org.autoplot.cdf

Class CdfUtil

java.lang.Object

org.autoplot.cdf.CdfUtil

public class CdfUtil
extends java.lang.Object

static methods supporting CdfFileDataSource

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CdfUtil.CdfVariableDescription information about a variable.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	OPTION_DATA_ONLY if "true" return only the data variables, not the support data.
static java.lang.String	OPTION_DEEP if "true" then return more detailed descriptions in HTML
static java.lang.String	OPTION_INCLUDE_EMPTY_RECORDS if "true", show empty records (true is default).
static java.lang.String	OPTION_IS_MASTER if "true", then don't show the number of records.
static java.lang.String	OPTION_RANK_LIMIT if greater than -1, then only read variables up to this rank.

Constructor Summary

Constructors

Constructor and Description
CdfUtil() Creates a new instance of CdfUtil

Method Summary

Modifier and Type	Method and Description
static void	doApplyAttributes(java.util.Map<java.lang.String,java.lang.Object> attr1, MutablePropertyDataSet result, java.lang.String os1, java.lang.String constraint) apply the ISTP metadata to the dataset.
static int[]	getDimensions(CDFReader cdf, java.lang.String variableName) This is cdf.getDimensions( variableName ), but then check varies to see if varies[0] is false (for rvariables).
protected static int	getEffectiveRank(boolean[] varies) returns effective rank.
static java.util.Map<java.lang.String,java.lang.String>	getPlottable(CDFReader cdf, boolean dataOnly, int rankLimit) Return a map where keys are the names of the variables, and values are descriptions.
static java.util.Map<java.lang.String,java.lang.String>	getPlottable(CDFReader cdf, boolean dataOnly, int rankLimit, java.util.Map<java.lang.String,java.lang.String> options) Return a map where keys are the names of the variables, and values are descriptions.
static java.util.LinkedHashMap<java.lang.String,CdfUtil.CdfVariableDescription>	getPlottable(CDFReader cdf, java.util.Map<java.lang.String,java.lang.String> options) retrieve information about all the variables.
static DatumRange	getRange(java.util.HashMap attrs) returns the range of the data by looking for the SCALEMIN/SCALEMAX params, or the required VALIDMIN/VALIDMAX parameters.
static java.lang.String	getScaleType(java.util.HashMap attrs)
static java.lang.String	getStringDataType(int type) return the data type for the encoding.
static boolean	hasAttribute(CDFReader cdf, java.lang.String var, java.lang.String attrname) return true if the attribute is set for the variable.
static int	jvmMemory(QDataSet ds) returns the amount of JVM memory in bytes occupied by the dataset.
static MutablePropertyDataSet	loadVariable(CDFReader cdf, java.lang.String svariable) Return the named variable as a QDataSet.
static MutablePropertyDataSet	loadVariable(CDFReader cdf, java.lang.String svariable, long recStart, long recCount, long recInterval, int slice1, ProgressMonitor mon) Return the named variable as a QDataSet.
static void	maybeAddValidRange(java.util.Map<java.lang.String,java.lang.Object> props, MutablePropertyDataSet ds) add the valid range only if it looks like it is correct.
static java.lang.String	maybeShorten(java.lang.String context, java.lang.String name) abbreviate names, motivated by Cluster CDF files which have Data__C1_CP_PEA_3DRH_cnts with DEPEND_0 of time_tags__C1_CP_PEA_3DRH_cnts.
protected static int	sizeOf(long itype) returns the size of the data type in bytes.
static MutablePropertyDataSet	wrapCdfData(CDFReader cdf, java.lang.String svariable) Deprecated. use loadCdfVariable instead
static MutablePropertyDataSet	wrapCdfData(CDFReader cdf, java.lang.String svariable, long recStart, long recCount, long recInterval, int slice1, boolean depend, ProgressMonitor mon) Deprecated. use loadCdfVariable instead

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

OPTION_INCLUDE_EMPTY_RECORDS

public static final java.lang.String OPTION_INCLUDE_EMPTY_RECORDS

if "true", show empty records (true is default).

See Also:

Constant Field Values

OPTION_IS_MASTER

public static final java.lang.String OPTION_IS_MASTER

if "true", then don't show the number of records.

See Also:

Constant Field Values

OPTION_DEEP

public static final java.lang.String OPTION_DEEP

if "true" then return more detailed descriptions in HTML

See Also:

Constant Field Values

OPTION_DATA_ONLY

public static final java.lang.String OPTION_DATA_ONLY

if "true" return only the data variables, not the support data.

See Also:

Constant Field Values

OPTION_RANK_LIMIT

public static final java.lang.String OPTION_RANK_LIMIT

if greater than -1, then only read variables up to this rank.

Constructor Detail

CdfUtil

public CdfUtil()

Creates a new instance of CdfUtil

Method Detail

getRange

public static DatumRange getRange(java.util.HashMap attrs)

returns the range of the data by looking for the SCALEMIN/SCALEMAX params, or the required VALIDMIN/VALIDMAX parameters. This is not used.

Parameters:

attrs - the properties for the variable

Returns:

the range

getScaleType

public static java.lang.String getScaleType(java.util.HashMap attrs)

maybeAddValidRange

public static void maybeAddValidRange(java.util.Map<java.lang.String,java.lang.Object> props,
                                      MutablePropertyDataSet ds)

add the valid range only if it looks like it is correct. It must contain some of the data.

Parameters:

props - the properties for the variable

ds - the dataset to which the valid range would be added.

sizeOf

protected static int sizeOf(long itype)

returns the size of the data type in bytes.

Parameters:

itype - type of data, such as CDFConstants.CDF_FLOAT

Returns:

the size the data atom in bytes TODO: this needs to be verified. Unsigned numbers may come back as next larger size.

getEffectiveRank

protected static int getEffectiveRank(boolean[] varies)

returns effective rank. Nand's code looks for 1-element dimensions, which messes up Seth's file rbspb_pre_ect-mageisHIGH. See files:

• vap+cdfj:ftp://cdaweb.gsfc.nasa.gov/pub/data/geotail/lep/2011/ge_k0_lep_20111016_v01.cdf?V0
• vap+cdfj:file:///home/jbf/ct/autoplot/data.backup/examples/cdf/seth/rbspb_pre_ect-mageisHIGH-sp-L1_20130709_v1.0.0.cdf?Histogram_prot

Parameters:

varies - array of boolean indicating if a dimension varies.

Returns:

the rank

wrapCdfData

public static MutablePropertyDataSet wrapCdfData(CDFReader cdf,
                                                 java.lang.String svariable)
                                          throws java.lang.Exception

Deprecated. use loadCdfVariable instead

Return the named variable as a QDataSet. This does not look at the metadata for DEPEND_0, etc, and only adds metadata to represent time units (e.g. the data is in TT2000) and ordinal data.

Parameters:

cdf - the value of CDF

svariable - name of the variable

Returns:

the dataset

Throws:

java.lang.Exception

loadVariable

public static MutablePropertyDataSet loadVariable(CDFReader cdf,
                                                  java.lang.String svariable)
                                           throws java.lang.Exception

Return the named variable as a QDataSet. This does not look at the metadata for DEPEND_0, etc, and only adds metadata to represent time units (e.g. the data is in TT2000) and ordinal data.

Parameters:

cdf - the value of CDF

svariable - name of the variable

Returns:

the dataset

Throws:

java.lang.Exception

wrapCdfData

public static MutablePropertyDataSet wrapCdfData(CDFReader cdf,
                                                 java.lang.String svariable,
                                                 long recStart,
                                                 long recCount,
                                                 long recInterval,
                                                 int slice1,
                                                 boolean depend,
                                                 ProgressMonitor mon)
                                          throws java.lang.Exception

Deprecated. use loadCdfVariable instead

Return the named variable as a QDataSet. This does not look at the metadata for DEPEND_0, etc, and only adds metadata to represent time units (e.g. the data is in TT2000) and ordinal data.

Parameters:

cdf - the value of CDF

svariable - name of the variable

recStart - the first record to retrieve (0 is the first record in the file).

recCount - the number of records to retrieve, -1 means the record is flag for slice

recInterval - the number of records to increment, typically 1 (e.g. 2= every other record).

slice1 - if non-negative, return the slice at this point.

depend - if false, don't do the non-varying expansion.

mon - progress monitor (currently not used), or null.

Returns:

the dataset

Throws:

java.lang.Exception

loadVariable

public static MutablePropertyDataSet loadVariable(CDFReader cdf,
                                                  java.lang.String svariable,
                                                  long recStart,
                                                  long recCount,
                                                  long recInterval,
                                                  int slice1,
                                                  ProgressMonitor mon)
                                           throws java.lang.Exception

Return the named variable as a QDataSet. This does not look at the metadata for DEPEND_0, etc, and only adds metadata to represent time units (e.g. the data is in TT2000) and ordinal data.

Parameters:

cdf - the value of CDF

svariable - name of the variable

recStart - the first record to retrieve (0 is the first record in the file).

recCount - the number of records to retrieve, -1 means the record is flag for slice

recInterval - the number of records to increment, typically 1 (e.g. 2= every other record).

slice1 - if non-negative, return the slice at this point.

mon - progress monitor (currently not used), or null.

Returns:

the dataset

Throws:

java.lang.Exception

jvmMemory

public static int jvmMemory(QDataSet ds)

returns the amount of JVM memory in bytes occupied by the dataset. This is an approximation, calculated by taking the element type size (e.g. float=4 bytes) times the number of elements for the dataset. This does not include the memory consumed by DEPEND_0, etc.

Parameters:

ds - the ArrayDataSet, or TrArrayDataSet, or BufferDataSet.

Returns:

the approximate memory consumption in bytes

getStringDataType

public static java.lang.String getStringDataType(int type)

return the data type for the encoding. From ftp://cdaweb.gsfc.nasa.gov/pub/cdf/doc/cdf33/cdf33ifd.pdf page 33.

Parameters:

type - integer type, such as 44 for CDF_FLOAT

Returns:

string like "CDF_FLOAT"

hasAttribute

public static boolean hasAttribute(CDFReader cdf,
                                   java.lang.String var,
                                   java.lang.String attrname)

return true if the attribute is set for the variable.

Parameters:

cdf - the cdf file reader

var - the variable name

attrname - the attribute name.

Returns:

true if the attribute is set for the variable.

getDimensions

public static int[] getDimensions(CDFReader cdf,
                                  java.lang.String variableName)
                           throws CDFException.ReaderError

This is cdf.getDimensions( variableName ), but then check varies to see if varies[0] is false (for rvariables). This will return "new int[0]" for scalar quantities like density.

Parameters:

cdf -

variableName -

Returns:

the dimensions for each record.

Throws:

CDFException.ReaderError

getPlottable

public static java.util.Map<java.lang.String,java.lang.String> getPlottable(CDFReader cdf,
                                                                            boolean dataOnly,
                                                                            int rankLimit)
                                                                     throws java.lang.Exception

Return a map where keys are the names of the variables, and values are descriptions.

Parameters:

cdf - the cdf reader reference.

dataOnly - show only the DATA and not SUPPORT_DATA. Note I reclaimed this parameter because I wasn't using it.

rankLimit - show only variables with no more than this rank.

Returns:

map of parameter name to short description

Throws:

java.lang.Exception

getPlottable

public static java.util.LinkedHashMap<java.lang.String,CdfUtil.CdfVariableDescription> getPlottable(CDFReader cdf,
                                                                                                    java.util.Map<java.lang.String,java.lang.String> options)
                                                                                             throws CDFException.ReaderError

retrieve information about all the variables. A LinkedHashMap will be returned to preserve the order.

Parameters:

cdf -

options - map of options like OPTION_DEEP and OPTION_DATA_ONLY

Returns:

Throws:

CDFException.ReaderError

maybeShorten

public static java.lang.String maybeShorten(java.lang.String context,
                                            java.lang.String name)

abbreviate names, motivated by Cluster CDF files which have Data__C1_CP_PEA_3DRH_cnts with DEPEND_0 of time_tags__C1_CP_PEA_3DRH_cnts.

Parameters:

context -

name -

Returns:

getPlottable

public static java.util.Map<java.lang.String,java.lang.String> getPlottable(CDFReader cdf,
                                                                            boolean dataOnly,
                                                                            int rankLimit,
                                                                            java.util.Map<java.lang.String,java.lang.String> options)
                                                                     throws java.lang.Exception

Return a map where keys are the names of the variables, and values are descriptions. This allows for a deeper query, getting detailed descriptions within the values, and also supports the mode where the master CDFs (used by the CDAWeb plugin) don't contain data and record counts should not be supported.

Parameters:

cdf -

dataOnly - show only the DATA and not SUPPORT_DATA. Note I reclaimed this parameter because I wasn't using it.

rankLimit - show only variables with no more than this rank.

options - see constants for parameter names.

Returns:

map of parameter name to short description

Throws:

java.lang.Exception

doApplyAttributes

public static void doApplyAttributes(java.util.Map<java.lang.String,java.lang.Object> attr1,
                                     MutablePropertyDataSet result,
                                     java.lang.String os1,
                                     java.lang.String constraint)

apply the ISTP metadata to the dataset. This is used to implement master files, where metadata from one file can override the data within another. Do not use this, as its location will probably change.

Parameters:

attr1 - the ISTP metadata

result - the data

os1 - if non-null, then modify the metadata for slice1

constraint - if non-null, then drop the render type.