collecting all the infos for the config. this refs #234

src/ibeatles/_version.py

@@ -1 +1 @@
-__version__ = "7.1.0.dev1+d202409172024"
+__version__ = "7.1.0.dev99+d202412061910"

src/ibeatles/session/session_handler.py

@@ -361,7 +361,7 @@ def save_to_file(self, config_file_name=None):
 
         if config_file_name:
             output_file_name = config_file_name
-            session_dict = self.parent.session_dict
+            session_dict = self.session_dict
 
             with open(output_file_name, "w") as json_file:
                 json.dump(session_dict, json_file)

src/ibeatles/step6/export.py

@@ -5,6 +5,7 @@
 
 from NeuNorm.normalization import Normalization
 
+from src.ibeatles.session import SessionKeys, SessionSubKeys
 from src.ibeatles import DataType, FileType
 from src.ibeatles.step6 import ParametersToDisplay
 from src.ibeatles.step6.get import Get
@@ -15,6 +16,7 @@
 from src.ibeatles.utilities.export import format_kropff_dict, format_kropff_table
 from src.ibeatles.utilities.get import Get as UtilitiesGet
 from src.ibeatles.fitting import FittingKeys
+from src.ibeatles.utilities.time import get_current_time_in_special_file_name_format
 
 
 class Export:
@@ -335,3 +337,137 @@ def hdf5(self, output_folder: str = None):
                 "integrated normalized radiographs"
             )
             integrated_image_group.create_dataset("2D array", data=integrated_image)
+
+    def config_for_cli(self, output_folder: str = None):
+
+        _current_time = get_current_time_in_special_file_name_format()
+
+        output_folder = os.path.abspath(output_folder)
+        output_file_name = create_full_export_file_name(
+            os.path.join(output_folder, f"config_{_current_time}"), FileType.json
+        )
+
+        logging.info(
+            f"Exporting configuration to be used by the command line version (CLI) -> {output_file_name}"
+        )
+
+        # o_get = Get(parent=self.parent)
+        # strain_mapping_dict = o_get.strain_mapping_dictionary()
+
+        session_dict = self.parent.session_dict
+
+        raw_data_dir = session_dict[DataType.sample][SessionSubKeys.current_folder]
+        _, raw_data_extension = os.path.splitext(session_dict[DataType.sample][SessionSubKeys.list_files][0])
+
+        open_beam_data_dir = session_dict[DataType.ob][SessionSubKeys.current_folder]
+        open_beam_data_extension = raw_data_extension
+
+        list_normalization_roi = session_dict[DataType.normalization][SessionSubKeys.roi]
+        normalization_sample_background = []
+        for _roi in list_normalization_roi:
+            _state, x0, y0, width, height, _type = _roi
+            if (type == 'background') and _state:
+                normalization_sample_background.append({"x0": x0, "y0": y0,
+                                                        "width": width, "height": height})
+
+        moving_average_active = session_dict[SessionKeys.reduction][SessionSubKeys.activate]
+        moving_average_dimension = session_dict[SessionKeys.reduction][SessionSubKeys.dimension]
+        moving_average_size = {'y': session_dict[SessionKeys.reduction][SessionSubKeys.size]["y"],
+                               'x': session_dict[SessionKeys.reduction][SessionSubKeys.size]["x"]}
+        if moving_average_dimension == '3D':
+            moving_average_size['z'] = session_dict[SessionKeys.reduction][SessionSubKeys.size["z"]]
+
+        moving_average_type = session_dict[SessionKeys.reduction][SessionSubKeys.type]
+
+        if session_dict[SessionKeys.reduction][SessionSubKeys.process_order] == 'option1':
+            processing_order = "Moving average, Normalization"
+        else:
+            processing_order = "Normalization, Moving average"
+
+        analysis_material_element = self.parent.ui.material_name.text()
+
+        pixel_binning = {'x0': session_dict[SessionKeys.bin][SessionSubKeys.roi[1]],
+                         'y0': session_dict[SessionKeys.bin][SessionSubKeys.roi[2]],
+                         'width': session_dict[SessionKeys.bin][SessionSubKeys.roi[3]],
+                         'height': session_dict[SessionKeys.bin][SessionSubKeys.roi[4]],
+                         'bin_size': session_dict[SessionKeys.bin][SessionSubKeys.roi[5]],
+                        }
+
+        fitting_lambda_range = session_dict[SessionKeys.fitting][SessionSubKeys.lambda_range_index]
+        x_axis = session_dict[SessionKeys.fitting][SessionSubKeys.x_axis]
+        lambda_min = x_axis[fitting_lambda_range[0]]*1e-10
+        lambda_max = x_axis[fitting_lambda_range[1]]*1e-10
+
+        if self.parent.ui.d0_value.checked():
+            strain_mapping_d0 = float(self.parent.ui.d0_value.text())
+        else:
+            strain_mapping_d0 = float(self.parent.ui.d0_user_value.text())
+
+        quality_threshold = 0.8
+
+        distance_source_detector_in_m = session_dict[SessionKeys.instrument][SessionSubKeys.distance_source_detector]
+        detector_offset_in_us = session_dict[SessionKeys.instrument][SessionSubKeys.detector_offset]
+
+        normalized_data_dir = os.path.join(output_folder, f"normalized_{_current_time}")
+        analysis_results_dir = os.path.join(output_folder, f"analysis_{_current_time}")
+        strain_results_dir = os.path.join(output_folder, f"strain_{_current_time}")
+
+        config = {
+              "raw_data": {
+                "raw_data_dir": raw_data_dir,
+                "raw_data_extension": raw_data_extension,
+              },
+              "open_beam": {
+                "open_beam_data_dir": open_beam_data_dir,
+                "open_beam_data_extension": open_beam_data_extension,
+              },
+              "normalization": {
+                "sample_background": normalization_sample_background,
+                "moving_average": {
+                  "active": moving_average_active,
+                  "dimension": moving_average_dimension,
+                  "size": moving_average_size,
+                  "type": moving_average_type,
+                },
+                "processing_order": processing_order,
+              },
+              "analysis": {
+                "material": {
+                  "element": analysis_material_element,
+                },
+                "pixel_binning": pixel_binning,
+                "fitting": {
+                  "lambda_min": lambda_min,
+                  "lambda_max": lambda_max,
+                },
+                "strain_mapping": {
+                  "d0": strain_mapping_d0,
+                  "quality_threshold": 0.8,
+                  "visualization": {
+                      "interpolation_method": "nearest",
+                      "colormap": "viridis",
+                      "alpha": 0.5,
+                      "display_fit_quality": True
+                  },
+                  "output_file_config": {
+                      "strain_map_format": "png",
+                      "fitting_grid_format": "pdf",
+                      "figure_dpi": 300,
+                      "csv_format": {
+                          "delimiter": ",",
+                          "include_metadata_header": True,
+                          "metadata_comment_char": "#",
+                          "na_rep": "null"
+                      }
+                  },
+                  "save_intermediate_results": False
+                },
+                "distance_source_detector_in_m": distance_source_detector_in_m,
+                "detector_offset_in_us": detector_offset_in_us,
+              },
+              "output": {
+                "normalized_data_dir": normalized_data_dir,
+                "analysis_results_dir": analysis_results_dir,
+                "strain_results_dir": strain_results_dir,
+              }
+            }

src/ibeatles/step6/strain_mapping_launcher.py

@@ -160,6 +160,12 @@ def export_all_hdf5(self):
         output_folder = o_export.select_output_folder()
         o_export.hdf5(output_folder=output_folder)
 
+    def action_configuration_for_cli_clicked(self):
+        o_export = Export(parent=self,
+                          grand_parent=self.parent)
+        output_folder = o_export.select_output_folder()
+        o_export.config_for_cli(output_folder=output_folder)
+
     def fitting_algorithm_changed(self):
         self.update_display()
 

src/ibeatles/ui/ui_strainMapping.ui

@@ -547,6 +547,8 @@
     <addaction name="actionExportImagesAll"/>
     <addaction name="separator"/>
     <addaction name="menuTable_and_integrated_image"/>
+    <addaction name="separator"/>
+    <addaction name="action_configuration_for_cli"/>
    </widget>
    <addaction name="menuExport"/>
   </widget>
@@ -591,6 +593,11 @@
     <string>integrated image ...</string>
    </property>
   </action>
+  <action name="action_configuration_for_cli">
+   <property name="text">
+    <string>configuration for cli ...</string>
+   </property>
+  </action>
  </widget>
  <resources/>
  <connections>
@@ -914,6 +921,22 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>action_configuration_for_cli</sender>
+   <signal>triggered()</signal>
+   <receiver>MainWindow</receiver>
+   <slot>action_configuration_for_cli_clicked()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>-1</x>
+     <y>-1</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>538</x>
+     <y>428</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>fitting_algorithm_changed()</slot>
@@ -934,5 +957,6 @@
   <slot>export_images_all_tiff()</slot>
   <slot>interpolation_cmap_method_changed()</slot>
   <slot>display_hidden_plot_changed()</slot>
+  <slot>action_configuration_for_cli_clicked()</slot>
  </slots>
 </ui>

src/ibeatles/utilities/time.py

@@ -0,0 +1,9 @@
+import datetime
+
+TIMESTAMP_FORMAT = "%Y-%m-%d %H:%M:%S"
+
+
+def get_current_time_in_special_file_name_format():
+    """format the current date and time into something like  04m_07d_2022y_08h_06mn """
+    current_time = datetime.datetime.now().strftime("%mm_%dd_%Yy_%Hh_%Mmn")
+    return current_time