tutorial as is

LSSTScienceCollaborations · Sep 6, 2018 · 79d561e · 79d561e
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diff --git a/Basics/DataInventory.ipynb b/Basics/DataInventory.ipynb
@@ -30,6 +30,13 @@
     "## Set-up"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/ImageProcessing/Re-RunHSC.ipynb b/ImageProcessing/Re-RunHSC.ipynb
@@ -7,7 +7,8 @@
     "# HSC Re-Run: Making Forced Photometry Light Curves from Scratch\n",
     "\n",
     "<br>Owner: **Justin Myles** ([@jtmyles](https://github.com/LSSTScienceCollaborations/StackClub/issues/new?body=@jtmyles))\n",
-    "<br>Last Verified to Run: **N/A -- in development**\n",
+    "<br>Last Verified to Run: **2018-08-10**\n",
+    "<br>Verified Stack Release: **16.0**\n",
     "\n",
     "This project addresses issue [#63: HSC Re-run](https://github.com/LSSTScienceCollaborations/StackClub/issues/63)\n",
     "\n",
@@ -32,12 +33,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
+    "os.system(\"eups list lsst_distrib\") #todo\n",
     "import sys\n",
+    "import matplotlib.pyplot as plt\n",
+    "%matplotlib inline\n",
     "import eups.setupcmd"
    ]
   },
@@ -63,14 +67,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
-    "!eups list lsst_distrib\n",
-    "datarepo = \"/home/jmyles/repositories/ci_hsc/\"\n",
-    "datadir = \"/home/jmyles/DATA/\"\n",
-    "os.system(\"mkdir -p {}\".format(datadir))"
+    "USER = \"jmyles\"\n",
+    "# todo: $USER\n",
+    "datarepo = \"/home/{}/repositories/ci_hsc/\".format(USER)\n",
+    "datadir = \"/home/{}/DATA/\".format(USER)\n",
+    "os.system(\"mkdir -p {}\".format(datadir));"
    ]
   },
   {
@@ -110,6 +115,7 @@
    "outputs": [],
    "source": [
     "# ingest script\n",
+    "# todo: $USER ()\n",
     "!ingestImages.py /home/jmyles/DATA /home/jmyles/repositories/ci_hsc/raw/*.fits --mode=link"
    ]
   },
@@ -171,12 +177,10 @@
    "outputs": [],
    "source": [
     "\"\"\"\n",
-    "# review what data will be processed\n",
-    "!processCcd.py DATA --rerun processCcdOutputs --id --show data\n",
-    "# id allows you to select data by data ID\n",
-    "# unspecified id selects all raw data\n",
-    "# example IDs: raw, filter, visit, ccd, field\n",
-    "# show data turns on dry-run mode\n",
+    "!processCcd.py DATA --rerun processCcdOutputs --id\n",
+    "# all cl tasks write output datasets to a Butler repo\n",
+    "# --rerun configured to write to processCcdOutputs\n",
+    "# other option is --output\n",
     "\"\"\""
    ]
   },
@@ -186,7 +190,52 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#!which processCcd.py"
+    "!which processCcd.py\n",
+    "\"\"\"\n",
+    "processCcd.py\n",
+    "from lsst.pipe.tasks.processCcd import ProcessCcdTask\n",
+    "\n",
+    "ProcessCcdTask.parseAndRun()\n",
+    "\"\"\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# show source of lsst.pipe.tasks.processCcd\n",
+    "# emacs /opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/16.0+1/python/lsst/pipe/tasks/processCcd.py\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lsst.pipe.tasks.processCcd import ProcessCcdTask, ProcessCcdConfig\n",
+    "processCcdTaskInstance = ProcessCcdTask(butler=butler)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from stackclub import where_is\n",
+    "where_is(processCcdTaskInstance, in_the=\"source\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "processCcdConfig = ProcessCcdConfig()"
    ]
   },
   {
@@ -196,13 +245,24 @@
    "outputs": [],
    "source": [
     "\"\"\"\n",
-    "!processCcd.py DATA --rerun processCcdOutputs --id\n",
-    "# all cl tasks write output datasets to a Butler repo\n",
-    "# --rerun configured to write to processCcdOutputs\n",
-    "# other option is --output\n",
+    "# review what data will be processed\n",
+    "!processCcd.py DATA --rerun processCcdOutputs --id --show data\n",
+    "# id allows you to select data by data ID\n",
+    "# unspecified id selects all raw data\n",
+    "# example IDs: raw, filter, visit, ccd, field\n",
+    "# show data turns on dry-run mode\n",
     "\"\"\""
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#!which processCcd.py"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -245,6 +305,117 @@
     "#           - TAN: tangent-plane projection\n",
     "\"\"\""
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Part 6: Multi-band catalog analysis\n",
+    "https://pipelines.lsst.io/getting-started/multiband-analysis.html"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import lsst.daf.persistence as dafPersist\n",
+    "datadir = \"/home/{}/DATA/\".format(os.environ['USER'])\n",
+    "butler = dafPersist.Butler(inputs=datadir + 'rerun/coaddForcedPhot/')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Access the sources identified from the coadd images"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rSources = butler.get('deepCoadd_forced_src', {'filter': 'HSC-R', 'tract': 0, 'patch': '1,1'})\n",
+    "iSources = butler.get('deepCoadd_forced_src', {'filter': 'HSC-I', 'tract': 0, 'patch': '1,1'})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Throw out negative fluxes, and convert fluxes to magnitudes."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rCoaddCalib = butler.get('deepCoadd_calexp_calib',  {'filter': 'HSC-R', 'tract': 0, 'patch': '1,1'})\n",
+    "iCoaddCalib = butler.get('deepCoadd_calexp_calib',  {'filter': 'HSC-I', 'tract': 0, 'patch': '1,1'})\n",
+    "\n",
+    "rCoaddCalib.setThrowOnNegativeFlux(False)\n",
+    "iCoaddCalib.setThrowOnNegativeFlux(False)\n",
+    "\n",
+    "rMags = rCoaddCalib.getMagnitude(rSources['base_PsfFlux_flux'])\n",
+    "iMags = iCoaddCalib.getMagnitude(iSources['base_PsfFlux_flux'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Select stars from catalog"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "deblended = rSources['deblend_nChild'] == 0\n",
+    "\n",
+    "refTable = butler.get('deepCoadd_ref', {'filter': 'HSC-R^HSC-I', 'tract': 0, 'patch': '1,1'})\n",
+    "inInnerRegions = refTable['detect_isPatchInner'] & refTable['detect_isTractInner'] # define inner regions\n",
+    "isSkyObject = refTable['merge_peak_sky'] # reject sky objects\n",
+    "isPrimary = refTable['detect_isPrimary']\n",
+    "\n",
+    "isStellar = iSources['base_ClassificationExtendedness_value'] < 1.\n",
+    "isGoodFlux = ~iSources['base_PsfFlux_flag']\n",
+    "selected = isPrimary & isStellar & isGoodFlux"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Make color-magnitude diagram."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.style.use('seaborn-notebook')\n",
+    "plt.figure(1, figsize=(4, 4), dpi=140)\n",
+    "plt.scatter(rMags[selected] - iMags[selected],\n",
+    "                        iMags[selected],\n",
+    "                        edgecolors='None', s=2, c='k')\n",
+    "plt.xlim(-0.5, 3)\n",
+    "plt.ylim(25, 14)\n",
+    "plt.xlabel('$r-i$')\n",
+    "plt.ylabel('$i$')\n",
+    "plt.subplots_adjust(left=0.125, bottom=0.1)\n",
+    "plt.show()"
+   ]
   }
  ],
  "metadata": {