Merge branch 'rename_ref_titles_to_flat_titles' into 'master'

[h52nx] rename some remaining `ref_titles` to `flat_titles`.

See merge request !83

doc/tutorials/h52nx.rst

@@ -153,7 +153,7 @@ an option from command line
                           Titles corresponding to zserie init scans
     --dark_titles DARK_TITLES, --dark-titles DARK_TITLES
                           Titles corresponding to dark scans
-    --ref_titles REF_TITLES, --ref-titles REF_TITLES
+    --flat_titles --flat_titles --ref_titles FLAT_TITLES, --ref-titles FLAT_TITLES
                           Titles corresponding to ref scans
     --proj_titles PROJ_TITLES, --proj-titles PROJ_TITLES
                           Titles corresponding to projection scans

nxtomomill/app/h52nx.py

@@ -82,7 +82,7 @@ Application to convert a bliss-hdf5 tomography dataset to Nexus - NXtomo (hdf5)
                             Titles corresponding to zserie init scans
       --dark_titles DARK_TITLES, --dark-titles DARK_TITLES
                             Titles corresponding to dark scans
-      --ref_titles REF_TITLES, --ref-titles REF_TITLES
+      --flat_titles --flat-titles --ref_titles REF_TITLES, --ref-titles FLAT_TITLES
                             Titles corresponding to ref scans
       --proj_titles PROJ_TITLES, --proj-titles PROJ_TITLES
                             Titles corresponding to projection scans
@@ -303,10 +303,11 @@ def main(argv):
         help="Titles corresponding to dark scans",
     )
     parser.add_argument(
-        "--ref_titles",
+        "--flat_titles" "--flat-titles" "--ref_titles",
         "--ref-titles",
         default=None,
         help="Titles corresponding to ref scans",
+        dest="flat_titles",
     )
     parser.add_argument(
         "--proj_titles",

nxtomomill/app/h5_3dxrd2nx.py

@@ -80,7 +80,7 @@ Application to convert a tomo dataset written in bliss- hdf5 - 3D-XRD into and h
                             Titles corresponding to zserie init scans
       --dark_titles DARK_TITLES, --dark-titles DARK_TITLES
                             Titles corresponding to dark scans
-      --ref_titles REF_TITLES, --ref-titles REF_TITLES
+      --flat-titles --flat_titles --ref_titles REF_TITLES, --ref-titles FLAT_TITLES
                             Titles corresponding to ref scans
       --proj_titles PROJ_TITLES, --proj-titles PROJ_TITLES
                             Titles corresponding to projection scans
@@ -293,10 +293,13 @@ def main(argv):
         help="Titles corresponding to dark scans",
     )
     parser.add_argument(
+        "--flat_titles",
+        "--flat-titles",
         "--ref_titles",
         "--ref-titles",
         default=None,
         help="Titles corresponding to ref scans",
+        dest="flat_titles",
     )
     parser.add_argument(
         "--proj_titles",

nxtomomill/converter/hdf5/hdf5converter.py

@@ -82,7 +82,8 @@ H5_DARK_TITLES = Tomo.H5.DARK_TITLES
 H5_INIT_TITLES = Tomo.H5.INIT_TITLES
 H5_ZSERIE_INIT_TITLES = Tomo.H5.ZSERIE_INIT_TITLES
 H5_PROJ_TITLES = Tomo.H5.PROJ_TITLES
-H5_REF_TITLES = Tomo.H5.REF_TITLES
+H5_FLAT_TITLES = Tomo.H5.FLAT_TITLES
+H5_REF_TITLES = H5_FLAT_TITLES
 H5_Y_ROT_KEY = Tomo.H5.Y_ROT_KEY
 H5_DIODE_KEYS = Tomo.H5.DIODE_KEYS
 
@@ -90,7 +91,7 @@ DEFAULT_SCAN_TITLES = H5ScanTitles(
     H5_INIT_TITLES,
     H5_ZSERIE_INIT_TITLES,
     H5_DARK_TITLES,
-    H5_REF_TITLES,
+    H5_FLAT_TITLES,
     H5_PROJ_TITLES,
     H5_ALIGNMENT_TITLES,
 )
@@ -759,7 +760,7 @@ def h5_to_nx(
     configuration.init_titles = scan_titles.init_titles
     configuration.zserie_init_titles = scan_titles.init_zserie_titles
     configuration.dark_titles = scan_titles.dark_titles
-    configuration.flat_titles = scan_titles.ref_titles
+    configuration.flat_titles = scan_titles.flat_titles
     configuration.projections_titles = scan_titles.proj_titles
     configuration.alignment_titles = scan_titles.align_titles
 

nxtomomill/converter/hdf5/utils.py

@@ -53,7 +53,7 @@ H5ScanTitles = namedtuple(
         "init_titles",
         "init_zserie_titles",
         "dark_titles",
-        "ref_titles",
+        "flat_titles",
         "proj_titles",
         "align_titles",
     ],

nxtomomill/io/config.py

@@ -192,7 +192,9 @@ class TomoHDF5Config:
 
     DARK_TITLES_DK = "dark_titles"
 
-    REF_TITLES_DK = "ref_titles"
+    FLAT_TITLES_DK = "flat_titles"
+
+    FLAT_TILES_ALIASES = ("ref_titles",)
 
     PROJ_TITLES_DK = "proj_titles"
 
@@ -213,7 +215,7 @@ class TomoHDF5Config:
         INIT_TITLES_DK: "List of title to consider the group/entry as a initialization (sequence start). Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
         ZSERIE_INIT_TITLES_DK: "List of title to consider the group/entry as a zserie initialization (sequence start). Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
         DARK_TITLES_DK: "List of title to consider the group/entry as a dark.  Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
-        REF_TITLES_DK: "List of title to consider the group/entry as a reference / flat.  Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
+        FLAT_TITLES_DK: "List of title to consider the group/entry as a reference / flat.  Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
         PROJ_TITLES_DK: "List of title to consider the group/entry as a projection.  Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
         ALIGNMENT_TITLES_DK: "List of title to consider the group/entry as an alignment.  Ignored if dark_groups, flat_groups, projection_groups ... are provided.",
         X_PIXEL_SIZE_KEYS_DK: "List of keys / paths to look for the x pixel size",
@@ -327,7 +329,7 @@ class TomoHDF5Config:
         self._init_titles = settings.Tomo.H5.INIT_TITLES
         self._zserie_init_titles = settings.Tomo.H5.ZSERIE_INIT_TITLES
         self._dark_titles = settings.Tomo.H5.DARK_TITLES
-        self._flat_titles = settings.Tomo.H5.REF_TITLES
+        self._flat_titles = settings.Tomo.H5.FLAT_TITLES
         self._projection_titles = settings.Tomo.H5.PROJ_TITLES
         self._alignment_titles = settings.Tomo.H5.ALIGNMENT_TITLES
         self._x_pixel_size_paths = settings.Tomo.H5.X_PIXEL_SIZE
@@ -877,7 +879,7 @@ class TomoHDF5Config:
                 TomoHDF5Config.INIT_TITLES_DK: self.init_titles or "",
                 TomoHDF5Config.ZSERIE_INIT_TITLES_DK: self.zserie_init_titles or "",
                 TomoHDF5Config.DARK_TITLES_DK: self.dark_titles or "",
-                TomoHDF5Config.REF_TITLES_DK: self.flat_titles or "",
+                TomoHDF5Config.FLAT_TITLES_DK: self.flat_titles or "",
                 TomoHDF5Config.PROJ_TITLES_DK: self.projections_titles or "",
                 TomoHDF5Config.ALIGNMENT_TITLES_DK: self.alignment_titles or "",
             },
@@ -1092,10 +1094,30 @@ class TomoHDF5Config:
             dark_titles = convert_str_to_tuple(dark_titles, none_if_empty=True)
             self.dark_titles = dark_titles
         # handle ref titles. empty string is consider as a valid value
-        flat_titles = dict_.get(TomoHDF5Config.REF_TITLES_DK, None)
-        if flat_titles is not None:
-            flat_titles = convert_str_to_tuple(flat_titles, none_if_empty=True)
-            self.flat_titles = flat_titles
+        flat_titles_dks = [
+            TomoHDF5Config.FLAT_TITLES_DK,
+        ]
+        flat_titles_dks.extend(TomoHDF5Config.FLAT_TILES_ALIASES)
+        flat_title_key_picked = None
+        ## handle flat titles
+        for alias in flat_titles_dks:
+            flat_titles = dict_.get(alias, None)
+            if flat_titles is not None:
+                if flat_title_key_picked is not None:
+                    _logger.warning(
+                        f"flat titles are provided twice under {flat_title_key_picked} and {alias}. Please clean your configuration file. {flat_title_key_picked} will be used"
+                    )
+                else:
+                    flat_titles = convert_str_to_tuple(flat_titles, none_if_empty=True)
+                    self.flat_titles = flat_titles
+                    flat_title_key_picked = alias
+        if (
+            flat_title_key_picked is not None
+            and flat_title_key_picked != TomoHDF5Config.FLAT_TITLES_DK
+        ):
+            _logger.warning(
+                f"{flat_title_key_picked} will be removed in the future. Please use {TomoHDF5Config.FLAT_TITLES_DK} instead"
+            )
         # handle projection titles. empty string is consider as a valid value
         proj_titles = dict_.get(TomoHDF5Config.PROJ_TITLES_DK, None)
         if proj_titles is not None:

nxtomomill/io/confighandler.py

@@ -250,7 +250,7 @@ class TomoHDF5ConfigHandler(BaseHDF5ConfigHandler):
                 self.get_tuple_of_keys_from_cmd,
             ),
             "dark_titles": ("dark_titles", self.get_tuple_of_keys_from_cmd),
-            "ref_titles": ("flat_titles", self.get_tuple_of_keys_from_cmd),
+            "flat_titles": ("flat_titles", self.get_tuple_of_keys_from_cmd),
             "proj_titles": ("projections_titles", self.get_tuple_of_keys_from_cmd),
             "align_titles": ("alignment_titles", self.get_tuple_of_keys_from_cmd),
             "set_params": ("param_already_defined", _extract_param_value),
@@ -279,7 +279,7 @@ class TomoHDF5ConfigHandler(BaseHDF5ConfigHandler):
                 "set_params",
                 "align_titles",
                 "proj_titles",
-                "ref_titles",
+                "flat_titles",
                 "dark_titles",
                 "init_zserie_titles",
                 "init_titles",
@@ -361,7 +361,7 @@ class XRD3DHDF5ConfigHandler(BaseHDF5ConfigHandler):
                 self.get_tuple_of_keys_from_cmd,
             ),
             "dark_titles": ("dark_titles", self.get_tuple_of_keys_from_cmd),
-            "ref_titles": ("flat_titles", self.get_tuple_of_keys_from_cmd),
+            "flat_titles": ("flat_titles", self.get_tuple_of_keys_from_cmd),
             "proj_titles": ("projections_titles", self.get_tuple_of_keys_from_cmd),
             "align_titles": ("alignment_titles", self.get_tuple_of_keys_from_cmd),
             "set_params": ("param_already_defined", _extract_param_value),
@@ -390,7 +390,7 @@ class XRD3DHDF5ConfigHandler(BaseHDF5ConfigHandler):
                 "set_params",
                 "align_titles",
                 "proj_titles",
-                "ref_titles",
+                "flat_titles",
                 "dark_titles",
                 "init_zserie_titles",
                 "init_titles",

nxtomomill/io/test/test_config.py

@@ -70,7 +70,7 @@ class TestH5Config(unittest.TestCase):
             titles_dict[TomoHDF5Config.PROJ_TITLES_DK], settings.Tomo.H5.PROJ_TITLES
         )
         self.assertEqual(
-            titles_dict[TomoHDF5Config.REF_TITLES_DK], settings.Tomo.H5.REF_TITLES
+            titles_dict[TomoHDF5Config.FLAT_TITLES_DK], settings.Tomo.H5.FLAT_TITLES
         )
         self.assertEqual(
             titles_dict[TomoHDF5Config.DARK_TITLES_DK], settings.Tomo.H5.DARK_TITLES
@@ -147,7 +147,7 @@ class TestH5Config(unittest.TestCase):
             TomoHDF5Config.PROJ_TITLES_DK,
             TomoHDF5Config.ZSERIE_INIT_TITLES_DK,
             TomoHDF5Config.INIT_TITLES_DK,
-            TomoHDF5Config.REF_TITLES_DK,
+            TomoHDF5Config.FLAT_TITLES_DK,
             TomoHDF5Config.DARK_TITLES_DK,
         ):
             with self.subTest(key=key):

nxtomomill/io/test/test_confighandler.py

@@ -47,7 +47,7 @@ class _ARParseMock(object):
         self.set_params = None
         self.align_titles = None
         self.proj_titles = None
-        self.ref_titles = None
+        self.flat_titles = None
         self.dark_titles = None
         self.init_zserie_titles = None
         self.init_titles = None

nxtomomill/settings.py

@@ -89,7 +89,7 @@ class Tomo:
         DARK_TITLES = ("dark images", "dark")
         """if a scan starts by one of those string then is considered as
         dark scan"""
-        REF_TITLES = ("flat", "reference images", "ref", "refend")
+        FLAT_TITLES = ("flat", "reference images", "ref", "refend")
         """if a scan starts by one of those string then is considered as
         reference scan"""
         PROJ_TITLES = ("projections", "ascan rot 0 ", "ascan diffrz 0 180 1600 0.1")