added --quite flag to cli to bypass sanity checks

sensospot_data/__init__.py

@@ -38,9 +38,16 @@ from .dynamic_range import blend, create_xdr, normalize_values  # noqa: F401
     default="raw_data.h5",
     help="Output file name",
 )
-def run(source, outfile):
+@click.option(
+    "-q",
+    "--quiet",
+    is_flag=True,
+    default=False,
+    help="Ignore Sanity Check",
+)
+def run(source, outfile, quiet=False):
     source_path = Path(source)
     # read the raw data of a folder
-    raw_data = parse_folder(source_path)
+    raw_data = parse_folder(source_path, quiet=quiet)
     hdf5_path = source_path / outfile
     raw_data.to_hdf(hdf5_path, key="raw_data", format="table")

sensospot_data/parser.py

@@ -124,16 +124,20 @@ def _sanity_check(data_frame):
     spot_positions = len(data_frame[RAW_DATA_POS_ID].unique())
     expected_rows = field_rows * field_cols * exposures * spot_positions
     if expected_rows != len(data_frame):
-        raise ValueError("Measurements are missing")
+        raise ValueError(
+            f"Measurements are missing: {expected_rows} != {len(data_frame)}"
+        )
     # set the right data type for measurement columns
     for raw_column in RAW_DATA_NORMALIZATION_MAP:
         data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column])   
     return data_frame
 
 
-def parse_folder(folder):
+def parse_folder(folder, quiet=False):
     """ parses all csv files in a folder to one large dataframe """
     file_list = list_csv_files(Path(folder))
     data_frame = parse_multiple_files(file_list)
     data_frame = add_optional_measurement_parameters(data_frame, folder)
+    if quiet:
+        return data_frame
     return _sanity_check(data_frame)