<reponame>adamrehn/charcoal-morphotypes<filename>dataprep_morphotypes.py
#!/usr/bin/env python3
from common import Configuration
import cv2, os, shutil, sys

# The morphotype classification mappings that Emma generated by hand using Taxonomist
MAPPINGS = {
	'TypeC': [
		'BWIL2-4.5-5cm-Training-Data-IMG_0032-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0039-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0041-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0041-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0046-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0047-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0050-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0052-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0053-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0054-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0066-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0071-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0082-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0083-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0087-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0087-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0092-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0095-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0100-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0110-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0117-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0118-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0119-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0120-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0125-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0139-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0140-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0140-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0142-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0143-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0147-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0148-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0151-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0152-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0158-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0161-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0161-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0166-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0169-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0169-3.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0174-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0175-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0177-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0177-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0179-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0182-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0184-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0186-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0188-3.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0190-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0190-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0191-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0197-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0200-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0202-2.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0207-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0208-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0209-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0211-0.png',
		'MAR2-1-1.95m-32-32cm-Training-Data-IMG_9288-2.png',
		'MAR2-1-1.95m-32-32cm-Training-Data-IMG_9290-0.png',
		'MAR2-1-1.95m-32-32cm-Training-Data-IMG_9294-0.png',
		'MAR2-1-1.95m-40-41cm-Training-Data-IMG_9307-0.png',
		'MAR2-1-1.95m-48-49cm-Training-Data-IMG_9330-0.png',
		'MAR2-1-1.95m-48-49cm-Training-Data-IMG_9331-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0215-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0217-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0222-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0224-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0225-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0234-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0239-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_0240-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9200-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9203-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9204-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9208-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9214-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9215-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9219-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9220-1.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9222-0.png',
		'MAR2-1.95-2.9m-12-13cm-Training-Data-IMG_9223-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9693-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9702-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9710-1.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9718-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9728-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9735-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9736-1.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9739-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9751-0.png',
		'MAR2-1.95-2.9m-4-5cm-Training-Data-IMG_9766-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_0001-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_0006-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_0006-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9787-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9793-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9806-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9806-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9808-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9812-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9816-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9817-7.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9818-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9820-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9821-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9822-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9822-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9823-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9824-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9825-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9829-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9831-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9833-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9834-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9834-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9837-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9837-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9838-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9840-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9841-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9842-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9842-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9843-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9844-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9844-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9844-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9856-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9856-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9857-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9857-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9858-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9859-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9859-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9861-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9862-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9863-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9864-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9867-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9867-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9870-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9875-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9876-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9877-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9877-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9877-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9879-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9881-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9882-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9882-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9884-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9886-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9889-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9889-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9889-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9891-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9894-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9902-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9903-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9905-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9906-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9909-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9914-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9917-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9917-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9918-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9919-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9922-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9922-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9926-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9928-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9931-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9931-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9933-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9936-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9936-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9942-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9944-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9945-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9945-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9947-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9948-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9949-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9952-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9952-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9953-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9954-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9955-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9959-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9966-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9966-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9971-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9971-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9972-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9973-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9976-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9978-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9979-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9984-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9986-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9987-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9995-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9996-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9997-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9998-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9998-3.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0533-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0541-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0543-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0546-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0551-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0555-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0556-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0566-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0567-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0574-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0576-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0577-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0580-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0581-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0581-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0582-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0582-5.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0583-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0594-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0594-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0595-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0600-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0601-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0605-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0606-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0613-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0624-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0626-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0629-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0630-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0631-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0633-0.png',
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		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9924-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9925-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9925-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9927-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9929-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9930-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9933-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9934-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9934-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9938-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9940-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9942-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9946-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9949-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9949-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9949-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9951-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9951-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9952-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9953-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9953-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9956-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9956-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9957-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9958-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9958-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9959-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9959-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9962-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9967-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9967-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9969-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9970-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9974-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9975-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9975-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9976-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9976-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9977-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9978-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9979-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9981-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9982-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9986-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9987-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9989-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9996-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9998-4.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0530-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0531-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0536-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0537-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0539-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0547-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0548-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0553-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0558-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0560-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0562-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0563-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0568-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0571-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0575-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0577-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0578-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0586-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0596-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0598-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0599-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0604-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0607-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0611-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0614-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0614-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0617-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0620-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0623-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0628-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0631-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0632-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0632-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0641-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0645-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0651-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0654-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0655-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0657-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0659-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0667-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0670-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0673-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0676-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0681-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0683-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0685-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0686-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0687-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0688-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0689-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0691-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0692-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0714-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0714-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0801-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0810-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0810-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0818-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_1434-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_1478-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1750-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1751-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1752-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1755-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1758-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1762-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1763-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1769-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1770-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1773-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1775-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1776-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1782-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1785-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1786-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1787-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1790-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1791-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1792-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1793-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1802-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1803-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1808-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1812-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1816-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1823-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9850-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9852-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9860-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9862-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9863-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9867-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9871-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9873-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9873-1.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9874-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0001-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0002-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0003-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0013-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0014-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0015-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0019-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-4.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0030-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0033-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0040-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0044-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0060-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0062-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0064-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0064-6.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0065-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0075-7.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0077-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0077-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0078-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0081-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0089-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0090-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0094-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0094-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0095-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0096-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0099-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0111-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0114-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0115-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0115-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0119-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0119-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0120-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0121-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0124-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0125-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0128-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0128-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0130-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-4.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-5.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0155-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0166-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0176-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0181-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0182-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0186-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0191-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0192-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0192-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0195-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0205-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0207-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0209-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0210-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0212-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0215-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0220-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0220-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0221-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9726-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9733-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9734-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9741-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9742-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9742-1.png'
	]
}

# Retrieve our input and output directory paths
inputDir = Configuration.path('segmentation_data_sliced')
outputDir = Configuration.path('classification_data')

# Iterate over each morphotype and copy the relevant files
for morphotype, images in MAPPINGS.items():
	
	# Ensure the subdirectory for the morphotype exists and is empty
	subdir = os.path.join(outputDir, morphotype)
	if os.path.exists(subdir) == True:
		shutil.rmtree(subdir)
	os.makedirs(subdir)
	
	# Progress output
	print('Copying {} images for morphotype {}...'.format(len(images), morphotype))
	sys.stdout.flush()
	
	# Copy each of the image files for the morphotype, stripping out the alpha channel
	# (Note: removing the alpha channel here isn't strictly necessary since the classification network will ignore it anyway,
	#  but doing so results in a better visual result when we generate the HTML report for the classification network.)
	for image in images:
		channels = cv2.imread(os.path.join(inputDir, image), flags=cv2.IMREAD_COLOR)
		cv2.imwrite(os.path.join(subdir, image), channels)

# Progress output
print('Done.')

#!/usr/bin/env python3
from common import Configuration
import cv2, os, shutil, sys

# The morphotype classification mappings that Emma generated by hand using Taxonomist
MAPPINGS = {
	'TypeC': [
		'BWIL2-4.5-5cm-Training-Data-IMG_0032-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0039-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0041-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0041-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0046-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0047-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0050-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0052-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0053-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0054-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0066-1.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0071-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0082-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0083-0.png',
		'BWIL2-4.5-5cm-Training-Data-IMG_0087-0.png',
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		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9949-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9951-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9951-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9952-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9953-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9953-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9956-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9956-4.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9957-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9958-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9958-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9959-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9959-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-5.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9960-6.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9962-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9967-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9967-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9969-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9970-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9974-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9975-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9975-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9976-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9976-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9977-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9978-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9979-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9981-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9982-0.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9986-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9987-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9989-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-1.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9992-3.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9996-2.png',
		'MAR2-1.95-2.9m-8-9cm-Training-Data-IMG_9998-4.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0530-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0531-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0536-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0537-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0539-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0547-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0548-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0553-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0558-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0560-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0562-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0563-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0568-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0571-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0575-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0577-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0578-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0586-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0596-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0598-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0599-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0604-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0607-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0611-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0614-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0614-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0617-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0620-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0622-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0623-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0628-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0631-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0632-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0632-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0641-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0645-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0651-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0654-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0655-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0657-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0659-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0667-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0670-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0673-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0676-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0681-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0683-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0685-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0686-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0687-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0688-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0689-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0691-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0692-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0714-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0714-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0801-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0810-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0810-1.png',
		'SAN1-3-3.5cm-Training-Data-IMG_0818-2.png',
		'SAN1-3-3.5cm-Training-Data-IMG_1434-0.png',
		'SAN1-3-3.5cm-Training-Data-IMG_1478-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1750-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1751-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1752-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1755-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1758-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1762-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1763-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1769-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1770-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1773-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1775-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1776-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1782-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1785-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1786-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1787-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1790-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1791-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1792-0.png',
		'SAN1-5-5.5cm-Training-Data-IMG_1793-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1802-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1803-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1808-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1812-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1816-0.png',
		'SAN1-5.5-6cm-Training-Data-IMG_1823-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9850-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9852-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9860-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9862-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9863-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9867-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9871-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9873-0.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9873-1.png',
		'SAN1-7.5-8cm-Training-Data-IMG_9874-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0001-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0002-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0003-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0013-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0014-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0015-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0019-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0020-4.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0030-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0033-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0040-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0044-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0060-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0062-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0064-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0064-6.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0065-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0075-7.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0077-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0077-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0078-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0081-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0089-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0090-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0094-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0094-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0095-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0096-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0099-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0111-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0114-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0115-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0115-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0119-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0119-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0120-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0121-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0124-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0125-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0128-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0128-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0130-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0131-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-4.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0153-5.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0155-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0166-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0176-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0181-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0182-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0186-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0190-3.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0191-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0192-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0192-2.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0195-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0205-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0207-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0209-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0210-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0212-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0215-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0220-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0220-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_0221-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9726-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9733-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9734-1.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9741-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9742-0.png',
		'SAN1-7-7.5cm-Training-Data-IMG_9742-1.png'
	]
}

# Retrieve our input and output directory paths
inputDir = Configuration.path('segmentation_data_sliced')
outputDir = Configuration.path('classification_data')

# Iterate over each morphotype and copy the relevant files
for morphotype, images in MAPPINGS.items():
	
	# Ensure the subdirectory for the morphotype exists and is empty
	subdir = os.path.join(outputDir, morphotype)
	if os.path.exists(subdir) == True:
		shutil.rmtree(subdir)
	os.makedirs(subdir)
	
	# Progress output
	print('Copying {} images for morphotype {}...'.format(len(images), morphotype))
	sys.stdout.flush()
	
	# Copy each of the image files for the morphotype, stripping out the alpha channel
	# (Note: removing the alpha channel here isn't strictly necessary since the classification network will ignore it anyway,
	#  but doing so results in a better visual result when we generate the HTML report for the classification network.)
	for image in images:
		channels = cv2.imread(os.path.join(inputDir, image), flags=cv2.IMREAD_COLOR)
		cv2.imwrite(os.path.join(subdir, image), channels)

# Progress output
print('Done.')
#!/usr/bin/env python3 # The morphotype classification mappings that Emma generated by hand using Taxonomist # Retrieve our input and output directory paths # Iterate over each morphotype and copy the relevant files # Ensure the subdirectory for the morphotype exists and is empty # Progress output # Copy each of the image files for the morphotype, stripping out the alpha channel # (Note: removing the alpha channel here isn't strictly necessary since the classification network will ignore it anyway, #  but doing so results in a better visual result when we generate the HTML report for the classification network.) # Progress output