Serialized Form

Package acquifer.ij
- Class acquifer.ij.BatchDialog extends fiji.util.gui.GenericDialogPlus implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - lastLeftPanelIndex
```
int lastLeftPanelIndex
```
    - headless
```
boolean headless
```
      True only when called in console with tag --headless.
      WARNING: without it, Fiji GUI is shown but not the plugin GUI, which can be an issue for functions relying on AWT/GUI.
    - imageDirectory
```
String imageDirectory
```
    - listChannels
```
Set<E> listChannels
```
    - listZslices
```
Set<E> listZslices
```
    - listTimepoints
```
Set<E> listTimepoints
```
    - listSubPositions
```
Set<E> listSubPositions
```
    - listWells
```
Set<E> listWells
```
    - plate
```
acquifer.core.Plate plate
```
    - nRows
```
int nRows
```
      Number of plate rows. The GUI has one more row of checkboxes (the 1st one) for full-column selections.
    - nColumns
```
int nColumns
```
      Number of plate columns. The GUI has one more column of checkboxes (the 1st one) for full-row selections.
    - nGroupCheckboxes
```
int nGroupCheckboxes
```
    - rowSelectionCheckboxes
```
List<E> rowSelectionCheckboxes
```
    - filenameFilter
```
acquifer.core.im.FilenameFilter filenameFilter
```
    - currentDataset
```
acquifer.core.Dataset currentDataset
```
      Dataset currently corresponding to the path in the input field. The dataset can be null if the path is not valid.
    - labelSubposition
```
java.awt.Label labelSubposition
```
    - labelChannels
```
java.awt.Label labelChannels
```
    - labelZ
```
java.awt.Label labelZ
```
    - labelTimepoint
```
java.awt.Label labelTimepoint
```
Package acquifer.ij.im.plugins
- Class acquifer.ij.im.plugins.BatchConverter extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - outDir
```
String outDir
```
    - outDirFile
```
File outDirFile
```
    - format
```
String format
```
    - crop
```
boolean crop
```
    - roiPath
```
String roiPath
```
    - scale
```
double scale
```
    - interpolationMethod
```
int interpolationMethod
```
    - averageWhenDownSizing
```
boolean averageWhenDownSizing
```
    - methods
```
String[] methods
```
- Class acquifer.ij.im.plugins.BatchCopy extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - destDir
```
String destDir
```
    - copyLog
```
boolean copyLog
```
    - COPY_DIRECTORIES
```
String COPY_DIRECTORIES
```
    - COPY_FILES
```
String COPY_FILES
```
    - COPY_ALL
```
String COPY_ALL
```
- Class acquifer.ij.im.plugins.BatchMacro extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  -3842365774173230771L
  - Serialized Fields
    - defaultDirectory
```
String defaultDirectory
```
    - BUTTON_LOAD_MACRO
```
String BUTTON_LOAD_MACRO
```
    - macro
```
String macro
```
- Class acquifer.ij.im.plugins.BatchScript extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - scriptService
```
org.scijava.script.DefaultScriptService scriptService
```
    - scriptPath
```
String scriptPath
```
    - scriptFile
```
File scriptFile
```
- Class acquifer.ij.im.plugins.BioformatConverter extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - destDir
```
String destDir
```
    - copyLog
```
boolean copyLog
```
    - COPY_DIRECTORIES
```
String COPY_DIRECTORIES
```
    - COPY_FILES
```
String COPY_FILES
```
    - COPY_ALL
```
String COPY_ALL
```
    - versionIM
```
int versionIM
```
- Class acquifer.ij.im.plugins.Hyperstack_Macro extends Hyperstack_Maker implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - macroCode
```
String macroCode
```
    - defaultDir
```
String defaultDir
```
    - output
```
String output
```
    - BUTTON_LOAD_MACRO
```
String BUTTON_LOAD_MACRO
```
- Class acquifer.ij.im.plugins.Hyperstack_Maker extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - metadataParser
```
acquifer.core.im.MetadataParser metadataParser
```
    - groupedImageInfos
```
acquifer.core.ImageSeries[] groupedImageInfos
```
    - showStack
```
boolean showStack
```
      If yes or no the stack should be shown
    - useVirtual
```
boolean useVirtual
```
      If VirtualStack should be used to display the stack.
      Faster but potential compatibility issues with macros (i.e need to duplicate).
    - saveStack
```
boolean saveStack
```
      If yes or no, the stack should be saved.
      If yes, it is saved in stackDir.
    - stackDir
```
String stackDir
```
      Where the stack should be saved if saveStack is true.
    - projectStack
```
boolean projectStack
```
      If yes or no the stack should be projected
    - showProjectionTickbox
```
boolean showProjectionTickbox
```
      If a tick box should be shown in the GUI to ask the user about yes/no project stack
    - showProjection
```
boolean showProjection
```
      Show stack projection (yes/no)
    - saveProjection
```
boolean saveProjection
```
      If the projection should be saved
    - METHODS
```
String[] METHODS
```
      Set of projection method for the stack
    - projMethod
```
String projMethod
```
      The selected projection method as a string
    - useCustomRange
```
boolean useCustomRange
```
      If a custom Z-slice range should be used for projection
    - startSlice
```
int startSlice
```
    - stopSlice
```
int stopSlice
```
    - projDir
```
String projDir
```
      Where to save the projection if saveProjection is true
    - stack
```
ij.ImagePlus stack
```
      Stack/hyperstack generated by the plugin at each iteration (each well).
    - proj
```
ij.ImagePlus proj
```
      Stack projection
- Class acquifer.ij.im.plugins.Hyperstack_Script extends Hyperstack_Maker implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - scriptService
```
org.scijava.script.DefaultScriptService scriptService
```
    - scriptPath
```
String scriptPath
```
      Path to script file to execute, provided by the user.
    - scriptFile
```
File scriptFile
```
- Class acquifer.ij.im.plugins.HyperstackBrowser extends fiji.util.gui.GenericDialogPlus implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isHyperstack
```
boolean isHyperstack
```
- Class acquifer.ij.im.plugins.PlateMontageMaker extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - downScalingFactor
```
int downScalingFactor
```
Package acquifer.ij.im03
- Class acquifer.ij.im03.BatchDialog extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
Package acquifer.ij.im03.plugins
- Class acquifer.ij.im03.plugins.Batch_Converter extends BatchConverter implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Batch_Copy extends BatchCopy implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Batch_Macro extends BatchMacro implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Batch_Script extends BatchScript implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.BioformatConverter extends BioformatConverter implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Hyperstack_Macro extends Hyperstack_Macro implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Hyperstack_Maker extends Hyperstack_Maker implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.Hyperstack_Script extends Hyperstack_Script implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im03.plugins.PlateMontageMaker extends PlateMontageMaker implements Serializable
  
  serialVersionUID:
  
  1L
Package acquifer.ij.im04
- Class acquifer.ij.im04.BatchDialog extends BatchDialog implements Serializable
  
  serialVersionUID:
  
  1L
Package acquifer.ij.im04.plugins
- Class acquifer.ij.im04.plugins.Batch_Converter extends BatchConverter implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Batch_Copy extends BatchCopy implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Batch_Macro extends BatchMacro implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Batch_Script extends BatchScript implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.BioformatConverter extends BioformatConverter implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Hyperstack_Macro extends Hyperstack_Macro implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Hyperstack_Maker extends Hyperstack_Maker implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.Hyperstack_Script extends Hyperstack_Script implements Serializable
  
  serialVersionUID:
  
  1L
- Class acquifer.ij.im04.plugins.PlateMontageMaker extends PlateMontageMaker implements Serializable
  
  serialVersionUID:
  
  1L

Serialized Form

Package acquifer.ij

Class acquifer.ij.BatchDialog extends fiji.util.gui.GenericDialogPlus implements Serializable

Serialized Fields

lastLeftPanelIndex

headless

imageDirectory

listChannels

listZslices

listTimepoints

listSubPositions

listWells

plate

nRows

nColumns

nGroupCheckboxes

rowSelectionCheckboxes

filenameFilter

currentDataset

labelSubposition

labelChannels

labelZ

labelTimepoint

Package acquifer.ij.im.plugins

Class acquifer.ij.im.plugins.BatchConverter extends BatchDialog implements Serializable

Serialized Fields

outDir

outDirFile

format

crop

roiPath

scale

interpolationMethod

averageWhenDownSizing

methods

Class acquifer.ij.im.plugins.BatchCopy extends BatchDialog implements Serializable

Serialized Fields

destDir

copyLog

COPY_DIRECTORIES

COPY_FILES

COPY_ALL

Class acquifer.ij.im.plugins.BatchMacro extends BatchDialog implements Serializable

Serialized Fields

defaultDirectory

BUTTON_LOAD_MACRO

macro

Class acquifer.ij.im.plugins.BatchScript extends BatchDialog implements Serializable

Serialized Fields

scriptService

scriptPath

scriptFile

Class acquifer.ij.im.plugins.BioformatConverter extends BatchDialog implements Serializable

Serialized Fields

destDir

copyLog

COPY_DIRECTORIES

COPY_FILES

COPY_ALL

versionIM

Class acquifer.ij.im.plugins.Hyperstack_Macro extends Hyperstack_Maker implements Serializable

Serialized Fields

macroCode

defaultDir

output

BUTTON_LOAD_MACRO

Class acquifer.ij.im.plugins.Hyperstack_Maker extends BatchDialog implements Serializable

Serialized Fields

metadataParser

groupedImageInfos

showStack

useVirtual

saveStack

stackDir

projectStack

showProjectionTickbox

showProjection

saveProjection

METHODS

projMethod