Merge pull request #1946 from HEXRD/cif-export

Cif export

Author: bnmajor

hexrdgui/hexrd_config.py

@@ -1289,9 +1289,16 @@ def load_materials(self, f):
         beam_energy = valWUnit('beam', 'energy', self.beam_energy, 'keV')
         self.materials = load_materials_hdf5(f, kev=beam_energy)
 
-    def save_materials(self, f, path=None):
+    def save_materials_hdf5(self, f, path=None):
         save_materials_hdf5(f, self.materials, path)
 
+    def save_material_cif(self, material, directory=None, filename=None):
+        if directory is None:
+            directory = HexrdConfig().working_dir
+        if filename is None:
+            filename = f"{material.name}.cif"
+        material.write_cif(f"{directory}/{filename}")
+
     def import_materials(self, file_paths: list[Path | str]):
         """Import materials from a list of files
 

hexrdgui/indexing/fit_grains_results_dialog.py

@@ -714,7 +714,7 @@ def full_path(file_name):
         HexrdConfig().working_dir = selected_directory
 
         HexrdConfig().save_indexing_config(full_path('workflow.yml'))
-        HexrdConfig().save_materials(full_path('materials.h5'))
+        HexrdConfig().save_materials_hdf5(full_path('materials.h5'))
         HexrdConfig().save_instrument_config(
             full_path('instrument.hexrd'),
             # Remove ROIs, since we are saving the imageseries without them

hexrdgui/main_window.py

@@ -203,8 +203,10 @@ def setup_connections(self):
             self.on_action_open_materials_triggered)
         self.ui.action_save_imageseries.triggered.connect(
             self.on_action_save_imageseries_triggered)
-        self.ui.action_save_materials.triggered.connect(
-            self.on_action_save_materials_triggered)
+        self.ui.action_save_materials_hdf5.triggered.connect(
+            self.on_action_save_materials_hdf5_triggered)
+        self.ui.action_save_materials_cif.triggered.connect(
+            self.on_action_save_materials_cif_triggered)
         self.ui.action_save_state.triggered.connect(
             self.on_action_save_state_triggered)
         self.ui.action_open_state.triggered.connect(
@@ -604,10 +606,14 @@ def images_loaded(self, enabled=True):
     def on_action_open_materials_triggered(self):
         selected_file, selected_filter = QFileDialog.getOpenFileName(
             self.ui, 'Load Materials File', HexrdConfig().working_dir,
-            'HDF5 files (*.h5 *.hdf5)')
+            'HDF5 files (*.h5 *.hdf5), CIF (*.cif)')
+        if not selected_file:
+            return
 
-        if selected_file:
-            HexrdConfig().working_dir = os.path.dirname(selected_file)
+        HexrdConfig().working_dir = os.path.dirname(selected_file)
+        if Path(selected_file).suffix == '.cif':
+            HexrdConfig().import_material(selected_file)
+        else:
             HexrdConfig().load_materials(selected_file)
 
     def on_action_save_imageseries_triggered(self):
@@ -618,7 +624,7 @@ def on_action_save_imageseries_triggered(self):
 
         SaveImagesDialog(self.ui).exec()
 
-    def on_action_save_materials_triggered(self):
+    def on_action_save_materials_hdf5_triggered(self):
         selected_file, selected_filter = QFileDialog.getSaveFileName(
             self.ui, 'Save Materials', HexrdConfig().working_dir,
             'HDF5 files (*.h5 *.hdf5)')
@@ -631,7 +637,18 @@ def on_action_save_materials_triggered(self):
             if not any(selected_file.endswith(x) for x in acceptable_exts):
                 selected_file += '.h5'
 
-            return HexrdConfig().save_materials(selected_file)
+            return HexrdConfig().save_materials_hdf5(selected_file)
+
+    def on_action_save_materials_cif_triggered(self):
+        caption = 'Select directory to save CIF files to'
+        selected_dir = QFileDialog.getExistingDirectory(
+            self.ui, caption, dir=HexrdConfig().working_dir)
+        if not selected_dir:
+            return
+
+        HexrdConfig().working_dir = selected_dir
+        for material in HexrdConfig().materials.values():
+            HexrdConfig().save_material_cif(material, selected_dir)
 
     def on_action_export_current_plot_triggered(self):
         filters = 'HDF5 files (*.h5 *.hdf5);; NPZ files (*.npz)'

hexrdgui/material_list_editor.py

@@ -32,6 +32,7 @@ def setup_connections(self):
 
         self.ui.import_from_cif.clicked.connect(self.import_from_cif)
         self.ui.import_from_defaults.clicked.connect(self.import_from_defaults)
+        self.ui.export_to_cif.clicked.connect(self.export_to_cif)
 
         HexrdConfig().materials_dict_modified.connect(self.update_editor_items)
 
@@ -67,6 +68,32 @@ def item_added(self, new_name):
         material.name = new_name
         HexrdConfig().add_material(new_name, material)
 
+    def export_to_cif(self):
+        selections = self.editor.selected_items
+        filename = None
+        if len(selections) == 1:
+            caption = 'Save CIF file as'
+            selected_file, _ = QFileDialog.getSaveFileName(
+                self.ui, caption, HexrdConfig().working_dir,
+                'CIF files (*.cif)')
+            filename = str(Path(selected_file).name)
+            selected_dir = str(Path(selected_file).parent)
+        else:
+            caption = 'Select directory to export CIF files to'
+            selected_dir = QFileDialog.getExistingDirectory(
+                self.ui, caption, dir=HexrdConfig().working_dir)
+
+        if not selected_dir:
+            return
+
+        HexrdConfig().working_dir = selected_dir
+        # Export selected materials or all materials if none selected
+        if not selections:
+            selections = HexrdConfig().materials.values()
+        for selected in selections:
+            material = HexrdConfig().material(selected)
+            HexrdConfig().save_material_cif(material, selected_dir, filename)
+
     def import_from_cif(self):
         selected_file, selected_filter = QFileDialog.getOpenFileName(
             self.ui, 'Import Material', HexrdConfig().working_dir,

hexrdgui/resources/ui/main_window.ui

@@ -92,10 +92,17 @@
       <addaction name="action_save_config_hexrd"/>
       <addaction name="action_save_config_yaml"/>
      </widget>
+     <widget class="QMenu" name="menu_save_materials">
+      <property name="title">
+       <string>&amp;Materials</string>
+      </property>
+      <addaction name="action_save_materials_hdf5"/>
+      <addaction name="action_save_materials_cif"/>
+     </widget>
      <addaction name="action_save_imageseries"/>
      <addaction name="action_save_state"/>
      <addaction name="menu_save_config"/>
-     <addaction name="action_save_materials"/>
+     <addaction name="menu_save_materials"/>
     </widget>
     <widget class="QMenu" name="menu_export">
      <property name="title">
@@ -542,11 +549,6 @@
     <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Show the saturation percentages of the images when in &amp;quot;Image View&amp;quot; mode. The saturation percentages will appear as white text in the bottom left corners of the images.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
    </property>
   </action>
-  <action name="action_save_materials">
-   <property name="text">
-    <string>&amp;Materials</string>
-   </property>
-  </action>
   <action name="action_run_laue_and_powder_calibration">
    <property name="enabled">
     <bool>false</bool>
@@ -902,6 +904,16 @@
     <string>Apply Median Filter</string>
    </property>
   </action>
+  <action name="action_save_materials_hdf5">
+   <property name="text">
+    <string>HDF5</string>
+   </property>
+  </action>
+  <action name="action_save_materials_cif">
+   <property name="text">
+    <string>CIF</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>

hexrdgui/resources/ui/material_list_editor.ui

@@ -27,22 +27,29 @@
     <number>6</number>
    </property>
    <item row="2" column="0">
-    <widget class="QPushButton" name="import_from_defaults">
+    <widget class="QPushButton" name="import_from_cif">
      <property name="text">
-      <string>Import from Defaults</string>
+      <string>Import from CIF</string>
      </property>
     </widget>
    </item>
-   <item row="1" column="0">
-    <widget class="QPushButton" name="import_from_cif">
+   <item row="3" column="0">
+    <widget class="QPushButton" name="import_from_defaults">
      <property name="text">
-      <string>Import from CIF</string>
+      <string>Import from Defaults</string>
      </property>
     </widget>
    </item>
    <item row="0" column="0">
     <layout class="QVBoxLayout" name="list_editor_layout"/>
    </item>
+   <item row="1" column="0">
+    <widget class="QPushButton" name="export_to_cif">
+     <property name="text">
+      <string>Export to CIF</string>
+     </property>
+    </widget>
+   </item>
   </layout>
  </widget>
  <tabstops>

hexrdgui/state.py

@@ -156,7 +156,7 @@ def save(h5_file):
     _save_config(h5_file, state)
 
     # Write out the materials
-    HexrdConfig().save_materials(h5_file, '/materials')
+    HexrdConfig().save_materials_hdf5(h5_file, '/materials')
 
     # Write out the instrument
     HexrdConfig().save_instrument_config(h5_file)