diff --git a/voluseg/VolusegProcessor.py b/voluseg/VolusegProcessor.py index d079d4c..3e8eeb1 100644 --- a/voluseg/VolusegProcessor.py +++ b/voluseg/VolusegProcessor.py @@ -23,4 +23,59 @@ class VolusegProcessor(ProcessorBase): def run( context: VolusegContext ): - pass \ No newline at end of file + import os + import lindi + import voluseg + + # set and save parameters + parameters0 = voluseg.parameter_dictionary() + parameters0["dir_ants"] = "/ants-2.5.3/bin/" + parameters0["dir_input"] = "/voluseg/data/" + parameters0["dir_output"] = "/tmp/voluseg_output" + + # user-defined parameters + parameters0["detrending"] = context.detrending + parameters0["registration"] = context.registration + parameters0["registration_restrict"] = context.registration_restrict + parameters0["diam_cell"] = context.diam_cell + parameters0["ds"] = context.ds + parameters0["planes_pad"] = context.planes_pad + parameters0["planes_packed"] = context.planes_packed + parameters0["parallel_clean"] = context.parallel_clean + parameters0["parallel_volume"] = context.parallel_volume + parameters0["save_volume"] = context.save_volume + parameters0["type_timepoints"] = context.type_timepoints + parameters0["type_mask"] = context.type_mask + parameters0["timepoints"] = context.timepoints + parameters0["f_hipass"] = context.f_hipass + parameters0["f_volume"] = context.f_volume + parameters0["n_cells_block"] = context.n_cells_block + parameters0["n_colors"] = context.n_colors + parameters0["res_x"] = context.res_x + parameters0["res_y"] = context.res_y + parameters0["res_z"] = context.res_z + parameters0["t_baseline"] = context.t_baseline + parameters0["t_section"] = context.t_section + parameters0["thr_mask"] = context.thr_mask + + voluseg.step0_process_parameters(parameters0) + filename_parameters = str( + os.path.join(parameters0["dir_output"], "parameters.json") + ) + parameters = voluseg.load_parameters(filename_parameters) + print("Parameters:\n", parameters) + + print("Process volumes...") + voluseg.step1_process_volumes(parameters) + + print("Align volumes...") + voluseg.step2_align_volumes(parameters) + + print("Mask volumes...") + voluseg.step3_mask_volumes(parameters) + + print("Detect cells...") + voluseg.step4_detect_cells(parameters) + + print("Clean cells...") + voluseg.step5_clean_cells(parameters) \ No newline at end of file