def test_no_activity(self):
f = Flywheel()
start_waiting = datetime.datetime.now()
second_count = f.wait_for_flywheel_to_stop(gui_q)
finish_waiting = datetime.datetime.now()
time_spent_waiting = timedelta_milliseconds(finish_waiting -
start_waiting)
self.assertAlmostEquals(time_spent_waiting / 1000,
NUM_SECONDS_INACTIVITY_PERIOD, 0)
self.assertEqual(second_count, NUM_SECONDS_INACTIVITY_PERIOD)
def add_n_spins_with_n_seconds_between_spins(self, num_spins,
delay_between_spins):
f = Flywheel()
#start new thread that adds n flywheel spins with n seconds between spins
try:
thread.start_new_thread(flywheel_simulated_input, (
num_spins,
delay_between_spins,
))
except:
print "Error: Unable to start thread"
start_waiting = datetime.datetime.now()
second_count = f.wait_for_flywheel_to_stop(gui_q)
finish_waiting = datetime.datetime.now()
time_spent_waiting = timedelta_milliseconds(finish_waiting -
start_waiting) / 1000
reset_time = NUM_SECONDS_INACTIVITY_PERIOD + (num_spins *
delay_between_spins)
self.assertAlmostEquals(time_spent_waiting, reset_time, 1)
self.assertEquals(second_count, NUM_SECONDS_INACTIVITY_PERIOD, 0)
import os
from os.path import join as pjoin
from subprocess import call, Popen, PIPE
from flywheel import Flywheel
import time
import sys
import pdb
#sys.path.insert(0, '/oak/stanford/groups/menon/projects/chamblin')
#from helper_funcs import print_out, split_path
from studies_template import studies_template, studies_rules
#log = open('../logs/fw_download_%s.log' % time.strftime('%m-%d-%Y'), 'w+')
#Get flywheel credentials
fw = Flywheel('lucascenter.flywheel.io:oglHDMF0DnDeKPmDnl')
me = fw.get_current_user()
#Generate a list of all scanids currently in rawdata_scsnl
rawdata_scanids = []
rawdata_root = '/oak/stanford/groups/menon/rawdata/scsnl'
pids = os.listdir(rawdata_root)
for pid in pids:
visits = os.listdir(pjoin(rawdata_root, pid))
for visit in visits:
sessions = os.listdir(pjoin(rawdata_root, pid, visit))
for session in sessions:
if session == 'assessments':
continue
sessnum = session[-1]
visitnum = visit[-1]
scanid = pid + '_' + visitnum + '_' + sessnum
from os.path import join as pjoin
from subprocess import call, Popen, PIPE
from flywheel import Flywheel
import flywheel
import time
import sys
#import pdb
#sys.path.insert(0, '/oak/stanford/groups/menon/projects/chamblin')
#from helper_funcs import print_out, split_path
#from studies_template import studies_template, studies_rules
#PARAMETERS
SUBLIST = 'mathwhiz_subjects.txt'
#Get flywheel credentials
fw = Flywheel('lucascenter.flywheel.io:oglHDMF0DnDeKPmDnl')
me = fw.get_current_user()
#listify file of scanids
study = SUBLIST.split('_subjects.txt')[0]
file = open(
pjoin(
'/oak/stanford/groups/menon/scsnlscripts/utilities/dataOrganization/study_sublists',
SUBLIST), 'r')
scans = file.readlines()
scans = [x.strip() for x in scans]
#generate dictionary of project ids to study names
projects_full = fw.get_all_projects()
#print(fw_projects_full)
projects_thin = {}
#Downloaded scanids (Set this!!!!)
downloaded_scanids = [['8088', 'visit1', 'session1'],
['0059', 'visit2', 'session1'],
['7483', 'visit7', 'session1'],
['7943', 'visit3', 'session1'],
['0224', 'visit2', 'session1'],
['0224', 'visit2', 'session2'],
['0281', 'visit2', 'session1'],
['0098', 'visit2', 'session1'],
['8082', 'visit2', 'session1'],
['7863', 'visit2', 'session1'],
['0098', 'visit2', 'session2']]
#Get flywheel credentials
fw = Flywheel('lucascenter.flywheel.io:oglHDMF0DnDeKPmDnl')
me = fw.get_current_user()
projects_full = fw.get_all_projects()
#print(fw_projects_full)
projects_thin = {}
for project in projects_full:
projects_thin[project['_id']] = project['label']
#Generate a list of all scanids currently in rawdata_scsnl
rawdata_scanids = []
rawdata_root = '/oak/stanford/groups/menon/rawdata/scsnl'
pids = os.listdir(rawdata_root)
for pid in pids:
visits = os.listdir(pjoin(rawdata_root, pid))
for visit in visits:
if not re.match('^[a-zA-Z0-9][a-zA-Z0-9_-]+$', GroupTagsBy):
print('Group By Tags is invalid.')
print(
'Valid values are: blank, alphanumeric including dashes and underscores'
)
sys.exit(1)
else:
GroupTagsBy = ""
# Load Flywheel Python SDK
print('Loading Python SDK')
from flywheel import Flywheel
# Get temporary API key
api_key = str(config['inputs']['api_key']['key'])
fw = Flywheel(api_key)
# Get fileid
fileid = config['inputs']['file']['hierarchy']['id']
# get project information from file
acquisition = fw.get_acquisition(fileid)
session = fw.get_session(acquisition['session'])
project = fw.get_project(session['project'])
projectid = project['_id']
projectname = project['label']
# read CSV into list
print('Reading in CSV')
csv_data = pd.read_csv(input_filepath)
csv_columns = csv.columns
0,
0,
tzinfo=tzutc())
end_date_dt = datetime.datetime(end_date[0],
end_date[1],
end_date[2],
23,
0,
0,
0,
tzinfo=tzutc())
start_date_unix = time.mktime(start_date_dt.timetuple())
end_date_unix = time.mktime(end_date_dt.timetuple())
fw = Flywheel('lucascenter.flywheel.io:oglHDMF0DnDeKPmDnl')
me = fw.get_current_user()
#generate dictionary of project ids to study names
projects_full = fw.get_all_projects()
#print(fw_projects_full)
projects_thin = {}
for project in projects_full:
projects_thin[project['label']] = project['_id']
projects_thin_inverted = dict([[v, k] for k, v in projects_thin.items()])
exams_full = fw.get_all_sessions()
print('scanid,timestamp,project')
for exam in exams_full: