Merge branch 'basemodel' into modes

specparam/objs/base.py

@@ -12,7 +12,7 @@
                                load_json, load_jsonlines, get_files)
 from specparam.core.modutils import copy_doc_func_to_method
 from specparam.plts.event import plot_event_model
-from specparam.objs.fit import BaseFit, BaseFit2D, BaseFit2DT, BaseFit3D
+from specparam.objs.results import BaseResults, BaseResults2D, BaseResults2DT, BaseResults3D
 from specparam.objs.data import BaseData, BaseData2D, BaseData2DT, BaseData3D
 
 ###################################################################################################
@@ -117,15 +117,15 @@ def _add_from_dict(self, data):
             setattr(self, key, data[key])
 
 
-class BaseObject(CommonBase, BaseFit, BaseData):
+class BaseObject(CommonBase, BaseResults, BaseData):
     """Define Base object for fitting models to 1D data."""
 
     def __init__(self, aperiodic_mode=None, periodic_mode=None, debug_mode=False, verbose=True):
 
         CommonBase.__init__(self)
         BaseData.__init__(self)
-        BaseFit.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
-                         debug_mode=debug_mode, verbose=verbose)
+        BaseResults.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
+                             debug_mode=debug_mode, verbose=verbose)
 
 
     def add_data(self, freqs, power_spectrum, freq_range=None, clear_results=True):
@@ -203,15 +203,15 @@ def _reset_data_results(self, clear_freqs=False, clear_spectrum=False, clear_res
         self._reset_results(clear_results)
 
 
-class BaseObject2D(CommonBase, BaseFit2D, BaseData2D):
+class BaseObject2D(CommonBase, BaseResults2D, BaseData2D):
     """Define Base object for fitting models to 2D data."""
 
     def __init__(self, aperiodic_mode=None, periodic_mode=None, debug_mode=False, verbose=True):
 
         CommonBase.__init__(self)
         BaseData2D.__init__(self)
-        BaseFit2D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
-                           debug_mode=debug_mode, verbose=verbose)
+        BaseResults2D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
+                               debug_mode=debug_mode, verbose=verbose)
 
 
     def add_data(self, freqs, power_spectra, freq_range=None, clear_results=True):
@@ -315,15 +315,15 @@ def _reset_data_results(self, clear_freqs=False, clear_spectrum=False,
         self._reset_results(clear_results)
 
 
-class BaseObject2DT(BaseObject2D, BaseFit2DT, BaseData2DT):
+class BaseObject2DT(BaseObject2D, BaseResults2DT, BaseData2DT):
     """Define Base object for fitting models to 2D data - tranpose version."""
 
     def __init__(self, aperiodic_mode=None, periodic_mode=None, debug_mode=False, verbose=True):
 
         BaseObject2D.__init__(self)
         BaseData2DT.__init__(self)
-        BaseFit2D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
-                           debug_mode=debug_mode, verbose=verbose)
+        BaseResults2D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
+                               debug_mode=debug_mode, verbose=verbose)
 
 
     def load(self, file_name, file_path=None, peak_org=None):
@@ -348,15 +348,15 @@ def load(self, file_name, file_path=None, peak_org=None):
             self.convert_results(peak_org)
 
 
-class BaseObject3D(BaseObject2DT, BaseFit3D, BaseData3D):
+class BaseObject3D(BaseObject2DT, BaseResults3D, BaseData3D):
     """Define Base object for fitting models to 3D data."""
 
     def __init__(self, aperiodic_mode=None, periodic_mode=None, debug_mode=False, verbose=True):
 
         BaseObject2DT.__init__(self)
         BaseData3D.__init__(self)
-        BaseFit3D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
-                           debug_mode=debug_mode, verbose=verbose)
+        BaseResults3D.__init__(self, aperiodic_mode=aperiodic_mode, periodic_mode=periodic_mode,
+                               debug_mode=debug_mode, verbose=verbose)
 
 
     def add_data(self, freqs, spectrograms, freq_range=None, clear_results=True):

specparam/objs/data.py

@@ -10,7 +10,7 @@
 from specparam.core.errors import DataError, InconsistentDataError
 from specparam.data import SpectrumMetaData
 from specparam.plts.settings import PLT_COLORS
-from specparam.plts.spectra import plot_spectra
+from specparam.plts.spectra import plot_spectra, plot_spectrogram
 from specparam.plts.utils import check_plot_kwargs
 
 ###################################################################################################
@@ -381,6 +381,12 @@ def add_data(self, freqs, spectrogram, freq_range=None):
         super().add_data(freqs, spectrogram, freq_range)
 
 
+    def plot(self, **plt_kwargs):
+        """Plot the spectrogram."""
+
+        plot_spectrogram(self.freqs, self.spectrogram, **plot_kwargs)
+
+
 class BaseData3D(BaseData2DT):
     """Base object for managing data for spectral parameterization - for 3D data."""
 
@@ -440,3 +446,9 @@ def add_data(self, freqs, spectrograms, freq_range=None):
         # Otherwise, pass through 2d array to underlying object method
         else:
             super().add_data(freqs, spectrograms, freq_range)
+
+
+    def plot(self, event_ind):
+        """Plot a selected spectrogram."""
+
+        plot_spectrogram(self.freqs, self.spectrograms[event_ind, :, :], **plot_kwargs)

specparam/objs/event.py

@@ -9,7 +9,7 @@
 from specparam.objs import SpectralModel
 from specparam.objs.base import BaseObject3D
 from specparam.objs.algorithm import SpectralFitAlgorithm
-from specparam.objs.fit import _progress
+from specparam.objs.results import _progress
 from specparam.plts.event import plot_event_model
 from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
 from specparam.data.utils import get_group_params, get_results_by_row, flatten_results_dict
@@ -68,8 +68,8 @@ def __init__(self, *args, **kwargs):
         BaseObject3D.__init__(self,
                               aperiodic_mode=kwargs.pop('aperiodic_mode', 'fixed'),
                               periodic_mode=kwargs.pop('periodic_mode', 'gaussian'),
-                              debug_mode=kwargs.pop('debug_mode', 'False'),
-                              verbose=kwargs.pop('verbose', 'True'))
+                              debug_mode=kwargs.pop('debug_mode', False),
+                              verbose=kwargs.pop('verbose', True))
 
         SpectralFitAlgorithm.__init__(self, *args, **kwargs)
 
@@ -222,8 +222,7 @@ def to_df(self, peak_org=None):
     def _check_width_limits(self):
         """Check and warn about bandwidth limits / frequency resolution interaction."""
 
-        # Only check & warn on first spectrogram
+        # Only check & warn on first spectrum
         #   This is to avoid spamming standard output for every spectrogram in the set
-        if np.all(self.spectrograms[0] == self.spectrogram):
-        #if self.power_spectra[0, 0] == self.power_spectrum[0]:
+        if np.all(self.power_spectrum == self.spectrograms[0, :, 0]):
             super()._check_width_limits()

specparam/objs/group.py

@@ -74,8 +74,8 @@ def __init__(self, *args, **kwargs):
         BaseObject2D.__init__(self,
                               aperiodic_mode=kwargs.pop('aperiodic_mode', 'fixed'),
                               periodic_mode=kwargs.pop('periodic_mode', 'gaussian'),
-                              debug_mode=kwargs.pop('debug_mode', 'False'),
-                              verbose=kwargs.pop('verbose', 'True'))
+                              debug_mode=kwargs.pop('debug_mode', False),
+                              verbose=kwargs.pop('verbose', True))
 
         SpectralFitAlgorithm.__init__(self, *args, **kwargs)
 

specparam/objs/fit.py → specparam/objs/results.py

@@ -20,8 +20,8 @@
 ###################################################################################################
 ###################################################################################################
 
-class BaseFit():
-    """Base object for managing fit procedures."""
+class BaseResults():
+    """Base object for managing results."""
     # pylint: disable=attribute-defined-outside-init, arguments-differ
 
     def __init__(self, aperiodic_mode, periodic_mode, debug_mode=False,
@@ -341,12 +341,13 @@ def _calc_error(self, metric=None):
             raise ValueError(error_msg)
 
 
-class BaseFit2D(BaseFit):
-    """Base object for managing fit procedures - 2D version."""
+class BaseResults2D(BaseResults):
+    """Base object for managing results - 2D version."""
 
     def __init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True):
 
-        BaseFit.__init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True)
+        BaseResults.__init__(self, aperiodic_mode, periodic_mode,
+                             debug_mode=debug_mode, verbose=verbose)
 
         self._reset_group_results()
 
@@ -617,12 +618,13 @@ def get_group(self, inds):
         return group
 
 
-class BaseFit2DT(BaseFit2D):
-    """Base object for managing fit procedures - 2D transpose version."""
+class BaseResults2DT(BaseResults2D):
+    """Base object for managing results - 2D transpose version."""
 
     def __init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True):
 
-        BaseFit2D.__init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True)
+        BaseResults2D.__init__(self, aperiodic_mode, periodic_mode,
+                               debug_mode=debug_mode, verbose=verbose)
 
         self._reset_time_results()
 
@@ -758,12 +760,13 @@ def convert_results(self, peak_org):
         self.time_results = group_to_dict(self.group_results, peak_org)
 
 
-class BaseFit3D(BaseFit2DT):
-    """Base object for managing fit procedures - 3D version."""
+class BaseResults3D(BaseResults2DT):
+    """Base object for managing results - 3D version."""
 
     def __init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True):
 
-        BaseFit2DT.__init__(self, aperiodic_mode, periodic_mode, debug_mode=False, verbose=True)
+        BaseResults2DT.__init__(self, aperiodic_mode, periodic_mode,
+                                debug_mode=debug_mode, verbose=verbose)
 
         self._reset_event_results()
 

specparam/objs/time.py

@@ -1,5 +1,7 @@
 """Time model object and associated code for fitting the model to spectrograms."""
 
+import numpy as np
+
 from specparam.objs import SpectralModel
 from specparam.objs.base import BaseObject2DT
 from specparam.objs.algorithm import SpectralFitAlgorithm
@@ -60,8 +62,8 @@ def __init__(self, *args, **kwargs):
         BaseObject2DT.__init__(self,
                                aperiodic_mode=kwargs.pop('aperiodic_mode', 'fixed'),
                                periodic_mode=kwargs.pop('periodic_mode', 'gaussian'),
-                               debug_mode=kwargs.pop('debug_mode', 'False'),
-                               verbose=kwargs.pop('verbose', 'True'))
+                               debug_mode=kwargs.pop('debug_mode', False),
+                               verbose=kwargs.pop('verbose', True))
 
         SpectralFitAlgorithm.__init__(self, *args, **kwargs)
 
@@ -156,3 +158,12 @@ def to_df(self, peak_org=None):
             df = dict_to_df(self.get_results())
 
         return df
+
+
+    def _check_width_limits(self):
+        """Check and warn about bandwidth limits / frequency resolution interaction."""
+
+        # Only check & warn on first power spectrum
+        #   This is to avoid spamming standard output for every spectrum in the group
+        if np.all(self.power_spectrum == self.spectrogram[:, 0]):
+            super()._check_width_limits()

specparam/tests/objs/test_base.py

@@ -48,7 +48,7 @@ def test_base2d():
     tobj2d = BaseObject2D()
     assert isinstance(tobj2d, CommonBase)
     assert isinstance(tobj2d, BaseObject2D)
-    assert isinstance(tobj2d, BaseFit2D)
+    assert isinstance(tobj2d, BaseResults2D)
     assert isinstance(tobj2d, BaseObject2D)
 
 ## 2DT Base Object
@@ -58,7 +58,7 @@ def test_base2dt():
     tobj2dt = BaseObject2DT()
     assert isinstance(tobj2dt, CommonBase)
     assert isinstance(tobj2dt, BaseObject2DT)
-    assert isinstance(tobj2dt, BaseFit2DT)
+    assert isinstance(tobj2dt, BaseResults2DT)
     assert isinstance(tobj2dt, BaseObject2DT)
 
 ## 3D Base Object
@@ -68,6 +68,6 @@ def test_base3d():
     tobj3d = BaseObject3D()
     assert isinstance(tobj3d, CommonBase)
     assert isinstance(tobj3d, BaseObject2DT)
-    assert isinstance(tobj3d, BaseFit2DT)
+    assert isinstance(tobj3d, BaseResults2DT)
     assert isinstance(tobj3d, BaseObject2DT)
     assert isinstance(tobj3d, BaseObject3D)