Pyriod 0.3.2__tar.gz → 0.3.4__tar.gz

{pyriod-0.3.2 → pyriod-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Pyriod
-Version: 0.3.2
+Version: 0.3.4
 Summary: Basic period detection and fitting routines for astronomical time series.
 Home-page: https://github.com/keatonb/Pyriod
 Author: Keaton Bell

{pyriod-0.3.2 → pyriod-0.3.4}/Pyriod/Pyriod.py

@@ -61,7 +61,7 @@ warnings.filterwarnings(action='ignore', category=XMLParsedAsHTMLWarning,
 
 # Definition of the basic model we fit
 def sin(x, freq, amp, phase):
-    """Model fit to time series."""
+    """Sinusoidal time series model."""
     return amp*np.sin(2.*np.pi*(freq*x+phase))
 
 
@@ -86,7 +86,7 @@ class Capturing(list):
 class lasso_selector(object):
     """Select indices from a matplotlib collection using `LassoSelector`.
 
-    Outline selected points with given color, otherwise don't outline
+    Highlight selected points with gold outline.
 
     Based on Lasso Selector Demo
     https://matplotlib.org/3.1.1/gallery/widgets/lasso_selector_demo_sgskip.html
@@ -142,6 +142,26 @@ class Pyriod(object):
         rescale_covar: (bool)
             Rescale covariance matrix when estimating uncertainties? The
             default is False.
+        **kwargs are passed to set_frequency_sampling() method, which takes arguments
+        ----------
+            frequency : array, optional
+                Explicit set of frequencies to compute periodogram at. The default
+                is None.
+            oversample_factor : FLOAT, optional
+                How many times more densely than the natural frequency resolution
+                of 1/duration to sample frequencies. The default is 5.
+            nyquist_factor : FLOAT, optional
+                How many time beyond the approximate Nyquist frequency to sample
+                periodograms. The default is 1. Overridden by maxfreq, if provided.
+                Note that the Nyquist frequency is estimated to equal 1/(2*dt),
+                where dt is the median time separation between adjacent samples.
+                This is only valid for evenly sampled data, and may be a very poor
+                approximation for unevenly sampled data.
+            minfreq : FLOAT
+                Minimum frequency of range to use. The default is 1/duration.
+            maxfreq : FLOAT
+                Maximum frequency of range to use. The default is based off of
+                nyquist_factor.
 
     Attributes
     ----------
@@ -278,6 +298,10 @@ class Pyriod(object):
         # Display toggle widget _perplot_orig_display
         # TODO: Add color picker _perplot_orig_color
 
+        # If gui, set up widgets (need checkbox for recalculating periodogram)
+        if self.gui:
+            self._init_periodogram_widgets()
+        
         # Compute original periodogram
         self.compute_pers(orig=True)
 
@@ -290,10 +314,8 @@ class Pyriod(object):
         # Make interpolator for residual periodogram
         self.interpls = interp1d(self.freqs, self.per_resid.power.value)
 
-        # Initialize widgets and plot
+        # Initialize periodogram plot
         if self.gui:
-            self._init_periodogram_widgets()
-
             # Set up figs/axes for periodogram plots
             self.perfig, self.perax = plt.subplots(
                 figsize=(7, 3), num='Periodogram ({:d})'.format(self.id))
@@ -625,9 +647,16 @@ class Pyriod(object):
         # Whether to extrapolate
         self._sig_extrapolate_widget = widgets.Checkbox(
             value = False,
-            description='Extrapolate?',
+            description='Extrapolate',
             style={'description_width': 'initial'}
         )
+        # Automatically recalculate sig threshold?
+        self._sig_auto_recalculate = widgets.Checkbox(
+            value = False,
+            description='Auto-recalculate',
+            style={'description_width': 'initial'},
+            layout=widgets.Layout(width='100%')
+        )
         # Calulate sig threshold button
         self._sig_calculate_button = widgets.Button(
             description='Calculate',
@@ -1040,7 +1069,7 @@ class Pyriod(object):
 
     def _valid_combo(self, combostr):
         """Check that provided combination string is a valid expression."""
-        parts = re.split('\+|\-|\*|\/', combostr.replace(" ", "").lower())
+        parts = re.split(r'\+|\-|\*|\/', combostr.replace(" ", "").lower())
         allvalid = np.all([(part in self.stagedvalues.index)
                            or part.replace('.', '', 1).isdigit()
                            for part in parts])
@@ -1095,11 +1124,11 @@ class Pyriod(object):
         for i in range(len(combostr)):
             combostr[i] = combostr[i].replace(" ", "").lower()
             # Evaluate combostring, replacing keys with values.
-            parts = re.split('\+|\-|\*|\/',
+            parts = re.split(r'\+|\-|\*|\/',
                              combostr[i].replace(" ", "").lower())
             keys = set([part for part in parts if part
                         in self.stagedvalues.index])
-            exploded = re.split('(\+|\-|\*|\/)',
+            exploded = re.split(r'(\+|\-|\*|\/)',
                                 combostr[i].replace(" ", "").lower())
             expression = "".join([str(self.stagedvalues.loc[val, 'freq'])
                                   if val in keys else val for val in exploded])
@@ -1196,7 +1225,7 @@ class Pyriod(object):
                     # Correct phase for tdiff
                     thisphase = (self.stagedvalues.phase[prefix]
                                  - (self.tshift * self.freq_conversion
-                                    * self.stagedvalues.freq[prefix]))
+                                    * self.stagedvalues.freq[prefix])) % 1
 
                     # Estimate phase for new signals with _brute_phase_est
                     # (or those with brute = True)
@@ -1213,10 +1242,10 @@ class Pyriod(object):
                     useprefix = 'c{}'.format(cnum)
                     signals[useprefix] = Model(sin, prefix=useprefix)
                     params.update(signals[useprefix].make_params())
-                    parts = re.split('\+|\-|\*|\/', prefix)
+                    parts = re.split(r'\+|\-|\*|\/', prefix)
                     keys = set([part for part in parts
                                 if part in self.stagedvalues.index])
-                    exploded = re.split('(\+|\-|\*|\/)', prefix)
+                    exploded = re.split(r'(\+|\-|\*|\/)', prefix)
                     expression = "".join([val+'freq' if val in keys else val
                                           for val in exploded])
                     params[useprefix+'freq'].set(expr=expression)
@@ -1226,7 +1255,7 @@ class Pyriod(object):
                     # Correct phase for tdiff
                     thisphase = (self.stagedvalues.phase[prefix]
                                  - (self.tshift * self.freq_conversion
-                                    * self.stagedvalues.freq[prefix]))
+                                    * self.stagedvalues.freq[prefix])) % 1
                     if np.isnan(thisphase):  # If new signal to fit
                         thisphase = self._brute_phase_est(
                             self.stagedvalues.freq[prefix],
@@ -1489,7 +1518,7 @@ class Pyriod(object):
     def _update_freq_dropdown(self):
         # Add new frequencies to dropdown options
         labels = [self.fitvalues.index[i]
-                  + ': {:.8f} '.format(self.fitvalues.freq[i])
+                  + ': {:.8f} '.format(self.fitvalues.freq.iloc[i])
                   + self.per_orig.frequency.unit.to_string()
                   for i in range(len(self.fitvalues))]
         currentind = self._select_fold_freq.index
@@ -1638,6 +1667,10 @@ class Pyriod(object):
                                  bounds_error=False,
                                  fill_value=self.per_resid.max_power.value)
         self._log_per_properties()
+        # If auto-recalculate set for significance threshold:
+        if self.gui:
+            if self._sig_auto_recalculate.value:
+                self._sigthreshfromgui()
         self._update_status(False)  # Calculation complete
 
     def _update_per_plots(self):
@@ -1833,7 +1866,7 @@ class Pyriod(object):
                                     self._sig_freqstep_widget,
                                     self._sig_winwidth_widget,
                                     self._sig_avgtype_widget,
-                                    self._sig_extrapolate_widget,
+                                    HBox([self._sig_extrapolate_widget,self._sig_auto_recalculate]),
                                     self._sig_calculate_button],
                                    layout=widgets.Layout(border='solid 1px'))
             options = HBox([displayconfig, thresholdconfig])

{pyriod-0.3.2 → pyriod-0.3.4}/Pyriod.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Pyriod
-Version: 0.3.2
+Version: 0.3.4
 Summary: Basic period detection and fitting routines for astronomical time series.
 Home-page: https://github.com/keatonb/Pyriod
 Author: Keaton Bell

{pyriod-0.3.2 → pyriod-0.3.4}/Pyriod.egg-info/SOURCES.txt

@@ -17,7 +17,6 @@ Pyriod/docs/Signals.md
 Pyriod/docs/TimeSeries.md
 docs/examples.md
 docs/index.md
-docs/tutorial.md
 docs/img/Log.png
 docs/img/Periodogram.png
 docs/img/Pyriod.png

pyriod-0.3.4/docs/index.md

@@ -0,0 +1,39 @@
+# Pyriod
+
+Python implementation of basic pre-whitening period detection and fitting routines for astronomical time series data.  
+
+Pyriod aims to provide most of the functionality of the wonderful program [Period04](https://www.period04.net/) in the Python environment for the modern astronomy workflow.
+
+The interactive GUI runs in a Jupyter Notebook environment.
+
+Please report any new bugs or request new features on the issues page on [GitHub](https://github.com/keatonb/Pyriod/issues).
+
+Pyriod is written and maintained by [Keaton Bell](https://keaton.commons.gc.cuny.edu/).
+
+Additional documentation and tutorials are under development.
+
+## Installation
+
+To install, use
+
+```pip install Pyriod```
+
+or download the latest (possibly unstable) version from [GitHub](https://github.com/keatonb/Pyriod) and run
+
+```python setup.py install```.
+
+## Dependencies
+
+Pyriod requires Python 3.
+
+You can view a list of package requirements [here](https://github.com/keatonb/Pyriod/blob/master/requirements.txt). Beyond fairly standard packages of astronomy research and plotting (Astropy, Pandas, ipywidgets, etc.), these few specific projects really made Pyriod possible, and are worth looking into if you want to understand or extend the code:
+
+ * [lightkurve](https://docs.lightkurve.org/) -- A friendly package for Kepler & TESS time series analysis in Python.
+ * [Lmfit](https://lmfit.github.io/lmfit-py/) -- Non-linear least-squares minimization and curve-fitting for Python.
+ * [qgrid](https://github.com/quantopian/qgrid) -- An interactive grid for sorting, filtering, and editing DataFrames in Jupyter notebooks. Huge thanks to [qgridnext](https://github.com/zhihanyue/qgridnext/) for keeping the functionality alive and compatible with modern python/dependencies.
+
+## Acknowledgement
+
+This material is based upon work supported by the National
+Science Foundation under Grant No. AST-2406917.
+