General skelaton for xrd reader.

pynxtools/dataconverter/readers/xrd/__init__.py

@@ -0,0 +1,15 @@
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

pynxtools/dataconverter/readers/xrd/reader.py

@@ -0,0 +1,100 @@
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+from typing import Tuple, Any, Dict, Union
+import json
+from pynxtools.dataconverter.readers.xrd.xrd_parser import parse_and_convert_file
+from pynxtools.dataconverter.readers.utils import flatten_and_replace, FlattenSettings
+import yaml
+from pynxtools.dataconverter.template import Template
+from pynxtools.dataconverter.readers.base.reader import BaseReader
+
+
+CONVERT_DICT = {
+    'Instrument': 'INSTRUMENT[instrument]',
+    'Software': 'SOFTWARE[software]',
+    'Hardware': 'Hardware[hardware]',
+    'Analyser': 'ELECTRONANALYSER[electronanalyser]',
+    'Beam': 'BEAM[beam]',
+    'unit': '@units',
+    'version': '@version',
+    'Sample': 'SAMPLE[sample]',
+    'User': 'USER[user]',
+    'Data': 'DATA[data]',
+    'Source': 'SOURCE[source]',
+    'Environment': 'ENVIRONMENT[environment]',
+    'Sample_bias': 'SAMPLE_BIAS[sample_bias]'
+}
+
+REPLACE_NESTED: Dict[str, str] = {}
+
+
+class STMReader(BaseReader):
+    """ Reader for XPS.
+    """
+
+    supported_nxdls = ["NXroot"]
+
+    def read(self,
+             template: dict = None,
+             file_paths: Tuple[str] = None,
+             objects: Tuple[Any] = None):
+        """
+            General read menthod to prepare the template.
+        """
+        # has_sxm_file: bool = False
+        # sxm_file: str = ""
+        # has_dat_file: bool = False
+        # dat_file: str = ""
+        filled_template: Union[Dict, None] = Template()
+        # config_dict: Union[Dict[str, Any], None] = None
+        eln_dict: Union[Dict[str, Any], None] = None
+        config_dict: Dict = {}
+
+        data_file: str = ""
+        for file in file_paths:
+            ext = file.rsplit('.', 1)[-1]
+            if ext == 'json':
+                with open(file, mode="r", encoding="utf-8") as fl_obj:
+                    config_dict = json.load(fl_obj)
+            elif ext in ['yaml', 'yml']:
+                with open(file, mode="r", encoding="utf-8") as fl_obj:
+                    eln_dict = flatten_and_replace(
+                        FlattenSettings(
+                            yaml.safe_load(fl_obj),
+                            CONVERT_DICT,
+                            REPLACE_NESTED
+                        )
+                    )
+            else:
+                xrd_dict = parse_and_convert_file(file)
+        # TODO combine nyaml, json, and xrd data here
+
+        # Get rid of empty concept and cleaning up Template
+        for key, val in template.items():
+
+            if val is None:
+                del template[key]
+            else:
+                filled_template[key] = val
+        if not filled_template.keys():
+            raise ValueError("Reader could not read anything! Check for input files and the"
+                             " corresponding extention.")
+        return filled_template
+
+
+READER = STMReader

pynxtools/dataconverter/readers/xrd/xrd_helper.py

@@ -0,0 +1,15 @@
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

src/nomad_measurements/xrd/xrd_parser.py → pynxtools/dataconverter/readers/xrd/xrd_parser.py

@@ -1,3 +1,23 @@
+"""
+XRD file parser collection.
+TODO: Extend the module level doc.
+"""
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import re # for regular expressions
 import os  # for file path operations
 import xml.etree.ElementTree as ET # for XML parsing
@@ -14,7 +34,7 @@ def __init__(self, file_path):
 
     def read_file(self):
         '''Reads the content of a file from the given file path.
-        
+
         Returns:
             str: The content of the file.
         '''
@@ -45,7 +65,7 @@ def parse_metadata(self):
         root = ET.fromstring(content)
 
         ns_version = root.tag.split("}")[0].strip("{")
-        ns = {'xrd': ns_version}    
+        ns = {'xrd': ns_version}
 
         xrd_measurement = root.find("xrd:xrdMeasurement", ns)
 
@@ -103,7 +123,7 @@ def __init__(self, file_path):
 
     def identify_format(self):
         '''Identifies the format of a given file.
-        
+
         Returns:
             str: The file extension of the file.
         '''