fix a few bugs.

src/pyMBIR_UI/algorithm_dictionary_creator.py

@@ -161,9 +161,6 @@ def build_dictionary(self, session_dict=None, config_file_name=None):
         n_vox_x = session_dict['advanced settings']['n_vox_x, n_vox_y']['n_vox_x_to_use']
         n_vox_y = session_dict['advanced settings']['n_vox_x, n_vox_y']['n_vox_y_to_use']
 
-        print("in build dictionary")
-        print(f"session_dict['advanced settings']['n_vox_z']: {session_dict['advanced settings']['n_vox_z']}")
-
         n_vox_z = session_dict['advanced settings']['n_vox_z']['n_vox_z_to_use']
         arguments['n_vox_x'] = n_vox_x
         arguments['n_vox_y'] = n_vox_y

src/pyMBIR_UI/recon_HFIR_script_batch.py

@@ -10,14 +10,12 @@
 # -----------------------------------------------------------------------
 
 import argparse
-import numpy as np
-import time
 from tomopy import remove_stripe_fw
 try:
     from dxchange.writer import write_tiff_stack
     from pyMBIR.reconEngine import analytic, MBIR
     from pyMBIR.utils import apply_proj_tilt
-    from readNeutronData import *
+    from src.pyMBIR_UI.readNeutronData import *
     import dxchange
 except ModuleNotFoundError:
     pass
@@ -36,22 +34,22 @@ def main():
     with open(args.input_json, "r") as read_file:
          input_dict = json.load(read_file)
 
-    # for testing only
-    import glob
-    list_files = glob.glob("/Volumes/G-DRIVE/IPTS/IPTS-25967-pymbir/output_folder/real_output_folder/*.tiff")
-
-    import time
-    import shutil
-    for _file in list_files:
-        time.sleep(.5)
-        shutil.copy(_file, input_dict['temp_op_dir'])
-
-    for _file in list_files:
-        shutil.copy(_file, input_dict['op_path'])
+    import pprint
+    pprint.pprint(input_dict)
 
-    return   # just for testing
+    # for testing only
+    #import glob
+   # list_files = glob.glob("/Volumes/G-DRIVE/IPTS/IPTS-25967-pymbir/output_folder/real_output_folder/*.tiff")
+
+    # #import time
+    # import shutil
+    # for _file in list_files:
+    #     time.sleep(.5)
+    #     shutil.copy(_file, input_dict['temp_op_dir'])
+    #
+    # for _file in list_files:
+    #     shutil.copy(_file, input_dict['op_path'])
 
-    pprint.pprint(input_dict)
     max_core = input_dict['max_core']
     num_wav_level = input_dict['wav_level']
     tot_col = input_dict['tot_col']
@@ -152,7 +150,7 @@ def main():
     import pyqtgraph as pg
     pg.image(rec_mbir);
     pg.QtGui.QApplication.exec_()
-    if input_dict.write_op == True:
+    if input_dict["write_op"] == True:
         dxchange.write_tiff_stack(rec_mbir, fname=input_dict["op_path"], start=z_start, overwrite=True)
 
 

src/pyMBIR_UI/reconstruction_launcher.py

@@ -139,7 +139,7 @@ def run(self):
         dictionary_of_arguments['running_mode'] = 'batch'
 
         # for debugging only !!! remove me
-        dictionary_of_arguments['n_vox_z'] = 6
+        #dictionary_of_arguments['n_vox_z'] = 6
 
 
 
@@ -166,7 +166,7 @@ def run(self):
         self.dictionary_of_arguments = dictionary_of_arguments
 
         logging.info(f"-> Saving config file to be called from command line script")
-        with open("/Users/j35/Desktop/config_to_test_batch_mode.json", 'w') as json_file:
+        with open("/home/j35/config_to_test_batch_mode.json", 'w') as json_file:
             json.dump(dictionary_of_arguments, json_file)
 
         current_location = os.path.abspath(os.path.dirname(__file__))
@@ -175,7 +175,7 @@ def run(self):
         proc = subprocess.Popen(['python',
                                  script_exe,
                                  '--input_json',
-                                 "/Users/j35/Desktop/config_to_test_batch_mode.json",
+                                 "/home/j35/config_to_test_batch_mode.json",
                                  ],
                                 shell=False)
         self.batch_process_id = proc

src/pyMBIR_UI/venkat_function.py

@@ -1,21 +1,17 @@
-import numpy as np
 import logging
-import json
-from qtpy.QtCore import QObject, QThread, Signal
+from qtpy.QtCore import QObject, Signal
 from tomopy import remove_stripe_fw
 try:
     from pyMBIR.reconEngine import analytic, MBIR
     from pyMBIR.utils import apply_proj_tilt
 except ModuleNotFoundError:
     pass
-from readNeutronData import *
+from pyMBIR_UI.readNeutronData import *
 from tomopy.misc.corr import median_filter
 import os
 import dxchange
 import time
 
-from .algorithm_dictionary_creator import AlgorithmDictionaryCreator
-
 
 class TestWorker(QObject):
     finished = Signal()