Changedate

notebooks/COS/AsnFile/test_asn.py

@@ -16,20 +16,33 @@
 outputdir = Path('./output/')
 plotsdir =  Path('./output/plots/')
 # %%
-######### SETTING THE lref VARIABLE:
+######### Setting the lref environment variable:
 ### YOU LIKELY NEED TO CHANGE THIS LOCATION !
 where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
 os.environ['lref'] = where_i_keep_my_ref_files
+assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
 
+# Copy the asn file we made into the directory where we moved all of our ldif* exposures' data
+shutil.copy("./output/ldifcombo_2_asn.fits", "./data/ldifcombo_2_asn.fits")
+
+# Run the CalCOS pipeline on our ldifcombo asn file
+calcos.calcos('./data/ldifcombo_2_asn.fits', verbosity=0, outdir=str(outputdir/"./calcos_processed_1"))
+
+# %%
+# Read in the processed data
 processed_data_tab = Table.read(str(outputdir/'calcos_processed_1/')+'/ldifcombo_x1dsum.fits')
+
+# Plot the processed data
 for segment in processed_data_tab:
     wvln, flux = segment["WAVELENGTH", "FLUX"]
     plt.plot(wvln, flux)
 
 plt.xlabel('Wavelength [$\AA$]')
 plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
 
-plt.title("If this graph looks reasonable, your ASN file seems to have worked\n")
+plt.title("If this graph looks at all reasonable, your ASN file seems to have worked\n")
 plt.tight_layout()
-plt.savefig(str(plotsdir/"AsnFile_test.png"), bbox_inches = 'tight', dpi = 200)
+plot_path = str(plotsdir/"AsnFile_test.png")
+plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+print(f"Saved plot to: {plot_path}")
 # %%

notebooks/COS/AsnFile/test_removed_exposure_asn.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+#%%[markdown]
+### From here, you can run the `CalCOS` pipeline on your association file where we've removed the empty exposure file.
+##### Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
+
+##### In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
+##### No matter *where* you place these files, you *must* create the lref environment variable.
+# %%
+import os, shutil
+import calcos
+from astropy.table import Table
+import matplotlib.pyplot as plt
+from pathlib import Path
+from astropy.io import fits
+# %%
+datadir = Path('./data/')
+mast_download_dir = datadir / "mastDownload"
+outputdir = Path('./output/')
+plotsdir =  Path('./output/plots/')
+# %%
+######### Setting the lref environment variable:
+### YOU LIKELY NEED TO CHANGE THIS LOCATION !
+where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
+os.environ['lref'] = where_i_keep_my_ref_files
+assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
+# %%
+remove_badfile_asn = "data/removed_badfile_asn.fits"
+# Run the CalCOS pipeline on our asn file
+calcos.calcos(remove_badfile_asn, verbosity=0, outdir=str(outputdir/"calcos_processed_remove_badfile/"))
+# %%
+# Read in the processed data
+processed_data_tab = Table.read(str(outputdir/'calcos_processed_remove_badfile/')+'/ldif01010_x1dsum.fits')
+
+# Plot the processed data
+for segment in processed_data_tab:
+    wvln, flux = segment["WAVELENGTH", "FLUX"]
+    plt.plot(wvln, flux)
+
+plt.xlabel('Wavelength [$\AA$]')
+plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
+
+plt.title("If this plot looks reasonable, your ASN file seems to have worked\n")
+plt.tight_layout()
+plot_path = str(plotsdir/"remove_badfile_AsnFile_test.png")
+plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+print(f"Saved plot to: {plot_path}")
+# %%

notebooks/COS/AsnFile/test_splitwave_asn.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+#%%[markdown]
+### From here, you can run the `CalCOS` pipeline on your new association SPLIT wavecal file.
+##### Running `CalCOS` is explained in *much* more detail in our [Notebook on running the pipeline](https://github.com/spacetelescope/notebooks/blob/master/notebooks/COS/CalCOS/CalCOS.ipynb)
+
+##### In short, to run the `CalCOS` pipeline, you will need the relavent reference files. These will need be hosted in the directory assigned the environmetn variable `lref`. 
+##### No matter *where* you place these files, you *must* create the lref environment variable.
+# %%
+import os, shutil
+import calcos
+from astropy.table import Table
+import matplotlib.pyplot as plt
+from pathlib import Path
+from astropy.io import fits
+# %%
+datadir = Path('./data/')
+mast_download_dir = datadir / "mastDownload"
+lp6_1exp_datadir = datadir / "lp6_1exp_datadir"
+lp6_1exp_datadir.mkdir(exist_ok=True)
+outputdir = Path('./output/')
+plotsdir =  Path('./output/plots/')
+# %%
+# Copy all of the relevant LP6 data files into the lp6_1exp_datadir
+splitwave_rawtags = [
+    shutil.copy(rt, lp6_1exp_datadir / rt.name) \
+        for rt in mast_download_dir.glob("**/*rawtag*fits") \
+            # Only grab the necessary files
+            if fits.getval(rt, "ROOTNAME").upper() in ['LETC01M6Q','LETC01MTQ','LETC01MVQ']
+]
+# Copy the LP6 single exposure asn file we made into the directory where we moved all of the relevant exposures' data
+lp6_1exp_asn = shutil.copy('data/letc01mtq_only_asn.fits', lp6_1exp_datadir)
+# %%
+######### Setting the lref environment variable:
+### YOU LIKELY NEED TO CHANGE THIS LOCATION !
+where_i_keep_my_ref_files = "/grp/hst/cdbs/lref/"
+os.environ['lref'] = where_i_keep_my_ref_files
+assert Path(os.environ['lref']).exists(), "Make sure to set the 'lref' environment variable to a valid path with all of your reference files."
+# %%
+# Run the CalCOS pipeline on our SPLIT wavecal asn file
+calcos.calcos(lp6_1exp_asn, verbosity=0, outdir=str(outputdir/"calcos_processed_lp6_1exp/"))
+# %%
+# Read in the processed data
+processed_data_tab = Table.read(str(outputdir/'calcos_processed_lp6_1exp/')+'/letc01mtq_only_x1dsum.fits')
+
+# Plot the processed data
+for segment in processed_data_tab:
+    wvln, flux = segment["WAVELENGTH", "FLUX"]
+    plt.plot(wvln, flux)
+
+plt.xlabel('Wavelength [$\AA$]')
+plt.ylabel('Flux [ergs/s/$cm^2$/$\AA$]')
+
+plt.title("If this plot looks reasonable, your ASN file seems to have worked\n")
+plt.tight_layout()
+plot_path = str(plotsdir/"LP6_1exposure_AsnFile_test.png")
+plt.savefig(plot_path, bbox_inches = 'tight', dpi = 200)
+print(f"Saved plot to: {plot_path}")
+# %%

notebooks/COS/DataDl/DataDl.ipynb

@@ -818,8 +818,9 @@
     "---\n",
     "## About this Notebook\n",
     "**Author:** Nat Kerman <[email protected]>\n",
+    "**Edited by:** Travis Fischer <[email protected]>\n",
     "\n",
-    "**Updated On:** 2022-02-25\n",
+    "**Updated On:** 2022-09-09\n",
     "\n",
     "> *This tutorial was generated to be in compliance with the [STScI style guides](https://github.com/spacetelescope/style-guides) and would like to cite the [Jupyter guide](https://github.com/spacetelescope/style-guides/blob/master/templates/example_notebook.ipynb) in particular.*\n",
     "\n",
@@ -913,7 +914,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.5 ('fs2')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -927,7 +928,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.9.7"
   },
   "vscode": {
    "interpreter": {