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FAIRmat-NFDI · Nov 21, 2023 · 61a945c · 61a945c
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commit 61a945c
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Showing 6 changed files with 8 additions and 12 deletions.
diff --git a/pynxtools/dataconverter/convert.py b/pynxtools/dataconverter/convert.py
@@ -164,7 +164,6 @@ def convert(input_file: Tuple[str],
             generate_template: bool = False,
             fair: bool = False,
             undocumented: bool = False,
-            temp_data_dict=None,   # pre generated empty template from nxdl name.
             **kwargs):
     """The conversion routine that takes the input parameters and calls the necessary functions."""
 
@@ -181,8 +180,6 @@ def convert(input_file: Tuple[str],
                                             **kwargs)
     if undocumented:
         logger.setLevel(UNDOCUMENTED)
-    # This is mainly if the filled template data is needed out of this function
-    temp_data_dict['data'] = temp_data
     if fair and temp_data.undocumented.keys():
         logger.warning("There are undocumented paths in the template. This is not acceptable!")
         return

diff --git a/pynxtools/dataconverter/readers/sts/helper.py b/pynxtools/dataconverter/readers/sts/helper.py
@@ -19,11 +19,9 @@
 
 from typing import Tuple
 import copy
-import json
 import numpy as np
 from pynxtools.dataconverter.helpers import (convert_data_dict_path_to_hdf5_path,
                                              transform_to_intended_dt,
-                                             nested_dict_to_slash_separated_path
                                              )
 
 
@@ -101,9 +99,9 @@ def overwrite_fields(template, data_dict,
                                                               else None)
         if unit in data_path:
             path_to_data = data_path[unit]
-            template[new_temp_key + "/@units"] = transform_to_intended_dt(data_dict[path_to_data]
-                                                                          if path_to_data in data_dict
-                                                                          else None)
+            unit = transform_to_intended_dt(data_dict[path_to_data] if path_to_data in data_dict
+                                            else None)
+            template[new_temp_key + "/@units"] =
 
 
 def nested_path_to_slash_separated_path(nested_dict: dict,

diff --git a/pynxtools/dataconverter/readers/sts/stm_file_parser.py b/pynxtools/dataconverter/readers/sts/stm_file_parser.py
@@ -367,8 +367,8 @@ def from_sxm_file_into_template(self, template, config_dict, eln_data_dict):
                                      c_key,
                                      nxdl_key_to_modified_key)
                 else:
-                    template[c_key] = transform_to_intended_dt(data_dict[c_val]) if c_val in data_dict \
-                        else None
+                    template[c_key] = transform_to_intended_dt(data_dict[c_val]) \
+                        if c_val in data_dict else None
         # The following function can be used later it link come true in application def.
         # link_implementation(template, nxdl_key_to_modified_key)
         link_seperation_from_hard_code(template, nxdl_key_to_modified_key)

diff --git a/pynxtools/dataconverter/readers/xrd/xrd_parser.py b/pynxtools/dataconverter/readers/xrd/xrd_parser.py
@@ -318,7 +318,7 @@ def parse(self):
             ValueError: If the file format is unsupported.
         '''
         file_format = self.get_file_format()
-
+        slash_sep_dict = {}
         if file_format == ".xrdml":
             slash_sep_dict = self.parse_xrdml()
         # elif file_format == ".udf":

diff --git a/pynxtools/definitions b/pynxtools/definitions
diff --git a/pyproject.toml b/pyproject.toml
@@ -39,6 +39,7 @@ dependencies = [
     "tzlocal<=4.3",
     "scipy>=1.7.1",
     "lark>=1.1.5",
+    "xrayutilities>=1.7.4",
     "requests",
     "requests_cache",
     "nanonispy@git+https://github.com/ramav87/nanonispy.git@a0da87c58482d29624a2bf5deecb763dd1274212"