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Update to remove explicit sys calls #312

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merged 11 commits into from
Oct 4, 2024
Merged

Update to remove explicit sys calls #312

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fdf5077
Calwf3 update to remove sys call
haticekaratay Sep 27, 2024
34a3ee2
Filter transformation nb update
haticekaratay Sep 27, 2024
80bfe98
Safely extract tar files
haticekaratay Oct 4, 2024
62b7967
Safely extract tar files, remove sys call in flux conv nb
haticekaratay Oct 4, 2024
7af2e9a
Safely extract files, remove sys call in phot nb
haticekaratay Oct 4, 2024
64e03a2
Remove sys call in the align_sparse_field nn
haticekaratay Oct 4, 2024
37d3e82
Remove sys call in align catalogs nb
haticekaratay Oct 4, 2024
22cb89b
remove explicit sys call in the reduction nb
haticekaratay Oct 4, 2024
24acb65
Rmv explicit sys call on the optimize img nb
haticekaratay Oct 4, 2024
05aba8c
remove explicit sys call in astrometry solutions nb
haticekaratay Oct 4, 2024
95d921c
Update mask_satellite nb
haticekaratay Oct 4, 2024
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7 changes: 3 additions & 4 deletions notebooks/ACS/acs_reduction/acs_reduction.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -330,8 +330,7 @@
"outputs": [],
"source": [
"for file in raw_files:\n",
" command_line_input = 'crds bestrefs --files {:} --sync-references=1 --update-bestrefs'.format(file)\n",
" os.system(command_line_input)"
" !crds bestrefs --files {file} --sync-references=1 --update-bestrefs"
]
},
{
Expand All @@ -357,7 +356,7 @@
"metadata": {},
"outputs": [],
"source": [
"os.system('calacs.e j9l960010_asn.fits')"
"!calacs.e j9l960010_asn.fits"
]
},
{
Expand Down Expand Up @@ -475,7 +474,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions notebooks/DrizzlePac/align_sparse_fields/align_sparse_fields.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -801,7 +801,7 @@
"# The following lines of code find and download the MDRIZTAB reference file.\n",
"mdz = fits.getval(input_files[0], 'MDRIZTAB', ext=0).split('$')[1]\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"get_mdriztab = os.system('crds sync --hst --files ' + mdz + ' --output-dir '+os.environ['jref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['jref']}"
]
},
{
Expand Down Expand Up @@ -1013,7 +1013,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions notebooks/DrizzlePac/align_to_catalogs/align_to_catalogs.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -789,7 +789,7 @@
"\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"\n",
"get_mdriztab = os.system('crds sync --hst --files '+mdz+' --output-dir '+os.environ['iref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['iref']}"
]
},
{
Expand Down Expand Up @@ -965,7 +965,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
14 changes: 5 additions & 9 deletions notebooks/DrizzlePac/mask_satellite/mask_satellite.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -200,9 +200,7 @@
" os.rename(file, os.path.basename(file))\n",
" for file in flc_download['Local Path']:\n",
" os.rename(file, os.path.basename(file))\n",
" shutil.rmtree('mastDownload')\n",
"else:\n",
" pass"
" shutil.rmtree('mastDownload')"
]
},
{
Expand Down Expand Up @@ -273,9 +271,7 @@
" os.rename(file, os.path.basename(file))\n",
" for file in flc_download['Local Path']:\n",
" os.rename(file, os.path.basename(file))\n",
" shutil.rmtree('mastDownload')\n",
"else:\n",
" pass"
" shutil.rmtree('mastDownload')"
]
},
{
Expand Down Expand Up @@ -533,7 +529,7 @@
"\n",
"mdz = fits.getval(input_images[0], 'MDRIZTAB', ext=0).split('$')[1]\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"get_mdriztab = os.system('crds sync --hst --files ' + mdz + ' --output-dir '+os.environ['jref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['jref']}"
]
},
{
Expand Down Expand Up @@ -998,7 +994,7 @@
"\n",
"mdz = fits.getval(input_images[0], 'MDRIZTAB', ext=0).split('$')[1]\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"get_mdriztab = os.system('crds sync --hst --files '+mdz+' --output-dir '+os.environ['iref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['iref']}"
]
},
{
Expand Down Expand Up @@ -1162,7 +1158,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions notebooks/DrizzlePac/optimize_image_sampling/optimize_image_sampling.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -349,7 +349,7 @@
"source": [
"mdz = fits.getval(flt_files[0], 'MDRIZTAB', ext=0).split('$')[1]\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"get_mdriztab = os.system('crds sync --hst --files '+mdz+' --output-dir '+os.environ['iref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['iref']}"
]
},
{
Expand Down Expand Up @@ -735,7 +735,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions ...ks/DrizzlePac/using_updated_astrometry_solutions/using_updated_astrometry_solutions.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -739,7 +739,7 @@
"input_images_f336w = sorted(glob.glob('iepw14g[46]q_flc.fits'))\n",
"mdz = fits.getval(input_images_f336w[0], 'MDRIZTAB', ext=0).split('$')[1]\n",
"print('Searching for the MDRIZTAB file:', mdz)\n",
"get_mdriztab = os.system('crds sync --hst --files '+mdz+' --output-dir '+os.environ['iref'])"
"!crds sync --hst --files {mdz} --output-dir {os.environ['iref']}"
]
},
{
Expand Down Expand Up @@ -981,7 +981,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
9 changes: 5 additions & 4 deletions notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,8 @@
"from drizzlepac import astrodrizzle\n",
"from stwcs import updatewcs\n",
"\n",
"from wfc3tools import calwf3, pstat"
"from wfc3tools import calwf3, pstat\n",
"from IPython.display import clear_output"
]
},
{
Expand Down Expand Up @@ -222,8 +223,8 @@
"raw_files = glob.glob('*_raw.fits')\n",
"\n",
"for file in raw_files:\n",
" command_line_input = f'crds bestrefs --files {file} --sync-references=1 --update-bestrefs'\n",
" os.system(command_line_input)"
" !crds bestrefs --files {file} --sync-references=1 --update-bestrefs\n",
"clear_output()"
]
},
{
Expand Down Expand Up @@ -768,7 +769,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
16 changes: 11 additions & 5 deletions notebooks/WFC3/filter_transformations/filter_transformations.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -110,8 +110,7 @@
"metadata": {},
"outputs": [],
"source": [
"cmd_input = 'curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"os.system(cmd_input)"
"!curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar"
]
},
{
Expand All @@ -131,10 +130,17 @@
"source": [
"tar_archive = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"extract_to = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed'\n",
"abs_extract_to = os.path.abspath(extract_to)\n",
"\n",
"with tarfile.open(tar_archive, 'r') as tar:\n",
" tar.extractall(path=extract_to)\n",
" for member in tar.getmembers():\n",
" member_path = os.path.abspath(os.path.join(abs_extract_to, member.name))\n",
" if member_path.startswith(abs_extract_to):\n",
" tar.extract(member, path=extract_to) \n",
" else:\n",
" print(f\"Skipped {member.name} due to potential security risk\")\n",
"\n",
"os.environ['PYSYN_CDBS'] = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed/grp/redcat/trds/'"
"os.environ['PYSYN_CDBS'] = os.path.join(abs_extract_to, 'grp/redcat/trds/')"
]
},
{
Expand Down Expand Up @@ -553,7 +559,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
24 changes: 11 additions & 13 deletions notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -116,8 +116,7 @@
"metadata": {},
"outputs": [],
"source": [
"cmd_input = 'curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"os.system(cmd_input)"
"!curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar"
]
},
{
Expand All @@ -137,10 +136,17 @@
"source": [
"tar_archive = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"extract_to = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed'\n",
"abs_extract_to = os.path.abspath(extract_to)\n",
"\n",
"with tarfile.open(tar_archive, 'r') as tar:\n",
" tar.extractall(path=extract_to)\n",
" for member in tar.getmembers():\n",
" member_path = os.path.abspath(os.path.join(abs_extract_to, member.name))\n",
" if member_path.startswith(abs_extract_to):\n",
" tar.extract(member, path=extract_to) \n",
" else:\n",
" print(f\"Skipped {member.name} due to potential security risk\")\n",
"\n",
"os.environ['PYSYN_CDBS'] = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed/grp/redcat/trds/'"
"os.environ['PYSYN_CDBS'] = os.path.join(abs_extract_to, 'grp/redcat/trds/')"
]
},
{
Expand Down Expand Up @@ -803,14 +809,6 @@
"[Top of Page](#title)\n",
"<img style=\"float: right;\" src=\"https://raw.githubusercontent.com/spacetelescope/notebooks/master/assets/stsci_pri_combo_mark_horizonal_white_bkgd.png\" alt=\"Space Telescope Logo\" width=\"200px\"/> "
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f708c513",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -829,7 +827,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
16 changes: 11 additions & 5 deletions notebooks/WFC3/photometry_examples/phot_examples.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -122,8 +122,7 @@
"metadata": {},
"outputs": [],
"source": [
"cmd_input = 'curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"os.system(cmd_input)"
"!curl -O https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar"
]
},
{
Expand All @@ -143,10 +142,17 @@
"source": [
"tar_archive = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar'\n",
"extract_to = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed'\n",
"abs_extract_to = os.path.abspath(extract_to)\n",
"\n",
"with tarfile.open(tar_archive, 'r') as tar:\n",
" tar.extractall(path=extract_to)\n",
" for member in tar.getmembers():\n",
" member_path = os.path.abspath(os.path.join(abs_extract_to, member.name))\n",
" if member_path.startswith(abs_extract_to):\n",
" tar.extract(member, path=extract_to) \n",
" else:\n",
" print(f\"Skipped {member.name} due to potential security risk\")\n",
"\n",
"os.environ['PYSYN_CDBS'] = 'hlsp_reference-atlases_hst_multi_everything_multi_v11_sed/grp/redcat/trds/'"
"os.environ['PYSYN_CDBS'] = os.path.join(abs_extract_to, 'grp/redcat/trds/')"
]
},
{
Expand Down Expand Up @@ -874,7 +880,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
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