endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/templates/admin/patient_finding_intervention.html

@@ -0,0 +1,253 @@
+{% extends "admin/base_site.html" %}
+{% block content %}
+
+<h2>Patient Finding Intervention</h2>
+
+<form method="POST" id="intervention-form">
+    {% csrf_token %}
+
+    <!-- Patient Selection -->
+    <div>
+        <label>Select Patient:</label><br>
+        <select name="patient" id="patient-dropdown">
+            <option value="">-- Select Patient --</option>
+            {% for patient in patients %}
+            <option value="{{ patient.id }}">{{ patient.first_name }} {{ patient.last_name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Examination Selection -->
+    <div>
+        <label>Select Examination:</label><br>
+        <select name="examination" id="examination-dropdown">
+            <option value="">-- Select Examination --</option>
+            {% for examination in examinations %}
+            <option value="{{ examination.id }}">{{ examination.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Finding Selection -->
+    <div>
+        <label>Select Finding:</label><br>
+        <select name="finding" id="finding-dropdown">
+            <option value="">-- Select Finding --</option>
+            {% for finding in findings %}
+            <option value="{{ finding.id }}">{{ finding.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Select Location -->
+    <div>
+        <label>Select Location:</label><br>
+        <select name="location" id="location-dropdown" onchange="updateFormAction(this)">
+            <option value="">-- Select Location --</option>
+            {% for location in locations %}
+            <option value="{{ location.id }}" {% if location.id == selected_location %}selected{% endif %}>
+                {{ location.name }}
+            </option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Select Location Choice -->
+    <div>
+        <label>Select Location Choice:</label><br>
+        <select name="location_choice" id="location-choice-dropdown">
+            <option value="">-- Select Location Choice --</option>
+            {% for choice in location_choices %}
+            <option value="{{ choice.id }}">{{ choice.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Select Morphology -->
+    <!-- Select Morphology (FindingMorphologyClassification) -->
+    <div>
+        <label>Select Morphology:</label><br>
+        <select name="morphology" id="morphology-dropdown">
+            <option value="">-- Select Morphology --</option>
+            {% for morphology in morphologies %}
+            <option value="{{ morphology.id }}">{{ morphology.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <!-- Select Morphology Choice (FindingMorphologyClassificationChoice) -->
+    <div>
+        <label>Select Morphology Choice:</label><br>
+        <select name="morphology_choice" id="morphology-choice-dropdown">
+            <option value="">-- Select Morphology Choice --</option>
+            {% for choice in morphology_choices %}
+            <option value="{{ choice.id }}">{{ choice.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+
+    <br>
+
+    <!-- Select Finding Interventions -->
+    <div>
+        <label>Select Finding Interventions:</label><br>
+        <select name="finding_intervention" id="finding-intervention-dropdown">
+            <option value="">-- Select Finding Intervention --</option>
+            {% for intervention in finding_interventions %}
+            <option value="{{ intervention.id }}">{{ intervention.name }}</option>
+            {% endfor %}
+        </select>
+    </div>
+
+    <br>
+
+    <div>
+        <button type="button" id="generate-report-btn">Generate Report</button>
+    </div>
+
+    <!-- Display Report Section -->
+    <div id="report-section" style="display:none; margin-top: 20px;">
+        <h3>Generated Report</h3>
+        <p><strong>Patient:</strong> <span id="report-patient"></span></p>
+        <p><strong>Examination:</strong> <span id="report-examination"></span></p>
+        <p><strong>Finding:</strong> <span id="report-finding"></span></p>
+        <p><strong>Location:</strong> <span id="report-location"></span></p>
+        <p><strong>Location Choice:</strong> <span id="report-location-choice"></span></p>
+        <p><strong>Morphology:</strong> <span id="report-morphology"></span></p>
+        <p><strong>Morphology Choice:</strong> <span id="report-morphology-choice"></span></p>
+        <p><strong>Finding Intervention:</strong> <span id="report-finding-intervention"></span></p>
+
+        <button id="download-report-btn">Download Report</button>
+    </div>
+
+</form>
+
+<script>
+    document.getElementById("location-dropdown").addEventListener("change", function() {
+        let locationId = this.value;
+        let locationChoiceDropdown = document.getElementById("location-choice-dropdown");
+
+        // Reset dropdown
+        locationChoiceDropdown.innerHTML = '<option value="">-- Select Location Choice --</option>';
+
+        // Fetch Choices Only If a Location is Selected
+        if (locationId) {
+            fetch(`/endoreg_db/get-location-choices/${locationId}/`)  
+            .then(response => response.json())
+            .then(data => {
+                if (data.location_choices.length === 0) {
+                    locationChoiceDropdown.innerHTML = `<option value="default">Rectum</option>`; // Default Value
+                } else {
+                    data.location_choices.forEach(choice => {
+                        locationChoiceDropdown.innerHTML += `<option value="${choice.id}">${choice.name}</option>`;
+                    });
+                }
+            })
+            .catch(error => {
+                console.error("Error loading location choices:", error);
+                alert("Error: Could not fetch location choices.");
+            });
+        } else {
+            locationChoiceDropdown.innerHTML = `<option value="default">Rectum</option>`; // Default Value
+        }
+    });
+</script>
+
+
+<script>
+    document.getElementById("generate-report-btn").addEventListener("click", function() {
+        let getText = (id, defaultValue = "Not Selected") => {
+            let element = document.getElementById(id);
+            return element.selectedOptions.length > 0 ? element.selectedOptions[0].text.trim() : defaultValue;
+        };
+
+        document.getElementById("report-patient").textContent = getText("patient-dropdown");
+        document.getElementById("report-examination").textContent = getText("examination-dropdown");
+        document.getElementById("report-finding").textContent = getText("finding-dropdown");
+        document.getElementById("report-location").textContent = getText("location-dropdown");
+        document.getElementById("report-location-choice").textContent = getText("location-choice-dropdown", "Rectum");
+        document.getElementById("report-morphology").textContent = getText("morphology-dropdown");
+        document.getElementById("report-morphology-choice").textContent = getText("morphology-choice-dropdown");
+        document.getElementById("report-finding-intervention").textContent = getText("finding-intervention-dropdown");
+
+        document.getElementById("report-section").style.display = "block";
+    });
+
+    document.getElementById("download-report-btn").addEventListener("click", function() {
+        let reportContent = `
+        Patient: ${document.getElementById("report-patient").textContent}
+        Examination: ${document.getElementById("report-examination").textContent}
+        Finding: ${document.getElementById("report-finding").textContent}
+        Location: ${document.getElementById("report-location").textContent}
+        Location Choice: ${document.getElementById("report-location-choice").textContent}
+        Morphology: ${document.getElementById("report-morphology").textContent}
+        Morphology Choice: ${document.getElementById("report-morphology-choice").textContent}
+        Finding Intervention: ${document.getElementById("report-finding-intervention").textContent}
+        `;
+
+        let blob = new Blob([reportContent], { type: "text/plain" });
+        let link = document.createElement("a");
+        link.href = URL.createObjectURL(blob);
+        link.download = "Patient_Finding_Report.txt";
+        document.body.appendChild(link);
+        link.click();
+        document.body.removeChild(link);
+    });
+</script>
+
+<script>
+    document.getElementById("morphology-dropdown").addEventListener("change", function() {
+        let morphologyId = this.value;
+        let morphologyChoiceDropdown = document.getElementById("morphology-choice-dropdown");
+
+        // Reset Morphology Choice Dropdown
+        morphologyChoiceDropdown.innerHTML = '<option value="">-- Select Morphology Choice --</option>';
+
+        // Fetch Choices Only If a Morphology is Selected
+        if (morphologyId) {
+            fetch(`/endoreg_db/get-morphology-choices/${morphologyId}/`)  
+            .then(response => {
+                if (!response.ok) {
+                    throw new Error(`HTTP error! Status: ${response.status}`);
+                }
+                return response.json();
+            })
+            .then(data => {
+                if (data.error) {
+                    console.error("Server Error:", data.error);
+                    alert("Error: " + data.error);
+                } else {
+                    if (data.morphology_choices.length === 0) {
+                        morphologyChoiceDropdown.innerHTML = `<option value="default">No Choices Available</option>`; // Default Value
+                    } else {
+                        data.morphology_choices.forEach(choice => {
+                            morphologyChoiceDropdown.innerHTML += `<option value="${choice.id}">${choice.name}</option>`;
+                        });
+                    }
+                }
+            })
+            .catch(error => {
+                console.error("Error loading morphology choices:", error);
+                alert("Error: Could not fetch morphology choices.");
+            });
+        }
+    });
+</script>
+
+
+
+
+{% endblock %}

endoreg_db/templates/admin/start_examination.html

@@ -0,0 +1,12 @@
+<!-- start_examination.html -->
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Start Examination</title>
+</head>
+<body>
+    <h1>Hello World</h1>
+</body>
+</html>

endoreg_db/templates/timeline.html

@@ -0,0 +1,176 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>Frames Timeline (Outside Label)</title>
+    <style>
+        body { font-family: Arial, sans-serif; text-align: center; margin: 20px; }
+        video { width: 80%; margin-bottom: 20px; }
+
+        /* Timeline Container */
+        .timeline-container {
+            position: relative;
+            width: 80%;
+            height: 50px;
+            margin: auto;
+            background: #f0f0f0;
+            border-radius: 5px;
+        }
+
+        /* Timeline Bar */
+        .timeline-bar {
+            width: 100%;
+            height: 8px;
+            background-color: #ccc;
+            position: absolute;
+            top: 50%;
+            transform: translateY(-50%);
+            border-radius: 4px;
+        }
+
+        /* Red Highlight for Outside Label Segments */
+        .segment-box {
+            position: absolute;
+            height: 8px;
+            background-color: rgba(255, 0, 0, 0.7);
+            border-radius: 4px;
+            top: 50%;
+            transform: translateY(-50%);
+            cursor: pointer;
+        }
+
+        /* Draggable Vertical Markers */
+        .frame-marker {
+            position: absolute;
+            width: 6px;
+            height: 20px;
+            background-color: blue;
+            cursor: grab;
+            top: 50%;
+            transform: translate(-50%, -50%);
+            border-radius: 3px;
+            transition: background-color 0.2s;
+        }
+
+        .frame-marker:hover {
+            background-color: red;
+        }
+
+        .frame-marker:active {
+            cursor: grabbing;
+        }
+
+    </style>
+</head>
+<body>
+    <h2>Frames Timeline (Outside Label)</h2>
+    
+    <video id="videoPlayer" controls>
+        <source src="{{ video_url }}" type="video/mp4">
+        Your browser does not support the video tag.
+    </video>
+
+    <div class="timeline-container">
+        <div class="timeline-bar"></div>
+        <div id="segments"></div>  <!-- Highlighted segments -->
+        <div id="frameMarkers"></div> <!-- Start & End markers -->
+    </div>
+
+    <script>
+        document.addEventListener("DOMContentLoaded", function () {
+            const segments = JSON.parse('{{ segments|safe }}');  // Get "outside" label segments
+            const video = document.getElementById("videoPlayer");
+            const timelineContainer = document.querySelector(".timeline-container");
+            const segmentsContainer = document.getElementById("segments");
+            const frameMarkersContainer = document.getElementById("frameMarkers");
+
+            let videoDuration = {{ video_duration|default:1 }};  // Ensure valid duration
+
+            console.log("Loaded Segments:", segments);
+            console.log("Video Duration:", videoDuration);
+
+            if (segments.length === 0) {
+                console.warn("No segments available!");
+                return;
+            }
+
+            // Create segment boxes
+            segments.forEach(segment => {
+                const segmentDiv = document.createElement("div");
+                segmentDiv.classList.add("segment-box");
+
+                // Convert times to percentage positions
+                let startPercent = (segment.start_time / videoDuration) * 100;
+                let endPercent = (segment.end_time / videoDuration) * 100;
+                let widthPercent = endPercent - startPercent;
+
+                // Ensure last segment does not go beyond 100%
+                startPercent = Math.min(100, startPercent);
+                endPercent = Math.min(100, endPercent);
+                widthPercent = Math.max(0, endPercent - startPercent);
+
+                segmentDiv.style.left = startPercent + "%";
+                segmentDiv.style.width = widthPercent + "%";
+
+                // Clicking on segment seeks video
+                segmentDiv.addEventListener("click", function () {
+                    video.currentTime = segment.start_time;
+                    video.play();
+                });
+
+                segmentsContainer.appendChild(segmentDiv);
+            });
+
+            // Create draggable markers
+            segments.forEach(segment => {
+                ["start_time", "end_time"].forEach(timeType => {
+                    const marker = document.createElement("div");
+                    marker.classList.add("frame-marker");
+
+                    // Position marker
+                    let percent = (segment[timeType] / videoDuration) * 100;
+                    percent = Math.min(100, Math.max(0, percent));  // Keep within bounds
+                    marker.style.left = percent + "%";
+
+                    // Store initial marker time
+                    marker.dataset.time = segment[timeType];
+
+                    // Enable dragging
+                    let isDragging = false;
+
+                    marker.addEventListener("pointerdown", (event) => {
+                        isDragging = true;
+                        marker.style.cursor = "grabbing";
+                        event.preventDefault();
+                    });
+
+                    document.addEventListener("pointermove", (event) => {
+                        if (!isDragging) return;
+
+                        const rect = timelineContainer.getBoundingClientRect();
+                        const offsetX = event.clientX - rect.left;
+                        let percentX = (offsetX / rect.width) * 100;
+                        
+                        // Keep marker within bounds (0-100%)
+                        percentX = Math.min(100, Math.max(0, percentX));
+                        
+                        const newTime = (percentX / 100) * videoDuration;
+
+                        marker.style.left = percentX + "%";
+                        video.currentTime = newTime;
+                    });
+
+                    document.addEventListener("pointerup", () => {
+                        if (isDragging) {
+                            isDragging = false;
+                            marker.style.cursor = "grab";
+                        }
+                    });
+
+                    frameMarkersContainer.appendChild(marker);
+                });
+            });
+
+        });
+    </script>
+</body>
+</html>

endoreg_db/utils/__init__.py

@@ -0,0 +1,36 @@
+"""Module for utility classes and functions."""
+
+from .dataloader import load_model_data_from_yaml
+from .parse_and_generate_yaml import collect_center_names
+from .validate_endo_roi import validate_endo_roi
+from .pydantic_models import DbConfig
+from .dates import random_day_by_month_year, random_day_by_year
+from .hashs import (
+    get_hash_string,
+    get_pdf_hash,
+    get_examiner_hash,
+    get_video_hash,
+    get_patient_examination_hash,
+)
+from .names import (
+    create_mock_patient_name,
+    create_mock_examiner_name,
+    guess_name_gender,
+)
+
+__all__ = [
+    "load_model_data_from_yaml",
+    "collect_center_names",
+    "validate_endo_roi",
+    "get_examiner_hash",
+    "DbConfig",
+    "random_day_by_month_year",
+    "random_day_by_year",
+    "get_hash_string",
+    "create_mock_examiner_name",
+    "create_mock_patient_name",
+    "guess_name_gender",
+    "get_pdf_hash",
+    "get_video_hash",
+    "get_patient_examination_hash",
+]

endoreg_db/utils/cropping.py

@@ -0,0 +1,29 @@
+from PIL import Image
+
+def crop_and_insert(image:Image, x, y, h, w, bg_color=(255, 255, 255)):
+    """
+    Crops a region from an inverted grayscale image and inserts it into a white image of the same size as the original.
+    
+    Parameters:
+    - fp: File path or a file object of the original image.
+    - x, y: The top-left coordinates of the rectangle to be cropped.
+    - h, w: The height and width of the rectangle to be cropped.
+    
+    Returns:
+    A PIL Image object containing the original image with the specified region replaced.
+    """
+    # Load the original image
+    original_image = image
+    
+    # Crop the specified region from the inverted image
+    crop_rectangle = (x, y, x + w, y + h)
+    cropped_content = original_image.crop(crop_rectangle)
+    
+    # Create a new white image of the same size as the original image
+    white_background = Image.new('RGB', original_image.size, bg_color)
+    
+    # Paste the cropped content onto the white image at the specified location
+    white_background.paste(cropped_content, (x, y))
+    
+    # The final image can be displayed or saved as needed
+    return white_background

endoreg_db/utils/dataloader.py

@@ -0,0 +1,118 @@
+import os
+import yaml
+from django.core.exceptions import ObjectDoesNotExist
+
+from icecream import ic
+
+
+def load_model_data_from_yaml(command, model_name, metadata, verbose):
+    """
+    Load model data from YAML files.
+
+    Args:
+        command: Command object for stdout writing.
+        model_name: Name of the model being loaded.
+        metadata: Metadata including directory and foreign key information.
+        verbose: Boolean indicating whether to print verbose output.
+    """
+    if verbose:
+        command.stdout.write(f"Start loading {model_name}")
+    model = metadata["model"]
+    dir_path = metadata["dir"]
+    foreign_keys = metadata["foreign_keys"]
+    foreign_key_models = metadata["foreign_key_models"]
+
+    _files = [f for f in os.listdir(dir_path) if f.endswith(".yaml")]
+    # sort
+    _files.sort()
+    for file in _files:
+        with open(os.path.join(dir_path, file), "r", encoding="utf-8") as file:
+            yaml_data = yaml.safe_load(file)
+
+        load_data_with_foreign_keys(
+            command, model, yaml_data, foreign_keys, foreign_key_models, verbose
+        )
+
+
+def load_data_with_foreign_keys(
+    command, model, yaml_data, foreign_keys, foreign_key_models, verbose
+):
+    """
+    Load data handling foreign keys and many-to-many relationships.
+
+    Args:
+        command: Command object for stdout writing.
+        model: The Django model for the data.
+        yaml_data: Data loaded from YAML.
+        foreign_keys: List of foreign keys.
+        foreign_key_models: Corresponding models for the foreign keys.
+        verbose: Boolean indicating whether to print verbose output.
+    """
+    for entry in yaml_data:
+        fields = entry.get("fields", {})
+        name = fields.pop("name", None)
+        m2m_relationships = {}  # Store many-to-many relationships
+        # print(entry)
+
+        # Handle foreign keys and many-to-many relationships
+        for fk_field, fk_model in zip(foreign_keys, foreign_key_models):
+            # print(fk_field, fk_model)
+            target_keys = fields.pop(fk_field, None)
+
+            # Ensure the foreign key exists
+            if target_keys is None:
+                if verbose:
+                    command.stdout.write(
+                        command.style.WARNING(
+                            f"Foreign key {fk_field} not found in fields"
+                        )
+                    )
+                continue  # Skip if no foreign key provided
+
+            # Process many-to-many fields or foreign keys
+            if isinstance(target_keys, list):  # Assume many-to-many relationship
+                related_objects = []
+                for key in target_keys:
+                    obj, created = fk_model.objects.get_or_create(name=key)
+                    if created and verbose:
+                        command.stdout.write(
+                            command.style.SUCCESS(f"Created {fk_model.__name__} {key}")
+                        )
+                    related_objects.append(obj)
+                m2m_relationships[fk_field] = related_objects
+            else:  # Single foreign key relationship
+                try:
+                    if model == "endoreg_db.case_template_rule":
+                        # print(fk_model, target_keys)
+                        pass
+                    obj = fk_model.objects.get_by_natural_key(target_keys)
+                except ObjectDoesNotExist:
+                    if verbose:
+                        command.stdout.write(
+                            command.style.WARNING(
+                                f"{fk_model.__name__} with key {target_keys} not found"
+                            )
+                        )
+                    continue
+                fields[fk_field] = obj
+
+        # Create or update the main object
+        if name is None:
+            obj, created = model.objects.get_or_create(**fields)
+        else:
+            obj, created = model.objects.update_or_create(defaults=fields, name=name)
+        if created and verbose:
+            command.stdout.write(
+                command.style.SUCCESS(f"Created {model.__name__} {name}")
+            )
+        elif verbose:
+            pass
+            # command.stdout.write(
+            #     command.style.WARNING(
+            #         f"Skipped {model.__name__} {name}, already exists"
+            #     )
+            # )
+
+        # Set many-to-many relationships
+        for field_name, related_objs in m2m_relationships.items():
+            getattr(obj, field_name).set(related_objs)

endoreg_db/utils/dates.py

@@ -0,0 +1,39 @@
+from datetime import datetime, date, timedelta
+from random import randint
+from calendar import monthrange
+
+# TODO replace used random_day_by_year function implementation when
+# creating pseudo patients with new function "random date by age_at_date and examination_date"
+
+
+def random_day_by_age_at_date(age_at_date: int, examination_date: date) -> date:
+    """
+    Return a random birth day for a patient with the specified age at the specified examination date.
+    """
+    examination_year = examination_date.year
+    latest_birthdate = examination_date.replace(year=examination_year - age_at_date)
+    valid_dates = [latest_birthdate - timedelta(days=i) for i in range(365)]
+
+    select = randint(0, len(valid_dates) - 1)
+    birth_date = valid_dates[select]
+
+    return birth_date
+
+
+def random_day_by_year(year: int) -> date:
+    """
+    Return a random birth day within the specified year.
+    """
+    month = randint(1, 12)
+    day = randint(1, monthrange(year, month)[1])
+
+    return date(year, month, day)
+
+
+def random_day_by_month_year(month: int, year) -> date:
+    """
+    Return a random birth day within the specified month and year.
+    """
+
+    day = randint(1, monthrange(year, month)[1])
+    return date(year, month, day)