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BUG: fix a couple bugs in PPVCube notebook #228

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Oct 9, 2023
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BUG: fix a couple bugs in PPVCube notebook #228

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81 changes: 35 additions & 46 deletions doc/source/PPVCube.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,6 @@
},
"outputs": [],
"source": [
"from yt.config import ytcfg\n",
"\n",
"import yt\n",
"import numpy as np\n",
"from yt.extensions.astro_analysis.ppv_cube.api import PPVCube\n",
Expand Down Expand Up @@ -125,11 +123,11 @@
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2017-08-10 16:21:34,359 Parameters: current_time = 0.0\n",
"yt : [INFO ] 2017-08-10 16:21:34,360 Parameters: domain_dimensions = [64 64 64]\n",
"yt : [INFO ] 2017-08-10 16:21:34,362 Parameters: domain_left_edge = [-0.5 -0.5 -0.5]\n",
"yt : [INFO ] 2017-08-10 16:21:34,363 Parameters: domain_right_edge = [ 0.5 0.5 0.5]\n",
"yt : [INFO ] 2017-08-10 16:21:34,364 Parameters: cosmological_simulation = 0.0\n"
"yt : [INFO ] 2023-10-02 09:48:06,889 Parameters: current_time = 0.0\n",
"yt : [INFO ] 2023-10-02 09:48:06,891 Parameters: domain_dimensions = [64 64 64]\n",
"yt : [INFO ] 2023-10-02 09:48:06,892 Parameters: domain_left_edge = [-0.5 -0.5 -0.5]\n",
"yt : [INFO ] 2023-10-02 09:48:06,893 Parameters: domain_right_edge = [0.5 0.5 0.5]\n",
"yt : [INFO ] 2023-10-02 09:48:06,894 Parameters: cosmological_simulation = 0\n"
]
}
],
Expand All @@ -153,7 +151,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"metadata": {
"collapsed": false
},
Expand All @@ -162,28 +160,33 @@
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2017-08-10 16:21:34,863 xlim = -0.500000 0.500000\n",
"yt : [INFO ] 2017-08-10 16:21:34,864 ylim = -0.500000 0.500000\n",
"yt : [INFO ] 2017-08-10 16:21:34,866 xlim = -0.500000 0.500000\n",
"yt : [INFO ] 2017-08-10 16:21:34,867 ylim = -0.500000 0.500000\n",
"yt : [INFO ] 2017-08-10 16:21:34,875 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800\n",
"yt : [INFO ] 2017-08-10 16:21:34,885 Making a fixed resolution buffer of (('gas', 'velocity_x')) 800 by 800\n",
"yt : [INFO ] 2017-08-10 16:21:34,893 Making a fixed resolution buffer of (('gas', 'velocity_y')) 800 by 800\n",
"yt : [INFO ] 2017-08-10 16:21:34,899 Making a fixed resolution buffer of (('gas', 'velocity_magnitude')) 800 by 800\n",
"yt : [WARNING ] 2017-08-10 16:21:34,920 Plot image for field ('gas', 'velocity_x') has both positive and negative values. Min = -16485822.496297, Max = 16485822.496296.\n",
"yt : [WARNING ] 2017-08-10 16:21:34,921 Switching to symlog colorbar scaling unless linear scaling is specified later\n",
"yt : [WARNING ] 2017-08-10 16:21:35,687 Plot image for field ('gas', 'velocity_y') has both positive and negative values. Min = -16485822.496296, Max = 16485822.496297.\n",
"yt : [WARNING ] 2017-08-10 16:21:35,688 Switching to symlog colorbar scaling unless linear scaling is specified later\n"
"yt : [INFO ] 2023-10-02 09:51:15,566 xlim = -0.500000 0.500000\n",
"yt : [INFO ] 2023-10-02 09:51:15,567 ylim = -0.500000 0.500000\n",
"yt : [INFO ] 2023-10-02 09:51:15,571 xlim = -0.500000 0.500000\n",
"yt : [INFO ] 2023-10-02 09:51:15,573 ylim = -0.500000 0.500000\n",
"yt : [INFO ] 2023-10-02 09:51:15,575 Making a fixed resolution buffer of (('gas', 'velocity_magnitude')) 800 by 800\n",
"yt : [INFO ] 2023-10-02 09:51:15,795 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800\n",
"yt : [INFO ] 2023-10-02 09:51:16,011 Making a fixed resolution buffer of (('gas', 'velocity_y')) 800 by 800\n",
"yt : [INFO ] 2023-10-02 09:51:16,235 Making a fixed resolution buffer of (('gas', 'velocity_x')) 800 by 800\n"
]
}
],
"source": [
"slc = yt.SlicePlot(ds, \"z\", [\"density\",\"velocity_x\",\"velocity_y\",\"velocity_magnitude\"])"
"slc = yt.SlicePlot(\n",
" ds,\n",
" \"z\",\n",
" fields=[\n",
" (\"gas\", \"density\"),\n",
" (\"gas\", \"velocity_x\"),\n",
" (\"gas\", \"velocity_y\"),\n",
" (\"gas\", \"velocity_magnitude\"),\n",
" ]\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 8,
"metadata": {
"collapsed": false,
"scrolled": false
Expand All @@ -203,10 +206,10 @@
}
],
"source": [
"slc.set_log(\"velocity_x\", False)\n",
"slc.set_log(\"velocity_y\", False)\n",
"slc.set_log(\"velocity_magnitude\", False)\n",
"slc.set_unit(\"velocity_magnitude\", \"km/s\")\n",
"slc.set_log((\"gas\", \"velocity_x\"), False)\n",
"slc.set_log((\"gas\", \"velocity_y\"), False)\n",
"slc.set_log((\"gas\", \"velocity_magnitude\"), False)\n",
"slc.set_unit((\"gas\", \"velocity_magnitude\"), \"km/s\")\n",
"slc.show()"
]
},
Expand All @@ -219,7 +222,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 9,
"metadata": {
"collapsed": false
},
Expand All @@ -238,7 +241,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {
"collapsed": false,
"scrolled": true
Expand All @@ -265,7 +268,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 11,
"metadata": {
"collapsed": false
},
Expand All @@ -274,10 +277,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2017-08-10 16:21:43,375 Making a FITS image of field density\n",
"yt : [WARNING ] 2017-08-10 16:21:43,389 update_all_headers is deprecated. Use update_header('all', key, value) instead.\n",
"yt : [WARNING ] 2017-08-10 16:21:43,390 update_all_headers is deprecated. Use update_header('all', key, value) instead.\n",
"WARNING: AstropyDeprecationWarning: \"clobber\" was deprecated in version 1.3 and will be removed in a future version. Use argument \"overwrite\" instead. [astropy.utils.decorators]\n"
"yt : [INFO ] 2023-10-02 09:51:37,535 Making a FITS image of field density\n"
]
}
],
Expand All @@ -294,22 +294,11 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2017-08-10 16:21:43,619 Making a FITS image of field density\n",
"yt : [WARNING ] 2017-08-10 16:21:43,629 update_all_headers is deprecated. Use update_header('all', key, value) instead.\n",
"yt : [WARNING ] 2017-08-10 16:21:43,629 update_all_headers is deprecated. Use update_header('all', key, value) instead.\n",
"WARNING: AstropyDeprecationWarning: \"clobber\" was deprecated in version 1.3 and will be removed in a future version. Use argument \"overwrite\" instead. [astropy.utils.decorators]\n"
]
}
],
"outputs": [],
"source": [
"sky_scale = (1.0, \"arcsec/kpc\")\n",
"sky_center = (30., 45.) # RA, Dec in degrees\n",
Expand Down