Fixes behavior of stc.save() as mentioned in issue #13158

doc/changes/devel/13165.bugfix.rst

@@ -0,0 +1,4 @@
+Fixes behavior of stc.save() as mentioned in issue #13158 :meth:`stc.save` and in `test_source_estimate.py` by `Shresth Keshari`.
+- Changed filetype to "auto"
+- saving a `.stc` file automatically saves two files with suffix `-lh.stc` and `-rh.stc`, which is intuitive and removes any confusion.
+- there were problems with pytest later on, which were tackled by minor tweaks.

mne/source_estimate.py

@@ -1884,7 +1884,7 @@ class SourceEstimate(_BaseSurfaceSourceEstimate):
     """
 
     @verbose
-    def save(self, fname, ftype="stc", *, overwrite=False, verbose=None):
+    def save(self, fname, ftype="auto", overwrite=False, verbose=None):
         """Save the source estimates to a file.
 
         Parameters
@@ -1894,18 +1894,29 @@ def save(self, fname, ftype="stc", *, overwrite=False, verbose=None):
             spaces are obtained by adding ``"-lh.stc"`` and ``"-rh.stc"`` (or
             ``"-lh.w"`` and ``"-rh.w"``) to the stem provided, for the left and
             the right hemisphere, respectively.
-        ftype : str
-            File format to use. Allowed values are ``"stc"`` (default),
-            ``"w"``, and ``"h5"``. The ``"w"`` format only supports a single
-            time point.
+        ftype : "auto" | "stc" | "w" | "h5"
+            File format to use. If "auto", the file format will be inferred from the
+            file extension if possible. Other allowed values are ``"stc"``, ``"w"``, and
+            ``"h5"``. The ``"w"`` format only supports a single time point.
         %(overwrite)s
 
             .. versionadded:: 1.0
         %(verbose)s
         """
         fname = str(_check_fname(fname=fname, overwrite=True))  # checked below
+        if ftype == "auto":
+            if fname.endswith((".stc", "-lh.stc", "-rh.stc")):
+                ftype = "stc"
+            elif fname.endswith((".w", "-lh.w", "-rh.w")):
+                ftype = "w"
+            elif fname.endswith(".h5"):
+                ftype = "h5"
+            else:
+                logger.info(
+                    "Cannot infer file type from `fname`; falling back to `.stc` format"
+                )
+                ftype = "stc"
         _check_option("ftype", ftype, ["stc", "w", "h5"])
-
         lh_data = self.data[: len(self.lh_vertno)]
         rh_data = self.data[-len(self.rh_vertno) :]
 
@@ -1918,6 +1929,8 @@ def save(self, fname, ftype="stc", *, overwrite=False, verbose=None):
                     "real numbers before saving."
                 )
             logger.info("Writing STC to disk...")
+            if fname.endswith(".stc"):
+                fname = fname[:-4]
             fname_l = str(_check_fname(fname + "-lh.stc", overwrite=overwrite))
             fname_r = str(_check_fname(fname + "-rh.stc", overwrite=overwrite))
             _write_stc(

mne/tests/test_source_estimate.py

@@ -480,9 +480,8 @@ def attempt_assignment(stc, attr, val):
 def test_io_stc(tmp_path):
     """Test IO for STC files."""
     stc = _fake_stc()
-    stc.save(tmp_path / "tmp.stc")
-    stc2 = read_source_estimate(tmp_path / "tmp.stc")
-
+    stc.save(tmp_path / "tmp.stc", overwrite=True)
+    stc2 = read_source_estimate(tmp_path / "tmp")
     assert_array_almost_equal(stc.data, stc2.data)
     assert_array_almost_equal(stc.tmin, stc2.tmin)
     assert_equal(len(stc.vertices), len(stc2.vertices))

sample.py

@@ -0,0 +1,42 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import numpy as np
+from mne.source_estimate import SourceEstimate
+
+# Create dummy data for the SourceEstimate
+n_vertices_lh = 10  # Number of vertices in the left hemisphere
+n_vertices_rh = 12  # Number of vertices in the right hemisphere
+n_times = 5         # Number of time points
+
+# Random data for the left and right hemispheres
+data = np.random.rand(n_vertices_lh + n_vertices_rh, n_times)
+
+# Vertices for the left and right hemispheres
+vertices = [np.arange(n_vertices_lh), np.arange(n_vertices_rh)]
+
+# Time parameters
+tmin = 0.0  # Start time in seconds
+tstep = 0.1  # Time step in seconds
+
+# Subject name
+subject = "sample_subject"
+
+# Create a SourceEstimate object
+stc = SourceEstimate(data, vertices, tmin, tstep, subject=subject)
+
+# Save the SourceEstimate in different formats
+output_dir = "./output_files"  # Directory to save the files
+import os
+os.makedirs(output_dir, exist_ok=True)
+
+stc.save("test.h5",overwrite=True)
+stc.save("test.stc",overwrite=True)
+# # Save as .stc file
+# stc.save(f"{output_dir}/dummy", ftype="stc", overwrite=True)
+
+# # Save as .h5 file
+# stc.save(f"{output_dir}/dummy.h5", ftype="h5", overwrite=True)
+
+# print(f"Dummy files saved in {output_dir}")