def _execute_sql_script(cls, name):
with app.app_context():
cursor = model.get_db().cursor()
filename = os.path.join(cls.RESOURCES_DIR, '{}.sql'.format(name))
with open(filename, 'r') as sql:
sqlscript = sql.read()
cursor.executescript(sqlscript)
cursor.close()
def get_context(patient_id=None):
context = {'theme': session['theme'] if 'theme' in session else 'dark'}
if patient_id:
db = model.get_db()
patient = db.execute(
'select p_first, p_last from patients where pid = ?',
(patient_id, )).fetchone()
context['patient_name'] = '{}, {}'.format(patient['P_Last'],
patient['P_First'])
return context
def manage():
db = model.get_db()
if request.method == 'POST':
if 'id' in request.form:
app.logger.info('Deleting patient with id {}'.format(
request.form['id']))
image_ids = []
for image in db.execute(
'select i.iid from images i \
join collections c on c.cid = i.cid where c.pid = ?',
(request.form['id'], )):
image_ids.append(image['IID'])
if len(image_ids):
s3delete(image_ids)
db.execute('delete from patients where pid = ?',
(request.form['id'], ))
else:
app.logger.info('Adding patient with name {} {}'.format(
request.form['f_name'], request.form['l_name']))
if request.form['f_name'] and request.form['l_name']:
first_name = request.form['f_name']
last_name = request.form['l_name']
db.execute(
'insert into patients(p_first, p_last) values (?, ?)', (
first_name,
last_name,
))
else:
flash('Error: patient name cannot be blank', 'error')
context = get_context()
context['items'] = []
for patient in db.execute('select pid, p_first, p_last from patients'):
context['items'].append({
'id':
patient['PID'],
'name':
'{}, {}'.format(patient['P_Last'], patient['P_First'])
})
return render_template('manage.html', **context)
def index():
db = model.get_db()
context = get_context()
context['patients'] = []
for patient in db.execute(
'select pid, p_first, p_last from patients order by p_last, p_first'
):
context['patients'].append({
'id':
patient['PID'],
'name':
'{}, {}'.format(patient['P_Last'], patient['P_First'])
})
return render_template('index.html', **context)
def manage_patient(patient_id):
db = model.get_db()
if request.method == 'POST':
if 'id' in request.form:
app.logger.info('Deleting collection with id {}'.format(
request.form['id']))
image_ids = []
for image in db.execute('select i.iid from images i where cid = ?',
(request.form['id'], )):
image_ids.append(image['IID'])
if len(image_ids):
s3delete(image_ids)
db.execute('delete from collections where cid = ?',
(request.form['id'], ))
context = get_context(patient_id)
context['items'] = []
for collection in db.execute(
'select c.cid, c.c_name, c.study \
from collections c where c.pid = ?', (patient_id, )):
# this might be able to be combined into the above query
count = db.execute(
'select count(*) as count from images where cid = ?',
(collection['CID'], )).fetchone()['count']
context['items'].append({
'id':
collection['CID'],
'name':
'{} ({} {})'.format(collection['C_Name'], count,
'images' if count != 1 else 'image')
})
return render_template('manage_patient.html', **context)
def upload(patient_id):
db = model.get_db()
if request.method == 'POST':
collection_id = int(request.form['collection'])
# collection_id < 0 means a new collection should be created
if collection_id < 0:
app.logger.info('Creating new collection with name {}'.format(
request.form['new_collection']))
if request.form['new_collection']:
db.execute(
'insert into collections(c_name, study, pid) values (?, ?, ?)',
(request.form['new_collection'], 'Other', patient_id))
collection_id = db.execute(
'select max(cid) as new_cid from collections').fetchone(
)['new_cid']
else:
collection_id = None
flash('Error: sequence name must not be blank', 'error')
if collection_id:
app.logger.info('Adding image(s) to collection with id {}'.format(
collection_id))
study = db.execute('select study from collections where cid = ?',
(collection_id, )).fetchone()['Study']
cur_idx = db.execute(
'select max(ind) as start_idx from images where cid = ?',
(collection_id, )).fetchone()['start_idx']
if not cur_idx:
cur_idx = 0
else:
cur_idx += 1
# TODO: add progress bar to show how many images are processed
for file in request.files.getlist('files'):
image_id = '{}.png'.format(uuid.uuid1())
print('[DEBUGGING] image_id is {}, file is {}'.format(
image_id, file))
# convert dicom to png. (based off of:
# https://github.com/pydicom/pydicom/issues/352#issuecomment-406767850)
try:
ds = pydicom.dcmread(file)
except pydicom.errors.InvalidDicomError:
flash('Error: Invalid dicom: {}'.format(file.filename),
'error')
continue
if study == 'Other':
study = ds.Modality
elif study != ds.Modality:
flash(
'Error: Image {} has a different modality than selected sequence'
.format(file.filename), 'error')
continue
try:
# 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)
image = png.from_array(image_2d_scaled, 'L')
# save image in memory and upload to s3
with io.BytesIO() as image_data:
image.save(image_data)
image_data.seek(0)
# upload image object
s3upload(image_id, image_data)
# insert into database once everything else has succeeded
db.execute(
'insert into images(iid, cid, ind) values (?,?,?)',
(image_id, collection_id, cur_idx))
cur_idx += 1
except NotImplementedError:
flash('Error converting image {}'.format(file.filename),
'error')
except RuntimeError:
flash('Error converting image {}'.format(file.filename),
'error')
if study != 'Other':
db.execute('update collections set study = ? where cid = ?', (
study,
collection_id,
))
context = get_context(patient_id=patient_id)
context['collections'] = []
for collection in db.execute(
'select cid, c_name, study from collections where pid = ?',
(patient_id, )):
context['collections'].append({
'id': collection['CID'],
'name': collection['C_Name']
})
return render_template('upload.html', **context)