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PeakMatching v1¶

PeakMatching dialog.

Table of Contents

Summary
- See Also
Properties
Description
- Input Table and datafile requirement
Usage
Source

Summary ¶

Matches peaks from table to a database to find probable transitions

Properties ¶

Name	Direction	Type	Default	Description
PeakTable	Input	TableWorkspace	Mandatory	Table containing peaks to match to database
PeakDatabase	Input	string		json file with peak database, if none is given default database will be used. Allowed values: [‘json’]
PeakCentreColumn	Input	string	centre	Name of column containing centre of peaks
SigmaColumn	Input	string	sigma	Name of column containing standard deviation of peaks
AllPeaks	Output	TableWorkspace	all_matches	Name of the table containing all of the peak matches
PrimaryPeaks	Output	TableWorkspace	primary_matches	Name of the table containing the primary peak matches
SecondaryPeaks	Output	TableWorkspace	secondary_matches	Name of the table containing the secondary peak matches
SortedByEnergy	Output	TableWorkspace	all_matches_sorted_by_energy	Name of the table containing all of the peak matches sorted by energy
ElementLikelihood	Output	TableWorkspace	element_likelihood	Name of the table containing the weighted count of elements in all matches

Description ¶

This algorithm takes a table of peak centres and standard deviations, then finds overlap with a database of known values to find probable energy transitions for peaks.

Input Table and datafile requirement ¶

input table must have at least 2 column in which one column is the peak centre and the other is the standard deviation, the names of the columns must be given if they differ from the default values: centre and sigma respectively.
json file can be loaded to override the default but must follow structure below:

{
  "Ag": {
    "Z": 47,
    "A": 107.87,
    "Primary": {
      "K(4->1)": 3177.7,
      "L(4->2)": 900.7,
      "M(4->3)": 304.7,
      "6->5": 141
    },
    "Secondary": {
      "K(2->1)": 3140.6,
      "L(8->2)": 1347.8,
      "M(10->3)": 567,
      "8->6": 122.2
    },
    "Gammas": {
      "72Ge(n,n')72Ge": 691,
      "73Ge(n,g)74Ge": null,
      "74Ge(n,n')74Ge": 595.7
    }
  }
}

Usage ¶

Example: Using all defaults*

from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy

def formatdict(row):
    row = dict([(column, "{:.2f}".format(value)) if type(value) == float else (column, value)  for column , value in row.items()])
    return row

table = CreateEmptyTableWorkspace(OutputWorkspace="input")
rows = [(900, 0.8), (306, 0.8), (567, 0.8), (3, 0.8)]

table.addColumn("double","centre")
table.addColumn("double","sigma")

for row in rows:
    table.addRow(row)

PeakMatching(table)

primary_matches = mtd['primary_matches']
secondary_matches = mtd['secondary_matches']
all_matches = mtd['all_matches']
sorted_by_energy = mtd['all_matches_sorted_by_energy']
element_likelihood = mtd[ 'element_likelihood']

print("--"*25)
print(formatdict(primary_matches.row(0)))
print("--"*25)
print(formatdict(secondary_matches.row(0)))
print("--"*25)
print(formatdict(all_matches.row(0)))
print("--"*25)
print(formatdict(sorted_by_energy.row(0)))
print("--"*25)
print(formatdict(element_likelihood.row(0)))

Output:

--------------------------------------------------
{'Peak centre': '3.00', 'Database Energy': '3.40', 'Element': 'Li', 'Transition': 'L(3d->2p)', 'Error': '0.80', 'Difference': '0.40'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '567.00', 'Element': 'Ag', 'Transition': 'M(7f->3d)', 'Error': '0.00', 'Difference': '0.00'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '567.00', 'Element': 'Ag', 'Transition': 'M(7f->3d)', 'Error': '0.00', 'Difference': '0.00'}
--------------------------------------------------
{'Peak centre': '3.00', 'Database Energy': '3.40', 'Element': 'Li', 'Transition': 'L(3d->2p)', 'Error': '0.80', 'Difference': '0.40'}
--------------------------------------------------
{'Element': 'Ag', 'Likelihood(arbitrary units)': 10}

Example: Renaming tables*

from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy

def formatdict(row):
    row = dict([(column, "{:.2f}".format(value)) if type(value) == float else (column, value)  for column , value in row.items()])
    return row

table = CreateEmptyTableWorkspace(OutputWorkspace="input")
rows = [(900, 0.8), (306, 0.8), (567, 0.8), (3, 0.8)]

table.addColumn("double","centre")
table.addColumn("double","sigma")

for row in rows:
    table.addRow(row)

PeakMatching(table,PrimaryPeaks="primary",SecondaryPeaks="secondary",AllPeaks="all",SortedByEnergy="sort",ElementLikelihood="count")

primary_matches = mtd['primary']
secondary_matches = mtd['secondary']
all_matches = mtd['all']
sorted_by_energy = mtd['sort']
element_likelihood = mtd[ 'count']

print("--"*25)
print(formatdict(primary_matches.row(1)))
print("--"*25)
print(formatdict(secondary_matches.row(1)))
print("--"*25)
print(formatdict(all_matches.row(1)))
print("--"*25)
print(formatdict(sorted_by_energy.row(1)))
print("--"*25)
print(formatdict(element_likelihood.row(1)))

Output:

--------------------------------------------------
{'Peak centre': '900.00', 'Database Energy': '900.70', 'Element': 'Ag', 'Transition': 'L(3d3/2->2p3/2)', 'Error': '0.80', 'Difference': '0.70'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '567.00', 'Element': 'In', 'Transition': 'M(6f->3d)', 'Error': '0.00', 'Difference': '0.00'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '567.00', 'Element': 'In', 'Transition': 'M(6f->3d)', 'Error': '0.00', 'Difference': '0.00'}
--------------------------------------------------
{'Peak centre': '306.00', 'Database Energy': '304.10', 'Element': 'W', 'Transition': 'O(7i->5g)', 'Error': '2.40', 'Difference': '1.90'}
--------------------------------------------------
{'Element': 'Tm', 'Likelihood(arbitrary units)': 6}

Example: Using non default column names*

from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy

def formatdict(row):
    row = dict([(column, "{:.2f}".format(value)) if type(value) == float else (column, value)  for column , value in row.items()])
    return row

table = CreateEmptyTableWorkspace(OutputWorkspace="input")
rows = [(900, 0.8), (306, 0.8), (567, 0.8), (3, 0.8)]

table.addColumn("double","center")
table.addColumn("double","standard deviation")

for row in rows:
    table.addRow(row)

PeakMatching(table, PeakCentreColumn = "center",SigmaColumn = "standard deviation")

primary_matches = mtd['primary_matches']
secondary_matches = mtd['secondary_matches']
all_matches = mtd['all_matches']
sorted_by_energy = mtd['all_matches_sorted_by_energy']
element_likelihood = mtd[ 'element_likelihood']

print("--"*25)
print(formatdict(primary_matches.row(2)))
print("--"*25)
print(formatdict(secondary_matches.row(2)))
print("--"*25)
print(formatdict(all_matches.row(2)))
print("--"*25)
print(formatdict(sorted_by_energy.row(2)))
print("--"*25)
print(formatdict(element_likelihood.row(2)))

Output:

--------------------------------------------------
{'Peak centre': '900.00', 'Database Energy': '899.20', 'Element': 'Au', 'Transition': 'M(4f5/2->3d3/2)', 'Error': '0.80', 'Difference': '0.80'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '566.70', 'Element': 'I', 'Transition': 'M(5f->3d)', 'Error': '0.80', 'Difference': '0.30'}
--------------------------------------------------
{'Peak centre': '567.00', 'Database Energy': '566.70', 'Element': 'I', 'Transition': 'M(5f->3d)', 'Error': '0.80', 'Difference': '0.30'}
--------------------------------------------------
{'Peak centre': '306.00', 'Database Energy': '304.50', 'Element': 'Tm', 'Transition': 'N(5g->4f)', 'Error': '1.60', 'Difference': '1.50'}
--------------------------------------------------
{'Element': 'In', 'Likelihood(arbitrary units)': 4}

Categories: AlgorithmIndex | Muon

Source ¶

Python: PeakMatching.py

PeakMatching v1¶

Summary¶

See Also¶

Properties¶

Description¶

Input Table and datafile requirement¶

Usage¶

Source¶

Summary ¶

See Also ¶

Properties ¶

Description ¶

Input Table and datafile requirement ¶

Usage ¶

Source ¶