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Merge pull request #234 from camipacifici/updates-niriss-im
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niriss imaging: updates to requirements and screenshots
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camipacifici authored Jul 31, 2024
2 parents ac151c3 + 416207a commit dd19779
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Binary file added notebooks/NIRISS/niriss_imaging/cal_science.png
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Binary file added notebooks/NIRISS/niriss_imaging/i2d_markers.png
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Binary file added notebooks/NIRISS/niriss_imaging/i2d_science.png
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200 changes: 180 additions & 20 deletions notebooks/NIRISS/niriss_imaging/niriss-imaging-tutorial.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,10 @@
"import zipfile\n",
"import numpy as np\n",
"import urllib.request\n",
"from IPython.display import Image\n",
"\n",
"# For visualizing images\n",
"import jdaviz\n",
"from jdaviz import Imviz\n",
"\n",
"# Astropy routines for visualizing detected sources:\n",
Expand All @@ -87,7 +89,8 @@
"from jwst.associations.lib.rules_level3_base import DMS_Level3_Base\n",
"\n",
"# To confirm which version of the pipeline you're running:\n",
"print(f\"jwst pipeline version: {jwst.__version__}\")"
"print(f\"jwst pipeline version: {jwst.__version__}\")\n",
"print(f\"jdaviz version: {jdaviz.__version__}\")"
]
},
{
Expand Down Expand Up @@ -232,9 +235,39 @@
"metadata": {},
"outputs": [],
"source": [
"viewer_uncal.stretch = 'sqrt'\n",
"viewer_uncal.set_colormap('Viridis')\n",
"viewer_uncal.cuts = '99.5%'"
"plotopt = imviz_uncal.plugins['Plot Options']\n",
"plotopt.stretch_function = 'sqrt'\n",
"plotopt.image_colormap = 'Viridis'\n",
"plotopt.stretch_preset = '99.5%'\n",
"plotopt.zoom_radius = 1024"
]
},
{
"cell_type": "markdown",
"id": "461d20dc-3d7b-42a2-a661-71fb34d74c08",
"metadata": {},
"source": [
"The viewer looks like this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "26c2d93f-ae6c-476d-b5be-bb04ed454c9f",
"metadata": {},
"outputs": [],
"source": [
"viewer_uncal.save('./uncal_science.png')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c68e2751-e6f2-4122-b9df-17a9460fa9f4",
"metadata": {},
"outputs": [],
"source": [
"Image('./uncal_science.png')"
]
},
{
Expand Down Expand Up @@ -383,9 +416,39 @@
"metadata": {},
"outputs": [],
"source": [
"viewer_rate.stretch = 'sqrt'\n",
"viewer_rate.set_colormap('Viridis')\n",
"viewer_rate.cuts = '95%'"
"plotopt = imviz_rate.plugins['Plot Options']\n",
"plotopt.stretch_function = 'sqrt'\n",
"plotopt.image_colormap = 'Viridis'\n",
"plotopt.stretch_preset = '95%'\n",
"plotopt.zoom_radius = 1024"
]
},
{
"cell_type": "markdown",
"id": "5d058328-4929-4508-8aa3-4b2bbc29fa78",
"metadata": {},
"source": [
"The viewer looks like this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f7a0f37d-c700-41fe-863e-6d528adeacb0",
"metadata": {},
"outputs": [],
"source": [
"viewer_rate.save('./rate_science.png')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1084538d-55af-45e6-bcfc-d1cfd26abcec",
"metadata": {},
"outputs": [],
"source": [
"Image('./rate_science.png')"
]
},
{
Expand Down Expand Up @@ -522,9 +585,39 @@
"metadata": {},
"outputs": [],
"source": [
"viewer_cal.stretch = 'sqrt'\n",
"viewer_cal.set_colormap('Viridis')\n",
"viewer_cal.cuts = '95%'"
"plotopt = imviz_cal.plugins['Plot Options']\n",
"plotopt.stretch_function = 'sqrt'\n",
"plotopt.image_colormap = 'Viridis'\n",
"plotopt.stretch_preset = '95%'\n",
"plotopt.zoom_radius = 1024"
]
},
{
"cell_type": "markdown",
"id": "96c99af7-77e4-42cf-ad11-782697eb8f30",
"metadata": {},
"source": [
"The viewer looks like this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4098cbfb-f303-494b-bd67-91825d8d238c",
"metadata": {},
"outputs": [],
"source": [
"viewer_cal.save('./cal_science.png')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e54d1b8c-c246-49cb-b736-bcbf04c1b575",
"metadata": {},
"outputs": [],
"source": [
"Image('./cal_science.png')"
]
},
{
Expand Down Expand Up @@ -693,9 +786,39 @@
"metadata": {},
"outputs": [],
"source": [
"viewer_i2d.stretch = 'sqrt'\n",
"viewer_i2d.set_colormap('Viridis')\n",
"viewer_i2d.cuts = '95%'"
"plotopt = imviz_i2d.plugins['Plot Options']\n",
"plotopt.stretch_function = 'sqrt'\n",
"plotopt.image_colormap = 'Viridis'\n",
"plotopt.stretch_preset = '95%'\n",
"plotopt.zoom_radius = 1024"
]
},
{
"cell_type": "markdown",
"id": "0c1d744e-7578-4b52-ab2a-1eae60099494",
"metadata": {},
"source": [
"The viewer looks like this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8741cd67-07dc-4fd6-b601-de585a889cf8",
"metadata": {},
"outputs": [],
"source": [
"viewer_i2d.save('./i2d_science.png')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7295d492-f955-4076-979f-6f95678a9f01",
"metadata": {},
"outputs": [],
"source": [
"Image('./i2d_science.png')"
]
},
{
Expand Down Expand Up @@ -757,15 +880,24 @@
"imviz_cat = Imviz()\n",
"viewer_cat = imviz_cat.default_viewer\n",
"imviz_cat.load_data(i2d)\n",
"\n",
"# Adjust settings for viewer\n",
"viewer_cat.stretch = 'sqrt'\n",
"viewer_cat.set_colormap('Viridis')\n",
"viewer_cat.cuts = '95%'\n",
"\n",
"imviz_cat.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e8271e84-d5b6-4ba9-9b32-cfeef22ff2e2",
"metadata": {},
"outputs": [],
"source": [
"# Adjust settings for viewer\n",
"plotopt = imviz_cat.plugins['Plot Options']\n",
"plotopt.stretch_function = 'sqrt'\n",
"plotopt.image_colormap = 'Viridis'\n",
"plotopt.stretch_preset = '95%'\n",
"plotopt.zoom_radius = 1024"
]
},
{
"cell_type": "markdown",
"id": "bb9dc081-7a24-442c-bf86-ed2faa6cf342",
Expand All @@ -792,6 +924,34 @@
"viewer_cat.add_markers(ext_coord, use_skycoord=True, marker_name='extended_sources')"
]
},
{
"cell_type": "markdown",
"id": "897cfc34-4978-44df-836e-1e3ee964bf49",
"metadata": {},
"source": [
"Viewer looks like this:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7a7e9494-8856-4fed-96a7-776a1ba41b07",
"metadata": {},
"outputs": [],
"source": [
"viewer_cat.save('./i2d_markers.png')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "afbd59ea-db29-444e-80a5-b412aa1460e3",
"metadata": {},
"outputs": [],
"source": [
"Image('./i2d_markers.png')"
]
},
{
"cell_type": "markdown",
"id": "1c1d9abd-b2d4-4c5d-a5ed-a1ef98e136fd",
Expand All @@ -817,7 +977,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.6"
"version": "3.11.9"
}
},
"nbformat": 4,
Expand Down
Binary file added notebooks/NIRISS/niriss_imaging/rate_science.png
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10 changes: 5 additions & 5 deletions notebooks/NIRISS/niriss_imaging/requirements.txt
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
numpy
crds
jwst>=1.2.3
jdaviz
astropy>=4.3.1
numpy>=1.26.4
crds>=11.17.23
jwst>=1.14.0
jdaviz>=3.10.2
astropy>=6.1.0
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