model

Class Importer

java.lang.Object

model.Importer

public class Importer
extends java.lang.Object

The importer class takes care of importing measurement data. Depending on the directory structure and filename it deduces what is an experiment, a sample, a field of view or a file. The level of a directory determines if it refers to an experiment, sample or field of view. For each file the channel is determined by its filename. Channels are (by default) determined by the following conditions:

acquisition

filename ends in 'acquisition.tif'

bright field

filename ends in 'bf.tif'

red channel

filename ends in '568.tif'

green channel

filename ends '514.tif'

blue channel

filename ends '488.tif'

Note that after 'bf', '568' and the other channels there might be an extra character. For example: '001 5682.tif'. The '2' indicates that it is the seconds part of the 568 image file.

Author:

C.M. Punter

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	acqRegEx The Acquisition regex.
static java.lang.String	bfRegEx The Bright Field regex.
static java.lang.String	blueRegEx The Blue channel regex.
static java.lang.String	greenRegEx The Green channel regex.
static java.lang.String	redRegEx The Red channel regex.

Constructor Summary

Constructors

Constructor and Description
Importer(DatabaseModel model) Instantiates a new importer.

Method Summary

Modifier and Type	Method and Description
void	importExperiment(java.io.File folder, boolean isTimeSampling) For a given root (node) and folder this method will import experiments.
void	importFieldOfViews(Sample sample) Import field of views.
void	importFile(Node node, java.io.File file)
void	importFile(Node node, java.io.File file, java.lang.String channel, java.lang.String name, java.lang.String path)
void	importFiles(Node fieldOfView) Import files.
void	importSamples(Experiment experiment) Import samples.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

acqRegEx

public static java.lang.String acqRegEx

The Acquisition regex.

bfRegEx

public static java.lang.String bfRegEx

The Bright Field regex.

redRegEx

public static java.lang.String redRegEx

The Red channel regex.

greenRegEx

public static java.lang.String greenRegEx

The Green channel regex.

blueRegEx

public static java.lang.String blueRegEx

The Blue channel regex.

Constructor Detail

Importer

public Importer(DatabaseModel model)

Instantiates a new importer.

Parameters:

model - the model

Method Detail

importExperiment

public void importExperiment(java.io.File folder,
                             boolean isTimeSampling)

For a given root (node) and folder this method will import experiments. You also need to specify if this experiment is time lapse or time sampling.

Parameters:

folder - the folder from which all samples are imported

isTimeSampling - determines if this experiment is time lapse or not

importSamples

public void importSamples(Experiment experiment)

Import samples.

Parameters:

experiment - the experiment

importFieldOfViews

public void importFieldOfViews(Sample sample)

Import field of views.

Parameters:

sample - the sample

importFiles

public void importFiles(Node fieldOfView)

Import files.

Parameters:

fieldOfView - the field of view

importFile

public void importFile(Node node,
                       java.io.File file)

importFile

public void importFile(Node node,
                       java.io.File file,
                       java.lang.String channel,
                       java.lang.String name,
                       java.lang.String path)