Merge pull request #12 from hamogu/spinspotter

Improve code pulled in from spinspotter

other_licenses/acf_functions_license

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2022, rae-holcomb
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

tessilator/acf_functions.py

@@ -1,7 +1,9 @@
+# Copyright (c) 2022, rae-holcomb
+# Licensed under a 3-clause BSD style license - see other_licenses/acf_functions_license
+# https://github.com/rae-holcomb/SpinSpotter/blob/main/spinspotter/function_library.py
 # Core SpinSpotter Library
-# Created: April 5, 2021
-# Last updated: June 2022 
-# (or possibly more recently, I honestly forget to update this line often)
+# Modified by the Tessilator team - see git history for details
+
 
 # imports
 import matplotlib.pyplot as plt
@@ -476,7 +478,7 @@ def process_LightCurve(lc, bs=cadence, precleaned=False,
         precleaned (:obj:`bool`, optional): set to True if the provided `lc` argument has already been cleaned and normalized.
         transit (:obj:`array`, optional): array of transit parameters like [period, epoch, duration] in units of days each entry can be an array if there are multiple planets. Also used by `default_cleaning_func`.
         max_lag (:obj:`float`, optional): the maximum lag to which to calculate the ACF in units of days.
-        smooth (:obj:`int`, optional): if supplied, will apply smoothing to the LC before fitting parabolas by convolving with a gaussian with a FWHM equal to this value.
+        smooth (:obj:`int`, optional): if supplißed, will apply smoothing to the LC before fitting parabolas by convolving with a gaussian with a FWHM equal to this value.
         sector_label (:obj:`int` or :obj:`str`, optional): tallows you to set a custom sector label, must be castable to a string.
         prot_prior_func (:obj:`func`, optional): the function to be used to identify the period_guess_index (pgi) for the rotation period. Defaults to `calc_fft_pgi()`
         prot_prior_func_kwargs (:obj:`dict`, optional): keyword arguments for the `prot_prior_func` function.
@@ -519,38 +521,21 @@ def process_LightCurve(lc, bs=cadence, precleaned=False,
 
 # # PLOTTING FUNCTIONS
 
-def custom_plot(x, y, ax=None, **plt_kwargs):
-    """
-    (Under construction) Custom plotting function.
-
-    Args:
-        x (:obj:`arr`): the x array.
-        y (:obj:`array`): the y array.
-        ax (:obj:`axis object`, optional): the axis object on which to plot.
-        peak_num (:obj:`int`): which alias you are trying to fit (1 being the original peak, 2 being the first alias.)
-        **plt_kwargs (:obj:`dict`): keyword arguments.
-
-    Returns:
-        ax (:obj:`obj`): the plotted function.
-    """
-    if ax is None:
-        ax = plt.gca()
-    ax.plot(x, y, **plt_kwargs) ## example plot here
-    return(ax)
-
-def plot_fft(fits_result,process_result, plot_peaks=True, **plt_kwargs):
+def plot_fft(process_result, plot_peaks=True, **plt_kwargs):
     """
     Given the result dictionaries from process_LightCurve, plots the FFT of the ACF. Returns a figure object.
 
-    Args:
-        fits_result (:obj:`dict`): dictionary containing information on the LC and ACF, as returned by `process_LightCurve()`.
-        process_result (:obj:`dict`): dictionary containing information on the parabola fits, as returned by `process_LightCurve()`.
-        plot_peaks (:obj:`dict`):  if True, places a marker on the five tallest peaks in the FFT.
-        plt_kwargs (:obj:`dict`):  keyword arguments for `matplotlib.plt.plot()`.
+    Parameters
+    ----------
+    process_result : dict
+        dictionary containing information on the parabola fits, as returned by `process_LightCurve()`.
+    plot_peaks : bool
+        if True, places a marker on the five tallest peaks in the FFT.
+    plt_kwargs : dict
+        keyword arguments for `matplotlib.plt.plot()`.
     """
     fft = process_result['fft']
-    fft_period = process_result['fft_period_days']
-    pgi = process_result['pgi']
+    fft_period = process_result["fft_period_days"]
     fft_pgi = process_result['fft_pgi']
 
     # make le plot!
@@ -573,39 +558,31 @@ def plot_fft(fits_result,process_result, plot_peaks=True, **plt_kwargs):
 
 
 # # PLOTTING AND PRINTING FUNCTIONS
-
-def print_summary(fits_result, process_result, bs=cadence):
-    """
-    Prints a summary of the descriptive parameters calculated by `process_LightCurve()`.
-    
-    Args:
-        fits_result (:obj:`dict`): dictionary containing information on the LC and ACF, as returned by `process_LightCurve()`.
-        process_result (:obj:`dict`): dictionary containing information on the parabola fits, as returned by `process_LightCurve()`.    
-    """
-    print('pgi: ' + "%.3f" % bins_to_days(process_result['pgi']/(24*30), bs=bs))
-    print('A_avg: ' + "%.3f" % (process_result['A_avg']))
-    print('B_avg: ' + "%.3f" % (process_result['B_avg']))
-    print('Rsq_avg: ' + "%.3f" % (process_result['R_avg']))
-    print('P_avg (days): ' + "%.3f" % bins_to_days(process_result['P_avg'], bs=bs))
-    print('P_err (days): ' + "%.3f" % bins_to_days(process_result['P_err'], bs=bs))
-    print('HWHM_err (days): ' + "%.3f" % bins_to_days(np.nanmean(process_result['hwhm_k']), bs=bs))
-    print()
-
-
 def plot_acf(fits_result,process_result, plot_peaks=True, plot_line=None, cut=10):
     """
     Prints a summary of the descriptive parameters calculated by `process_LightCurve()`.
-    
-    Args:
-        fits_result (:obj:`dict`): dictionary containing information on the LC and ACF, as returned by `process_LightCurve()`.
-        process_result (:obj:`dict`): dictionary containing information on the parabola fits, as returned by `process_LightCurve()`.   
-        plot_peaks (:obj:`bool`): if set to True, will overplot the parabola fits to the ACF peaks on the ACF plot
-        plot_line (:obj:`float`): if given a lag time in days, will plot a vertical line on the ACF at that x-value, indended to plot the found period for visual comparison
-        cut (:obj:`int`): plots look better when you cut the first few points off the ACF, to avoid the high peak at (0,1). This keyword lets you adjust how many points get cut off the front.
-    
-    Returns:
-        fig (:obj:`obj`): the figure object. 
-        ax (:obj:`obj`): the axis object with the plotted function. 
+
+    Parameters
+    ----------
+    fits_result : dict
+        dictionary containing information on the LC and ACF, as returned by `process_LightCurve()`.
+    process_result : dict
+        dictionary containing information on the parabola fits, as returned by `process_LightCurve()`.
+    plot_peaks : bool
+        if set to True, will overplot the parabola fits to the ACF peaks on the ACF plot
+    plot_line : float or None
+        if given a lag time in days, will plot a vertical line on the ACF at that x-value,
+        intended to plot the found period for visual comparison.
+    cut : int
+        plots look better when you cut the first few points off the ACF, to avoid the high peak at (0,1).
+        This keyword lets you adjust how many points get cut off the front.
+
+    Returns
+    -------
+        fig :
+            the figure object.
+        ax :
+            the axis object with the plotted function.
     """
     # make the base plot
     # fig_num=plt.figure().number + 1