PYME.LMVis.pipeline module¶
- class PYME.LMVis.pipeline.Pipeline(filename=None, visFr=None, execute_on_invalidation=True)¶
Bases:
object- ClearGenerated()¶
- CloseFiles()¶
- GenQuads(max_leaf_size=10)¶
- OpenChannel(filename='', ds=None, channel_name='', **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
- OpenFile(filename='', ds=None, clobber_recipe=True, **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
- namestr
The column name
- valuesarray like
The values
- defaultfloat
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
- dskeystr
The name of the new data source
- dsan tabular.inputFilter derived class
The new data source
- property chromaticShifts¶
- property colour_mapper¶
Search for a colour mapper rather than use a hard coded reference - allows loading of saved pipelines with colour mapping
- property dataSources¶
- property dtypes¶
- property fluorSpecies¶
- property fluorSpeciesDyes¶
- getBlobs()¶
- getEdb()¶
- getNeighbourDists(forceRetriang=False)¶
- getTriangles(recalc=False)¶
- get_layer_data(dsname)¶
Returns layer data for a given name. The principle difference to just accessing self.dataSources directly is that we do some magic relating to allow colour channels to be accessed with the dot notation e.g. dsname.colour_channel
- keys()¶
- property layer_data_source_names¶
Return a list of names of datasources we can use with dotted channel selection
There is a little bit of magic here as we augment the names with dotted names for colour channel selection
- property layer_datasources¶
- measureObjects()¶
- new_ds_name(stub, return_count=False)¶
Generate a name for a new, unused, pipeline step output based on a stub
FIXME - should this be in ModuleCollection instead? FIXME - should this use recipe.outputs as well?
- Parameters
- stub - string to start the name with
- Returns
- property output¶
- save_hdf(filename)¶
- save_txt(outFile, keys=None)¶
- selectDataSource(dskey)¶
Set the currently selected data source
- Parameters
- dskeystring
The data source name
- property selectedDataSource¶
The currently selected data source (an instance of tabular.inputFilter derived class)
- toDataFrame(keys=None)¶
- to_recarray(keys=None)¶