Merge pull request #86 from mwcraig/update-notebooks-exoplanets

Update notebooks exoplanets

stellarphot/io/__init__.py

@@ -1,4 +1,4 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
 from .aij import *
-from .tess_submission import *
+from .tess import *

stellarphot/io/tess.py

@@ -0,0 +1,253 @@
+from dataclasses import dataclass
+from pathlib import Path
+import re
+
+from astropy.coordinates import SkyCoord
+from astropy.table import Table
+from astropy.time import Time
+from astropy import units as u
+from astropy.utils.data import download_file
+
+from astroquery.mast import Catalogs
+
+import requests
+
+from stellarphot.analysis.exotic import get_tic_info
+
+__all__ = ["TessSubmission", "TOI", "TessTargetFile"]
+
+# Makes me want to vomit, but....
+DEFAULT_TABLE_LOCATION = "who.the.fuck.knows"
+TOI_TABLE_URL = "https://exofop.ipac.caltech.edu/tess/download_toi.php?output=csv"
+TIC_regex = re.compile(r"[tT][iI][cC][^\d]?(?P<star>\d+)(?P<planet>\.\d\d)?")
+
+
+@dataclass
+class TessSubmission:
+    telescope_code: str
+    filter: str
+    utc_start: int
+    tic_id: int
+    planet_number: int
+
+    def __post_init__(self, *args, **kwargs):
+        self._tic_info = None
+
+    @classmethod
+    def from_header(cls, header, telescope_code="", planet=0):
+        # Set some default dummy values
+
+        tic_id = 0
+        filter = ""
+        fails = {}
+        try:
+            dateobs = header['date-obs']
+        except KeyError:
+            fails["utc_start"] = "UTC date of first image"
+        else:
+            dateobs = dateobs.split("T")[0].replace("-", "")
+
+        try:
+            filter = header['filter']
+        except KeyError:
+            fails["filter"] = ("filter/passband")
+
+        try:
+            obj = header['object']
+        except KeyError:
+            fails['tic_id'] = "TIC ID number"
+        else:
+            result = TIC_regex.match(obj)
+            if result:
+                tic_id = int(result.group("star"))
+                # Explicit argument overrules the header
+                if result.group("planet") and not planet:
+                    # Drop the leading period from the match
+                    planet = int(result.group("planet")[1:])
+            else:
+                # No star from the object after all
+                fails['tic_id'] = "TIC ID number"
+
+        fail_msg = ""
+        fail = []
+        for k, v in fails.items():
+            fail.append(f"Unable to determine {k}, {v}, from header.")
+
+        fail = "\n".join(fail)
+
+        if fail:
+            raise ValueError(fail)
+
+        return cls(utc_start=dateobs,
+                   filter=filter,
+                   telescope_code=telescope_code,
+                   tic_id=tic_id,
+                   planet_number=planet)
+
+    def _valid_tele_code(self):
+        return len(self.telescope_code) > 0
+
+    def _valid_planet(self):
+        return self.planet_number > 0
+
+    def _valid_tic_num(self):
+        return self.tic_id < 10_000_000_000
+
+    def _valid(self):
+        """
+        Check whether the information so far is valid, meaning:
+         + Telescope code is not the empty string
+         + Planet number is not zero
+         + TIC ID is not more than 10 digits
+        """
+        valid = (
+            self._valid_tele_code() and
+            self._valid_planet() and
+            self._valid_tic_num()
+        )
+        return valid
+
+    @property
+    def base_name(self):
+        if self._valid():
+            pieces = [
+                f"TIC{self.tic_id}-{self.planet_number:02d}",
+                self.utc_start,
+                self.telescope_code,
+                self.filter
+            ]
+            return "_".join(pieces)
+
+    @property
+    def seeing_profile(self):
+        return self.base_name + "_seeing-profile.png"
+
+    @property
+    def field_image(self):
+        return self.base_name + "_field.png"
+
+    @property
+    def field_image_zoom(self):
+        return self.base_name + "_field-zoom.png"
+
+    @property
+    def apertures(self):
+        return self.base_name + "_measurements.apertures"
+
+    @property
+    def tic_coord(self):
+        if not self._tic_info:
+            self._tic_info = get_tic_info(self.tic_id)
+        return SkyCoord(ra=self._tic_info['ra'][0], dec=self._tic_info['dec'][0], unit='degree')
+
+    def invalid_parts(self):
+        if self._valid():
+            return
+
+        if not self._valid_tele_code():
+            print(f"Telescope code {self.telescope_code} is not valid")
+
+        if not self._valid_planet():
+            print(f"Planet number {self.planet_number} is not valid")
+
+        if not self._valid_tic_num():
+            print(f"TIC ID {self.tic_id} is not valid.")
+
+
+class TOI:
+    def __init__(self, tic_id, toi_table=DEFAULT_TABLE_LOCATION, allow_download=True):
+        path = Path(toi_table)
+        if not path.is_file():
+            if not allow_download:
+                raise ValueError(f"File {toi_table} not found.")
+            toi_table = download_file(TOI_TABLE_URL, cache=True, show_progress=True, timeout=60)
+
+        self._toi_table = Table.read(toi_table, format="ascii.csv")
+        self._toi_table = self._toi_table[self._toi_table['TIC ID'] == tic_id]
+        if len(self._toi_table) != 1:
+            raise RuntimeError(f"Found {len(self._toi_table)} rows in table, expected one.")
+        self._tic_info = get_tic_info(tic_id)
+
+    @property
+    def tess_mag(self):
+        return self._toi_table['TESS Mag'][0]
+
+    @property
+    def tess_mag_error(self):
+        return self._toi_table['TESS Mag err'][0]
+
+    @property
+    def depth(self):
+        """
+        Depth, parts per thousand.
+        """
+        return self._toi_table['Depth (ppm)'][0] / 1000
+
+    @property
+    def depth_error(self):
+        """
+        Error in depth, parts per thousand.
+        """
+        return self._toi_table['Depth (ppm) err'][0] / 1000
+
+    @property
+    def epoch(self):
+        return Time(self._toi_table['Epoch (BJD)'][0], scale='tdb', format='jd')
+
+    @property
+    def epoch_error(self):
+        return self._toi_table['Epoch (BJD) err'][0] * u.day
+
+    @property
+    def period(self):
+        return self._toi_table['Period (days)'][0] * u.day
+
+    @property
+    def period_error(self):
+        return self._toi_table['Period (days) err'][0] * u.day
+
+    @property
+    def duration(self):
+        return self._toi_table['Duration (hours)'][0] * u.hour
+
+    @property
+    def duration_error(self):
+        return self._toi_table['Duration (hours) err'][0] * u.hour
+
+    @property
+    def coord(self):
+        return SkyCoord(ra=self._tic_info['ra'][0], dec=self._tic_info['dec'][0], unit='degree')
+
+
+@dataclass
+class TessTargetFile:
+    coord : SkyCoord
+    magnitude : float
+    depth : float
+    file : str = "aperture_locations.csv"
+    aperture_server : str = "https://www.astro.louisville.edu/"
+
+    def __post_init__(self):
+        self._path = Path(self.file)
+        self.target_file = self._retrieve_target_file()
+        self.target_table = self._build_table()
+
+    def _retrieve_target_file(self):
+        params = dict(
+            ra = self.coord.ra.to_string(unit='hour', decimal=False, sep=":"),
+            dec = self.coord.dec.to_string(unit='degree', decimal=False, sep=":"),
+            mag=self.magnitude,
+            depth=self.depth
+        )
+        result = requests.get(self.aperture_server + "cgi-bin/gaia_to_aij/upload_request.cgi", params=params)
+        links = re.search('href="(.+)"', result.text.replace('\n', ''), )
+        download_link = self.aperture_server + links[1]
+        target_file_contents = requests.get(download_link)
+        with open(self._path, "w") as f:
+            f.write(target_file_contents.text)
+
+
+    def _build_table(self):
+        from stellarphot.visualization.comparison_functions import read_file
+
+        self.table = read_file(self._path)

stellarphot/io/tests/test_tess_submission.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from stellarphot.io.tess_submission import TessSubmission
+from stellarphot.io.tess import TessSubmission
 
 GOOD_HEADER = {
     "date-obs": "2022-06-04T05:44:28.010",
@@ -49,7 +49,7 @@ def test_base_name():
 
 def test_seeing_profile():
     tsub = TessSubmission.from_header(GOOD_HEADER_WITH_PLANET, telescope_code="ABS")
-    assert tsub.seeing_profile == "TIC237205154-01_20220604_ABS_ip_seeing-profile"
+    assert tsub.seeing_profile == "TIC237205154-01_20220604_ABS_ip_seeing-profile.png"
 
 
 def test_valid_method():