Merge pull request #293 from fooof-tools/checkmodes

[MNT] - Fix management of check modes

Author: TomDonoghue

doc/api.rst

@@ -91,6 +91,7 @@ Objects to store settings, metadata and results for power spectrum models.
    :template: data_object.rst
 
    FOOOFSettings
+   FOOOFRunModes
    FOOOFMetaData
    FOOOFResults
 

fooof/core/info.py

@@ -17,6 +17,7 @@ def get_description():
 
     - results : parameters for and measures of the model
     - settings : model settings
+    - run_modes: checks performed and errors raised
     - data : input data
     - meta_data : meta data of the inputs
     - arrays : data stored in arrays
@@ -29,6 +30,7 @@ def get_description():
                   'settings' : ['peak_width_limits', 'max_n_peaks',
                                 'min_peak_height', 'peak_threshold',
                                 'aperiodic_mode'],
+                  'run_modes': ['_debug', '_check_freqs', '_check_data'],
                   'data' : ['power_spectrum', 'freq_range', 'freq_res'],
                   'meta_data' : ['freq_range', 'freq_res'],
                   'arrays' : ['freqs', 'power_spectrum', 'aperiodic_params_',

fooof/data/__init__.py

@@ -1,3 +1,3 @@
 """Data sub-module for FOOOF."""
 
-from .data import FOOOFSettings, FOOOFMetaData, FOOOFResults, SimParams
+from .data import FOOOFSettings, FOOOFRunModes, FOOOFMetaData, FOOOFResults, SimParams

fooof/data/data.py

@@ -38,6 +38,25 @@ class FOOOFSettings(namedtuple('FOOOFSettings', ['peak_width_limits', 'max_n_pea
     __slots__ = ()
 
 
+class FOOOFRunModes(namedtuple('FOOOFRunModes', ['debug', 'check_freqs', 'check_data'])):
+    """Checks performed and errors raised by the model.
+
+    Parameters
+    ----------
+    debug :  bool
+       Whether to run in debug mode.
+    check_freqs : bool
+        Whether to run in check freqs mode.
+    check_data : bool
+        Whether to run in check data mode.
+
+    Notes
+    -----
+    This object is a data object, based on a NamedTuple, with immutable data attributes.
+    """
+    __slots__ = ()
+
+
 class FOOOFMetaData(namedtuple('FOOOFMetaData', ['freq_range', 'freq_res'])):
     """Metadata information about a power spectrum.
 

fooof/objs/fit.py

@@ -45,9 +45,11 @@
 _debug : bool
     Whether the object is set in debug mode.
     This should be controlled by using the `set_debug_mode` method.
-_check_data : bool
-    Whether to check added data for NaN or Inf values, and fail out if present.
-    This should be controlled by using the `set_check_data_mode` method.
+_check_data, _check_freqs : bool
+    Whether to check added inputs for incorrect inputs, failing if present.
+    Frequency data is checked for linear spacing.
+    Power values are checked for data for NaN or Inf values.
+    These modes default to True, and can be controlled with the `set_check_modes` method.
 
 Code Notes
 ----------
@@ -76,7 +78,7 @@
 from fooof.plts.fm import plot_fm
 from fooof.utils.data import trim_spectrum
 from fooof.utils.params import compute_gauss_std
-from fooof.data import FOOOFResults, FOOOFSettings, FOOOFMetaData
+from fooof.data import FOOOFSettings, FOOOFRunModes, FOOOFMetaData, FOOOFResults
 from fooof.data.conversions import model_to_dataframe
 from fooof.sim.gen import gen_freqs, gen_aperiodic, gen_periodic, gen_model
 
@@ -199,7 +201,7 @@ def __init__(self, peak_width_limits=(0.5, 12.0), max_n_peaks=np.inf, min_peak_h
         # Set default debug mode - controls if an error is raised if model fitting is unsuccessful
         self._debug = False
         # Set default data checking modes - controls which checks get run on input data
-        #   check_freqs: check the frequency values, and raises an error for uneven spacing
+        #   check_freqs: checks the frequency values, and raises an error for uneven spacing
         self._check_freqs = True
         #   check_data: checks the power values and raises an error for any NaN / Inf values
         self._check_data = True
@@ -568,6 +570,19 @@ def get_settings(self):
                              for key in OBJ_DESC['settings']})
 
 
+    def get_run_modes(self):
+        """Return run modes of the current object.
+
+        Returns
+        -------
+        FOOOFRunModes
+            Object containing the run modes from the current object.
+        """
+
+        return FOOOFRunModes(**{key.strip('_') : getattr(self, key) \
+                             for key in OBJ_DESC['run_modes']})
+
+
     def get_meta_data(self):
         """Return data information from the current object.
 
@@ -723,6 +738,24 @@ def set_debug_mode(self, debug):
         self._debug = debug
 
 
+    def set_check_modes(self, check_freqs=None, check_data=None):
+        """Set check modes, which controls if an error is raised based on check on the inputs.
+
+        Parameters
+        ----------
+        check_freqs : bool, optional
+            Whether to run in check freqs mode, which checks the frequency data.
+        check_data : bool, optional
+            Whether to run in check data mode, which checks the power spectrum values data.
+        """
+
+        if check_freqs is not None:
+            self._check_freqs = check_freqs
+        if check_data is not None:
+            self._check_data = check_data
+
+
+    # This kept for backwards compatibility, but to be removed in 2.0 in favor of `set_check_modes`
     def set_check_data_mode(self, check_data):
         """Set check data mode, which controls if an error is raised if NaN or Inf data are added.
 
@@ -732,7 +765,24 @@ def set_check_data_mode(self, check_data):
             Whether to run in check data mode.
         """
 
-        self._check_data = check_data
+        self.set_check_modes(check_data=check_data)
+
+
+    def set_run_modes(self, debug, check_freqs, check_data):
+        """Simultaneously set all run modes.
+
+        Parameters
+        ----------
+        debug : bool
+            Whether to run in debug mode.
+        check_freqs : bool
+            Whether to run in check freqs mode.
+        check_data : bool
+            Whether to run in check data mode.
+        """
+
+        self.set_debug_mode(debug)
+        self.set_check_modes(check_freqs, check_data)
 
 
     def to_df(self, peak_org):

fooof/objs/group.py

@@ -456,9 +456,9 @@ def get_fooof(self, ind, regenerate=True):
             The FOOOFResults data loaded into a FOOOF object.
         """
 
-        # Initialize a FOOOF object, with same settings & check data mode as current FOOOFGroup
+        # Initialize a FOOOF object, with same settings & run modes as current FOOOFGroup
         fm = FOOOF(*self.get_settings(), verbose=self.verbose)
-        fm.set_check_data_mode(self._check_data)
+        fm.set_run_modes(*self.get_run_modes())
 
         # Add data for specified single power spectrum, if available
         #   The power spectrum is inverted back to linear, as it is re-logged when added to FOOOF
@@ -494,8 +494,9 @@ def get_group(self, inds):
         # Check and convert indices encoding to list of int
         inds = check_inds(inds)
 
-        # Initialize a new FOOOFGroup object, with same settings as current FOOOFGroup
+        # Initialize a new FOOOFGroup object, with same settings and run modes as current FOOOFGroup
         fg = FOOOFGroup(*self.get_settings(), verbose=self.verbose)
+        fg.set_run_modes(*self.get_run_modes())
 
         # Add data for specified power spectra, if available
         #   The power spectra are inverted back to linear, as they are re-logged when added to FOOOF

fooof/sim/params.py

@@ -146,13 +146,16 @@ def _check_values(start, stop, step):
             If the given values for defining the iteration range are inconsistent.
         """
 
-        if any(ii < 0 for ii in [start, stop, step]):
-            raise ValueError("Inputs 'start', 'stop', and 'step' should all be positive values.")
+        if any(ii < 0 for ii in [start, stop]):
+            raise ValueError("Inputs 'start' and 'stop' should be positive values.")
 
-        if not start < stop:
-            raise ValueError("Input 'start' should be less than 'stop'.")
+        if (stop - start) * step < 0:
+            raise ValueError("The sign of input 'step' does not align with 'start' / 'stop' values.")
 
-        if not step < (stop - start):
+        if start == stop:
+            raise ValueError("Input 'start' and 'stop' must be different values.")
+
+        if not abs(step) < abs(stop - start):
             raise ValueError("Input 'step' is too large given values for 'start' and 'stop'.")
 
 

fooof/tests/core/test_info.py

@@ -15,7 +15,6 @@ def test_get_description(tfm):
         for it in va:
             assert it in objs
 
-
 def test_get_peak_indices():
 
     indices = get_peak_indices()
@@ -33,7 +32,6 @@ def test_get_ap_indices():
     for ind, val in enumerate(['offset', 'exponent']):
         assert indices_fixed[val] == ind
 
-
     indices_knee = get_indices('knee')
 
     assert indices_knee

fooof/tests/data/test_data.py

@@ -19,6 +19,14 @@ def test_fooof_settings():
     for field in OBJ_DESC['settings']:
         assert getattr(settings, field)
 
+def test_fooof_run_modes():
+
+    run_modes = FOOOFRunModes(True, True, True)
+    assert run_modes
+
+    for field in OBJ_DESC['run_modes']:
+        assert getattr(run_modes, field.strip('_'))
+
 def test_fooof_meta_data():
 
     meta_data = FOOOFMetaData([1, 50], 0.5)

fooof/tests/objs/test_fit.py

@@ -414,17 +414,24 @@ def test_fooof_debug():
     with raises(FitError):
         tfm.fit(*gen_power_spectrum([3, 50], [50, 2], [10, 0.5, 2, 20, 0.3, 4]))
 
-def test_fooof_check_data():
-    """Test FOOOF in with check data mode turned off, including with NaN data."""
+def test_fooof_set_check_modes(tfm):
+    """Test changing check_modes using set_check_modes, and that checks get turned off.
+    Note that testing for checks raising errors happens in test_fooof_checks.`"""
 
     tfm = FOOOF(verbose=False)
 
-    tfm.set_check_data_mode(False)
+    tfm.set_check_modes(False, False)
+    assert tfm._check_freqs is False
     assert tfm._check_data is False
 
-    # Add data, with check data turned off
-    #   In check data mode, adding data with NaN should run
-    freqs = gen_freqs([3, 50], 0.5)
+    # Add bad frequency data, with check freqs turned off
+    freqs = np.array([1, 2, 4])
+    powers = np.array([1, 2, 3])
+    tfm.add_data(freqs, powers)
+    assert tfm.has_data
+
+    # Add bad power values data, with check data turned off
+    freqs = gen_freqs([3, 30], 1)
     powers = np.ones_like(freqs) * np.nan
     tfm.add_data(freqs, powers)
     assert tfm.has_data
@@ -433,6 +440,18 @@ def test_fooof_check_data():
     tfm.fit()
     assert not tfm.has_model
 
+    # Reset check modes to true
+    tfm.set_check_modes(True, True)
+    assert tfm._check_freqs is True
+    assert tfm._check_data is True
+
+def test_set_run_modes():
+
+    tfm = FOOOF(verbose=False)
+    tfm.set_run_modes(False, False, False)
+    for field in OBJ_DESC['run_modes']:
+        assert getattr(tfm, field) is False
+
 def test_fooof_to_df(tfm, tbands, skip_if_no_pandas):
 
     df1 = tfm.to_df(2)