endoreg-db 0.5.3__py3-none-any.whl → 0.6.1__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/urls.py

@@ -0,0 +1,173 @@
+from django.urls import path, include
+from rest_framework.routers import DefaultRouter
+from .views.patient_views import (
+    PatientViewSet,
+    start_examination,
+    get_location_choices,
+    get_morphology_choices, 
+)
+from .views.csrf import csrf_token_view
+#from .views.feature_selection_view import FetchSingleFramePredictionView // its implemented in ando-ai other project need to add here
+from .views.video_segmentation_views import VideoView, VideoLabelView,UpdateLabelSegmentsView
+from .views.views_for_timeline import video_timeline_view
+from .views.raw_video_meta_validation_views import VideoFileForMetaView
+router = DefaultRouter()
+router.register(r'patients', PatientViewSet)
+
+urlpatterns = [
+    path('start-examination/', start_examination, name="start_examination"),
+    path('get-location-choices/<int:location_id>/', get_location_choices, name="get_location_choices"),
+    path('get-morphology-choices/<int:morphology_id>/', get_morphology_choices, name="get_morphology_choices"),
+    path('api/', include(router.urls)),
+    path('api/conf/', csrf_token_view, name='csrf_token'),
+    
+
+
+#--------------------------------------VIDEO SEGMENTATION END POINTS--------------------------------------
+
+       # The dropdown contains video names and their corresponding IDs, which are retrieved from the database(RawVideoFile). Additionally, this route(api/videos) also fetches labels along with their names and IDs from the label table.
+       # We will modify this implementation later as per our requirements.
+        #Based on the selected video ID, relevant data will be fetched from the database, and the video, along with its associated details, 
+        # will be displayed on the frontend using route(api/video/<int:video_id>/).
+        # once label is selected from the dropdown,using its name, details can be fetched from rawvideofile using route("api/video/<int:video_id>/label/<str:label_name>/) 
+        #If editing is required, a form will be available for each label. This form dynamically updates when the selected label changes. It will display all segments associated with the selected label, each with a delete option. Below these segments, there may be a button for adding more segments.
+        #If any values in the form are modified, the updated data will be saved in the database table.
+    
+    
+    
+    
+    # Fetch all videos for the dropdown
+    # Fetch all available videos (for the video selection dropdown in frontend)
+    # Usage in frontend: Call this API to get a list of available videos.
+    # Example request: GET /api/videos/
+    # Response: Returns a JSON list of videos (id, file path, video_url, sequences, label_names).
+    # it also fetch the label from teh label table
+    path("api/videos/", VideoView.as_view(), name="video_list"),
+    
+    #need to change this route
+    #path('api/prediction/', FetchSingleFramePredictionView.as_view(), name='fetch-single-frame-prediction'),#.as_view() converts the class-based view into a function that Django can use for routing.
+    
+    # Fetch video details + labels based on selected video
+    # Usage in frontend: Call this when a user selects a video from the dropdown.
+    # Example request: GET /api/video/1/
+    # Response: Returns metadata, file path, video URL, sequences, and available label names.
+    # Frontend should use this api for `label_names`, to display label selection (dropdown or tabs).
+    path("api/video/<int:video_id>/", VideoView.as_view(), name="video_handler"),
+    
+
+    # Fetch time segments along with frame predictions and filenames for a selected label
+    # 
+    # **Usage in frontend:**
+    # - Call this API when a user selects a label from the dropdown in the timeline.
+    # - The API returns time segments (start & end times in seconds) where the label appears in the video.
+    # - Each segment includes frame-wise predictions and the corresponding frame filenames.
+    #
+    # **Example request:**
+    #   GET /api/video/1/label/outside/
+    #
+    # **Example response:**
+    # {
+    #     "label": "outside",
+    #     "time_segments": [
+    #         {   "segment_start": 0,
+     #       "segment_end": 463,
+    #             "start_time": 0.0,
+    #             "end_time": 9.26,
+    #             "frames": {
+    #                 "0": {
+    #                     "frame_filename": "frame_0000000.jpg",
+    #                     "frame_file_path": "/home/admin/test-data/video_frames/abc123/frame_0000000.jpg",
+    #                     "predictions": {
+    #                         "appendix": 0.0150,
+    #                         and others
+    #                     }
+    #                 },
+    #                 "1": {
+    #                     "frame_filename": "frame_0000001.jpg",
+    #                     "frame_file_path": "/home/admin/test-data/video_frames/abc123/frame_0000001.jpg",
+    #                     "predictions": {
+    #                         "appendix": 0.0124,
+    #                         and otehrs
+    #                     }}}}]}
+    #                 
+    # start_time and end_time are in seconds, converted from frame indices.
+    # frames contains all frames in the segment with:
+    # frame_filename (e.g., frame_0000001.jpg)
+    # frame_file_path (full path for easy access)
+    #  predictions (frame-wise probability scores for each category)
+    #we need label name for this not id as we donot have id in rawvideofile table
+    path("api/video/<int:video_id>/label/<str:label_name>/", VideoLabelView.as_view(), name="video_label_times"),
+
+    # Update or create label segments for a specific video and label
+    # - Call this API when a user updates the start and end frames of a label segment(adding new , deleting or changing the values).
+    # - The API will:
+    #   - **Update** existing segments if they match the given `video_id` and `label_id`.
+    #   - **Create** new segments if they do not already exist.
+    #   - **Delete** segments from the database if they were removed from the frontend.
+    # - This ensures that the database reflects exactly what is sent from the frontend.
+    #
+    # **Example request (Updating segments for label ID 12 in video ID 1):**
+    #   PUT /api/video/1/label/12/update_segments/
+    #
+    # **Request body (JSON):**
+    # {
+    #     "video_id": 1,
+    #     "label_id": 12,
+    #     "segments": [
+    #         {
+    #             "start_frame_number": 0,
+    #             "end_frame_number": 463
+    #         },{
+    #             "start_frame_number": 500,
+    #             "end_frame_number": 700
+    #         }]}
+    #
+    # **Expected response (If successful):**
+    # {
+    #     "updated_segments": [
+    #         {
+    #             "id": 1,
+    #             "video_id": 1,
+    #             "label_id": 12,
+    #             "start_frame_number": 0,
+    #             "end_frame_number": 463
+    #         }
+    #     ],
+    #     "new_segments": [
+    #         {
+    #             "id": 2,
+    #             "video_id": 1,
+    #             "label_id": 12,
+    #             "start_frame_number": 500,
+    #             "end_frame_number": 700
+    #         }
+    #     ],
+    #     "deleted_segments": 1  # Number of deleted segments if any were removed
+    # }
+ 
+    # **Frontend Integration:**
+    # - Vue.js should send this request when the user **saves changes** to segments.
+    # - The **"Add Segment"** button should allow users to add new segments dynamically.
+    # - The **"Delete Segment"** button should remove segments from the list before submitting.
+    # - The request should be triggered via an `axios.put` call:
+    #
+    path("api/video/<int:video_id>/label/<int:label_id>/update_segments/", UpdateLabelSegmentsView.as_view(), name="update_label_segments"),
+
+#----------------------------------END--VIDEO SEGMENTATION SECTION-------------------------------
+    #this is for to test the timeline
+    #need to delete this url and also endoreg_db_production/endoreg_db/views/views_for_timeline.py and endoreg_db_production/endoreg_db/templates/timeline.html
+    path('video/<int:video_id>/timeline/', video_timeline_view, name='video_timeline'),
+
+    
+    
+    
+    #  const url = lastId ? `http://localhost:8000/api/video/meta/?last_id=${lastId}` : "http://localhost:8000/api/video/meta/";
+    path("api/video/sensitivemeta/", VideoFileForMetaView.as_view(), name="video_meta"),  # Single endpoint for both first and next video    
+    ]
+
+
+
+
+
+
+#https://biigle.de/manual/tutorials/videos/navigating-timeline#for time line example

endoreg_db/utils/__init__.py

@@ -1 +1,36 @@
-from .dataloader import load_model_data_from_yaml
+"""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",
+]