Structure of the emgfile
What is the emgfile¶
The emgfile is the basic data structure of the openhdemg framework. In practical terms, it is a Python object containing all the information of the decomposed HD-EMG file loaded in the working environment via the dedicated openhdemg functions.
For example:
# Import the library with the short name 'emg'
import openhdemg.library as emg
# Load the sample file and assign it to the emgfile object
emgfile = emg.emg_from_samplefile()
Loads the decomposed sample file provided with openhdemg and assigns its content to the object emgfile.
Structure of the emgfile¶
The emgfile has a simple structure. Indeed, it is a Python dictionary with keys:
# Import the library with the short name 'emg'
import openhdemg.library as emg
# Load the sample file and assign it to the emgfile object
emgfile = emg.emg_from_samplefile()
# Visualise the type of the emgfile
print(type(emgfile))
"""Output
<class 'dict'>
"""
# Visualise the keys of the emgfile dictionary
print(emgfile.keys())
"""Output
dict_keys(['SOURCE', 'FILENAME', 'RAW_SIGNAL', 'REF_SIGNAL', 'ACCURACY', 'IPTS', 'MUPULSES', 'FSAMP', 'IED', 'EMG_LENGTH', 'NUMBER_OF_MUS', 'BINARY_MUS_FIRING', 'EXTRAS'])
"""
That means that the emgfile contains the following keys (or variables, in simpler terms):
- "SOURCE" : source of the file (i.e., "CUSTOMCSV", "DEMUSE", "OTB", "DELSYS")
- "FILENAME" : the name of the original file
- "RAW_SIGNAL" : the raw EMG signal
- "REF_SIGNAL" : the reference signal
- "ACCURACY" : accuracy score (depending on source file type)
- "IPTS" : pulse train (decomposed source)
- "MUPULSES" : instants of firing
- "FSAMP" : sampling frequency
- "IED" : interelectrode distance
- "EMG_LENGTH" : length of the emg file (in samples)
- "NUMBER_OF_MUS" : total number of MUs
- "BINARY_MUS_FIRING" : binary representation of MUs firings
- "EXTRAS" : additional custom values
Each key has a specific content and structure that will be presented in the next code block.
It must be noted that some of these keys might be empty (e.g., absence of a reference signal) and, therefore, the specific content of each key must be assessed from case to case. This can be simply done taking advantage of the info class:
# Import the library with the short name 'emg'
import openhdemg.library as emg
# Load the sample file and assign it to the emgfile object
emgfile = emg.emg_from_samplefile()
# Obtain info on the content of the emgfile
info = emg.info()
info.data(emgfile)
"""Output
Data structure of the emgfile
-----------------------------
emgfile type is:
<class 'dict'>
emgfile keys are:
dict_keys(['SOURCE', 'FILENAME', 'RAW_SIGNAL', 'REF_SIGNAL', 'ACCURACY', 'IPTS', 'MUPULSES', 'FSAMP', 'IED', 'EMG_LENGTH', 'NUMBER_OF_MUS', 'BINARY_MUS_FIRING', 'EXTRAS'])
Any key can be acced as emgfile[key].
emgfile['SOURCE'] is a <class 'str'> of value:
OTB
emgfile['FILENAME'] is a <class 'str'> of value:
otb_testfile.mat
MUST NOTE: emgfile from OTB has 64 channels, from DEMUSE 65 (includes empty channel).
emgfile['RAW_SIGNAL'] is a <class 'pandas.core.frame.DataFrame'> of value:
0 1 2 3 4 5 6 7 8 ... 55 56 57 58 59 60 61 62 63
0 10.172526 5.086263 12.715657 11.189778 9.155273 8.138021 9.155273 13.224284 2.034505 ... 7.120768 6.612142 10.172526 8.138021 10.681152 2.034505 14.750163 4.577637 11.698405
1 14.750163 8.138021 12.715657 12.715657 10.681152 6.612142 13.732910 16.276041 3.051758 ... 4.577637 3.560384 11.698405 7.120768 10.681152 0.508626 10.681152 4.069010 11.698405
2 6.103516 1.017253 6.103516 15.767415 6.103516 3.051758 6.103516 11.698405 2.034505 ... 1.525879 1.525879 3.560384 -1.017253 4.069010 -4.577637 8.138021 -1.525879 5.086263
3 -3.051758 -7.120768 -3.051758 4.577637 -4.069010 -8.138021 -2.543132 2.543132 -7.120768 ... -8.646647 -9.155273 -3.560384 -9.155273 -6.103516 -13.732910 -1.017253 -11.698405 -2.543132
4 -11.189778 -15.767415 -15.767415 -5.086263 -11.698405 -13.732910 -7.120768 -3.560384 -12.207031 ... -15.767415 -18.310547 -12.207031 -12.715657 -11.189778 -17.293295 -8.646647 -17.293295 -11.189778
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
66555 11.189778 17.801920 16.276041 17.801920 2.034505 22.379557 8.646647 14.750163 14.750163 ... -2.034505 0.508626 2.034505 2.034505 13.224284 0.000000 10.172526 10.172526 17.801920
66556 12.715657 22.888184 21.362305 20.853678 10.172526 26.448568 12.207031 19.836426 16.276041 ... 2.034505 7.120768 4.577637 8.646647 14.241536 5.086263 18.819174 16.276041 16.276041
66557 6.103516 7.120768 12.207031 12.715657 0.508626 16.276041 3.051758 9.663899 5.594889 ... -5.594889 -1.525879 -6.103516 -1.525879 6.103516 -1.525879 7.629395 8.646647 8.646647
66558 -9.663899 -9.663899 -7.120768 -7.629395 -14.241536 -1.017253 -14.750163 -7.629395 -10.681152 ... -23.905436 -17.801920 -22.888184 -20.853678 -10.681152 -17.801920 -13.224284 -8.646647 -9.155273
66559 0.508626 1.017253 0.000000 4.577637 -2.543132 6.612142 -3.051758 1.525879 -2.034505 ... -12.715657 -6.612142 -14.750163 -10.172526 0.000000 -6.103516 1.017253 -3.051758 -2.543132
[66560 rows x 64 columns]
emgfile['REF_SIGNAL'] is a <class 'pandas.core.frame.DataFrame'> of value:
0
0 1.640534
1 1.660370
2 1.700043
3 1.719879
4 1.739716
... ...
66555 1.462006
66556 1.481842
66557 1.501679
66558 1.481842
66559 1.481842
[66560 rows x 1 columns]
emgfile['ACCURACY'] is a <class 'pandas.core.frame.DataFrame'> of value:
0
0 0.879079
1 0.955819
2 0.917190
3 0.899082
4 0.919601
emgfile['IPTS'] is a <class 'pandas.core.frame.DataFrame'> of value:
0 1 2 3 4
0 -1.208628e-04 3.242122e-09 0.000004 0.000186 0.000038
1 -4.316778e-04 -8.801236e-05 -0.000053 0.000095 -0.000063
2 -6.112677e-06 -1.158515e-04 0.000619 -0.000379 0.000035
3 5.843681e-05 -1.308242e-05 -0.000033 -0.000001 -0.000168
4 4.365258e-06 5.634868e-05 -0.000423 -0.000112 0.000001
... ... ... ... ... ...
66555 -6.366898e-08 0.000000e+00 0.000000 0.000000 0.000000
66556 -5.846209e-05 0.000000e+00 0.000000 0.000000 0.000000
66557 -4.853265e-05 0.000000e+00 0.000000 0.000000 0.000000
66558 1.100347e-05 0.000000e+00 0.000000 0.000000 0.000000
66559 1.217465e-04 0.000000e+00 0.000000 0.000000 0.000000
[66560 rows x 5 columns]
emgfile['MUPULSES'] is a <class 'list'> of length depending on total MUs number.
MUPULSES for each MU can be accessed as emgfile['MUPULSES'][MUnumber].
emgfile['MUPULSES'][0] is a <class 'numpy.ndarray'> of value:
[ 4990 6659 8310 8581 9424 9662 9905 10046 10200 10543 10762 11179
11469 11743 11973 12243 12580 12795 13038 13258 13396 13642 13890 14161
14357 14672 14975 15250 15564 15920 16281 16572 16837 17182 17321 17634
17973 18999 19388 19906 20178 20331 20523 20797 21020 21321 21705 21863
22190 22283 22656 23297 23397 23445 23598 24045 24206 24430 24678 24764
24982 25095 25277 25939 26581 26942 27652 28303 28515 28602 28893 29136
29363 30399 30604 31277 32005 32227 32780 33030 33255 33550 34239 34889
35261 37394 37932 38439 39061 39564 40393 41056 41919 43357 43742 44039
44335 44721 45182 45913 46083 46745 47076 47343 47635 47976 48147 48578
48880 49428 49742 49887 50516 50850 50957 51194 51350 51678 52110 52892
53161 53390 53795 54154 54386 54823 55032 55283 55653 56026 56282 56538
56931 57578 57871 58429 59077]
emgfile['FSAMP'] is a <class 'float'> of value:
2048.0
emgfile['IED'] is a <class 'float'> of value:
8.0
emgfile['EMG_LENGTH'] is a <class 'int'> of value:
66560
emgfile['NUMBER_OF_MUS'] is a <class 'int'> of value:
5
emgfile['BINARY_MUS_FIRING'] is a <class 'pandas.core.frame.DataFrame'> of value:
0 1 2 3 4
0 0.0 0.0 0.0 0.0 0.0
1 0.0 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0 0.0
... ... ... ... ... ...
66555 0.0 0.0 0.0 0.0 0.0
66556 0.0 0.0 0.0 0.0 0.0
66557 0.0 0.0 0.0 0.0 0.0
66558 0.0 0.0 0.0 0.0 0.0
66559 0.0 0.0 0.0 0.0 0.0
[66560 rows x 5 columns]
emgfile['EXTRAS'] is a <class 'pandas.core.frame.DataFrame'> of value:
Empty DataFrame
Columns: [0]
Index: []
"""
As you can see, info.data(emgfile) provides you with all the information regarding the content of the emgfile, on how it is structured and on how each element can be accessed. This information is crucial to interact with the emgfile and, understanding its structure, is fundamental to performed advanced customisation of the functions and to exploit the full flexibility/customisability of the openhdemg framework.
Please take some time to learn this!
Alternative structures of the emgfile¶
At the moment, the only alternative to the basic emgfile structure is reserved for the loading of those files containing only the reference signal. This can be, for example, the case of the force signal used to calculate the maximum voluntary contraction (MVC) value.
In this case, the emg_refsig is a Python dictionary with the following keys:
- "SOURCE": source of the file (i.e., "CUSTOMCSV_REFSIG", "OTB_REFSIG", "DELSYS_REFSIG")
- "FSAMP": sampling frequency
- "REF_SIGNAL": the reference signal
- "EXTRAS" : additional custom values
Modify the emgfile to fit your needs¶
This is a fundamental part of this tutorial. You can modify the emgfile as you wish, but there are 2 simple rules that must be followed to allow a seamless integration with the openhdemg functions.
- Do not alter the
emgfilekeys. You should not add or remove keys and you should not alter the data type under each key. If you need to do so, please remember that some of the built-in functions might not work anymore and you might encounter unexpected errors. - Preserve data structures. If there is missing data you should fill the
emgfilekeys with the original data structure. The original data structure is the one presented in section Structure of the emgfile. For example, the reference signal is by default contained in a pd.DataFrame. Therefore, if the reference signal is absent, the dict key "REF_SIGNAL" should contain an empty pd.DataFrame.
To modify the emgfile you can simply act as for modifying any Python dictionary:
# Import the necessary libraries
import openhdemg.library as emg
import pandas as pd
import numpy as np
# Load the sample file and assign it to the emgfile object
emgfile = emg.emg_from_samplefile()
# Visualise the keys of the emgfile dictionary
print(emgfile.keys())
"""Output
dict_keys(['SOURCE', 'FILENAME', 'RAW_SIGNAL', 'REF_SIGNAL', 'ACCURACY', 'IPTS', 'MUPULSES', 'FSAMP', 'IED', 'EMG_LENGTH', 'NUMBER_OF_MUS', 'BINARY_MUS_FIRING', 'EXTRAS'])
"""
# Visualise the original data structure contained in the 'REF_SIGNAL' key
print(type(emgfile['REF_SIGNAL']))
"""Output
<class 'pandas.core.frame.DataFrame'>
"""
# Replace the current 'REF_SIGNAL' with a random reference signal.
random_data = np.random.randint(0 ,20, size=(emgfile['EMG_LENGTH'], 1))
rand_ref = pd.DataFrame(random_data, columns=[0])
emgfile['REF_SIGNAL'] = rand_ref
print(emgfile['REF_SIGNAL'])
"""Output
0
0 2
1 15
2 13
3 18
4 3
... ..
66555 13
66556 11
66557 13
66558 1
66559 7
"""
Create your own emgfile¶
openhdemg offers a number of built-in functions to load the data from different sources. However, there might be special circumnstances that require more flexibility. In this case, the user can create custom functions to load any type of decomposed HD-EMG files. However, in order to interact with the openhdemg functions, the emgfile loaded with any custom function must respect the original structure.
In case your decomposed HD-EMG file does not contain a specific variable, you should mantain the original emgfile keys and the original data structure, although empty.
More questions?¶
We hope that this tutorial was useful. If you need any additional information, do not hesitate to read the answers or ask a question in the openhdemg discussion section. If you are not familiar with GitHub discussions, please read this post. This will allow the openhdemg community to answer your questions.