Fix updating metadata format

magmap/io/importer.py

@@ -541,16 +541,23 @@ def load_metadata(path, check_ver=False, assign=True):
         if output:
             # metadata is in first document
             output = output[0]
-    except FileNotFoundError:
+    except FileNotFoundError as err:
         # fall back to pre-v1.4 NPZ file format
-        libmag.warn("Could not find metadata file '{}', will check NPZ format"
-                    .format(path))
+        _logger.warn("Could not load metadata file '%s', will check NPZ format",
+                     path)
+        _logger.debug(err)
         path_npz = f"{os.path.splitext(path)[0]}.npz"
         try:
+            # load NPZ and resave as YML format
             output = np_io.read_np_archive(np.load(path_npz))
-        except FileNotFoundError:
-            libmag.warn("Could not find metadata file '{}', skipping"
-                        .format(path_npz))
+            path_yml = f"{os.path.splitext(path)[0]}.yml"
+            yaml_io.save_yaml(path_yml, output, True)
+            _logger.info(
+                "Metadata file from '%s' updated to '%s'", path_npz, path_yml)
+        except FileNotFoundError as err2:
+            _logger.warn(
+                "Could not load metadata file '%s', skipping", path_npz)
+            _logger.debug(err2)
             return None, image5d_ver_num
 
     try:

magmap/io/yaml_io.py

@@ -2,7 +2,6 @@
 # Author: David Young, 2020
 """YAML file format input/output."""
 
-import numpy as np
 import yaml
 
 from magmap.io import libmag
@@ -49,6 +48,9 @@ def load_yaml(path, enums=None):
     Returns:
         List[dict]: Sequence of parsed dictionaries for each document within
         a YAML file.
+
+    Raises:
+        FileNotFoundError: if ``path`` could not be found or loaded.
 
     """
     def parse_enum_val(val):
@@ -63,18 +65,21 @@ def parse_enum_val(val):
                 # replace with the corresponding Enum class
                 val = enums[val_split[0]][val_split[1]]
         return val
-
-    with open(path) as yaml_file:
-        # load all documents into a generator
-        docs = yaml.load_all(yaml_file, Loader=yaml.FullLoader)
-        data = []
-        for doc in docs:
-            if not doc:
-                # skip empty document
-                continue
-            if enums:
-                doc = _filter_dict(doc, parse_enum_val)
-            data.append(doc)
+
+    try:
+        with open(path) as yaml_file:
+            # load all documents into a generator
+            docs = yaml.load_all(yaml_file, Loader=yaml.FullLoader)
+            data = []
+            for doc in docs:
+                if not doc:
+                    # skip empty document
+                    continue
+                if enums:
+                    doc = _filter_dict(doc, parse_enum_val)
+                data.append(doc)
+    except (FileNotFoundError, UnicodeDecodeError) as e:
+        raise FileNotFoundError(e)
     return data
 
 

magmap/settings/profiles.py

@@ -14,6 +14,8 @@
 from magmap.io import yaml_io
 from magmap.settings import config
 
+_logger = config.logger.getChild(__name__)
+
 
 class RegKeys(Enum):
     """Register setting enumerations."""
@@ -142,11 +144,14 @@ def add_modifier(self, mod_name, profiles, sep):
                     print(mod_path, "profile file not found, skipped")
                     return
             self.timestamps[mod_path] = os.path.getmtime(mod_path)
-            yamls = yaml_io.load_yaml(mod_path, _PROFILE_ENUMS)
-            mods = {}
-            for yaml in yamls:
-                mods.update(yaml)
-            print("loaded {}:\n{}".format(mod_path, mods))
+            try:
+                yamls = yaml_io.load_yaml(mod_path, _PROFILE_ENUMS)
+                mods = {}
+                for yaml in yamls:
+                    mods.update(yaml)
+                _logger.info("Loaded profile from '%s':\n%s", mod_path, mods)
+            except FileNotFoundError:
+                _logger.warn("Unable to load profile from: %s", mod_path)
         else:
             if mod_name == self.DEFAULT_NAME:
                 # update entries from a new instance for default values;
@@ -194,8 +199,8 @@ def update_settings(self, names_str):
             self.add_modifier(profile, self.profiles, self.delimiter)
 
         if config.verbose:
-            print("settings for {}:", self[self.NAME_KEY])
-            pprint.pprint(self)
+            _logger.debug("settings for '%s':", self[self.NAME_KEY])
+            _logger.debug(pprint.pprint(self))
 
     def check_file_changed(self):
         """Check whether any profile files have changed since last loaded.