Fix bugs

superdsm/c2freganal.py

@@ -123,7 +123,7 @@ class C2F_RegionAnalysis(repype.stage.Stage):
     inputs  = ['y', 'dsm_cfg']
     outputs = ['y_mask', 'atoms', 'adjacencies', 'seeds', 'clusters']
 
-    def process(y, dsm_cfg, pipeline, config, status=None):
+    def process(self, y, dsm_cfg, pipeline, config, status=None):
         seed_connectivity = config.get('seed_connectivity', 8)
         min_atom_radius = config.get('min_atom_radius', 15)
         max_atom_norm_energy = config.get('max_atom_norm_energy', 0.05)
@@ -187,7 +187,7 @@ def process(y, dsm_cfg, pipeline, config, status=None):
             'clusters': clusters
         }
 
-    def configure(pipeline, input_id, *args, radius, **kwargs):
+    def configure(self, pipeline, input_id, *args, radius, **kwargs):
         return {
             'min_atom_radius': (radius, 0.33, dict(type=int)),
         }

superdsm/dsmcfg.py

@@ -71,15 +71,15 @@ class DSM_Config(repype.stage.Stage):
     id = 'dsm'
     outputs = ['dsm_cfg']
 
-    def process(pipeline, config, status=None):
+    def process(self, pipeline, config, status=None):
         dsm_cfg = {
             key: config.get(key, DSM_CONFIG_DEFAULTS[key]) for key in DSM_CONFIG_DEFAULTS.keys()
         }
         return {
             'dsm_cfg': dsm_cfg
         }
 
-    def configure(pipeline, input_id, *args, scale, **kwargs):
+    def configure(self, pipeline, input_id, *args, scale, **kwargs):
         return {
             'alpha': (scale ** 2, 0.0005),
             'smooth_amount':     (scale, 0.2, dict(type=int, min=4)),

superdsm/globalenergymin.py

@@ -142,7 +142,7 @@ class GlobalEnergyMinimization(repype.stage.Stage):
     inputs  = ['y', 'y_mask', 'atoms', 'adjacencies', 'dsm_cfg']
     outputs = ['y_img', 'cover', 'objects', 'performance']
 
-    def process(y, y_mask, atoms, adjacencies, dsm_cfg, pipeline, config, status=None, log_root_dir=None):
+    def process(self, y, y_mask, atoms, adjacencies, dsm_cfg, pipeline, config, status=None, log_root_dir=None):
         y_img             = Image.create_from_array(y, normalize=False, mask=y_mask)
         pruning           = config.get(          'pruning', 'exact')
         beta              = config.get(             'beta',  0)
@@ -177,7 +177,7 @@ def process(y, y_mask, atoms, adjacencies, dsm_cfg, pipeline, config, status=Non
             'performance': performance,
         }
 
-    def configure(pipeline, input_id, *args, scale, diameter, **kwargs):
+    def configure(self, pipeline, input_id, *args, scale, diameter, **kwargs):
         return {
             'beta': (scale ** 2, 0.66),
             'max_seed_distance': (diameter, np.inf),

superdsm/pipeline.py

@@ -67,7 +67,7 @@ class LoadInput(repype.stage.Stage):
     inputs = ['input_id']
     outputs = ['g_raw']
 
-    def process(input_id: InputID, pipeline: Pipeline, config: repype.config.Config, status: Optional[repype.status.Status] = None) -> Dict[str, Any]:
+    def process(self, input_id: InputID, pipeline: Pipeline, config: repype.config.Config, status: Optional[repype.status.Status] = None) -> Dict[str, Any]:
         img_filepath = pipeline.resolve('input', input_id)
         return dict(
             g_raw = superdsm.io.imread(img_filepath)

superdsm/postprocess.py

@@ -121,7 +121,7 @@ class Postprocessing(repype.stage.Stage):
     inputs  = ['cover', 'y_img', 'atoms', 'g_raw', 'dsm_cfg']
     outputs = ['postprocessed_objects']
 
-    def process(cover, y_img, atoms, g_raw, dsm_cfg, pipeline, config, status=None, log_root_dir=None):
+    def process(self, cover, y_img, atoms, g_raw, dsm_cfg, pipeline, config, status=None, log_root_dir=None):
         # simple post-processing
         max_norm_energy           = config.get(          'max_norm_energy',    0.2)
         discard_image_boundary    = config.get(   'discard_image_boundary',  False)
@@ -238,7 +238,7 @@ def process(cover, y_img, atoms, g_raw, dsm_cfg, pipeline, config, status=None,
             'postprocessed_objects': postprocessed_objects
         }
 
-    def configure(pipeline, input_id, *args, radius, **kwargs):
+    def configure(self, pipeline, input_id, *args, radius, **kwargs):
         return {
             'min_object_radius': (radius, 0.0),
             'max_object_radius': (radius, np.inf),

superdsm/preprocess.py

@@ -32,7 +32,7 @@ class Preprocessing(repype.stage.Stage):
     inputs  = ['g_raw']
     outputs = ['y']
 
-    def process(g_raw, pipeline, config, status=None):
+    def process(self, g_raw, pipeline, config, status=None):
         sigma1 = config.get('sigma1', math.sqrt(2))
         sigma2 = config.get('sigma2', 40)
         offset_clip  = config.get('offset_clip', 3)
@@ -61,7 +61,7 @@ def process(g_raw, pipeline, config, status=None):
             'y': y,
         }
 
-    def configure(pipeline, input_id, *args, scale, **kwargs):
+    def configure(self, pipeline, input_id, *args, scale, **kwargs):
         return {
             'sigma2': (scale, 1.0),
         }