create_table :categories do |t|
    t.string :name, :null => false
    t.text :description
    t.boolean :user_defined
    t.timestamps
end

add_index :categories, :name

create_table :cat_values do |t|
	t.string :name, :null => false
	t.text :description
	t.boolean :user_defined
	t.references :category
	t.timestamps
end
add_index :cat_values, :category_id
add_index :cat_values, :name

create_table :subjects do |t|
    t.string :subject_tag, :null => false
    t.references :specimen, :null => false
    t.string :sex
    t.text :conditions
    t.float :age
    t.timestamps
end
add_index :subjects, :subject_tag
add_index :subjects, :specimen_id

create_table :experiments do |t|
    t.string :name, :null => false
    t.text :description
    t.date :exp_date
	t.references :tracer
	t.references :user, :null => false
	t.references :machine
	t.references :subject, :null => false
	t.boolean :is_gated
	t.string :data_description
	t.integer :data_compression
	t.integer :data_encode
	t.string :type_of_data
	t.integer :num_images
	t.string :image_data_format
	t.integer :num_energy_window
	t.boolean :flood_corrected
	t.boolean :decay_corrected
	t.integer :num_angle_steps
	t.integer :angle_start
	t.integer :total_angle_rotation
	t.integer :angle_direction
	t.integer :num_projections
	t.integer :extent_rotation
	t.string :process_status
	t.integer :time_per_projection
	t.integer :study_duration
	t.string :patient_orientation
	t.references :modality, :null => false
	t.string :type
	t.text :search_field
	t.timestamps
end
add_index :experiments, :modality_id
add_index :experiments, :user_id
add_index :experiments, :subject_id
add_index :experiments, :machine_id
add_index :experiments, :tracer_id
add_index :experiments, :exp_date


create_table :collimators do |t|
	t.integer :dect_number, :null => false
	t.references :experiment, :null => false
	t.string :collimator_type
	t.string :material
	t.float :radius
	t.float :length
	t.timestamps
end
add_index :collimators, :experiment_id

create_table :files do |t|
	t.string :filename, :null => false
	t.string :filetype, :null => false
	t.float :file_size
	t.text :location, :null => false
	t.text :description
	t.string :file_checksum
    t.integer :num_bytes_per_pixel
    t.string :image_byte_order
	t.timestamps
end

create_table :file_associations, :id => false do |t|
	t.references :experiment, :null => false
	t.references :file_1, :null => false
	t.references :file_2
    t.text :tags
	t.timestamps
end
add_index :file_associations, :experiment_id

create_table :vnvgeometries do |t|
	t.references :experiment, :null => false
	t.integer :NumVoxel_X
	t.integer :NumVoxel_Y
	t.integer :NumVoxel_Z
	t.integer :AttnZCount
	t.float :Voxel_Xwidth
	t.float :Voxel_Ywidth
	t.float :Voxel_Zwidth
	t.text :description
	t.timestamps
end
add_index :vnvgeometries, :experiment_id

create_table :machines do |t|
	t.string :name, :null => false
	t.string :company
	t.references :location, :null => false
	t.timestamps
end
add_index :machines, :name
add_index :machines, :location_id

create_table :detector_heads do |t|
    t.references :machine, :null => false
    t.timestamps
end
add_index :detector_heads, :machine_id

create_table :experiment_detectors do |t|
    t.references :experiment, :null => false
    t.references :detector_head, :null => false
    t.decimal :energy_window_lower_level
    t.decimal :energy_window_upper_level
    t.string :dect_material
    t.timestamps
end
add_index :experiment_detectors, :experiment_id
add_index :experiment_detectors, :detector_head_id

create_table :users do |t|
	t.string :username, :null => false
	t.string :firstname
	t.string :lastname
	t.string :email, :null => false
	t.string :department
	t.string :institution
	t.string :position
	t.string :crypted_password
	t.string :password_salt
	t.string :persistence_token
	t.timestamps
end
add_index :users, :username

create_table :roles do |t|
	t.string :name, :null => false
	t.string :description
	t.timestamps
end
add_index :roles, :name

create_table :user_roles, :id => false do |t|
	t.references :user, :null => false
 	t.references :role, :null => false
	t.timestamps
end
execute "ALTER TABLE user_roles ADD UNIQUE INDEX user_id_role_id (user_id, role_id)"

create_table :experiment_approvals, :id => false do |t|
  	t.references :experiment, :null => false
  	t.references :user
	t.timestamps
end
add_index :experiment_approvals, :experiment_id
add_index :experiment_approvals, :user_id