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Update wfc3 notebook dependencies #299

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Sep 4, 2024
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Update wfc3 notebook dependencies #299

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b416169
Update WFC3 requirements
haticekaratay Aug 1, 2024
121a458
Update requirements.txt
haticekaratay Aug 1, 2024
a150288
Replace ginga zscale with astropy visualization zscale
haticekaratay Aug 2, 2024
f058cf6
Install hst-cal via conda-forge
haticekaratay Aug 2, 2024
68d031d
Remove the numpy pinning on the uvis_pam nb
haticekaratay Aug 27, 2024
0d94775
Revert hstcal to old version to demo specific API
haticekaratay Aug 29, 2024
108de13
Pin photutils
haticekaratay Aug 29, 2024
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4 changes: 2 additions & 2 deletions notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
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Expand Up @@ -10,7 +10,7 @@
"\n",
"## Learning Goals\n",
"\n",
"This notebook shows two reprocessing examples for WFC3/IR observations impacted by time-variable background (TVB).\n",
"This notebook shows two reprocessing examples for WFC3/IR observations impacted by time-variable background (TVB). \n",
"\n",
"By the end of this tutorial, you will:\n",
"- Analyze exposure statistics for each read in an IMA file using `pstat`.\n",
Expand Down Expand Up @@ -768,7 +768,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.12.4"
}
},
"nbformat": 4,
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19 changes: 10 additions & 9 deletions notebooks/WFC3/calwf3_recalibration/requirements.txt
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@@ -1,9 +1,10 @@
astropy==5.3.3
astroquery==0.4.6
ccdproc==2.4.0
crds==11.17.9
drizzlepac==3.5.1
matplotlib==3.7.0
numpy==1.23.4
stwcs==1.7.2
wfc3tools==1.4.0
photutils==1.12.0 # The notebook uses deprecated methods such as DAOGroup.
astropy>=5.3.3
astroquery>=0.4.6
ccdproc>=2.4.0
crds>=11.17.9
drizzlepac>=3.5.1
matplotlib>=3.7.0
numpy>=1.23.4
stwcs>=1.7.2
wfc3tools>=1.4.0
4 changes: 2 additions & 2 deletions notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
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Expand Up @@ -14,7 +14,7 @@
"\n",
"By the end of this tutorial, you will:\n",
"\n",
"- Download a raw WFC3 image from MAST.\n",
"- Download a raw WFC3 image from MAST. \n",
"- Find the necessary reference files needed for calibration.\n",
"- Edit header keywords.\n",
"- Run `calwf3` `v3.5.2` to calibrate the raw image with the v1.0 pixel based CTE-correction.\n",
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instructions need updating for only using hstcal 2.5?

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wait! my bad, it's been a minute and I forgot calXXX versions don't track hstcal. I see hstcal 2.5 tracking calwf3 at v3.5.2

12-Aug-2020 - MDD - Version 3.5.2

Expand Down Expand Up @@ -990,7 +990,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.12.4"
},
"varInspector": {
"cols": {
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2 changes: 1 addition & 1 deletion notebooks/WFC3/calwf3_v1.0_cte/pre-requirements.sh
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Is there a reason that hstcal is being installed from the older ssb server and not conda-forge?
https://anaconda.org/conda-forge/hstcal

hstcal on the ssb server is at 2.7.1 and conda-forge has 3.0.2

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No special reason. Good catch! I will update to conda-forge in the upcoming commits.

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@bjkuhn bjkuhn Aug 2, 2024 •
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The calwf3_v1.0_cte notebook actually does need the old version of hstcal. This is because we're showing users how to access the older v1.0 CTE correction, which was available in calwf3 versions 3.3 to 3.5.2. I have specifically pinned hstcal v2.5.0 because it provides access to calwf3 v3.5.2, the most recent version to still include the v1.0 CTE correction. I don't believe hstcal version 2.5.0 is hosted on conda-forge so we therefore need to continue using the ssb server. @haticekaratay Please keep hstcal pinned to v2.5.0

Original file line number Diff line number Diff line change
@@ -1 +1 @@
conda install --yes -c http://ssb.stsci.edu/astroconda hstcal==2.5.0
conda install --yes -c http://ssb.stsci.edu/astroconda hstcal
35 changes: 20 additions & 15 deletions notebooks/WFC3/filter_transformations/filter_transformations.ipynb
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Expand Up @@ -6,7 +6,7 @@
"metadata": {},
"source": [
"<a id=\"title\"></a>\n",
"# WFC3/UVIS Filter Transformations with stsynphot\n",
"# WFC3/UVIS Filter Transformations with stsynphot \n",
"***\n",
"## Learning Goals\n",
"\n",
Expand Down Expand Up @@ -289,7 +289,8 @@
"STMAG = True\n",
"VEGAMAG = False\n",
"\n",
"mags = [('ABMAG', u.ABmag, ABMAG), ('STMAG', u.STmag, STMAG), ('VEGAMAG', su.VEGAMAG, VEGAMAG)]"
"mags = [('ABMAG', u.ABmag, ABMAG), ('STMAG', u.STmag, STMAG),\n",
" ('VEGAMAG', su.VEGAMAG, VEGAMAG)]"
]
},
{
Expand Down Expand Up @@ -363,12 +364,12 @@
"for pair in filter_pairs:\n",
" comparison_filter, uvis_filter = pair # Unpack filters\n",
" filt_str = comparison_filter + ' - ' + uvis_filter\n",
" \n",
"\n",
" for i, toggle in enumerate(chips):\n",
" if not toggle:\n",
" continue\n",
" chip_str = 'UVIS' + str(i + 1)\n",
" \n",
"\n",
" # Generate observation mode strings, bandpasses, observations\n",
" comparison_obsmode = comparison_filter\n",
" uvis_obsmode = 'wfc3, ' + chip_str + ', ' + uvis_filter\n",
Expand All @@ -383,11 +384,13 @@
" for name, unit, toggle in mags:\n",
" if not toggle:\n",
" continue\n",
" comparison_countrate = comparison_observation.effstim(flux_unit=unit, vegaspec=vegaspec) \n",
" uvis_countrate = uvis_observation.effstim(flux_unit=unit, vegaspec=vegaspec)\n",
" color = comparison_countrate - uvis_countrate # Find color term\n",
" comparison_countrate = comparison_observation.effstim(\n",
" flux_unit=unit, vegaspec=vegaspec)\n",
" uvis_countrate = uvis_observation.effstim(\n",
" flux_unit=unit, vegaspec=vegaspec)\n",
" color = comparison_countrate - uvis_countrate # Find color term\n",
" row.append(f'{color.value:.3f}') # Append color term\n",
" \n",
"\n",
" rows.append(row) # Append row to list of rows"
]
},
Expand Down Expand Up @@ -448,27 +451,29 @@
"metadata": {},
"outputs": [],
"source": [
"fig, axs = plt.subplots(1, len(filter_pairs), sharey=True, figsize=(4*len(filter_pairs), 5)) # Instantiate subplots\n",
"fig, axs = plt.subplots(1, len(filter_pairs), sharey=True, figsize=(\n",
" 4*len(filter_pairs), 5)) # Instantiate subplots\n",
"axs[0].set_ylabel('Throughput')\n",
"for i, pair in enumerate(filter_pairs):\n",
" \n",
"\n",
" f1, f2 = pair\n",
" bp1 = stsyn.band(f1)\n",
" bp2 = stsyn.band('wfc3, uvis1,' + f2)\n",
" \n",
"\n",
" # Create wavelength array for subplot based on average bandpass wavelength and width\n",
" avgwave = (bp1.avgwave().to(u.nm) + bp2.avgwave().to(u.nm))/2\n",
" width = (bp1.rectwidth().to(u.nm) + bp2.rectwidth().to(u.nm))/2\n",
" left = max((avgwave - 1.5 * width).value, 1)\n",
" right = (avgwave + 1.5 * width).value\n",
" \n",
"\n",
" wl = np.arange(left, right) * u.nm\n",
"\n",
" # Normalize curves to fit on one set of axes\n",
" bp1_norm = bp1(wl) / np.max(bp1(wl)) * np.max(bp2(wl))\n",
" spec_norm = source_spectrum(wl) / np.max(source_spectrum(wl)) * np.max(bp2(wl))\n",
" \n",
" # Plot bandpasses and spectrum on subplot \n",
" spec_norm = source_spectrum(\n",
" wl) / np.max(source_spectrum(wl)) * np.max(bp2(wl))\n",
"\n",
" # Plot bandpasses and spectrum on subplot\n",
" axs[i].plot(wl, bp1_norm, ls='--', label=f1, c='tab:blue')\n",
" axs[i].plot(wl, bp2(wl), ls='-.', label=f2, c='tab:red')\n",
" axs[i].plot(wl, spec_norm, label='source spectrum', c='tab:purple')\n",
Expand Down
10 changes: 5 additions & 5 deletions notebooks/WFC3/filter_transformations/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
astropy
matplotlib==3.8.3
numpy==1.26.4
pandas==2.2.1
stsynphot==1.2.0
synphot==1.1.1
matplotlib>=3.8.3
numpy>=1.26.4
pandas>=2.2.1
stsynphot>=1.2.0
synphot>=1.1.1
64 changes: 36 additions & 28 deletions notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
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Expand Up @@ -6,7 +6,7 @@
"metadata": {},
"source": [
"<a id=\"title\"></a>\n",
"# Flux Unit Conversions with synphot and stsynphot\n",
"# Flux Unit Conversions with synphot and stsynphot \n",
"***\n",
"## Learning Goals\n",
"By the end of this tutorial, you will:\n",
Expand Down Expand Up @@ -275,7 +275,7 @@
"value_in = 0.0\n",
"unit_in = su.VEGAMAG\n",
"waveband_in = 'johnson, v'\n",
"wavelength_unit = u.nm "
"wavelength_unit = u.nm"
]
},
{
Expand Down Expand Up @@ -349,7 +349,7 @@
"source": [
"quantity_in = value_in * unit_in\n",
"mag_systems = [u.STmag, u.ABmag, su.VEGAMAG]\n",
"flux_systems = ['spectral flux density', 'spectral flux density wav', \n",
"flux_systems = ['spectral flux density', 'spectral flux density wav',\n",
" 'photon flux density', 'photon flux density wav']"
]
},
Expand Down Expand Up @@ -392,7 +392,7 @@
" plot_flux_in = convert_flux(wavelength_in, flux_in, plot_unit)\n",
"elif unit_in.physical_type in flux_systems:\n",
" flux_in = quantity_in\n",
" wavelength_in = waveband_in * wavelength_unit \n",
" wavelength_in = waveband_in * wavelength_unit\n",
" plot_unit = unit_in\n",
" plot_flux_in = convert_flux(wavelength_in, flux_in, plot_unit)\n",
"else:\n",
Expand Down Expand Up @@ -431,7 +431,7 @@
"elif unit_out.physical_type in flux_systems:\n",
" wavelength_out = waveband_out * wavelength_unit\n",
"else:\n",
" print('unit_out not a flux density unit or magnitude system') "
" print('unit_out not a flux density unit or magnitude system')"
]
},
{
Expand All @@ -449,7 +449,8 @@
"metadata": {},
"outputs": [],
"source": [
"scale = convert_flux(wavelength_in, flux_in, su.PHOTLAM) / spectrum(wavelength_in)\n",
"scale = convert_flux(wavelength_in, flux_in, su.PHOTLAM) / \\\n",
" spectrum(wavelength_in)\n",
"scaled_spectrum = spectrum * scale"
]
},
Expand All @@ -474,11 +475,14 @@
"if unit_out in mag_systems:\n",
" flux_out = convert_flux(wavelength_out, scaled_spectrum(wavelength_out), unit_out,\n",
" vegaspec=vegaspec)\n",
" plot_flux_out = convert_flux(wavelength_out, scaled_spectrum(wavelength_out), plot_unit)\n",
" plot_flux_out = convert_flux(\n",
" wavelength_out, scaled_spectrum(wavelength_out), plot_unit)\n",
"else:\n",
" flux_out = convert_flux(wavelength_out, scaled_spectrum(wavelength_out), unit_out)\n",
" plot_flux_out = convert_flux(wavelength_out, scaled_spectrum(wavelength_out), plot_unit)\n",
" \n",
" flux_out = convert_flux(\n",
" wavelength_out, scaled_spectrum(wavelength_out), unit_out)\n",
" plot_flux_out = convert_flux(\n",
" wavelength_out, scaled_spectrum(wavelength_out), plot_unit)\n",
"\n",
"value_out = flux_out.value"
]
},
Expand Down Expand Up @@ -550,7 +554,7 @@
"if wavelength_in.value > wavelength_out.value:\n",
" c_in = 'r'\n",
" c_out = 'b'\n",
"else: \n",
"else:\n",
" c_in = 'b'\n",
" c_out = 'r'"
]
Expand All @@ -573,19 +577,20 @@
"plt.figure()\n",
"\n",
"# Plot spectrum\n",
"plt.plot(wavelength_space, scaled_spectrum(wavelength_space, flux_unit=plot_unit), c='k', label='Source Spectrum')\n",
"plt.plot(wavelength_space, scaled_spectrum(wavelength_space,\n",
" flux_unit=plot_unit), c='k', label='Source Spectrum')\n",
"\n",
"# Plot input\n",
"plt.plot(wavelength_in.value, plot_flux_in.value,\n",
" marker='o', color=c_in, ls='none', \n",
" marker='o', color=c_in, ls='none',\n",
" label='Input: {:.4} {} at {:.1f} {}'.format(\n",
" float(value_in), str(unit_in), wavelength_in.value, str(wavelength_in.unit)))\n",
" float(value_in), str(unit_in), wavelength_in.value, str(wavelength_in.unit)))\n",
"\n",
"# Plot output\n",
"plt.plot(wavelength_out.value, plot_flux_out.value,\n",
" marker='s', color=c_out, ls='none', \n",
" marker='s', color=c_out, ls='none',\n",
" label='Output: {:.4} {} at {:.1f} {}'.format(\n",
" float(value_out), str(unit_out), wavelength_out.value, str(wavelength_out.unit)))\n",
" float(value_out), str(unit_out), wavelength_out.value, str(wavelength_out.unit)))\n",
"\n",
"# Set heights for dotted lines to markers as % of plot range\n",
"bottom, top = plt.ylim()\n",
Expand All @@ -594,13 +599,15 @@
"outheight = (plot_flux_out.value - bottom) / yrange\n",
"\n",
"# Plot dotted lines to markers\n",
"plt.axvline(wavelength_in.to(wavelength_unit).value, ymax=inheight, ls=':', c=c_in)\n",
"plt.axvline(wavelength_out.to(wavelength_unit).value, ymax=outheight, ls=':', c=c_out)\n",
"plt.axvline(wavelength_in.to(wavelength_unit).value,\n",
" ymax=inheight, ls=':', c=c_in)\n",
"plt.axvline(wavelength_out.to(wavelength_unit).value,\n",
" ymax=outheight, ls=':', c=c_out)\n",
"\n",
"# Miscellaneous\n",
"plt.ylabel('Flux ({})'.format(str(plot_unit)))\n",
"plt.xlabel('Wavelength ({})'.format(str(wavelength_unit)))\n",
"plt.legend(fontsize='small') \n",
"plt.legend(fontsize='small')\n",
"plt.tight_layout()"
]
},
Expand All @@ -627,15 +634,15 @@
"outputs": [],
"source": [
"# Input: 3631 Jy at 550. nm\n",
"value_in = 3631. \n",
"value_in = 3631.\n",
"unit_in = u.Jy\n",
"waveband_in = 550.\n",
"wavelength_unit = u.nm\n",
"\n",
"# Output: Johnson V mag (AB)\n",
"unit_out = u.ABmag\n",
"waveband_out = 'Johnson, V'\n",
" \n",
"\n",
"# Spectrum: Flat power law in F_nu\n",
"pl_index = 0\n",
"model = PowerLawFlux1D(amplitude=flux_in, x_0=wavelength_in, alpha=pl_index)\n",
Expand All @@ -660,15 +667,15 @@
"outputs": [],
"source": [
"# Input: 1.234e-8 flam at 500. nm\n",
"value_in = 1.234e-8 \n",
"value_in = 1.234e-8\n",
"unit_in = su.FLAM\n",
"waveband_in = 500.\n",
"wavelength_unit = u.nm\n",
"\n",
"# Output: flam at 800. nm\n",
"unit_out = su.FLAM\n",
"waveband_out = 800.\n",
" \n",
"\n",
"# Spectrum: 5800 K blackbody\n",
"bb_temp = 5800 * u.K\n",
"model = BlackBody1D(bb_temp)\n",
Expand All @@ -693,15 +700,15 @@
"outputs": [],
"source": [
"# Input: 1.234e-21 fnu at 686. nm\n",
"value_in = 1.234e-21 \n",
"value_in = 1.234e-21\n",
"unit_in = su.FNU\n",
"waveband_in = 686.\n",
"wavelength_unit = u.nm\n",
"\n",
"# Output: photnu at 686. nm\n",
"unit_out = su.PHOTNU\n",
"waveband_out = 686.\n",
" \n",
"\n",
"# Spectrum: 5800 K blackbody\n",
"bb_temp = 5800 * u.K\n",
"model = BlackBody1D(bb_temp)\n",
Expand All @@ -726,18 +733,19 @@
"outputs": [],
"source": [
"# Input: STmag = 12.240, F606W filter on WFC3 UVIS 2\n",
"value_in = 12.240 \n",
"value_in = 12.240\n",
"unit_in = u.STmag\n",
"waveband_in = 'wfc3, uvis2, f606w, mjd#59367'\n",
"wavelength_unit = u.nm\n",
"\n",
"# Output: Johnson V mag (AB)\n",
"unit_out = u.STmag\n",
"waveband_out = 'Johnson, V'\n",
" \n",
"\n",
"# Spectrum: Flat power law in F_lambda\n",
"pl_index = 0\n",
"model = PowerLawFlux1D(amplitude=convert_flux(606 * u.nm, 1., su.FLAM), x_0=606 * u.nm, alpha=pl_index)\n",
"model = PowerLawFlux1D(amplitude=convert_flux(\n",
" 606 * u.nm, 1., su.FLAM), x_0=606 * u.nm, alpha=pl_index)\n",
"spec = SourceSpectrum(model)\n",
"model = PowerLawFlux1D(amplitude=flux_in, x_0=wavelength_in, alpha=pl_index)"
]
Expand Down
8 changes: 4 additions & 4 deletions notebooks/WFC3/flux_conversion_tool/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
astropy
matplotlib==3.8.3
numpy==1.26.4
stsynphot==1.2.0
synphot==1.1.1
matplotlib>=3.8.3
numpy>=1.26.4
stsynphot>=1.2.0
synphot>=1.1.1
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