Update all file readers with command line interface so we can run them as a subprocess. Added also registry.yaml to decouple code from user-based instrument adaptations or extensions.

instruments/filereader_registry.py

@@ -1,15 +1,20 @@
 import os
 import sys
+import subprocess
+import yaml
 #root_dir = os.path.abspath(os.curdir)
 #sys.path.append(root_dir)
 
-try:
-    from dima.instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
-    from dima.instruments.readers.g5505_text_reader import read_txt_files_as_dict
+#try:
+#    from dima.instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
+#    from dima.instruments.readers.g5505_text_reader import read_txt_files_as_dict
     
-except ModuleNotFoundError:
-    from instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
-    from instruments.readers.g5505_text_reader import read_txt_files_as_dict
+#except ModuleNotFoundError as e:
+#    print(e)    
+from instruments.readers.xps_ibw_reader import read_xps_ibw_file_as_dict
+from instruments.readers.g5505_text_reader import read_txt_files_as_dict
+from instruments.readers.acsm_tofware_reader import read_acsm_files_as_dict
+from instruments.readers.acsm_flag_reader import read_jsonflag_as_dict
 
 file_extensions = ['.ibw','.txt','.dat','.h5','.TXT','.csv','.pkl','.json','.yaml']
 
@@ -19,24 +24,37 @@ default_instruments_dir = None  # or provide an absolute path
 file_readers = {
     'ibw': lambda a1: read_xps_ibw_file_as_dict(a1),
     'txt': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False),
-#    'TXT': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False),
     'dat': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False),
-    'csv': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False)
-}
+    'csv': lambda a1: read_txt_files_as_dict(a1, instruments_dir=default_instruments_dir, work_with_copy=False),
+    'ACSM_TOFWARE_txt' : lambda x: read_acsm_files_as_dict(x, instruments_dir=default_instruments_dir, work_with_copy=False),
+    'ACSM_TOFWARE_csv' : lambda x: read_acsm_files_as_dict(x, instruments_dir=default_instruments_dir, work_with_copy=False),
+    'ACSM_TOFWARE_flags_json' : lambda x: read_jsonflag_as_dict(x)}
 
-# Add new "instrument reader (Data flagging app data)"
+REGISTRY_FILE = "registry.yaml" #os.path.join(os.path.dirname(__file__), "registry.yaml")
 
-from instruments.readers.acsm_tofware_reader import read_acsm_files_as_dict
-file_extensions.append('.txt') 
-file_readers.update({'ACSM_TOFWARE_txt' : lambda x: read_acsm_files_as_dict(x, instruments_dir=default_instruments_dir, work_with_copy=False)})
+def load_registry():
 
-file_extensions.append('.csv') 
-file_readers.update({'ACSM_TOFWARE_csv' : lambda x: read_acsm_files_as_dict(x, instruments_dir=default_instruments_dir, work_with_copy=False)})
+    module_dir = os.path.dirname(__file__)
+    instruments_dir = os.path.join(module_dir, '..')
 
-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)})
+    # Normalize the path (resolves any '..' in the path)
+    registry_path = os.path.abspath(os.path.join(module_dir,REGISTRY_FILE))
 
+    with open(registry_path, "r") as file:
+        return yaml.safe_load(file)["instruments"]
+    
+def find_reader(instrument_folder, file_extension):
+
+
+
+    registry = load_registry()
+    
+    for entry in registry:
+        if entry["instrumentFolderName"] == instrument_folder and entry["fileExtension"] == file_extension:
+            return entry["fileReaderPath"], entry["InstrumentDictionaryPath"]
+    
+    return None, None  # Not found
+    
 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. 
@@ -81,4 +99,45 @@ def select_file_reader(path):
         return file_readers[extension]
     
     # Default case if no reader is found
-    return lambda x : None
+    return lambda x : None
+
+
+
+def run_reader(hdf5_file_path, src_file_path, dst_group_name):
+    try:
+        thisFilePath = os.path.abspath(__file__)
+    except NameError:
+        print("Error: __file__ is not available. Ensure the script is being run from a file.")
+        print("[Notice] Path to DIMA package may not be resolved properly.")
+        thisFilePath = os.getcwd()  # Use current directory or specify a default
+
+    projectPath = os.path.normpath(os.path.join(thisFilePath, "..",'..'))  # Move up to project root
+
+    # 
+    full_string, file_extension = compute_filereader_key_from_path(dst_group_name)
+    full_string_parts = full_string.split("_")
+    full_string_parts.remove(file_extension)
+    instrument_folder = '_'.join(full_string_parts)
+
+
+
+    reader_path, dict_path = find_reader(instrument_folder, file_extension)
+    
+
+    if reader_path:
+        reader_path = os.path.normpath(os.path.join(projectPath, reader_path))
+        if not os.path.exists(reader_path):
+            raise FileNotFoundError(f"File reader {reader_path} not found for key {full_string}. Verify the reader is properly referenced in registry.yaml.")
+        else:
+            print(f'Attempting to run {reader_path}')
+
+
+        command = ["python", reader_path, hdf5_file_path, src_file_path, instrument_folder]
+        #if dict_path:
+        #    args.append(dict_path)        
+        print(f"Running: {command}")
+        output = subprocess.run(command, capture_output=True)#, check=True)
+        print('Subprocess output',output.stdout)
+    else:
+        print(f'There is no file reader available to process files in {instrument_folder}.')
+        #logging.info(instFoldermsdEnd )