    001/*****************************************************************************
    002 * Copyright by The HDF Group.                                               *
    003 * Copyright by the Board of Trustees of the University of Illinois.         *
    004 * All rights reserved.                                                      *
    005 *                                                                           *
    006 * This file is part of the HDF Java Products distribution.                  *
    007 * The full copyright notice, including terms governing use, modification,   *
    008 * and redistribution, is contained in the COPYING file, which can be found  *
    009 * at the root of the source code distribution tree,                         *
    010 * or in https://www.hdfgroup.org/licenses.                                  *
    011 * If you do not have access to either file, you may request a copy from     *
    012 * help@hdfgroup.org.                                                        *
    013 ****************************************************************************/
    014
    015package hdf.object.fits;
    016
    017import java.lang.reflect.Array;
    018import java.math.BigInteger;
    019import java.util.Arrays;
    020import java.util.Collection;
    021import java.util.HashMap;
    022import java.util.List;
    023import java.util.Map;
    024
    025import org.slf4j.Logger;
    026import org.slf4j.LoggerFactory;
    027
    028import hdf.object.Attribute;
    029import hdf.object.DataFormat;
    030import hdf.object.Dataset;
    031import hdf.object.Datatype;
    032import hdf.object.FileFormat;
    033import hdf.object.Group;
    034import hdf.object.HObject;
    035import hdf.object.ScalarDS;
    036
    037/**
    038 * An attribute is a (name, value) pair of metadata attached to a primary data object such as a dataset, group or named
    039 * datatype.
    040 *
    041 * Like a dataset, an attribute has a name, datatype and dataspace.
    042 *
    043 * For more details on attributes, <a href="https://hdfgroup.github.io/hdf5/_h5_a__u_g.html#sec_attribute">HDF5
    044 * Attributes in HDF5 User Guide</a>
    045 *
    046 * The following code is an example of an attribute with 1D integer array of two elements.
    047 *
    048 * <pre>
    049 * // Example of creating a new attribute
    050 * // The name of the new attribute
    051 * String name = "Data range";
    052 * // Creating an unsigned 1-byte integer datatype
    053 * Datatype type = new Datatype(Datatype.CLASS_INTEGER, // class
    054 *                              1,                      // size in bytes
    055 *                              Datatype.ORDER_LE,      // byte order
    056 *                              Datatype.SIGN_NONE);    // unsigned
    057 * // 1-D array of size two
    058 * long[] dims = {2};
    059 * // The value of the attribute
    060 * int[] value = {0, 255};
    061 * // Create a new attribute
    062 * FitsAttribute dataRange = new FitsAttribute(name, type, dims);
    063 * // Set the attribute value
    064 * dataRange.setValue(value);
    065 * // See FileFormat.writeAttribute() for how to attach an attribute to an object,
    066 * &#64;see hdf.object.FileFormat#writeAttribute(HObject, Attribute, boolean)
    067 * </pre>
    068 *
    069 *
    070 * For an atomic datatype, the value of an FitsAttribute will be a 1D array of integers, floats and strings. For a
    071 * compound datatype, it will be a 1D array of strings with field members separated by a comma. For example, "{0, 10.5},
    072 * {255, 20.0}, {512, 30.0}" is a compound attribute of {int, float} of three data points.
    073 *
    074 * @see hdf.object.Datatype
    075 *
    076 * @version 2.0 4/2/2018
    077 * @author Peter X. Cao, Jordan T. Henderson
    078 */
    079public class FitsAttribute extends ScalarDS implements Attribute {
    080
    081    private static final long serialVersionUID = 2072473407027648309L;
    082
    083    private static final Logger log = LoggerFactory.getLogger(FitsAttribute.class);
    084
    085    /** The HObject to which this NC2Attribute is attached, Attribute interface */
    086    protected HObject         parentObject;
    087
    088    /** additional information and properties for the attribute, Attribute interface */
    089    private transient Map<String, Object> properties;
    090
    091    /**
    092     * Create an attribute with specified name, data type and dimension sizes.
    093     *
    094     * For scalar attribute, the dimension size can be either an array of size one
    095     * or null, and the rank can be either 1 or zero. Attribute is a general class
    096     * and is independent of file format, e.g., the implementation of attribute
    097     * applies to both HDF4 and HDF5.
    098     *
    099     * The following example creates a string attribute with the name "CLASS" and
    100     * value "IMAGE".
    101     *
    102     * <pre>
    103     * long[] attrDims = { 1 };
    104     * String attrName = &quot;CLASS&quot;;
    105     * String[] classValue = { &quot;IMAGE&quot; };
    106     * Datatype attrType = null;
    107     * try {
    108     *     attrType = new FitsDatatype(Datatype.CLASS_STRING, classValue[0].length() + 1, Datatype.NATIVE, Datatype.NATIVE);
    109     * }
    110     * catch (Exception ex) {}
    111     * FitsAttribute attr = new FitsAttribute(attrName, attrType, attrDims);
    112     * attr.setValue(classValue);
    113     * </pre>
    114     *
    115     * @param parentObj
    116     *            the HObject to which this Attribute is attached.
    117     * @param attrName
    118     *            the name of the attribute.
    119     * @param attrType
    120     *            the datatype of the attribute.
    121     * @param attrDims
    122     *            the dimension sizes of the attribute, null for scalar attribute
    123     *
    124     * @see hdf.object.Datatype
    125     */
    126    public FitsAttribute(HObject parentObj, String attrName, Datatype attrType, long[] attrDims) {
    127        this(parentObj, attrName, attrType, attrDims, null);
    128    }
    129
    130    /**
    131     * Create an attribute with specific name and value.
    132     *
    133     * For scalar attribute, the dimension size can be either an array of size one
    134     * or null, and the rank can be either 1 or zero. Attribute is a general class
    135     * and is independent of file format, e.g., the implementation of attribute
    136     * applies to both HDF4 and HDF5.
    137     *
    138     * The following example creates a string attribute with the name "CLASS" and
    139     * value "IMAGE".
    140     *
    141     * <pre>
    142     * long[] attrDims = { 1 };
    143     * String attrName = &quot;CLASS&quot;;
    144     * String[] classValue = { &quot;IMAGE&quot; };
    145     * Datatype attrType = null;
    146     * try {
    147     *     attrType = new FitsDatatype(Datatype.CLASS_STRING, classValue[0].length() + 1, Datatype.NATIVE, Datatype.NATIVE);
    148     * }
    149     * catch (Exception ex) {}
    150     * FitsAttribute attr = new FitsAttribute(attrName, attrType, attrDims, classValue);
    151     * </pre>
    152     *
    153     * @param parentObj
    154     *            the HObject to which this FitsAttribute is attached.
    155     * @param attrName
    156     *            the name of the attribute.
    157     * @param attrType
    158     *            the datatype of the attribute.
    159     * @param attrDims
    160     *            the dimension sizes of the attribute, null for scalar attribute
    161     * @param attrValue
    162     *            the value of the attribute, null if no value
    163     *
    164     * @see hdf.object.Datatype
    165     */
    166    @SuppressWarnings({ "rawtypes", "unchecked", "deprecation" })
    167    public FitsAttribute(HObject parentObj, String attrName, Datatype attrType, long[] attrDims, Object attrValue) {
    168        super((parentObj == null) ? null : parentObj.getFileFormat(), attrName,
    169                (parentObj == null) ? null : parentObj.getFullName(), null);
    170
    171        log.trace("FitsAttribute: start {}", parentObj);
    172        this.parentObject = parentObj;
    173
    174        unsignedConverted = false;
    175
    176        datatype = attrType;
    177
    178        if (attrValue != null) {
    179            data = attrValue;
    180            originalBuf = attrValue;
    181            isDataLoaded = true;
    182        }
    183        properties = new HashMap();
    184
    185        if (attrDims == null) {
    186            rank = 1;
    187            dims = new long[] { 1 };
    188        }
    189        else {
    190            dims = attrDims;
    191            rank = dims.length;
    192        }
    193
    194        selectedDims = new long[rank];
    195        startDims = new long[rank];
    196        selectedStride = new long[rank];
    197
    198        log.trace("attrName={}, attrType={}, attrValue={}, rank={}, isUnsigned={}",
    199                attrName, getDatatype().getDescription(), data, rank, getDatatype().isUnsigned());
    200
    201        resetSelection();
    202    }
    203
    204    /*
    205     * (non-Javadoc)
    206     *
    207     * @see hdf.object.HObject#open()
    208     */
    209    @Override
    210    public long open() {
    211        if (parentObject == null) {
    212            log.debug("open(): attribute's parent object is null");
    213            return -1;
    214        }
    215
    216        return -1;
    217    }
    218
    219    /*
    220     * (non-Javadoc)
    221     *
    222     * @see hdf.object.HObject#close(int)
    223     */
    224    @Override
    225    public void close(long aid) {
    226    }
    227
    228    @Override
    229    public void init() {
    230        if (inited) {
    231            resetSelection();
    232            log.trace("init(): FitsAttribute already inited");
    233            return;
    234        }
    235    }
    236
    237    /**
    238     * Reads the data from file.
    239     *
    240     * read() reads the data from file to a memory buffer and returns the memory
    241     * buffer. The dataset object does not hold the memory buffer. To store the
    242     * memory buffer in the dataset object, one must call getData().
    243     *
    244     * By default, the whole dataset is read into memory. Users can also select
    245     * a subset to read. Subsetting is done in an implicit way.
    246     *
    247     * @return the data read from file.
    248     *
    249     * @see #getData()
    250     *
    251     * @throws Exception
    252     *             if object can not be read
    253     * @throws OutOfMemoryError
    254     *             if memory is exhausted
    255     */
    256    @Override
    257    public Object read() throws Exception, OutOfMemoryError {
    258        if (!inited) init();
    259
    260        return data;
    261    }
    262
    263    /* Implement abstract Dataset */
    264
    265    /*
    266     * (non-Javadoc)
    267     * @see hdf.object.Dataset#copy(hdf.object.Group, java.lang.String, long[], java.lang.Object)
    268     */
    269    @Override
    270    public Dataset copy(Group pgroup, String dstName, long[] dims, Object buff)
    271            throws Exception {
    272        // not supported
    273        throw new UnsupportedOperationException("copy operation unsupported for FITS.");
    274    }
    275
    276    /*
    277     * (non-Javadoc)
    278     * @see hdf.object.Dataset#readBytes()
    279     */
    280    @Override
    281    public byte[] readBytes() throws Exception {
    282        // not supported
    283        throw new UnsupportedOperationException("readBytes operation unsupported for FITS.");
    284    }
    285
    286    /**
    287     * Writes a memory buffer to the object in the file.
    288     *
    289     * @param buf
    290     *            the data to write
    291     *
    292     * @throws Exception
    293     *             if data can not be written
    294     */
    295    @Override
    296    public void write(Object buf) throws Exception {
    297        // not supported
    298        throw new UnsupportedOperationException("write operation unsupported for FITS.");
    299    }
    300
    301    /**
    302     * Returns the HObject to which this Attribute is currently "attached".
    303     *
    304     * @return the HObject to which this Attribute is currently "attached".
    305     */
    306    public HObject getParentObject() {
    307        return parentObject;
    308    }
    309
    310    /**
    311     * Sets the HObject to which this Attribute is "attached".
    312     *
    313     * @param pObj
    314     *            the new HObject to which this Attribute is "attached".
    315     */
    316    public void setParentObject(HObject pObj) {
    317        parentObject = pObj;
    318    }
    319
    320    /**
    321     * set a property for the attribute.
    322     *
    323     * @param key the attribute Map key
    324     * @param value the attribute Map value
    325     */
    326    public void setProperty(String key, Object value) {
    327        properties.put(key, value);
    328    }
    329
    330    /**
    331     * get a property for a given key.
    332     *
    333     * @param key the attribute Map key
    334     *
    335     * @return the property
    336     */
    337    public Object getProperty(String key) {
    338        return properties.get(key);
    339    }
    340
    341    /**
    342     * get all property keys.
    343     *
    344     * @return the Collection of property keys
    345     */
    346    public Collection<String> getPropertyKeys() {
    347        return properties.keySet();
    348    }
    349
    350    /**
    351     * Returns the name of the object. For example, "Raster Image #2".
    352     *
    353     * @return The name of the object.
    354     */
    355    public final String getAttributeName() {
    356        return getName();
    357    }
    358
    359    /**
    360     * Retrieves the attribute data from the file.
    361     *
    362     * @return the attribute data.
    363     *
    364     * @throws Exception
    365     *             if the data can not be retrieved
    366     */
    367    public final Object getAttributeData() throws Exception, OutOfMemoryError {
    368        return getData();
    369    }
    370
    371    /**
    372     * Returns the datatype of the attribute.
    373     *
    374     * @return the datatype of the attribute.
    375     */
    376    public final Datatype getAttributeDatatype() {
    377        return getDatatype();
    378    }
    379
    380    /**
    381     * Returns the space type for the attribute. It returns a
    382     * negative number if it failed to retrieve the type information from
    383     * the file.
    384     *
    385     * @return the space type for the attribute.
    386     */
    387    public final int getAttributeSpaceType() {
    388        return getSpaceType();
    389    }
    390
    391    /**
    392     * Returns the rank (number of dimensions) of the attribute. It returns a
    393     * negative number if it failed to retrieve the dimension information from
    394     * the file.
    395     *
    396     * @return the number of dimensions of the attribute.
    397     */
    398    public final int getAttributeRank() {
    399        return getRank();
    400    }
    401
    402    /**
    403     * Returns the selected size of the rows and columns of the attribute. It returns a
    404     * negative number if it failed to retrieve the size information from
    405     * the file.
    406     *
    407     * @return the selected size of the rows and colums of the attribute.
    408     */
    409    public final int getAttributePlane() {
    410        return (int)getWidth() * (int)getHeight();
    411    }
    412
    413    /**
    414     * Returns the array that contains the dimension sizes of the data value of
    415     * the attribute. It returns null if it failed to retrieve the dimension
    416     * information from the file.
    417     *
    418     * @return the dimension sizes of the attribute.
    419     */
    420    public final long[] getAttributeDims() {
    421        return getDims();
    422    }
    423
    424    /**
    425     * @return true if the dataspace is a NULL; otherwise, returns false.
    426     */
    427    @Override
    428    public boolean isAttributeNULL() {
    429        return isNULL();
    430    }
    431
    432    /**
    433     * @return true if the data is a single scalar point; otherwise, returns false.
    434     */
    435    public boolean isAttributeScalar() {
    436        return isScalar();
    437    }
    438
    439    /**
    440     * Not for public use in the future.
    441     *
    442     * setData() is not safe to use because it changes memory buffer
    443     * of the dataset object. Dataset operations such as write/read
    444     * will fail if the buffer type or size is changed.
    445     *
    446     * @param d  the object data -must be an array of Objects
    447     */
    448    public void setAttributeData(Object d) {
    449        setData(d);
    450    }
    451
    452    /**
    453     * Writes the memory buffer of this dataset to file.
    454     *
    455     * @throws Exception if buffer can not be written
    456     */
    457    public void writeAttribute() throws Exception {
    458        write();
    459    }
    460
    461    /**
    462     * Writes the given data buffer into this attribute in a file.
    463     *
    464     * The data buffer is a vector that contains the data values of compound fields. The data is written
    465     * into file as one data blob.
    466     *
    467     * @param buf
    468     *            The vector that contains the data values of compound fields.
    469     *
    470     * @throws Exception
    471     *             If there is an error at the library level.
    472     */
    473    public void writeAttribute(Object buf) throws Exception {
    474        write(buf);
    475    }
    476
    477    /**
    478     * Returns a string representation of the data value. For
    479     * example, "0, 255".
    480     *
    481     * For a compound datatype, it will be a 1D array of strings with field
    482     * members separated by the delimiter. For example,
    483     * "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int,
    484     * float} of three data points.
    485     *
    486     * @param delimiter
    487     *            The delimiter used to separate individual data points. It
    488     *            can be a comma, semicolon, tab or space. For example,
    489     *            toString(",") will separate data by commas.
    490     *
    491     * @return the string representation of the data values.
    492     */
    493    public String toAttributeString(String delimiter) {
    494        return toString(delimiter, -1);
    495    }
    496
    497    /**
    498     * Returns a string representation of the data value. For
    499     * example, "0, 255".
    500     *
    501     * For a compound datatype, it will be a 1D array of strings with field
    502     * members separated by the delimiter. For example,
    503     * "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int,
    504     * float} of three data points.
    505     *
    506     * @param delimiter
    507     *            The delimiter used to separate individual data points. It
    508     *            can be a comma, semicolon, tab or space. For example,
    509     *            toString(",") will separate data by commas.
    510     * @param maxItems
    511     *            The maximum number of Array values to return
    512     *
    513     * @return the string representation of the data values.
    514     */
    515    public String toAttributeString(String delimiter, int maxItems) {
    516        return toString(delimiter, maxItems);
    517    }
    518}