diff --git a/jdat_notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb b/jdat_notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
index 3c2fa3f8..044aed18 100644
--- a/jdat_notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
+++ b/jdat_notebooks/IFU_cube_continuum_fit/NGC4151_FeII_ContinuumFit.ipynb
@@ -59,8 +59,7 @@
"from specutils import Spectrum1D\n",
"\n",
"from jdaviz.app import Application\n",
- "from IPython.display import HTML\n",
- "\n"
+ "from IPython.display import HTML"
]
},
{
@@ -72,7 +71,7 @@
"# load and configure matplotlib\n",
"%matplotlib inline\n",
"import matplotlib.pyplot as plt\n",
- "plt.rcParams.update({'figure.max_open_warning': 0})\n"
+ "plt.rcParams.update({'figure.max_open_warning': 0})"
]
},
{
@@ -92,13 +91,81 @@
" return pickle.load(f)"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "tags": []
+ },
+ "source": [
+ "
Reviewer note: Begin PEP8 check cells (delete below when finished)
"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# disable all imported packages' loggers\n",
+ "import logging\n",
+ "logging.root.manager.loggerDict = {}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1: E999 SyntaxError: invalid syntax\n",
+ "INFO:pycodestyle:3:13: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:3:25: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:30: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:35: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
+ "source": [
+ "# enable PEP8 checker for this notebook\n",
+ "%load_ext pycodestyle_magic\n",
+ "%flake8_on --ignore E261,E501,W291,W293\n",
+ "\n",
+ "# only allow the checker to throw warnings when there's a violation\n",
+ "logging.getLogger('flake8').setLevel('ERROR')\n",
+ "logging.getLogger('stpipe').setLevel('ERROR')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Reviewer note: End PEP8 check cells (delete above when finished)
"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:10:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:15:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:17:7: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:17:31: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:17:34: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:23:29: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#This cell accesses the datacube file, defines the wavelength grid from header information and then plots a simple\n",
"# 1-D collapsed spectrum of the IFU data.\n",
@@ -153,7 +220,19 @@
"metadata": {
"scrolled": true
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:24:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:32:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:37:75: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"\n",
"#This cell defines the wavelength regions of interest: around the emission line, and the location\n",
@@ -199,7 +278,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"print(wave)\n",
"#print(wave-wave_emission_limit1)\n",
@@ -307,6 +395,13 @@
"Here is a video illustrating how to load and manipulate data for this particular notebook."
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "IFrame(\"https://data.science.stsci.edu/redirect/JWST/jwst-data_analysis_tools/IFU_cube_continuum_fit/cubeviz1.mov\", width=700, height=500)\n"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -329,7 +424,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#PART 1\n",
"HTML('')"
@@ -339,7 +442,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#PART 2\n",
"HTML('')\n"
@@ -363,7 +474,22 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:63: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:2:76: E262 inline comment should start with '# '\n",
+ "INFO:pycodestyle:3:63: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:76: E262 inline comment should start with '# '\n",
+ "INFO:pycodestyle:4:63: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:4:76: E262 inline comment should start with '# '\n",
+ "INFO:pycodestyle:5:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Extract spectra corresponding to the colored regions in cubeviz\n",
"spectrum1 = cubeviz.app.get_data_from_viewer('spectrum-viewer','Subset 1') #AGN Center\n",
@@ -377,7 +503,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#regions = cubeviz.specviz.get_spectral_regions()\n",
"#regions"
@@ -387,7 +522,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#regions = cubeviz.app.get_data_from_viewer('flux-viewer')['Subset 4'] #AGN Center\n",
"#regions"
@@ -397,7 +541,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#regions = cubeviz.app.get"
]
@@ -408,7 +560,26 @@
"metadata": {
"scrolled": true
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ },
+ {
+ "ename": "KeyError",
+ "evalue": "'Subset 4'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m/var/folders/ls/7lh0_8jn0ndbm6g7plbzw8n400028t/T/ipykernel_48321/1159788268.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0mregions\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mline_region\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mregions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Subset 4\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 7\u001b[0m \u001b[0mcontinuum_region\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mregions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Subset 5\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mKeyError\u001b[0m: 'Subset 4'"
+ ]
+ }
+ ],
"source": [
"#Extract the spectral regions defined in the spectral viewer\n",
"from specutils.spectra import SpectralRegion\n",
@@ -423,7 +594,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Define Missing Spectral Regions if User Did Not in Cubeviz\n",
"if not regions:\n",
@@ -437,7 +616,24 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:5:29: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:5:49: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:5:79: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:14:34: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:14:48: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:14:72: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:23:35: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:23:49: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:23:73: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#Apply the spectral region\n",
"from specutils.manipulation import extract_region\n",
@@ -474,7 +670,17 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:32: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:46: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#Visualize new subsets\n",
"plt.figure()\n",
@@ -485,7 +691,19 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:38: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:58: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:4:37: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:4:56: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#Visualize new subsets\n",
"plt.figure()\n",
@@ -517,7 +735,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#VIDEO OF CONTINUUM FITTING\n",
"#PART 1\n",
@@ -528,7 +755,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#PART 2\n",
"HTML('')"
@@ -552,7 +787,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#List Data from Viewer\n",
"regions = cubeviz.app.get_data_from_viewer(\"uncert-viewer\")\n",
@@ -563,7 +806,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Extract Continuum Model from Cubeviz above\n",
"cont_psf_cube = cubeviz.app.get_data_from_viewer(\"uncert-viewer\", \"LinFitCont [Cube] 1\")\n",
@@ -581,7 +833,19 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:4:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:6:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:10:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:12:3: E111 indentation is not a multiple of 4\n"
+ ]
+ }
+ ],
"source": [
"#Delete any existing output in current directory\n",
"import os\n",
@@ -601,7 +865,35 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:8:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:12:18: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:12:31: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:12:34: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:13:18: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:13:31: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:13:34: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:17:27: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:17:29: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:21:28: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:21:30: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:21:33: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:22:28: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:22:30: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:22:33: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:32:9: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:33:9: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:38:9: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:39:9: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Subtract Continuum\n",
"\n",
@@ -652,7 +944,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:7: E225 missing whitespace around operator\n"
+ ]
+ }
+ ],
"source": [
"#You can also read out your model fit parameters \n",
"params=cubeviz.get_model_parameters(model_label=\"LinFitCont\")\n",
@@ -663,7 +964,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#And this is just an example of how you can acces the model fit parameter values\n",
"#params['LinFitCont_3d']['slope']"
@@ -673,7 +983,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Open up a new instance of Cubeviz to visualize continuum subtracted data\n",
"from jdaviz import CubeViz\n",
@@ -722,7 +1040,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#VIDEO PART1\n",
"HTML('')"
@@ -732,7 +1058,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#VIDEO PART2\n",
"HTML('')\n"
@@ -742,7 +1076,26 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:7:1: E265 block comment should start with '# '\n"
+ ]
+ },
+ {
+ "ename": "KeyError",
+ "evalue": "'Subset 1'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m/var/folders/ls/7lh0_8jn0ndbm6g7plbzw8n400028t/T/ipykernel_48321/4088308880.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mregions\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mline_region\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mregions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Subset 1\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 12\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mline_region\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0mline_region\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSpectralRegion\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1.6322\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mum\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1.6563\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mum\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mKeyError\u001b[0m: 'Subset 1'"
+ ]
+ }
+ ],
"source": [
"# Wow, that multi-component fit looks great. Good deal.\n",
"\n",
@@ -763,7 +1116,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:5: E225 missing whitespace around operator\n"
+ ]
+ }
+ ],
"source": [
"#List spectra available in spectrum-viewer\n",
"spec=cubeviz2.app.get_data_from_viewer('spectrum-viewer') \n",
@@ -774,7 +1136,20 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:63: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:2:93: E262 inline comment should start with '# '\n",
+ "INFO:pycodestyle:3:65: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:3:78: E262 inline comment should start with '# '\n",
+ "INFO:pycodestyle:4:86: E262 inline comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Get Gauss Model Spectrum and Model Cube\n",
"all_spec = cubeviz2.app.get_data_from_viewer('spectrum-viewer','Continuum Subtracted[SCI]') #AGN Center Data Cube\n",
@@ -786,7 +1161,30 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:5:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:8:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:9:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:10:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:11:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:13:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:14:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:15:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:16:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:17:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:19:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:20:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:21:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"##Save your Gauss Model Cube If Necessary\n",
"#import os\n",
@@ -815,7 +1213,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Check to see if user used Cubeviz (above), and, if not, read in premade data\n",
"if not gauss_cube:\n",
@@ -837,7 +1243,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:7: E225 missing whitespace around operator\n"
+ ]
+ }
+ ],
"source": [
"#You can also read out your model fit parameters \n",
"params=cubeviz2.get_model_parameters(model_label=\"GaussAll\")\n",
@@ -848,7 +1263,17 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Save Parameters as a Pickle File if necessary\n",
"#save_obj(params, \"gauss_params.pkl\")\n",
@@ -859,7 +1284,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:4:11: E225 missing whitespace around operator\n"
+ ]
+ }
+ ],
"source": [
"#Check to see if user used Cubeviz (above), and, if not, read in premade data\n",
"if not params:\n",
@@ -872,7 +1306,24 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:3:1: E402 module level import not at top of file\n",
+ "INFO:pycodestyle:8:13: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:9:13: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:10:11: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:11:11: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:12:15: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:13:15: E225 missing whitespace around operator\n",
+ "INFO:pycodestyle:16:32: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:16:34: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#Overwrite Gauss Model with only 2 of the components of interest\n",
"gauss_cube_2component = gauss_cube*0\n",
@@ -896,7 +1347,16 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:5:5: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#Add the continuum cube to the new model cube\n",
"continuum_file = 'NGC4151_Hband_ContinuumPSF.fits'\n",
@@ -911,7 +1371,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:2:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"# subtract the model to create the final cube where the [Fe II] emission is isolated.\n",
"#Re-read in original IFU cube for manipulation\n",
@@ -926,7 +1394,19 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:4:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:6:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:10:3: E111 indentation is not a multiple of 4\n",
+ "INFO:pycodestyle:12:3: E111 indentation is not a multiple of 4\n"
+ ]
+ }
+ ],
"source": [
"#Delete any existing output in current directory\n",
"import os\n",
@@ -946,7 +1426,15 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n"
+ ]
+ }
+ ],
"source": [
"#del newfull_header['MODE']\n",
"del newfinalsub_header['MODE']\n",
@@ -959,7 +1447,27 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:pycodestyle:1:1: E265 block comment should start with '# '\n",
+ "INFO:pycodestyle:5:50: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:5:53: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:5:57: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:6:49: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:6:52: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:6:56: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:7:46: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:7:49: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:7:53: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:8:50: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:8:53: E231 missing whitespace after ','\n",
+ "INFO:pycodestyle:8:61: E231 missing whitespace after ','\n"
+ ]
+ }
+ ],
"source": [
"#Make the final plots to illustrated\n",
"plt.figure()\n",
@@ -976,9 +1484,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3 (ipykernel)",
+ "display_name": "Python [conda env:dat-ifu-cont-adv] *",
"language": "python",
- "name": "python3"
+ "name": "conda-env-dat-ifu-cont-adv-py"
},
"language_info": {
"codemirror_mode": {
@@ -990,7 +1498,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.9.6"
+ "version": "3.8.10"
}
},
"nbformat": 4,