SequenceSettings

java.lang.Object
- org.micromanager.acquisition.SequenceSettings

```
public final class SequenceSettings
extends java.lang.Object
```
SequenceSettings objects contain the parameters describing how to run a single acquisition. Various methods of the AcquisitionManager will consume or generate SequenceSettings, and you can create your own to configure your custom acquisitions. Maintainer note: This should be an interface, but kept as a class for backward compatibility.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SequenceSettings.Builder

Nested Classes
Modifier and Type	Class and Description
`static class`	`SequenceSettings.Builder`

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`cameraTimeout` Deprecated. use Builder and cameraTimeout() instead
`java.lang.String`	`channelGroup` Deprecated. use Builder and channelGroup() instead
`java.util.ArrayList<ChannelSpec>`	`channels` Deprecated. use Builder and channels() instead
`java.lang.String`	`comment` Deprecated. use Builder and comment() instead
`java.util.ArrayList<java.lang.Double>`	`customIntervalsMs` Deprecated. use Builder and customIntervalsMs() instead
`double`	`intervalMs` Deprecated. use Builder and intervalMs() instead
`boolean`	`keepShutterOpenChannels` Deprecated. use Builder and keepShutterOpenChannels() instead
`boolean`	`keepShutterOpenSlices` Deprecated. use Builder and keepShutterOpenSlices() instead
`int`	`numFrames` Deprecated. use Builder and numFrames() instead
`java.lang.String`	`prefix` Deprecated. use Builder and prefix() instead
`boolean`	`relativeZSlice` Deprecated. use Builder and relativeZSlice() instead
`java.lang.String`	`root` Deprecated. use Builder and root() instead
`boolean`	`save` Deprecated. use Builder and save() instead
`boolean`	`shouldDisplayImages` Deprecated. use Builder and shouldDisplayImages() instead
`int`	`skipAutofocusCount` Deprecated. use Builder and skipAutofocusCount() instead
`java.util.ArrayList<java.lang.Double>`	`slices` Deprecated. use Builder and slices() instead
`boolean`	`slicesFirst` Deprecated. use Builder and slicesFirst() instead
`boolean`	`timeFirst` Deprecated. use Builder and timeFirst() instead
`boolean`	`useAutofocus` Deprecated. use Builder and useAutofocus() instead
`boolean`	`useCustomIntervals` Deprecated. use Builder and useCustomIntervals() instead
`boolean`	`usePositionList` Deprecated. use Builder and usePositionList() instead
`static double`	`Version`
`double`	`zReference` Deprecated. use Builder and zReference() instead

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`int`	`acqOrderMode()` Order of the various axes during acquisition as defined in `AcqOrderMode` Currently available orders: 0 - `AcqOrderMode.TIME_POS_SLICE_CHANNEL` 1 - `AcqOrderMode.TIME_POS_CHANNEL_SLICE` 2 - `AcqOrderMode.POS_TIME_SLICE_CHANNEL` 3 - `AcqOrderMode.POS_TIME_CHANNEL_SLICE`
`int`	`cameraTimeout()` Minimum camera timeout, in ms, for sequence acquisitions (actual timeout depends on exposure time and other factors)
`java.lang.String`	`channelGroup()` Configuration group used to define channels used in the acquisition
`java.util.ArrayList<ChannelSpec>`	`channels()` LIst with channel definitions to be used in the acquisition
`java.lang.String`	`comment()` Text comment to be attached to the acquired data
`SequenceSettings`	`copy()` Deprecated. When used correctly, SequenceSettings are immutable. If you really need a copy, use copyBuilder().build();
`SequenceSettings.Builder`	`copyBuilder()`
`java.util.ArrayList<java.lang.Double>`	`customIntervalsMs()` Time intervals between the starts of time points in milliseconds
`int`	`displayTimeUnit()` Time unit, only used to store preferred way to display the time
`static SequenceSettings`	`fromJSONStream(java.lang.String stream)`
`double`	`intervalMs()` Desired interval between the start of two consecutive time points in milliseconds.
`boolean`	`keepShutterOpenChannels()` Whether to keep shutter open during channel changes
`boolean`	`keepShutterOpenSlices()` Whether to keep shutter open during z-stack stage movements
`int`	`numFrames()` Number of time points to be acquired.
`java.lang.String`	`prefix()` Acquisition name.
`boolean`	`relativeZSlice()` Whether to base the z Top and Bottom for a z stack relative to a referent position or treat them as absolute values
`java.lang.String`	`root()` Directory where data will be saved
`boolean`	`save()` Whether the data acquisition should be stored on disk
`Datastore.SaveMode`	`saveMode()` File format to be used to save this acquisition when `save()` is set.
`boolean`	`shouldDisplayImages()` Whether to display acquired data
`int`	`skipAutofocusCount()` how many autofocus opportunities to skip
`java.util.ArrayList<java.lang.Double>`	`slices()` Z- drive positions to be used to acquire a z-stack
`double`	`sliceZBottomUm()` Start position of the z-stack in microns.
`double`	`sliceZStepUm()` Distance the z-drive should travel between steps when acquiring a z-stack
`double`	`sliceZTopUm()` End position of the z-stack in microns.
`static java.lang.String`	`toJSONStream(SequenceSettings settings)`
`boolean`	`useAutofocus()` Whether to use autofocus before each time point / position
`boolean`	`useChannels()` Whether to acquire multiple channels during the acquisition.
`boolean`	`useCustomIntervals()` Whether to use custom time intervals defined `customIntervalsMs()`
`boolean`	`useFrames()` Whether to acquire multiple time points during the acquisition.
`boolean`	`usePositionList()` Whether to acquire at multiple positions (defined in the positionLost
`boolean`	`useSlices()` Whether to acquire z stacks during the acquisition.
`double`	`zReference()` referent z position for relative moves

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

- Field Detail
  - Version
```
public static final double Version
```
    See Also:
    
    Constant Field Values
  - numFrames
```
@Deprecated
public int numFrames
```
    Deprecated. use Builder and numFrames() instead
  - intervalMs
```
@Deprecated
public double intervalMs
```
    Deprecated. use Builder and intervalMs() instead
  - useCustomIntervals
```
@Deprecated
public boolean useCustomIntervals
```
    Deprecated. use Builder and useCustomIntervals() instead
    
    Whether or not to use custom time intervals. Do not set this to true if customIntervalsMs is null!
  - customIntervalsMs
```
@Deprecated
public java.util.ArrayList<java.lang.Double> customIntervalsMs
```
    Deprecated. use Builder and customIntervalsMs() instead
    
    sequence of custom intervals or null
  - channels
```
@Deprecated
public java.util.ArrayList<ChannelSpec> channels
```
    Deprecated. use Builder and channels() instead
    
    an array of ChannelSpec settings (one for each channel) no member of the array should ever by null
  - slices
```
@Deprecated
public java.util.ArrayList<java.lang.Double> slices
```
    Deprecated. use Builder and slices() instead
    
    slice Z coordinates
  - relativeZSlice
```
@Deprecated
public boolean relativeZSlice
```
    Deprecated. use Builder and relativeZSlice() instead
    
    are Z coordinates relative or absolute
  - slicesFirst
```
@Deprecated
public boolean slicesFirst
```
    Deprecated. use Builder and slicesFirst() instead
    
    slice coordinate changes first
  - timeFirst
```
@Deprecated
public boolean timeFirst
```
    Deprecated. use Builder and timeFirst() instead
    
    frame coordinate changes first
  - keepShutterOpenSlices
```
@Deprecated
public boolean keepShutterOpenSlices
```
    Deprecated. use Builder and keepShutterOpenSlices() instead
    
    do we keep shutter open during slice changes
  - keepShutterOpenChannels
```
@Deprecated
public boolean keepShutterOpenChannels
```
    Deprecated. use Builder and keepShutterOpenChannels() instead
    
    do we keep shutter open channel changes
  - useAutofocus
```
@Deprecated
public boolean useAutofocus
```
    Deprecated. use Builder and useAutofocus() instead
    
    are we going to run autofocus before acquiring each position/frame
  - skipAutofocusCount
```
@Deprecated
public int skipAutofocusCount
```
    Deprecated. use Builder and skipAutofocusCount() instead
    
    how many autofocus opportunities to skip
  - save
```
@Deprecated
public boolean save
```
    Deprecated. use Builder and save() instead
    
    save to disk?
  - root
```
@Deprecated
public java.lang.String root
```
    Deprecated. use Builder and root() instead
    
    root directory name
  - prefix
```
@Deprecated
public java.lang.String prefix
```
    Deprecated. use Builder and prefix() instead
    
    acquisition name
  - zReference
```
@Deprecated
public double zReference
```
    Deprecated. use Builder and zReference() instead
    
    referent z position for relative moves
  - comment
```
@Deprecated
public java.lang.String comment
```
    Deprecated. use Builder and comment() instead
    
    comment text
  - channelGroup
```
@Deprecated
public java.lang.String channelGroup
```
    Deprecated. use Builder and channelGroup() instead
    
    which configuration group is used to define channels
  - usePositionList
```
@Deprecated
public boolean usePositionList
```
    Deprecated. use Builder and usePositionList() instead
    
    true if we want to have multiple positions
  - cameraTimeout
```
@Deprecated
public int cameraTimeout
```
    Deprecated. use Builder and cameraTimeout() instead
    
    Minimum camera timeout, in ms, for sequence acquisitions (actual timeout depends on exposure time and other factors)
  - shouldDisplayImages
```
@Deprecated
public boolean shouldDisplayImages
```
    Deprecated. use Builder and shouldDisplayImages() instead
    
    Whether or not to display images generated by the acquisition.
- Method Detail
  - copy
```
@Deprecated
public SequenceSettings copy()
```
    Deprecated. When used correctly, SequenceSettings are immutable. If you really need a copy, use copyBuilder().build();
    
    Create a copy of this SequenceSettings. All parameters will be copied, with new objects being created as necessary (i.e. this is a deep copy).
    
    Returns:
    
    Copy of this SequenceSettings.
  - copyBuilder
```
public SequenceSettings.Builder copyBuilder()
```
  - numFrames
```
public int numFrames()
```
    Number of time points to be acquired. Defines a sequence of time points together with intervalMs(). Will be overriden when useCustomIntervals() and customIntervalsMs() are set.
  - intervalMs
```
public double intervalMs()
```
    Desired interval between the start of two consecutive time points in milliseconds. Defines a sequence of time points together r with numFrames(). Will be overriden when useCustomIntervals() and customIntervalsMs() are set.
  - displayTimeUnit
```
public int displayTimeUnit()
```
    Time unit, only used to store preferred way to display the time
    
    Returns:
    
    0-milliseconds, 1-seconds, 2-minutes
  - useCustomIntervals
```
public boolean useCustomIntervals()
```
    Whether to use custom time intervals defined customIntervalsMs()
    
    Returns:
    
    use custom time intervals when true
  - customIntervalsMs
```
public java.util.ArrayList<java.lang.Double> customIntervalsMs()
```
    Time intervals between the starts of time points in milliseconds
  - channels
```
public java.util.ArrayList<ChannelSpec> channels()
```
    LIst with channel definitions to be used in the acquisition
    
    Returns:
    
    LIst with channel definitions to be used in the acquisition
  - slices
```
public java.util.ArrayList<java.lang.Double> slices()
```
    Z- drive positions to be used to acquire a z-stack
    
    Returns:
    
    List of Z- drive positions to be used to acquire a z-stack
  - relativeZSlice
```
public boolean relativeZSlice()
```
    Whether to base the z Top and Bottom for a z stack relative to a referent position or treat them as absolute values
    
    Returns:
    
    true when values are relative
  - keepShutterOpenSlices
```
public boolean keepShutterOpenSlices()
```
    Whether to keep shutter open during z-stack stage movements
  - keepShutterOpenChannels
```
public boolean keepShutterOpenChannels()
```
    Whether to keep shutter open during channel changes
  - useAutofocus
```
public boolean useAutofocus()
```
    Whether to use autofocus before each time point / position
    
    Returns:
    
    Whether to use autofocus before each time point / position
  - skipAutofocusCount
```
public int skipAutofocusCount()
```
    how many autofocus opportunities to skip
  - save
```
public boolean save()
```
    Whether the data acquisition should be stored on disk
    
    Returns:
    
    save when true, otherwise to RAMM only
  - saveMode
```
public Datastore.SaveMode saveMode()
```
    File format to be used to save this acquisition when save() is set. Formats are defined in Datastore.SaveMode. Currently: 0 - Datastore.SaveMode.SINGLEPLANE_TIFF_SERIES 1 - Datastore.SaveMode.MULTIPAGE_TIFF
    
    Returns:
    
    integer representing Datastore.SaveMode
  - root
```
public java.lang.String root()
```
    Directory where data will be saved
    
    Returns:
    
    irectory where data will be saved
  - prefix
```
public java.lang.String prefix()
```
    Acquisition name. Will be used in storage and display
    
    Returns:
    
    acquisition anme
  - zReference
```
public double zReference()
```
    referent z position for relative moves
  - comment
```
public java.lang.String comment()
```
    Text comment to be attached to the acquired data
    
    Returns:
    
    text comment
  - channelGroup
```
public java.lang.String channelGroup()
```
    Configuration group used to define channels used in the acquisition
  - usePositionList
```
public boolean usePositionList()
```
    Whether to acquire at multiple positions (defined in the positionLost
    
    Returns:
    
    True if positions in the list should all be visited, when false, only acquired at current position
  - cameraTimeout
```
public int cameraTimeout()
```
    Minimum camera timeout, in ms, for sequence acquisitions (actual timeout depends on exposure time and other factors)
  - shouldDisplayImages
```
public boolean shouldDisplayImages()
```
    Whether to display acquired data
  - useSlices
```
public boolean useSlices()
```
    Whether to acquire z stacks during the acquisition.
  - useFrames
```
public boolean useFrames()
```
    Whether to acquire multiple time points during the acquisition.
  - useChannels
```
public boolean useChannels()
```
    Whether to acquire multiple channels during the acquisition.
  - sliceZStepUm
```
public double sliceZStepUm()
```
    Distance the z-drive should travel between steps when acquiring a z-stack
  - sliceZBottomUm
```
public double sliceZBottomUm()
```
    Start position of the z-stack in microns. Can be absolute or relative to current position.
  - sliceZTopUm
```
public double sliceZTopUm()
```
    End position of the z-stack in microns. Can be absolute or relative to current position.
  - acqOrderMode
```
public int acqOrderMode()
```
    Order of the various axes during acquisition as defined in AcqOrderMode Currently available orders: 0 - AcqOrderMode.TIME_POS_SLICE_CHANNEL 1 - AcqOrderMode.TIME_POS_CHANNEL_SLICE 2 - AcqOrderMode.POS_TIME_SLICE_CHANNEL 3 - AcqOrderMode.POS_TIME_CHANNEL_SLICE
    
    Returns:
    
    integer representing enum AcqOrderMode
  - toJSONStream
```
public static java.lang.String toJSONStream(SequenceSettings settings)
```
  - fromJSONStream
```
public static SequenceSettings fromJSONStream(java.lang.String stream)
```

Class SequenceSettings

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

Version

numFrames

intervalMs

useCustomIntervals

customIntervalsMs

channels

slices

relativeZSlice

slicesFirst

timeFirst

keepShutterOpenSlices

keepShutterOpenChannels

useAutofocus

skipAutofocusCount

save

root

prefix

zReference

comment

channelGroup

usePositionList

cameraTimeout

shouldDisplayImages

Method Detail

copy

copyBuilder

numFrames

intervalMs

displayTimeUnit

useCustomIntervals

customIntervalsMs

channels

slices

relativeZSlice

keepShutterOpenSlices

keepShutterOpenChannels

useAutofocus

skipAutofocusCount

save

saveMode

root

prefix

zReference

comment

channelGroup

usePositionList

cameraTimeout

shouldDisplayImages

useSlices

useFrames

useChannels

sliceZStepUm

sliceZBottomUm

sliceZTopUm

acqOrderMode

toJSONStream

fromJSONStream