSubclass
```
public class NetcdfFile
extends Object
implements ucar.nc2.util.cache.FileCacheable, Closeable
```
Read-only scientific datasets that are accessible through the netCDF API. Immutable after setImmutable() is called. However, reading data is not thread-safe.

Be sure to close the file when done. Either enclose in a try/finally block:
```
 NetcdfFile ncfile = null;
 try {
  ncfile = NetcdfFile.open(fileName);
  // do stuff
 } finally {
  if(ncfile != null) { ncfile.close(); }
 }
 
```
Or better yet, use try-with-resources:
```
 try (NetcdfFile ncfile = NetcdfFile.open(fileName)) {
  // do stuff
 }
 
```
Naming

Each object has a name (aka "full name") that is unique within the entire netcdf file, and a "short name" that is unique within the parent group. These coincide for objects in the root group, and so are backwards compatible with version 3 files.
1. Variable: group1/group2/varname
2. Structure member Variable: group1/group2/varname.s1.s2
3. Group Attribute: group1/group2@attName
4. Variable Attribute: group1/group2/varName@attName

Field Summary

Fields
Modifier and Type	Field and Description
`protected ucar.nc2.util.cache.FileCacheIF`	`cache`
`protected String`	`cacheName`
`protected static boolean`	`debugCompress`
`protected static boolean`	`debugSPI`
`protected List<Dimension>`	`dimensions`
`protected List<Attribute>`	`gattributes`
`protected String`	`id`
`static String`	`IOSP_MESSAGE_ADD_RECORD_STRUCTURE`
`static String`	`IOSP_MESSAGE_CONVERT_RECORD_STRUCTURE`
`static String`	`IOSP_MESSAGE_RANDOM_ACCESS_FILE`
`static String`	`IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE`
`protected String`	`location`
`static String`	`reservedCdl`
`static String`	`reservedFullName`
`static String`	`reservedSectionSpec`
`protected Group`	`rootGroup`
`protected static boolean`	`showRequest`
`protected IOServiceProvider`	`spi`
`protected String`	`title`
`protected List<Variable>`	`variables`

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`NetcdfFile()` For subclass construction.
`protected`	`NetcdfFile(IOServiceProvider spi, RandomAccessFile raf, String location, CancelTask cancelTask)` Open an existing netcdf file, passing in the iosp and the raf.
`protected`	`NetcdfFile(IOServiceProvider spi, String location)` Open an existing netcdf file (read only) , but dont do nuttin else Use NetcdfFileSubclass to access this constructor
`protected`	`NetcdfFile(NetcdfFile ncfile)` Copy constructor, used by NetcdfDataset.
	`NetcdfFile(String filename)` Deprecated. use NetcdfFile.open( location) or NetcdfDataset.openFile( location)
`protected`	`NetcdfFile(String iospClassName, Object iospParam, String location, int buffer_size, CancelTask cancelTask)` Open an existing netcdf file (read only), using the specified iosp.
	`NetcdfFile(URL url)` Deprecated. use NetcdfFile.open( http:location) or NetcdfDataset.openFile( http:location)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`Attribute`	`addAttribute(Group parent, Attribute att)` Add an attribute to a group.
`Attribute`	`addAttribute(Group parent, String name, String value)` Add optional String attribute to a group.
`Dimension`	`addDimension(Group parent, Dimension d)` Add a shared Dimension to a Group.
`Group`	`addGroup(Group parent, Group g)` Add a group to the parent group.
`Variable`	`addStringVariable(Group g, String shortName, String dims, int strlen)` Create a new Variable of type Datatype.CHAR, and add to the given group.
`Variable`	`addVariable(Group g, String shortName, DataType dtype, String dims)` Create a new Variable, and add to the given group.
`Variable`	`addVariable(Group g, Variable v)` Add a Variable to the given group.
`Attribute`	`addVariableAttribute(Variable v, Attribute att)` Add a variable attribute.
`static String`	`canonicalizeUriString(String location)` Removes the `"file:"` or `"file://"` prefix from the location, if necessary.
`static boolean`	`canOpen(String location)` Find out if the file can be opened, but dont actually open it.
`void`	`close()` Close all resources (files, sockets, etc) associated with this file.
`void`	`empty()` Completely empty the objects in the netcdf file.
`Attribute`	`findAttribute(String fullNameEscaped)` Find an attribute, with the specified (escaped full) name.
`String`	`findAttValueIgnoreCase(Variable v, String attName, String defaultValue)` Find a String-valued global or variable Attribute by Attribute name (ignore case), return the Value of the Attribute.
`Dimension`	`findDimension(String fullName)` Finds a Dimension with the specified full name.
`Attribute`	`findGlobalAttribute(String name)` Look up global Attribute by (full) name.
`Attribute`	`findGlobalAttributeIgnoreCase(String name)` Look up global Attribute by name, ignore case.
`Group`	`findGroup(String fullName)` Find a Group, with the specified (full) name.
`Variable`	`findVariable(Group g, String shortName)`
`Variable`	`findVariable(String fullNameEscaped)` Find a Variable, with the specified (escaped full) name.
`Variable`	`findVariableByAttribute(Group g, String attName, String attValue)`
`void`	`finish()` Finish constructing the object model.
`String`	`getCacheName()` Public by accident.
`String`	`getDetailInfo()` Access to iosp debugging info.
`void`	`getDetailInfo(Formatter f)`
`List<Dimension>`	`getDimensions()` Get the shared Dimensions used in this file.
`String`	`getFileTypeDescription()` Get a human-readable description for this file type.
`String`	`getFileTypeId()` Get the file type id for the underlying data source.
`String`	`getFileTypeVersion()` Get the version of this file type.
`List<Attribute>`	`getGlobalAttributes()` Returns the set of global attributes associated with this file.
`String`	`getId()` Get the globally unique dataset identifier, if it exists.
`IOServiceProvider`	`getIosp()` DO NOT USE - public by accident
`long`	`getLastModified()`
`String`	`getLocation()` Get the NetcdfFile location.
`Group`	`getRootGroup()` Get the root group.
`protected StructureDataIterator`	`getStructureIterator(Structure s, int bufferSize)`
`String`	`getTitle()` Get the human-readable title, if it exists.
`Dimension`	`getUnlimitedDimension()` Return the unlimited (record) dimension, or null if not exist.
`List<Variable>`	`getVariables()` Get all of the variables in the file, in all groups.
`boolean`	`hasUnlimitedDimension()` Return true if this file has one or more unlimited (record) dimension.
`static boolean`	`iospDeRegister(Class iospClass)` See if a specific IOServiceProvider is registered and if so, remove it.
`static boolean`	`iospRegistered(Class iospClass)` See if a specific IOServiceProvider is registered
`static void`	`main(String[] arg)` debugging - do not use
`protected static String`	`makeFullName(CDMNode v)` Given a CDMNode, create its full name with appropriate backslash escaping.
`protected static String`	`makeFullName(CDMNode node, String reservedChars)` Given a CDMNode, create its full name with appropriate backslash escaping of the specified characters.
`protected static String`	`makeFullNameSectionSpec(CDMNode v)` Given a CDMNode, create its full name with appropriate backslash escaping for use in a section spec.
`protected String`	`makeFullNameWithString(Group parent, String name)` Create a synthetic full name from a group plus a string
`static String`	`makeNameUnescaped(String vname)` Unescape any escaped characters in a name.
`protected Boolean`	`makeRecordStructure()` If there is an unlimited dimension, make all variables that use it into a Structure.
`protected Group`	`makeRootGroup()`
`static String`	`makeValidCDLName(String vname)` Escape special characters in a netcdf short name when it is intended for use in CDL.
`static String`	`makeValidCdmObjectName(String shortName)` Create a valid CDM object name.
`static String`	`makeValidPathName(String vname)` Escape special characters in a netcdf short name when it is intended for use in a fullname
`static String`	`makeValidSectionSpecName(String vname)` Escape special characters in a netcdf short name when it is intended for use in a sectionSpec
`static NetcdfFile`	`open(RandomAccessFile raf, String location, CancelTask cancelTask, Object iospMessage)`
`static NetcdfFile`	`open(String location)` Open an existing netcdf file (read only).
`static NetcdfFile`	`open(String location, CancelTask cancelTask)` Open an existing file (read only), with option of cancelling.
`static NetcdfFile`	`open(String location, int buffer_size, CancelTask cancelTask)` Open an existing file (read only), with option of cancelling, setting the RandomAccessFile buffer size for efficiency.
`static NetcdfFile`	`open(String location, int buffer_size, CancelTask cancelTask, Object iospMessage)` Open an existing file (read only), with option of cancelling, setting the RandomAccessFile buffer size for efficiency, with an optional special object for the iosp.
`static NetcdfFile`	`open(String location, String iospClassName, int bufferSize, CancelTask cancelTask, Object iospMessage)` Open an existing file (read only), specifying which IOSP is to be used.
`static NetcdfFile`	`openInMemory(String filename)` Read a local CDM file into memory.
`static NetcdfFile`	`openInMemory(String name, byte[] data)` Open an in-memory netcdf file.
`static NetcdfFile`	`openInMemory(String name, byte[] data, String iospClassName)` Open an in-memory netcdf file, with a specific iosp.
`static NetcdfFile`	`openInMemory(URI uri)` Read a remote CDM file into memory.
`void`	`reacquire()`
`Array`	`read(String variableSection, boolean flatten)` Deprecated. use readSection(), flatten=false no longer supported
`List<Array>`	`readArrays(List<Variable> variables)` Do a bulk read on a list of Variables and return a corresponding list of Array that contains the results of a full read on each Variable.
`double`	`readAttributeDouble(Variable v, String attName, double defValue)`
`int`	`readAttributeInteger(Variable v, String attName, int defValue)`
`protected Array`	`readData(Variable v, Section ranges)`
`Array`	`readSection(String variableSection)` Read a variable using the given section specification.
`protected long`	`readToByteChannel(Variable v, Section section, WritableByteChannel wbc)` Read data from a top level Variable and send data to a WritableByteChannel.
`protected long`	`readToOutputStream(Variable v, Section section, OutputStream out)`
`static void`	`registerIOProvider(Class iospClass)` Register an IOServiceProvider.
`static void`	`registerIOProvider(Class iospClass, boolean last)` Register an IOServiceProvider.
`static void`	`registerIOProvider(String className)` Register an IOServiceProvider, using its class string name.
`static void`	`registerIOProviderPreferred(Class iospClass, Class target)` Register an IOServiceProvider.
`void`	`release()`
`boolean`	`removeDimension(Group g, String dimName)` Remove a shared Dimension from a Group by name.
`protected Boolean`	`removeRecordStructure()`
`boolean`	`removeVariable(Group g, String varName)` Remove a Variable from the given group by name.
`Object`	`sendIospMessage(Object message)` Generic way to send a "message" to the underlying IOSP.
`protected void`	`setCacheName(String cacheName)` Public by accident.
`static void`	`setDebugFlags(DebugFlags debugFlag)` debugging
`void`	`setFileCache(ucar.nc2.util.cache.FileCacheIF cache)` Public by accident.
`void`	`setId(String id)` Set the globally unique dataset identifier.
`NetcdfFile`	`setImmutable()` Make this immutable.
`void`	`setLocation(String location)` Set the location, a URL or local filename.
`static void`	`setProperty(String name, String value)` Set properties.
`void`	`setTitle(String title)` Set the dataset "human readable" title.
`protected void`	`showCached(Formatter f)`
`protected void`	`showProxies(Formatter f)`
`boolean`	`syncExtend()` Extend the file if needed, in a way that is compatible with the current metadata, that is, does not invalidate structural metadata held by the application.
`String`	`toNcML(String url)` CDL representation of Netcdf header info, non strict
`String`	`toString()` CDL representation of Netcdf header info, non strict
`protected String`	`toStringDebug(Object o)` Access to iosp debugging info.
`void`	`toStringEnd(PrintWriter pw)`
`protected void`	`toStringStart(Formatter f, Indent indent, boolean strict)`
`void`	`toStringStart(PrintWriter pw, boolean strict)`
`protected void`	`writeCDL(Formatter f, Indent indent, boolean strict)`
`void`	`writeCDL(OutputStream out, boolean strict)` Write CDL representation to OutputStream.
`void`	`writeCDL(PrintWriter pw, boolean strict)` Write CDL representation to PrintWriter.
`void`	`writeNcML(OutputStream os, String uri)` Write the NcML representation: dont show coodinate values
`void`	`writeNcML(Writer writer, String uri)` Write the NcML representation: dont show coodinate values

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - IOSP_MESSAGE_ADD_RECORD_STRUCTURE
```
public static final String IOSP_MESSAGE_ADD_RECORD_STRUCTURE
```
    See Also:
    
    Constant Field Values
  - IOSP_MESSAGE_CONVERT_RECORD_STRUCTURE
```
public static final String IOSP_MESSAGE_CONVERT_RECORD_STRUCTURE
```
    See Also:
    
    Constant Field Values
  - IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE
```
public static final String IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE
```
    See Also:
    
    Constant Field Values
  - IOSP_MESSAGE_RANDOM_ACCESS_FILE
```
public static final String IOSP_MESSAGE_RANDOM_ACCESS_FILE
```
    See Also:
    
    Constant Field Values
  - debugSPI
```
protected static boolean debugSPI
```
  - debugCompress
```
protected static boolean debugCompress
```
  - showRequest
```
protected static boolean showRequest
```
  - location
```
protected String location
```
  - id
```
protected String id
```
  - title
```
protected String title
```
  - cacheName
```
protected String cacheName
```
  - rootGroup
```
protected Group rootGroup
```
  - cache
```
protected ucar.nc2.util.cache.FileCacheIF cache
```
  - spi
```
protected IOServiceProvider spi
```
  - variables
```
protected List<Variable> variables
```
  - dimensions
```
protected List<Dimension> dimensions
```
  - gattributes
```
protected List<Attribute> gattributes
```
  - reservedFullName
```
public static final String reservedFullName
```
    See Also:
    
    Constant Field Values
  - reservedSectionSpec
```
public static final String reservedSectionSpec
```
    See Also:
    
    Constant Field Values
  - reservedCdl
```
public static final String reservedCdl
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - NetcdfFile
```
public NetcdfFile(String filename)
           throws IOException
```
    Deprecated. use NetcdfFile.open( location) or NetcdfDataset.openFile( location)
    
    This is can only be used for local netcdf-3 files.
    
    Parameters:
    
    filename - location
    
    Throws:
    
    IOException - if error
  - NetcdfFile
```
public NetcdfFile(URL url)
           throws IOException
```
    Deprecated. use NetcdfFile.open( http:location) or NetcdfDataset.openFile( http:location)
    
    This can only be used for netcdf-3 files served over HTTP
    
    Parameters:
    
    url - HTTP URL location
    
    Throws:
    
    IOException - if error
  - NetcdfFile
```
protected NetcdfFile(String iospClassName,
                     Object iospParam,
                     String location,
                     int buffer_size,
                     CancelTask cancelTask)
              throws IOException,
                     IllegalAccessException,
                     InstantiationException,
                     ClassNotFoundException
```
    Open an existing netcdf file (read only), using the specified iosp. The ClassLoader for the NetcdfFile class is used. Use NetcdfFileSubclass to access this constructor
    
    Parameters:
    
    iospClassName - the name of the class implementing IOServiceProvider
    
    iospParam - parameter to pass to the IOSP (before open is called)
    
    location - location of file. This is a URL string, or a local pathname.
    
    buffer_size - use this buffer size on the RandomAccessFile
    
    cancelTask - allow user to cancel
    
    Throws:
    
    ClassNotFoundException - if the iospClassName cannot be found
    
    IllegalAccessException - if the class or its nullary constructor is not accessible.
    
    InstantiationException - if the class cannot be instatiated, eg if it has no nullary constructor
    
    IOException - if I/O error
  - NetcdfFile
```
protected NetcdfFile(IOServiceProvider spi,
                     RandomAccessFile raf,
                     String location,
                     CancelTask cancelTask)
              throws IOException
```
    Open an existing netcdf file, passing in the iosp and the raf. Use NetcdfFileSubclass to access this constructor
    
    Parameters:
    
    spi - use this IOServiceProvider instance
    
    raf - read from this RandomAccessFile
    
    cancelTask - allow user to cancel
    
    location - location of data
    
    Throws:
    
    IOException - if I/O error
  - NetcdfFile
```
protected NetcdfFile(IOServiceProvider spi,
                     String location)
```
    Open an existing netcdf file (read only) , but dont do nuttin else Use NetcdfFileSubclass to access this constructor
    
    Parameters:
    
    spi - use this IOServiceProvider instance
    
    location - location of data
  - NetcdfFile
```
protected NetcdfFile()
```
    For subclass construction. Call finish() when completed construction. Use NetcdfFileSubclass to access this constructor
  - NetcdfFile
```
protected NetcdfFile(NetcdfFile ncfile)
```
    Copy constructor, used by NetcdfDataset. Shares the iosp.
    
    Parameters:
    
    ncfile - copy from here
- Method Detail
  - registerIOProvider
```
public static void registerIOProvider(String className)
                               throws IllegalAccessException,
                                      InstantiationException,
                                      ClassNotFoundException
```
    Register an IOServiceProvider, using its class string name.
    
    Parameters:
    
    className - Class that implements IOServiceProvider.
    
    Throws:
    
    IllegalAccessException - if class is not accessible.
    
    InstantiationException - if class doesnt have a no-arg constructor.
    
    ClassNotFoundException - if class not found.
  - registerIOProvider
```
public static void registerIOProvider(Class iospClass)
                               throws IllegalAccessException,
                                      InstantiationException
```
    Register an IOServiceProvider. A new instance will be created when one of its files is opened.
    
    Parameters:
    
    iospClass - Class that implements IOServiceProvider.
    
    Throws:
    
    IllegalAccessException - if class is not accessible.
    
    InstantiationException - if class doesnt have a no-arg constructor.
    
    ClassCastException - if class doesnt implement IOServiceProvider interface.
  - registerIOProvider
```
public static void registerIOProvider(Class iospClass,
                                      boolean last)
                               throws IllegalAccessException,
                                      InstantiationException
```
    Register an IOServiceProvider. A new instance will be created when one of its files is opened.
    
    Parameters:
    
    iospClass - Class that implements IOServiceProvider.
    
    last - true=>insert at the end of the list; otherwise front
    
    Throws:
    
    IllegalAccessException - if class is not accessible.
    
    InstantiationException - if class doesnt have a no-arg constructor.
    
    ClassCastException - if class doesnt implement IOServiceProvider interface.
  - registerIOProviderPreferred
```
public static void registerIOProviderPreferred(Class iospClass,
                                               Class target)
                                        throws IllegalAccessException,
                                               InstantiationException
```
    Register an IOServiceProvider. A new instance will be created when one of its files is opened. This differs from the above in that it specifically locates the target iosp and inserts the new one in front of it in order to override the target. If the iospclass is already registered, remove it and reinsert. If the target class is not present, then insert at front of the registry
    
    Parameters:
    
    iospClass - Class that implements IOServiceProvider.
    
    target - Class to override
    
    Throws:
    
    IllegalAccessException - if class is not accessible.
    
    InstantiationException - if class doesnt have a no-arg constructor.
    
    ClassCastException - if class doesnt implement IOServiceProvider interface.
  - iospRegistered
```
public static boolean iospRegistered(Class iospClass)
```
    See if a specific IOServiceProvider is registered
    
    Parameters:
    
    iospClass - Class for which to search
  - iospDeRegister
```
public static boolean iospDeRegister(Class iospClass)
```
    See if a specific IOServiceProvider is registered and if so, remove it.
    
    Parameters:
    
    iospClass - Class for which to search and remove
    
    Returns:
    
    true if class was present
  - setDebugFlags
```
public static void setDebugFlags(DebugFlags debugFlag)
```
    debugging
    
    Parameters:
    
    debugFlag - debug flags
  - setProperty
```
public static void setProperty(String name,
                               String value)
```
    Set properties. Currently recognized: "syncExtendOnly", "true" or "false" (default). if true, can only extend file on a sync.
    
    Parameters:
    
    name - name of property
    
    value - value of property
  - open
```
public static NetcdfFile open(String location)
                       throws IOException
```
    Open an existing netcdf file (read only).
    
    Parameters:
    
    location - location of file.
    
    Returns:
    
    the NetcdfFile.
    
    Throws:
    
    IOException - if error
  - open
```
public static NetcdfFile open(String location,
                              CancelTask cancelTask)
                       throws IOException
```
    Open an existing file (read only), with option of cancelling.
    
    Parameters:
    
    location - location of the file.
    
    cancelTask - allow task to be cancelled; may be null.
    
    Returns:
    
    NetcdfFile object, or null if cant find IOServiceProver
    
    Throws:
    
    IOException - if error
  - open
```
public static NetcdfFile open(String location,
                              int buffer_size,
                              CancelTask cancelTask)
                       throws IOException
```
    Open an existing file (read only), with option of cancelling, setting the RandomAccessFile buffer size for efficiency.
    
    Parameters:
    
    location - location of file.
    
    buffer_size - RandomAccessFile buffer size, if <= 0, use default size
    
    cancelTask - allow task to be cancelled; may be null.
    
    Returns:
    
    NetcdfFile object, or null if cant find IOServiceProver
    
    Throws:
    
    IOException - if error
  - open
```
public static NetcdfFile open(String location,
                              int buffer_size,
                              CancelTask cancelTask,
                              Object iospMessage)
                       throws IOException
```
    Open an existing file (read only), with option of cancelling, setting the RandomAccessFile buffer size for efficiency, with an optional special object for the iosp.
    Parameters:
    location - location of file. This may be a
    
    local netcdf-3 filename (with a file: prefix or no prefix)
    remote netcdf-3 filename (with an http: prefix)
    local netcdf-4 filename (with a file: prefix or no prefix)
    local hdf-5 filename (with a file: prefix or no prefix)
    local iosp filename (with a file: prefix or no prefix)
    http://thredds.ucar.edu/thredds/fileServer/grib/NCEP/GFS/Alaska_191km/files/GFS_Alaska_191km_20130416_0600.grib1 If file ends with ".Z", ".zip", ".gzip", ".gz", or ".bz2", it will uncompress/unzip and write to new file without the suffix, then use the uncompressed file. It will look for the uncompressed file before it does any of that. Generally it prefers to place the uncompressed file in the same directory as the original file. If it does not have write permission on that directory, it will use the directory defined by ucar.nc2.util.DiskCache class.
    buffer_size - RandomAccessFile buffer size, if <= 0, use default size
    
    cancelTask - allow task to be cancelled; may be null.
    
    iospMessage - special iosp tweaking (sent before open is called), may be null
    
    Returns:
    
    NetcdfFile object, or null if cant find IOServiceProver
    
    Throws:
    
    IOException - if error
  - canOpen
```
public static boolean canOpen(String location)
                       throws IOException
```
    Find out if the file can be opened, but dont actually open it. Experimental.
    
    Parameters:
    
    location - same as open
    
    Returns:
    
    true if can be opened
    
    Throws:
    
    IOException - on read error
  - open
```
public static NetcdfFile open(String location,
                              String iospClassName,
                              int bufferSize,
                              CancelTask cancelTask,
                              Object iospMessage)
                       throws ClassNotFoundException,
                              IllegalAccessException,
                              InstantiationException,
                              IOException
```
    Open an existing file (read only), specifying which IOSP is to be used.
    
    Parameters:
    
    location - location of file
    
    iospClassName - fully qualified class name of the IOSP class to handle this file
    
    bufferSize - RandomAccessFile buffer size, if <= 0, use default size
    
    cancelTask - allow task to be cancelled; may be null.
    
    iospMessage - special iosp tweaking (sent before open is called), may be null
    
    Returns:
    
    NetcdfFile object, or null if cant find IOServiceProver
    
    Throws:
    
    IOException - if read error
    
    ClassNotFoundException - cannat find iospClassName in thye class path
    
    InstantiationException - if class cannot be instantiated
    
    IllegalAccessException - if class is not accessible
  - canonicalizeUriString
```
public static String canonicalizeUriString(String location)
```
    Removes the "file:" or "file://" prefix from the location, if necessary. Also replaces back slashes with forward slashes.
    
    Parameters:
    
    location - a URI string.
    
    Returns:
    
    a canonical URI string.
  - openInMemory
```
public static NetcdfFile openInMemory(String name,
                                      byte[] data,
                                      String iospClassName)
                               throws IOException,
                                      ClassNotFoundException,
                                      IllegalAccessException,
                                      InstantiationException
```
    Open an in-memory netcdf file, with a specific iosp.
    
    Parameters:
    
    name - name of the dataset. Typically use the filename or URI.
    
    data - in-memory netcdf file
    
    iospClassName - fully qualified class name of the IOSP class to handle this file
    
    Returns:
    
    NetcdfFile object, or null if cant find IOServiceProver
    
    Throws:
    
    IOException - if read error
    
    ClassNotFoundException - cannat find iospClassName in the class path
    
    InstantiationException - if class cannot be instantiated
    
    IllegalAccessException - if class is not accessible
  - openInMemory
```
public static NetcdfFile openInMemory(String name,
                                      byte[] data)
                               throws IOException
```
    Open an in-memory netcdf file.
    
    Parameters:
    
    name - name of the dataset. Typically use the filename or URI.
    
    data - in-memory netcdf file
    
    Returns:
    
    memory-resident NetcdfFile
    
    Throws:
    
    IOException - if error
  - openInMemory
```
public static NetcdfFile openInMemory(String filename)
                               throws IOException
```
    Read a local CDM file into memory. All reads are then done from memory.
    
    Parameters:
    
    filename - location of CDM file, must be a local file.
    
    Returns:
    
    a NetcdfFile, which is completely in memory
    
    Throws:
    
    IOException - if error reading file
  - openInMemory
```
public static NetcdfFile openInMemory(URI uri)
                               throws IOException
```
    Read a remote CDM file into memory. All reads are then done from memory.
    
    Parameters:
    
    uri - location of CDM file, must be accessible through url.toURL().openStream().
    
    Returns:
    
    a NetcdfFile, which is completely in memory
    
    Throws:
    
    IOException - if error reading file
  - open
```
public static NetcdfFile open(RandomAccessFile raf,
                              String location,
                              CancelTask cancelTask,
                              Object iospMessage)
                       throws IOException
```
    Throws:
    
    IOException
  - close
```
public void close()
           throws IOException
```
    Close all resources (files, sockets, etc) associated with this file. If the underlying file was acquired, it will be released, otherwise closed. if isClosed() already, nothing will happen
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface ucar.nc2.util.cache.FileCacheable
    
    Throws:
    
    IOException - if error when closing
  - release
```
public void release()
             throws IOException
```
    Specified by:
    
    release in interface ucar.nc2.util.cache.FileCacheable
    
    Throws:
    
    IOException
  - reacquire
```
public void reacquire()
               throws IOException
```
    Specified by:
    
    reacquire in interface ucar.nc2.util.cache.FileCacheable
    
    Throws:
    
    IOException
  - setFileCache
```
public void setFileCache(ucar.nc2.util.cache.FileCacheIF cache)
```
    Public by accident. Optional file caching.
    
    Specified by:
    
    setFileCache in interface ucar.nc2.util.cache.FileCacheable
  - getCacheName
```
public String getCacheName()
```
    Public by accident. Get the name used in the cache, if any.
    
    Returns:
    
    name in the cache.
  - setCacheName
```
protected void setCacheName(String cacheName)
```
    Public by accident.
    
    Parameters:
    
    cacheName - name in the cache, should be unique for this NetcdfFile. Usually the location.
  - getLocation
```
public String getLocation()
```
    Get the NetcdfFile location. This is a URL, or a file pathname.
    
    Specified by:
    
    getLocation in interface ucar.nc2.util.cache.FileCacheable
    
    Returns:
    
    location URL or file pathname.
  - getId
```
public String getId()
```
    Get the globally unique dataset identifier, if it exists.
    
    Returns:
    
    id, or null if none.
  - getTitle
```
public String getTitle()
```
    Get the human-readable title, if it exists.
    
    Returns:
    
    title, or null if none.
  - getRootGroup
```
public Group getRootGroup()
```
    Get the root group.
    
    Returns:
    
    root group
  - getVariables
```
public List<Variable> getVariables()
```
    Get all of the variables in the file, in all groups. This is part of "version 3 compatibility" interface. Alternatively, use groups.
    
    Returns:
    
    List of type Variable.
  - findGroup
```
public Group findGroup(String fullName)
```
    Find a Group, with the specified (full) name. An embedded "/" is interpreted as separating group names.
    
    Parameters:
    
    fullName - eg "/group/subgroup/wantGroup". Null or empty string returns the root group.
    
    Returns:
    
    Group or null if not found.
  - findVariable
```
public Variable findVariable(Group g,
                             String shortName)
```
  - findVariable
```
public Variable findVariable(String fullNameEscaped)
```
    Find a Variable, with the specified (escaped full) name. It may possibly be nested in multiple groups and/or structures. An embedded "." is interpreted as structure.member. An embedded "/" is interpreted as group/variable. If the name actually has a ".", you must escape it (call NetcdfFile.escapeName(varname)) Any other chars may also be escaped, as they are removed before testing.
    
    Parameters:
    
    fullNameEscaped - eg "/group/subgroup/name1.name2.name".
    
    Returns:
    
    Variable or null if not found.
  - findVariableByAttribute
```
public Variable findVariableByAttribute(Group g,
                                        String attName,
                                        String attValue)
```
  - getDimensions
```
public List<Dimension> getDimensions()
```
    Get the shared Dimensions used in this file. This is part of "version 3 compatibility" interface.
    If the dimensions are in a group, the dimension name will have the group name, in order to disambiguate the dimensions. This means that a Variable's dimensions will not match Dimensions in this list. Therefore it is better to get the shared Dimensions directly from the Groups.
    
    Returns:
    
    List of type Dimension.
  - findDimension
```
public Dimension findDimension(String fullName)
```
    Finds a Dimension with the specified full name. It may be nested in multiple groups. An embedded "/" is interpreted as a group separator. A leading slash indicates the root group. That slash may be omitted, but the fullName will be treated as if it were there. In other words, the first name token in fullName is treated as the short name of a Group or Dimension, relative to the root group.
    
    Parameters:
    
    fullName - Dimension full name, e.g. "/group/subgroup/dim".
    
    Returns:
    
    the Dimension or null if it wasn't found.
  - hasUnlimitedDimension
```
public boolean hasUnlimitedDimension()
```
    Return true if this file has one or more unlimited (record) dimension.
    
    Returns:
    
    if this file has an unlimited Dimension(s)
  - getUnlimitedDimension
```
public Dimension getUnlimitedDimension()
```
    Return the unlimited (record) dimension, or null if not exist. If there are multiple unlimited dimensions, it will return the first one.
    
    Returns:
    
    the unlimited Dimension, or null if none.
  - getGlobalAttributes
```
public List<Attribute> getGlobalAttributes()
```
    Returns the set of global attributes associated with this file. This is part of "version 3 compatibility" interface. Alternatively, use groups.
    
    Returns:
    
    List of type Attribute
  - findGlobalAttribute
```
public Attribute findGlobalAttribute(String name)
```
    Look up global Attribute by (full) name.
    
    Parameters:
    
    name - the name of the attribute
    
    Returns:
    
    the attribute, or null if not found
  - findGlobalAttributeIgnoreCase
```
public Attribute findGlobalAttributeIgnoreCase(String name)
```
    Look up global Attribute by name, ignore case.
    
    Parameters:
    
    name - the name of the attribute
    
    Returns:
    
    the attribute, or null if not found
  - findAttribute
```
public Attribute findAttribute(String fullNameEscaped)
```
    Find an attribute, with the specified (escaped full) name. It may possibly be nested in multiple groups and/or structures. An embedded "." is interpreted as structure.member. An embedded "/" is interpreted as group/group or group/variable. An embedded "@" is interpreted as variable@attribute If the name actually has a ".", you must escape it (call NetcdfFile.escapeName(varname)) Any other chars may also be escaped, as they are removed before testing.
    
    Parameters:
    
    fullNameEscaped - eg "@attName", "/group/subgroup/@attName" or "/group/subgroup/varname.name2.name@attName"
    
    Returns:
    
    Attribute or null if not found.
  - findAttValueIgnoreCase
```
public String findAttValueIgnoreCase(Variable v,
                                     String attName,
                                     String defaultValue)
```
    Find a String-valued global or variable Attribute by Attribute name (ignore case), return the Value of the Attribute. If not found return defaultValue
    
    Parameters:
    
    v - the variable or null for global attribute
    
    attName - the (full) name of the attribute, case insensitive
    
    defaultValue - return this if attribute not found
    
    Returns:
    
    the attribute value, or defaultValue if not found
  - readAttributeDouble
```
public double readAttributeDouble(Variable v,
                                  String attName,
                                  double defValue)
```
  - readAttributeInteger
```
public int readAttributeInteger(Variable v,
                                String attName,
                                int defValue)
```
  - toString
```
public String toString()
```
    CDL representation of Netcdf header info, non strict
    
    Overrides:
    
    toString in class Object
  - toNcML
```
public String toNcML(String url)
              throws IOException
```
    CDL representation of Netcdf header info, non strict
    
    Throws:
    
    IOException
  - writeCDL
```
public void writeCDL(OutputStream out,
                     boolean strict)
```
    Write CDL representation to OutputStream.
    
    Parameters:
    
    out - write to this OutputStream
    
    strict - if true, make it stricly CDL, otherwise, add a little extra info
  - writeCDL
```
public void writeCDL(PrintWriter pw,
                     boolean strict)
```
    Write CDL representation to PrintWriter.
    
    Parameters:
    
    pw - write to this PrintWriter
    
    strict - if true, make it stricly CDL, otherwise, add a little extra info
  - toStringStart
```
public void toStringStart(PrintWriter pw,
                          boolean strict)
```
  - toStringEnd
```
public void toStringEnd(PrintWriter pw)
```
  - writeCDL
```
protected void writeCDL(Formatter f,
                        Indent indent,
                        boolean strict)
```
  - toStringStart
```
protected void toStringStart(Formatter f,
                             Indent indent,
                             boolean strict)
```
  - writeNcML
```
public void writeNcML(OutputStream os,
                      String uri)
               throws IOException
```
    Write the NcML representation: dont show coodinate values
    
    Parameters:
    
    os - : write to this OutputStream. Will be closed at end of the method.
    
    uri - use this for the url attribute; if null use getLocation(). // ??
    
    Throws:
    
    IOException - if error
    
    See Also:
    
    NcMLWriter.writeToStream(org.jdom2.Element, java.io.OutputStream)
  - writeNcML
```
public void writeNcML(Writer writer,
                      String uri)
               throws IOException
```
    Write the NcML representation: dont show coodinate values
    
    Parameters:
    
    writer - : write to this Writer, should have encoding of UTF-8 if applicable. Will be closed at end of the method.
    
    uri - use this for the url attribute; if null use getLocation().
    
    Throws:
    
    IOException - if error
    
    See Also:
    
    NcMLWriter.writeToWriter(org.jdom2.Element, java.io.Writer)
  - syncExtend
```
public boolean syncExtend()
                   throws IOException
```
    Extend the file if needed, in a way that is compatible with the current metadata, that is, does not invalidate structural metadata held by the application. For example, ok if dimension lengths, data has changed. All previous object references (variables, dimensions, etc) remain valid.
    
    Returns:
    
    true if file was extended.
    
    Throws:
    
    IOException - if error
  - getLastModified
```
public long getLastModified()
```
    Specified by:
    
    getLastModified in interface ucar.nc2.util.cache.FileCacheable
  - addAttribute
```
public Attribute addAttribute(Group parent,
                              Attribute att)
```
    Add an attribute to a group.
    
    Parameters:
    
    parent - add to this group. If group is null, use root group
    
    att - add this attribute
    
    Returns:
    
    the attribute that was added
  - addAttribute
```
public Attribute addAttribute(Group parent,
                              String name,
                              String value)
```
    Add optional String attribute to a group.
    
    Parameters:
    
    parent - add to this group. If group is null, use root group
    
    name - attribute name, may not be null
    
    value - attribute value, may be null, in which case, do not addd
    
    Returns:
    
    the attribute that was added
  - addGroup
```
public Group addGroup(Group parent,
                      Group g)
```
    Add a group to the parent group.
    
    Parameters:
    
    parent - add to this group. If group is null, use root group
    
    g - add this group
    
    Returns:
    
    the group that was added
  - addDimension
```
public Dimension addDimension(Group parent,
                              Dimension d)
```
    Add a shared Dimension to a Group.
    
    Parameters:
    
    parent - add to this group. If group is null, use root group
    
    d - add this Dimension
    
    Returns:
    
    the dimension that was added
  - removeDimension
```
public boolean removeDimension(Group g,
                               String dimName)
```
    Remove a shared Dimension from a Group by name.
    
    Parameters:
    
    g - remove from this group. If group is null, use root group
    
    dimName - name of Dimension to remove.
    
    Returns:
    
    true if found and removed.
  - addVariable
```
public Variable addVariable(Group g,
                            Variable v)
```
    Add a Variable to the given group.
    
    Parameters:
    
    g - add to this group. If group is null, use root group
    
    v - add this Variable
    
    Returns:
    
    the variable that was added
  - addVariable
```
public Variable addVariable(Group g,
                            String shortName,
                            DataType dtype,
                            String dims)
```
    Create a new Variable, and add to the given group.
    
    Parameters:
    
    g - add to this group. If group is null, use root group
    
    shortName - short name of the Variable
    
    dtype - data type of the Variable
    
    dims - list of dimension names
    
    Returns:
    
    the new Variable
  - addStringVariable
```
public Variable addStringVariable(Group g,
                                  String shortName,
                                  String dims,
                                  int strlen)
```
    Create a new Variable of type Datatype.CHAR, and add to the given group.
    
    Parameters:
    
    g - add to this group. If group is null, use root group
    
    shortName - short name of the Variable
    
    dims - list of dimension names
    
    strlen - dimension length of the inner (fastest changing) dimension
    
    Returns:
    
    the new Variable
  - removeVariable
```
public boolean removeVariable(Group g,
                              String varName)
```
    Remove a Variable from the given group by name.
    
    Parameters:
    
    g - remove from this group. If group is null, use root group
    
    varName - name of variable to remove.
    
    Returns:
    
    true is variable found and removed
  - addVariableAttribute
```
public Attribute addVariableAttribute(Variable v,
                                      Attribute att)
```
    Add a variable attribute.
    
    Parameters:
    
    v - add to this Variable.
    
    att - add this attribute
    
    Returns:
    
    the added Attribute
  - sendIospMessage
```
public Object sendIospMessage(Object message)
```
    Generic way to send a "message" to the underlying IOSP. This message is sent after the file is open. To affect the creation of the file, you must send into the factory method.
    Parameters:
    message - iosp specific message Special:
    
    NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE : tells Netcdf-3 files to make record (unlimited) variables into a structure. return true if it has a Nectdf-3 record structure
    Returns:
    
    iosp specific return, may be null
  - makeRecordStructure
```
protected Boolean makeRecordStructure()
```
    If there is an unlimited dimension, make all variables that use it into a Structure. A Variable called "record" is added. You can then access these through the record structure.
    
    Returns:
    
    true if it has a Nectdf-3 record structure
  - removeRecordStructure
```
protected Boolean removeRecordStructure()
```
  - setId
```
public void setId(String id)
```
    Set the globally unique dataset identifier.
    
    Parameters:
    
    id - the id
  - setTitle
```
public void setTitle(String title)
```
    Set the dataset "human readable" title.
    
    Parameters:
    
    title - the title
  - setLocation
```
public void setLocation(String location)
```
    Set the location, a URL or local filename.
    
    Parameters:
    
    location - the location
  - setImmutable
```
public NetcdfFile setImmutable()
```
    Make this immutable.
    
    Returns:
    
    this
  - empty
```
public void empty()
```
    Completely empty the objects in the netcdf file. Used for rereading the file on a sync().
  - makeRootGroup
```
protected Group makeRootGroup()
```
  - finish
```
public void finish()
```
    Finish constructing the object model. This construsts the "global" variables, attributes and dimensions. It also looks for coordinate variables.
  - readData
```
protected Array readData(Variable v,
                         Section ranges)
                  throws IOException,
                         InvalidRangeException
```
    Throws:
    
    IOException
    
    InvalidRangeException
  - readSection
```
public Array readSection(String variableSection)
                  throws IOException,
                         InvalidRangeException
```
    Read a variable using the given section specification. The result is always an array of the type of the innermost variable. Its shape is the accumulation of all the shapes of its parent structures.
    
    Parameters:
    
    variableSection - the constraint expression.
    
    Returns:
    
    data requested
    
    Throws:
    
    IOException - if error
    
    InvalidRangeException - if variableSection is invalid
    
    See Also:
    
    SectionSpecification
  - readToByteChannel
```
protected long readToByteChannel(Variable v,
                                 Section section,
                                 WritableByteChannel wbc)
                          throws IOException,
                                 InvalidRangeException
```
    Read data from a top level Variable and send data to a WritableByteChannel. Experimental.
    
    Parameters:
    
    v - a top-level Variable
    
    section - the section of data to read. There must be a Range for each Dimension in the variable, in order. Note: no nulls allowed. IOSP may not modify.
    
    wbc - write data to this WritableByteChannel
    
    Returns:
    
    the number of bytes written to the channel
    
    Throws:
    
    IOException - if read error
    
    InvalidRangeException - if invalid section
  - readToOutputStream
```
protected long readToOutputStream(Variable v,
                                  Section section,
                                  OutputStream out)
                           throws IOException,
                                  InvalidRangeException
```
    Throws:
    
    IOException
    
    InvalidRangeException
  - getStructureIterator
```
protected StructureDataIterator getStructureIterator(Structure s,
                                                     int bufferSize)
                                              throws IOException
```
    Throws:
    
    IOException
  - readArrays
```
public List<Array> readArrays(List<Variable> variables)
                       throws IOException
```
    Do a bulk read on a list of Variables and return a corresponding list of Array that contains the results of a full read on each Variable. This is mostly here so DODSNetcdf can override it with one call to the server.
    
    Parameters:
    
    variables - List of type Variable
    
    Returns:
    
    List of Array, one for each Variable in the input.
    
    Throws:
    
    IOException - if read error
  - read
```
public Array read(String variableSection,
                  boolean flatten)
           throws IOException,
                  InvalidRangeException
```
    Deprecated. use readSection(), flatten=false no longer supported
    
    Read a variable using the given section specification.
    
    Parameters:
    
    variableSection - the constraint expression.
    
    flatten - MUST BE TRUE
    
    Returns:
    
    Array data read.
    
    Throws:
    
    IOException - if error
    
    InvalidRangeException - if variableSection is invalid
    
    See Also:
    
    SectionSpecification
  - toStringDebug
```
protected String toStringDebug(Object o)
```
    Access to iosp debugging info.
    
    Parameters:
    
    o - must be a Variable, Dimension, Attribute, or Group
    
    Returns:
    
    debug info for this object.
  - getDetailInfo
```
public String getDetailInfo()
```
    Access to iosp debugging info.
    
    Returns:
    
    debug / underlying implementation details
  - getDetailInfo
```
public void getDetailInfo(Formatter f)
```
  - showCached
```
protected void showCached(Formatter f)
```
  - showProxies
```
protected void showProxies(Formatter f)
```
  - getIosp
```
public IOServiceProvider getIosp()
```
    DO NOT USE - public by accident
    
    Returns:
    
    the IOSP for this NetcdfFile
  - getFileTypeId
```
@Nonnull
public String getFileTypeId()
```
    Get the file type id for the underlying data source.
    
    Returns:
    
    registered id of the file type
    
    See Also:
    
    "http://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"
  - getFileTypeDescription
```
public String getFileTypeDescription()
```
    Get a human-readable description for this file type.
    
    Returns:
    
    description of the file type
    
    See Also:
    
    "http://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"
  - getFileTypeVersion
```
public String getFileTypeVersion()
```
    Get the version of this file type.
    
    Returns:
    
    version of the file type
    
    See Also:
    
    "http://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"
  - main
```
public static void main(String[] arg)
                 throws Exception
```
    debugging - do not use
    
    Throws:
    
    Exception
  - makeValidCdmObjectName
```
public static String makeValidCdmObjectName(String shortName)
```
    Create a valid CDM object name. Control chars (< 0x20) are not allowed. Trailing and leading blanks are not allowed and are stripped off. A space is converted into an underscore "_". A forward slash "/" is converted into an underscore "_".
    
    Parameters:
    
    shortName - from this name
    
    Returns:
    
    valid CDM object name
  - makeValidCDLName
```
public static String makeValidCDLName(String vname)
```
    Escape special characters in a netcdf short name when it is intended for use in CDL.
    
    Parameters:
    
    vname - the name
    
    Returns:
    
    escaped version of it
  - makeValidPathName
```
public static String makeValidPathName(String vname)
```
    Escape special characters in a netcdf short name when it is intended for use in a fullname
    
    Parameters:
    
    vname - the name
    
    Returns:
    
    escaped version of it
  - makeValidSectionSpecName
```
public static String makeValidSectionSpecName(String vname)
```
    Escape special characters in a netcdf short name when it is intended for use in a sectionSpec
    
    Parameters:
    
    vname - the name
    
    Returns:
    
    escaped version of it
  - makeNameUnescaped
```
public static String makeNameUnescaped(String vname)
```
    Unescape any escaped characters in a name.
    
    Parameters:
    
    vname - the escaped name
    
    Returns:
    
    unescaped version of it
  - makeFullName
```
protected static String makeFullName(CDMNode v)
```
    Given a CDMNode, create its full name with appropriate backslash escaping. Warning: do not use for a section spec.
    
    Parameters:
    
    v - the cdm node
    
    Returns:
    
    full name
  - makeFullNameSectionSpec
```
protected static String makeFullNameSectionSpec(CDMNode v)
```
    Given a CDMNode, create its full name with appropriate backslash escaping for use in a section spec.
    
    Parameters:
    
    v - the cdm node
    
    Returns:
    
    full name
  - makeFullName
```
protected static String makeFullName(CDMNode node,
                                     String reservedChars)
```
    Given a CDMNode, create its full name with appropriate backslash escaping of the specified characters.
    
    Parameters:
    
    node - the cdm node
    
    reservedChars - the set of characters to escape
    
    Returns:
    
    full name
  - makeFullNameWithString
```
protected String makeFullNameWithString(Group parent,
                                        String name)
```
    Create a synthetic full name from a group plus a string
    
    Parameters:
    
    parent - parent group
    
    name - synthetic name string
    
    Returns:
    
    synthetic name

Class NetcdfFile

Naming

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

IOSP_MESSAGE_ADD_RECORD_STRUCTURE

IOSP_MESSAGE_CONVERT_RECORD_STRUCTURE

IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE

IOSP_MESSAGE_RANDOM_ACCESS_FILE

debugSPI

debugCompress

showRequest

location

id

title

cacheName

rootGroup

cache

spi

variables

dimensions

gattributes

reservedFullName

reservedSectionSpec

reservedCdl

Constructor Detail

NetcdfFile

NetcdfFile

NetcdfFile

NetcdfFile

NetcdfFile

NetcdfFile

NetcdfFile

Method Detail

registerIOProvider

registerIOProvider

registerIOProvider

registerIOProviderPreferred

iospRegistered

iospDeRegister

setDebugFlags

setProperty

open

open

open

open

canOpen

open

canonicalizeUriString

openInMemory

openInMemory

openInMemory

openInMemory

open

close

release

reacquire

setFileCache

getCacheName

setCacheName

getLocation

getId

getTitle

getRootGroup

getVariables

findGroup

findVariable

findVariable

findVariableByAttribute

getDimensions

findDimension

hasUnlimitedDimension

getUnlimitedDimension

getGlobalAttributes

findGlobalAttribute

findGlobalAttributeIgnoreCase

findAttribute

findAttValueIgnoreCase