Integrate StartTime BIDS physio parameter

physiopy · Aug 19, 2024 · bbe49a6 · bbe49a6
1 parent 82d6ee9
commit bbe49a6
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 10 deletions.
diff --git a/physutils/io.py b/physutils/io.py
@@ -76,15 +76,15 @@ def load_from_bids(
 
     config_file = bids_file[0].get_metadata()
     fs = config_file["SamplingFrequency"]
-    t_start = config_file["StartTime"]  # noqa
+    t_start = config_file["StartTime"] if "StartTime" in config_file else 0
     columns = config_file["Columns"]
     logger.debug(f"Loaded structure contains columns: {columns}")
 
     physio_objects = {}
     data = np.loadtxt(bids_file[0].path)
 
     if "time" in columns:
-        idx_0 = np.argmax(data[:, columns.index("time")] >= 0)
+        idx_0 = np.argmax(data[:, columns.index("time")] >= t_start)
     else:
         idx_0 = 0
         logger.warning(

diff --git a/physutils/physio.py b/physutils/physio.py
@@ -563,12 +563,6 @@ class MRIConfig:
     def __init__(self, slice_timings=None, n_scans=None, tr=None):
         if np.ndim(slice_timings) > 1:
             raise ValueError("Slice timings must be a 1-dimensional array.")
-        if np.size(slice_timings) != n_scans:
-            raise ValueError(
-                "Number of slice timings ({}) must match number of scans ({}).".format(
-                    np.size(slice_timings), n_scans
-                )
-            )
 
         self._slice_timings = np.asarray(slice_timings)
         self._n_scans = int(n_scans)

diff --git a/physutils/tests/test_io.py b/physutils/tests/test_io.py
@@ -63,8 +63,8 @@ def test_load_from_bids():
 
     for col in phys_array.keys():
         assert isinstance(phys_array[col], physio.Physio)
-        # The data saved are the ones after t_0 = 0s
-        assert phys_array[col].data.size == 70000
+        # The data saved are the ones after t_0 = -3s
+        assert phys_array[col].data.size == 80000
         assert phys_array[col].fs == 10000.0
         assert phys_array[col].history[0][0] == "physutils.io.load_from_bids"
 

diff --git a/physutils/tests/utils.py b/physutils/tests/utils.py
@@ -138,9 +138,11 @@ def create_random_bids_structure(data_dir):
     # Initialize tsv file with random data columns and a time column
     num_rows = 100000
     num_cols = 6
+    time_offset = 2
     time = (
         np.arange(num_rows) / physio_json["SamplingFrequency"]
         + physio_json["StartTime"]
+        - time_offset
     )
     data = np.column_stack((time, np.random.rand(num_rows, num_cols - 1).round(8)))
     df = pd.DataFrame(data)