📝 updating docs

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 127
+max-complexity = 20
+count = True
+show-source = True
+extend-ignore = E203, E741

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "vetting"
-version = "0.1.8"
+version = "0.1.9"
 description = "Simple, stand-alone vetting tools for transiting signals in Keper, K2 and TESS data"
 authors = ["Christina Hedges <christina.l.hedges@nasa.gov>"]
 license = "MIT"

src/vetting/__init__.py

@@ -1,7 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import
+import os
 
 from .centroiding import centroid_test
 
+PACKAGEDIR = os.path.abspath(os.path.dirname(__file__))
+
 __all__ = ["centroid_test"]

src/vetting/centroiding.py

@@ -1,11 +1,10 @@
-import numpy as np
-import matplotlib.pyplot as plt
-from astropy.convolution import convolve, Gaussian1DKernel
 import astropy.units as u
+import corner
 import lightkurve as lk
-
+import matplotlib.pyplot as plt
+import numpy as np
+from astropy.convolution import Gaussian1DKernel, convolve
 from scipy.stats import ttest_ind
-import corner
 
 
 def _label(tpf):
@@ -81,8 +80,8 @@ def centroid_test(
         r : dict
             Dictionary of results, containing 'figs' (a list of matplotlib figures) and 'pvalues', which is a list of tuples.
             Each tuple contains the p-value for the input planets. There are as many tuples as input TPFs.
-
     """
+
     if isinstance(tpfs, lk.targetpixelfile.TargetPixelFile):
         tpfs = [tpfs]
     if isinstance(tpfs, lk.collections.TargetPixelFileCollection):
@@ -118,7 +117,6 @@ def centroid_test(
         for key in ["1sigma_error"]:
             r[key] = []
 
-    offsets = np.logspace(-6, np.log10(3), 100)[::-1]
     for tpf in tpfs:
         if tpf.mission.lower() in ["kepler", "ktwo", "k2"]:
             pixel_scale = 4
@@ -133,7 +131,8 @@ def centroid_test(
         if crwd is not None:
             if crwd < 0.8:
                 raise ValueError(
-                    f"Aperture is significantly crowded (CROWDSAP = {crwd}). This method will not work to centroid these cases."
+                    f"Aperture is significantly crowded (CROWDSAP = {crwd}). "
+                    "This method will not work to centroid these cases."
                 )
 
         aper = tpf._parse_aperture_mask(aperture_mask)
@@ -167,7 +166,6 @@ def centroid_test(
         ycent = np.average(Y, weights=fe, axis=1)
         xcent = np.asarray([np.nanmean(xcent, axis=1), np.nanstd(xcent, axis=1)]).T
         ycent = np.asarray([np.nanmean(ycent, axis=1), np.nanstd(ycent, axis=1)]).T
-        import pdb
 
         # If the mission is K2, we need to use SFF to detrend the centroids.
         if tpf.mission.lower() in ["ktwo", "k2"]:
@@ -266,13 +264,23 @@ def centroid_test(
                 with plt.style.context("seaborn-white"):
                     xc1 = (xcent[:, 0][k1] - xtr[k1]) * scale
                     yc1 = (ycent[:, 0][k1] - ytr[k1]) * scale
+
+                    xrange = np.nanpercentile(xc1, (1, 99))
+                    dx = np.diff(xrange) / 100
+                    xrange[0] -= dx * 15
+                    xrange[1] += dx * 15
+                    yrange = np.nanpercentile(yc1, (1, 99))
+                    dy = np.diff(yrange) / 100
+                    yrange[0] -= dy * 15
+                    yrange[1] += dy * 15
+
                     corner.hist2d(
                         xc1,
                         yc1,
                         ax=axs[idx],
                         range=[
-                            np.nanpercentile(xc1, (1, 99)),
-                            np.nanpercentile(yc1, (1, 99)),
+                            xrange,
+                            yrange,
                         ],
                     )
                     axs[idx].errorbar(
@@ -283,7 +291,7 @@ def centroid_test(
                         marker=".",
                         markersize=1,
                         c=f"C{idx}",
-                        lw=1,
+                        lw=0.5,
                         ls="",
                         label=f"Transit {labels[idx]} Cadences",
                     )
@@ -304,10 +312,7 @@ def centroid_test(
                 a2 = weighted_average(xcent[k2, 0] - xtr[k2], 1 / xcent[k2, 1])
                 b2 = weighted_average(ycent[k2, 0] - ytr[k2], 1 / ycent[k2, 1])
                 pos_err = np.hypot(np.hypot(a1[1], b1[1]), np.hypot(a2[1], b2[1]))
-
-            if transit_depths is not None:
                 sigma1.append(pixel_scale * pos_err / transit_depths[idx])
-
             if k2.sum() == 0:
                 pvalue = 1
             else:

src/vetting/version.py

@@ -1,3 +1,3 @@
 # It is important to store the version number in a separate file
 # so that we can read it from setup.py without importing the package
-__version__ = "0.1.8"
+__version__ = "0.1.9"

tests/test_centroids.py

@@ -1,25 +1,35 @@
-import pytest
 import os
-import matplotlib.pyplot as plt
 
 import lightkurve as lk
+import matplotlib.pyplot as plt
+import pytest
+import numpy as np
+
 from vetting import centroid_test
+from vetting import PACKAGEDIR
+
+testdir = "/".join(PACKAGEDIR.split("/")[:-2])
 
-lib_path = os.getcwd()
-tpf = lk.KeplerTargetPixelFile(
-    f"{lib_path}/tests/data/kplr005562784-2011271113734_lpd-targ.fits.gz"
-)
+
+def is_action():
+    try:
+        return os.environ["GITHUB_ACTIONS"]
+    except KeyError:
+        return False
 
 
 def test_centroid_test():
+    tpf = lk.KeplerTargetPixelFile(
+        f"{testdir}/tests/data/kplr005562784-2011271113734_lpd-targ.fits.gz"
+    )
     period, t0, dur = 25.3368592, 192.91552, 8.85 / 24
     r = centroid_test(tpf, period, t0, dur, aperture_mask="pipeline", plot=False)
     assert r["pvalues"][0][0] < 0.01
     assert len(r["pvalues"][0]) == 1
 
     r = centroid_test(tpf, period, t0, dur, aperture_mask="pipeline", plot=True)
     assert len(r["figs"]) == 1
-    r["figs"][0].savefig(f"{lib_path}/demo.png", dpi=200, bbox_inches="tight")
+    r["figs"][0].savefig(f"{PACKAGEDIR}/demo.png", dpi=200, bbox_inches="tight")
 
     r = centroid_test(
         tpf,
@@ -70,3 +80,73 @@ def test_centroid_test():
         transit_depths=0.001499,
         labels="c",
     )
+
+
+@pytest.mark.skipif(
+    is_action(),
+    reason="Can not run on GitHub actions, because it's a pain to download.",
+)
+def test_FPs():
+    """Produce some figures that show centroid offsets"""
+    names = [
+        "KIC 5391911",
+        "KIC 5866724",
+        "EPIC 220256496",
+        "EPIC 210957318",
+        "TIC 293435336",
+        "TIC 13023738",
+    ]
+    kwargs = [
+        {"quarter": 3},
+        {"quarter": 3},
+        {"campaign": 8},
+        {"campaign": 4},
+        {},
+        {"sector": 2},
+    ]
+
+    periods = [0.782068488, 2.154911236, 0.669558, 4.098503000, 1.809886, 8.0635]
+    t0s = [
+        131.8940201,
+        133.498613,
+        2457393.81364 - 2454833,
+        2457063.80710000 - 2454833,
+        2456107.85507 - 2457000,
+        2459104.87232 - 2457000,
+    ]
+    durs = np.asarray([1.239, 3.1341, 1, 2.3208, 3.694, 3.396]) / 24
+    depths = [
+        0.01157 * 0.01,
+        0.00850 * 0.01,
+        0.015450 ** 2,
+        1.603 * 0.01,
+        1.189 * 0.01,
+        5180 * 1e-6,
+    ]
+
+    for name, period, t0, dur, kwarg, depth in zip(
+        names, periods, t0s, durs, kwargs, depths
+    ):
+        tpf = lk.search_targetpixelfile(name, **kwarg).download()
+        r = centroid_test(
+            tpf,
+            period,
+            t0,
+            dur,
+            aperture_mask="pipeline",
+            plot=True,
+            transit_depths=depth,
+        )
+        r["figs"][0].savefig(
+            f"{testdir}/docs/{name.replace(' ','').lower()}.png",
+            dpi=200,
+            bbox_inches="tight",
+        )
+        # nb = int(1 // np.median(np.diff(tpf.time.value)))
+        # nb = [nb if nb % 2 == 1 else nb + 1][0]
+        # ax = tpf.to_lightcurve().flatten(nb).fold(period, t0).bin(period / 200).plot()
+        # plt.savefig(
+        #     f"{testdir}/docs/{name.replace(' ','').lower()}_lc.png",
+        #     dpi=200,
+        #     bbox_inches="tight",
+        # )