n_vox_x, y and z are now integers. GPU number is at least 1. this refs …

…#49

src/pyMBIR_UI/advanced_settings/advanced_settings_initialization.py

@@ -57,27 +57,27 @@ 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(image_width / vox_xy_to_use) * det_x_to_use
-                n_vox_y = int(image_width / vox_xy_to_use) * det_x_to_use
+                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(crop_width / vox_xy_to_use) * det_x_to_use
+                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
         n_vox_y_to_use = n_vox_y
 
         n_vox_z_mode = config['n_vox_z']["mode"]
         if n_vox_z_mode == "user":
-            n_vox_z = config['n_vox_z']['user_value']
+            n_vox_z = int(config['n_vox_z']['user_value'])
         else:
             if session_dict.get('crop', None) is None:
                 image_height = self.parent.image_size['height']
-                n_vox_z = int(image_height / vox_z_to_use) * det_y_to_use
+                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(crop_height / vox_z_to_use) * det_y_to_use
+                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']

src/pyMBIR_UI/pyMBIR_UI.py

@@ -105,8 +105,6 @@ class PyMBIRUILauncher(QMainWindow):
     # batch mode - last time a file was added to output folder
     list_file_found_in_output_folder = None
 
-
-
     def __init__(self, parent=None):
 
         super(PyMBIRUILauncher, self).__init__(parent)

src/pyMBIR_UI/reconstruction_launcher.py

@@ -22,7 +22,7 @@
 from .status_message_config import show_status_message, StatusMessageStatus
 from .event_handler import EventHandler
 from NeuNorm.normalization import Normalization
-from .utilities.file_utilities import make_or_reset_folder
+from .utilities.file_utilities import make_or_reset_folder, make_folder
 from .venkat_function import MBIR_fromGUI
 # from .recon_HFIR_script_batch import recon_HFIR_script_launcher
 from .reconstructed_output_handler import ReconstructedOutputHandler
@@ -138,28 +138,23 @@ def run(self):
         dictionary_of_arguments = o_dictionary.get_dictionary()
         dictionary_of_arguments['running_mode'] = 'batch'
 
-        # for debugging only !!! remove me
-        #dictionary_of_arguments['n_vox_z'] = 6
-
         base_output_folder = os.path.basename(dictionary_of_arguments['data_path'])
         full_output_folder = os.path.join(dictionary_of_arguments['op_path'])
 
  #       full_output_folder = os.path.join(dictionary_of_arguments['op_path'], base_output_folder +
  #                                         "_pymbir_reconstructed")
 #        dictionary_of_arguments['op_path'] = full_output_folder
         logging.info(f"Final image will be output in {full_output_folder}")
-        make_or_reset_folder(dictionary_of_arguments['op_path'])
-        logging.info(f"Reset output folder: {full_output_folder}")
+        make_folder(dictionary_of_arguments['op_path'])
+        logging.info(f"Making sure output folder ({full_output_folder}) exists!")
 
-        dictionary_of_arguments['temp_op_dir'] = os.path.join(dictionary_of_arguments['op_path'], "temporary_pymbir_reconstructed")
+        self.tmp_output_folder = os.path.join(dictionary_of_arguments['op_path'], "temporary_pymbir_reconstructed")
+        dictionary_of_arguments['temp_op_dir'] = self.tmp_output_folder
+        logging.info(f"-> reset temporary folder: {dictionary_of_arguments['temp_op_dir']}")
         make_or_reset_folder(dictionary_of_arguments['temp_op_dir'])
 
         logging.info(f"-> Dictionary of arguments: {dictionary_of_arguments}")
 
-        logging.info(f"-> reset temporary folder: {dictionary_of_arguments['temp_op_dir']}")
-        make_or_reset_folder(dictionary_of_arguments['temp_op_dir'])
-        self.tmp_output_folder = dictionary_of_arguments['temp_op_dir']
-
         self.parent.ui.reconstruction_launch_pushButton.setEnabled(False)
         self.parent.ui.reconstruction_display_latest_output_file_pushButton.setEnabled(True)
         self.parent.ui.reconstruction_batch_stop_pushButton.setEnabled(True)

src/pyMBIR_UI/utilities/file_utilities.py

@@ -75,3 +75,8 @@ def make_or_reset_folder(folder_name):
     if os.path.exists(folder_name):
         shutil.rmtree(folder_name)
     os.makedirs(folder_name)
+
+
+def make_folder(folder_name):
+    if not os.path.exists(folder_name):
+        os.makedirs(folder_name)

src/pyMBIR_UI/utilities/get.py

@@ -157,7 +157,7 @@ def get_number_of_gpu():
             return nbr_gpu
 
         except FileNotFoundError:
-            return 0
+            return 1
 
     @staticmethod
     def full_home_file_name(base_file_name):