cosmoHammer.util package

Submodules

cosmoHammer.util.FlatPositionGenerator module

class cosmoHammer.util.FlatPositionGenerator.FlatPositionGenerator[source]

Bases: object

Generates samples in a flat random space using center + (random values * 2 -1) * width

generate()[source]

generates the positions

setup(sampler)[source]

setup the generator

cosmoHammer.util.IPythonUtil module

cosmoHammer.util.InMemoryStorageUtil module

class cosmoHammer.util.InMemoryStorageUtil.InMemoryStorageUtil(master=True)[source]

Bases: object

Stores the data in memory
Variables:
  • samplesBurin – samples from the burn in
  • probBurnin – likelihoods from the burn in
  • samples – samples from the burn in
  • prob –

    likelihoods from the burn in

    param master:True if the sampler instance is the master
importFromFile(filePath)[source]
importRandomState(filePath)[source]
persistBurninValues(pos, prob, data)[source]
persistSamplingValues(pos, prob, data)[source]
storeRandomState(filePath, randomState)[source]

cosmoHammer.util.IterationStopCriteriaStrategy module

class cosmoHammer.util.IterationStopCriteriaStrategy.IterationStopCriteriaStrategy[source]

Bases: object

A very simple implementation of a stop criteria strategy which does not stop the sampling until the max iteration is reached.

hasFinished()[source]

always returns false

setup(sampler)[source]

setup the strategy

cosmoHammer.util.MpiUtil module

class cosmoHammer.util.MpiUtil.MpiPool(mapFunction)[source]

Bases: object

Implementation of a mpi based pool. Currently it supports only the map function.

Parameters:mapFunction – the map function to apply on the mpi nodes
isMaster()[source]

Returns true if the rank is 0

map(function, sequence)[source]

Emulates a pool map function using Mpi. Retrieves the number of mpi processes and splits the sequence of walker position in order to allow each process its block

Parameters:
  • function – the function to apply on the items of the sequence
  • sequence – a sequence of items
Returns sequence:
 

sequence of results
cosmoHammer.util.MpiUtil.mergeList(lists)[source]

Merges the lists into one single list

Parameters:lists – a list of lists
Returns list:the merged list
cosmoHammer.util.MpiUtil.mpiBCast(value)[source]

Mpi bcasts the value and Returns the value from the master (rank = 0).

cosmoHammer.util.MpiUtil.splitList(list, n)[source]

Splits the list into block of equal sizes (listlength/n)

Parameters:
  • list – a sequence of items
  • n – the number of blocks to create
Returns sequence:
 

a list of blocks

cosmoHammer.util.Params module

Created on Aug 5, 2015

author: jakeret

class cosmoHammer.util.Params.Params(*args)[source]

Bases: object

A key-value parameter store preserving the order of the params passed to the intializer.

Examples:

$ params = Params(("key1", [1,2,3]),
                  ("key2", [1,2,3]))

$ print(params.keys)
> ['key1', 'key2']

$ print(params.key1)
> [1, 2, 3]

$ params[:,0] = 0

$ print(params.values)
> [[0 2 3]
   [0 2 3]]
   
$ print(params[:,1])
> [2 2]
copy()[source]
get(key)[source]
keys
values

cosmoHammer.util.SampleBallPositionGenerator module

class cosmoHammer.util.SampleBallPositionGenerator.SampleBallPositionGenerator[source]

Bases: object

Generates samples in a very thight n-dimensional ball

generate()[source]

generates the positions

setup(sampler)[source]

setup the generator

cosmoHammer.util.SampleFileUtil module

class cosmoHammer.util.SampleFileUtil.SampleFileUtil(filePrefix, master=True, reuseBurnin=False)[source]

Bases: object

Util for handling sample files

Parameters:
  • filePrefix – the prefix to use
  • master – True if the sampler instance is the master
  • reuseBurnin – True if the burn in data from a previous run should be used
close()[source]
finalize()[source]
importFromFile(filePath)[source]
importRandomState(filePath)[source]
persistBurninValues(pos, prob, data)[source]
persistSamplingValues(pos, prob, data)[source]
persistValues(posFile, probFile, pos, prob, data)[source]

Writes the walker positions and the likelihood to the disk

storeRandomState(filePath, randomState)[source]

Module contents