From a329c814adde6f1c6a683439c1d0159fd8f3f49a Mon Sep 17 00:00:00 2001 From: Hwihyun Kim <8321492+hwihyun@users.noreply.github.com> Date: Tue, 26 Aug 2025 14:15:44 -0700 Subject: [PATCH] Update IGRINSDR_users_manual.ipynb --- docs/IGRINSDR_users_manual.ipynb | 38 +++++++++++++++++--------------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/docs/IGRINSDR_users_manual.ipynb b/docs/IGRINSDR_users_manual.ipynb index 00aa222..b602a60 100644 --- a/docs/IGRINSDR_users_manual.ipynb +++ b/docs/IGRINSDR_users_manual.ipynb @@ -14,7 +14,7 @@ "\n", "\n", "
\n", - "At this stage of development, plesae understand that the primary purpose of this document is to receive (early) feedback on high-level workflow. But any comment will be welcomed.\n", + "At this stage of development, please understand that the primary purpose of this document is to receive (early) feedback on high-level workflow. But any comment will be welcomed.\n", "
\n" ] }, @@ -27,7 +27,7 @@ "source": [ "## Install\n", "\n", - "If you have not, please consult \"Preparation for dragons version.ipynb\" and install IGRINSDR.\n" + "If you have not installed the IGRINS-2 pipeline yet, please consult \"Preparation for DRAGONS version.ipynb\" to install IGRINSDR.\n" ] }, { @@ -39,19 +39,19 @@ "source": [ "## Setting up\n", "\n", - "The original version of this document is a jupyter notebook, mixed with shell comannds and python code. It may be better to look at the original notebook file.\n", + "The original version of this document is a Jupyter notebook, mixed with shell commands and Python code. It probably is easier to follow the original notebook.\n", "\n", - "To reduce number of typing, we make aliases for `dataselect` and `reduce` so that they load ingrisdr packages automtically.\n", + "To reduce number of typing, we make aliases for `dataselect` and `reduce` so that they load igrinsdr packages automtically.\n", "\n", "\n", - "On the shell, you may do something like\n", + "In the shell, type the following lines.\n", "\n", "```sh\n", "> alias dataselect_ig=\"dataselect --adpkg=igrins_instruments\"\n", "> alias reduce_ig=\"reduce --drpkg=igrinsdr --adpkg=igrins_instruments\"\n", "```\n", "\n", - "Below we will us ipython magic commands for aliasing." + "Below we will use iPython magic commands for aliasing." ] }, { @@ -83,7 +83,7 @@ "id": "9d49c858-511b-4ea0-a4d2-7ea42cc562e5", "metadata": {}, "source": [ - "Below are initial import statements for the pyton codes." + "Import Python libraries to run IGRINSDR." ] }, { @@ -109,13 +109,14 @@ "id": "bbd5455f-1024-4e35-be79-926456000f0b" }, "source": [ - "## Download data\n", + "## Download data (Before download data, it would be good to have a section describing MEF extensions. It would be good to have a log file that keeps track of the process something like logutils.) \n", "\n", - "We will use engineering data of \"gn-2024a-eng-142\" which is available from\n", - "Gemini archive. Download data from 2024-04-29.\n", + "We will use the engineering data of \"gn-2024a-eng-142\", which is available in\n", + "Gemini archive. Download the data taken on 2024-04-29.\n", "\n", - "The MEF files from the archive need to be unbundled to H and K bands files. Assuming that files from gemini archive is extracted in the directory \"mef_20240429\" (the files need to be unzipped if zipped). 'reduce' can be used to unbundle these files.\n", + "The IGRINS-2 MEF files in the archive need to be unbundled to H and K bands files. Assuming that the files from the Gemini archive are extracted in the directory \"mef_20240429\" (the files need to be unzipped if zipped). 'reduce' can be used to unbundle these files.\n", "\n", + "### Prepare a list of MEFs and unbubdle them to run DRAGONS\n", "```bash\n", "> dataselect_ig --tags BUNDLE mef_20240429/N*.fits -o list_of_bundles.txt\n", "> reduce_ig @list_of_bundles.txt\n", @@ -360,7 +361,7 @@ "/home/jjlee/git_personal/IGRINSDR/test_i2\n" ] } - ], + ], "source": [ "%cd -" ] @@ -410,9 +411,10 @@ }, "source": [ "## Running REDUCE\n", + "REDUCE command will process flat, sky, standard star (A0V type star), and science target, following the work-flow below. Here we will show each step (recipe) of running REDUCE.\n", "1. FLAT\n", "2. SKY\n", - "3. STANDARD\n", + "3. STANDARD (A0V)\n", "4. TARGET" ] }, @@ -425,7 +427,7 @@ "source": [ "## FLAT\n", "\n", - "Then create a file lising the FALT image from the fixed fits files.\n", + "First create a file lising the FALT image from the fixed fits files.\n", "\n", "> dataselect_ig --tags FLAT,H unbundled_20240429/N*_H.fits -o list_of_flat_h.txt\n", "\n", @@ -896,14 +898,14 @@ "source": [ "## SKY\n", "\n", - "(this recipe is a combined version of register-sky and wvlsol-sky from the PLP)\n", + "The SKY recipe is a combined version of register-sky and wvlsol-sky from the PLP. It uses the OH lines in the sky frame to get a crude wavelength solution, then finetunes it in the second iteration.\n", "\n", "Create a file containg sky frames.\n", "\n", "> dataselect_ig --tags SKY,H unbundled_20240429/N*_H.fits -o list_of_sky_h.txt\n", "\n", "
\n", - "CALDB support is not properly integrated yet. You need to explicitly speicy calibrations file with the \"--user_cal\" options.\n", + "CALDB support is not properly integrated yet. You need to explicitly specify calibrations file with the \"--user_cal\" options.\n", "
\n", "\n", "We will run reduce, but we need to explicitly set the calibration file.\n", @@ -1263,7 +1265,7 @@ "source": [ "## A0V\n", "\n", - "Let's do telluric standar star. We will select images from observation_id of\n", + "The next step is processing telluric standard (A0V type) star. We will select data from observation_id of\n", "'GN-2024A-ENG-142-261'.\n", "\n", "> dataselect_ig --tags STANDARD,H unbundled_20240429/N*_H.fits -o list_of_std_h.txt --expr \"observation_id=='GN-2024A-ENG-142-120'\"\n", @@ -1642,7 +1644,7 @@ "source": [ "## SCIENCE\n", "\n", - "For science target, select 900078.\n", + "For science target, select the object 900078.\n", "\n", "> dataselect_ig --tags SCIENCE,H unbundled_20240429/N*_H.fits -o list_of_900078_h.txt --expr \"object=='900078'\"\n", "\n",