matlabefd asked . 2022-04-09

Extract data from text file

I have this 'sample data' data not in the right form. I need to read this text file and extract the data and tabulate it in the order as shown in figure below. I am not sure how can I do it.

=========== REPORT TEXT ==========







RADIOLOGICAL REPORT
Patient AAA 
Date of Birth 17/10/2020
Request Number 2020100000000 
RN Number 123456789123 / 123456789 
Referring Doctor 
Examination Date 09/10/2020 





MRI - Heart / Cardiac ( Contrast )


Indication
blablabla

Medication/Contrast
blablabla

Complications
Nil

Sequences
GRE 2C, 4C, SA - CINE
GRE LVOT
GRE 2C, 4C, SA - 
MDE

Findings
The LV longitudinal and circumferential function is reduced.
The right ventricular contractility is normal. The RVOT is normal.
No mitral regurgitation.
Aortic valve appears normal with 3 cusps seen, mobile and not calcified. No tricuspid regurgitation.
No thrombus seen. Mild aortic regurgitation.
Normal pericardium. No pericardial effusion.
The visualized liver and thoracic spine are normal.





Left Ventricular Segments No Wall Motion Perfusion At Rest Perfusion At Stress Delayed Gadolinium 
Enhancement 
Basal Anterior 1 Hypokinetic Nil Nil 50% 
Basal Anteroseptal 2 Dyskinetic Present Present Full thickness 
Basal Inferoseptal 3 Hypokinetic Present Present 50% 
Basal Inferior 4 Hypokinetic Nil Present 50% 
Basal Inferolateral 5 Normal Nil Nil Nil 
Basal Anterolateral 6 Normal Nil Nil Nil 
Mid Anterior 7 Hypokinetic Nil Nil <50% 
Mid Anteroseptal 8 Dyskinetic Present Present Full thickness 
Mid Inferoseptal 9 Akinetic Present Present Full thickness 
Mid Inferior 10 Hypokinetic Nil Present <50% 
Mid Inferolateral 11 Normal Nil Nil Nil 
Mid Anterolateral 12 Normal Nil Nil <50% 
Apical Anterior 13 Akinetic Nil Nil 50% 
Apical Septal 14 Akinetic Nil Nil < 50% 
Apical Inferior 15 Akinetic Nil Nil > 50% 
Apical Lateral 16 Hypokinetic Nil Nil Full thickness 
Apex 17 Akinetic Nil Nil Full thickness 

LVESV is 138 ml. 
LVEDV is 172 ml. 
LVEF is 20 %.
The anterior septal wall thickness in is 0.8 cm. (Diastole)
The posterior lateral wall thickness is 0.9 cm. (Diastole)


Impression
1. Poor LV systolic function.
2. Infarcted and nonviable LAD territory. 
3. Some scarring in the RCA territory. However, inferior wall myocardium has to be considered viable.
4. Stress induced ischaemia of RCA territory.
5. Mild AR.


Computer generated report. No signature required.




========== REPORT TEXT END =========

Really appreciate it if someone can help to guide me. Thank you.

text file , extract data , data extraction , AI, Data Science, and Statistics , Text Analytics Too

Expert Answer

Prashant Kumar answered . 2024-12-21 15:22:02

That is a very badly formatted file. For example, the field delimiters are space characters and space characters also occur within the fields (without any text delimiters to group the fields together). There is no robust general solution for parsing such a poorly formatted file, altough in some limited cases (such as with prior knowledge of the field contents) you might be able to parse it but parsing such files will always be fragile. On that basis I assumed that the fields contain only the text in the number and types that you have shown, i.e. each line contains exactly:

1 or 2 words (starts with 'Basal' or 'Mid' or 'Apical', or constitutes 'Apex')
1 number
1 word
('Nil' or 'Present')
('Nil' or 'Present')
('Nil' or 'Full thickness' or a percentage)

This matches all of the seventeen rows in your example data file:

=========== REPORT TEXT ==========







RADIOLOGICAL REPORT
Patient AAA 
Date of Birth 17/10/2020
Request Number 2020100000000 
RN Number 123456789123 / 123456789 
Referring Doctor 
Examination Date 09/10/2020 





MRI - Heart / Cardiac ( Contrast )


Indication
blablabla

Medication/Contrast
blablabla

Complications
Nil

Sequences
GRE 2C, 4C, SA - CINE
GRE LVOT
GRE 2C, 4C, SA - 
MDE

Findings
The LV longitudinal and circumferential function is reduced.
The right ventricular contractility is normal. The RVOT is normal.
No mitral regurgitation.
Aortic valve appears normal with 3 cusps seen, mobile and not calcified. No tricuspid regurgitation.
No thrombus seen. Mild aortic regurgitation.
Normal pericardium. No pericardial effusion.
The visualized liver and thoracic spine are normal.





Left Ventricular Segments No Wall Motion Perfusion At Rest Perfusion At Stress Delayed Gadolinium 
Enhancement 
Basal Anterior 1 Hypokinetic Nil Nil 50% 
Basal Anteroseptal 2 Dyskinetic Present Present Full thickness 
Basal Inferoseptal 3 Hypokinetic Present Present 50% 
Basal Inferior 4 Hypokinetic Nil Present 50% 
Basal Inferolateral 5 Normal Nil Nil Nil 
Basal Anterolateral 6 Normal Nil Nil Nil 
Mid Anterior 7 Hypokinetic Nil Nil <50% 
Mid Anteroseptal 8 Dyskinetic Present Present Full thickness 
Mid Inferoseptal 9 Akinetic Present Present Full thickness 
Mid Inferior 10 Hypokinetic Nil Present <50% 
Mid Inferolateral 11 Normal Nil Nil Nil 
Mid Anterolateral 12 Normal Nil Nil <50% 
Apical Anterior 13 Akinetic Nil Nil 50% 
Apical Septal 14 Akinetic Nil Nil < 50% 
Apical Inferior 15 Akinetic Nil Nil > 50% 
Apical Lateral 16 Hypokinetic Nil Nil Full thickness 
Apex 17 Akinetic Nil Nil Full thickness 

LVESV is 138 ml. 
LVEDV is 172 ml. 
LVEF is 20 %.
The anterior septal wall thickness in is 0.8 cm. (Diastole)
The posterior lateral wall thickness is 0.9 cm. (Diastole)


Impression
1. Poor LV systolic function.
2. Infarcted and nonviable LAD territory. 
3. Some scarring in the RCA territory. However, inferior wall myocardium has to be considered viable.
4. Stress induced ischaemia of RCA territory.
5. Mild AR.


Computer generated report. No signature required.




========== REPORT TEXT END =========

str = fileread('sample data.txt');
rgx = ['(Apex|(Basal|Mid|Apical)\s+[A-Z][a-z]+)\s+(\d+)\s+([A-Z][a-z]+)',...
	'\s+(Nil|Present)\s+(Nil|Present)\s+(Nil|Full thickness|([<>]\s?)?\d+\%)'];
tkn = regexpi(str,rgx,'tokens');
tkn = vertcat(tkn{:})

Giving:

tkn = 
    'Basal Anterior'         '1'     'Hypokinetic'    'Nil'        'Nil'        '50%'           
    'Basal Anteroseptal'     '2'     'Dyskinetic'     'Present'    'Present'    'Full thickness'
    'Basal Inferoseptal'     '3'     'Hypokinetic'    'Present'    'Present'    '50%'           
    'Basal Inferior'         '4'     'Hypokinetic'    'Nil'        'Present'    '50%'           
    'Basal Inferolateral'    '5'     'Normal'         'Nil'        'Nil'        'Nil'           
    'Basal Anterolateral'    '6'     'Normal'         'Nil'        'Nil'        'Nil'           
    'Mid Anterior'           '7'     'Hypokinetic'    'Nil'        'Nil'        '<50%'          
    'Mid Anteroseptal'       '8'     'Dyskinetic'     'Present'    'Present'    'Full thickness'
    'Mid Inferoseptal'       '9'     'Akinetic'       'Present'    'Present'    'Full thickness'
    'Mid Inferior'           '10'    'Hypokinetic'    'Nil'        'Present'    '<50%'          
    'Mid Inferolateral'      '11'    'Normal'         'Nil'        'Nil'        'Nil'           
    'Mid Anterolateral'      '12'    'Normal'         'Nil'        'Nil'        '<50%'          
    'Apical Anterior'        '13'    'Akinetic'       'Nil'        'Nil'        '50%'           
    'Apical Septal'          '14'    'Akinetic'       'Nil'        'Nil'        '< 50%'         
    'Apical Inferior'        '15'    'Akinetic'       'Nil'        'Nil'        '> 50%'         
    'Apical Lateral'         '16'    'Hypokinetic'    'Nil'        'Nil'        'Full thickness'
    'Apex'                   '17'    'Akinetic'       'Nil'        'Nil'        'Full thickness'
>> size(tkn)
ans =
    17     6
>>

Clearly you can put that into a table if you really want to:

>> hdr = {'LeftVentricularSegments','No','WallMotion','PerfusionAtRest','PerfusionAtStress','DelayedGadoliniumEnhancement'};
>> T = cell2table(tkn,'VariableNames',hdr)
T = 
    LeftVentricularSegments     No      WallMotion      PerfusionAtRest    PerfusionAtStress    DelayedGadoliniumEnhancement
    _______________________    ____    _____________    _______________    _________________    ____________________________
    'Basal Anterior'           '1'     'Hypokinetic'    'Nil'              'Nil'                '50%'                       
    'Basal Anteroseptal'       '2'     'Dyskinetic'     'Present'          'Present'            'Full thickness'            
    'Basal Inferoseptal'       '3'     'Hypokinetic'    'Present'          'Present'            '50%'                       
    'Basal Inferior'           '4'     'Hypokinetic'    'Nil'              'Present'            '50%'                       
    'Basal Inferolateral'      '5'     'Normal'         'Nil'              'Nil'                'Nil'                       
    'Basal Anterolateral'      '6'     'Normal'         'Nil'              'Nil'                'Nil'                       
    'Mid Anterior'             '7'     'Hypokinetic'    'Nil'              'Nil'                '<50%'                      
    'Mid Anteroseptal'         '8'     'Dyskinetic'     'Present'          'Present'            'Full thickness'            
    'Mid Inferoseptal'         '9'     'Akinetic'       'Present'          'Present'            'Full thickness'            
    'Mid Inferior'             '10'    'Hypokinetic'    'Nil'              'Present'            '<50%'                      
    'Mid Inferolateral'        '11'    'Normal'         'Nil'              'Nil'                'Nil'                       
    'Mid Anterolateral'        '12'    'Normal'         'Nil'              'Nil'                '<50%'                      
    'Apical Anterior'          '13'    'Akinetic'       'Nil'              'Nil'                '50%'                       
    'Apical Septal'            '14'    'Akinetic'       'Nil'              'Nil'                '< 50%'                     
    'Apical Inferior'          '15'    'Akinetic'       'Nil'              'Nil'                '> 50%'                     
    'Apical Lateral'           '16'    'Hypokinetic'    'Nil'              'Nil'                'Full thickness'            
    'Apex'                     '17'    'Akinetic'       'Nil'              'Nil'                'Full thickness'

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