BatchReader (Incenp.org ImageJ Plugins 0.9.6 API)

java.lang.Object
- org.incenp.imagej.BatchReader

```
public class BatchReader
extends Object
```
A class to open images from a CSV file containing filenames and optional associated data.
A BatchReader object reads a CSV file whose first column is expected to contain pathnames pointing to image files. If the pathnames are not absolute, they are supposed to be relative to the directory containing the CSV file itself.
Typical usage is as follows:
```
 BatchReader reader = new BatchReader("filename.csv");
 while ( reader.next() ) {
     ImagePlus image = reader.getImage();
     String[] fields = reader.getRow();
     
     // Work with the image and the associated fields...
     
     image.close()
 }
 
```
Blank lines and lines starting with a '#' are ignored. The first line of the CSV file is treated as a header line.

Constructor Summary

Constructors
Constructor and Description
`BatchReader(File file)` Creates a new reader.
`BatchReader(File file, boolean noHeaders)` Creates a new reader.
`BatchReader(String filename)` Creates a new reader.
`BatchReader(String filename, boolean noHeaders)` Creates a new reader.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()` Closes any opened images.
`void`	`fillResultsTable(ij.measure.ResultsTable rt)` Update a ResultsTable with the contents of the current row.
`String`	`getCell(int index)` Gets the contents of a specific cell within the current row.
`String`	`getCell(String name)` Gets the contents of a specific cell within the current row.
`String`	`getCell(String[] names)` Gets the contents of a specific cell within the current row.
`String`	`getCell(String[] names, String fallback)` Gets the contents of a specific cell within the current row.
`String`	`getCSVRow()` Gets the current row as a single string containing comma-separated values.
`String`	`getCSVRow(char separator)` Gets the current row as a single string, with values separated by the specified character.
`String[]`	`getHeaders()` Gets the headers as found in the CSV file.
`ij.ImagePlus`	`getImage()` Gets the current image.
`String[]`	`getRow()` Gets a copy of the current row.
`boolean`	`hasImage()` Indicates if there’s an image ready to be processed.
`boolean`	`next()` Moves to the next available image.
`void`	`readCSV()` Reads the entire CSV file.
`void`	`setCaseSensitive(boolean caseSensitive)` Sets the case-sensitivity option.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BatchReader
```
public BatchReader(String filename,
                   boolean noHeaders)
```
    Creates a new reader.
    
    Parameters:
    
    filename - pathname to the file to read
    
    noHeaders - if true, the first non-comment line will not be treated as a header line
  - BatchReader
```
public BatchReader(String filename)
```
    Creates a new reader.
    
    Parameters:
    
    filename - pathname to the file to read
  - BatchReader
```
public BatchReader(File file)
```
    Creates a new reader.
    
    Parameters:
    
    file - the file object to read from
  - BatchReader
```
public BatchReader(File file,
                   boolean noHeaders)
```
    Creates a new reader.
    
    Parameters:
    
    file - the file object to read from
    
    noHeaders - if true, the first non-comment line will not be treated as a header line
- Method Detail
  - setCaseSensitive
```
public void setCaseSensitive(boolean caseSensitive)
```
    Sets the case-sensitivity option. If set to true, the getCell(String) method and its overloaded variants will match header names in a case-sensitive way. The default is false.
    
    Parameters:
    
    caseSensitive - true to match header names case-sensitively.
  - next
```
public boolean next()
```
    Moves to the next available image. Once this method has been called and if it returned true, the image can be obtained by calling the getImage() method.
    
    Returns:
    
    true if there is another image available, false otherwise
  - hasImage
```
public boolean hasImage()
```
    Indicates if there’s an image ready to be processed. This method is mostly intended for private use within the BatchReader class, but is made public anyway just in case.
    
    Returns:
    
    true if an image is available, false otherwise
  - getImage
```
public ij.ImagePlus getImage()
```
    Gets the current image.
    
    Returns:
    
    the current image, if one is available; otherwise null
  - getRow
```
public String[] getRow()
```
    Gets a copy of the current row.
    
    Returns:
    
    an array containing the fields of the current row.
  - getCell
```
public String getCell(int index)
```
    Gets the contents of a specific cell within the current row.
    
    Parameters:
    
    index - a 0-based column index
    
    Returns:
    
    the contents of the specified cell
  - getCell
```
public String getCell(String[] names,
                      String fallback)
```
    Gets the contents of a specific cell within the current row. The cell is searched for using several equally accepted names.
    
    Parameters:
    
    names - an array of accepted column names
    
    fallback - the default value to return if the cell is not found
    
    Returns:
    
    the contents of the specified cell
  - getCell
```
public String getCell(String[] names)
```
    Gets the contents of a specific cell within the current row. The cell is searched for using several equally accepted names.
    
    Parameters:
    
    names - an array of accepted column names
    
    Returns:
    
    the contents of the specified cell
  - getCell
```
public String getCell(String name)
```
    Gets the contents of a specific cell within the current row.
    
    Parameters:
    
    name - the column name, as indicated in the header row
    
    Returns:
    
    the contents of the specified cell
  - getCSVRow
```
public String getCSVRow(char separator)
```
    Gets the current row as a single string, with values separated by the specified character.
    
    Parameters:
    
    separator - the column separator character
    
    Returns:
    
    the current row as a string
  - getCSVRow
```
public String getCSVRow()
```
    Gets the current row as a single string containing comma-separated values.
    
    Returns:
    
    the current row as string
  - getHeaders
```
public String[] getHeaders()
                    throws IOException
```
    Gets the headers as found in the CSV file. If the constructor was called with the withHeaders parameter set to false, then this method will only return a 1-sized array containing the single header “image”,
    
    Returns:
    
    the CSV file headers
    
    Throws:
    
    IOException
  - fillResultsTable
```
public void fillResultsTable(ij.measure.ResultsTable rt)
```
    Update a ResultsTable with the contents of the current row.
    
    Parameters:
    
    rt - the ResultsTable object to update.
  - close
```
public void close()
```
    Closes any opened images. Calling this method is only necessary if the client code wishes to stop batch processing before the next() method returns false.
    Note that this only closes images that have not been reached yet by any call to next(). Closing previous images is the responsibility of the caller.
  - readCSV
```
public void readCSV()
             throws IOException
```
    Reads the entire CSV file. This method is automatically called by the next() or getHeaders() methods if needed.
    
    Throws:
    
    IOException - if any I/O error occurs while attempting to read the file

Class BatchReader

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BatchReader

BatchReader

BatchReader

BatchReader

Method Detail

setCaseSensitive

next

hasImage

getImage

getRow

getCell

getCell

getCell

getCell

getCSVRow

getCSVRow

getHeaders

fillResultsTable

close

readCSV