Merge pull request #280 from scottclowe/api_rename-to-matfile

API: Rename run_fissa argument export_to_matlab -> export_to_matfile

examples/Basic usage - Function.ipynb

@@ -617,7 +617,7 @@
     "\n",
     "The results can easily be exported to a MATLAB-compatible [MAT-file](https://mathworks.com/help/matlab/import_export/mat-file-versions.html) as follows.\n",
     "\n",
-    "If we provide `export_to_matlab=True` to `fissa.run_fissa`, it will export the data a matfile named `\"separated.mat\"` within the cache directory (the cache directory as provided with the `folder` argument)."
+    "If we provide `export_to_matfile=True` to `fissa.run_fissa`, it will export the data a matfile named `\"separated.mat\"` within the cache directory (the cache directory as provided with the `folder` argument)."
    ]
   },
   {
@@ -627,15 +627,15 @@
    "outputs": [],
    "source": [
     "result, raw = fissa.run_fissa(\n",
-    "    images_location, rois_location, folder=output_folder, export_to_matlab=True\n",
+    "    images_location, rois_location, folder=output_folder, export_to_matfile=True\n",
     ")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Alternatively, we can export to a matfile with a custom file name by setting the `export_to_matlab` argument to the target path."
+    "Alternatively, we can export to a matfile with a custom file name by setting the `export_to_matfile` argument to the target path."
    ]
   },
   {
@@ -645,7 +645,7 @@
    "outputs": [],
    "source": [
     "result, raw = fissa.run_fissa(\n",
-    "    images_location, rois_location, export_to_matlab=\"experiment_results.mat\"\n",
+    "    images_location, rois_location, export_to_matfile=\"experiment_results.mat\"\n",
     ")"
    ]
   },

examples/basic_usage_func.py

@@ -21,4 +21,4 @@
 output_dir = "fissa_example"
 
 # Run FISSA on this data
-result = fissa.run_fissa(images, rois, output_dir, export_to_matlab=True)
+result = fissa.run_fissa(images, rois, output_dir, export_to_matfile=True)

examples/basic_usage_func_windows.py

@@ -24,4 +24,4 @@
     output_dir = "fissa_example"
 
     # Run FISSA on this data
-    result = fissa.run_fissa(images, rois, output_dir, export_to_matlab=True)
+    result = fissa.run_fissa(images, rois, output_dir, export_to_matfile=True)

fissa/core.py

@@ -1870,7 +1870,7 @@ def run_fissa(
     freq=None,
     return_deltaf=False,
     deltaf_across_trials=True,
-    export_to_matlab=False,
+    export_to_matfile=False,
     **kwargs
 ):
     r"""
@@ -1928,10 +1928,10 @@ def run_fissa(
         Δf/f\ :sub:`0` value will be relative to the trial-specific f0.
         Default is ``True``.
 
-    export_to_matlab : bool or str or None, default=False
+    export_to_matfile : bool or str or None, default=False
         Whether to export the data to a MATLAB-compatible .mat file.
-        If `export_to_matlab` is a string, it is used as the path to the output
-        file. If ``export_to_matlab=True``, the matfile is saved to the
+        If `export_to_matfile` is a string, it is used as the path to the output
+        file. If ``export_to_matfile=True``, the matfile is saved to the
         default path of ``"separated.mat"`` within the `folder` directory, and
         `folder` must be set. If this is ``None``, the matfile is exported to
         the default path if `folder` is set, and otherwise is not exported.
@@ -1963,20 +1963,22 @@ def run_fissa(
     fissa.core.Experiment
     """
     # Parse arguments
-    if export_to_matlab is None:
-        export_to_matlab = folder is not None
+    if export_to_matfile is None:
+        export_to_matfile = folder is not None
     if return_deltaf and freq is None:
         raise ValueError("The argument `freq` must be set to determine df/f0.")
     # Make a new Experiment object
     experiment = Experiment(images, rois, folder=folder, **kwargs)
     # Run separation
     experiment.separate()
     # Calculate Δf/f0
-    if return_deltaf or (export_to_matlab and freq is not None):
+    if return_deltaf or (export_to_matfile and freq is not None):
         experiment.calc_deltaf(freq=freq, across_trials=deltaf_across_trials)
     # Save to matfile
-    if export_to_matlab:
-        matlab_fname = None if isinstance(export_to_matlab, bool) else export_to_matlab
+    if export_to_matfile:
+        matlab_fname = (
+            None if isinstance(export_to_matfile, bool) else export_to_matfile
+        )
         experiment.to_matfile(matlab_fname)
     # Return appropriate data
     if return_deltaf:

fissa/tests/test_core.py

@@ -1913,7 +1913,7 @@ def test_func(self):
         image_path = os.path.join(self.resources_dir, self.images_dir)
         roi_path = os.path.join(self.resources_dir, self.roi_zip_path)
         actual_result, actual_raw = core.run_fissa(
-            image_path, roi_path, self.output_dir, export_to_matlab=None
+            image_path, roi_path, self.output_dir, export_to_matfile=None
         )
         self.compare_result(actual_result)
         self.compare_raw(actual_raw)
@@ -1925,7 +1925,7 @@ def test_func_explict_matlab(self):
         image_path = os.path.join(self.resources_dir, self.images_dir)
         roi_path = os.path.join(self.resources_dir, self.roi_zip_path)
         actual_result, actual_raw = core.run_fissa(
-            image_path, roi_path, self.output_dir, export_to_matlab=True
+            image_path, roi_path, self.output_dir, export_to_matfile=True
         )
         self.compare_result(actual_result)
         self.compare_raw(actual_raw)
@@ -1936,7 +1936,7 @@ def test_func_explict_nomatlab(self):
         image_path = os.path.join(self.resources_dir, self.images_dir)
         roi_path = os.path.join(self.resources_dir, self.roi_zip_path)
         actual_result, actual_raw = core.run_fissa(
-            image_path, roi_path, self.output_dir, export_to_matlab=False
+            image_path, roi_path, self.output_dir, export_to_matfile=False
         )
         self.compare_result(actual_result)
         self.compare_raw(actual_raw)
@@ -1948,7 +1948,7 @@ def test_func_manual_matlab(self):
         roi_path = os.path.join(self.resources_dir, self.roi_zip_path)
         fname = os.path.join(self.output_dir, "test_output.mat")
         actual_result, actual_raw = core.run_fissa(
-            image_path, roi_path, self.output_dir, export_to_matlab=fname
+            image_path, roi_path, self.output_dir, export_to_matfile=fname
         )
         self.compare_result(actual_result)
         self.compare_raw(actual_raw)