[general]
raw_files = "images/*.silc"
pixel_size = 28
log_level = "INFO"
log_file = "pyopia.log"

[steps.classifier]
pipeline_class = "pyopia.classify.Classify"
model_path = "pyopia-default-classifier-20250409.keras"

[steps.load]
pipeline_class = "pyopia.instrument.silcam.SilCamLoad"

[steps.correctbackground]
pipeline_class = "pyopia.background.CorrectBackgroundAccurate"
average_window = 5
bgshift_function = "accurate"
image_source = "imraw"
divide_bg = true

[steps.imageprep]
pipeline_class = "pyopia.instrument.silcam.ImagePrep"
image_level = "im_corrected"

[steps.segmentation]
pipeline_class = "pyopia.process.Segment"
threshold = 0.85
segment_source = "im_minimum"

[steps.statextract]
pipeline_class = "pyopia.process.CalculateStats"
export_outputpath = "roi"
roi_source = "imref"

[steps.output]
pipeline_class = "pyopia.io.StatsToDisc"
output_datafile = "processed/testpyopia"
append = false
project_metadata_file = "metadata.json"
auxillary_data_file = "auxillarydata/auxillary_data.csv"