Temp files are given unique name and deleted after dcm pdf is created. Removed stone web viewer.

OrthancExplorer.js

@@ -68,62 +68,3 @@ $('#instance').live('pageshow', function() {
     }
   });
 });
-
-
-$('#study').live('pagebeforecreate', function() {
-  var b = $('<a>')
-      .attr('data-role', 'button')
-      .attr('href', '#')
-      .attr('data-icon', 'search')
-      .attr('data-theme', 'e')
-      .text('Stone Web Viewer (for mammography)');
-
-  b.insertBefore($('#study-delete').parent().parent());
-  b.click(function() {
-    if ($.mobile.pageData) {
-      $.ajax({
-        url: '../studies/' + $.mobile.pageData.uuid,
-        dataType: 'json',
-        cache: false,
-        success: function(study) {
-          var studyInstanceUid = study.MainDicomTags.StudyInstanceUID;
-          window.open('../mammography-viewer/index.html?study=' + studyInstanceUid);
-        }
-      });
-    }
-  });
-});
-
-
-$('#series').live('pagebeforecreate', function() {
-  var b = $('<a>')
-      .attr('data-role', 'button')
-      .attr('href', '#')
-      .attr('data-icon', 'search')
-      .attr('data-theme', 'e')
-      .text('Stone Web Viewer (for mammography)');
-
-  b.insertBefore($('#series-delete').parent().parent());
-  b.click(function() {
-    if ($.mobile.pageData) {
-      $.ajax({
-        url: '../series/' + $.mobile.pageData.uuid,
-        dataType: 'json',
-        cache: false,
-        success: function(series) {
-          $.ajax({
-            url: '../studies/' + series.ParentStudy,
-            dataType: 'json',
-            cache: false,
-            success: function(study) {
-              var studyInstanceUid = study.MainDicomTags.StudyInstanceUID;
-              var seriesInstanceUid = series.MainDicomTags.SeriesInstanceUID;
-              window.open('../mammography-viewer/index.html?study=' + studyInstanceUid +
-                          '&series=' + seriesInstanceUid);
-            }
-          });
-        }
-      });
-    }
-  });
-});

dicom_sr_to_pdf.py

@@ -4,9 +4,10 @@ from pydicom.dataset import FileMetaDataset
 from pydicom.uid import MediaStorageDirectoryStorage, EncapsulatedPDFStorage, generate_uid
 import matplotlib
 matplotlib.use("Agg")  # Use non-GUI backend to avoid Tkinter issues
-import matplotlib.pyplot as plt  # Now import pyplot
+import matplotlib.pyplot as plt
 from reportlab.pdfgen import canvas
 from datetime import datetime, date
+import os
 
 
 def extract_measurements(sr):
@@ -28,10 +29,10 @@ def extract_measurements(sr):
     return measurements, probabilities
 
 
-def overlay_measurements(image, measurements, probabilities):
+def overlay_measurements(dcm_image_pixels, measurements, probabilities, image_path):
     """Overlays extracted measurements onto the mammography image."""
     fig, ax = plt.subplots()
-    ax.imshow(image, cmap='gray')
+    ax.imshow(dcm_image_pixels, cmap='gray')
 
     # Draw each polyline
     for i in range(0, len(measurements), 1):
@@ -44,11 +45,11 @@ def overlay_measurements(image, measurements, probabilities):
     ax.axis("off")
 
     # Save the overlay as an image
-    plt.savefig("temp.png", bbox_inches='tight', pad_inches=0)
+    plt.savefig(image_path, bbox_inches='tight', pad_inches=0)
     plt.close(fig)
 
 
-def create_pdf(temp_image_path, measurements, sr, pdf_path):
+def create_pdf(image_path, measurements, sr, pdf_path):
     """Creates a PDF with the mammography image and extracted measurements."""
     c = canvas.Canvas(pdf_path)
 
@@ -63,7 +64,7 @@ def create_pdf(temp_image_path, measurements, sr, pdf_path):
     # Reset font for other text
     c.setFont("Helvetica", 12)
 
-    # Add patient info to the PDF
+    # Add patient and study info to the PDF
     c.drawString(70, 800, f"Patient ID: {sr.PatientID}")
     c.drawString(70, 785, f"Patient name: {sr.PatientName}")
     c.drawString(70, 770, f"Patient birth date: {formateted_datetime(sr.PatientBirthDate)}")
@@ -73,13 +74,13 @@ def create_pdf(temp_image_path, measurements, sr, pdf_path):
     c.drawString(70, 700, f"Referring physician: {sr.ReferringPhysicianName}")
 
     # Add the image to the PDF
-    c.drawImage(temp_image_path, 70, 300)
+    c.drawImage(image_path, 70, 300)
 
     c.save()
 
-# Convert DICOM date
-def formateted_datetime(dicom_date, dicom_time = None):
 
+def formateted_datetime(dicom_date, dicom_time = None):
+    """Convert DICOM date and time format."""
     if dicom_date is None or dicom_date == '':
         return ''
 
@@ -98,7 +99,8 @@ def formateted_datetime(dicom_date, dicom_time = None):
     # Combined datetime
     return f"{formatted_date} {formatted_time}"
 
-def create_dcm_pdf(sr, pdf_path):
+
+def create_dcm_pdf(sr, pdf_path, instance_uid):
     ds = Dataset()
 
     # Add general DICOM metadata
@@ -123,7 +125,7 @@ def create_dcm_pdf(sr, pdf_path):
     ds.Manufacturer = "MammographyAI"
     ds.ConversionType = "DI"
 
-    ds.SOPInstanceUID = generate_uid()
+    ds.SOPInstanceUID = instance_uid
     ds.SOPClassUID = EncapsulatedPDFStorage
 
     # Open the PDF file and read it as binary data
@@ -156,8 +158,23 @@ def create_dcm_pdf(sr, pdf_path):
     
     return ds
 
-def create(image, sr):
+
+def create(dcm_image_pixels, sr):
+    instance_uid = generate_uid()
+    temp_image_path = f"{instance_uid}.png"
+    temp_pdf_path = f"{instance_uid}.pdf"
+    
     measurements, probabilities = extract_measurements(sr)
-    overlay_measurements(image, measurements, probabilities)
+    overlay_measurements(dcm_image_pixels, measurements, probabilities, temp_image_path)
-    create_pdf("temp.png", measurements, sr, "temp.pdf")
+    create_pdf(temp_image_path, measurements, sr, temp_pdf_path)
-    return create_dcm_pdf(sr, "temp.pdf",)
+    dcm_pdf = create_dcm_pdf(sr, temp_pdf_path, instance_uid)
+    
+    print("Current Working Directory:", os.getcwd())
+    
+    if os.path.exists(temp_image_path):
+        os.remove(temp_image_path)
+    
+    if os.path.exists(temp_pdf_path):
+        os.remove(temp_pdf_path)
+    
+    return dcm_pdf

mammography.py

@@ -24,6 +24,7 @@
 import sys
 import json
 import orthanc
+import os
 
 config = json.loads(orthanc.GetConfiguration()).get('Mammography', {})
 venv = config.get('VirtualEnv')
@@ -32,61 +33,7 @@ if venv != None:
     # https://orthanc.uclouvain.be/book/plugins/python.html#working-with-virtual-environments
     sys.path.insert(0, venv)
 
-
-##
-## Install the Stone Web viewer
-##
-
-STONE_VERSION = '2024-08-31-StoneWebViewer-DICOM-SR'
-VIEWER_PREFIX = '/mammography-viewer/'
-
-import os
 SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
-VIEWER_DIR = os.path.join(SCRIPT_DIR, 'viewer')
-
-sys.path.append(os.path.join(SCRIPT_DIR, '..'))
-import download
-
-os.makedirs(VIEWER_DIR, exist_ok = True)
-
-download.get(os.path.join(VIEWER_DIR, '%s.zip' % STONE_VERSION),
-             'https://github.com/jodogne/orthanc-mammography/raw/master/viewer/%s.zip' % STONE_VERSION,
-             4815178, '86b52a17f86e4769d12e9ae680c4a99f')
-
-import zipfile
-stone_assets = zipfile.ZipFile(os.path.join(VIEWER_DIR, '%s.zip' % STONE_VERSION))
-
-MIME_TYPES = {
-    '.css'  : 'text/css',
-    '.gif'  : 'image/gif',
-    '.html' : 'text/html',
-    '.jpeg' : 'image/jpeg',
-    '.js'   : 'text/javascript',
-    '.png'  : 'image/png',
-}
-
-def serve_stone_web_viewer(output, uri, **request):
-    if not uri.startswith(VIEWER_PREFIX):
-        output.SendHttpStatusCode(404)
-    elif request['method'] != 'GET':
-        output.SendMethodNotAllowed('GET')
-    else:
-        try:
-            path = '%s/%s' % (STONE_VERSION, uri[len(VIEWER_PREFIX):])
-            extension = os.path.splitext(path) [1]
-            if not extension in MIME_TYPES:
-                mime = 'application/octet-stream'
-            else:
-                mime = MIME_TYPES[extension]
-
-            with stone_assets.open(path) as f:
-                output.AnswerBuffer(f.read(), mime)
-        except:
-            output.SendHttpStatusCode(500)
-
-
-orthanc.RegisterRestCallback('%s(.*)' % VIEWER_PREFIX, serve_stone_web_viewer)
-
 
 ##
 ## Load the deep learning model