Package ucar.nc2

Class NetcdfFile

  • All Implemented Interfaces:
    Closeable, AutoCloseable, FileCacheable
    Direct Known Subclasses:
    CdmRemote, DapNetcdfFile, DODSNetcdfFile, NetcdfDataset, NetcdfFileSubclass, NetcdfFileWriteable
    public class NetcdfFile
extends Object
implements FileCacheable, Closeable

    Read-only scientific datasets that are accessible through the netCDF API. Immutable after setImmutable() is called. Reading data is not thread-safe because of the use of RandomAccessFile.

    Using this class's Builder scheme to create a NetcdfFile object could, for example, be accomplished as follows, using a try/finally block to ensure that the NetcdfFile is closed when done. 

     NetcdfFile ncfile = null;
 try {
   ncfile = NetcdfFile.builder().setLocation(fileName).build();
   // do stuff
 } finally {
   if (ncfile != null) {
     ncfile.close();
   }
 }
    More conveniently, a NetcdfFile object may be created using one of the static methods in NetcdfFiles: 
     NetcdfFile ncfile = null;
 try {
   ncfile = NetcdfFiles.open(fileName);
   // do stuff
 } finally {
   if (ncfile != null) {
     ncfile.close();
   }
 }
    Or better yet, use try-with-resources: 
     try (NetcdfFile ncfile = NetcdfFiles.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

    • Constructor Detail

      • NetcdfFile

        @Deprecated
public NetcdfFile​(String filename)
           throws IOException
        Deprecated.
        use NetcdfFiles.open( location) or NetcdfDatasets.openFile( location)
        This is can only be used for local netcdf-3 files.
        Parameters:
        filename - location
        Throws:
        IOException - if error

      • NetcdfFile

        @Deprecated
public NetcdfFile​(URL url)
           throws IOException
        Deprecated.
        use NetcdfFiles.open( http:location) or NetcdfDatasets.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

        @Deprecated
protected NetcdfFile​(String iospClassName,
                     Object iospParam,
                     String location,
                     int buffer_size,
                     CancelTask cancelTask)
              throws IOException,
                     IllegalAccessException,
                     InstantiationException,
                     ClassNotFoundException
        Deprecated.
        use NetcdfFile.builder()
        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

        @Deprecated
protected NetcdfFile​(IOServiceProvider spi,
                     RandomAccessFile raf,
                     String location,
                     CancelTask cancelTask)
              throws IOException
        Deprecated.
        use NetcdfFile.builder()
        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

        @Deprecated
protected NetcdfFile​(IOServiceProvider spi,
                     String location)
        Deprecated.
        use NetcdfFile.builder()
        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

        @Deprecated
protected NetcdfFile()
        Deprecated.
        use NetcdfFile.builder()
        For subclass construction. Use NetcdfFileSubclass to access this constructor

      • NetcdfFile

        @Deprecated
protected NetcdfFile​(NetcdfFile ncfile)
        Deprecated.
        use NetcdfFile.builder()
        Copy constructor, used by NetcdfDataset. Shares the iosp.
        Parameters:
        ncfile - copy from here

    • Method Detail

      • setDebugFlags

        @Deprecated
public static void setDebugFlags​(DebugFlags debugFlag)
        Deprecated.
        do not use

      • registerIOProvider

        @Deprecated
public static void registerIOProvider​(Class iospClass,
                                      boolean last)
                               throws IllegalAccessException,
                                      InstantiationException
        Deprecated.
        use NetcdfFiles.registerIOProvider
        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

        @Deprecated
public static void registerIOProviderPreferred​(Class iospClass,
                                               Class target)
                                        throws IllegalAccessException,
                                               InstantiationException
        Deprecated.
        use NetcdfFiles.registerIOProvider
        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

        @Deprecated
public static boolean iospRegistered​(Class iospClass)
        Deprecated.
        use NetcdfFiles.iospRegistered
        See if a specific IOServiceProvider is registered
        Parameters:
        iospClass - Class for which to search

      • iospDeRegister

        @Deprecated
public static boolean iospDeRegister​(Class iospClass)
        Deprecated.
        use NetcdfFiles.iospDeRegister
        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

      • setProperty

        @Deprecated
public static void setProperty​(String name,
                               String value)
        Deprecated.
        do not use
        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

        @Deprecated
public static NetcdfFile open​(String location)
                       throws IOException
        Deprecated.
        use NetcdfFiles.open
        Open an existing netcdf file (read only).
        Parameters:
        location - location of file.
        Returns:
        the NetcdfFile.
        Throws:
        IOException - if error

      • open

        @Deprecated
public static NetcdfFile open​(String location,
                              CancelTask cancelTask)
                       throws IOException
        Deprecated.
        use NetcdfFiles.open
        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

        @Deprecated
public static NetcdfFile open​(String location,
                              int buffer_size,
                              CancelTask cancelTask)
                       throws IOException
        Deprecated.
        use NetcdfFiles.open
        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

        @Deprecated
public static NetcdfFile open​(String location,
                              int buffer_size,
                              CancelTask cancelTask,
                              Object iospMessage)
                       throws IOException
        Deprecated.
        use NetcdfFiles.open
        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
        1. local netcdf-3 filename (with a file: prefix or no prefix)
        2. remote netcdf-3 filename (with an http: prefix)
        3. local netcdf-4 filename (with a file: prefix or no prefix)
        4. local hdf-5 filename (with a file: prefix or no prefix)
        5. 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

        @Deprecated
public static boolean canOpen​(String location)
                       throws IOException
        Deprecated.
        use NetcdfFiles.canOpen
        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

      • canonicalizeUriString

        @Deprecated
public static String canonicalizeUriString​(String location)
        Deprecated.
        use NetcdfFiles.canonicalizeUriString
        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

        @Deprecated
public static NetcdfFile openInMemory​(String name,
                                      byte[] data)
                               throws IOException
        Deprecated.
        use NetcdfFiles.openInMemory
        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

        @Deprecated
public static NetcdfFile openInMemory​(String filename)
                               throws IOException
        Deprecated.
        use NetcdfFiles.openInMemory
        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

        @Deprecated
public static NetcdfFile openInMemory​(URI uri)
                               throws IOException
        Deprecated.
        use NetcdfFiles.openInMemory
        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

        @Deprecated
public static NetcdfFile open​(RandomAccessFile raf,
                              String location,
                              CancelTask cancelTask,
                              Object iospMessage)
                       throws IOException
        Deprecated.
        use NetcdfFiles.open
        Open a RandomAccessFile as a NetcdfFile, if possible.
        Parameters:
        raf - The open raf, is not cloised by this method.
        location - human readable locatoin of this dataset.
        cancelTask - used to monitor user cancellation; may be null.
        iospMessage - send this message to iosp; may be null.
        Returns:
        NetcdfFile or throw an Exception.
        Throws:
        IOException - if cannot open as a CDM NetCDF.

      • 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 AutoCloseable
        Specified by:
        close in interface Closeable
        Specified by:
        close in interface FileCacheable
        Throws:
        IOException - if error when closing

      • setFileCache

        @Deprecated
public void setFileCache​(FileCacheIF cache)
        Deprecated.
        do not use
        Public by accident. Optional file caching.
        Specified by:
        setFileCache in interface FileCacheable
        Parameters:
        cache - must store this, use it on close as above.

      • getCacheName

        @Deprecated
public String getCacheName()
        Deprecated.
        do not use
        Public by accident. Get the name used in the cache, if any.
        Returns:
        name in the cache.

      • setCacheName

        @Deprecated
protected void setCacheName​(String cacheName)
        Deprecated.
        do not use
        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 FileCacheable
        Returns:
        location URL or file pathname.

      • getId

        @Nullable
public String getId()
        Get the globally unique dataset identifier, if it exists.
        Returns:
        id, or null if none.

      • getTitle

        @Nullable
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

      • findGroup

        @Nullable
public Group findGroup​(@Nullable
                       String fullName)
        Find a Group, with the specified (full) name. A full name should start with a '/'. For backwards compatibility, we accept full names that omit the leading '/'. An embedded '/' separates subgroup names.
        Parameters:
        fullName - eg "/group/subgroup/wantGroup". Null or empty string returns the root group.
        Returns:
        Group or null if not found.

      • findVariable

        @Deprecated
@Nullable
public Variable findVariable​(Group g,
                             String shortName)
        Deprecated.
        use g.findVariable(shortName)
        Find a Variable by short name, in the given group.
        Parameters:
        g - A group in this file. Null for root group.
        shortName - short name of the Variable.
        Returns:
        Variable if found, else null.

      • findVariable

        @Nullable
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 NetcdfFiles.makeValidPathName(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

        @Deprecated
@Nullable
public Variable findVariableByAttribute​(Group g,
                                        String attName,
                                        String attValue)
        Deprecated.
        use g.findVariableByAttribute(String attName, String attValue)
        Look in the given Group and in its nested Groups for a Variable with a String valued Attribute with the given name and value.
        Parameters:
        g - start with this Group, null for the root Group.
        attName - look for an Attribuite with this name.
        attValue - look for an Attribuite with this value.
        Returns:
        the first Variable that matches, or null if none match.

      • findDimension

        @Nullable
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

        @Nullable
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.

      • getDimensions

        @Deprecated
public com.google.common.collect.ImmutableList<Dimension> getDimensions()
        Deprecated.
        use ncfile.getRootGroup().getDimensions() for files without nested groups, or recurse through nested groups to get dimensions.
        Get the shared Dimensions used in this file.

        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.

      • getVariables

        public com.google.common.collect.ImmutableList<Variable> getVariables()
        Get all of the variables in the file, in all groups. Alternatively, use groups.

      • getGlobalAttributes

        public com.google.common.collect.ImmutableList<Attribute> getGlobalAttributes()
        Returns the set of global attributes associated with this file, which are the attributes associated with the root group, or any subgroup. Alternatively, use groups.

      • findGlobalAttribute

        @Nullable
public Attribute findGlobalAttribute​(String attName)
        Look up an Attribute by (short) name in the root Group or nested Groups, exact match.
        Parameters:
        attName - the name of the attribute
        Returns:
        the first Group attribute with given name, or null if not found

      • findGlobalAttributeIgnoreCase

        @Nullable
public Attribute findGlobalAttributeIgnoreCase​(String name)
        Look up an Attribute by (short) name in the root Group or nested Groups, ignore case.
        Parameters:
        name - the name of the attribute
        Returns:
        the first group attribute with given Attribute name, ignoronmg case, or null if not found

      • findAttribute

        @Nullable
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 NetcdfFiles.makeValidPathName(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

        @Deprecated
public String findAttValueIgnoreCase​(Variable v,
                                     String attName,
                                     String defaultValue)
        Deprecated.
        use getRootGroup() or Variable attributes().findAttributeString().
        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 to look in the root group.
        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

        @Deprecated
public double readAttributeDouble​(Variable v,
                                  String attName,
                                  double defValue)
        Deprecated.
        use use getRootGroup() or Variable attributes().findAttributeDouble

      • readAttributeInteger

        @Deprecated
public int readAttributeInteger​(Variable v,
                                String attName,
                                int defValue)
        Deprecated.
        use use getRootGroup() or Variable attributes().findAttributeInteger

      • toString

        public String toString()
        CDL representation of Netcdf header info, non strict
        Overrides:
        toString in class Object

      • toNcml

        public String toNcml​(String url)
        NcML representation of Netcdf header info, non strict

      • writeNcml

        public void writeNcml​(OutputStream os,
                      String uri)
               throws IOException
        Write the NcML representation: dont show coordinate 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

      • writeNcml

        public void writeNcml​(Writer writer,
                      String uri)
               throws IOException
        Write the NcML representation: dont show coordinate values
        Parameters:
        writer - : write to this Writer, should have encoding of UTF-8. Will be closed at end of the method.
        uri - use this for the url attribute; if null use getLocation().
        Throws:
        IOException - if error

      • writeCDL

        @Deprecated
public void writeCDL​(OutputStream out,
                     boolean strict)
        Deprecated.
        use CDLWriter
        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

        @Deprecated
public void writeCDL​(PrintWriter pw,
                     boolean strict)
        Deprecated.
        use CDLWriter
        Write CDL representation to PrintWriter.
        Parameters:
        pw - write to this PrintWriter
        strict - if true, make it stricly CDL, otherwise, add a little extra info

      • writeCDL

        protected void writeCDL​(Formatter f,
                        Indent indent,
                        boolean strict)

      • syncExtend

        @Deprecated
public boolean syncExtend()
                   throws IOException
        Deprecated.
        do not use
        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

        @Deprecated
public long getLastModified()
        Deprecated.
        Description copied from interface: FileCacheable
        Returns the time that the underlying file(s) were last modified. If they've changed since they were stored in the cache, they will be closed and reopened with FileFactory.
        Specified by:
        getLastModified in interface FileCacheable
        Returns:
        a long value representing the time the file(s) were last modified or 0L if the last-modified time couldn't be determined for any reason.

      • addAttribute

        @Deprecated
public Attribute addAttribute​(Group parent,
                              Attribute att)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Attribute addAttribute​(Group parent,
                              String name,
                              String value)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Group addGroup​(Group parent,
                      Group g)
        Deprecated.
        Use NetcdfFile.builder()
        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

      • setRootGroup

        @Deprecated
public void setRootGroup​(Group rootGroup)
        Deprecated.
        Use NetcdfFile.builder()
        Public by accident.

      • addDimension

        @Deprecated
public Dimension addDimension​(Group parent,
                              Dimension d)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public boolean removeDimension​(Group g,
                               String dimName)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Variable addVariable​(Group g,
                            Variable v)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Variable addVariable​(Group g,
                            String shortName,
                            DataType dtype,
                            String dims)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Variable addStringVariable​(Group g,
                                  String shortName,
                                  String dims,
                                  int strlen)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public boolean removeVariable​(Group g,
                              String varName)
        Deprecated.
        Use NetcdfFile.builder()
        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

        @Deprecated
public Attribute addVariableAttribute​(Variable v,
                                      Attribute att)
        Deprecated.
        Use NetcdfFile.builder()
        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, use a factory method like NetcdfFile.open(). In ver6, IOSP_MESSAGE_ADD_RECORD_STRUCTURE, IOSP_MESSAGE_REMOVE_RECORD_STRUCTURE will not work here.
        Parameters:
        message - iosp specific message
        Returns:
        iosp specific return, may be null

      • makeRecordStructure

        @Deprecated
protected Boolean makeRecordStructure()
        Deprecated.
        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

        @Deprecated
protected Boolean removeRecordStructure()
        Deprecated.

      • setId

        @Deprecated
public void setId​(String id)
        Deprecated.
        Use NetcdfFile.builder()
        Set the globally unique dataset identifier.
        Parameters:
        id - the id

      • setTitle

        @Deprecated
public void setTitle​(String title)
        Deprecated.
        Use NetcdfFile.builder()
        Set the dataset "human readable" title.
        Parameters:
        title - the title

      • setLocation

        @Deprecated
public void setLocation​(String location)
        Deprecated.
        Use NetcdfFile.builder()
        Set the location, a URL or local filename.
        Parameters:
        location - the location

      • setImmutable

        @Deprecated
public NetcdfFile setImmutable()
        Deprecated.
        Use NetcdfFile.builder()
        Make this immutable.
        Returns:
        this

      • empty

        @Deprecated
public void empty()
        Deprecated.
        Completely empty the objects in the netcdf file. Used for rereading the file on a sync().

      • finish

        @Deprecated
public void finish()
        Deprecated.
        Use NetcdfFile.builder()
        Finish constructing the object model. This construsts the "global" variables, attributes and dimensions. It also looks for coordinate variables.

      • 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

        @Deprecated
protected long readToByteChannel​(Variable v,
                                 Section section,
                                 WritableByteChannel wbc)
                          throws IOException,
                                 InvalidRangeException
        Deprecated.
        do not use
        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

      • readArrays

        @Deprecated
public List<Array> readArrays​(List<Variable> variables)
                       throws IOException
        Deprecated.
        will be moved to DODSNetcdfFile in version 6.
        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

      • 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()
        Show debug / underlying implementation details

      • getDetailInfo

        public void getDetailInfo​(Formatter f)

      • showProxies

        protected void showProxies​(Formatter f)

      • getFileTypeId

        public String getFileTypeId()
        Get the file type id for the underlying data source.
        Returns:
        registered id of the file type
        See Also:
        "https://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:
        "https://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:
        "https://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"

      • makeValidCdmObjectName

        @Deprecated
public static String makeValidCdmObjectName​(String shortName)
        Deprecated.
        use NetcdfFiles.makeValidCdmObjectName
        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

        @Deprecated
public static String makeValidCDLName​(String vname)
        Deprecated.
        use NetcdfFiles.makeValidCDLName
        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

        @Deprecated
public static String makeValidPathName​(String vname)
        Deprecated.
        use NetcdfFiles.makeValidPathName
        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

        @Deprecated
public static String makeValidSectionSpecName​(String vname)
        Deprecated.
        use NetcdfFiles.makeValidSectionSpecName
        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

        @Deprecated
public static String makeNameUnescaped​(String vname)
        Deprecated.
        use NetcdfFiles.makeNameUnescaped
        Unescape any escaped characters in a name.
        Parameters:
        vname - the escaped name
        Returns:
        unescaped version of it

      • makeFullName

        @Deprecated
protected static String makeFullName​(CDMNode v)
        Deprecated.
        use NetcdfFiles.makeFullName
        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

        @Deprecated
protected static String makeFullNameSectionSpec​(CDMNode v)
        Deprecated.
        use NetcdfFiles.makeFullNameSectionSpec
        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

        @Deprecated
protected static String makeFullName​(CDMNode node,
                                     String reservedChars)
        Deprecated.
        use NetcdfFiles.makeFullName
        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

        @Deprecated
protected String makeFullNameWithString​(Group parent,
                                        String name)
        Deprecated.
        use NetcdfFiles.makeFullNameWithString
        Create a synthetic full name from a group plus a string
        Parameters:
        parent - parent group
        name - synthetic name string
        Returns:
        synthetic name

      • toBuilder

        public NetcdfFile.Builder<?> toBuilder()
        Turn into a mutable Builder. Can use toBuilder().build() to copy.

      • builder

        public static NetcdfFile.Builder<?> builder()
        Get Builder for this class. Allows subclassing.
        See Also:
        "https://community.oracle.com/blogs/emcmanus/2010/10/24/using-builder-pattern-subclasses"