Package org.anchoranalysis.plugin.io.bean.file.group

Class GroupFiles

Object
AnchorBean<InputManager<NamedChannelsInput>>
InputManager<NamedChannelsInput>
InputManagerWithStackReader<NamedChannelsInput>
GroupFiles
public class GroupFiles extends InputManagerWithStackReader<NamedChannelsInput>
An InputManagerWithStackReader that can unify separate images in separate files to form a single Stack.

A time-series of Stacks may also be formed.

The criteria on how to unify is defined by a pattern in the file path (via regular expressions).

A regular expression is applied on the set of input file paths, to identify one or more groups:

  1. One group is the image key (something that uniquely identifies each image).
  2. One group is the slice-identifier (identifies the z slice, must be positive integer.
  3. One group is the channel-identifier (identifies the channel, must be positive integer).

For each image key, an image is loaded using the slice and channel-identifiers.

Integer numbers are simply loaded in ascending numerical order. So gaps are allowed, and starting numbers are irrelevant.

It is more powerful than MultiFileReader, which expects only one image per directory. This class allows multiple images per directory and only performs a single glob for filenames.

Author:
Owen Feehan

  • Constructor Details

    • GroupFiles

      public GroupFiles()

  • Method Details

    • inputs

      public InputsWithDirectory<NamedChannelsInput> inputs(InputManagerParameters parameters) throws InputReadFailedException
      Description copied from class: InputManager
      Creates a list of inputs given particular parameters.
      Specified by:
      inputs in class InputManager<NamedChannelsInput>
      Parameters:
      parameters - the parameters.
      Returns:
      the list of inputs, together with any associated parent directory.
      Throws:
      InputReadFailedException - if inputs cannot be successfully read from the file-system.

    • getFileInput

      public NamedFiles getFileInput()

    • setFileInput

      public void setFileInput(NamedFiles fileInput)

    • getPathParser

      public FilePathParser getPathParser()

    • setPathParser

      public void setPathParser(FilePathParser pathParser)

    • isRequireAllFilesMatch

      public boolean isRequireAllFilesMatch()

    • setRequireAllFilesMatch

      public void setRequireAllFilesMatch(boolean requireAllFilesMatch)

    • getImgChannelMapCreator

      public ChannelMapCreator getImgChannelMapCreator()

    • setImgChannelMapCreator

      public void setImgChannelMapCreator(ChannelMapCreator imgChannelMapCreator)

    • getNamer

      public FileNamer getNamer()

    • setNamer

      public void setNamer(FileNamer namer)

    • getCheckParsedFilePathBag

      public CheckParsedFilePathBag getCheckParsedFilePathBag()
      Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.

    • setCheckParsedFilePathBag

      public void setCheckParsedFilePathBag(CheckParsedFilePathBag checkParsedFilePathBag)
      Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.