Hopefully no longer passing NaN pixels into libraries that don't like…

… such things.
spacetelescope · Jul 11, 2019 · 6b30b0b · 6b30b0b
1 parent 88ba9b3
commit 6b30b0b
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Showing 9 changed files with 428 additions and 535 deletions.
diff --git a/jwst_pancake/engine.py b/jwst_pancake/engine.py
@@ -329,7 +329,8 @@ def calculate_subtracted(raw_config, target=None, reference=None, ta_error=False
     for r in sgd_results:
         slope = r['2d']['detector']
         sgd_slopes.append(slope)
-        reg = register_to_target(slope, target_slope, rescale_reference=True)
+        mask = np.where(np.isnan(slope), 1., 0.)
+        reg = register_to_target(slope, target_slope, mask=mask, rescale_reference=True)
         sgd_reg.append(reg)
 
     sgd_reg = np.array(sgd_reg)

diff --git a/notebooks/covariance_contrast.ipynb b/notebooks/covariance_contrast.ipynb
diff --git a/notebooks/miri_pandeia_pancake.ipynb b/notebooks/miri_pandeia_pancake.ipynb
diff --git a/notebooks/miri_photon_noise_and_contrast.ipynb b/notebooks/miri_photon_noise_and_contrast.ipynb
@@ -649,7 +649,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/miri_small_grid_dither.ipynb b/notebooks/miri_small_grid_dither.ipynb
@@ -24,7 +24,9 @@
     "from pandeia.engine.perform_calculation import perform_calculation\n",
     "\n",
     "from copy import deepcopy\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "import time"
    ]
   },
   {
@@ -184,13 +186,14 @@
     "options.on_the_fly_PSFs = True\n",
     "otf_options = options.current_options\n",
     "\n",
-    "print(\"Calculating Target\")\n",
+    "print(\"Calculating Target at {}\".format(time.ctime()))\n",
     "otf_targ_results = pancake.engine.calculate_target(config)\n",
     "otf_sgd_results = []\n",
     "for i, s in enumerate(sgd_configs):\n",
-    "    print(\"Calculating SGD {} of {}\".format(i+1, len(sgd_configs)))\n",
+    "    print(\"Calculating SGD {} of {} at {}\".format(i+1, len(sgd_configs), time.ctime()))\n",
     "    otf_sgd_results.append(pancake.engine.calculate_reference(s))\n",
     "\n",
+    "print(\"Done SGD\")\n",
     "options.current_options = initial_options"
    ]
   },
@@ -280,9 +283,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (pancake p13 w08)",
+   "display_name": "Python (pancake)",
    "language": "python",
-   "name": "pancake_p13_w08"
+   "name": "pancake"
   },
   "language_info": {
    "codemirror_mode": {
@@ -294,7 +297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/nircam_pandeia_pancake.ipynb b/notebooks/nircam_pandeia_pancake.ipynb
@@ -419,20 +419,13 @@
    "source": [
     "In this case, the above figures show that pancake's ```calculate_subtracted``` convenience function manages to compensate for the PSF changes with target offset, whereas pandeia does not perform quite as well."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (pancake p13 w08)",
+   "display_name": "Python (pancake)",
    "language": "python",
-   "name": "pancake_p13_w08"
+   "name": "pancake"
   },
   "language_info": {
    "codemirror_mode": {
@@ -444,7 +437,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/nircam_photon_noise_and_contrast.ipynb b/notebooks/nircam_photon_noise_and_contrast.ipynb
diff --git a/notebooks/nircam_small_grid_dither.ipynb b/notebooks/nircam_small_grid_dither.ipynb
@@ -284,9 +284,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:test_pancake]",
+   "display_name": "Python (pancake)",
    "language": "python",
-   "name": "conda-env-test_pancake-py"
+   "name": "pancake"
   },
   "language_info": {
    "codemirror_mode": {
@@ -298,7 +298,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/stsci_pancake_installation.ipynb b/notebooks/stsci_pancake_installation.ipynb