From 9b24117f6e1397fe2903f1179652f493c545bc16 Mon Sep 17 00:00:00 2001
From: karnem <mikhail.karnevskiy@desy.de>
Date: Tue, 16 Jul 2019 15:59:26 +0200
Subject: [PATCH] Small refactoring
---
cal_tools/cal_tools/tools.py | 2 +-
notebooks/LPD/LPDChar_Darks_NBC.ipynb | 14 ++++++++------
xfel_calibrate/calibrate.py | 13 ++++++++++---
3 files changed, 19 insertions(+), 10 deletions(-)
diff --git a/cal_tools/cal_tools/tools.py b/cal_tools/cal_tools/tools.py
index 8eb72105f..c82137238 100644
--- a/cal_tools/cal_tools/tools.py
+++ b/cal_tools/cal_tools/tools.py
@@ -54,7 +54,7 @@ def combine_report(run_path, calibration):
with open("{}/{}.rst".format(sphinx_path, group),
"a") as gfile:
if conc_param != "None":
- title = "{}. {} = {}".format(calibration, name_param,
+ title = "{}, {} = {}".format(calibration, name_param,
conc_param)
gfile.write(title + "\n")
gfile.write("=" * len(title) + "\n")
diff --git a/notebooks/LPD/LPDChar_Darks_NBC.ipynb b/notebooks/LPD/LPDChar_Darks_NBC.ipynb
index 360eebee4..00fcd83e1 100644
--- a/notebooks/LPD/LPDChar_Darks_NBC.ipynb
+++ b/notebooks/LPD/LPDChar_Darks_NBC.ipynb
@@ -6,7 +6,7 @@
"source": [
"# Offset, Noise and Dead Pixels Characterization #\n",
"\n",
- "Author: S. Hauf, Version: 0.1\n",
+ "Author: S. Hauf\n",
"\n",
"This notebook performs recharacterize of dark images to get offset, noise and bad-pixel maps. All 3 type of constants are evaluated per pixel and per memory cell.\n",
"\n",
@@ -14,13 +14,15 @@
"\n",
"Evaluated calibration constants are stored locally and injected in the calibration data base.\n",
"\n",
- "**Offset** ($O$) is defined as median ($M$) of dark signal ($Ds$) over trains ($t$) for a given pixel ($x,y$) and memory cell ($c$). **Noise** $N$ is a standard deviation $\\delta$ of dark signal.\n",
+ "**Offset** ($O$) is defined as median ($M$) of dark signal ($Ds$) over trains ($t$) for a given pixel ($x,y$) and memory cell ($c$). \n",
+ "\n",
+ "**Noise** $N$ is a standard deviation $\\delta$ of dark signal.\n",
"\n",
"$$ O_{x,y,c} = M(Ds)_{t} ,\\,\\,\\,\\,\\,\\, N_{x,y,c} = \\delta(Ds)_{t}$$\n",
"\n",
"**Bad-pixel** mask is evaluated bitweise.\n",
"\n",
- "** Bit: \"Offset_out_of_threshold\": **\n",
+ "**Bit: \"OFFSET_OUT_OF_THRESHOLD\":**\n",
"\n",
"Offset outside of bounds:\n",
"\n",
@@ -30,7 +32,7 @@
"\n",
"$$thresholds\\_offset\\_hard\\_low < O < thresholds\\_offset\\_hard\\_high $$\n",
"\n",
- "** Bit: \"Noise_out_of_threshold\": **\n",
+ "**Bit: \"NOISE_OUT_OF_THRESHOLD\":**\n",
"\n",
"Noise outside of bounds:\n",
"\n",
@@ -40,7 +42,7 @@
"\n",
"$$thresholds\\_noise\\_hard\\_low < N < thresholds\\_noise\\_hard\\_high $$\n",
"\n",
- "** Bit: \"\"OFFSET_NOISE_EVAL_ERROR\": **\n",
+ "**Bit: \"OFFSET_NOISE_EVAL_ERROR\":**\n",
"\n",
"Offset and Noise both not $nan$ values \n",
"\n",
@@ -1088,7 +1090,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Aggregate values, and per cell behaviour ##\n",
+ "## Aggregate values and per cell behaviour ##\n",
"\n",
"Following tables and plots give an overview of statistical aggregates for each constant, as well as per cell behavior, averaged across pixels."
]
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index c8d9d859e..d1353b09e 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -407,7 +407,8 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
parms = extract_parameters(nb)
params = parameter_values(parms, **args)
new_nb = replace_definitions(nb, params, execute=False)
- first_markdown_cell(new_nb).source = ''
+ if len(job_list) > 0 and not final_job:
+ first_markdown_cell(new_nb).source = ''
set_figure_format(new_nb, args["vector_figs"])
base_name = nbname.replace(".ipynb", "")
new_name = "{}__{}__{}.ipynb".format(
@@ -658,15 +659,21 @@ def run():
cmd = ('"from cal_tools.tools import finalize; ' +
'finalize({{joblist}}, $1, \'{run_path}\', \'{out_path}\', ' +
'\'{project}\', \'{calibration}\', \'{author}\', '
- '\'{version}\', \'{report_to}\')"')
+ '\'{version}\', \'{report_to}\', \'{in_folder}\' )"')
report_to = title.replace(" ", "")
if args["report_to"] is not None:
report_to = args["report_to"]
+ folder = ''
+ for p in parms:
+ if p.name == 'in_folder':
+ folder = p.value
+
fmtcmd = cmd.format(run_path=run_tmp_path, out_path=out_path,
project=title, calibration=title,
- author=author, version=version, report_to=report_to)
+ author=author, version=version,
+ report_to=report_to, in_folder=folder)
joblist = []
if concurrency.get("parameter", None) is None:
--
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