boilerplate pipeline

voluseg/VolusegProcessor.py

@@ -23,4 +23,59 @@ class VolusegProcessor(ProcessorBase):
     def run(
         context: VolusegContext
     ):
-        pass
+        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)