Update wfc3 notebook dependencies (#299)

* Update WFC3 requirements * Update requirements.txt * Replace ginga zscale with astropy visualization zscale * Install hst-cal via conda-forge * Remove the numpy pinning on the uvis_pam nb * Revert hstcal to old version to demo specific API * Pin photutils
spacetelescope · Sep 4, 2024 · c54f2ef · c54f2ef
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diff --git a/notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb b/notebooks/WFC3/calwf3_recalibration/calwf3_recal_tvb.ipynb
@@ -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",
@@ -768,7 +768,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/WFC3/calwf3_recalibration/requirements.txt b/notebooks/WFC3/calwf3_recalibration/requirements.txt
@@ -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
diff --git a/notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb b/notebooks/WFC3/calwf3_v1.0_cte/calwf3_with_v1.0_PCTE.ipynb
@@ -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",
@@ -990,7 +990,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.12.4"
   },
   "varInspector": {
    "cols": {

diff --git a/notebooks/WFC3/calwf3_v1.0_cte/requirements.txt b/notebooks/WFC3/calwf3_v1.0_cte/requirements.txt
@@ -4,6 +4,6 @@ crds
 jupyter
 matplotlib
 numpy
-photutils
+photutils==1.12.0
 scipy
 wfc3tools
diff --git a/notebooks/WFC3/filter_transformations/filter_transformations.ipynb b/notebooks/WFC3/filter_transformations/filter_transformations.ipynb
@@ -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",
@@ -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)]"
    ]
   },
   {
@@ -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",
@@ -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"
    ]
   },
@@ -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",

diff --git a/notebooks/WFC3/filter_transformations/requirements.txt b/notebooks/WFC3/filter_transformations/requirements.txt
@@ -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
diff --git a/notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb b/notebooks/WFC3/flux_conversion_tool/flux_conversion_tool.ipynb
@@ -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",
@@ -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"
    ]
   },
   {
@@ -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']"
    ]
   },
@@ -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",
@@ -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')"
    ]
   },
   {
@@ -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"
    ]
   },
@@ -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"
    ]
   },
@@ -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'"
    ]
@@ -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",
@@ -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()"
    ]
   },
@@ -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",
@@ -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",
@@ -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",
@@ -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)"
    ]

diff --git a/notebooks/WFC3/flux_conversion_tool/requirements.txt b/notebooks/WFC3/flux_conversion_tool/requirements.txt
@@ -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