def getRiMappedImage(case_id, index_1, index_2):
#if username is in session then the call is web call, so use that username
if 'username' in session and len(session['username']) > 0:
username = session['username']
elif 'key' not in request.args or len(request.args['key']) == 0:
abort(403)
return ""
else:
auth_result = Auth.checkKeyValidity(request.args['key'])
if not auth_result['valid']:
abort(403)
return ""
username = auth_result['username']
if not PatientCases.userHasAuthentication(case_id, username):
abort(403)
return ""
#TODO get the ri-buffer from a controller module and send it to the Response
#for testing only
f = PatientCases.findImage(case_id, index_1, index_2)
if f == None:
abort(404)
buffer = Conversions(f['disk_filename']).dicomToRIColoredImage()
return Response(buffer, mimetype='image/jpeg')
def getAllCaseImages(case_id):
result = {'error': {}}
#if username is in session then the call is web call, so use that username
if 'username' in session and len(session['username']) > 0:
username = session['username']
else:
if 'key' not in request.args or len(request.args['key']) == 0:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not specified"
return jsonify(result)
auth_result = Auth.checkKeyValidity(request.args['key'])
if not auth_result['valid']:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not valid"
return jsonify(result)
username = auth_result['username']
if not PatientCases.userHasAuthentication(case_id, username):
result['error']['error'] = True
result['error'][
'error_msgessage'] = "logged in user do not have permission to acccess this case"
return jsonify(result)
case_result = PatientCases.findCase(case_id)
if case_result == None:
result['error']['error'] = True
result['error']['error_msgessage'] = "Case id not valid"
return jsonify(result)
#Now that the authentication is done process the result and respond according to the api refference
#take the files from the case result
files = case_result['files']
result['error']['error'] = False
result['images'] = []
i = 0 #to keep track of index_1
for file in files:
series = {}
series['series_description'] = file['series_description']
series['series_time'] = file['series_time']
series['images'] = []
j = 0 #to keep track of index_2
for image in file['images']:
img = {}
img['filename'] = image['org_filename']
img['url'] = BASE_URL + url_for('patient_cases_api.getImage',
case_id=case_id,
index_1=i,
index_2=j)
j += 1
series['images'].append(img)
i += 1
result['images'].append(series)
return jsonify(result)
def getSeriesRiImages(case_id, index_1):
result = {'error': {}}
#if username is in session then the call is web call, so use that username
if 'username' in session and len(session['username']) > 0:
username = session['username']
else:
if 'key' not in request.args or len(request.args['key']) == 0:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not specified"
return jsonify(result)
auth_result = Auth.checkKeyValidity(request.args['key'])
if not auth_result['valid']:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not valid"
return jsonify(result)
username = auth_result['username']
if not PatientCases.userHasAuthentication(case_id, username):
result['error'][
'error_msgessage'] = "logged in user do not have permission to acccess this case"
return jsonify(result)
series_result = PatientCases.findSeries(case_id, index_1)
if series_result == None:
result['error']['error'] = True
result['error']['error_msgessage'] = "Case id not valid"
return jsonify(result)
if 't2' not in series_result[
'series_description'] and 'T2' not in series_result[
'series_description']:
result['error']['error'] = True
result['error'][
'error_msgessage'] = "The series selected is not a T2 series. Cannot be RI mapped"
return jsonify(result)
result['error']['error'] = False
result['images'] = []
i = 0
for image in series_result['images']:
img = {}
img['filename'] = image['org_filename']
img['url'] = BASE_URL + url_for('patient_cases_api.getRiMappedImage',
case_id=case_id,
index_1=index_1,
index_2=i)
i += 1
result['images'].append(img)
return jsonify(result)
def getImage(case_id, index_1, index_2):
# get the case from db
series = PatientCases.findSeries(case_id, index_1)
if series == None:
abort(404)
elif PatientCases.userHasAuthentication(case_id, session['username']):
result = {
'status': 'success',
'series': series,
'index_1': index_1,
'index_2': index_2
}
else:
result = {
'status': 'error',
'msg':
'You do not have sufficient authentication to access the file'
}
return render_template('image-view.html', result=result)
def getImageCount(case_id, index_1):
result = {'error': {}}
#if username is in session then the call is web call, so use that username
if 'username' in session and len(session['username']) > 0:
username = session['username']
else:
if 'key' not in request.args or len(request.args['key']) == 0:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not specified"
return jsonify(result)
auth_result = Auth.checkKeyValidity(request.args['key'])
if not auth_result['valid']:
result['error']['error'] = True
result['error']['error_msgessage'] = "key not valid"
return jsonify(result)
username = auth_result['username']
if not PatientCases.userHasAuthentication(case_id, username):
result['error']['error'] = True
result['error'][
'error_msgessage'] = "logged in user do not have permission to acccess this case"
return jsonify(result)
series_result = PatientCases.findSeries(case_id, index_1)
if series_result == None:
result['error']['error'] = True
result['error']['error_msgessage'] = "Case id not valid"
return jsonify(result)
result['error']['error'] = False
result['count'] = len(series_result['images'])
return jsonify(result)
def analyseSingleImage(case_id, index_1, index_2):
result = {'error': {'error': False}}
#if username is in session then the call is web call, so use that username
if 'username' in session and len(session['username']) > 0:
username = session['username']
elif 'key' not in request.args or len(request.args['key']) == 0:
abort(403)
return ""
else:
auth_result = Auth.checkKeyValidity(request.args['key'])
if not auth_result['valid']:
abort(403)
return ""
username = auth_result['username']
if not PatientCases.userHasAuthentication(case_id, username):
abort(403)
return ""
f = PatientCases.findImage(case_id, index_1, index_2)
if f == None:
return abort(404)
result['error']['error'] = False
if 're_analysis' not in request.args or request.args[
're_analysis'] == 'false':
analysis = AnalysisResult.findByCase(case_id, index_1, index_2)
if analysis == None:
flag = True
else:
analysis['error'] = result['error']
analysis['analysis_image'] = BASE_URL + url_for(
'patient_cases_api.analysisImage',
case_id=case_id,
index_1=index_1,
index_2=index_2,
analysis_id=str(analysis['_id']))
#pop fields that are not required as response to api
analysis_index = 0
for infected_area in analysis['infected_areas']:
#pop fields that are not required as response to api
infected_area.pop('points')
infected_area.pop('box_width')
infected_area.pop('box_height')
#add the update url
infected_area['update_actual_result_url'] = BASE_URL + url_for(
'patient_cases_api.uploadAnlysis',
case_id=case_id,
index_1=index_1,
index_2=index_2,
analysis_id=str(analysis['_id']),
analysis_index=analysis_index)
analysis_index += 1
#pop fields that are not required as response to api
analysis.pop('_id')
analysis.pop('case_id')
analysis.pop('index_1')
analysis.pop('index_2')
return jsonify(analysis)
else:
flag = True
if flag:
dicom = Conversions(f['disk_filename'])
cluster = SingleClusterer(dicom)
result['infected_areas'] = []
infected_areas = []
AnalysisResult.delete(case_id, index_1, index_2)
for _disease_key in cluster.diseases.keys():
disease_clusters = cluster.diseases_clusters[_disease_key]
if len(disease_clusters.keys()) > 0:
for disease_cluster_key in disease_clusters.keys():
c = disease_clusters[disease_cluster_key]
c.compute()
#c.searchForDiseases()
i_area = {}
i_area['detected_result'] = _disease_key
i_area['coordinate'] = c.p1
i_area['area'] = c.getTightArea()
i_area['tumor_width'] = c.tumorwidth
i_area['tumor_height'] = c.tumorheight
i_area['average_chemical_composition'] = {
'x': (0, 0.5, 0.8, 1.3, 1.4, 1.5, 1.6, 1.8, 2, 2.4,
2.6, 2.8, 3, 3.2, 3.4, 3.6, 3.7, 3.9, 4, 4.4),
'y':
c.getAverageChemicalComposition(),
'labels':
('', '', 'LIP', '', 'LAC', '', '', '', 'NAA', 'GLM',
'', '', 'CR', '', 'CHO', '', 'MI', '', 'CR2', '')
}
infected_areas.append(
InfectedAreas((c.p1[0], c.p1[1]), c.getWidth(),
c.getHeight(), c.tumorwidth,
c.tumorheight,
i_area['average_chemical_composition'],
c.getArea(), _disease_key, c.elements))
result['infected_areas'].append(i_area)
#result['diseases'].append(disease)
if len(infected_areas) != 0:
analysisResult = AnalysisResult(case_id, index_1, index_2,
infected_areas)
analysis_id = analysisResult.save()
result['analysis_image'] = BASE_URL + url_for(
'patient_cases_api.analysisImage',
case_id=case_id,
index_1=index_1,
index_2=index_2,
analysis_id=analysis_id)
analysis_index = 0
for infected_area in result['infected_areas']:
infected_area['update_actual_result_url'] = BASE_URL + url_for(
'patient_cases_api.uploadAnlysis',
case_id=case_id,
index_1=index_1,
index_2=index_2,
analysis_id=analysis_id,
analysis_index=analysis_index)
analysis_index += 1
return jsonify(result)
'status': 'success',
'cases': cases
})
#the page to view all the series in a case
#return 403 if the logged in user is not authorized to access the image
@case_bp.route('/<case_id>/images/', methods=['GET'])
@case_bp.route('/<case_id>/', methods=['GET'])
@login_required
def getCase(case_id):
# get the case from db
case = PatientCases.findCase(case_id)
if case == None:
abort(404)
elif PatientCases.userHasAuthentication(case_id, session['username']):
result = {'status': 'success', 'case': case}
else:
result = {
'status': 'error',
'msg':
'You do not have sufficient authentication to access the file'
}
return render_template('series-view.html', result=result)
#the page to view all the images in a series
#return 403 if the logged in user is not authorized to access the image
@case_bp.route('/<case_id>/images/<int:index_1>/', methods=['GET'])
@case_bp.route('/<case_id>/<int:index_1>/', methods=['GET'])
@login_required