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38 changes: 20 additions & 18 deletions docs/IGRINSDR_users_manual.ipynb
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Expand Up @@ -14,7 +14,7 @@
"</div>\n",
"\n",
"<div class=\"alert alert-success\">\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",
"</div>\n"
]
},
Expand All @@ -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"
]
},
{
Expand All @@ -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."
]
},
{
Expand Down Expand Up @@ -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."
]
},
{
Expand All @@ -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",
Expand Down Expand Up @@ -360,7 +361,7 @@
"/home/jjlee/git_personal/IGRINSDR/test_i2\n"
]
}
],
],
"source": [
"%cd -"
]
Expand Down Expand Up @@ -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"
]
},
Expand All @@ -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",
Expand Down Expand Up @@ -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",
"<div class=\"alert alert-info\">\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",
"</div>\n",
"\n",
"We will run reduce, but we need to explicitly set the calibration file.\n",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down