Merge pull request #130 from JuanCab/gui_reorg

Initial reorganization of code

CHANGES.rst

@@ -6,6 +6,8 @@ New Features
 
 Other Changes and Additions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
++ Major reorganizaiton of code including moving functions to new modules. [#130]
+
 
 Bug Fixes
 ^^^^^^^^^

stellarphot/differential_photometry/__init__.py

@@ -1,4 +1,2 @@
-from .magnitude_transforms import *
-from .catalog_search import *
-from .vsx_mags import *
 from .aij_rel_fluxes import *
+from .vsx_mags import *

stellarphot/visualization/__init__.py → stellarphot/gui_tools/__init__.py

@@ -1,9 +1,6 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
-from .multi_night_plots import *
-from .aij_plots import *
-from .comparison_functions import *
 from .fits_opener import *
+from .comparison_functions import *
 from .photometry_widget_functions import *
 from .seeing_profile_functions import *
-from .transit_plots import *

stellarphot/visualization/comparison_functions.py → stellarphot/gui_tools/comparison_functions.py

@@ -1,8 +1,6 @@
 import functools
 from pathlib import Path
 
-import pandas
-
 import ipywidgets as ipw
 
 import numpy as np
@@ -20,227 +18,18 @@
     from astrowidgets.ginga import ImageWidget
 
 from stellarphot.differential_photometry import *
-from stellarphot.io import TessSubmission, TOI, TessTargetFile
 from stellarphot.photometry import *
-from stellarphot.visualization.seeing_profile_functions import set_keybindings
-from stellarphot.visualization.fits_opener import FitsOpener
+from stellarphot.io import TessSubmission, TOI, TessTargetFile
+from stellarphot.gui_tools.seeing_profile_functions import set_keybindings
+from stellarphot.gui_tools.fits_opener import FitsOpener
+from stellarphot.utils.comparison_utils import read_file, set_up, crossmatch_APASS2VSX, mag_scale, in_field
 
 
-__all__ = ['read_file', 'set_up', 'crossmatch_APASS2VSX', 'mag_scale',
-           'in_field', 'make_markers', 'wrap', 'ComparisonViewer']
+__all__ = ['make_markers', 'wrap', 'ComparisonViewer']
 
 DESC_STYLE = {"description_width": "initial"}
 
 
-def read_file(radec_file):
-    """
-    Read an AIJ radec file with target and/or comparison positions
-
-    Parameters
-    ----------
-
-    radec_file : str
-        Name of the file
-
-    Returns
-    -------
-
-    `astropy.table.Table`
-        Table with target information, including a
-        `astropy.coordinates.SkyCoord` column.
-    """
-    df = pandas.read_csv(radec_file, names=['RA', 'Dec', 'a', 'b', 'Mag'])
-    target_table = Table.from_pandas(df)
-    ra = target_table['RA']
-    dec = target_table['Dec']
-    target_table['coords'] = SkyCoord(ra=ra, dec=dec, unit=(u.hour, u.degree))
-    return target_table
-
-
-def set_up(sample_image_for_finding_stars, directory_with_images='.'):
-    """
-    Read in sample image and find known variables in the field of view.
-
-    Parameters
-    ----------
-
-    sample_image_for_finding_stars : str
-        Name or URL of a FITS image of the field of view.
-
-    directory_with_images : str, optional
-        Folder in which the image is located. Ignored if the sample image
-        is a URL.
-
-    Returns
-    -------
-
-    ccd: `astropy.nddata.CCDData`
-        Sample image.
-
-    vsx: `astropy.table.Table`
-        Table with known variables in the field of view.
-
-    """
-    if sample_image_for_finding_stars.startswith('http'):
-        path = sample_image_for_finding_stars
-    else:
-        path = Path(directory_with_images) / sample_image_for_finding_stars
-
-    ccd = CCDData.read(path)
-    try:
-        vsx = find_known_variables(ccd)
-    except RuntimeError:
-        vsx = []
-    else:
-        ra = vsx['RAJ2000']
-        dec = vsx['DEJ2000']
-        vsx['coords'] = SkyCoord(ra=ra, dec=dec, unit=(u.hour, u.degree))
-
-    return ccd, vsx
-
-
-def crossmatch_APASS2VSX(CCD, RD, vsx):
-    """
-    Find APASS stars in FOV and matches APASS stars to VSX and APASS to input targets.
-
-    Parameters
-    ----------
-
-    CCD : `astropy.nddata.CCDData`
-        Sample image.
-
-    RD : `astropy.table.Table`
-        Table with target information, including a
-        `astropy.coordinates.SkyCoord` column.
-
-    vsx : `astropy.table.Table`
-        Table with known variables in the field of view.
-
-    Returns
-    -------
-
-    apass : `astropy.table.Table`
-        Table with APASS stars in the field of view.
-
-    v_angle : `astropy.units.Quantity`
-        Angular separation between APASS stars and VSX stars.
-
-    RD_angle : `astropy.units.Quantity`
-        Angular separation between APASS stars and input targets.
-    """
-    apass, apass_in_bright = find_apass_stars(CCD)
-    ra = apass['RAJ2000']
-    dec = apass['DEJ2000']
-    apass['coords'] = SkyCoord(ra=ra, dec=dec, unit=(u.hour, u.degree))
-    apass_coord = apass['coords']
-
-    if vsx:
-        v_index, v_angle, v_dist = \
-            apass_coord.match_to_catalog_sky(vsx['coords'])
-    else:
-        v_angle = []
-
-    if RD:
-        RD_index, RD_angle, RD_dist = \
-            apass_coord.match_to_catalog_sky(RD['coords'])
-    else:
-        RD_angle = []
-
-    return apass, v_angle, RD_angle
-
-
-def mag_scale(cmag, apass, v_angle, RD_angle,
-              brighter_dmag=0.44, dimmer_dmag=0.75):
-    """
-    Select comparison stars that are 1) not close the VSX stars or to other
-    target stars and 2) fall within a particular magnitude range.
-
-    Parameters
-    ----------
-
-    cmag : float
-        Magnitude of the target star.
-
-    apass : `astropy.table.Table`
-        Table with APASS stars in the field of view.
-
-    v_angle : `astropy.units.Quantity`
-        Angular separation between APASS stars and VSX stars.
-
-    RD_angle : `astropy.units.Quantity`
-        Angular separation between APASS stars and input targets.
-
-    brighter_dmag : float, optional
-        Maximum difference in magnitude between the target and comparison stars.
-
-    dimmer_dmag : float, optional
-        Minimum difference in magnitude between the target and comparison stars.
-
-    Returns
-    -------
-
-    apass_good_coord : `astropy.coordinates.SkyCoord`
-        Coordinates of the comparison stars.
-
-    good_stars : `astropy.table.Table`
-        Table with the comparison stars.
-    """
-    high_mag = apass['r_mag'] < cmag + dimmer_dmag
-    low_mag = apass['r_mag'] > cmag - brighter_dmag
-    if len(v_angle)>0:
-        good_v_angle = v_angle > 1.0 * u.arcsec
-    else:
-        good_v_angle = True
-
-    if len(RD_angle)>0:
-        good_RD_angle = RD_angle > 1.0 * u.arcsec
-    else:
-        good_RD_angle = True
-
-    good_stars = high_mag & low_mag & good_RD_angle & good_v_angle
-    good_apass = apass[good_stars]
-    apass_good_coord = good_apass['coords']
-    return apass_good_coord, good_stars
-
-
-def in_field(apass_good_coord, ccd, apass, good_stars):
-    """
-    Return APASS stars in the field of view.
-
-    Parameters
-    ----------
-
-    apass_good_coord : `astropy.coordinates.SkyCoord`
-        Coordinates of the comparison stars.
-
-    ccd : `astropy.nddata.CCDData`
-        Sample image.
-
-    apass : `astropy.table.Table`
-        Table with APASS stars in the field of view.
-
-    good_stars : `astropy.table.Table`
-        Table with the comparison stars.
-
-    Returns
-    -------
-
-    ent : `astropy.table.Table`
-        Table with APASS stars in the field of view.
-    """
-    apassx, apassy = ccd.wcs.all_world2pix(
-        apass_good_coord.ra, apass_good_coord.dec, 0)
-    ccdx, ccdy = ccd.shape
-
-    xin = (apassx < ccdx) & (0 < apassx)
-    yin = (apassy < ccdy) & (0 < apassy)
-    xy_in = xin & yin
-    apass_good_coord[xy_in]
-    nt = apass[good_stars]
-    ent = nt[xy_in]
-    return ent
-
-
 def make_markers(iw, ccd, RD, vsx, ent, name_or_coord=None):
     """
     Add markers for APASS, TESS targets, VSX.  Also center on object/coordinate.

stellarphot/visualization/seeing_profile_functions.py → stellarphot/gui_tools/seeing_profile_functions.py

@@ -17,8 +17,8 @@
 import matplotlib.pyplot as plt
 
 from stellarphot.io import TessSubmission
-from stellarphot.visualization import seeing_plot
-from stellarphot.visualization.fits_opener import FitsOpener
+from stellarphot.gui_tools.fits_opener import FitsOpener
+from stellarphot.plotting import seeing_plot
 
 __all__ = ['set_keybindings', 'find_center', 'radial_profile',
            'RadialProfile', 'box', 'SeeingProfileWidget']

stellarphot/visualization/tests/test_seeing_profile.py → stellarphot/gui_tools/tests/test_seeing_profile.py

@@ -6,7 +6,7 @@
 from astropy.table import Table
 from astrowidgets import ImageWidget
 
-from stellarphot.visualization import seeing_profile_functions as spf
+from stellarphot.gui_tools import seeing_profile_functions as spf
 
 # Make a few round stars
 STARS = Table(dict(amplitude=[1000, 200, 300],

stellarphot/io/tess.py

@@ -466,6 +466,6 @@ def _retrieve_target_file(self):
 
 
     def _build_table(self):
-        from stellarphot.visualization.comparison_functions import read_file
+        from stellarphot.utils.comparison_utils import read_file
 
         self.table = read_file(self._path)

stellarphot/notebooks/comp-star-plots.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
@@ -18,7 +18,7 @@
     "\n",
     "from stellarphot.io import parse_aij_table\n",
     "\n",
-    "from stellarphot.visualization import multi_night\n",
+    "from stellarphot.plotting import multi_night\n",
     "\n",
     "from astropy.table import Table, Column"
    ]
@@ -239,7 +239,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

stellarphot/notebooks/comp-stars-template.ipynb

@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,11 +39,13 @@
     "from astropy.table import Table\n",
     "from astropy.coordinates import SkyCoord\n",
     "\n",
-    "from stellarphot.visualization.comparison_functions import (\n",
-    "    read_file, set_up, crossmatch_APASS2VSX, mag_scale, in_field, wrap, make_markers,\n",
-    "    viewer\n",
+    "from stellarphot.utils.comparison_utils import (\n",
+    "    read_file, set_up, crossmatch_APASS2VSX, in_field, mag_scale\n",
+    ")\n",
+    "from stellarphot.gui_tools.comparison_functions import (\n",
+    "    wrap, make_markers\n",
     ")\n",
-    "from stellarphot.visualization.seeing_profile_functions import set_keybindings"
+    "from stellarphot.gui_tools.seeing_profile_functions import set_keybindings"
    ]
   },
   {
@@ -324,7 +326,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,