formating

Author: skbarber

docs/image_analysis/examples/HTT_magspec_analysis_tests.ipynb

@@ -27,10 +27,10 @@
     "import numpy as np\n",
     "import pandas as pd\n",
     "\n",
+    "\n",
     "from image_analysis.offline_analyzers.magspec_manual_calib_analyzer import (\n",
     "    MagSpecManualCalibAnalyzer,\n",
     ")\n",
-    "from image_analysis.offline_analyzers.beam_analyzer import BeamAnalyzer\n",
     "\n",
     "logging.getLogger(\"image_analysis\").setLevel(logging.WARNING)\n",
     "logging.getLogger(\"geecs_data_utils\").setLevel(logging.WARNING)\n",
@@ -46,7 +46,7 @@
     "\n",
     "# calibrations are stored in the repo, provide their path\n",
     "img_analysis_dir = Path(os.getcwd()).parents[2] / \"ImageAnalysis\" / \"image_analysis\"\n",
-    "magspec_calibrations_dir = img_analysis_dir / 'data' / \"HTT-MagSpce-Calibrations\""
+    "magspec_calibrations_dir = img_analysis_dir / \"data\" / \"HTT-MagSpce-Calibrations\""
    ]
   },
   {
@@ -80,22 +80,27 @@
     "shot = 3\n",
     "\n",
     "sd = ScanData.from_date(\n",
-    "    year=2026, month=3, day=23, number=scan_number, experiment=\"Thomson\", append_paths=True\n",
+    "    year=2026,\n",
+    "    month=3,\n",
+    "    day=23,\n",
+    "    number=scan_number,\n",
+    "    experiment=\"Thomson\",\n",
+    "    append_paths=True,\n",
     ")\n",
     "\n",
     "bkg = ScanData.from_date(\n",
     "    year=2026, month=3, day=23, number=bkg_scan, experiment=\"Thomson\", append_paths=True\n",
     ")\n",
     "\n",
     "# this was looked up in the sfile. Note, this can be defined in the config file, but we\n",
-    "# explicitly set it here for the example \n",
-    "bfield = {'HTT-MagTeslameter-DTM141 Field':0.4265}\n",
+    "# explicitly set it here for the example\n",
+    "bfield = {\"HTT-MagTeslameter-DTM141 Field\": 0.4265}\n",
     "\n",
     "\n",
     "# setup for constrcuting magcam1 analyzer\n",
     "dev_name_1 = \"HTT-C23_1_MagSpec1\"\n",
     "config_name_1 = \"HTT-MagCam1\"\n",
-    "file_path_1 = sd.data_frame[f\"{dev_name_1}_expected_path\"][shot-1]\n",
+    "file_path_1 = sd.data_frame[f\"{dev_name_1}_expected_path\"][shot - 1]\n",
     "bkg_path_1 = bkg.data_frame[f\"{dev_name_1}_expected_path\"][3]\n",
     "\n",
     "analyzer_1 = MagSpecManualCalibAnalyzer(camera_config_name=config_name_1)\n",
@@ -104,17 +109,16 @@
     "new_bkg_1 = cfg.BackgroundConfig()\n",
     "new_bkg_1.method = \"from_file\"\n",
     "new_bkg_1.file_path = bkg_path_1\n",
-    "new_bkg_1.additional_constant=0.9\n",
+    "new_bkg_1.additional_constant = 0.9\n",
     "analyzer_1.update_config(background=new_bkg_1)\n",
     "\n",
-    "#construct the analyzer for magcam1\n",
-    "res_1 = analyzer_1.analyze_image_file(image_filepath=file_path_1, \n",
-    "                                      auxiliary_data=bfield)\n",
+    "# construct the analyzer for magcam1\n",
+    "res_1 = analyzer_1.analyze_image_file(image_filepath=file_path_1, auxiliary_data=bfield)\n",
     "\n",
     "# setup for constrcuting magcam2 analyzer\n",
     "dev_name_2 = \"HTT-C23_2_MagSpec2\"\n",
     "config_name_2 = \"HTT-MagCam2\"\n",
-    "file_path_2 = sd.data_frame[f\"{dev_name_2}_expected_path\"][shot-1]\n",
+    "file_path_2 = sd.data_frame[f\"{dev_name_2}_expected_path\"][shot - 1]\n",
     "bkg_path_2 = bkg.data_frame[f\"{dev_name_2}_expected_path\"][3]\n",
     "\n",
     "new_bkg_2 = cfg.BackgroundConfig()\n",
@@ -125,10 +129,9 @@
     "new_bkg_2 = cfg.BackgroundConfig()\n",
     "new_bkg_2.method = \"from_file\"\n",
     "new_bkg_2.file_path = bkg_path_2\n",
-    "new_bkg_2.additional_constant=1.7\n",
+    "new_bkg_2.additional_constant = 1.7\n",
     "analyzer_2.update_config(background=new_bkg_2)\n",
-    "res_2 = analyzer_2.analyze_image_file(image_filepath=file_path_2,\n",
-    "                                      auxiliary_data=bfield)"
+    "res_2 = analyzer_2.analyze_image_file(image_filepath=file_path_2, auxiliary_data=bfield)"
    ]
   },
   {
@@ -231,10 +234,11 @@
     }
    ],
    "source": [
-    "sn = str(scan_number).rjust(3,\"0\")\n",
-    "shot_str = str(shot).rjust(3,\"0\")\n",
-    "analyzed_data_path = (sd.paths.get_analysis_folder() / \n",
-    "                      f\"MgspcHtt/Scan{sn}_MgspcHttSpec_{shot_str}.txt\" )\n",
+    "sn = str(scan_number).rjust(3, \"0\")\n",
+    "shot_str = str(shot).rjust(3, \"0\")\n",
+    "analyzed_data_path = (\n",
+    "    sd.paths.get_analysis_folder() / f\"MgspcHtt/Scan{sn}_MgspcHttSpec_{shot_str}.txt\"\n",
+    ")\n",
     "df = pd.read_csv(analyzed_data_path, sep=\"\\t\")\n",
     "\n",
     "signal_calib_1 = np.sum(res_1.processed_image, axis=0) / 1000\n",
@@ -278,7 +282,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "from image_analysis.offline_analyzers.magspec_manual_calib_analyzer import (\n",
     "    DnnAxisCalibration,\n",
     ")\n",
@@ -350,9 +353,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python (geecs-plugins, poetry)",
    "language": "python",
-   "name": "python3"
+   "name": "geecs-plugins-py310"
   },
   "language_info": {
    "codemirror_mode": {
@@ -364,7 +367,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.18"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,