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Merge pull request #45 from desihub/fiberassign_fixes
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Update fiberassign notebooks to use a nominal focalplane
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@sbailey
sbailey authored Mar 20, 2020
2 parents 1340ab1 + dd5b0ba commit f8f3cac
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33 changes: 26 additions & 7 deletions FiberAssign.ipynb
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Expand Up @@ -40,6 +40,7 @@
"%pylab inline\n",
"import os, sys, subprocess\n",
"from collections import Counter\n",
"from datetime import datetime\n",
"\n",
"import numpy as np\n",
"from astropy.table import Table\n",
Expand All @@ -64,6 +65,8 @@
"metadata": {},
"outputs": [],
"source": [
"# You can set this to a local path if you have the software installed and a copy of the data.\n",
"# workdir = os.path.join(os.environ['HOME'], 'scratch', 'desi', 'tutorials', 'fiberassign_obs')\n",
"workdir = os.path.join(os.environ['SCRATCH'], 'desi', 'test', 'fiberassign')\n",
"os.makedirs(workdir, exist_ok=True)\n",
"os.chdir(workdir)\n",
Expand Down Expand Up @@ -193,7 +196,17 @@
"metadata": {},
"source": [
"Let's compare that tiling coverage to the fiber coverage. We'll see that the coverage of\n",
"actual fibers (positioners) is less than that of the tile, and has a more complex spatial structure."
"actual fibers (positioners) is less than that of the tile, and has a more complex spatial structure. By default, desimodel returns the realistic state of the focalplane at the time you run this notebook. That is great for working in realtime on real data. For this exercise, we will be using a focalplane from a time prior to commissioning so that we will have all positioners working and with their nominal properties."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"rundatestr = \"2020-01-01T00:00:00\"\n",
"rundate = datetime.strptime(rundatestr, \"%Y-%m-%dT%H:%M:%S\")"
]
},
{
Expand All @@ -203,8 +216,11 @@
"outputs": [],
"source": [
"def plot_positioners(tilera, tiledec, alpha=0.1):\n",
" fiberpos = desimodel.io.load_fiberpos()\n",
" ra, dec = desimodel.focalplane.xy2radec(tilera, tiledec, fiberpos['X'], fiberpos['Y'])\n",
" fp, exclude, state, tmstr = desimodel.io.load_focalplane(time=rundate)\n",
" # Select just science positioners\n",
" rows = np.where(fp['DEVICE_TYPE'] == 'POS')[0]\n",
" fp = fp[rows]\n",
" ra, dec = desimodel.focalplane.xy2radec(tilera, tiledec, fp['OFFSET_X'], fp['OFFSET_Y'])\n",
" plot(ra, dec, '.', alpha=alpha)\n",
"\n",
"figure(figsize=(8,4))\n",
Expand Down Expand Up @@ -345,7 +361,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Run fiberassign on those targets/standards/sky"
"## Run fiberassign on those targets/standards/sky\n",
"\n",
"Fiberassign calls desimodel to get focalplane properties. By default this uses the current time when you run this notebook. Instead, we will use the same historical time above in order to get a nominal focalplane prior to commissioning will all positioners working."
]
},
{
Expand All @@ -355,6 +373,7 @@
"outputs": [],
"source": [
"cmd = 'fiberassign --overwrite --mtl mtl.fits --stdstar stdstars.fits --sky sky.fits'\n",
"cmd += ' --rundate {}'.format(rundatestr)\n",
"cmd += ' --footprint ./tiles.fits'\n",
"cmd += ' --outdir ./output/'\n",
"cmd = cmd.format(outdir=outdir)\n",
Expand Down Expand Up @@ -771,9 +790,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "DESI master",
"display_name": "Python 3",
"language": "python",
"name": "desi-master"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -785,7 +804,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.6"
"version": "3.7.5"
}
},
"nbformat": 4,
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105 changes: 97 additions & 8 deletions FiberAssignDECaLS.ipynb
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Expand Up @@ -52,6 +52,8 @@
"metadata": {},
"outputs": [],
"source": [
"# You can set this to a local path if you have the software installed and a copy of the data.\n",
"# workdir = os.path.join(os.environ['HOME'], 'scratch', 'desi', 'tutorials', 'fiberassign_obs')\n",
"workdir = os.path.join(os.environ['SCRATCH'], 'desi', 'test', 'fiberassign_obs')\n",
"os.makedirs(workdir, exist_ok=True)\n",
"os.chdir(workdir)\n",
Expand All @@ -72,6 +74,13 @@
"metadata": {},
"outputs": [],
"source": [
"# Change this if you are running locally.\n",
"# paths = {\n",
"# \"targets\": \"/home/kisner/scratch/desi/tutorials\", \n",
"# \"skies\": \"/home/kisner/scratch/desi/tutorials\", \n",
"# \"gfas\": \"/home/kisner/scratch/desi/tutorials\",\n",
"# }\n",
"\n",
"paths = {\"targets\": \"/global/cfs/cdirs/desi/target/catalogs/dr8/0.31.1/targets/main/resolve/\", \n",
" \"skies\": \"/global/cfs/cdirs/desi/target/catalogs/dr8/0.32.0/skies/\", \n",
" \"gfas\": \"/global/cfs/cdirs/desi/target/catalogs/dr8/0.32.0/gfas/\",\n",
Expand Down Expand Up @@ -227,16 +236,33 @@
"plt.ylabel('DEC [deg]')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"By default, fiberassign uses the real focalplane geometry and properties at the current time. During operations, if a fiber broke yesterday and you run fiberassign today with an up-to-date desimodel data checkout, then that fiber will not be assigned. For this tutorial, we will run fiberassign with a *rundate* set to a time in the past before the start of commissioning. This will give us a nominal focalplane layout with all positioners working."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"assign_date = \"2020-01-01T00:00:00\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd = 'fiberassign --overwrite --mtl mtl.fits --sky sky.fits'\n",
"cmd += ' --footprint ./tiles.fits'\n",
"cmd += ' --outdir ./output/'\n",
"cmd = cmd.format(outdir=outdir)\n",
"cmd += ' --rundate {}'.format(assign_date)\n",
"cmd += ' --footprint {}'.format(tilefile)\n",
"cmd += ' --outdir {}'.format(outdir)\n",
"\n",
"print(cmd)"
]
},
Expand Down Expand Up @@ -275,8 +301,8 @@
"# Gather all outputs\n",
"assignments = list()\n",
"for tileid in tiles['TILEID']:\n",
" tilefile = '{}/fiberassign-{:06d}.fits'.format(outdir, tileid)\n",
" assignments.append(Table.read(tilefile, hdu=1))\n",
" outtile = '{}/fiberassign-{:06d}.fits'.format(outdir, tileid)\n",
" assignments.append(Table.read(outtile, hdu=1))\n",
" \n",
"assigned_targetids = np.concatenate([tmp['TARGETID'] for tmp in assignments])\n",
"isAssigned = np.in1d(targets['TARGETID'], assigned_targetids)\n",
Expand All @@ -300,13 +326,76 @@
"plt.xlabel('RA [deg]')\n",
"plt.ylabel('DEC [deg]')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can now run some basic QA on these outputs. We run this on the merged outputs so that we have access to more target information."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"cmd = 'fba_run_qa --prefix fiberassign-'\n",
"cmd += ' --rundate {}'.format(assign_date)\n",
"cmd += ' --footprint {}'.format(tilefile)\n",
"cmd += ' --dir {}'.format(outdir)\n",
"\n",
"print(cmd)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print('RUNNING: '+cmd)\n",
"try:\n",
" results = subprocess.check_output(cmd.split(), stderr=subprocess.STDOUT)\n",
" print(results.decode())\n",
" print('--- SUCCESS ---')\n",
"except subprocess.CalledProcessError as ex:\n",
" print('--- ERROR {} ---'.format(ex.returncode))\n",
" print(ex.output.decode())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Load the results back in and print\n",
"import json\n",
"from pprint import PrettyPrinter\n",
"\n",
"qa_file = os.path.join(outdir, \"qa.json\")\n",
"qa_data = None\n",
"with open(qa_file, \"r\") as f:\n",
" qa_data = json.load(f)\n",
"\n",
"pp = PrettyPrinter(indent=2)\n",
"pp.pprint(qa_data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "DESI master",
"display_name": "Python 3",
"language": "python",
"name": "desi-master"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -318,7 +407,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.6"
"version": "3.7.5"
}
},
"nbformat": 4,
Expand Down
23 changes: 20 additions & 3 deletions FiberAssignMocks.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,22 @@
"plt.ylabel('DEC')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"By default, fiberassign uses the real focalplane geometry and properties at the current time. During operations, if a fiber broke yesterday and you run fiberassign today with an up-to-date desimodel data checkout, then that fiber will not be assigned. For this tutorial, we will run fiberassign with a *rundate* set to a time in the past before the start of commissioning. This will give us a nominal focalplane layout with all positioners working."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"assign_date = \"2020-01-01T00:00:00\""
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -195,6 +211,7 @@
"source": [
"# Run fiberassign\n",
"cmd = 'fiberassign --overwrite --mtl mtl-dark.fits --sky sky.fits'\n",
"cmd += ' --rundate {}'.format(assign_date)\n",
"cmd += ' --footprint ./tiles.fits'\n",
"cmd += ' --outdir ./output/'\n",
"cmd = cmd.format(outdir=outdir)"
Expand Down Expand Up @@ -281,9 +298,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "DESI master",
"display_name": "Python 3",
"language": "python",
"name": "desi-master"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -295,7 +312,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.6"
"version": "3.7.5"
}
},
"nbformat": 4,
Expand Down

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