Package gov.nih.mipav.model.file

Class FileMinc

    • Field Detail

      • DEFAULT_NON_HEADER_START_LOCATION

        private static final int DEFAULT_NON_HEADER_START_LOCATION
        The location, in bytes, of the portion of the minc file being written directly after the header. Does not include data added to the header by the dynamically generated history attribute or dicom-exported tags.
        See Also:
        Constant Field Values

      • dicomConvertedTagTable

        private java.util.Hashtable<java.lang.String,​java.util.Hashtable<java.lang.String,​java.lang.String>> dicomConvertedTagTable
        Table of tags extracted from a dicom file info to be written to the minc file. Generated in writeHeader(), then used again later in writeImage() to output placeholder values outside of the header.

      • endianess

        private boolean endianess
        The endianess of the image being written or read.

        TODO: this variable either needs to be local to the read/write methods or consistently used globally. As it stands right now, it is used in both ways and confuses things greatly.

      • fileDir

        private java.lang.String fileDir
        The directory containing the minc file being written out or read in.

      • fileName

        private java.lang.String fileName
        The name of the minc file to be read in or written out.

      • imgBegin

        private int imgBegin
        The location, in bytes, of the image data in the minc file being written out.

      • imgSize

        private int imgSize
        The size of the image data that will be written out, in bytes.

      • location

        private int location
        TODO: THIS VARIABLE MUST BE REMOVED! It is used as if local in places and global in others. A number of methods change it, causing subtle side effects which must be carefully managed.

      • newExtents

        private int[] newExtents

    • Constructor Detail

      • FileMinc

        public FileMinc​(java.lang.String fName,
                java.lang.String fDir)
         throws java.io.IOException
        MINC reader/writer constructor.
        Parameters:
        fName - File name.
        fDir - File directory.
        Throws:
        java.io.IOException - if there is an error constructing the files

    • Method Detail

      • finalize

        public void finalize()
        Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
        Overrides:
        finalize in class FileBase

      • isMinc

        public boolean isMinc()
               throws java.io.IOException
        Looks for the CDF tag at the start of the image 'C''D''F''\001' in image header ID. If present, the image is a MINC format.
        Returns:
        boolean true if the header contains CDF tag 'C''D''F''\001'
        Throws:
        java.io.IOException - Indicates error reading the file

      • readHeader

        public FileInfoMinc readHeader()
                        throws java.io.IOException
        Reads in all the tags available in the file and stores them in FileInfoMinc.

        Format:
        header := magic numrecs dim_array gatt_array var_array
        magic := 'C' 'D' 'F' '\001'
        numrecs := non negative integer
        dim_array := NC_DIMENSION nelems [dim...]
        gatt_array := att_array
        att_array := NC_ATTRIBUTE nelems [attr...]
        var_array := NC_VARIABLE nelems [var...]
        nelems is # of elements in following array.
        dim := name dim_length
        dim is the extents; the name is xspace, yspace, or zspace.
        attr := name nc_type nelems [values]
        name is the name of the attribute; nc_type is the type (integer, char, etc.); values are the values of this attribute. It seems that attributes are mostly of type char, so the entire attribute is just a string.
        var := name nelems [dimid...] vatt_array nc_type vsize begin
        name is the name of the variable; dimid is Dimension id (for dimensions variables); vatt_array is an array of attributes for this variable; nc_type is the type of the variable; vsize is the size of the variable; begin is where in the file the variable data begins.

        Image extents are orginally determined under NC_DIMENSION with the MIPAV dimension ordering being the reverse of the MINC dimension ordering. However, under NC_VARIABLE refer to dimid.length of the variable with the string name of image to determine how many of these variables to retain. The contents of the dimid array under variable image give the dimid indices of the dimensions found in NC_DIMENSION which should be retained.
        Returns:
        true confirms a successful read.
        Throws:
        java.io.IOException - if there is an error reading the file
        See Also:
        FileInfoMinc

      • readImage

        public ModelImage readImage​(boolean one,
                            boolean readData)
                     throws java.io.IOException
        Reads a MINC image file and stores the data in file info.
        Parameters:
        one - Flag indicating if only one image should be read in
        readData -
        Returns:
        The image.
        Throws:
        java.io.IOException - if there is an error reading the file
        See Also:
        FileRaw

      • writeImage

        public void writeImage​(ModelImage _image,
                       FileWriteOptions options)
                throws java.io.IOException
        Writes a MINC format type image. Calls the appropriate header method.
        Parameters:
        _image - Image model where the data is stored.
        options - Information about how to write this file.
        Throws:
        java.io.IOException - if there is an error writing the file
        See Also:
        FileInfoMinc, FileMinc

      • extractDicomTags

        private static java.util.Hashtable<java.lang.String,​java.util.Hashtable<java.lang.String,​java.lang.String>> extractDicomTags​(FileInfoBase fileInfo)
        Extracts any Dicom tags from a given FileInfoBase (if the file info is dicom) and puts them into a Hashtable.
        Parameters:
        fileInfo - the file info to extract dicom tags from
        Returns:
        Hashtable keyed on tag group, containing Hashtables keyed on tag element, containing the tag values. Returns an empty Hashtable if the file info is not dicom.

      • getDefaultMax

        public static double getDefaultMax​(FileInfoBase fileInfo)
        Return the default volume maximum for different file data types. This is used to rescale the image data before storing it on disk (the reader then uses the same values to scale the data back).
        Parameters:
        fileInfo - The fileInfo containing information about the image being saved.
        Returns:
        The default volume maximum for a given fileInfo.

      • getDefaultMin

        public static double getDefaultMin​(FileInfoBase fileInfo)
        Return the default volume minimum for different file data types. This is used to rescale the image data before storing it on disk (the reader then uses the same values to scale the data back).
        Parameters:
        fileInfo - The fileInfo containing information about the image being saved.
        Returns:
        The default volume minimum for a given fileInfo.

      • getDicomValueAsString

        private static java.lang.String getDicomValueAsString​(FileDicomTag tag)
        Returns the value of a dicom tag, represented as a string. Null tag values are ignored, as are array value types.
        Parameters:
        tag - The dicom tag (including its value).
        Returns:
        the value of the given dicom tag (null if the value is null or is an array (which we don't support at the moment))

      • getMincModality

        public static java.lang.String getMincModality​(int modality)
        Get the minc modality string from the mipav modality type.
        Parameters:
        modality - The mipav image modality.
        Returns:
        The appropriate minc modality string if there is one; null if there is not equivalent minc modality or if the mipav modality is unknown.

      • getNextElem

        private java.lang.Object getNextElem​(int type,
                                     boolean endianess)
                              throws java.io.IOException
        Gets the next element, switching on the type.
        Parameters:
        type - Short, byte, float, etc, defined in FileInfoMinc.
        endianess - Endianess, FileBase.BIG_ENDIAN or FileBase.LITTLE_ENDIAN.
        Returns:
        The element read in.
        Throws:
        java.io.IOException - if an error is encountered reading from the file

      • getPadding

        private int getPadding​(int size)
        Returns the amount of padding needed (to the nearest 4 byte boundary) after a variable of length size.
        Parameters:
        size - The length of the variable.
        Returns:
        The amount of padding needed for that variable.

      • getSizeOfExportedDicomTags

        private int getSizeOfExportedDicomTags​(java.util.Hashtable<java.lang.String,​java.util.Hashtable<java.lang.String,​java.lang.String>> tagTable)
        Get the size, in bytes, of the data which would be written to the header to store a set of dicom tags.
        Parameters:
        tagTable - hashtable of exported dicom tags. Hashtable inside of a Hashtable ultimately storing Strings (tagValue = table[tagGroup][tagElement]).
        Returns:
        the size of the data which will be written to the header for the exported dicom tags

      • getSizeOfWrittenName

        private int getSizeOfWrittenName​(java.lang.String string,
                                 int addedByte)
        Returns the number of bytes that would be written to disk by calling writeName() on a given string.
        Parameters:
        string - the string which would be passed to writeName()
        addedByte - the number of bytes of explicit padding to put after the string (see the second param of writeName())
        Returns:
        the number of bytes that would be written to disk if the given string was passed to writeName()
        See Also:
        writeName(String, int, boolean)

      • getVattArray

        private void getVattArray​(int index,
                          FileInfoMinc fileInfo)
                   throws java.io.IOException
        Gets the attribute array within a variable.
        Parameters:
        index - Index into the variable array; i.e., which variable this is.
        fileInfo - The file info to fill with data from the Vatt array read in from the minc file
        Throws:
        java.io.IOException - If an error is encountered while reading from the file

      • padding

        private void padding()
              throws java.io.IOException
        Pads to the nearest 4 byte boundary. Everything in MINC files is padded this way.
        Throws:
        java.io.IOException - If an error is encountered while reading from the file

      • writeDicomTagsToHeader

        private void writeDicomTagsToHeader​(java.util.Hashtable<java.lang.String,​java.util.Hashtable<java.lang.String,​java.lang.String>> tagTable,
                                    int beginningOffset)
                             throws java.io.IOException
        Writes the dicom-extracted tags contained in tagTable to disk.
        Parameters:
        tagTable - a tag-group keyed table, containing a tag-element keyed table of string values
        beginningOffset - the location, in bytes, directly after the data section pointed to by the previous NC_VARIABLE section (usually image-min)
        Throws:
        java.io.IOException - If an error is encountered while writing to the file
        See Also:
        extractDicomTags(FileInfoBase)

      • writeHeader

        private void writeHeader​(FileInfoMinc fileInfo)
                  throws java.io.IOException
        Writes a header for MINC to MINC. This is much easier than the other-format-to-MINC writeHeader; in this case, we already have all the information we need to write. Therefore, the process is just to go through the dimArray, gattArray, and varArray and write out the variables.
        Parameters:
        fileInfo - File info needed to write the header.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writeHeader

        private void writeHeader​(FileInfoBase fileInfo,
                         FileWriteOptions options,
                         int nSlices,
                         int nVolumes)
                  throws java.io.IOException
        Writes the header for non-MINC to MINC. MINC has a very structured format. Many of the things written out I don't understand, but they seem to be consistent across the MINC files we've seen (e.g., varid, vartype, and version attributes). The header begins with a dimension array with a specific ordering of the spaces which dictates orientation. Then there's a global attribute array, which in our case is just the history of how this file was created. Then there's a variable array. Each variable contains an attribute array, a type, a size, and a begin location. The actual value of the variable is written at its begin location, after all other header info is written. So the rootvariable's value, for example, is written after the info for image-min, which is the last variable in the array. It seems that conventionally the image-max and image-min variables are after the image variable; thus, the values of those variables are written after the "value of the image" which is the actual image data. Consequently, this function exits just before the image is to be written, even though the image-max and image-min values have yet to be written.

        This is a public method because it is called from FileIO. Previously it was called from writeImage, but this would create a file even if the dialog was cancelled. Obviously that is undesirable behavior.

        Parameters:
        fileInfo - Info to use when writing the header.
        options - The structure that returns important information about the image to be written.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writeName

        private void writeName​(java.lang.String name,
                       int add,
                       boolean endianess)
                throws java.io.IOException
        Write a string name by writing the length of the string plus padding length, writing the string, and writing the padding.
        Parameters:
        name - Value to write.
        add - Length of padding to add.
        endianess - Endianess, FileBase.BIG_ENDIAN or FileBase.LITTLE_ENDIAN.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writeNextElem

        private void writeNextElem​(java.lang.Object value,
                           int type,
                           boolean endianess)
                    throws java.io.IOException
        Writes the next element, switching on the type.
        Parameters:
        value - The value to write out.
        type - Short, byte, float, etc, defined in FileInfoMinc.
        endianess - Endianess, FileBase.BIG_ENDIAN or FileBase.LITTLE_ENDIAN.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writePadding

        private void writePadding()
                   throws java.io.IOException
        Pads to the nearest 4 byte boundary. Everything in MINC files is padded this way.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writeSpace

        private void writeSpace​(double step,
                        double start,
                        java.lang.String space,
                        boolean endianess,
                        boolean isNormal)
                 throws java.io.IOException
        Writes the "space", as in xspace, yspace, zspace. The space gives information on that dimension, such as length (what we call extents), step, and start. Start tells the real talirach value of where the space starts, so -50 would be something like 50 inches away from the center of the brain to the right, depending on which space we're in. Step is the step you take per slice from the start, so the third slice in would be start + 3*step.
        Parameters:
        step - Step, see above.
        start - Start, see above.
        space - The string label used for the space ('xspace', 'yspace', 'zspace', or 'time')
        endianess - Endianess, FileBase.BIG_ENDIAN or FileBase.LITTLE_ENDIAN.
        isNormal - No longer used to determine the space direction comment. Consider removal.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file

      • writeValuesArray

        private void writeValuesArray​(java.lang.Object[] values,
                              int type,
                              boolean endianess)
                       throws java.io.IOException
        Writes the array, switching on the type.
        Parameters:
        values - Array to write.
        type - Short, byte, float, etc, defined in FileInfoMinc.
        endianess - Endianess, FileBase.BIG_ENDIAN or FileBase.LITTLE_ENDIAN.
        Throws:
        java.io.IOException - If an error is encountered while writing to the file