Merge pull request #286 from choosehappy/v2-ui

replace v1 UI with v2 UI

histoqc/ui/HQC_html.py

@@ -0,0 +1,116 @@
+from flask import render_template, Blueprint, request, current_app, send_file
+import os
+from argparse import Namespace
+from cohortfinder import runCohortFinder
+import json
+from PIL import Image
+import io
+# constants 
+cf_results_filename = 'results_cohortfinder.tsv'
+
+
+html = Blueprint('html', __name__, template_folder='templates')
+
+@html.route('/')
+def index():
+    return render_template('index.html')
+
+
+@html.route('/image_extensions/<foldername>', methods=['GET'])
+def image_extensions(foldername):
+    """
+    Returns the suffixes of the thumbnails that are available for a given folder.
+    """
+    folderpath = os.path.join(current_app.config['data_directory'], foldername)
+    thumbnail_suffixes = [f.split(foldername)[1] for f in os.listdir(folderpath) if f.endswith('.png')]
+    return thumbnail_suffixes
+
+
+@html.route('/image/<foldername>/<suffix>', methods=['GET'])
+@html.route('/image/<foldername>/<suffix>/<height>', methods=['GET'])
+def image(foldername, suffix, height=None):
+
+    # read image from file system and send over http
+    img_name = foldername + suffix
+    img_path = os.path.join(current_app.config['data_directory'], foldername, img_name)
+    # return send_from_directory(current_app.config['assets_path'], fn)
+    if height is None:
+        return send_file(img_path)
+    elif int(height) > 0:
+        # Read image from file system
+        img_path = os.path.join(current_app.config['data_directory'], foldername, img_name)
+        image_buffer = io.BytesIO()
+
+        image = Image.open(img_path)
+        height = int(height)
+        width = image.width * height // image.height
+        image.thumbnail((width, height))
+        image.save(image_buffer, format='PNG')
+        image_buffer.seek(0)
+
+        # Return the image buffer
+        return send_file(image_buffer, mimetype='image/png')
+
+
+@html.route('/results_path', methods=['GET'])
+def datadir():
+    results_path = os.path.join(current_app.config['data_directory'], current_app.config['results_filename'])
+    return results_path
+
+
+@html.route('/hqc_results', methods=['GET'])
+def hqc_results():
+    """
+    Returns the HQC results file as a Flask response object.
+    """
+    results_path = os.path.join(current_app.config['data_directory'], current_app.config['results_filename'])
+
+    # if the user provided an incorrect path, raise an error here.
+    if not os.path.isfile(results_path):
+        raise FileNotFoundError('The results file path provided is not valid: {}'.format(results_path))
+
+    current_app.logger.info('results file path: %s', results_path)
+
+    return send_file(results_path)
+
+
+@html.route('/run_cohort_finder', methods=['GET'])
+def run_cohort_finder():
+    # check if cohortFinder has already been run (with output saved)
+    fp = os.path.join(current_app.config['data_directory'], '**', cf_results_filename)[0]
+    if os.path.isfile(fp):
+        pass
+
+    current_app.logger.info('running CohortFinder...')
+    cf_args = Namespace()
+
+    # ---------------- default values ----------------
+
+    cf_args.labelcolumn = None
+    cf_args.sitecolumn = None
+    cf_args.patientidcolumn = None
+    cf_args.batcheffectsitetest = False
+    cf_args.batcheffectlabeltest = False
+    cf_args.randomseed = None
+    cf_args.resultsfilepath = os.path.join(current_app.config['data_directory'], current_app.config['results_filename'])
+    cf_args.disable_save = True
+    cf_args.quality_control_tool = "histoqc"
+
+    # ---------------- user input ----------------
+
+    cf_args.cols = request.args.get('featuresSelected')
+    cf_args.nclusters = int(request.args.get('numClusters'))
+    cf_args.testpercent = float(request.args.get('testSetPercent'))  
+    # add line to check if cohortFinder has already been run (with output saved). If so, load the results.tsv file and return.
+    output, sil_score, db_score, ch_score = runCohortFinder(cf_args)
+    out_dict = {
+        'embed_x': output['embed_x'].tolist(),
+        'embed_y': output['embed_y'].tolist(),
+        'groupid': output['groupid'].tolist(),
+        'testind': output['testind'].tolist(),
+        'sil_score': float(sil_score),
+        'db_score': float(db_score),
+        'ch_score': float(ch_score)
+    }
+
+    return out_dict