ecg_report_dicom_sr_to_fhir.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from typing import List, Optional, Dict\n",
    "import uuid\n",
    "import pydicom\n",
    "from fhir.resources.patient import Patient\n",
    "from fhir.resources.observation import Observation\n",
    "from fhir.resources.diagnosticreport import DiagnosticReport\n",
    "from fhir.resources.codeableconcept import CodeableConcept\n",
    "from fhir.resources.coding import Coding\n",
    "from fhir.resources.reference import Reference\n",
    "from datetime import datetime\n",
    "import highdicom as hd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def recursive_search_for_coded_concept(\n",
    "        ds: pydicom.Dataset, \n",
    "        coded_concept: hd.sr.CodedConcept\n",
    ") -> List[pydicom.Dataset]:\n",
    "    return_items = []\n",
    "    for content_item in ds.ContentSequence:\n",
    "        if hasattr(content_item, 'ConceptNameCodeSequence'):\n",
    "            concept = content_item.ConceptNameCodeSequence[0]\n",
    "\n",
    "            concept = hd.sr.CodedConcept(\n",
    "                value=concept.CodeValue,\n",
    "                scheme_designator=concept.CodingSchemeDesignator,\n",
    "                meaning=concept.CodeMeaning\n",
    "            )\n",
    "\n",
    "            if concept == coded_concept:\n",
    "                return_items.append(content_item)\n",
    "        \n",
    "        if hasattr(content_item, 'ContentSequence'):\n",
    "            _return_items = recursive_search_for_coded_concept(content_item, coded_concept=coded_concept)\n",
    "            return_items += _return_items\n",
    "    return return_items\n",
    "\n",
    "\n",
    "def create_observation_resource(\n",
    "        code_value: str, \n",
    "        code_system: str, \n",
    "        code_display: str, \n",
    "        patient_id: str,\n",
    "        value_quantity: Optional[Dict] = None\n",
    ") -> Observation:\n",
    "    return Observation(\n",
    "        id=str(uuid.uuid4()),\n",
    "        status=\"final\",\n",
    "        code=CodeableConcept(\n",
    "            coding=[Coding(\n",
    "                system=code_system,\n",
    "                code=code_value,\n",
    "                display=code_display\n",
    "            )]\n",
    "        ),\n",
    "        subject=Reference(reference=f\"Patient/{patient_id}\"),\n",
    "        effectiveDateTime=datetime.now().isoformat(),\n",
    "        valueQuantity=value_quantity\n",
    "    )\n",
    "\n",
    "\n",
    "def string_observation(\n",
    "        ds: pydicom.Dataset, \n",
    "        coded_concept: hd.sr.CodedConcept\n",
    ") -> List[Observation]:\n",
    "    items = recursive_search_for_coded_concept(ds, coded_concept)\n",
    "    observations = []\n",
    "    for item in items:\n",
    "        item = item.ConceptCodeSequence[0]\n",
    "        observation = create_observation_resource(\n",
    "            code_value=item.CodeValue,\n",
    "            code_system=item.CodingSchemeDesignator,\n",
    "            code_display=item.CodeMeaning,\n",
    "            patient_id=ds.PatientID\n",
    "        )\n",
    "        observations.append(observation)\n",
    "\n",
    "    return observations\n",
    "\n",
    "\n",
    "def numeric_measurements(\n",
    "        ds: pydicom.Dataset, \n",
    "        coded_concept: hd.sr.CodedConcept\n",
    ") -> List[Observation]:\n",
    "    items = recursive_search_for_coded_concept(ds, coded_concept)\n",
    "    observations = []\n",
    "    for item in items:\n",
    "        measurement = item.MeasuredValueSequence[0].NumericValue\n",
    "        unit = item.MeasuredValueSequence[0].MeasurementUnitsCodeSequence[0]\n",
    "        value_quantity = {\n",
    "            \"value\": float(measurement),\n",
    "            \"unit\": unit.CodeMeaning,\n",
    "            \"system\": unit.CodingSchemeDesignator,\n",
    "            \"code\": unit.CodeMeaning\n",
    "        }\n",
    "        observation = create_observation_resource(\n",
    "            code_value=coded_concept.CodeValue,\n",
    "            code_system=coded_concept.CodingSchemeDesignator,\n",
    "            code_display=coded_concept.CodeMeaning,\n",
    "            patient_id=ds.PatientID,\n",
    "            value_quantity=value_quantity\n",
    "        )\n",
    "        observations.append(observation)\n",
    "\n",
    "    return observations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
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       "(0002, 0002) Media Storage SOP Class UID         UI: Comprehensive SR Storage\n",
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       "-------------------------------------------------\n",
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       "(0008, 0020) Study Date                          DA: '20240101'\n",
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       "(0008, 0050) Accession Number                    SH: '1'\n",
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       "(0008, 0070) Manufacturer                        LO: ''\n",
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       "   (0008, 0104) Code Meaning                        LO: 'ECG Report'\n",
       "   ---------\n",
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       "      (0008, 1199)  Referenced SOP Sequence  1 item(s) ---- \n",
       "         (0008, 1150) Referenced SOP Class UID            UI: 12-lead ECG Waveform Storage\n",
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       "   ---------\n",
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       "   (0040, db00) Template Identifier                 CS: '3700'\n",
       "   ---------\n",
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       "   (0040, a010) Relationship Type                   CS: 'HAS CONCEPT MOD'\n",
       "   (0040, a040) Value Type                          CS: 'CODE'\n",
       "   (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "      (0008, 0100) Code Value                          SH: '121049'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Language of Content Item and Descendants'\n",
       "      ---------\n",
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       "      (0008, 0100) Code Value                          SH: 'de-DE'\n",
       "      (0008, 0102) Coding Scheme Designator            SH: 'RFC5646'\n",
       "      (0008, 0104) Code Meaning                        LO: 'German (Germany)'\n",
       "      ---------\n",
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       "   (0040, a040) Value Type                          CS: 'CODE'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Observer Type'\n",
       "      ---------\n",
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       "      (0008, 0100) Code Value                          SH: '121006'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Person'\n",
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       "   (0040, a040) Value Type                          CS: 'PNAME'\n",
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       "      (0008, 0100) Code Value                          SH: '121008'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Person Observer Name'\n",
       "      ---------\n",
       "   (0040, a123) Person Name                         PN: 'Mustermann^Max'\n",
       "   ---------\n",
       "   (0040, a010) Relationship Type                   CS: 'HAS OBS CONTEXT'\n",
       "   (0040, a040) Value Type                          CS: 'CODE'\n",
       "   (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "      (0008, 0100) Code Value                          SH: '121005'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Observer Type'\n",
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       "      (0008, 0100) Code Value                          SH: '121007'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Device'\n",
       "      ---------\n",
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       "   (0040, a040) Value Type                          CS: 'UIDREF'\n",
       "   (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "      (0008, 0100) Code Value                          SH: '121012'\n",
       "      (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "      (0008, 0104) Code Meaning                        LO: 'Device Observer UID'\n",
       "      ---------\n",
       "   (0040, a124) UID                                 UI: 1.2.826.0.1.3680043.10.511.3.45142667692843894368719330329688917\n",
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       "      (0008, 0100) Code Value                          SH: '55111-9'\n",
       "      (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "      (0008, 0104) Code Meaning                        LO: 'Current Procedure Descriptions'\n",
       "      ---------\n",
       "   (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "   (0040, a504)  Content Template Sequence  1 item(s) ---- \n",
       "      (0008, 0105) Mapping Resource                    CS: 'DCMR'\n",
       "      (0040, db00) Template Identifier                 CS: '3708'\n",
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       "   (0040, a730)  Content Sequence  5 item(s) ---- \n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'DATETIME'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '122146'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Procedure DateTime'\n",
       "         ---------\n",
       "      (0040, a120) DateTime                            DT: '20240902164439.548779'\n",
       "      ---------\n",
       "      (0008, 1199)  Referenced SOP Sequence  1 item(s) ---- \n",
       "         (0008, 1150) Referenced SOP Class UID            UI: 12-lead ECG Waveform Storage\n",
       "         (0008, 1155) Referenced SOP Instance UID         UI: 1.2.826.0.1.3680043.8.498.89623170437663723329382978340499119689\n",
       "         ---------\n",
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       "      (0040, a040) Value Type                          CS: 'WAVEFORM'\n",
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       "         (0008, 0100) Code Value                          SH: 'C0018799'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Electrocardiogram'\n",
       "         ---------\n",
       "      ---------\n",
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       "      (0040, a040) Value Type                          CS: 'CODE'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '10:11345'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'MDC'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Lead System'\n",
       "         ---------\n",
       "      (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '10:11265'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'MDC'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Standard 12-lead positions, electrodes placed individually'\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
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       "         (0008, 0100) Code Value                          SH: '122142'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Acquisition Device Type'\n",
       "         ---------\n",
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       "      ---------\n",
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       "         (0008, 0104) Code Meaning                        LO: 'Equipment Identification'\n",
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       "      (0008, 0104) Code Meaning                        LO: 'Current Procedure Descriptions'\n",
       "      ---------\n",
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       "         (0008, 0100) Code Value                          SH: '122158'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'ECG Global Measurements'\n",
       "         ---------\n",
       "      (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
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       "            (0008, 0104) Code Meaning                        LO: 'Ventricular Heart Rate'\n",
       "            ---------\n",
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       "            (0008, 0104) Code Meaning                        LO: 'QT interval global'\n",
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       "            (0008, 0102) Coding Scheme Designator            SH: 'MDC'\n",
       "            (0008, 0104) Code Meaning                        LO: 'QRS duration global'\n",
       "            ---------\n",
       "         (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "            (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: 'ms'\n",
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       "               (0008, 0104) Code Meaning                        LO: 'millisecond'\n",
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       "            (0040, a30a) Numeric Value                       DS: '100.0'\n",
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       "         (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "         (0040, a040) Value Type                          CS: 'NUM'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '2:16168'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'MDC'\n",
       "            (0008, 0104) Code Meaning                        LO: 'RR interval global'\n",
       "            ---------\n",
       "         (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "            (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: 'ms'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'UCUM'\n",
       "               (0008, 0104) Code Meaning                        LO: 'millisecond'\n",
       "               ---------\n",
       "            (0040, a161) Floating Point Value                FD: 800.0\n",
       "            (0040, a30a) Numeric Value                       DS: '800.0'\n",
       "            ---------\n",
       "         ---------\n",
       "      ---------\n",
       "   ---------\n",
       "   (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "   (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "   (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "      (0008, 0100) Code Value                          SH: '11329-0'\n",
       "      (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "      (0008, 0104) Code Meaning                        LO: 'History'\n",
       "      ---------\n",
       "   (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "   (0040, a504)  Content Template Sequence  1 item(s) ---- \n",
       "      (0008, 0105) Mapping Resource                    CS: 'DCMR'\n",
       "      (0040, db00) Template Identifier                 CS: '3802'\n",
       "      ---------\n",
       "   (0040, a730)  Content Sequence  4 item(s) ---- \n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '11450-4'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Problem List'\n",
       "         ---------\n",
       "      (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "      (0040, a730)  Content Sequence  2 item(s) ---- \n",
       "         (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "         (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '121430'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Concern'\n",
       "            ---------\n",
       "         (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "         (0040, a504)  Content Template Sequence  1 item(s) ---- \n",
       "            (0008, 0105) Mapping Resource                    CS: 'DCMR'\n",
       "            (0040, db00) Template Identifier                 CS: '3829'\n",
       "            ---------\n",
       "         (0040, a730)  Content Sequence  2 item(s) ---- \n",
       "            (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "            (0040, a040) Value Type                          CS: 'CODE'\n",
       "            (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '418799008'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'Finding reported by patient/informant'\n",
       "               ---------\n",
       "            (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '400047006'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'Peripheral vascular disease'\n",
       "               ---------\n",
       "            ---------\n",
       "            (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "            (0040, a040) Value Type                          CS: 'DATETIME'\n",
       "            (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '121431'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "               (0008, 0104) Code Meaning                        LO: 'DateTime Concern Noted'\n",
       "               ---------\n",
       "            (0040, a120) DateTime                            DT: '20240902164439.583187'\n",
       "            ---------\n",
       "         ---------\n",
       "         (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "         (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '121430'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Concern'\n",
       "            ---------\n",
       "         (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "         (0040, a504)  Content Template Sequence  1 item(s) ---- \n",
       "            (0008, 0105) Mapping Resource                    CS: 'DCMR'\n",
       "            (0040, db00) Template Identifier                 CS: '3829'\n",
       "            ---------\n",
       "         (0040, a730)  Content Sequence  3 item(s) ---- \n",
       "            (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "            (0040, a040) Value Type                          CS: 'CODE'\n",
       "            (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '418799008'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'Finding reported by patient/informant'\n",
       "               ---------\n",
       "            (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '399211009'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'History of myocardidal infarction'\n",
       "               ---------\n",
       "            ---------\n",
       "            (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "            (0040, a040) Value Type                          CS: 'DATETIME'\n",
       "            (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '121431'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "               (0008, 0104) Code Meaning                        LO: 'DateTime Concern Noted'\n",
       "               ---------\n",
       "            (0040, a120) DateTime                            DT: '20240902164439.582513'\n",
       "            ---------\n",
       "            (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "            (0040, a040) Value Type                          CS: 'CODE'\n",
       "            (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '277132007'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'Therapy'\n",
       "               ---------\n",
       "            (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '232717009'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "               (0008, 0104) Code Meaning                        LO: 'Coronary artery bypass graft'\n",
       "               ---------\n",
       "            ---------\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '29762-2'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Social History'\n",
       "         ---------\n",
       "      (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "      (0040, a730)  Content Sequence  1 item(s) ---- \n",
       "         (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "         (0040, a040) Value Type                          CS: 'CODE'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '365981007'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Tobacco Smoking Behavior'\n",
       "            ---------\n",
       "         (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '77176002'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Current Smoker'\n",
       "            ---------\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '10167-5'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Past Surgical History'\n",
       "         ---------\n",
       "      (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "      (0040, a730)  Content Sequence  2 item(s) ---- \n",
       "         (0040, a010) Relationship Type                   CS: 'HAS CONCEPT MOD'\n",
       "         (0040, a040) Value Type                          CS: 'CODE'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '387713003'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Surgical Procedure'\n",
       "            ---------\n",
       "         (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '232717009'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Coronary artery bypass graft'\n",
       "            ---------\n",
       "         ---------\n",
       "         (0040, a010) Relationship Type                   CS: 'HAS CONCEPT MOD'\n",
       "         (0040, a040) Value Type                          CS: 'CODE'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '387713003'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Surgical Procedure'\n",
       "            ---------\n",
       "         (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '307280005'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Implantation of cardiac pacemaker'\n",
       "            ---------\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '30954-2'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Relevant Diagnostic Tests and/or Laboratory Data'\n",
       "         ---------\n",
       "      (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "      (0040, a730)  Content Sequence  2 item(s) ---- \n",
       "         (0040, a010) Relationship Type                   CS: 'HAS PROPERTIES'\n",
       "         (0040, a040) Value Type                          CS: 'NUM'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '2086-7'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Cholesterol in HDL'\n",
       "            ---------\n",
       "         (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "            (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '1'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'UCUM'\n",
       "               (0008, 0104) Code Meaning                        LO: 'no units'\n",
       "               ---------\n",
       "            (0040, a161) Floating Point Value                FD: 75.0\n",
       "            (0040, a30a) Numeric Value                       DS: '75.0'\n",
       "            ---------\n",
       "         ---------\n",
       "         (0040, a010) Relationship Type                   CS: 'HAS PROPERTIES'\n",
       "         (0040, a040) Value Type                          CS: 'NUM'\n",
       "         (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '2089-1'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'LN'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Cholesterol in LDL'\n",
       "            ---------\n",
       "         (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "            (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "               (0008, 0100) Code Value                          SH: '1'\n",
       "               (0008, 0102) Coding Scheme Designator            SH: 'UCUM'\n",
       "               (0008, 0104) Code Meaning                        LO: 'no units'\n",
       "               ---------\n",
       "            (0040, a161) Floating Point Value                FD: 160.0\n",
       "            (0040, a30a) Numeric Value                       DS: '160.0'\n",
       "            ---------\n",
       "         ---------\n",
       "      ---------\n",
       "   ---------\n",
       "   (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "   (0040, a040) Value Type                          CS: 'CONTAINER'\n",
       "   (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "      (0008, 0100) Code Value                          SH: '121118'\n",
       "      (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "      (0008, 0104) Code Meaning                        LO: 'Patient Characteristics'\n",
       "      ---------\n",
       "   (0040, a050) Continuity Of Content               CS: 'CONTINUOUS'\n",
       "   (0040, a504)  Content Template Sequence  1 item(s) ---- \n",
       "      (0008, 0105) Mapping Resource                    CS: 'DCMR'\n",
       "      (0040, db00) Template Identifier                 CS: '3704'\n",
       "      ---------\n",
       "   (0040, a730)  Content Sequence  6 item(s) ---- \n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'NUM'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '121033'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Subject Age'\n",
       "         ---------\n",
       "      (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "         (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '7456'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'CID'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Age Unit'\n",
       "            ---------\n",
       "         (0040, a30a) Numeric Value                       DS: '60.0'\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'TEXT'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '121032'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Subject Sex'\n",
       "         ---------\n",
       "      (0040, a160) Text Value                          UT: 'M'\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'NUM'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '271649006'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Systolic blood pressure (observable entity)'\n",
       "         ---------\n",
       "      (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "         (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '3500'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'CID'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Pressure Unit'\n",
       "            ---------\n",
       "         (0040, a161) Floating Point Value                FD: 160.0\n",
       "         (0040, a30a) Numeric Value                       DS: '160.0'\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'NUM'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '271650006'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Diastolic blood pressure (observable entity)'\n",
       "         ---------\n",
       "      (0040, a300)  Measured Value Sequence  1 item(s) ---- \n",
       "         (0040, 08ea)  Measurement Units Code Sequence  1 item(s) ---- \n",
       "            (0008, 0100) Code Value                          SH: '3500'\n",
       "            (0008, 0102) Coding Scheme Designator            SH: 'CID'\n",
       "            (0008, 0104) Code Meaning                        LO: 'Pressure Unit'\n",
       "            ---------\n",
       "         (0040, a161) Floating Point Value                FD: 100.0\n",
       "         (0040, a30a) Numeric Value                       DS: '100.0'\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CODE'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '109054'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'DCM'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Patient State'\n",
       "         ---------\n",
       "      (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '128975004'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Resting state'\n",
       "         ---------\n",
       "      ---------\n",
       "      (0040, a010) Relationship Type                   CS: 'CONTAINS'\n",
       "      (0040, a040) Value Type                          CS: 'CODE'\n",
       "      (0040, a043)  Concept Name Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: '441509002'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'SCT'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Pacemaker in situ'\n",
       "         ---------\n",
       "      (0040, a168)  Concept Code Sequence  1 item(s) ---- \n",
       "         (0008, 0100) Code Value                          SH: 'D'\n",
       "         (0008, 0102) Coding Scheme Designator            SH: 'NBG'\n",
       "         (0008, 0104) Code Meaning                        LO: 'Dual (A+V)'\n",
       "         ---------\n",
       "      ---------\n",
       "   ---------"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ds = pydicom.dcmread('example_ecg_sr.dcm')\n",
    "ds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Convert DICOM Patient Information to FHIR Patient Resource\n",
    "patient = Patient(\n",
    "    id=ds.PatientID,\n",
    "    name=[{\n",
    "        \"family\": ds.PatientName.family_name,\n",
    "        \"given\": ds.PatientName.given_name.split('^')\n",
    "    }],\n",
    "    birthDate=ds.PatientBirthDate,\n",
    "    gender=\"male\" if ds.PatientSex == \"M\" else \"female\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "dbp_code = hd.sr.CodedConcept(\n",
    "    value='271650006',\n",
    "    scheme_designator='SCT',\n",
    "    meaning='Diastolic blood pressure (observable entity)'\n",
    ")\n",
    "dbp_observations = numeric_measurements(ds, dbp_code)\n",
    "\n",
    "sbp_code = hd.sr.CodedConcept(\n",
    "    value=\"271649006\",\n",
    "    scheme_designator='SCT',\n",
    "    meaning=\"Systolic blood pressure (observable entity)\"\n",
    ")\n",
    "sbp_oberservations = numeric_measurements(ds, sbp_code)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "surgical_procedure_code = hd.sr.CodedConcept(\n",
    "    value='387713003', \n",
    "    scheme_designator='SCT',\n",
    "    meaning='Surgical Procedure'\n",
    ")\n",
    "\n",
    "surgical_procedure_observations = string_observation(ds, surgical_procedure_code)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "observations = [\n",
    "    *dbp_observations, *sbp_oberservations, *surgical_procedure_observations\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# # Convert DICOM SR Document to FHIR DiagnosticReport\n",
    "diagnostic_report = DiagnosticReport(\n",
    "    status=\"final\",\n",
    "    code=CodeableConcept(\n",
    "        coding=[Coding(\n",
    "            system=\"http://loinc.org\",\n",
    "            code=\"11524-0\",\n",
    "            display=\"ECG Report\"\n",
    "        )]\n",
    "    ),\n",
    "    subject=Reference(reference=f\"Patient/{ds.PatientID}\"),\n",
    "    effectiveDateTime=datetime.now().isoformat(),\n",
    "    result=[Reference(reference=f\"Observation/{obs.id}\") for obs in observations]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "OrderedDict([('resourceType', 'DiagnosticReport'),\n",
       "             ('status', 'final'),\n",
       "             ('code',\n",
       "              OrderedDict([('coding',\n",
       "                            [OrderedDict([('system', 'http://loinc.org'),\n",
       "                                          ('code', '11524-0'),\n",
       "                                          ('display', 'ECG Report')])])])),\n",
       "             ('subject', OrderedDict([('reference', 'Patient/0123456789')])),\n",
       "             ('effectiveDateTime',\n",
       "              datetime.datetime(2024, 9, 3, 17, 58, 38, 238806)),\n",
       "             ('result',\n",
       "              [OrderedDict([('reference',\n",
       "                             'Observation/2e5dd4ea-e4b2-4301-88f2-74a430c3c5e3')]),\n",
       "               OrderedDict([('reference',\n",
       "                             'Observation/d5dca584-85f7-4462-af47-7d0e3a968fc8')]),\n",
       "               OrderedDict([('reference',\n",
       "                             'Observation/9347876e-0ba2-4bdb-b547-0386bc1fe714')]),\n",
       "               OrderedDict([('reference',\n",
       "                             'Observation/625fe33e-7c5b-4aca-ad98-f9e4280b8dbf')])])])"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "diagnostic_report.dict()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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