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hpos-web/scripts/result_generation.ipynb

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result generation python code
2023-08-28 11:25:36 +00:00
{
"cells": [
{
"cell_type": "code",
"execution_count": 3,
"id": "30bd0387-b182-49a0-9591-6136df91f9b7",
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: xhtml2pdf in c:\\users\\acer\\anaconda3\\lib\\site-packages (0.2.11)\n",
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"Requirement already satisfied: Pillow>=8.1.1 in c:\\users\\acer\\anaconda3\\lib\\site-packages (from xhtml2pdf) (9.4.0)\n",
"Requirement already satisfied: pyHanko>=0.12.1 in c:\\users\\acer\\anaconda3\\lib\\site-packages (from xhtml2pdf) (0.20.0)\n",
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"Requirement already satisfied: charset-normalizer<4,>=2 in c:\\users\\acer\\anaconda3\\lib\\site-packages (from requests>=2.24.0->pyHanko>=0.12.1->xhtml2pdf) (2.0.4)\n",
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}
],
"source": [
"\n",
"import sys\n",
"import csv\n",
"#import qrcode\n",
"! pip install xhtml2pdf\n",
"from xhtml2pdf import pisa\n",
"from jinja2 import Environment, FileSystemLoader\n",
"import os\n",
"import pandas as pd\n",
"\n",
"# Capture our current directory\n",
"THIS_DIR = os.path.dirname(os.path.abspath(r\"C:\\Users\\acer\\Desktop\\SMI\"))\n",
"print(os.getcwd())\n",
"\n",
"#def generateQRCode(rptD):\n",
" # qrc = qrcode.QRCode(version=10,error_correction=qrcode.constants.ERROR_CORRECT_H)\n",
" # data = \"SRF ID : {} \\n ICMR ID: {} \\n IISc ID: {} \\n Name: {} \\n Age: {} \\n Gender: {} \\n Swab Collected On: {} \\n Lab Name: Indian Institute of Science, Bangalore\\n Result Date: {} \\n Test Type: RT-PCR\\n Test Result: {}.\\n\".format(rptD['srfid'],rptD['sampleICMRID'],rptD['sampleIIScID'],rptD['patientName'],rptD['patientAge'],rptD['patientGender'],rptD['sampleCollectionDate'],rptD['testDate'],rptD['testResult'])\n",
" # qrc.add_data(data)\n",
" #qrImg = qrc.make_image(fill_color=\"black\", back_color=\"white\")\n",
" #qrImg.save(rptD['qrcodeImgFile'])\n",
" #return\n",
"\n",
"def prepareData(row):\n",
" rptData = {}\n",
"\n",
" rptData['Person Name'] = row['Name']\n",
" rptData['Age'] = row['Age']\n",
" rptData['Gender'] = row['Gender']\n",
" rptData['Age / Sex'] = f\"{rptData['Age']} ({rptData['Gender']})\"\n",
" rptData['Sample type'] = 'Capillary Whole Blood'\n",
" rptData['Family History of Sickle Cell Anemia'] = 'Unknown'\n",
" rptData['Marital Status'] = row['Marital Status']\n",
" rptData['Test Date'] = pd.to_datetime(row['testTime']).date()\n",
" rptData['Patient ID'] = row['ABHA ID']\n",
" rptData['Sample ID'] = row['_id']\n",
" rptData['value'] = row['Measured Deovix Ratio']\n",
" #rptData['qrcodeImgFile'] = 'qr_' + row['SRF ID'] + '.png'\n",
" # generateQRCode(rptData)\n",
" return rptData\n",
"\n",
"def generatePDFReport(row):\n",
" outFilename = row['_id'] + '.pdf'\n",
" # fill template with sample result values\n",
" # generate report\n",
" # generate qr code\n",
" # convert to pdf\n",
" print(\"Creating report %s ...\" % outFilename)\n",
" j2_env = Environment(loader=FileSystemLoader(THIS_DIR),\n",
" trim_blocks=True)\n",
" rd = prepareData(row)\n",
" # template_path = os.path.join(THIS_DIR, 'report_template.html')\n",
"\n",
" report_template =r'''\n",
"<!DOCTYPE html>\n",
"<html>\n",
"\n",
"<head>\n",
" <style>\n",
" @media print {\n",
" body {\n",
" -webkit-print-color-adjust: exact;\n",
" }\n",
" }\n",
"\n",
" .person-details-row {\n",
" display: flex;\n",
" flex-direction: row;\n",
" }\n",
"\n",
" .person-details-col {\n",
" display: flex;\n",
" flex-direction: column;\n",
" height: 90px;\n",
" width: 50%;\n",
" margin: 1px;\n",
" border: 0;\n",
" }\n",
"\n",
" .test-details-row {\n",
" border: 0;\n",
" }\n",
"\n",
" .test-details-col {\n",
" height: 100px;\n",
" }\n",
"\n",
" .test-cell-div {\n",
" /* border: 1px solid black; */\n",
" border-collapse: collapse;\n",
" height: 20px;\n",
" padding: 10px;\n",
" }\n",
"\n",
" .table-header {\n",
" border: 1px solid black;\n",
" margin: 0 0 -10px 10px;\n",
" background-color: rgb(191, 191, 191);\n",
" text-align: center;\n",
" justify-content: center;\n",
" align-items: center;\n",
" display: flex;\n",
" font-weight: 600;\n",
" height: 50px;\n",
" width: 98%;\n",
" }\n",
"\n",
" @media print {\n",
" .table-header {\n",
" background-color: rgb(191, 191, 191) !important;\n",
" print-color-adjust: exact;\n",
" }\n",
" }\n",
"\n",
" @media print {\n",
" .vendorListHeading th {\n",
" color: white !important;\n",
" }\n",
" }\n",
"\n",
" .test-method {\n",
" font-weight: 200 !important;\n",
" color: rgb(191, 191, 191);\n",
" }\n",
"\n",
" .result-value {\n",
" justify-content: center;\n",
" align-items: center;\n",
" display: flex;\n",
" }\n",
"\n",
" .end-of-report {\n",
" display: flex;\n",
" align-items: center;\n",
" justify-content: center;\n",
" }\n",
"\n",
" .logo {\n",
" display: flex;\n",
" justify-content: center;\n",
" align-items: center;\n",
" }\n",
"\n",
" table,\n",
" th,\n",
" td {\n",
" border: 1px solid black;\n",
" border-collapse: collapse;\n",
" }\n",
"\n",
" ul {\n",
" list-style-type: none;\n",
" /* margin: 0; */\n",
" /* padding: 0; */\n",
" }\n",
" </style>\n",
"</head>\n",
"\n",
"<body>\n",
" <div>\n",
" <div class=\"logo\">\n",
" <img src=\"C:\\Users\\acer\\Desktop\\SMI\\logo_nobg.png\" width=\"128\" height=\"128\" alt=\"sickle cell logo\" />\n",
" </div>\n",
" <table style=\"border: 1px solid black; margin: 10px; width: 98%;\">\n",
" <tr class=\"person-details-row\">\n",
" <td class=\"person-details-col\" style=\"border-right: 2; width: 70%;\">\n",
" <div><strong>Person Name:</strong> {{ reportData[\"Person Name\"] }}</div>\n",
" <div><strong>Age / Sex:</strong> {{reportData['Age']}} / {{reportData['Gender']}}</div>\n",
" <div><strong>Sample type:</strong>{{ reportData[\"Sample type\"] }}</div>\n",
" <div><strong>Family History of Sickle Cell Anemia:</strong>{{ reportData[\"Family History of Sickle Cell Anemia\"] }}</div>\n",
" </td>\n",
" <td class=\"person-details-col\" style=\"width: 30%;\">\n",
" <div><strong>Marital Status:</strong>{{ reportData[\"Marital Status\"] }}</div>\n",
" <div><strong>Test Date:</strong>{{ reportData[\"Test Date\"] }}</div> \n",
" <div><strong>ABHA ID:</strong>{{ reportData[\"Patient ID\"] }}</div>\n",
" <div><strong>Sample ID:</strong>{{ reportData[\"Sample ID\"] }}</div>\n",
" </td>\n",
" </tr>\n",
" </table>\n",
" </div>\n",
"\n",
"\n",
" <div style=\"height: 2px;width: 98%; background-color: rgb(56, 105, 166); margin: 30px 10px 40px 10px;\"></div>\n",
"\n",
"\n",
" <div>\n",
" <div class=\"table-header\">POINT OF CARE SICKLE CELL ANEMIA TEST</div>\n",
" <table class=\"test-details-table\" style=\"border: 1px solid black; margin: 10px; width: 98%;\">\n",
" <tr style=\"height: 50px;\">\n",
" <th>\n",
" Test Description\n",
" </th>\n",
" <th>\n",
" RESULT\n",
" </th>\n",
" <th>\n",
" REFERENCE RANGES\n",
" </th>\n",
" </tr>\n",
" <tr class=\"test-details-row\">\n",
" <td class=\"test-details-col\" style=\"width: 20%; margin: 10px;\">\n",
" <div style=\"margin: 10px;\">Sickle Cell\n",
" Anemia\n",
" <div class=\"test-method\">(Method: HPOS)</div>\n",
" </div>\n",
" </td>\n",
" <td style=\"width: 30%;\">\n",
" <div class=\"result-value\">Ra = {{ reportData[\"value\"] }}</div>\n",
" <!-- <div class=\"test-cell-div\">Normal</div>\n",
" <div class=\"test-cell-div\">Sickle Cell Trait</div>\n",
" <div class=\"test-cell-div\">Sickle Cell Disease</div>\n",
" <div class=\"test-cell-div\">Negative Borderline</div>\n",
" <div class=\"test-cell-div\">Positive Borderline</div> -->\n",
" </td>\n",
" <td style=\"width: 50%;\">\n",
" <div class=\"test-cell-div\">\n",
" < 0.16: Normal (HbA)</div>\n",
" <div class=\"test-cell-div\">0.165 – 0.235: Sickle-cell Trait (HbAS)</div>\n",
" <div class=\"test-cell-div\">> 0.24: Sickle-cell Disease (HbSS)</div>\n",
" <div class=\"test-cell-div\">0.16-0.165: Inconclusive (Negative Borderline)</div>\n",
" <div class=\"test-cell-div\">0.235 – 0.24: Inconclusive (Positive Borderline)</div>\n",
" </td>\n",
" <!-- <td style=\"width: 25%;\">\n",
" <div class=\"test-cell-div\">Normal</div>\n",
" <div class=\"test-cell-div\">Sickle Cell Trait</div>\n",
" <div class=\"test-cell-div\">Sickle Cell Disease</div>\n",
" <div class=\"test-cell-div\">Recommended for HPLC or Electrophoresis Tests</div>\n",
" <div class=\"test-cell-div\">Recommended for HPLC or Electrophore</div>\n",
" </td> -->\n",
" </tr>\n",
" </table>\n",
" </div>\n",
"\n",
" <div>\n",
" <!-- <div style=\"font-weight: 600; margin: 10px;\">INTERPRETATION:</div> -->\n",
"\n",
" <div style=\"margin: 10px;\">\n",
" <strong>Test Principle:</strong> This point of care quantitative diagnostic test for sickle-cell anemia\n",
" works on the principle of absorption\n",
" spectroscopy. The test helps in differentiating heterozygous/homozygous hemoglobin from normal hemoglobin.\n",
" </div>\n",
"\n",
" <div style=\"margin: 10px;\">\n",
" <strong>Method:</strong> High Performance Optical Spectroscopy (HPOS) for detection of Sickle cell trait and\n",
" sickle cell disease in whole blood capillary blood samples.\n",
" </div>\n",
"\n",
" <div style=\"margin: 10px;\">\n",
" <strong> Note:</strong>\n",
" <!-- <ul>\n",
" <li>a. Blood transfusion may have an impact on the test results.</li>\n",
"\n",
" <li>\n",
" b. Patients already on sickle-cell medications may impact test results.\n",
" </li>\n",
" </ul> -->\n",
"\n",
" Borderline cases are reported as inconclusive. It may occur due to several factors such as medication,\n",
" transfusion, field conditions and assay process. Further clinical tests are recommended in these cases for\n",
" diagnosis.\n",
" </div>\n",
"\n",
" <!-- <div\n",
" style=\"margin: 80px 10px 20px 50px; width: 88%; display: flex; flex-direction: row; justify-content: space-between; align-items: center;\">\n",
" <div style=\"margin: 5px;\">DATE:</div>\n",
" <div style=\"margin: 5px;\">Hematologist</div>\n",
" </div> -->\n",
"\n",
" <!-- <div style=\"margin: 30px;\">\n",
" This report is for the perusal of doctor only. Not for medico legal cases. Clinical correlation is\n",
" essential.\n",
" Please contact us in case of unexpected result.\n",
" </div> -->\n",
" <div style=\"height: 3px;width: 98%; background-color: black; margin-top: 150px;\"></div>\n",
" <div class=\"end-of-report\">\n",
" *** END OF REPORT ***</div>\n",
" <div style=\"display: flex; justify-content: center; align-items: center; flex-direction: column;\">\n",
" <div style=\"font-style: italic; color: rgb(191, 191, 191);\">\n",
" This is an electronically generated report. Generated at HH:MM hrs on DD-MMM-YYYY.\n",
" </div>\n",
" <div>\n",
" Note: Assay results should be correlated clinically with other clinical findings\n",
" </div>\n",
" </div>\n",
" </div>\n",
"</body>\n",
"\n",
"</html>\n",
"'''\n",
" rptHtml = j2_env.from_string(report_template).render(reportData=rd)\n",
" reportFile = open('reports/' + rd['Sample ID'] + '.pdf','w+b')\n",
" pisa_status = pisa.CreatePDF(rptHtml, dest=reportFile)\n",
" if not pisa_status.err:\n",
" print(\"Created PDF report %s.\" % outFilename)\n",
" #os.remove(rd['qrcodeImgFile'])\n",
" return\n",
"\n",
"if (len(sys.argv) < 2):\n",
" print(\"Usage: genLabReport.py <results_file.csv>\")\n",
" sys.exit(1)\n",
"\n",
"csv_file_path = r\"C:\\Users\\acer\\Desktop\\SMI\\TILL AUG5.csv\" # Replace this with the actual path to your CSV file\n",
"\n",
"\n",
"with open(csv_file_path) as resultsCSVFile:\n",
" reader = csv.DictReader(resultsCSVFile)\n",
" for row in reader:\n",
" generatePDFReport(row)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "90a2f709-7521-41ed-ba1b-99cbbf108ab0",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "3e31b418-eb4c-48e1-9a4f-bdfdc50365f4",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.3"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Reference in New Issue Copy Permalink