PYME.recipes.processing module

Created on Mon May 25 17:15:01 2015

@author: david

class PYME.recipes.processing.BinaryDilation(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.BinaryErosion(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.BinaryFillHoles(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.Deconvolve(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

GetDec(dp, vshint) Get a (potentially cached) deconvolution object
GetPSF(vshint)
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
default_traits_view()
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
GetDec(dp, vshint)

Get a (potentially cached) deconvolution object

GetPSF(vshint)
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
default_traits_view()
class PYME.recipes.processing.DeconvolveMotionCompensating(parent=None, **kwargs)

Bases: PYME.recipes.processing.Deconvolve

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

GetDec(dp, vshint) Get a (potentially cached) deconvolution object
GetPSF(vshint)
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
default_traits_view()
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
GetDec(dp, vshint)

Get a (potentially cached) deconvolution object

applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.DirectionToMask3D(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Estimates the direction from a pixel to the edge of a mask.

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

calc_grad(data, chanNum)
execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
calc_grad(data, chanNum)
execute(namespace)
class PYME.recipes.processing.DistanceTransform(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.FractionalThreshold(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Chose a threshold such that the given fraction of the total labelling is included in the mask.

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
class PYME.recipes.processing.Gradient2D(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

calc_grad(data, chanNum)
execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
calc_grad(data, chanNum)
execute(namespace)
class PYME.recipes.processing.Gradient3D(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

calc_grad(data, chanNum)
execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
calc_grad(data, chanNum)
execute(namespace)
class PYME.recipes.processing.GreyDilation(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.GreyErosion(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
class PYME.recipes.processing.Label(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Asigns a unique integer label to each contiguous region in the input mask. Optionally throws away all regions which are smaller than a cutoff size.

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
class PYME.recipes.processing.LocalMaxima(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
class PYME.recipes.processing.OpticalFlow(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

calc_flow(data, chanNum)
completeMetadata(im)
execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
calc_flow(data, chanNum)
completeMetadata(im)
execute(namespace)
class PYME.recipes.processing.ProjectOnVector(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Project onto a set of direction vectors, producing p and s components

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

calc_proj(inpX, inpY, dirX, dirY, chanNum)
do_proj(inpX, inpY, dirX, dirY) project onto basis vectors
execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
calc_proj(inpX, inpY, dirX, dirY, chanNum)
do_proj(inpX, inpY, dirX, dirY)

project onto basis vectors

execute(namespace)
class PYME.recipes.processing.SelectLabel(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Creates a mask corresponding to all pixels with the given label

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
class PYME.recipes.processing.SimpleThreshold(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)
completeMetadata(im)
class PYME.recipes.processing.VectorfieldCurl(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates the curl of a vector field defined by three inputs.

rac{del F_z}{del y} - rac{del F_y}{del z}, rac{del F_x}{del z} - rac{del F_z}{del x}, rac{del F_y}{del x} - rac{del F_x}{del y})$$

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.processing.VectorfieldNorm(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates the norm of a vector field defined by three inputs.

Notes

returns .. math:

sqrt(x*x + y*y + z*z)

Also works for 2D vector fields if inputZ is an empty string.

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.processing.Watershed(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Module with one image input and one image output

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(image, markers[, mask])
execute(namespace)
filter(image, markers[, mask])
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(image, markers, mask=None)
execute(namespace)
filter(image, markers, mask=None)
class PYME.recipes.processing.WhiteTophat(parent=None, **kwargs)

Bases: PYME.recipes.base.Filter

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

applyFilter(data, chanNum, frNum, im)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
applyFilter(data, chanNum, frNum, im)