Typos and other cleanup

.gitignore

@@ -58,6 +58,7 @@ distribute-*.tar.gz
 .pydevproject
 .settings
 .vscode
+_personal_docs
 
 # Mac OSX
 .DS_Store

docs/conf.py

@@ -106,7 +106,7 @@
 
 
 html_theme_options = {
-    'logotext1': 'glowing-waffles',  # white,  semi-bold
+    'logotext1': 'stellarphot',  # white,  semi-bold
     'logotext2': '',  # orange, light
     'logotext3': ':docs'   # white,  light
     }

docs/index.rst

@@ -1,7 +1,7 @@
 Documentation
 =============
 
-This is the documentation for glowing-waffles.
+This is the documentation for stellarphot.
 This is a package for doing stellar photometry that relies on astropy.
 
 .. toctree::
@@ -11,5 +11,5 @@ This is a package for doing stellar photometry that relies on astropy.
 
 .. note:: The layout of this directory is simply a suggestion.  To follow
           traditional practice, do *not* edit this page, but instead place
-          all documentation for the package inside ``glowing_waffles/``.
+          all documentation for the package inside ``stellarphot/``.
           You can follow this practice or choose your own layout.

docs/stellarphot/index.rst

@@ -21,7 +21,10 @@ Reference/API
 =============
 
 .. automodapi:: stellarphot
+.. automodapi:: stellarphot.analysis
+.. automodapi:: stellarphot.core
 .. automodapi:: stellarphot.photometry
 .. automodapi:: stellarphot.differential_photometry
+.. automodapi:: stellarphot.source_detection
 .. automodapi:: stellarphot.visualization
 .. automodapi:: stellarphot.io

stellarphot/analysis/__init__.py

@@ -0,0 +1,2 @@
+from .exotic import *
+from .transit_fitting import *

stellarphot/analysis/exotic.py

@@ -10,6 +10,11 @@
 from astropy.utils.data import get_pkg_data_filename
 
 
+__all__ = ['MyValid', 'get_tic_info', 'make_checker','validate_exposure_time',
+           'populate_TIC_boxes', 'populate_TOI_boxes', 'exotic_settings_widget',
+           'set_values_from_json_file', 'get_values_from_widget','generate_json_file_name']
+
+
 template_types = ['known', 'candidate']
 template_json = {}
 to_fill = {}
@@ -71,7 +76,7 @@ def get_tic_info(TIC_ID):
 
 def make_checker(indicator_widget, value_widget):
     """
-    Build an observer thatchecks TIC number and, if it is a valid
+    Build an observer that checks TIC number and, if it is a valid
     TIC number, looks up information about the TIC object from
     MAST copy of TIC as priors for EXOTIC. It also sets the visible checkbox
     to the appropriate state.

stellarphot/analysis/transit_fitting.py

@@ -29,6 +29,7 @@
                 'or\n'
                 'pip install batman-package')
 
+__all__ = ['VariableArgsFitter', 'TransitModelFit']
 
 class VariableArgsFitter(LevMarLSQFitter):
     """

stellarphot/differential_photometry/__init__.py

@@ -1,3 +1,4 @@
 from .magnitude_transforms import *
 from .catalog_search import *
 from .vsx_mags import *
+from .aij_rel_fluxes import *

stellarphot/differential_photometry/catalog_search.py

@@ -97,7 +97,7 @@ def catalog_search(frame_wcs_or_center, shape, desired_catalog,
     if clip_by_frame:
         in_fov = in_frame(frame_wcs_or_center, cat_coords, padding=padding)
     else:
-        in_fov = np.ones([len(cat_coords)], dtype=np.bool)
+        in_fov = np.ones([len(cat_coords)], dtype=bool)
     return cat[in_fov]
 
 
@@ -131,7 +131,7 @@ def catalog_clean(catalog, remove_rows_with_mask=True,
     }
 
     recognized_comparison_ops = '|'.join(comparisons.keys())
-    keepers = np.ones([len(catalog)], dtype=np.bool)
+    keepers = np.ones([len(catalog)], dtype=bool)
 
     if remove_rows_with_mask and catalog.masked:
         for c in catalog.columns:
@@ -146,7 +146,7 @@ def catalog_clean(catalog, remove_rows_with_mask=True,
         comparison_func = comparisons[results.group(1)]
         comparison_value = results.group(2)
         new_keepers = comparison_func(catalog[column],
-                                      np.float(comparison_value))
+                                      float(comparison_value))
         keepers = keepers & new_keepers
 
     return catalog[keepers]

stellarphot/differential_photometry/tests/test_magnitude_transforms.py

@@ -38,7 +38,7 @@ def generate_star_coordinates(n_stars,
     """
     # The plus one guarantees we'll have enough positions for
     # all of our stars.
-    max_index = np.int(np.sqrt(n_stars)) + 1
+    max_index = int(np.sqrt(n_stars)) + 1
 
     grids = np.mgrid[:max_index, :max_index]
     dec_grid, ra_grid = grids

stellarphot/io/aij.py

@@ -7,7 +7,7 @@
 
 import numpy as np
 
-__all__ = ['parse_aij_table', 'ApertureFileAIJ']
+__all__ = ['parse_aij_table', 'ApertureAIJ', 'ApertureFileAIJ', 'MultiApertureAIJ', 'Star', 'generate_aij_table']
 
 
 class ApertureAIJ:

stellarphot/notebooks/example_interactive_plot.ipynb

@@ -144,8 +144,8 @@
     "    # that the event.x is a number from 0 to 1 covering the whole drawing \n",
     "    # canvas, but event.xdata is the position indicated in the units \n",
     "    # on the axes.\n",
-    "    click_x_data = np.int(event.xdata)\n",
-    "    click_y_data = np.int(event.ydata)\n",
+    "    click_x_data = int(event.xdata)\n",
+    "    click_y_data = int(event.ydata)\n",
     "    \n",
     "    # Define a slice centered on the click\n",
     "    slice_x = slice(click_x_data - stamp_size/2, click_x_data + stamp_size/2)\n",
@@ -202,8 +202,8 @@
     "def mouse_moved(event):\n",
     "    # Yuck. This code duplicates the click stuff above.\n",
     "    stamp_size = 20\n",
-    "    click_x_data = np.int(event.xdata)\n",
-    "    click_y_data = np.int(event.ydata)\n",
+    "    click_x_data = int(event.xdata)\n",
+    "    click_y_data = int(event.ydata)\n",
     "    slice_x = slice(click_x_data-stamp_size/2, click_x_data+stamp_size/2)\n",
     "    slice_y = slice(click_y_data-stamp_size/2, click_y_data+stamp_size/2)\n",
     "    cutout = image_cut[slice_y, slice_x]\n",

stellarphot/notebooks/photometry/06-transit-fit-template.ipynb

@@ -207,7 +207,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cycle_number = np.int((then - epoch) / period + 1)\n",
+    "cycle_number = int((then - epoch) / period + 1)\n",
     "that_transit = cycle_number * period + epoch\n",
     "that_transit"
    ]

stellarphot/photometry.py

@@ -14,7 +14,6 @@
 from astropy.stats import sigma_clipped_stats
 from astropy.nddata import NoOverlapError
 
-from .coordinates import convert_pixel_wcs
 from .source_detection import compute_fwhm
 
 __all__ = ['photutils_stellar_photometry',
@@ -122,7 +121,7 @@ def photutils_stellar_photometry(ccd_image, sources,
 
     # Obtain RA/Dec coordinates and add them to table
     try:
-        ra, dec = convert_pixel_wcs(ccd_image, coords[0], coords[1], 1)
+        ra, dec = ccd_image.wcs.all_pix2world(coords[0], coords[1], 0)
         phot_table['RA_center'] = ra
         phot_table['Dec_center'] = dec
     except AttributeError:
@@ -339,7 +338,7 @@ def add_to_photometry_table(phot, ccd, annulus, apertures, fname='',
     phot['date-obs'] = [ccd.header['DATE-OBS']] * len(phot)
     night = Time(ccd.header['DATE-OBS'], scale='utc')
     night.format = 'mjd'
-    phot['night'] = np.int(np.floor(night.value - 0.5))
+    phot['night'] = int(np.floor(night.value - 0.5))
     phot['aperture_net_flux'] = (phot['aperture_sum'] -
                                  (phot['aperture_area'] *
                                   phot['sky_per_pix_avg']))
@@ -593,7 +592,7 @@ def find_times(phot_column, exposure,
                ra=331.1170417, dec=81.5659444,
                latitude=46.86678, longitude=263.54672):
     """
-    Returns a numpy array of barycentric julien date times
+    Returns a numpy array of barycentric Julian date times
 
     Parameters
     ----------
@@ -621,7 +620,7 @@ def find_times(phot_column, exposure,
     -------
 
     new_time : numpy array
-        array of barycentric times by julien date
+        array of barycentric times by Julian date
 
     """
     location = EarthLocation(lat=latitude, lon=longitude)

stellarphot/source_detection.py

@@ -13,7 +13,6 @@
 
 __all__ = ['source_detection', 'compute_fwhm']
 
-
 def _fit_2dgaussian(data):
     """
     Fit a 2d Gaussian to data.

stellarphot/tests/test_detection.py

@@ -138,7 +138,7 @@ def test_aperture_photometry_with_outlier_rejection(reject):
     # adding these moves the average pixel value by quite a bit,
     # so we'll only get the correct net flux if these are removed.
     for source in fake_image.sources:
-        center_px = (np.int(source['x_mean']), np.int(source['y_mean']))
+        center_px = (int(source['x_mean']), int(source['y_mean']))
         begin = center_px[0] + inner_annulus + 1
         end = begin + (outer_annulus - inner_annulus - 1)
         # Yes, x and y are deliberately reversed below.

stellarphot/visualization/__init__.py

@@ -2,3 +2,8 @@
 
 from .multi_night_plots import *
 from .aij_plots import *
+from .comparison_functions import *
+from .fits_opener import *
+from .photometry_widget_functions import *
+from .seeing_profile_functions import *
+from .transit_plots import *

stellarphot/visualization/comparison_functions.py

@@ -28,7 +28,7 @@
 
 
 __all__ = ['read_file', 'set_up', 'match', 'mag_scale',
-           'in_field', 'make_markers', 'wrap']
+           'in_field', 'make_markers', 'wrap', 'ComparisonViewer']
 
 DESC_STYLE = {"description_width": "initial"}
 

stellarphot/visualization/fits_opener.py

@@ -7,6 +7,8 @@
 from ipyfilechooser import FileChooser
 
 
+__all__ = ['FitsOpener']
+
 class FitsOpener:
     def __init__(self, title="Choose an image", filter_pattern=None, **kwargs):
         self._fc = FileChooser(title=title, **kwargs)

stellarphot/visualization/photometry_widget_functions.py

@@ -5,6 +5,9 @@
 from ipyfilechooser import FileChooser
 
 
+__all__ = ['PhotometrySettings']
+
+
 class PhotometrySettings:
     def __init__(self):
         self._image_dir = FileChooser(title="Choose folder with images", show_only_dirs=True)

stellarphot/visualization/seeing_profile_functions.py

@@ -20,7 +20,7 @@
 from stellarphot.visualization import seeing_plot
 from stellarphot.visualization.fits_opener import FitsOpener
 
-__all__ = ['set_keybindings', 'box', 'make_show_event']
+__all__ = ['set_keybindings', 'box', 'SeeingProfileWidget']
 
 desc_style = {"description_width": "initial"}
 
@@ -176,7 +176,7 @@ def radial_profile(data, center, size=30, return_scaled=True):
 
     r = np.sqrt((xd - sub_center[0])**2 + (yd - sub_center[1])**2)
     r_exact = r.copy()
-    r = r.astype(np.int)
+    r = r.astype(int)
 
     sub_data = sub_image.data
 

stellarphot/visualization/transit_plots.py

@@ -1,6 +1,9 @@
 import numpy as np
 
 
+__all__ = ['plot_many_factors', 'bin_data', 'scale_and_shift']
+
+
 def plot_many_factors(photometry, low, high, shift, scale):
     airmass = photometry['airmass'] / np.mean(photometry['airmass'])
     x = photometry['xcenter'] / np.mean(photometry['xcenter'])