def add_patient(patient_id):
from forms import PatientForm
if patient_id:
id = int(patient_id.replace('P00', '').replace(
'P0', '').replace('P', ''))
patient = Patient.query.get(id)
else:
patient = Patient()
form = PatientForm(obj=patient)
if form.validate_on_submit():
if 'photo' not in request.files:
flash('No file part')
return redirect(request.url)
file = request.files['photo']
# if user does not select file, browser also
# submit an empty part without filename
if file.filename == '':
flash('No selected file')
return redirect(request.url)
if file and allowed_file(file.filename):
filename = uuid.uuid4().hex+'.' + \
secure_filename(file.filename).split('.')[-1].lower()
form.photo.data.save(os.path.join(
app.config['UPLOAD_FOLDER'], 'patients', filename))
form.populate_obj(patient)
patient.photo = filename
patient.gender = Gender(form.gender.data)
db.session.add(patient)
db.session.commit()
url = url_for('patient_profile', patient_id=repr(patient))
flash(
'Patient saved with ID: {}, <a href="{}">view patient profile</a>'.format(repr(patient), url))
return redirect(url_for('add_patient'))
return render_template('add-patient.html', form=form)
def patient():
form = PatientForm()
req = request.form
if form.validate_on_submit():
session["Patient"] = req.get("Patient")
session["age"] = req.get("age")
session["Schuljahre"] = req.get("Schuljahre")
session["gender"] = req.get("gender")
return redirect(url_for('messwerte'))
return render_template('patient.html', title='Patientendaten Extern',
form=form)
def patient_create():
patient_form_create = PatientForm()
if patient_form_create.validate_on_submit():
form_data = patient_form_create.data
id = patient_form_create.patient_id.data
qry = db.patient_insert_sql(form_data)
db.insert(qry)
flash('New patient record created', 'success')
return redirect(f'/patient_created/{id}.html')
return render_template('patient_create.html',
template_form=patient_form_create)
def setup():
pform = PatientForm()
error = None
if pform.validate_on_submit():
#user input
name = pform.name.data
dob = pform.dob.data
street = pform.street_address.data
city = pform.city.data
state = pform.state.data
country = pform.country.data
telephone = pform.telephone.data
patient = models.add_patient(name, dob, street, city, state, country, telephone)
error = 'A patient with that patient id already exists'
return redirect('/patient')
return render_template('setup.html', error = error, form = pform)
def editPatientData(id):
# Initialize form from forms.py
form = PatientForm()
# if form is sent back (POST) to the server
if form.validate_on_submit():
# capture data from form
form_data = form.data
# build SQL query in update table
qry = db.patient_update_sql(form_data)
# update table with new data
try:
db.insert(qry)
except:
flash('Not able to update patient record', 'warning')
return render_template(f'edit-patient-data.html',
template_form=form,
id=id)
# redirect user to patient updated page
return redirect(f'/patient_updated/{id}.html')
# get values for this row from the database
sql = f"SELECT * FROM patient WHERE patient_id = '{id}'"
res = db.query(sql)
# populate values to the form
form.patient_id.data = res[0][0]
form.name.data = res[0][1]
form.address_street.data = res[0][2]
form.address_city.data = res[0][3]
form.address_state.data = res[0][4]
form.address_zip.data = res[0][5]
form.phone.data = res[0][6]
form.admitted.data = res[0][7]
form.discharged.data = res[0][8]
form.county_id.data = res[0][9]
form.health_info.data = res[0][10]
form.age.data = res[0][11]
form.race.data = res[0][12]
form.gender.data = res[0][13]
return render_template('edit-patient-data.html', template_form=form, id=id)
def edit_patient(patient_id):
pform = PatientForm()
#return redirect('/login')
error = None
patient_details = models.get_patient(patient_id)
if pform.validate_on_submit():
#user input
name = pform.name.data
dob = pform.dob.data
street = pform.street_address.data
city = pform.city.data
state = pform.state.data
country = pform.country.data
telephone = pform.telephone.data
models.update_patient(patient_id, name, dob, street, city, state, country, telephone)
return redirect('/patient')
return render_template('edit_patient.html', id=patient_id, form = pform, existing=patient_details)
def form():
form = PatientForm()
print("form generated")
if form.validate_on_submit():
print("form submitted and succeeded")
feature = Features(age=int(escape(form.age.data)),
apoe4=int(escape(form.apoe4.data)),
mmse=escape(form.mmse.data),
adas11=escape(form.adas11.data),
adas13=escape(form.adas13.data),
ICV=escape(form.ICV.data),
Ventricles=escape(form.Ventricles.data),
Entorhinal=escape(form.Entorhinal.data),
CEREBRUM=escape(form.CEREBRUM.data),
HIPPO=escape(form.HIPPO.data),
CSF=escape(form.CSF.data),
RAVLT_immediate=escape(form.RAVLT_immediate.data),
ABETA=escape(form.ABETA.data),
FAQTOTAL=escape(form.FAQTOTAL.data),
PTGENDER=escape(form.PTGENDER.data),
PTMARRY=escape(form.PTMARRY.data),
PTEDUCAT=escape(form.PTEDUCAT.data),
PTRACCAT=escape(form.PTRACCAT.data))
mrn = escape(form.medicalRecordNum.data)
# here we need to take the raw form values for imaging data and turn them into ratios in respect to ICV
# print("feature 2: ", featureList[2])
db.session.add(feature)
db.session.commit()
to_predict_list = [
int(escape(form.age.data)),
int(escape(form.apoe4.data)),
int(escape(form.mmse.data)),
int(escape(form.adas11.data)),
int(escape(form.adas13.data)),
int(escape(form.ICV.data)),
float(escape(form.Ventricles.data)),
float(escape(form.Entorhinal.data)),
float(escape(form.CEREBRUM.data)),
float(escape(form.HIPPO.data)),
float(escape(form.CSF.data)),
int(escape(form.RAVLT_immediate.data)),
int(escape(form.ABETA.data)),
int(escape(form.FAQTOTAL.data)),
int(escape(form.PTGENDER.data)),
int(escape(form.PTMARRY.data)),
int(escape(form.PTEDUCAT.data)),
int(escape(form.PTRACCAT.data))
]
print(to_predict_list)
sample = np.array(to_predict_list)
result = ModelClassification(to_predict_list)
proba = LIME(to_predict_list, sample)
print("Patient Data Submitted!")
flash('Patient data has been submitted!', 'success')
return redirect(url_for('result', result=result, mrn=mrn, proba=proba))
return render_template('form.html', title='Form', form=form)
