Data manager 2.0


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The 2. With it, we want to provide access to many aspects of the program that were previously hidden in internal classes. For example, it is now much more straightforward to access acquisition image data, control image display windows, read and modify acquisition metadata, and save data to disk. Additionally, we have rearranged the org. The Javadocs should prove useful to anyone wanting to familiarize themselves with the API.

This page provides some more focused and descriptive guidance, with reference to the Javadocs where appropriate. The org. In particular, there are several new classes that you should familiarize yourself with if you want to read, modify, or create acquisition data or metadata. As a general note, many of the classes in particular, Image , Coords , Metadata , and SummaryMetadata below are immutable.

This means that a given instance of the class cannot be modified — it will have methods to read its state, but no methods to modify them. If you want a modified version of a class, instead you make a copy that is different in the relevant ways. Immutability provides many advantages for ensuring coherency of data in complex workflows.

However, it can take some getting used to. DataProvider is a new class that holds the image data and summary metadata of an acquisition. Whereas data can only be read from a DataProvider i. Datastore which otherwise has the same functionality as a DataProvider. Every acquisition has an associated Datastore, and you can create your own Datastores to perform custom acquisitions see the section on the DataManager , below.

A RewriteableDatastore lets you replace already present images with new ones, whereas a Datastore will not let you do that. The Image class replaces the old TaggedImage class as our internal representation of a single 2D, monochromatic image. In addition there are various methods for creating copies of the Image with different metadata or at different coordinates.

While Image is intended to completely supplant TaggedImage , the latter class is not completely gone; it is still generated by various MMCore functions. The new classes have pre-defined supported fields that are strongly-typed, and can be rapidly constructed based on a template metadata object.

If you have extra fields that you wish to include in the metadata or summary metadata, there is a userData field with the type of PropertyMap , which allows for storing semi-arbitrary key-value pairs.

You can add whatever fields you like to this object. A Coords is a zero-based location in N-dimensional space. If you attempt to add an Image to a Datastore whose Coords match those of an image that is already in the Datastore, an error will occur whereas you can replace existing images with the same Coords in a RewritableDatastore.

You are not restricted to the classic 4 axes of channel, time, z slice, and stage position. You can freely add additional axes and call them whatever you like. The only axis that Micro-Manager treats specially is the channel axis, and then only in the display code. Additionally, you are not required to provide a position along any given axis.

If you ask a Coords what its position is for an axis it does not have, it will return 0. Note that this is not a useful way to figure out if a DataProvider contains images for the given axis, since it will also return 0 for the first image along each axis.

In the future we will add support for saving arbitrary axes to disk. As with the Metadata and SummaryMetadat classes, Coords are generated using a builder. Because the API only exposes interfaces i. The DataManager provides that functionality for you via e. The DataManager can be accessed via the Studio. The display package contains the API for creating, controlling, and manipulating image display windows.

It provides the ability to create new display windows, programatically control them including both adjusting the parameters used to draw the image, and the ability to draw overlays , and listen to certain events they generate when interacted with.

DataViewer is the class that all Micro-Manager image display windows implement. Each DataViewer is associated with a single Datastore , and displays the images in that store. However, there may be multiple DataViewers for a single Datastore. The DataViewer class exposes a large number of methods for selecting which images are displayed and controlling how they are displayed.

For example, the setDisplayedImageTo method takes a Coords object described above and changes the displayed image to be the one at the specified coordinates. Most of the properties of the display, like the channel colors, contrast settings, and magnification, are encompassed by the DisplaySettings object see below.

This object can be accessed with getDisplaySettings and changed with setDisplaySettings. StackWindow as it was in the 1. Micro-Manager strives to maintain backwards compatibility by creating a hidden StackWindow that transparently redirects most calls to the DataViewer; this allows ImageJ plugins and tools to still largely operate as expected.

However, direct window manipulations e. If you need to find a DataViewer i. If you need to manipulate a DataViewer as a Java window for example to change its position onscreen , use the DataViewer. As with Datastore , each DisplayWindow has a com. EventBus , whose events you can subscribe to using the registerForEvents method.

In particular, you should listen to the RequestToCloseEvent if you want to be notified when the user clicks on the close button of the window. DisplayWindows cannot close unless their forceClosed method is called. If you are not interested in handling this logic, read about DisplayWindow tracking in the DisplayManager section, below.

The DisplaySettings class tracks most aspects of how exactly images are displayed in a particular DisplayWindow. As with the Metadata and SummaryMetadata classes discussed earlier, it is constructed with a Builder pattern. Whenever the DisplayWindow receives new DisplaySettings e. The various controls in the window listen for this event, and automatically update themselves to reflect the new settings.

Your own code may also listen for this event if you have controls that need to be updated to reflect the new state of the display. The DisplayManager class accessible via Studio. In addition to the above, DisplayManager also handles management of Datastores. Additionally, before the last DisplayWindow is allowed to close, either the Datastore must have saved its data, or the user must have explicitly confirmed closing without saving.

If you want to transfer this responsibility to Micro-Manager, call the manage method of DisplayManager. It will automatically find all DisplayWindows associated with the Datastore, and register on their EventBuses. All DisplayWindows except the last are allowed to close when the user clicks the close button. When the last one tries to close, the DisplayManager will ensure that the user has a chance to save their data. All Datastores that Micro-Manager creates for its own purposes for example, for storing the results of a multi-dimensional acquisition are automatically managed.

You can access the Album via the Studio. Effectively it is a subset of the old ScriptInterface object from 1. You can access the CompatibilityInterface via the Studio. The Micro-Manager Core is unchanged compared to 1.

You can access it using Studio. The EventManager is used to register for various system-wide events, as listed in the org. You can access the EventManager via the Studio. It can be accessed via the Studio. The LogManager is used to log and display messages, which can be useful for indicating when important events occur or when something goes wrong.

Accessed via the Studio. The UserProfile stores information specific to the current user of the microscope, such as preferred window positions and remembered form inputs. When the user starts Micro-Manager, they are prompted to select a profile to use; relevant information is then pulled from that profile. ScriptController is a small entity for interacting with the BeanShell scripting system. Access via the Studio.

Edit page History How do I edit this website? Acquisition data: the data API The org. The DataProvider and Datastore classes org. The primary functions you will likely be interested in are: putImage and getImage , which allow you to add and retrieve Images from the Datastore see the Image class, below. The Datastore has a com. EventBus that signals events; appropriate methods with the com.

Subscribe annotation will be called when the event occurs. For example: import com. Subscribe; import org. Datastore; import org. Image; import org. NewImageEvent; import org. Who should use Micro-Manager Version 2.



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data manager 2.0

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