Merge pull request #44 from AdebayoBraimah/dev5

Dev5

CHANGES.rst

@@ -1,6 +1,14 @@
 CHANGES
 =========
 
+0.2.0a12
+---------
+
+This version is an alpha release that contains several bug fixes and updates.
+
+* BUG FIX: Fixed bug in which if a singular b-value was read from a b-value text file, then errors would be thrown.
+* BUG FIX: Fixed bug in which unprocessed source data was not converted to BIDS NIFTI data.
+
 0.2.0a11
 ---------
 

convert_source/cs_utils/database.py

@@ -758,7 +758,8 @@ def query_db(database:str,
     """Database query wrapper function that writes and performs a query for some provided value.
 
     NOTE:
-        The SQL query performed in this function assumes that the value is of datatype ``TEXT``.
+        * The SQL query performed in this function assumes that the value is of datatype ``TEXT``.
+        * If ``column`` is not provided, then it is assumed that ``table`` and ``column`` share the same name.
 
     Usage example:
         >>> sub_id = query_db(database='file.db',

convert_source/cs_utils/utils.py

@@ -649,8 +649,16 @@ def get_bvals(bval_file: Optional[str] = ""
     if bval_file and os.path.exists(bval_file):
         bval_file: str = os.path.abspath(bval_file)
         vals = np.loadtxt(bval_file)
-        vals_int = [ int(i) for i in vals ]
-        vals_nonzero = [ i for i in vals_int if i != 0 ]
+
+        # NOTE: This try-except statement is here for situtions
+        #   in which a singular b-value is found in the b-value
+        #   text file.
+        try:
+            vals_int: List[int] = [ int(i) for i in vals ]
+        except TypeError:
+            vals_int: List[int] = [ int(vals) ]
+
+        vals_nonzero: List[int] = [ i for i in vals_int if i != 0 ]
         bvals: List[float] = list(np.unique(vals_nonzero))
         return [ int(i) for i in bvals ]
     else:
@@ -1142,7 +1150,13 @@ def collect_info(parent_dir: str,
                                     prim_key='rel_path',
                                     column='file_id',
                                     value=db_info.get('rel_path',''))
-            if file_id:
+
+            bids_name: str = query_db(database=database, 
+                                      table='bids_name', 
+                                      prim_key='file_id', 
+                                      value=file_id)
+
+            if file_id and bids_name:
                 if log:
                     log.log("Imaging data has already been processed and is stored in the database.")
             else:

convert_source/version.txt

@@ -1 +1 @@
-0.2.0a11
+0.2.0a12