ExampleGenFeatsParameters.txt

# version=param_v1.0.0

run_pipeline{

	# Set run to 0 to execute individual driver programs
	run=0

}

gen_feats{

	# Set window and frame width and height
	window_width=500
	window_height=500
	frame_width=250
	frame_height=250

	# Set to a txt file where each new line is the absolute path to a svs file
	image_files_list="/data/isip/exp/tuh_dpath/exp_0288/Machine-Learning-Applications-In-Digital-Pathology/ExampleImages.list"

	# Set to a txt file where each new line is the absolute path to the corresponding xml file of the svs files above
	annotation_files_list="/data/isip/exp/tuh_dpath/exp_0288/Machine-Learning-Applications-In-Digital-Pathology/ExampleAnnotations.list"

	# This is where the feature files, corresponding list of generated feature_files, and PCA joblib file will be output
	output_directory="/data/isip/exp/tuh_dpath/exp_0288/Machine-Learning-Applications-In-Digital-Pathology/nedc_mladp/data/example_features_output"

	
	# 1 to write feature files 0 to not write features
	write_features=1


	# Set minimum amount windows must overlap with a annotated region before they are considered a labelled frame
	window_region_overlap_threshold=.5

	## Begin of if fitting PCA

	# 0 if trained PCA doesn't exist
	existing_PCA=0

	# Number of components for PCA to train on
	PCA_components=2


	# Amount to compress exported PCA
	PCA_compression=0

	## End of if fitting PCA

	## Begin of if trained PCA does exist

	#PCA_path="some_path/PCA.joblib"

	## End of it trained PCA does exist
}