PYME.LMVis.pipeline module

class PYME.LMVis.pipeline.Pipeline(filename=None, visFr=None)

Attributes

chromaticShifts
dataSources
dtypes
layer_datasources
selectedDataSource The currently selected data source (an instance of tabular.inputFilter derived class)

Methods

ClearGenerated()
CloseFiles()
GenQuads()
OpenFile([filename, ds]) Open a file - accepts optional keyword arguments for use with files saved as .txt and .mat.
Rebuild(**kwargs) Rebuild the pipeline.
addColumn(name, values[, default]) Adds a column to the currently selected data source.
addDataSource(dskey, ds[, add_missing_vars]) Add a new data source
getBlobs()
getEdb()
getNeighbourDists([forceRetriang])
getTriangles([recalc])
keys()
measureObjects()
save_hdf(filename)
save_txt(outFile[, keys])
selectDataSource(dskey) Set the currently selected data source
toDataFrame([keys])
ClearGenerated()
CloseFiles()
GenQuads()
OpenFile(filename='', ds=None, **kwargs)

Open a file - accepts optional keyword arguments for use with files saved as .txt and .mat. These are:

FieldNames: a list of names for the fields in the text file or
matlab variable.
VarName: the name of the variable in the .mat file which
contains the data.

SkipRows: Number of header rows to skip for txt file data

PixelSize: Pixel size if not in nm

Rebuild(**kwargs)

Rebuild the pipeline. Called when the selected data source is changed/modified and/or the filter is changed.

addColumn(name, values, default=0)

Adds a column to the currently selected data source. Attempts to guess whether the size matches the input or the output, and adds padding values appropriately if it matches the output.

Parameters:

name : str

The column name

values : array like

The values

default : float

The default value to pad with if we’ve given an output-sized array

addDataSource(dskey, ds, add_missing_vars=True)

Add a new data source

Parameters:

dskey : str

The name of the new data source

ds : an tabular.inputFilter derived class

The new data source

chromaticShifts
dataSources
dtypes
getBlobs()
getEdb()
getNeighbourDists(forceRetriang=False)
getTriangles(recalc=False)
keys()
layer_datasources
measureObjects()
save_hdf(filename)
save_txt(outFile, keys=None)
selectDataSource(dskey)

Set the currently selected data source

Parameters:

dskey : string

The data source name

selectedDataSource

The currently selected data source (an instance of tabular.inputFilter derived class)

toDataFrame(keys=None)