Better document the first fitting notebook

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

@@ -33,7 +33,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 0. Get some data"
+    "### 0. Get some data\n",
+    "\n",
+    "+ Select photometry file with relative flux\n",
+    "+ Select passband\n",
+    "+ Select TESS info file"
    ]
   },
   {
@@ -83,7 +87,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 👇👇👇 use this to exclude some data (only if needed!) 👇👇👇"
+    "### 👇👇👇 use this to exclude some data (only if needed!) 👇👇👇\n",
+    "\n",
+    "Option to filter by date..even though you do not know yet what the data looks like"
    ]
   },
   {
@@ -101,6 +107,13 @@
     "use_no_data_after = Time(2499999, format=\"jd\", scale=\"tdb\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Read the photometry and TESS info"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -116,6 +129,13 @@
     "#     tess_info = pickle.load(f)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Actually filter out data by date"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -165,6 +185,16 @@
     "### You may need to alter some of the settings here"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Fit settings\n",
+    "\n",
+    "+ Do any detrending by a covariate?\n",
+    "+ Which parameters are fixed?"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -200,6 +230,13 @@
     "fit_width = False"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Create separate variables for a bunch of things because it was a PITA to write to code later in the notebook \n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -223,10 +260,19 @@
     "# Enter object name\n",
     "obj = f\"TIC {tess_info.tic_id}\"\n",
     "\n",
+    "\n",
+    "# 👇👇👇 BUG 🐛 BUG 🐛 BUG 🐛 BUG 👇👇👇👇\n",
     "# Enter filter\n",
     "phot_filter = \"rp\""
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Plot settings 🤦‍♂️"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -249,6 +295,13 @@
    "outputs": [],
    "source": []
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Get just the target star and some information about it"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -273,6 +326,13 @@
     "Looks like we need to normalize the data first....."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Keep only the data in the right filter"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -283,18 +343,17 @@
    "source": [
     "band_filter = photometry[\"passband\"] == phot_filter\n",
     "\n",
-    "target_and_filter = target_star & band_filter"
+    "target_and_filter = target_star & band_filter\n",
+    "photometry = photometry[target_and_filter]"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
    "source": [
-    "photometry = photometry[target_and_filter]"
+    "### Find the transit number....this is off by one if we observe only the second half of the transit"
    ]
   },
   {
@@ -310,6 +369,13 @@
     "that_transit"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Find the OOT region and use it to get normalization factor"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -334,13 +400,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Bin Data\n",
-    "\n",
-    "Need\n",
-    "* data table\n",
-    "* start\n",
-    "* end\n",
-    "* bin_size"
+    "#### WTF?"
    ]
   },
   {
@@ -352,6 +412,23 @@
     "len(normalization_factor * photometry[\"relative_flux_error\"].value)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Bin Data\n",
+    "\n",
+    "Need\n",
+    "* data table\n",
+    "* start\n",
+    "* end\n",
+    "* bin_size\n",
+    "\n",
+    "Data is binned twice because the method for finding error is different in each\n",
+    "\n",
+    "**Also make times smaller**"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -397,6 +474,14 @@
     "# binned_time = BinnedTimeSeries(photometry['bjd'], time_bin_start=first_time, time_bin_end=last_time, time_bin_size=bin_size)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Model mash-up....weird mix of model and data filtering\n",
+    "### OMG so many places we subtract by 2400000"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -492,7 +577,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 3.5 Constrain the fits if you want\n",
+    "### 3.5 Constrain the fits if you want...this approach is terrible\n",
     "\n",
     "#### Exoplanet parameters"
    ]
@@ -534,6 +619,13 @@
     "mod.model.width_trend.fixed = not fit_width"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Detrending string, including a spelling error"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -579,7 +671,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 5. Let's try a plot...."
+    "### 5. Let's try a plot....maybe need some way here to deal with discrepant points???"
    ]
   },
   {
@@ -620,6 +712,13 @@
     "# mod._fitter.fit_info"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Remove trends from the data if desired"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -632,6 +731,13 @@
     "flux_full_detrend_model = mod.model_light_curve(detrend_by=\"all\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Calculate RMS before and after detrending, hopefully correctly...."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -648,6 +754,13 @@
     "rel_flux_rms = np.std(mod.data)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Random isolated plot command..."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -659,6 +772,13 @@
     "grid_y_ticks = np.arange(low, high, 0.02)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Make the big plot"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -751,6 +871,13 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Cruft"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -773,6 +900,13 @@
     "mod._all_detrend_params"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Attempt to calculate BIC, but...this seems to have side effects on the rest of notebook "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,