holtair 1.0.4

Package for reading data from Holter blood pressure test results.

Project description

HoltAir is a tool for python that reads and analyzes data from Holter blood pressure test results in PDF format.

Usage

Quickstart:

from holtair import exams

# you have to specify the tesseract executable in your PATH:
tesseract_path = r'<full_path_to_your_tesseract_executable>'
#also you have to specify the pdf2image poppler executable in your PATH:
poppler_path =  r'<full_path_to_your_poppler_executable>'

#create Exam object with test result data
exam = exams.get_exam(r'test_file.pdf',poppler_path,tesseract_path)

#get pandas dataframe with raw data  
print(exam.results_df)

#create ExamStatistics object calculated statistics 
statistics = exam.exam_statistics

#get basic statistics such sa mean,std,min and max for different blood pressure indicators
print(statistics.basic_overall)

# get basic statistics for detected night:
print(statistics.basic_night)

# create Patient with information about patient
patient = exam.patient

# get patient id 
print(patient.patient_id)

Necessary files:

Windows

• Poppler: https://github.com/oschwartz10612/poppler-windows/releases/
• Tesseract https://github.com/UB-Mannheim/tesseract/wiki

Linux

• Poppler (using conda): conda install -c conda-forge poppler
• Tesseract : sudo apt install tesseract-ocr, sudo apt install libtesseract-dev

Functions and classes description

get_exam() function

This function is used to return the ExamFromImage or ExamFromText object that contain all the analysis and test results data.

Parameters:
get_exam(fielpath,popplerpath,tesseractpath)

• filepath Path to the PDF file containing the exam result.
• popplerpath Path to the poppler executable used in the pdf2image package.
• tesseractpath Path to the Tesseract executable used in pytesseract package.

Exam class

ExamFromImage and ExamFromText inherit from Exam class. Their objects store all the analysis and information data regarding test result. ExamFromText object contains exam information that is read directly from the pdf file and ExamFromImage object contains the information that is read from not readable pdf using Tesseract OCR.

Attributes:

• results_df Dataframe containing measure values from the exam.
• exam_statistics ExamStatistics object storing dataframes with calculated statistics.
• patient Patient object which stores data about patient.
• scan_end_time String value with time of the end of the exam.
• scan_start_time String value with time of the start of the exam.

ExamStatistics class

ExemStatistics objects stores dataframes with calculated statistics from data from exam results for day, night, both and dictionary with pb_load values.

Attributes:

• basic_overall Dataframe with statistics for day and night.
• basic_day Dataframe with basic statistics for a day.
• basic_night Dataframe with basic statistics for a night.
• param bp_load Dictionary with pb_load values for day, night and joined.

Patient

Patient object stores the basic information about the patient.

Attributes:

• first_name Patient first name.
• last_name Patient second name.
• patient_id Patient ID.
• birrthdate Patient birthdate.