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Merge pull request #104 from lsst/tickets/SP-2732
Tickets/sp 2732
2 parents 3a0318e + 108ffc4 commit 3407d7a

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‎DP0.2/13a_Image_Cutout_SciDemo.ipynb‎

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"<img align=\"left\" src = https://project.lsst.org/sites/default/files/Rubin-O-Logo_0.png width=250 style=\"padding: 10px\" alt=\"Rubin Observatory logo, a graphical representation of turning stars into data.\">\n",
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"<br>\n",
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"Contact author: Christina Williams <br>\n",
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"Last verified to run: 2025-09-02 <br>\n",
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"Last verified to run: 2025-12-15 <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Container Size: medium <br>\n",
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"Targeted learning level: beginner <br>"
@@ -445,7 +445,7 @@
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" # from_resource: creates a instance from\n",
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" # a number of records and a Datalink Resource.\n",
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" sq = SodaQuery.from_resource(dl,\n",
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" dl.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=auth_session)\n",
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"\n",
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" sq.circle = (spherePoint.getRa().asDegrees() * u.deg,\n",
@@ -753,7 +753,7 @@
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"outputs": [],
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"source": [
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"sq = SodaQuery.from_resource(dl_results,\n",
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" dl_results.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_results.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=auth_session)"
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]
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},
@@ -916,7 +916,7 @@
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"outputs": [],
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"source": [
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"sq2 = SodaQuery.from_resource(dl_results,\n",
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" dl_results.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_results.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=auth_session)\n",
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"sphereRadius1 = 0.03 * u.deg\n",
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"sphereRadius2 = 0.01 * u.deg\n",

‎DP0.2/18_Galaxy_Photometry.ipynb‎

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"<img align=\"left\" src = https://noirlab.edu/public/media/archives/logos/svg/logo250.svg width=250 style=\"background-color:white; padding:10px\" alt=\"Rubin Observatory logo, a graphical representation of turning stars into data.\">\n",
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"</div>\n",
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"Contact author(s): Christina Williams <br>\n",
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"Last verified to run: 2025-09-02 <br>\n",
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"Last verified to run: 2025-12-14 <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Container Size: medium <br>"
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]
@@ -327,7 +327,7 @@
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" session=auth_session)\n",
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"\n",
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" sq = SodaQuery.from_resource(dl,\n",
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" dl.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=auth_session)\n",
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"\n",
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" sq.circle = (spherePoint.getRa().asDegrees() * u.deg,\n",

‎DP1/100_How_to_Use_RSP_Tools/103_Image_access_and_display/103_4_Small_Image_Cutout.ipynb‎

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"Data Release: DP1 <br>\n",
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"Container Size: large <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Last verified to run: 2025-11-20 <br>\n",
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"Last verified to run: 2025-12-16 <br>\n",
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"Repository: <a href=\"https://github.com/lsst/tutorial-notebooks\">github.com/lsst/tutorial-notebooks</a> <br>"
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]
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},
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"source": [
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"import numpy as np\n",
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"import matplotlib.pyplot as plt\n",
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"import os\n",
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"\n",
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"import lsst.afw.display as afwDisplay\n",
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"import lsst.afw.image as afwImage\n",
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"from lsst.afw.image import ExposureF\n",
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"from lsst.afw.fits import MemFileManager\n",
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"\n",
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"\n",
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"from lsst.rsp.utils import get_pyvo_auth\n",
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"from lsst.rsp.service import get_siav2_service\n",
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"\n",
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"\n",
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"from astropy import units as u\n",
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"from astropy.coordinates import Angle\n",
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"from astropy.time import Time"
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"from astropy.time import Time\n",
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"\n",
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"from astropy.io import fits\n",
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"import io\n"
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]
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},
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{
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"id": "d945e191-7ee4-458a-bb0f-fb00cd219e30",
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"metadata": {},
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"source": [
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"Lastly, call the Rubin Image Cutout Service. This is the IVOA procedure `cutout-sync` that is called using `get_adhocservice_by_id`. It is done by feeding the data link created above (called `dl_result`) to `from_resource`. Since the Rubin DP1 imaging is proprietary it is necessary to again provide the authorization for the current RSP session. Do this using the `get_pyvo_auth` function."
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"Lastly, call the Rubin Image Cutout Service. This notebook demonstrates two types of cutout services: `cutout-sync` which, by default, returns just the image extension of the LSST imaging; `cutout-sync-exposure`, which returns the full set of metadata and image extensions that are contained in the `ExposureF` data type. This section will demonstrate the use of `cutout-sync-exposure` and Section 4 below will demonstrate the other. \n",
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"\n",
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"To use the cutout service in this example, the IVOA procedure `cutout-sync-exposure` is called using `get_adhocservice_by_id`. It is done by feeding the data link created above (called `dl_result`) to `from_resource`. Since the Rubin DP1 imaging is proprietary it is necessary to again provide the authorization for the current RSP session. Do this using the `get_pyvo_auth` function."
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]
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},
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{
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"outputs": [],
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"source": [
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"sq = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=get_pyvo_auth())"
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]
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},
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"sq.raise_if_error()\n",
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"mem = MemFileManager(len(cutout_bytes))\n",
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"mem.setData(cutout_bytes, len(cutout_bytes))\n",
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"exposure = ExposureF(mem)"
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"exposure = ExposureF(mem)\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "324be87a-337b-4db7-b57d-842f14614613",
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"metadata": {},
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"source": [
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"Display the cutout."
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"Display the image extension of the `ExposureF` cutout."
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"# from astropy.io import fits\n",
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"\n",
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"# fits.info(sodaCutout)\n",
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"\n",
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"# sodaCutout_small = os.path.join(tempdir, 'cutout-circle_small.fits')\n",
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"outputs": [],
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"source": [
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"sqp = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=get_pyvo_auth())\n",
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"\n",
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"ra_edge = 0.02 * u.deg\n",
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"outputs": [],
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"source": [
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"sq2 = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=get_pyvo_auth())\n",
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"\n",
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"edge1 = Radius\n",
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"cosd = np.cos(a.radian)\n",
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"\n",
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"sq3 = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=get_pyvo_auth())\n",
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"\n",
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"sq3.polygon = (spherePoint.getRa().asDegrees() * u.deg - edge1/cosd,\n",
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"The zooniverse package should be used instead of this procedure for citizen science applications. "
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]
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},
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{
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"cell_type": "markdown",
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"id": "99e75a7a-348e-409e-88f6-871b68a4e9dc",
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"metadata": {},
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"source": [
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"## 4. Single extension image cutouts\n",
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"\n",
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"As mentioned in Section 3, there are three types of cutout services: `cutout-sync-exposure` to return an `ExposureF` type image with all LSST image extensions (demonstrated above); `cutout-sync` which returns just the image extension. The latter will be demonstrated below.\n",
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"\n",
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"First, reuse the data link `dl_result` that was defined in Section 3 to define a new cutout, this time using `cutout-sync`. Call this soda query `sq4` to differentiate from the earlier ones. Define the cutout as a square subtended by a circle of radius 0.01 degrees, as done in Section 3.\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "837fbd2a-c3e2-4ee3-a06d-69f4df50823b",
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"metadata": {},
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"outputs": [],
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"source": [
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"sq4 = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" session=get_pyvo_auth())\n",
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"\n",
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"spherePoint = geom.SpherePoint(target_ra*geom.degrees, target_dec*geom.degrees)\n",
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"Radius = 0.01 * u.deg\n",
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"\n",
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"sq4.circle = (spherePoint.getRa().asDegrees() * u.deg,\n",
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" spherePoint.getDec().asDegrees() * u.deg,\n",
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" Radius)\n",
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"\n",
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"cutout_bytes = sq4.execute_stream().read()\n",
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"sq4.raise_if_error()\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "454a017b-df88-48cc-975e-cac4ff3a37b5",
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"metadata": {},
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"source": [
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"Receive the cutout into memory, as in Section 3."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "516dbd86-d573-4d81-a017-2ebbce8fb445",
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"metadata": {},
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"outputs": [],
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"source": [
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"mem = MemFileManager(len(cutout_bytes))\n",
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"mem.setData(cutout_bytes, len(cutout_bytes))\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "2ae72a88-8002-46b5-8eee-164a2c903314",
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"metadata": {},
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"source": [
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"Use the `getData` method from the `MemFileManager` class to return and store the bytes associated with the cutout. "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ed3f7908-a256-42f5-939f-61f38645c7ca",
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"metadata": {},
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"outputs": [],
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"source": [
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"data = mem.getData()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "441a49fb-42be-4f37-853e-141419f1da14",
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"metadata": {},
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"source": [
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"Use the astropy.io fits package to access the bytes and store in an HDUList object. Then, the image extension `image_hdu`, and pixel values `image_data` (a numpy array) can be accessed similar to opening a fits file. "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d23a0397-6500-4e36-b956-7917ed6a7173",
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"metadata": {},
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"outputs": [],
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"source": [
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"hdul = fits.open(io.BytesIO(data))\n",
768+
"hdul.info()\n",
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"\n",
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"image_hdu = hdul[1]\n",
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"image_data = image_hdu.data\n"
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]
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},
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{
775+
"cell_type": "markdown",
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"id": "c0eea8e5-ae86-456d-9d67-798557a4a707",
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"metadata": {},
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"source": [
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"To enable image display, first store `image_data` as an LSST `ImageF` object."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "78e1c658-916c-4a73-8c0b-a50d281f4764",
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"metadata": {},
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"outputs": [],
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"source": [
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"image = afwImage.ImageF(image_data.astype(\"float32\"))\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "6a19e7cd-4096-44b9-832f-baa6b6c40482",
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"metadata": {},
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"source": [
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"Display the image cutout."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "1aa9009a-b493-41ea-bc3c-e0c79adef913",
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"metadata": {},
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"outputs": [],
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"source": [
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"display = afwDisplay.Display()\n",
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"display.scale('asinh', 'zscale')\n",
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"display.image(image)\n",
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"plt.show()"
811+
]
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},
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{
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"attachments": {
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"923e951d-30c0-4a8f-a1b0-8bb851f1cb5f.png": {
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"id": "acbe9638-e7b7-4229-8301-3f57eb0b0c5b",
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"metadata": {},
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"source": [
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"## 4. Exercise for the learner\n",
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"## 5. Exercise for the learner\n",
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"\n",
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"Reproduce the cutout below, whose center is (ra, dec) = 59.1, -48.8 with 0.06 degrees on a side.\n",
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"\n",
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"\n",
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"</div>\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6b611f9f-aaa5-4e2b-b4a5-b7acc6aecbf9",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {

‎DP1/200_Data_Products/203_Maps/203_1_Survey_property_maps.ipynb‎

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"Data Release: <a href=\"https://dp1.lsst.io/\">Data Preview 1</a> <br>\n",
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"Container Size: large <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Last verified to run: 2025-09-02 <br>\n",
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"Last verified to run: 2025-12-17 <br>\n",
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"Repository: <a href=\"https://github.com/lsst/tutorial-notebooks\">github.com/lsst/tutorial-notebooks</a> <br>"
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]
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"# from astropy.wcs import WCS\n",
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"# temp = deep_coadd.image.array.flatten()\n",
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"# norm = ImageNormalize(temp, interval=ZScaleInterval(),\n",
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"# stretch=LinearStretch())\n",

‎DP1/300_Science_Demos/303_Galaxies/303_2_Galaxy_Shapes.ipynb‎

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"Data Release: <a href=\"https://dp1.lsst.io/\">Data Preview 1</a> <br>\n",
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"Container Size: Large <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Last verified to run: 2025-09-02 <br>\n",
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"Last verified to run: 2025-12-11 <br>\n",
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"Repository: <a href=\"https://github.com/lsst/tutorial-notebooks\">github.com/lsst/tutorial-notebooks</a> <br>"
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]
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},
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" dl = DatalinkResults.from_result_url(datalink_url, session=get_pyvo_auth())\n",
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"\n",
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" sq = SodaQuery.from_resource(dl,\n",
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" dl.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=get_pyvo_auth())\n",
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"\n",
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" sq.circle = (spherePoint.getRa().asDegrees() * u.deg,\n",

‎DP1/300_Science_Demos/306_Extragalactic_transients/306_2_Candidate_transient_identification.ipynb‎

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"Data Release: <a href=\"https://dp1.lsst.io/\">Data Preview 1</a> <br>\n",
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"Container Size: large <br>\n",
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"LSST Science Pipelines version: r29.2.0 <br>\n",
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"Last verified to run: 2025-09-17 <br>\n",
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"Last verified to run: 2025-12-11 <br>\n",
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"Repository: <a href=\"https://github.com/lsst/tutorial-notebooks\">github.com/lsst/tutorial-notebooks</a> <br>"
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]
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},
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"source": [
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"def get_cutout(dl_result, spherePoint, session, fov):\n",
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" sq = SodaQuery.from_resource(dl_result,\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync\"),\n",
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" dl_result.get_adhocservice_by_id(\"cutout-sync-exposure\"),\n",
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" session=session)\n",
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" sphereRadius = fov * u.deg\n",
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" sq.circle = (spherePoint.getRa().asDegrees() * u.deg,\n",
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"source": [
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"> **Figure 4**: The cutout triplet for the first detection of this `DiaObject`, a candidate SN Ia."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "89ed684b-147e-4ed5-a340-205491c0f096",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {

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