NSLS-II-CHX · genematx · Mar 28, 2025
diff --git a/AutoRun_functions/AutoRun_functions.py b/AutoRun_functions/AutoRun_functions.py
diff --git a/AutoRun_functions/__pycache__/AutoRun_functions.cpython-310.pyc b/AutoRun_functions/__pycache__/AutoRun_functions.cpython-310.pyc
diff --git a/AutoRun_functions/__pycache__/AutoRun_functions.cpython-311.pyc b/AutoRun_functions/__pycache__/AutoRun_functions.cpython-311.pyc
diff --git a/AutoRun_functions/__pycache__/AutoRun_functions_development.cpython-311.pyc b/AutoRun_functions/__pycache__/AutoRun_functions_development.cpython-311.pyc
diff --git a/AutoRun_functions/backup/AutoRun_functions_03112024.py b/AutoRun_functions/backup/AutoRun_functions_03112024.py
diff --git a/Auto_Analysis_Functions/Auto_Analysis_Functions.py b/Auto_Analysis_Functions/Auto_Analysis_Functions.py
diff --git a/Auto_Analysis_Functions/__pycache__/Auto_Analysis_Functions.cpython-311.pyc b/Auto_Analysis_Functions/__pycache__/Auto_Analysis_Functions.cpython-311.pyc
diff --git a/Data_Processing/WAXS/Pilatus800k_WAXS_analysis.ipynb b/Data_Processing/WAXS/Pilatus800k_WAXS_analysis.ipynb
diff --git a/Data_Processing/WAXS/SAXS_WAXS_Database.ipynb b/Data_Processing/WAXS/SAXS_WAXS_Database.ipynb
diff --git a/Data_Processing/WAXS/WAXS_Batch_Processing.ipynb b/Data_Processing/WAXS/WAXS_Batch_Processing.ipynb
diff --git a/Data_Processing/WAXS/WAXS_Geometry_Calibration.ipynb b/Data_Processing/WAXS/WAXS_Geometry_Calibration.ipynb
diff --git a/Data_Processing/WAXS/WAXS_ReProcessing_Export.ipynb b/Data_Processing/WAXS/WAXS_ReProcessing_Export.ipynb
diff --git a/Data_Processing/WAXS/WAXS_auto_processing.ipynb b/Data_Processing/WAXS/WAXS_auto_processing.ipynb
@@ -0,0 +1,163 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b84c70d5-022d-4a1e-ba89-f968de728eba",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Tiled version 0.1.0a120\n",
+      "/nsls2/conda/envs/2024-2.0-py311-tiled/lib/python3.11/site-packages/databroker/v1.py:72: UserWarning: In databroker 2.x, there are separate notions of 'server' and 'client', and register_handler(...) has no effect on the client. Likely this is being done for you on the server side, so you should not worry about this message unless you encounter trouble loading large array data.\n",
+      "  warnings.warn(\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32mrunning on: jupyter_hub   environment: standard\n",
+      "\u001b[0m\n",
+      "\u001b[36msetting '_base_path_' as /nsls2/data/chx/legacy/analysis/\u001b[0m\n",
+      "\u001b[36msetting '_mask_path_' as /nsls2/data/chx/shared/CHX_Setup/Detector_masks/\n",
+      "\u001b[0m\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Tiled version 0.1.0a120\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32mRe-imported pyCHX from /nsls2/data/chx/shared/CHX_Software/packages/pyCHX/\u001b[0m\n",
+      "\u001b[32mRe-imported chx_compress from /nsls2/data/chx/shared/CHX_Software/packages/pyCHX/chx_compress.py\u001b[0m\n",
+      "\u001b[35m\n",
+      "environment dependent settings and patches:\u001b[0m\n",
+      "using \"%matplotlib inline\" for plotting\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/nsls2/conda/envs/2024-2.0-py311-tiled/lib/python3.11/site-packages/databroker/v1.py:72: UserWarning: In databroker 2.x, there are separate notions of 'server' and 'client', and register_handler(...) has no effect on the client. Likely this is being done for you on the server side, so you should not worry about this message unless you encounter trouble loading large array data.\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pyCHX.chx_packages import *\n",
+    "plt.rcParams.update({'figure.max_open_warning': 0})\n",
+    "plt.rcParams.update({ 'image.origin': 'lower'   })\n",
+    "plt.rcParams.update({ 'image.interpolation': 'none'   })\n",
+    "import json\n",
+    "import sys\n",
+    "sys.path.insert(0, \"/nsls2/data/chx/shared/CHX_Software/packages/waxs_auto_processing/\")\n",
+    "from waxs_auto_processing import *\n",
+    "\n",
+    "\n",
+    "%run /nsls2/data/chx/shared/CHX_Software/packages/environment_management/chx_analysis_setup_test_pyCHX.ipynb"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "ede9e0e4-128f-466f-beaf-7f28d575a7a4",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "data_dir = '/nsls2/data/chx/legacy/analysis/2024_2/AutoRuns/lwiegart/' # folder with the json dict in\n",
+    "fn='waxs_uids.json'\n",
+    "waxs_uids_dict_file=data_dir+fn\n",
+    "\n",
+    "analyst = 'lwiegart'\n",
+    "calibration_uid = 149555 # WAXS detector position optimized for polypropylene sample (scan_id is likely to work, but provide uid if you can)\n",
+    "insert_dict={'template_name':'Pilatus800k_WAXS_analysis','analyst':analyst} # need the template name, IF 'analyst' is missing, we assume it's the same as 'user'\n",
+    "txt_filename = 'waxs_dataprocessing.txt' # will be saved in same directory as waxs_uids_dict_file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "5a199867-3711-436b-a7a1-66351118f68c",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Mon Aug  5 17:12:10 2024:   waiting for uids to be processed...\n"
+     ]
+    },
+    {
+     "ename": "KeyboardInterrupt",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mrun_waxs_papermill_loop\u001b[49m\u001b[43m(\u001b[49m\u001b[43mwaxs_uids_dict_file\u001b[49m\u001b[43m,\u001b[49m\u001b[43mcalibration_uid\u001b[49m\u001b[43m,\u001b[49m\u001b[43minsert_dict\u001b[49m\u001b[43m,\u001b[49m\u001b[43mtxt_filename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m_base_path_\u001b[49m\u001b[43m,\u001b[49m\u001b[43mempty_list_timeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m/nsls2/data/chx/shared/CHX_Software/packages/waxs_auto_processing/waxs_auto_processing.py:135\u001b[0m, in \u001b[0;36mrun_waxs_papermill_loop\u001b[0;34m(waxs_uids_dict_file, calibration_uid, insert_dict, txt_filename, _base_path_, empty_list_timeout, verbose)\u001b[0m\n\u001b[1;32m    133\u001b[0m     run_condition\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m    134\u001b[0m     \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mTIMEOUT: stopping to look for new uids.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m--> 135\u001b[0m time\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;241m10\u001b[39m)\n",
+      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+     ]
+    }
+   ],
+   "source": [
+    "run_waxs_papermill_loop(waxs_uids_dict_file,calibration_uid,insert_dict,txt_filename,_base_path_,empty_list_timeout=None,verbose=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9f067c36-faf0-4780-a07b-41349d29c9a1",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed28146b-d10d-4337-85ca-c2555319b55a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/Data_Processing/WAXS/WAXS_queue.ipynb b/Data_Processing/WAXS/WAXS_queue.ipynb