eda_plugin.utility.writers.Writer

class eda_plugin.utility.writers.Writer(*args: Any, **kwargs: Any)

Bases: QObject

Writer that writes images, metadata and EDA specific data to have all information for EDA.

With this one everything will be written as OME_NGFF with some additional folders for additional Metadata for both Micro-Manager and EDA specific information.

__init__(event_bus: EventBus)

Connect the necessary signals

Methods

__init__(event_bus)	Connect the necessary signals
new_save_location(event)	A new acquisition was started leading to a new path for saving
prepare_nn_image(image, dims)	Padding here, could be something else in a subclass.
reset_local_image_store()
save_decision_parameter(param, elapsed, ...)	Received new interpretation from interpreter, save value into the EDA file
save_image(py_image)	Gather one timepoint for the original data and save it.
save_imagej_metadata([tif])	Get the ImageJ metadata from the original tiff file and save it
save_metadata()	Save all the metadata once the acquisition is over.
save_mmacq_settings()	Save acquisition settings but strip off the Java objects first.
save_mmdev_settings(event)	Sace Micro-Manager settings
save_network_image(image, dims)	Save network image to zarr store
save_ome_metadata([tif, xml])	Get the OME metadata from the original tiff file and save it
save_thresholds()	New Acquisition is starting, save the thresholds used for this acquisition.
update_parameters(params)	Update the parameters for the Interpreter used.

new_save_location(event)

A new acquisition was started leading to a new path for saving

prepare_nn_image(image, dims)

Padding here, could be something else in a subclass.

Note, that the cropping was done at the end of the image in the KerasRescaleWorker.

save_decision_parameter(param: float, elapsed: float, timepoint: int)

Received new interpretation from interpreter, save value into the EDA file

save_image(py_image: pymm_eventserver.data_structures.PyImage)

Gather one timepoint for the original data and save it.

save_imagej_metadata(tif: tifffile.TiffFile | None = None)

Get the ImageJ metadata from the original tiff file and save it

save_metadata()

Save all the metadata once the acquisition is over.

save_mmacq_settings()

Save acquisition settings but strip off the Java objects first.

save_mmdev_settings(event)

Sace Micro-Manager settings

save_network_image(image: numpy.ndarray, dims: tuple)

Save network image to zarr store

save_ome_metadata(tif: tifffile.TiffFile | None = None, xml: str | None = None)

Get the OME metadata from the original tiff file and save it

save_thresholds()

New Acquisition is starting, save the thresholds used for this acquisition.

update_parameters(params: pymm_eventserver.data_structures.ParameterSet | dict)

Update the parameters for the Interpreter used.