Merge pull request #5 from eipm/update-ai-biopsy

Update ai biopsy

.dockerignore

@@ -1,4 +1,5 @@
 README.md
 
 data
+env
 .git

Dockerfile

@@ -1,18 +1,16 @@
-FROM python:3.6.8-stretch
+FROM python:3.7.9-buster
 #===============================#
 # Docker Image Configuration	#
 #===============================#
 LABEL vendor='Englander Institute for Precision Medicine' \
     description='AI Biopsy' \
-    maintainer='[email protected]' \
-    base_image='python' \
-    base_image_version='3.6.8-stretch' \
-    base_image_SHA256='sha256:ab2670ec57d486f73e49e7352de6a80b6767e3c996c1c0d0c158f17ae6f2d113'
+    maintainer='[email protected]'
 
 ENV APP_NAME='ai_biopsy' \
     TZ='US/Eastern' \
     AI_BIOPSY_SRC_DIR='/ai_biopsy/src/ai_biopsy_src' \
     PREDICT_DIR='/ai_biopsy/src/ai_biopsy_src/slim'
+
 ENV RESULT_DIR=${AI_BIOPSY}/result \
     PROCESS_DIR=${AI_BIOPSY}/process \
     PYTHONPATH=${PYTHONPATH}:${AI_BIOPSY}:${PREDICT_DIR}

README.md

@@ -1,11 +1,10 @@
-# AI Biopsy
-
-Needs to be updated
+<p align="center">
+    <img src="docs/images/logo.png" width="256">
+</p>
 
-[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+# AI Biopsy
 
-![AI Biopsy Logo](docs/images/logo.png)
+[![Python 3.7.9](https://img.shields.io/badge/python-3.7.9-blue.svg)](https://www.python.org/downloads/release/python-379/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 ## AI Biopsy Requirements
 

requirements.txt

@@ -1,37 +1,39 @@
-absl-py==0.7.0
-astor==0.7.1
-cachetools==2.1.0
-certifi==2018.10.15
+absl-py==0.10.0
+astor==0.8.1
+cachetools==4.1.1
+certifi==2020.6.20
 chardet==3.0.4
-Click==7.0
+Click==7.1.2
 CouchDB==1.2
-Flask==1.0.2
-Flask-Cors==3.0.7
+Flask==1.1.2
+Flask-Cors==3.0.9
 Flask-Uploads==0.2.1
 gast==0.2.2
-grpcio==1.15.0
-h5py==2.9.0
-idna==2.7
+grpcio==1.32.0
+h5py==2.10.0
+idna==2.10
 itsdangerous==1.1.0
-Jinja2==2.10
-Keras-Applications==1.0.6
+Jinja2==2.11.2
+Keras-Applications==1.0.8
 Keras-Preprocessing==1.0.5
-Markdown==3.0.1
-MarkupSafe==1.1.0
-numpy==1.15.2
-protobuf==3.6.1
+Markdown==3.2.2
+MarkupSafe==1.1.1
+numpy==1.16.0
+protobuf==3.13.0
 pyasn1==0.4.4
 pyasn1-modules==0.2.2
 pytz==2018.5
-requests==2.20.0
-rsa==4.0
-selenium==3.14.1
-six==1.12.0
-tensorboard==1.12.2
-tensorflow==1.12.0
+requests==2.24.0
+rsa==4.6
+selenium==3.141.0
+six==1.15.0
+tensorboard==1.15.0
+tensorflow==1.15.3
 termcolor==1.1.0
-urllib3==1.24
-virtualenv==16.2.0
-Werkzeug==0.14.1
+urllib3==1.25.10
+virtualenv==20.0.31
+Werkzeug==1.0.1
 opencv-python==4.0.0.21
-matplotlib==3.0.3
+matplotlib==3.3.2
+pydicom==2.0.0
+pypng==0.0.20

src/ai_biopsy_src/slim/predict.py

@@ -14,7 +14,7 @@
 session = tf.Session()
 
 def get_test_images(mypath):
-	return [mypath + '/' + f for f in listdir(mypath) if isfile(join(mypath, f)) and f.find('.jpg') != -1]
+	return [mypath + '/' + f for f in listdir(mypath) if isfile(join(mypath, f)) and f.find('.png') != -1]
 
 def transform_img_fn(path_list):
     out = []

src/api/app.py

@@ -9,6 +9,8 @@
 import glob
 import ntpath
 import datetime
+import numpy as np
+import png, pydicom
 from ast import literal_eval
 
 # Relative Imports
@@ -20,7 +22,7 @@
 STATIC_DIR = '/ai_biopsy/src'
 RESULT_DIR = '/ai_biopsy/src/ai_biopsy_src/result/'
 
-ALLOWED_EXTENSIONS = set(['jpg', 'png', 'tif', 'tiff'])
+ALLOWED_EXTENSIONS = set(['jpg', 'png', 'tif', 'tiff', 'dcm'])
 
 static_file_dir = os.path.join(STATIC_DIR, 'static')
 
@@ -103,10 +105,29 @@ def upload_image():
 
     # 3. Normalize images to jpeg format
     for image in glob.glob(os.path.join(request_dir, '*.*')):
-        img = cv2.imread(image)
-        os.remove(image)
-        filename = '%s.jpg' % os.path.splitext(image)[0]
-        cv2.imwrite(os.path.join(request_dir, filename), img)
+        filename = os.path.splitext(image)[0]
+        if os.path.splitext(image)[1] == '.dcm':
+            ds = pydicom.dcmread(image)
+            shape = ds.pixel_array.shape
+
+            # Convert to float to avoid overflow or underflow losses.
+            image_2d = ds.pixel_array.astype(float)
+
+            # Rescaling grey scale between 0-255
+            image_2d_scaled = (np.maximum(image_2d,0) / image_2d.max()) * 255.0
+
+            # Convert to uint
+            image_2d_scaled = np.uint8(image_2d_scaled)
+
+            # Write the PNG file
+            with open(os.path.join(request_dir, filename) + '.png' , 'wb') as png_file:
+                w = png.Writer(shape[1], shape[0], greyscale=True)
+                w.write(png_file, image_2d_scaled)
+        else:
+            img = cv2.imread(image)
+            os.remove(image)
+            filename = '%s.png' % filename
+            cv2.imwrite(os.path.join(request_dir, filename), img)
 
     # 4. Specify Output log
     output_filename = 'output_' + request_id + '.txt'

src/api/version.py

@@ -1,4 +1,4 @@
-version = '1.0.0'
+version = '1.1.0'
 
 def api_version():
     return version

src/static/assets/ai_biopsy.js

@@ -6,6 +6,8 @@ const baseApiUrl = 'api'
 let token = getCookie('ai-biopsy-auth');
 checkTokenAndRedirectIfEmpty();
 
+document.getElementById('year').innerHTML = new Date().getFullYear();
+
 setInterval(function(){
     checkTokenAndRedirectIfEmpty();
 }, 5000);
@@ -68,8 +70,8 @@ function average(array) {
 }
 
 function isAnImage(file) {
-    if (file && file.type) {
-        return file.type.startsWith('image/jpeg') || file.type.startsWith('image/png') || file.type.startsWith('image/tiff');
+    if (file && (file.type || file.name)) {
+        return file.type.startsWith('image/jpeg') || file.type.startsWith('image/png') || file.type.startsWith('image/tiff') || file.name.endsWith('.dcm');
     }
 
     return false;
@@ -198,6 +200,64 @@ function clearAllImageCards() {
     });
 };
 
+async function getDcmImage(file) {
+    const width = 256;
+    const height = 256;
+    let pixelData = null;
+
+    function str2ab(str) {
+        var buf = new ArrayBuffer(str.length*2); // 2 bytes for each char
+        var bufView = new Uint16Array(buf);
+        var index = 0;
+        for (var i=0, strLen=str.length; i<strLen; i+=2) {
+            var lower = str.charCodeAt(i);
+            var upper = str.charCodeAt(i+1);
+            bufView[index] = lower + (upper <<8);
+            index++;
+        }
+        return bufView;
+    };
+
+    const toBase64 = file => new Promise((resolve, reject) => {
+        const reader = new FileReader();
+        reader.readAsDataURL(file);
+        reader.onload = () => resolve(reader.result);
+        reader.onerror = error => reject(error);
+    });
+
+    const base64 = await toBase64(file);
+    const base64PixelData = base64.substring(base64.indexOf('base64,') + 'base64,'.length);
+    const pixelDataAsString = atob(base64PixelData);
+    pixelData = str2ab(pixelDataAsString);
+
+    function getPixelData() {
+        return pixelData;
+    }
+
+    var image = {
+        imageId: file.name,
+        minPixelValue : 0,
+        maxPixelValue : 257,
+        slope: 1.0,
+        intercept: 0,
+        windowCenter : 127,
+        windowWidth : 256,
+        getPixelData: getPixelData,
+        rows: height,
+        columns: width,
+        height: height,
+        width: width,
+        color: false,
+        columnPixelSpacing: .8984375,
+        rowPixelSpacing: .8984375,
+        sizeInBytes: width * height * 2
+    };
+
+    return new Promise((resolve) => {
+        resolve(image);
+    });
+}
+
 function createImagesUIFromFiles(files, imagesPlaceholder) {
     if (files === null || files === undefined || imagesPlaceholder === null || imagesPlaceholder === undefined) {
         return;
@@ -209,9 +269,7 @@ function createImagesUIFromFiles(files, imagesPlaceholder) {
         imagePlaceholder.id = `image-card-${file.name}`;
         imagePlaceholder.innerHTML = `
             <div class="card image-container">
-                <div class="card-image">
-                    <img alt="${file.name}" width="330px" />
-                </div>
+                <div class="card-image" ></div>
                 <div class="card-file-name">${file.name}</div>
                 
                 <div class="loader"></div> 
@@ -227,8 +285,18 @@ function createImagesUIFromFiles(files, imagesPlaceholder) {
                 </div>
             </div>`;
         imagesPlaceholder.appendChild(imagePlaceholder);
+        const cardImage = imagePlaceholder.getElementsByClassName('card-image')[0];
+
+        if (file.name.endsWith('.dcm')) {
+            cornerstone.enable(cardImage);
+            getDcmImage(file).then(function(image) {
+                cornerstone.displayImage(cardImage, image);
+            });
+        } else {
+            cardImage.innerHTML = `<img alt="${file.name}" width="330px" />`;
+        }
 
-        const image = imagePlaceholder.getElementsByTagName('img')[0];
+        const image = cardImage.children[0];
         const reader = new FileReader();
         reader.onload = function (e) {
             image.setAttribute('src', e.target.result);

src/static/index.html

@@ -6,6 +6,7 @@
         <link rel="stylesheet" href="assets/materialize.min.css">
         <link href="assets/font-material-icons.css" rel="stylesheet">
         <link href="assets/ai_biopsy.css" rel="stylesheet">
+        <script src="https://unpkg.com/cornerstone-core/dist/cornerstone.min.js"></script>
         <!-- Global site tag (gtag.js) - Google Analytics -->
         <script async src="https://www.googletagmanager.com/gtag/js?id=UA-53992417-18"></script>
         <script>
@@ -27,7 +28,7 @@
                     <label for="file-select" id="add-images-button" class="btn">
                         <i class="material-icons left">add</i>Add Images
                     </label>
-                    <input type="file" id="file-select" multiple="multiple" accept="image/jpeg, image/png, image/tiff" class="hidden" />
+                    <input type="file" id="file-select" multiple="multiple" class="hidden" />
                     <div id="error-message" class="error-message hidden">You can add up to 100 images</div>
                 </div >
 
@@ -53,8 +54,8 @@
             <div class="push"></div>
         </div>
         <footer>
-            <div>Copyright © 2019 Englander Institute for Precision Medicine</div>
-            <div>AI Biopsy Version 1.0.0</div>
+            <div>Copyright © <span id="year"></span> Englander Institute for Precision Medicine</div>
+            <div>AI Biopsy Version 1.1.0</div>
             <img alt="logo" class="footer-logo" src="assets/LOGO_ENGLANDER_2LINE_RGB.png">
          </footer>
 

src/static/login.html

@@ -31,8 +31,8 @@ <h5 class="login-title">Log in</h5>
             </div>
         </div>
         <footer>
-            <div>Copyright © 2019 Englander Institute for Precision Medicine</div>
-            <div>AI Biopsy Version 1.0.0</div>
+            <div>Copyright © <span id="year"></span> Englander Institute for Precision Medicine</div>
+            <div>AI Biopsy Version 1.1.0</div>
             <img alt="logo" class="footer-logo" src="assets/LOGO_ENGLANDER_2LINE_RGB.png">
         </footer>
         <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.2.1/jquery.min.js"></script>