DeepD3 training
generator
- class deepd3.training.generator.Arrange
- addData()
Add selected d3data files
- createSet()
Create d3set from selected d3data files.
- keyPressEvent(self, a0: QKeyEvent)
- removeSelection()
Remove selected d3data sets
- class deepd3.training.generator.Selector
- arrangeTrainingData()
Arrange training data (d3data files) in a d3set
- createTrainingData()
Create d3data set
- viewTrainingData()
View training data
- class deepd3.training.generator.Viewer(fn)
- plane()
Overlay current annotation plane
- save()
Save d3data set
- class deepd3.training.generator.addStackWidget
- changeOverlay()
Show the dendrite and spine annotations as overlay in addition to the original stack
- keyPressEvent(a0: QKeyEvent) None
Key press event to enable shortcuts
- Parameters
a0 (QKeyEvent) – Key event
- save()
Save a d3data set
- selectDendrite()
Select dendrite annotation file
- selectSpines()
Select a spine annotation
- selectStack()
Select a microscopy stack
- updateProgress(a, b)
Update progress bar
- Parameters
a (int, float) – maximum of progress bar
b (int, float) – current value of progress bar
- updateROI()
Updates the ROI chosen as dataset
- updateZ(a, b)
Updates z-level in stack
- Parameters
a (int) – z-stack begin, first plane
b (int) – z-stack end, last plane
- class deepd3.training.generator.askSpacing
- spacing()
Converts spacing
- Returns
spacing in µm in x, y and z
- Return type
tuple(float, float, float)
- deepd3.training.generator.main()
Main entry point to GUI
stream
- class deepd3.training.stream.DataGeneratorStream(fn, batch_size, samples_per_epoch=50000, size=(1, 128, 128), target_resolution=None, augment=True, shuffle=True, seed=42, normalize=[-1, 1], min_content=0.0)
- _getSample(squeeze=True)
Retrieves a sample
- Parameters
squeeze (bool, optional) – Squeezes return shape. Defaults to True.
- Returns
Tuple of stack (X), dendrite (Y0) and spines (Y1)
- Return type
tuple
- _get_augmenter()
Defines used augmentations
- getSample(squeeze=True)
Get a sample from the provided data
- Parameters
squeeze (bool, optional) – if plane is 2D, skip 3D. Defaults to True.
- Returns
stack image with respective labels
- Return type
list(np.ndarray, np.ndarray, np.ndarray)