x-axis file produced. this refs #245

Author: JeanBilheux

notebooks/__code/normalization_tof/normalization_for_timepix.py

@@ -87,6 +87,22 @@ def retrieve_list_of_tif(folder: str) -> list:
     return list_tif
 
 
+def create_x_axis_file(lambda_array: np.ndarray = None, 
+                       energy_array: np.ndarray = None, 
+                       output_folder: str = "./") -> str:
+    """create x axis file with lambda, energy and tof arrays"""
+    x_axis_data = {
+        "file_index": np.arange(len(lambda_array)),
+        "lambda (Angstroms)": lambda_array,
+        "energy (eV)": energy_array,
+    }
+    x_axis_file_name = os.path.join(output_folder, "x_axis.txt")
+    pd_dataframe = pd.DataFrame(x_axis_data)
+    pd_dataframe.to_csv(x_axis_file_name, index=False, sep=",")
+
+    logging.info(f"X axis file created: {x_axis_file_name}")
+
+
 def normalization_with_list_of_runs(sample_run_numbers: list = None, 
                                     ob_run_numbers: list = None, 
                                     output_folder: str ="./", 
@@ -137,13 +153,15 @@ def normalization_with_list_of_runs(sample_run_numbers: list = None,
     export_corrected_integrated_sample_data = export_mode.get("sample_integrated", False)
     export_corrected_integrated_ob_data = export_mode.get("ob_integrated", False)
     export_corrected_integrated_normalized_data = export_mode.get("normalized_integrated", False)
+    export_x_axis = export_mode.get("x_axis", True)
 
     logging.info(f"{export_corrected_stack_of_sample_data = }")
     logging.info(f"{export_corrected_stack_of_ob_data = }")
     logging.info(f"{export_corrected_stack_of_normalized_data = }")
     logging.info(f"{export_corrected_integrated_sample_data = }")
     logging.info(f"{export_corrected_integrated_ob_data = }")
     logging.info(f"{export_corrected_integrated_normalized_data = }")
+    logging.info(f"{export_x_axis = }")
 
     sample_master_dict, sample_status_metadata = create_master_dict(list_run_numbers=sample_run_numbers, 
                                                              data_type=DataType.sample,
@@ -387,6 +405,12 @@ def normalization_with_list_of_runs(sample_run_numbers: list = None,
                 spectra_file = sample_master_dict[_sample_run_number][MasterDictKeys.spectra_file_name]
                 shutil.copy(spectra_file, full_output_folder)
 
+                # create x-axis file
+                create_x_axis_file(lambda_array=lambda_array,
+                                   energy_array=energy_array,
+                                   output_folder=output_stack_folder,
+                                   )
+
     logging.info(f"Normalization and export is done!")
     if verbose:
         display(HTML(f"Normalization and export is done!"))

notebooks/__code/normalization_tof/normalization_tof.py

@@ -425,8 +425,10 @@ def run_normalization_with_list_of_runs(self, preview=False):
                        'normalized_stack': self.export_corrected_stack_of_normalized_data.value,
                        'sample_integrated': self.export_corrected_integrated_sample_data.value,
                        'ob_integrated': self.export_corrected_integrated_ob_data.value,
-                       'normalized_integrated': self.export_corrected_integrated_normalized_data.value,}
-        
+                       'normalized_integrated': self.export_corrected_integrated_normalized_data.value,
+                       'x_axis': True,  # always export x axis
+                       }
+
         detecor_delay_us = None
         if self.instrument == "SNAP":
             detecor_delay_us = self.detector_offset_us.value

notebooks/normalization_tof.ipynb

@@ -216,6 +216,20 @@
    "source": [
     "o_norm.run_normalization_with_list_of_runs(preview=True)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {