From 4f9c9dd7e2f96ebb3d3297476e93b150242a8c9b Mon Sep 17 00:00:00 2001
From: JeanBilheux <bilheuxjm@ornl.gov>
Date: Wed, 16 Feb 2022 16:23:16 -0500
Subject: [PATCH] fixing error when no crop provided. this refs #50

---
 .../advanced_settings_initialization.py            | 10 +++++-----
 src/pyMBIR_UI/reconstruction_launcher.py           | 14 ++------------
 2 files changed, 7 insertions(+), 17 deletions(-)

diff --git a/src/pyMBIR_UI/advanced_settings/advanced_settings_initialization.py b/src/pyMBIR_UI/advanced_settings/advanced_settings_initialization.py
index 0e88ef3..50c28c0 100644
--- 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)
-                n_vox_y = int(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) - 1
+                n_vox_y = int(int(image_width / vox_xy_to_use) * det_x_to_use) - 1
                 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)
+                n_vox_x_y_value = int(int(crop_width / vox_xy_to_use) * det_x_to_use) - 1
                 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)
+                n_vox_z = int(int(image_height / vox_z_to_use) * det_y_to_use) - 1
             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)
+                n_vox_z = int(int(crop_height / vox_z_to_use) * det_y_to_use) - 1
         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
index 63fcad2..d510973 100644
--- a/src/pyMBIR_UI/reconstruction_launcher.py
+++ b/src/pyMBIR_UI/reconstruction_launcher.py
@@ -138,12 +138,8 @@ def run(self):
         dictionary_of_arguments = o_dictionary.get_dictionary()
         dictionary_of_arguments['running_mode'] = 'batch'
 
-        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_folder(dictionary_of_arguments['op_path'])
         logging.info(f"Making sure output folder ({full_output_folder}) exists!")
@@ -161,9 +157,9 @@ def run(self):
 
         self.dictionary_of_arguments = dictionary_of_arguments
 
-        logging.info(f"-> Saving config file to be called from command line script")
         home_folder = os.path.expanduser("~")
         json_file_name = os.path.join(home_folder, "config_batch_mode.json")
+        logging.info(f"-> Saving config file to be called from command line script into {json_file_name}")
         with open(json_file_name, 'w') as json_file:
             json.dump(dictionary_of_arguments, json_file)
 
@@ -173,8 +169,7 @@ def run(self):
         proc = subprocess.Popen(['python',
                                  script_exe,
                                  '--input_json',
-                                 json_file_name,
-],
+                                 json_file_name],
                                 shell=False)
         self.batch_process_id = proc
 
@@ -292,14 +287,9 @@ def check_output_file(self):
         o_event.update_output_plot()
 
     def check_output_3d_volume(self):
-        print("in check 3D")
-        base_output_folder = os.path.basename(self.dictionary_of_arguments['data_path'])
         output_folder = self.dictionary_of_arguments['op_path']
-        print(f"output_folder: {output_folder}")
         list_tiff_files_in_output_folder = glob.glob(os.path.join(output_folder, "*.tif?"))
-        print(f"list tiff:{list_tiff_files_in_output_folder}")
         number_of_files_in_output_folder = len(list_tiff_files_in_output_folder)
-        print(f"number of files: {number_of_files_in_output_folder}")
         if number_of_files_in_output_folder == 0:
             self.parent.ui.tabWidget_3.setTabEnabled(1, False)
             return