From 098a79531c9d0e91277f5cb440191e0ec609387a Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Thu, 3 Oct 2024 09:07:06 +0200
Subject: [PATCH] Added new instrument (flagging app) file reading
 capabilities. It includes two files a flag_reader.py that takes flag.json
 files produced by the app into a standard intermidiate representation, and a
 yaml file with instrument dependent description terms. Last, we modified the
 filereader_registry.py to find the new instrument file reader.

---
 .../dictionaries/ACSM_TOFWARE_flags.yaml      |  0
 instruments/readers/filereader_registry.py    |  5 +++
 instruments/readers/flag_reader.py            | 36 +++++++++++++++++++
 3 files changed, 41 insertions(+)
 create mode 100644 instruments/dictionaries/ACSM_TOFWARE_flags.yaml
 create mode 100644 instruments/readers/flag_reader.py

diff --git a/instruments/dictionaries/ACSM_TOFWARE_flags.yaml b/instruments/dictionaries/ACSM_TOFWARE_flags.yaml
new file mode 100644
index 0000000..e69de29
diff --git a/instruments/readers/filereader_registry.py b/instruments/readers/filereader_registry.py
index 2d893fb..de5d717 100644
--- a/instruments/readers/filereader_registry.py
+++ b/instruments/readers/filereader_registry.py
@@ -22,6 +22,11 @@ file_readers = {
     'ACSM_TOFWARE_csv': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False)
 }
 
+# Add new "instrument reader (Data flagging app data)"
+from instruments.readers.flag_reader import read_jsonflag_as_dict
+file_extensions.append('.json') 
+file_readers.update({'ACSM_TOFWARE_flags_json' : lambda x: read_jsonflag_as_dict(x)})
+
 def compute_filereader_key_from_path(hdf5_file_path):
     """Constructs the key 'instrumentname_ext' based on hdf5_file_path, structured as
     /instrumentname/to/filename.ext, which access the file reader that should be used to read such a file. 
diff --git a/instruments/readers/flag_reader.py b/instruments/readers/flag_reader.py
new file mode 100644
index 0000000..35df85e
--- /dev/null
+++ b/instruments/readers/flag_reader.py
@@ -0,0 +1,36 @@
+import os
+import sys
+#root_dir = os.path.abspath(os.curdir)
+#sys.path.append(root_dir)
+
+import json
+import dima.utils.g5505_utils as utils
+
+
+
+def read_jsonflag_as_dict(path_to_file):
+
+
+    file_dict = {}
+    path_tail, path_head = os.path.split(path_to_file)
+
+    file_dict['name'] = path_head
+    # TODO: review this header dictionary, it may not be the best way to represent header data
+    file_dict['attributes_dict'] = {}
+    file_dict['datasets'] = []
+
+    try:
+        with open(path_to_file, 'r') as stream:
+            flag = json.load(stream)#, Loader=json.FullLoader)
+    except (FileNotFoundError, json.JSONDecodeError) as exc:
+        print(exc)
+
+    dataset = {}
+    dataset['name'] = 'data_table'#_numerical_variables'
+    dataset['data'] = utils.convert_attrdict_to_np_structured_array(flag) #df_numerical_attrs.to_numpy()
+    dataset['shape'] = dataset['data'].shape
+    dataset['dtype'] = type(dataset['data'])  
+
+    file_dict['datasets'].append(dataset)
+
+    return file_dict
\ No newline at end of file