Merge pull request #255 from larrybradley/fix-bkgsub

Fix background subtraction notebook
spacetelescope · Oct 31, 2024 · aa0a499 · aa0a499
2 parents e1a7136 + 60e16d5
commit aa0a499
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Showing 3 changed files with 28 additions and 20 deletions.
diff --git a/notebooks/NIRCam/psf_photometry/requirements.txt b/notebooks/NIRCam/psf_photometry/requirements.txt
@@ -2,7 +2,7 @@ numpy>=1.25.2
 pandas>=2.1.0
 jwst>=1.11.4
 astropy>=5.3.3
-photutils>=1.11.0
+photutils>=2.0.2
 ipywidgets>=8.1.1
 matplotlib>=3.7.2
 webbpsf>=1.2.1

diff --git a/...ks/cross_instrument/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb b/...ks/cross_instrument/background_estimation_imaging/Imaging_Sky_Background_Estimation.ipynb
@@ -63,7 +63,7 @@
     "from photutils.background import (Background2D,\n",
     "                                  BkgIDWInterpolator, BkgZoomInterpolator,\n",
     "                                  MedianBackground)\n",
-    "from photutils.datasets import make_gaussian_sources_image\n",
+    "from photutils.datasets import make_model_image\n",
     "from photutils.segmentation import detect_sources, make_2dgaussian_kernel\n",
     "from scipy.ndimage import median_filter"
    ]
@@ -413,7 +413,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "source_img = make_gaussian_sources_image(sky_bkgd.shape, sources)\n",
+    "model = models.Gaussian2D()\n",
+    "source_img = make_model_image(sky_bkgd.shape, model, sources, \n",
+    "                              x_name='x_mean', y_name='y_mean')\n",
     "scene = source_img + sky_bkgd"
    ]
   },
@@ -485,7 +487,8 @@
     "                   bkg_estimator=MedianBackground(),\n",
     "                   interpolator=BkgZoomInterpolator(order=3))\n",
     "plt.figure(figsize=(6, 6))\n",
-    "plt.imshow(bkg.background-noiseless_sky, vmin=0.1*zmin, vmax=0.1*zmax, origin='lower')"
+    "bkgimg = bkg.background\n",
+    "plt.imshow(bkgimg-noiseless_sky, vmin=0.1*zmin, vmax=0.1*zmax, origin='lower')"
    ]
   },
   {
@@ -525,9 +528,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mask_2sigma = make_source_mask(scene-bkg.background, nsigma=2, npixels=3,\n",
+    "mask_2sigma = make_source_mask(scene-bkgimg, nsigma=2, npixels=3,\n",
     "                               dilate_size=5, filter_fwhm=3)\n",
-    "mask_3sigma = make_source_mask(scene-bkg.background, nsigma=3, npixels=3,\n",
+    "mask_3sigma = make_source_mask(scene-bkgimg, nsigma=3, npixels=3,\n",
     "                               dilate_size=5, filter_fwhm=3)\n",
     "plot_two(mask_2sigma, mask_3sigma, 0, 1)"
    ]
@@ -551,7 +554,9 @@
     "                    sigma_clip=sigma_clip, bkg_estimator=bkg_estimator)\n",
     "bkg2 = Background2D(scene, (15, 15), filter_size=(3, 3), mask=mask_3sigma,\n",
     "                    sigma_clip=sigma_clip, bkg_estimator=bkg_estimator)\n",
-    "plot_two(bkg1.background-noiseless_sky, bkg2.background-noiseless_sky,\n",
+    "bkg1img = bkg1.background\n",
+    "bkg2img = bkg2.background\n",
+    "plot_two(bkg1img-noiseless_sky, bkg2img-noiseless_sky,\n",
     "         0.1*zmin, 0.1*zmax, titles=['bkg1', 'bkg2'])"
    ]
   },
@@ -862,7 +867,8 @@
    "outputs": [],
    "source": [
     "bkg3 = my_background(scene, box_size=10, filter_size=5, mask=mask)\n",
-    "plot_bkgd(scene, mask, bkg1.background, noiseless_sky, sources, zmin, zmax)"
+    "bkg3img = bkg3.background\n",
+    "plot_bkgd(scene, mask, bkg3img, noiseless_sky, sources, zmin, zmax)"
    ]
   },
   {
@@ -885,7 +891,8 @@
     "interpolator = BkgIDWInterpolator(n_neighbors=20, power=1, reg=30)\n",
     "bkg4 = my_background(scene, box_size=10, filter_size=5, mask=mask,\n",
     "                     interp=interpolator, exclude_percentile=90)\n",
-    "plot_bkgd(scene, mask, bkg4.background, noiseless_sky, sources, zmin, zmax)"
+    "bkg4img = bkg4.background\n",
+    "plot_bkgd(scene, mask, bkg4img, noiseless_sky, sources, zmin, zmax)"
    ]
   },
   {
@@ -902,10 +909,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sm = SourceMask(scene-bkg4.background, nsigma=1.5)\n",
+    "sm = SourceMask(scene-bkg4img, nsigma=1.5)\n",
     "mask = sm.multiple(filter_fwhm=[1, 3, 5],\n",
     "                   tophat_size=[4, 2, 1])\n",
-    "plot_mask(scene, bkg4.background, mask, zmin, zmax)\n",
+    "plot_mask(scene, bkg4img, mask, zmin, zmax)\n",
     "mask.sum()"
    ]
   },
@@ -926,7 +933,8 @@
     "interpolator = BkgIDWInterpolator(n_neighbors=20, power=0, reg=30)\n",
     "bkg5 = my_background(scene, box_size=6, filter_size=3, mask=mask,\n",
     "                     interp=interpolator, exclude_percentile=90)\n",
-    "plot_bkgd(scene, mask, bkg5.background, noiseless_sky, sources, zmin, zmax)"
+    "bkg5img = bkg5.background\n",
+    "plot_bkgd(scene, mask, bkg5img, noiseless_sky, sources, zmin, zmax)"
    ]
   },
   {
@@ -946,7 +954,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bkgd = bkg5.background\n",
+    "bkgd = bkg5img\n",
     "residual_image = bkgd-noiseless_sky\n",
     "\n",
     "# Create columns in the table for the background estimate, the residual,\n",
@@ -1196,11 +1204,11 @@
    "source": [
     "rms = Table()\n",
     "widths = rms['widths'] = np.arange(3, 30, 1)\n",
-    "rms['bkg1'] = calculate_stats(scene-bkg1.background, mask, widths)\n",
-    "rms['bkg2'] = calculate_stats(scene-bkg2.background, mask, widths)\n",
-    "rms['bkg3'] = calculate_stats(scene-bkg3.background, mask, widths)\n",
-    "rms['bkg4'] = calculate_stats(scene-bkg4.background, mask, widths)\n",
-    "rms['bkg5'] = calculate_stats(scene-bkg5.background, mask, widths)\n",
+    "rms['bkg1'] = calculate_stats(scene-bkg1img, mask, widths)\n",
+    "rms['bkg2'] = calculate_stats(scene-bkg2img, mask, widths)\n",
+    "rms['bkg3'] = calculate_stats(scene-bkg3img, mask, widths)\n",
+    "rms['bkg4'] = calculate_stats(scene-bkg4img, mask, widths)\n",
+    "rms['bkg5'] = calculate_stats(scene-bkg5img, mask, widths)\n",
     "rms['perfect'] = calculate_stats(sky_bkgd-noiseless_sky, mask, widths)"
    ]
   },
@@ -1252,7 +1260,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/cross_instrument/background_estimation_imaging/requirements.txt b/notebooks/cross_instrument/background_estimation_imaging/requirements.txt
@@ -2,6 +2,6 @@ numpy >= 2.0.0
 astropy >= 6.1.1
 matplotlib >= 3.9.1
 scipy >= 1.14.0
-photutils >= 1.13.0
+photutils >= 2.0.2
 scikit-image >= 0.21.0
 jdaviz >= 3.10.2