From a58bf4f0196b66ddf9712c447a739307b0c17673 Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Tue, 26 Mar 2024 13:57:19 +0100
Subject: [PATCH] Refactored import dependencies.

---
 src/g5505_file_reader.py        | 15 +++++----------
 src/hdf5_lib.py                 | 28 ++++++++++++++++++----------
 src/smog_chamber_file_reader.py | 14 +++++++++-----
 3 files changed, 32 insertions(+), 25 deletions(-)

diff --git a/src/g5505_file_reader.py b/src/g5505_file_reader.py
index 2589448..c86a2ee 100644
--- a/src/g5505_file_reader.py
+++ b/src/g5505_file_reader.py
@@ -1,17 +1,13 @@
+import os
+
 import numpy as np
 import pandas as pd
-import matplotlib.pyplot as plt
-import plotly.express as px
-import plotly.graph_objects as go
-from plotly.subplots import make_subplots
 from igor2.binarywave import load as loadibw
 
-#import h5py
-import os
-import tempfile
-import shutil
+import src.g5505_utils as utils
+
+
 import h5py
-import g5505_utils as utils
 
 ROOT_DIR = os.path.abspath(os.curdir)
 
@@ -125,7 +121,6 @@ def read_txt_files_as_dict(filename : str ):
 
                 print(line_number, len(column_names ))
                 break
-            
             # Subdivide line into words, and join them by single space. 
             # I asumme this can produce a cleaner line that contains no weird separator characters \t \r or extra spaces and so on.
             list_of_substrings = line.split()
diff --git a/src/hdf5_lib.py b/src/hdf5_lib.py
index ad41383..7126179 100644
--- a/src/hdf5_lib.py
+++ b/src/hdf5_lib.py
@@ -1,17 +1,20 @@
-import pandas as pd
-import h5py
+import sys
 import os
-#import sys
-#from itertools import product
+root_dir = os.path.abspath(os.curdir)
+sys.path.append(root_dir)
+
+import pandas as pd
 import numpy as np
 
 
 
 #import g5505_file_reader
-import g5505_utils as utils
-#import smog_chamber_file_reader 
+import src.g5505_utils as utils
+import input_files.config_file as config_file
+import src.hdf5_vis as hdf5_vis
 
-import config_file
+import h5py
+import yaml
 
 
 def read_mtable_as_dataframe(filename):
@@ -456,8 +459,14 @@ def main():
     select_file_keywords = config_file.select_file_keywords #['20220726','2022.07.26']
 
     output_filename_path = os.path.join(config_file.outputfile_dir,config_file.output_filename)   
-    create_hdf5_file_from_filesystem_path(output_filename_path,inputfile_dir,select_dir_keywords,select_file_keywords)
-    #display_group_hierarchy_on_a_treemap(output_filename_path)
+    if not os.path.exists(output_filename_path):
+        create_hdf5_file_from_filesystem_path(output_filename_path,inputfile_dir,select_dir_keywords,select_file_keywords)
+
+    # hdf5_vis.display_group_hierarchy_on_a_treemap(output_filename_path)
+    output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(output_filename_path)
+
+
+    return output_filename_path, output_yml_filename_path
 
 def main_mtable_h5_from_dataframe():
 
@@ -503,7 +512,6 @@ def main_mtable_h5_from_dataframe():
 
     print(':)')
 
-
 if __name__ == '__main__':
 
     main()
diff --git a/src/smog_chamber_file_reader.py b/src/smog_chamber_file_reader.py
index 61f145c..5bdb8ec 100644
--- a/src/smog_chamber_file_reader.py
+++ b/src/smog_chamber_file_reader.py
@@ -1,9 +1,13 @@
-
-import pandas as pd
-import numpy as np
-import matplotlib.pyplot as plt
 import os
-import g5505_utils as utils
+
+import numpy as np
+import pandas as pd
+from igor2.binarywave import load as loadibw
+
+import src.g5505_utils as utils
+
+
+import h5py
 
 #def read_txt_files_as_dict(filename : str ,instrument_folder : str):
 def read_txt_files_as_dict(filename : str ):