Modified esis.data.Level_1.from_level_0() to flip the short axis of the CCD to match actual observations. (#51)

Author: jacobdparker

.github/workflows/docs.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Set Swap Space
         uses: pierotofy/set-swap-space@master
         with:
-          swap-size-gb: 32
+          swap-size-gb: 48
 
       - name: Checkout
         uses: actions/checkout@v4

docs/index.rst

@@ -51,7 +51,7 @@ Below is an example of one image captured during the 2019 flight.
     )
     ax.text(
         x=0.01,
-        y=0.98,
+        y=0.05,
         s=a.channel.ndarray,
         transform=ax.transAxes,
         ha="left",
@@ -60,7 +60,7 @@ Below is an example of one image captured during the 2019 flight.
     )
     ax.text(
         x=.99,
-        y=0.98,
+        y=0.05,
         s=a.inputs.time.ndarray,
         transform=ax.transAxes,
         ha="right",

docs/reports/level-1.ipynb

@@ -444,18 +444,22 @@
    ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "darks = electrons.darks.despiked",
    "id": "7b482a566ba8ae28",
+   "metadata": {},
+   "source": [
+    "darks = electrons.darks.despiked"
+   ],
    "outputs": [],
    "execution_count": null
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "dark = darks.mean(darks.axis_time)",
    "id": "1667176b2b7fa5e2",
+   "metadata": {},
+   "source": [
+    "dark = darks.mean(darks.axis_time)"
+   ],
    "outputs": [],
    "execution_count": null
   },
@@ -472,9 +476,7 @@
   {
    "cell_type": "code",
    "id": "e02eff69",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "source": [
     "fig, ax = na.plt.subplots(\n",
     "    axis_rows=axis_channel,\n",
@@ -574,12 +576,10 @@
   {
    "cell_type": "code",
    "id": "94c2f8c1",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "source": [
     "hist = na.histogram(\n",
-    "    residual.taps.outputs, \n",
+    "    residual.taps.outputs,\n",
     "    axis=axis_txy,\n",
     "    bins=dict(values=51),\n",
     "    min=-20 * u.electron,\n",
@@ -765,7 +765,12 @@
    "cell_type": "raw",
    "id": "9d4a66db",
    "metadata": {
-    "raw_mimetype": "text/restructuredtext"
+    "editable": true,
+    "raw_mimetype": "text/restructuredtext",
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
    },
    "source": [
     "Compute the `Pearson correlation coefficient <https://en.wikipedia.org/wiki/Pearson_correlation_coefficient>`_\n",
@@ -786,7 +791,13 @@
   {
    "cell_type": "code",
    "id": "51302e0b",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
    "source": [
     "scipy.stats.pearsonr(\n",
     "    x=where_spike.ndarray,\n",
@@ -801,18 +812,53 @@
    "cell_type": "raw",
    "id": "1cda4f3f",
    "metadata": {
-    "raw_mimetype": "text/restructuredtext"
+    "editable": true,
+    "raw_mimetype": "",
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
    },
    "source": [
     "As we can see, the spikes are slightly correlated with the image.\n",
     "This means that there are some small fraction of pixels wrongly identified as spikes."
    ]
   },
+  {
+   "cell_type": "raw",
+   "id": "88c64473-2a29-4e51-8fc7-f68f444fe19c",
+   "metadata": {
+    "editable": true,
+    "raw_mimetype": "text/x-rst",
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
+   "source": [
+    "To match oberservations, we need to undo an electronic flip of the image incident on the ESIS CCDs about the `detector_y` axis."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "id": "b05a4b3e849e0451",
+   "metadata": {},
+   "source": [
+    "flipped_outputs = despiked.outputs[dict(detector_y=slice(None, None, -1))]"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
   {
    "cell_type": "raw",
    "id": "5e090187",
    "metadata": {
-    "raw_mimetype": "text/restructuredtext"
+    "editable": true,
+    "raw_mimetype": "text/restructuredtext",
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
    },
    "source": [
     "The last thing to do is to convert the output to an instance of :class:`esis.data.Level_1`.\n",
@@ -826,7 +872,7 @@
    "source": [
     "level_1 = esis.data.Level_1(\n",
     "    inputs=despiked.inputs,\n",
-    "    outputs=despiked.outputs,\n",
+    "    outputs=flipped_outputs,\n",
     "    axis_time=axis_time,\n",
     "    axis_channel=axis_channel,\n",
     "    axis_x=axis_x,\n",
@@ -874,7 +920,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.1"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

esis/data/_level_1/_level_1.py

@@ -58,7 +58,7 @@ def from_level_0(
 
         return cls(
             inputs=a.inputs,
-            outputs=a.outputs,
+            outputs=a.outputs[dict(detector_y=slice(None, None, -1))],
             instrument=instrument,
             axis_time=a.axis_time,
             axis_channel=a.axis_channel,

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
     "ipython",
     "numpy",
     "matplotlib",
-    "astropy@git+https://github.com/astropy/astropy.git",
+    "astropy~=7.2",
     "joblib",
     "optika>=0.13.0",
     "msfc-ccd>=0.6.0",