1 - Creating a blank IDF#
First import the IDF class from pyIBA (see Installation)
[1]:
# if pyIBA has been installed with pip3,
# the above 4 lines can be removed
import sys
from os.path import abspath
path_pyIBA = abspath('../../../..')
sys.path.insert(0, path_pyIBA)
# import pyIBA
from pyIBA import IDF
To create a new IDF, we first create a blank IDF object:
[2]:
idf_file = IDF()
Adding spectrum data#
We now data to this object. Adding a RBS spectrum is possible via two ways:
load the data manually (e.g. the result of some analysis) and use
set_spectrum_data(data_x, data_y)load the data directly from a file using
set_spectrum_data_from_file(path_to_file)Note: To see the documentation of a method in python you can use help(method) as shown below. Moreover, in jupyter notebooks you can use shift + tab while the cursor is inside the method to pull its documentation.
[3]:
help(idf_file.set_spectrum_data_from_file)
Help on method set_spectrum_data_from_file in module pyIBA.main_idf:
set_spectrum_data_from_file(file_name, save_file_name=True, mode='channels vs yield', spectra_id=0, simulation=False) method of pyIBA.IDF.IDF instance
Read the spectrum data from the file and sets it on the IDF file.
Example:
Load experimental data from file and plot it (see also ``self.get_dataxy()`` and
``self.get_spectrum_file_name()``::
#create a blank IDF file
idf_file = IDF()
#set the spectrum data from the txt file
idf_file.set_spectrum_data_from_file(path_to_exp_data.txt)
#load and plot the data using the file name as label
xx, yy = self.get_dataxy()
plt.figure()
plt.plot(xx, yy, label = idf_file.get_spectrum_file_name())
plt.legend()
Args:
file_name (str): Path to the file with the data
save_file_name (bool, optional, default = True): If True, saves the original file name
mode (str, optional, default = 'channels vs yield'): Mode of the data file options:
mode = 'channels vs yield' if txt file has two columns (xx, yy)
mode = '8 columns' if txt file has 8 columns with yields and assumes linear xx-scale
spectra_id (int, optional): ID of the spectrum to change
simulation (bool, optional): Not used as of now
Returns:
DOM Element or None: The XML entry of spectrum[spectra_id].
using set_spectrum_data()#
As an example, we will load the spectrum data from a two column file using numpy.loadtxt():
[4]:
import numpy as np
[5]:
path_data = 'RBS2PT50CO50_30.odf'
data = np.loadtxt(path_data)
data_x = data[:,0]
data_y = data[:,1]
In fact, we can also use the auxiliary function pyIBA.auxiliar.load_spectrum_from_file(path_to_file) to obtain the raw data from a file:
[6]:
from pyIBA.auxiliar import load_spectrum_from_file
[7]:
data_x, data_y = load_spectrum_from_file(path_data)
Either way, once you have you x, y data you add it to the IDF object using:
[8]:
idf_file.set_spectrum_data(data_x, data_y);
using set_spectrum_data_from_file()#
set_spectrum_data_from_file() is a much more efficient method of adding spectrum files to the IDF object. Repeating the example above:
[9]:
path_data = 'RBS2PT50CO50_30.odf'
idf_file.set_spectrum_data_from_file(path_data);
Note that set_spectrum_data_from_file is also saving the file name (save_file_name = True) and assumes mode = ‘channels vs yield’. If the input file has 8 columns with yields and assumes linear xx-scale, then use mode = ‘8 columns’.
To validate the process we can load the x,y data from the IDF object and plot it using matplolib:
[10]:
import matplotlib.pyplot as plt
[11]:
#load the x and y from the object:
xx, yy = idf_file.get_dataxy()
#create figure and plot it
plt.figure()
plt.plot(xx, yy)
plt.xlabel('Channels')
plt.ylabel('Counts')
[11]:
Text(0, 0.5, 'Counts')
Adding beam parameters#
We now add the beam parameters:
[12]:
idf_file.set_beam_energy(2000)
idf_file.set_beam_energy_spread(20)
idf_file.set_beam_particles('4He')
idf_file.set_charge(5)
idf_file.set_geometry_type('IBM')
idf_file.set_incident_angle(30)
idf_file.set_scattering_angle(140)
idf_file.set_detector_solid_angle(11)
idf_file.set_energy_calibration(2.28, 105.5)
or, instead we can use set_geo_parameters() to add the all the parameters at once. For this, we first define a dictionary with the parameters:
[13]:
geo_params = {'beam_energy': 2000.0,
'beam_FWHM': 20.0,
'projectile': '4He',
'charge': 5,
'geometry': 'IBM',
'angles': ['30', '140'],
'dect_solid': '11',
'energy_calib': [2.28, 105.5]
}
idf_file.set_geo_parameters(geo_params)
Adding the sample details#
Elements#
We begin by defining the elements dictionary forming the sample and use set_elements() to add it to the IDF object (see also help(idf_file.set_elements)). In this example we have a sample with CoPt, SiO2 and Si.
[14]:
#define the elements dictionary
elements = {
#number of elements
'nelements':3,
#element 1
0: {'name': 'Co 1 Pt 1',
'density': '',
'concentration': ['0','1'],
'depth': ['0','1000']},
#element 2
1: {'name': 'Si 1 O 2',
'density': '',
'concentration': ['0','1'],
'depth': ['0','1000']},
#element 3
2: {'name': 'Si',
'density': '',
'concentration': ['0', '1'],
'depth': ['300','1e6']},
}
idf_file.set_elements(elements)
Depth profile#
Similar to the process above, to include the depth profile of the sample, we define first the profile dictionary and then load it into the IDF object using idf_file.set_profile(). Here, our sample has 3 layers - CoPt/SiO\(_2\)/Si. Therefore, the profile dictionary is:
[15]:
#dictionary defining the depth profile of the sample
profile_dic = {
'nlayers': '3',
'names': ['Co 1 Pt 1', 'Si 1 O 2', 'Si'],
0: {'thickness': 390, 'concentrations': [100, 0, 0]},
1: {'thickness': 550, 'concentrations': [ 0, 100, 0]},
2: {'thickness': 4000000, 'concentrations': [ 0, 0, 100]}
}
#add the profile to the IDF object
idf_file.set_profile(profile_dic)
Add a note#
It is also possible to add notes and turn IDF into a logbook.
[16]:
#define note
note = 'This file was created during Example 1, it relates to a RBS measurement of a CoPt/SiO2 sample.'
#add note to idf_file
idf_file.set_note(note)
#if you want to add more notes afterwards, it is possible to append them to the previous ones
note = 'Something I did after the first note'
idf_file.set_note(note, append=True)
#check the notes
print(idf_file.get_notes())
#it is also possible to define the author of the file
author = 'Miguel Sequeira'
idf_file.set_user(author)
['This file was created during Example 1, it relates to a RBS measurement of a CoPt/SiO2 sample.', 'Something I did after the first note']
Saving the IDF object#
Until this point, nothing has been saved into the disk. To save the idf_file object into the file, using the IDF file format, we use idf_file.save_idf().
[17]:
#define the path to the new file
path_to_save = 'idf_example1.xml'
#create the idf file
idf_file.save_idf(path_to_save);
Checking the file#
If you want to check the contents of the IDF object (or file), you use idf_file.printout_idf_file(). However, it is much more efficient to use the GUI IDFViewer (see Example A2).
[18]:
idf_file.print_idf_file()
=============== idf_example1 ===============
idf_example1.xml
Miguel Sequeira
------------------ Notes ------------------
This file was created during Example 1, it relates to a RBS measurement of a CoPt/SiO2 sample.
Something I did after the first note
------------------ Elements -----------------
nelements 3
- - - Element 0 - - -
name Co 1 Pt 1
density
concentration ['0', '1']
depth ['0', '1000']
- - - Element 1 - - -
name Si 1 O 2
density
concentration ['0', '1']
depth ['0', '1000']
- - - Element 2 - - -
name Si
density
concentration ['0', '1']
depth ['300', '1e6']
------------------ Profile -----------------
nlayers 2
names ['Co 1 Pt 1', 'Si 1 O 2', 'Si']
- - - Layer 0 - - -
thickness 390
concentrations ['100', '0', '0']
- - - Layer 1 - - -
thickness 550
concentrations ['0', '100', '0']
- - - Layer 2 - - -
thickness 4000000
concentrations ['0', '0', '100']
-------- Spectrum 0 (RBS2PT50CO50_30.odf) --------
Technique RBS
(4He, 4He)
Projectile 4He
Beam energy 2000.0
Beam fwhm 20.0
Geometry IBM
Angles ['30', '140']
Dect solid 11
Energy calib [2.28, 105.5]
Charge 5
If you want to directly check the XML file, you can set mode = 'XML':
[19]:
idf_file.print_idf_file(mode='XML')
<?xml version="1.0" ?>
<idf xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://idf.schemas.itn.pt" xmlns:idf="http:/idf.schemas.itn.pt" xmlns:ndf="http:/ndf.schemas.itn.pt" xsi:schemaLocation="http:/idf.schemas.itn.pt idfv1.xsd http://ndf.schemas.itn.pt ndfv1.xsd">
<users>
<user>Miguel Sequeira</user>
</users>
<notes>
<note>This file was created during Example 1, it relates to a RBS measurement of a CoPt/SiO2 sample.</note>
<note>Something I did after the first note</note>
</notes>
<attributes>
<idfversion/>
<filename/>
<createtime/>
</attributes>
<sample>
<users>
<user/>
</users>
<notes>
<note/>
</notes>
<description/>
<structure>
<layeredstructure>
<nlayers>3</nlayers>
<layers>
<layer>
<layerthickness units="1e15at/cm2">390</layerthickness>
<layerelements>
<layerelement>
<name>Co 1 Pt 1</name>
<concentration units="fraction">100</concentration>
</layerelement>
<layerelement>
<name>Si 1 O 2</name>
<concentration units="fraction">0</concentration>
</layerelement>
<layerelement>
<name>Si</name>
<concentration units="fraction">0</concentration>
</layerelement>
</layerelements>
</layer>
<layer>
<layerthickness units="1e15at/cm2">550</layerthickness>
<layerelements>
<layerelement>
<name>Co 1 Pt 1</name>
<concentration units="fraction">0</concentration>
</layerelement>
<layerelement>
<name>Si 1 O 2</name>
<concentration units="fraction">100</concentration>
</layerelement>
<layerelement>
<name>Si</name>
<concentration units="fraction">0</concentration>
</layerelement>
</layerelements>
</layer>
<layer>
<layerthickness units="1e15at/cm2">4000000</layerthickness>
<layerelements>
<layerelement>
<name>Co 1 Pt 1</name>
<concentration units="fraction">0</concentration>
</layerelement>
<layerelement>
<name>Si 1 O 2</name>
<concentration units="fraction">0</concentration>
</layerelement>
<layerelement>
<name>Si</name>
<concentration units="fraction">100</concentration>
</layerelement>
</layerelements>
</layer>
</layers>
</layeredstructure>
</structure>
<spectra>
<spectrum>
<notes>
<note/>
<note> </note>
<note> </note>
<note/>
</notes>
<beam>
<beamparticle>4He</beamparticle>
<beamZ/>
<beammass units="amu"/>
<beamenergy units="keV">2000.0</beamenergy>
<beamfluence units="uC"/>
<beamenergyspread mode="FWHM" units="keV">20.0</beamenergyspread>
<charge>5</charge>
</beam>
<geometry>
<geometrytype>IBM</geometrytype>
<incidenceangle units="degree">30</incidenceangle>
<scatteringangle units="degree">140</scatteringangle>
<exitangle units="degree"/>
</geometry>
<detection>
<detector>
<detectortype/>
<solidangle units="msr">11</solidangle>
</detector>
</detection>
<calibrations>
<energycalibrations>
<energycalibration>
<calibrationmode>energy</calibrationmode>
<calibrationparameters>
<calibrationparameter units="keV">105.5</calibrationparameter>
<calibrationparameter units="keV/channel">2.28</calibrationparameter>
</calibrationparameters>
<calibrationion>4He</calibrationion>
</energycalibration>
<energycalibration/>
</energycalibrations>
</calibrations>
<reactions>
<technique/>
<reactionlist>
<reaction>
<initialtargetparticle></initialtargetparticle>
<incidentparticle>4He</incidentparticle>
<exitparticle>4He</exitparticle>
<finaltargetparticle></finaltargetparticle>
<reactionQ units="keV"></reactionQ>
</reaction>
</reactionlist>
</reactions>
<data>
<simpledata>
<xaxis>
<axisname>energy</axisname>
<axisunit>channel</axisunit>
</xaxis>
<yaxis>
<axisname>yield</axisname>
<axisunit>counts</axisunit>
</yaxis>
<x>0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0 31.0 32.0 33.0 34.0 35.0 36.0 37.0 38.0 39.0 40.0 41.0 42.0 43.0 44.0 45.0 46.0 47.0 48.0 49.0 50.0 51.0 52.0 53.0 54.0 55.0 56.0 57.0 58.0 59.0 60.0 61.0 62.0 63.0 64.0 65.0 66.0 67.0 68.0 69.0 70.0 71.0 72.0 73.0 74.0 75.0 76.0 77.0 78.0 79.0 80.0 81.0 82.0 83.0 84.0 85.0 86.0 87.0 88.0 89.0 90.0 91.0 92.0 93.0 94.0 95.0 96.0 97.0 98.0 99.0 100.0 101.0 102.0 103.0 104.0 105.0 106.0 107.0 108.0 109.0 110.0 111.0 112.0 113.0 114.0 115.0 116.0 117.0 118.0 119.0 120.0 121.0 122.0 123.0 124.0 125.0 126.0 127.0 128.0 129.0 130.0 131.0 132.0 133.0 134.0 135.0 136.0 137.0 138.0 139.0 140.0 141.0 142.0 143.0 144.0 145.0 146.0 147.0 148.0 149.0 150.0 151.0 152.0 153.0 154.0 155.0 156.0 157.0 158.0 159.0 160.0 161.0 162.0 163.0 164.0 165.0 166.0 167.0 168.0 169.0 170.0 171.0 172.0 173.0 174.0 175.0 176.0 177.0 178.0 179.0 180.0 181.0 182.0 183.0 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<datafile>
<filename>RBS2PT50CO50_30.odf</filename>
</datafile>
</data>
<process>
<simulations>
<simulation/>
</simulations>
</process>
</spectrum>
</spectra>
<elementsandmolecules>
<molecules>
<nmolecules>3</nmolecules>
<molecule>
<name>Co 1 Pt 1</name>
<density units="1e22at/cm3"></density>
<concentrationmin>0</concentrationmin>
<concentrationmax>1</concentrationmax>
<depthmin>0</depthmin>
<depthmax>1000</depthmax>
</molecule>
<molecule>
<name>Si 1 O 2</name>
<density units="1e22at/cm3"></density>
<concentrationmin>0</concentrationmin>
<concentrationmax>1</concentrationmax>
<depthmin>0</depthmin>
<depthmax>1000</depthmax>
</molecule>
<molecule>
<name>Si</name>
<density units="1e22at/cm3"></density>
<concentrationmin>0</concentrationmin>
<concentrationmax>1</concentrationmax>
<depthmin>300</depthmin>
<depthmax>1e6</depthmax>
</molecule>
</molecules>
</elementsandmolecules>
</sample>
</idf>
[ ]: