# LOCATION VARIABLES

#TODO: Ensure that these can be run from other machines easily.

location = 'data/stanford/'

clinical = location + 'labels/full_clinical_file.csv'

recurrence = location + 'labels/recurrence_cleaned.csv'

images = location + 'images_original/'

segs = location + 'segmentations_cleaned/'

cropped = location + 'cropped_nodules/'

pyradiomics = location + 'pyradiomics_features/'

genomics = location + 'genomics_cleaned.csv'

densenet = cropped

csv_location = location + 'labels/recurrence_labels/'

# OTHER VARIABLES

mutation_mapping = {'Mutant': 1,

                    'Wildtype': 0,

                    'Not collected': 'N/A',

                    'Unknown': 'N/A'}

recurrence_mapping = {'yes': 1, 'no': 0, 'Not collected': 'N/A'}

survival_mapping = {'Dead': 1, 'Alive': 0}

class_weights = {'Recurrence': {'no':0.3, 'yes':0.7},

                 'Survival Status': {'Dead':0.8, 'Alive':0.2}}

location_dict = {'Checked': 1, 'Unchecked':0}

smoking_dict = {'Nonsmoker': 0,

                'Former' : 1,

                'Current' : 2}

gg_dict = {'0%': 0,

           '>0 - 25%': 1,

           '25 - 50%': 2,

           '50 - 75%' : 3,

           '75 - < 100%' : 4,

           '100%' : 5,

           'Not Assessed': 0}