io.scif.formats

Class ScancoISQFormat

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractFormat

io.scif.formats.ScancoISQFormat

All Implemented Interfaces:

Format, SCIFIOPlugin, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

public class ScancoISQFormat
extends AbstractFormat

The file format reader for Scanco ISQ files

ISQ images are generated by Scanco X-ray microtomography scanners

Scanco ISQ Header Information:

• Scanco uses OpenVMS on Alpha workstations
• Little endian byte order (the least significant bit occupies the lowest memory position)

 BYTE
 00   char    check[16]; // CTDATA-HEADER_V1
 16   int     data_type;
 20   int     nr_of_bytes;
 24   int     nr_of_blocks;
 28   int     patient_index;
 32   int     scanner_id;
 36   int     creation_date[2];
 44   int     dimx_p;
 48   int     dimy_p;
 52   int     dimz_p;
 56   int     dimx_µm;
 60   int     dimy_µm;
 64   int     dimz_µm;
 68   int     slice_thickness_µm;
 72   int     slice_increment_µm;
 76   int     slice_1_pos_µm;
 80   int     min_data_value;
 84   int     max_data_value;
 88   int     mu_scaling;
 92   int     nr_of_samples;
 96   int     nr_of_projections;
 100  int     scandist_µm;
 104  int     scanner_type;
 108  int     sampletime_µs;
 112  int     index_measurement;
 116  int     site;
 120  int     reference_line_µm;
 124  int     recon_alg;
 128  char    name[40];
 168  int     energy; // V
 172  int     intensity; // µA
 ...
 508  int     data_offset; // Number of optional header blocks
 

Author:

B. Koller (SCANCO Medical AG, April 2005), K.-H. Kunzelmann (Operative Dentistry, LMU-München, Ger, April 2006), Michael Doube (Royal Veterinary College, London), Richard Domander (Royal Veterinary College, London)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ScancoISQFormat.Checker
static class	ScancoISQFormat.Metadata
static class	ScancoISQFormat.Parser
static class	ScancoISQFormat.Reader

Field Summary

Fields

Modifier and Type	Field and Description
static String	ISQ_ID The header byte sequence which identifies Scanco ISQ files

Constructor Summary

Constructors

Constructor and Description
ScancoISQFormat()

Method Summary

Modifier and Type	Method and Description
protected String[]	makeSuffixArray() Helper method to cache the suffix array for a format.

Methods inherited from class io.scif.AbstractFormat

createChecker, createMetadata, createParser, createReader, createWriter, getCheckerClass, getFormatName, getMetadataClass, getParserClass, getReaderClass, getSuffixes, getWriterClass, isEnabled, setEnabled

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.Format

ownsLocationType

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Field Detail

ISQ_ID

public static final String ISQ_ID

The header byte sequence which identifies Scanco ISQ files

See Also:

Constant Field Values

Constructor Detail

ScancoISQFormat

public ScancoISQFormat()

Method Detail

makeSuffixArray

protected String[] makeSuffixArray()

Description copied from class: AbstractFormat

Helper method to cache the suffix array for a format. Concrete format classes should implement this method, returning an array of supported suffixes.

Specified by:

makeSuffixArray in class AbstractFormat

Returns:

Valid suffixes for this file format.