fixed offset convention. this refs #50

ornlneutronimaging · Feb 16, 2022 · bde6a79 · bde6a79
1 parent 4f9c9dd
commit bde6a79
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Showing 3 changed files with 29 additions and 7 deletions.
diff --git a/src/pyMBIR_UI/advanced_settings/advanced_settings_initialization.py b/src/pyMBIR_UI/advanced_settings/advanced_settings_initialization.py
@@ -57,12 +57,12 @@ def from_config_to_session_dict(self):
             session_dict = self.parent.session_dict
             if session_dict.get('crop', None) is None:
                 image_width = self.parent.image_size['width']
-                n_vox_x = int(int(image_width / vox_xy_to_use) * det_x_to_use) - 1
-                n_vox_y = int(int(image_width / vox_xy_to_use) * det_x_to_use) - 1
+                n_vox_x = int(int(image_width / vox_xy_to_use) * det_x_to_use)
+                n_vox_y = int(int(image_width / vox_xy_to_use) * det_x_to_use)
                 n_vox_x_y_value = n_vox_x
             else:
                 crop_width = session_dict['crop']['width']
-                n_vox_x_y_value = int(int(crop_width / vox_xy_to_use) * det_x_to_use) - 1
+                n_vox_x_y_value = int(int(crop_width / vox_xy_to_use) * det_x_to_use)
                 n_vox_x = n_vox_x_y_value
                 n_vox_y = n_vox_x_y_value
         n_vox_x_to_use = n_vox_x
@@ -74,10 +74,10 @@ def from_config_to_session_dict(self):
         else:
             if session_dict.get('crop', None) is None:
                 image_height = self.parent.image_size['height']
-                n_vox_z = int(int(image_height / vox_z_to_use) * det_y_to_use) - 1
+                n_vox_z = int(int(image_height / vox_z_to_use) * det_y_to_use)
             else:
                 crop_height = session_dict['crop']['to slice - from slice']
-                n_vox_z = int(int(crop_height / vox_z_to_use) * det_y_to_use) - 1
+                n_vox_z = int(int(crop_height / vox_z_to_use) * det_y_to_use)
         n_vox_z_to_use = n_vox_z
 
         write_output_flag = config['write output']

diff --git a/src/pyMBIR_UI/reconstruction_launcher.py b/src/pyMBIR_UI/reconstruction_launcher.py
@@ -128,6 +128,12 @@ def initialization(self):
         ReconstructionLauncher.initialization(self)
         self.parent.list_file_found_in_output_folder = None
 
+    @staticmethod
+    def _fix_n_vox(dictionary_of_arguments):
+        dictionary_of_arguments["n_vox_x"] = dictionary_of_arguments["n_vox_x"] - 1
+        dictionary_of_arguments["n_vox_y"] = dictionary_of_arguments["n_vox_y"] - 1
+        dictionary_of_arguments["n_vox_z"] = dictionary_of_arguments["n_vox_z"] - 1
+
     def run(self):
         logging.info("Running reconstruction in Batch mode")
         logging.info(f"-> algorithm selected: {self.reconstruction_algorithm_selected}")
@@ -149,6 +155,10 @@ def run(self):
         logging.info(f"-> reset temporary folder: {dictionary_of_arguments['temp_op_dir']}")
         make_or_reset_folder(dictionary_of_arguments['temp_op_dir'])
 
+        # fix n_vox_x, n_vox_y and n_vox_z to follow pymbir convention
+        # n_vox_x, y and z have a start index of 1 in the UI, 0 in the algorithm
+        ReconstructionBatchLauncher._fix_n_vox(dictionary_of_arguments)
+
         logging.info(f"-> Dictionary of arguments: {dictionary_of_arguments}")
 
         self.parent.ui.reconstruction_launch_pushButton.setEnabled(False)

diff --git a/src/pyMBIR_UI/ui/advanced_settings.ui b/src/pyMBIR_UI/ui/advanced_settings.ui
@@ -615,7 +615,7 @@
            <item>
             <widget class="QLabel" name="n_vox_x_n_vox_y_fixed_value">
              <property name="text">
-              <string>0</string>
+              <string>1</string>
              </property>
             </widget>
            </item>
@@ -661,6 +661,9 @@
              <property name="enabled">
               <bool>false</bool>
              </property>
+             <property name="minimum">
+              <number>1</number>
+             </property>
              <property name="maximum">
               <number>10000</number>
              </property>
@@ -705,6 +708,9 @@
              <property name="enabled">
               <bool>false</bool>
              </property>
+             <property name="minimum">
+              <number>1</number>
+             </property>
              <property name="maximum">
               <number>10000</number>
              </property>
@@ -738,6 +744,9 @@
              <property name="enabled">
               <bool>false</bool>
              </property>
+             <property name="minimum">
+              <number>1</number>
+             </property>
              <property name="maximum">
               <number>10000</number>
              </property>
@@ -789,7 +798,7 @@
            <item>
             <widget class="QLabel" name="n_vox_z_fixed_value">
              <property name="text">
-              <string>0</string>
+              <string>1</string>
              </property>
             </widget>
            </item>
@@ -832,6 +841,9 @@
              <property name="enabled">
               <bool>false</bool>
              </property>
+             <property name="minimum">
+              <number>1</number>
+             </property>
              <property name="maximum">
               <number>10000</number>
              </property>