From a324b12f9a3c26715b26ee1e76d1e9a47627cd06 Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Thu, 18 Mar 2021 12:25:04 +0100
Subject: [PATCH] Cleanup
---
...IPD_Retrieve_Constants_Precorrection.ipynb | 39 ++++++-------------
1 file changed, 12 insertions(+), 27 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
index f6b40e513..664f20837 100644
--- a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
+++ b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
@@ -51,7 +51,7 @@
"xray_gain = True # do relative gain correction based on xray data\n",
"blc_noise = False # if set, baseline correction via noise peak location is attempted\n",
"blc_stripes = False # if set, baseline corrected via stripes\n",
- "blc_hmatch = False # if set, base line correction via histogram matching is attempted \n",
+ "blc_hmatch = False # if set, base line correction via histogram matching is attempted\n",
"match_asics = False # if set, inner ASIC borders are matched to the same signal level\n",
"adjust_mg_baseline = False # adjust medium gain baseline to match highest high gain value"
]
@@ -205,14 +205,11 @@
"outputs": [],
"source": [
"def retrieve_constants(\n",
- " qm_files: List[Path],\n",
- " qm: str,\n",
- " karabo_da: str,\n",
- " idx: int\n",
+ " qm_files: List[Path], qm: str, karabo_da: str, idx: int\n",
") -> Tuple[str, str, float, float, str, dict]:\n",
" \"\"\"\n",
" Retrieve constants for a module.\n",
- " \n",
+ "\n",
" :return:\n",
" qm: module virtual name i.e. Q1M1.\n",
" karabo_da: karabo data aggregator.\n",
@@ -236,7 +233,7 @@
" if local_max_cells is None:\n",
" raise ValueError(f\"No raw images found for {qm} for all sequences\")\n",
"\n",
- " if acq_rate == 0: \n",
+ " if acq_rate == 0:\n",
" local_acq_rate = agipdlib.get_acq_rate(fast_paths=(f, karabo_id, idx))\n",
" else:\n",
" local_acq_rate = acq_rate\n",
@@ -244,7 +241,7 @@
" # avoid retrieving constant, if requested.\n",
" if nodb_with_dark:\n",
" return\n",
- " \n",
+ "\n",
" const_dict = agipdlib.assemble_constant_dict(\n",
" corr_bools,\n",
" pc_bools,\n",
@@ -359,13 +356,11 @@
"source": [
"mod_dev = dict()\n",
"mdata_dict = dict()\n",
- "for r in results:\n",
- " if r:\n",
- " qm, md_dict, karabo_da, acq_rate, max_cells, err = r\n",
- " mod_dev[karabo_da] = {\"mod\": qm, \"err\": err}\n",
- " if err:\n",
- " print(f\"Error for module {qm}: {err}\")\n",
- " mdata_dict[karabo_da] = md_dict\n",
+ "for qm, md_dict, karabo_da, acq_rate, max_cells, err in results:\n",
+ " mod_dev[karabo_da] = {\"mod\": qm, \"err\": err}\n",
+ " if err:\n",
+ " print(f\"Error for module {qm}: {err}\")\n",
+ " mdata_dict[karabo_da] = md_dict\n",
"# check if it is requested not to retrieve any constants from the database\n",
"if nodb_with_dark:\n",
" print(\"No constants were retrieved as calibrated files will be used.\")\n",
@@ -390,12 +385,11 @@
"metadata": {},
"outputs": [],
"source": [
- "print(\"Constants are retrieved with creation time: \")\n",
- "i = 0\n",
+ "print(\"Constants are retrieved with creation time:\")\n",
"timestamps = {}\n",
"\n",
"for k_da, dinfo in mod_dev.items():\n",
- " print(dinfo[\"mod\"], \":\")\n",
+ " print(f\"{dinfo['mod']}:\")\n",
" module_timestamps = {}\n",
" module_name = dinfo[\"mod\"]\n",
" if k_da in mdata_dict:\n",
@@ -403,8 +397,6 @@
" if hasattr(mdata[\"creation-time\"], 'strftime'):\n",
" mdata[\"creation-time\"] = mdata[\"creation-time\"].strftime('%y-%m-%d %H:%M')\n",
" print(f'{cname:.<12s}', mdata[\"creation-time\"])\n",
- " # Store few time stamps if exists\n",
- " # Add NA to keep array structure\n",
" for cname in ['Offset', 'SlopesPC', 'SlopesFF']:\n",
" if k_da not in mdata_dict or dinfo[\"err\"]:\n",
" module_timestamps[cname] = \"Err\"\n",
@@ -418,13 +410,6 @@
" module_timestamps[cname] = \"NA\"\n",
" timestamps[module_name] = module_timestamps\n",
"\n",
- " i += 1\n",
- " if sequences:\n",
- " seq_num = sequences[0]\n",
- " else:\n",
- " # if sequences[0] changed to None as it was -1\n",
- " seq_num = 0\n",
- "\n",
"time_summary = metadata.setdefault(\"retrieved-constants\", {}).setdefault(\"time-summary\", {})\n",
"time_summary[\"SAll\"] = timestamps\n",
"\n",
--
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