org.micromanager.data

Interface SummaryMetadata

public interface SummaryMetadata

This class defines the summary metadata that applies to all images in a dataset. It is immutable; construct it with a SummaryMetadataBuilder. All fields of the SummaryMetadata that are not explicitly initialized will default to null. You are not expected to implement this interface; it is here to describe how you can interact with SummaryMetadata created by Micro-Manager itself. If you need to create a new SummaryMetadata, either use the getSummaryMetadataBuilder() method of the DataManager class, or call the copy() method of an existing SummaryMetadata instance.

This class uses a Builder pattern. Please see https://micro-manager.org/wiki/Using_Builders for more information.

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static interface	SummaryMetadata.Builder Builder for SummaryMetadata.
static interface	SummaryMetadata.SummaryMetadataBuilder Deprecated. - Use SummaryMetadata.Builder instead

Method Summary

Modifier and Type	Method and Description
SummaryMetadata.SummaryMetadataBuilder	copy() Deprecated. - Use SummaryMetadata.Builder.copyBuilder instead
SummaryMetadata.Builder	copyBuilder()
java.lang.String[]	getAxisOrder() Deprecated. - Use getOrdereddAxes() instead
java.lang.String	getChannelGroup() The config group that was used to switch between channels.
java.util.List<java.lang.String>	getChannelNameList()
java.lang.String[]	getChannelNames() Deprecated. - Use getChannelNameList() instead
java.lang.String	getComputerName() The name of the computer the data was collected on.
java.lang.Double[]	getCustomIntervalsMs() Deprecated. - Use double[] getCustomIntervalsMsArray() instead
double[]	getCustomIntervalsMsArray()
java.util.List<java.lang.Double>	getCustomIntervalsMsList() When using a variable amount of time between timepoints, this array has the list of wait times.
java.lang.String	getDirectory() The directory the data was originally saved to.
java.lang.Integer	getImageHeight() ImageHeight in pixels.
java.lang.Integer	getImageWidth() ImageWidth in pixels.
Coords	getIntendedDimensions() The expected number of images along each axis that were to be collected.
java.lang.Boolean	getKeepShutterOpenChannels() For acquisitions with more than one channel, whether or not the shutter was left open in between each channel.
java.lang.Boolean	getKeepShutterOpenSlices() For acquisitions with more than one Z slice, whether or not the shutter was left open in between each slice.
java.lang.String	getMetadataVersion() The version of the metadata when the data was collected.
java.lang.String	getMicroManagerVersion() The version of Micro-Manager used to collect the data.
java.util.List<java.lang.String>	getOrderedAxes() The order in which axes changed when adding images to the dataset.
java.lang.String	getPrefix() The user-supplied portion of the filename, plus any additional numerical identifier needed to ensure uniqueness.
java.lang.String	getProfileName() The name of the Micro-Manager profile used to collect this data.
java.lang.String	getSafeChannelName(int index) Retrieve the name of the specified channel.
SequenceSettings	getSequenceSettings() Settings that define the Multi-Dimensional Acquisition specified by the user to acquire this data set.
java.util.List<MultiStagePosition>	getStagePositionList() The stage positions that were to be visited in the acquisition.
MultiStagePosition[]	getStagePositions() Deprecated. - Use getStagePositionList() instead
java.lang.String	getStartDate() The date and time at which the acquisition started.
PropertyMap	getUserData() Any general-purpose user meta data.
java.lang.String	getUserName() The signed-in user of the machine that collected this data.
java.lang.Double	getWaitInterval() Amount of time to wait between timepoints.
java.lang.Double	getZStepUm() Distance between slices in a volume of data, in microns.

Method Detail

copyBuilder

SummaryMetadata.Builder copyBuilder()

copy

@Deprecated
SummaryMetadata.SummaryMetadataBuilder copy()

Deprecated. - Use SummaryMetadata.Builder.copyBuilder instead

Deprecated.

Returns:

- A copy of the SummaryMetadataBuilder

getPrefix

java.lang.String getPrefix()

The user-supplied portion of the filename, plus any additional numerical identifier needed to ensure uniqueness. This should in practice be the name of the directory that the data is saved in.

Returns:

user-supplied portion of the filename.

getUserName

java.lang.String getUserName()

The signed-in user of the machine that collected this data.

Returns:

signed-in user of the machine that collected this data

getProfileName

java.lang.String getProfileName()

The name of the Micro-Manager profile used to collect this data.

Returns:

name of the micro-Manager profile used to collect this data

getMicroManagerVersion

java.lang.String getMicroManagerVersion()

The version of Micro-Manager used to collect the data.

Returns:

version of Micro-Manager used to collect the data

getMetadataVersion

java.lang.String getMetadataVersion()

The version of the metadata when the data was collected.

Returns:

version of the metadata when the data was collected

getComputerName

java.lang.String getComputerName()

The name of the computer the data was collected on.

Returns:

name of the computer the data was collected on

getDirectory

java.lang.String getDirectory()

The directory the data was originally saved to.

Returns:

directory the data was originally saved to

getChannelGroup

java.lang.String getChannelGroup()

The config group that was used to switch between channels.

Returns:

name of the channel config group

getChannelNameList

java.util.List<java.lang.String> getChannelNameList()

getChannelNames

@Deprecated
java.lang.String[] getChannelNames()

Deprecated. - Use getChannelNameList() instead

Deprecated.

Returns:

Array with channelname

getSafeChannelName

java.lang.String getSafeChannelName(int index)

Retrieve the name of the specified channel. Ordinarily this is simply an index into the channelNames array (per getChannelNames()), but if there is no name there (channelNames is unset, or not long enough, or contains a null), then the name will be "channel N" where N is the channel index.

Parameters:

index - Channel index to get the name for.

Returns:

Name of the channel.

getZStepUm

java.lang.Double getZStepUm()

Distance between slices in a volume of data, in microns.

Returns:

distance between slices in a volume of data, in microns

getWaitInterval

java.lang.Double getWaitInterval()

Amount of time to wait between timepoints.

Returns:

amount of time to wait between timepoints

getCustomIntervalsMsList

java.util.List<java.lang.Double> getCustomIntervalsMsList()

When using a variable amount of time between timepoints, this array has the list of wait times.

Returns:

list of wait times between timepoints

getCustomIntervalsMsArray

double[] getCustomIntervalsMsArray()

getCustomIntervalsMs

@Deprecated
java.lang.Double[] getCustomIntervalsMs()

Deprecated. - Use double[] getCustomIntervalsMsArray() instead

Deprecated.

Returns:

- Array with custom intervals

getOrderedAxes

java.util.List<java.lang.String> getOrderedAxes()

The order in which axes changed when adding images to the dataset. The first entry in this array is the first axis to have a nonzero value; the second entry is the second to have a nonzero value, etc. In other words, the entries should be ordered from changes-most-frequently to changes-least-frequently. RewritableDatastores will automatically update this property as images are added to the Datastore, if the property is not set manually. Other Datastore types cannot change the SummaryMetadata as images are added; thus this property will need to be set manually in those cases.

Returns:

Axis names in order of change rate.

getAxisOrder

@Deprecated
java.lang.String[] getAxisOrder()

Deprecated. - Use getOrdereddAxes() instead

Deprecated.

Returns:

- Array with Axis ordered as described for getOrderedAxes()

getIntendedDimensions

Coords getIntendedDimensions()

The expected number of images along each axis that were to be collected. The actual dimensions may differ if the acquisition was aborted partway through for any reason.

Returns:

expected number of images along each axis that were to be collected

getKeepShutterOpenSlices

java.lang.Boolean getKeepShutterOpenSlices()

For acquisitions with more than one Z slice, whether or not the shutter was left open in between each slice.

Returns:

whether shutter was left open between Z slices.

getKeepShutterOpenChannels

java.lang.Boolean getKeepShutterOpenChannels()

For acquisitions with more than one channel, whether or not the shutter was left open in between each channel.

Returns:

whether shutter was left open between channels.

getStartDate

java.lang.String getStartDate()

The date and time at which the acquisition started.

Returns:

date and time at which the acquisition started

getStagePositionList

java.util.List<MultiStagePosition> getStagePositionList()

The stage positions that were to be visited in the acquisition.

Returns:

stage positions that were to be visited in the acquisition

getStagePositions

@Deprecated
MultiStagePosition[] getStagePositions()

Deprecated. - Use getStagePositionList() instead

Deprecated.

Returns:

see getStagePostionList()

getUserData

PropertyMap getUserData()

Any general-purpose user meta data.

Returns:

Any general-purpose user meta data

getSequenceSettings

SequenceSettings getSequenceSettings()

Settings that define the Multi-Dimensional Acquisition specified by the user to acquire this data set.

Returns:

The settings that define this MDA.

getImageWidth

java.lang.Integer getImageWidth()

ImageWidth in pixels.

Returns:

ImageWidth in pixels. Null if Image Width is not known.

getImageHeight

java.lang.Integer getImageHeight()

ImageHeight in pixels.

Returns:

ImageHeight in pixels. Null if Image Height is not know.