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java.lang.Objectloci.formats.AxisGuesser
public class AxisGuesser
AxisGuesser guesses which blocks in a file pattern correspond to which dimensional axes (Z, T or C), potentially recommending an adjustment in dimension order within the files, depending on the confidence of each guess.
Field Summary | |
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protected int[] |
axisTypes
Guessed axis types. |
protected static String[] |
C
Prefix endings indicating channel dimension. |
static int |
C_AXIS
Axis type for channels. |
protected boolean |
certain
Whether the guesser is confident that all axis types are correct. |
protected String |
dimOrder
Original ordering of internal dimensional axes. |
protected FilePattern |
fp
File pattern identifying dimensional axis blocks. |
protected String |
newOrder
Adjusted ordering of internal dimensional axes. |
protected static String[] |
T
Prefix endings indicating time dimension. |
static int |
T_AXIS
Axis type for time points. |
protected static BigInteger |
THREE
|
protected static BigInteger |
TWO
|
static int |
UNKNOWN_AXIS
Axis type for unclassified axes. |
protected static String[] |
Z
Prefix endings indicating space dimension. |
static int |
Z_AXIS
Axis type for focal planes. |
Constructor Summary | |
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AxisGuesser(FilePattern fp,
String dimOrder,
int sizeZ,
int sizeT,
int sizeC,
boolean isCertain)
Guesses dimensional axis assignments corresponding to the given file pattern, using the specified dimensional information from within each file as a guide. |
Method Summary | |
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String |
getAdjustedOrder()
Gets the adjusted dimension order. |
int |
getAxisCount(int axisType)
Gets the number of axes in the pattern of the given type. |
int |
getAxisCountC()
Gets the number of C axes in the pattern. |
int |
getAxisCountT()
Gets the number of T axes in the pattern. |
int |
getAxisCountZ()
Gets the number of Z axes in the pattern. |
int[] |
getAxisTypes()
Gets the guessed axis type for each dimensional block. |
FilePattern |
getFilePattern()
Gets the file pattern. |
String |
getOriginalOrder()
Gets the original dimension order. |
boolean |
isCertain()
Gets whether the guesser is confident that all axes are correct. |
static void |
main(String[] args)
Method for testing pattern guessing logic. |
void |
setAxisTypes(int[] axes)
Sets the axis type for each dimensional block. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int UNKNOWN_AXIS
public static final int Z_AXIS
public static final int T_AXIS
public static final int C_AXIS
protected static final String[] Z
protected static final String[] T
protected static final String[] C
protected static final BigInteger TWO
protected static final BigInteger THREE
protected FilePattern fp
protected String dimOrder
protected String newOrder
protected int[] axisTypes
protected boolean certain
Constructor Detail |
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public AxisGuesser(FilePattern fp, String dimOrder, int sizeZ, int sizeT, int sizeC, boolean isCertain)
fp
- The file pattern of the filesdimOrder
- The dimension order (e.g., XYZTC) within each filesizeZ
- The number of Z positions within each filesizeT
- The number of T positions within each filesizeC
- The number of C positions within each fileisCertain
- Whether the dimension order given is known to be good,
or merely a guessFilePattern
Method Detail |
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public FilePattern getFilePattern()
public String getOriginalOrder()
public String getAdjustedOrder()
public boolean isCertain()
public int[] getAxisTypes()
public void setAxisTypes(int[] axes)
axes
- An array containing values from the enumeration:
public int getAxisCountZ()
public int getAxisCountT()
public int getAxisCountC()
public int getAxisCount(int axisType)
axisType
- One of:
public static void main(String[] args) throws FormatException, IOException
FormatException
IOException
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