run_dark_subarray.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import iris_pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "%run ~/p/software/iris_pipeline/setup_local_crds.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "iris_pipeline.monkeypatch_jwst_datamodels()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "r2019-03-18_i_001_001_0.fits  r2019-03-18_i_001_001_3.fits\n",
      "r2019-03-18_i_001_001_1.fits  r2019-03-18_i_001_001_4.fits\n",
      "r2019-03-18_i_001_001_2.fits  raw_science_frame_subarray.fits\n"
     ]
    }
   ],
   "source": [
    "ls readouts/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "raw_science_frame = iris_pipeline.datamodels.IRISImageModel(\"/home/azonca/p/software/iris_pipeline/iris_pipeline/tests/data/raw_science_frame_sci.fits\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "import jwst"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2019-12-17 22:06:28,100 - stpipe.Step - INFO - Step instance created.\n"
     ]
    }
   ],
   "source": [
    "full_dark_filename = jwst.stpipe.Step().get_reference_file(raw_science_frame, \"dark\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/azonca/crds_cache/references/tmt/iris/tmt_iris_dark_0001.fits'"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "full_dark_filename"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_dark = iris_pipeline.datamodels.IRISImageModel(full_dark_filename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [],
   "source": [
    "subarray = jwst.datamodels.open(\"readouts/raw_science_frame_subarray.fits\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "980"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "subarray.meta.subarray.xstart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_dark.data = full_dark.data[subarray.meta.subarray.xstart:subarray.meta.subarray.xstart+subarray.meta.subarray.xsize,\n",
    "                                subarray.meta.subarray.ystart:subarray.meta.subarray.ystart+subarray.meta.subarray.ysize]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_dark.write(\"subarray_dark.fits\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[14.545454 ,  7.272727 , 13.181818 , ...,  9.545454 , 10.454545 ,\n",
       "         9.545454 ],\n",
       "       [ 9.090909 , 11.818182 , 12.727272 , ..., 11.818182 , 11.363636 ,\n",
       "        10.       ],\n",
       "       [13.636363 , 12.727272 , 15.909091 , ..., 14.545454 , 12.272727 ,\n",
       "        12.272727 ],\n",
       "       ...,\n",
       "       [10.909091 ,  9.545454 , 11.363636 , ..., 10.909091 , 15.       ,\n",
       "         9.545454 ],\n",
       "       [13.181818 , 13.636363 ,  6.8181815, ..., 11.363636 , 10.454545 ,\n",
       "        11.363636 ],\n",
       "       [10.       , 13.636363 ,  8.636363 , ...,  9.545454 , 16.363636 ,\n",
       "         7.7272725]], dtype=float32)"
      ]
     },
     "execution_count": 71,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "full_dark.data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Overwriting dark.cfg\n"
     ]
    }
   ],
   "source": [
    "%%file dark.cfg\n",
    "\n",
    "override_dark = subarray_dark.fits"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "override_dark = subarray_dark.fits\n"
     ]
    }
   ],
   "source": [
    "cat dark.cfg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2019-12-17 22:32:51,963 - stpipe.DarkCurrentStep - INFO - DarkCurrentStep instance created.\n",
      "2019-12-17 22:32:52,210 - stpipe.DarkCurrentStep - INFO - Step DarkCurrentStep running with args ('readouts/raw_science_frame_subarray.fits',).\n",
      "2019-12-17 22:32:52,386 - stpipe.DarkCurrentStep - INFO - Using DARK reference file /home/azonca/p/issues/201912_subarrays/subarray_dark.fits\n",
      "2019-12-17 22:32:52,674 - stpipe.DarkCurrentStep - INFO - Step DarkCurrentStep done\n"
     ]
    }
   ],
   "source": [
    "out = iris_pipeline.dark_current.DarkCurrentStep.call(\"readouts/raw_science_frame_subarray.fits\", config_file=\"dark.cfg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 86.454544, 106.72727 ,  90.818184, ...,  72.454544,  78.545456,\n",
       "         80.454544],\n",
       "       [ 79.90909 ,  85.181816,  69.27273 , ...,  80.181816, 103.63637 ,\n",
       "         91.      ],\n",
       "       [ 81.36364 ,  82.27273 ,  59.090908, ...,  76.454544,  91.72727 ,\n",
       "         84.72727 ],\n",
       "       ...,\n",
       "       [ 83.09091 ,  75.454544,  79.63637 , ...,  65.09091 ,  52.      ,\n",
       "         69.454544],\n",
       "       [ 57.818184,  72.36364 ,  59.18182 , ...,  80.63637 ,  74.545456,\n",
       "         69.63637 ],\n",
       "       [ 69.      ,  55.363636,  68.36364 , ...,  72.454544,  59.636364,\n",
       "         73.27273 ]], dtype=float32)"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "out.data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "np.testing.assert_allclose(out.data, subarray.data - full_dark.data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "jwst",
   "language": "python",
   "name": "jwst"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}