Update Include the X and Y axis in NXdata.

src/pynxtools_stm/configs/nanonis_sxm_generic_afm.py

@@ -560,7 +560,7 @@
                     "@units": "/DATA/INFO/Excitation/Unit",
                 },
                 "@title": "Excitation Plot of AFM Experiment (Backward Direction)",
-                "grp_name": "excitation _backward",
+                "grp_name": "excitation_backward",
             },
             {
                 "data": {

src/pynxtools_stm/configs/nanonis_sxm_generic_stm.py

@@ -533,7 +533,7 @@
                     "raw_path": "/Z/forward",
                     "@units": "@default:m",
                 },
-                # If axis will be provided use the following structure
+                # Syntax Note: If axis will be provided use the following structure
                 # "0": {
                 #     "name": "Bias Voltage",
                 #     "raw_path": [

src/pynxtools_stm/nxformatters/base_formatter.py

@@ -119,13 +119,15 @@ def _get_eln_dict(self, eln_file: str):
         return eln_dict
 
     def work_though_config_nested_dict(self, config_dict: Dict, parent_path: str):
+        # This concept is just note where the group will be
+        # handeld or somthing like that.
         if "#note" in config_dict:
             return
         for key, val in config_dict.items():
             if val is None or val == "":
                 continue
-            # Special case, will be handled in a specific function registerd in
-            # self._grp_to_func
+            # Special case, will be handled in a specific function registerd
+            # in self._grp_to_func
             if key in self._grp_to_func:
                 # First fill the default values
                 self.work_though_config_nested_dict(
@@ -146,11 +148,18 @@ def work_though_config_nested_dict(self, config_dict: Dict, parent_path: str):
                 if other_attrs:
                     for k, v in other_attrs.items():
                         self.template[f"{parent_path}/{key}/@{k}"] = v
+            # Handle to construct nxdata group that comes alon as a dict
+            elif ("@title" in val or "grp_name" in val) and "data" in val:
+                _ = self._NXdata_grp_from_conf_description(
+                    partial_conf_dict=val,
+                    parent_path=parent_path,
+                    group_name=key,
+                )
             # variadic fields that would have several values according to the dimentions
             elif isinstance(val, list) and isinstance(val[0], dict):
                 for item in val:
                     # Handle to construct nxdata group
-                    if "@title" in item or "grp_name" in item and "data" in item:
+                    if ("@title" in item or "grp_name" in item) and "data" in item:
                         _ = self._NXdata_grp_from_conf_description(
                             partial_conf_dict=item,
                             parent_path=parent_path,
@@ -195,9 +204,9 @@ def rearrange_data_according_to_axes(self, data):
                 np.flip(data)
         elif self.NXScanControl.fast_axis == "-y":
             if self.NXScanControl.slow_axis == "x":
-                return np.flipud(data)
+                return np.transpose(np.flipud(data))
             elif self.NXScanControl.slow_axis == "-x":
-                return np.flip(data)
+                return np.transpose(data)
         elif self.NXScanControl.fast_axis == "y":
             if self.NXScanControl.slow_axis == "-x":
                 return np.fliplr(data)

src/pynxtools_stm/nxformatters/nanonis_sxm_stm.py

@@ -22,6 +22,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import copy
 from pynxtools_stm.nxformatters.base_formatter import SPMformatter
 from typing import Dict, Optional, Union
 from pathlib import Path
@@ -275,7 +276,7 @@ def construct_scan_data_grps(
             data_dict=self.raw_data,
             end_dict=partial_conf_dict,
         )
-        # Example of data des and info and each column is separated by tab
+        ## Example of data des and info and each column is separated by tab
         # Channel	Name	Unit	Direction	Calibration	Offset
         # 14	Z	m	both	9.000E-9	0.000E+0
         # 0	Current	A	both	1.000E-9	-1.132E-13
@@ -403,3 +404,40 @@ def _construct_nxscan_controllers(
                 parent_path=f"{parent_path}/{group_name}",
                 group_name=scan_pattern_grp,
             )
+
+    def _NXdata_grp_from_conf_description(
+        self, partial_conf_dict, parent_path, group_name, group_index=0
+    ):
+        """Specialization of the generic funciton to create NXdata group or plots."""
+        store_partial_dict = copy.deepcopy(partial_conf_dict)
+        super()._NXdata_grp_from_conf_description(
+            partial_conf_dict, parent_path, group_name, group_index
+        )
+        print(" ################### ", partial_conf_dict)
+        nxdata_group_nm = store_partial_dict["grp_name"]
+        axis_x = "x"
+        axis_y = "y"
+        print(" ######################### ", group_name)
+        self.template[f"{parent_path}/{nxdata_group_nm}/@axes"] = [
+            axis_x,
+            axis_y,
+        ]
+        self.template[f"{parent_path}/{nxdata_group_nm}/@{axis_x}_indices"] = 0
+        self.template[f"{parent_path}/{nxdata_group_nm}/{axis_x}"] = np.linspace(
+            self.NXScanControl.x_start,
+            self.NXScanControl.x_end,
+            int(self.NXScanControl.x_points),
+        )
+        self.template[f"{parent_path}/{nxdata_group_nm}/{axis_x}/@units"] = (
+            self.NXScanControl.x_start_unit
+        )
+
+        self.template[f"{parent_path}/{nxdata_group_nm}/@{axis_y}_indices"] = 1
+        self.template[f"{parent_path}/{nxdata_group_nm}/{axis_y}"] = np.linspace(
+            self.NXScanControl.y_start,
+            self.NXScanControl.y_end,
+            int(self.NXScanControl.y_points),
+        )
+        self.template[f"{parent_path}/{nxdata_group_nm}/{axis_y}/@units"] = (
+            self.NXScanControl.y_start_unit
+        )

tests/data/nanonis/afm/version_gen_4_with_described_nxdata/config.json

@@ -524,7 +524,7 @@
                     "@units": "/DATA/INFO/Excitation/Unit"
                 },
                 "@title": "Excitation Plot of AFM Experiment (Backward Direction)",
-                "grp_name": "excitation _backward"
+                "grp_name": "excitation_backward"
             },
             {
                 "data": {

update_example_script.sh

@@ -0,0 +1,26 @@
+!#/local/bin/bash
+
+# STS Nanonis
+echo " !!! Converting Nanonis STS data !!! "
+find tests/data/nanonis/sts/version_gen_5e_default_config -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXspm --reader spm --output sts_5e_default_config.nxs
+find tests/data/nanonis/sts/version_gen_5e_default_config -type f -name '*.nxs' | xargs mv sts_5e_default_config.nxs
+
+find tests/data/nanonis/sts/version_gen_5e_with_described_nxdata -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXspm --reader spm --output sts_5e_with_described_nxdata.nxs
+find tests/data/nanonis/sts/version_gen_5e_with_described_nxdata -type f -name '*.nxs' | xargs mv sts_5e_with_described_nxdata.nxs
+
+# AFM Nanonis
+echo " !!! Converting Nanonis AFM data !!! "
+find tests/data/nanonis/afm/version_gen_4_default_config -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXafm --reader spm --output afm_4_with_default_config.nxs
+find tests/data/nanonis/afm/version_gen_4_default_config -type f -name '*.nxs' | xargs mv afm_4_with_default_config.nxs
+
+find tests/data/nanonis/afm/version_gen_4_with_described_nxdata -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXafm --reader spm --output afm_4_with_described_nxdata.nxs
+find tests/data/nanonis/afm/version_gen_4_with_described_nxdata -type f -name '*.nxs' | xargs mv afm_4_with_described_nxdata.nxs
+
+# STM Nanonis
+echo " !!! Converting Nanonis STM data !!! "
+find tests/data/nanonis/stm/version_gen_4_5_default_config -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXstm --reader spm --output stm_4_5_default_config.nxs
+find tests/data/nanonis/stm/version_gen_4_5_default_config -type f -name '*.nxs' | xargs mv stm_4_5_default_config.nxs
+
+find tests/data/nanonis/stm/version_gen_4_5_with_described_nxdata -type f ! -name '*.nxs' | xargs dataconverter --nxdl NXstm --reader spm --output stm_4_5_with_described_nxdata.nxs
+find tests/data/nanonis/stm/version_gen_4_5_with_described_nxdata -type f -name '*.nxs' | xargs mv stm_4_5_with_described_nxdata.nxs
+