Merge pull request #485 from mwcraig/fix-bjd-column

Fix bjd column among other exoplanet fixes

.jp_app_launcher_stellarphot.yaml

@@ -54,7 +54,23 @@
 
 - title: Initial exoplanet model
   description: Do an initial fit to a transit
-  source: ../stellarphot/tess-intial-model-fit.ipynb
+  source: ../stellarphot/tess-initial-model-fit.ipynb
+  icon: ../stellarphot/stellarphot-logo.svg
+  cwd: not_used
+  type: notebook
+  catalog: Stellarphot analysis and tools
+
+- title: Second exoplanet model fit
+  description: Second transit model fit
+  source: ../stellarphot/tess-second-model-fit.ipynb
+  icon: ../stellarphot/stellarphot-logo.svg
+  cwd: not_used
+  type: notebook
+  catalog: Stellarphot analysis and tools
+
+- title: Exoplanet model fit with EXOTIC
+  description: The final exoplanet fit
+  source: ../stellarphot/tess-EXOTIC-fit.ipynb
   icon: ../stellarphot/stellarphot-logo.svg
   cwd: not_used
   type: notebook

stellarphot/differential_photometry/aij_rel_fluxes.py

@@ -2,6 +2,7 @@
 import numpy as np
 from astropy.coordinates import SkyCoord
 from astropy.table import QTable, Table
+from astropy.time import Time
 
 from stellarphot import PhotometryData, SourceListData
 
@@ -240,13 +241,20 @@ def add_relative_flux_column(
     if "bjd" not in flux_table.colnames:
         if verbose:
             print("Adding BJD column to photometry data")
-        # Add dummy BJD column so the whole table has one
-        flux_table["bjd"] = np.nan
+        # Accumulate the BJD here
+        bjds = []
+
         flux_group = flux_table.group_by("file")
         for group in flux_group.groups:
             mean_ra = group["ra"].mean()
             mean_dec = group["dec"].mean()
             group.add_bjd_col(bjd_coordinates=SkyCoord(mean_ra, mean_dec))
+            bjds.extend(group["bjd"].jd)
+
+    # Each (ephemeral) group had a BJD, this adds the column to the
+    # original table.
+    flux_group["bjd"] = Time(bjds, scale="tdb", format="jd")
+
     if verbose:
         print("Writing photometry data with relative flux columns")
-    flux_table.write(output_file, overwrite=True)
+    flux_group.write(output_file, overwrite=True)

stellarphot/notebooks/photometry/07-transit-fit-with-exotic.ipynb → stellarphot/notebooks/tess-EXOTIC-fit.ipynb

@@ -10,15 +10,16 @@
     "from pathlib import Path\n",
     "import pickle\n",
     "\n",
-    "import numpy as np\n",
+    "import numpy as np \n",
     "\n",
-    "from astropy.table import Table\n",
+    "from astropy.table import Table \n",
     "\n",
     "#from try_json_editing_rev1 import whole_thing, generate_json_file_name, exotic_arguments, get_values_from_widget\n",
     "from stellarphot.transit_fitting.gui import generate_json_file_name, exotic_arguments, get_values_from_widget, exotic_settings_widget, populate_TOI_boxes\n",
     "from stellarphot.settings.fits_opener import FitsOpener\n",
     "from stellarphot import PhotometryData\n",
-    "from stellarphot.io import TOI"
+    "from stellarphot.io import TOI\n",
+    "from stellarphot.gui_tools.photometry_widget_functions import TessAnalysisInputControls"
    ]
   },
   {
@@ -30,15 +31,49 @@
     "This notebook will do a different kind of fit to your exoplanet data. It takes longer to run than the fitting we've done so far, which is why we didn't begin with this type of fit."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 0. Get some data\n",
+    "\n",
+    "+ Select photometry file with relative flux\n",
+    "+ Select passband\n",
+    "+ Select TESS info file"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "fits_opener = FitsOpener(title=\"Select your photometry/relative flux file\", filter_pattern=[\"*.ecsv\"])\n",
+    "taic = TessAnalysisInputControls()\n",
+    "taic"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "# 👉 File with photometry, including flux\n",
+    "photometry_file = taic.photometry_data_file\n",
+    "inp_photometry = taic.phot_data\n",
     "\n",
-    "fits_opener.file_chooser"
+    "# 👉 File with exoplanet info in\n",
+    "tess_info_output_file = taic.tic_info_file\n",
+    "tess_info = TOI.model_validate_json(tess_info_output_file.read_text())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Get just the target star and some information about it"
    ]
   },
   {
@@ -47,10 +82,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_data_file = fits_opener.path\n",
-    "toi_info_file = Path(\"TIC-194461202-info.json\")\n",
-    "\n",
-    "tess_info = TOI.model_validate_json(toi_info_file.read_text())"
+    "if np.isnan(inp_photometry['bjd']).all():\n",
+    "    inp_photometry.add_bjd_col()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "photometry = inp_photometry.lightcurve_for(1, flux_column=\"relative_flux\", passband=taic.passband).remove_nans()"
    ]
   },
   {
@@ -70,12 +112,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "inp_data = PhotometryData.read(input_data_file)\n",
-    "inp_data = inp_data[inp_data['star_id'] == 1]\n",
-    "inp_data.add_bjd_col()\n",
-    "# inp_data = inp_data[inp_data['BJD'] > 2459795.75]\n",
     "\n",
-    "out_data = inp_data['bjd', 'relative_flux', 'relative_flux_error', 'airmass']\n",
+    "out_data = photometry['bjd', 'relative_flux', 'relative_flux_error', 'airmass']\n",
     "out_data.write(exotic_data_file, overwrite=True)"
    ]
   },
@@ -90,6 +128,13 @@
     "populate_TOI_boxes(tess_info, settings.value_widget)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## YOU MAY NEED DATA FROM HERE:  https://exofop.ipac.caltech.edu/tess/\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -145,9 +190,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!exotic --override --pre TIC_194461202-2024-10-08-SR.json"
+    "!exotic --override --pre TIC_370981403-2024-10-18-SG.json"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -158,7 +210,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "stelldev-pyd2",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -172,7 +224,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

stellarphot/notebooks/tess-intial-model-fit.ipynb → stellarphot/notebooks/tess-initial-model-fit.ipynb

@@ -69,6 +69,16 @@
     "### Get just the target star and some information about it"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if np.isnan(inp_photometry['bjd']).all():\n",
+    "    inp_photometry.add_bjd_col()\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -198,7 +208,7 @@
     "binned2 = aggregate_downsample(ts2, time_bin_size=model_options.bin_size * u.min, aggregate_func=add_quad)\n",
     "\n",
     "binned[\"normalized_flux_error\"] = binned2[\"normalized_flux_error\"]\n",
-    "# binned_time = BinnedTimeSeries(photometry['bjd'], time_bin_start=first_time, time_bin_end=last_time, time_bin_size=bin_size)"
+    "binned = binned[~np.isnan(binned[\"normalized_flux\"])]"
    ]
   },
   {
@@ -389,7 +399,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,