replace several `create_ini_ref` and `create_final_ref` by `create_ini_flat`...

replace several `create_ini_ref` and `create_final_ref` by `create_ini_flat` and `create_final_dark`

nxtomomill/app/test/test_patch_nx_app.py

@@ -54,8 +54,8 @@ def test_patch_nx_application():
             n_proj=nproj,
             n_ini_proj=nproj,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=dim,
         ).scan
         main(

nxtomomill/test/test_utils.py

@@ -58,8 +58,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=self.nproj,
             n_ini_proj=self.nproj,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         with h5py.File(self._simple_nx.master_file, mode="r") as h5s:
@@ -73,8 +73,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=0,
             n_ini_proj=0,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         self._create_vds(
@@ -94,8 +94,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=0,
             n_ini_proj=0,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         self._create_vds(
@@ -852,8 +852,8 @@ class TestChangeImageKeyControl(unittest.TestCase):
             n_proj=self.nproj,
             n_ini_proj=self.nproj,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
             dim=self.dim,
             n_refs=4,
         )
@@ -1096,8 +1096,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
             n_proj=10,
             n_ini_proj=2,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         # 1. add first level of indirection for dark and flat and check the VDS
@@ -1123,8 +1123,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
             n_proj=10,
             n_ini_proj=2,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         # 2. create a second level of indirection for dark and flat and check