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,