diff --git a/cal_tools/cal_tools/tools.py b/cal_tools/cal_tools/tools.py
index 904140d10f4d5a509690dae3f815f103c01a1cbc..2b1e99b10cd5629558b1fa17402449c492b5a887 100644
--- a/cal_tools/cal_tools/tools.py
+++ b/cal_tools/cal_tools/tools.py
@@ -8,7 +8,7 @@ from os.path import isfile, isdir, splitext
from queue import Queue
import re
import shutil
-from subprocess import Popen, PIPE, check_output
+from subprocess import Popen, PIPE, check_output, check_call
import textwrap
from time import sleep
import time
@@ -56,6 +56,50 @@ def combine_report(run_path, calibration):
shutil.copytree("{}/{}".format(run_path, entry), "{}/{}".format(sphinx_path, entry))
return sphinx_path
+
+def prepare_plots(run_path, threshold=1000000):
+ """
+ Convert svg file to pdf or png to be used for latex
+
+ Conversion of svg to vector graphics pdf is performed using svglib3.
+ This procedure is CPU consuming. In order to speed up process
+ large svg files are converted to png format.
+
+ The links in the rst files are adapted accordingly to the
+ converted image files.
+
+ :param run_path: Run path of the slurm job
+ :param threshold: Max svg file size (in bytes) to be converted to pdf
+ """
+ print('Convert svg to pdf and png')
+ run_path = os.path.abspath(run_path)
+
+ rst_files = glob.glob('{}/*rst'.format(run_path))
+ for rst_file in rst_files:
+ rst_file_name = os.path.basename(rst_file)
+ rst_file_name = os.path.splitext(rst_file_name)[0]
+
+ svg_files = glob.glob(
+ '{}/{}_files/*svg'.format(run_path, rst_file_name))
+ for f_path in svg_files:
+ f_name = os.path.basename(f_path)
+ f_name = os.path.splitext(f_name)[0]
+
+ if (os.stat(f_path)).st_size < threshold:
+ check_call(["svg2pdf", "{}".format(f_path)], shell=False)
+ new_ext = 'pdf'
+ else:
+ check_call(["convert", "{}".format(f_path),
+ "{}.png".format(f_name)], shell=False)
+ new_ext = 'png'
+
+ check_call(["sed",
+ "-i",
+ "s/{}.svg/{}.{}/g".format(f_name, f_name, new_ext),
+ rst_file],
+ shell=False)
+
+
def make_report(run_path, tmp_path, out_path, project, author, version, report_to):
run_path = os.path.abspath(run_path)
report_path, report_name = os.path.split(report_to)
@@ -166,6 +210,7 @@ def finalize(joblist, run_path, out_path, project, calibration, author, version,
if len(found_jobs) == 0:
break
sleep(10)
+ prepare_plots(run_path)
sphinx_path = combine_report(run_path, calibration)
make_report(sphinx_path, run_path, out_path, project, author, version, report_to)
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index 7703e461630363b5b856aecf15963e87b4a6a693..a56db134f1f74d4ee5bec8eaab7525f7b9d5eaeb 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -53,6 +53,9 @@ def make_initial_parser():
parser.add_argument('--priority', type=int, default=2,
help="Priority of batch jobs. If priority<=1, reserved nodes become available.")
+ parser.add_argument('--vector-figs', action="store_true", default=False,
+ help="Use vector graphics for figures in the report.")
+
parser.add_argument_group('required arguments')
return parser
@@ -112,12 +115,7 @@ def deconsolize_args(args):
def extract_title_author_version(nb):
""" Tries to extract title, author and versions from markdown """
- def find_first_markdown(nb):
- for cell in nb.cells:
- if cell.cell_type == 'markdown':
- return cell
-
- first_md = find_first_markdown(nb)
+ first_md = first_markdown_cell(nb)
source = first_md["source"]
title = re.findall(r'\#+\s*(.*)\s*\#+', source)
author = re.findall(
@@ -130,18 +128,31 @@ def extract_title_author_version(nb):
return title, author, version
+def get_cell_n(nb, cell_type, cell_n):
+ """
+ Return notebook cell with given number and given type
+
+ :param nb: jupyter notebook
+ :param cell_type: cell type, 'code' or 'markdown'
+ :param cell_n: cell number (count from 0)
+ :return: notebook cell
+ """
+ counter = 0
+ for cell in nb.cells:
+ if cell.cell_type == cell_type:
+ if counter == cell_n:
+ return cell
+ counter=+1
+
+
def first_code_cell(nb):
""" Return the first code cell of a notebook """
- for cell in nb.cells:
- if cell.cell_type == 'code':
- return cell
+ return get_cell_n(nb, 'code', 0)
def first_markdown_cell(nb):
""" Return the first markdown cell of a notebook """
- for cell in nb.cells:
- if cell.cell_type == 'markdown':
- return cell
+ return get_cell_n(nb, 'markdown', 0)
def make_epilog(nb, caltype=None):
@@ -359,6 +370,23 @@ def flatten_list(l):
return "_".join([str(flatten_list(v)) for v in l]) if isinstance(l, list) else l
+def set_figure_format(nb, enable_vector_format):
+ """
+ Set svg format in inline backend for figures
+
+ If parameter 'vector_figs' is set to True svg format will
+ be used for figures in the notebook rendering. Subsequently vector
+ graphics figures will be used for report.
+
+ :param nb: jupyter notebook
+ :param param: value of corresponding parameter
+ """
+
+ if enable_vector_format:
+ cell = get_cell_n(nb, 'code', 1)
+ cell.source += "\n%config InlineBackend.figure_formats = ['svg']\n"
+
+
def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
final_job=False, job_list=[], fmtcmd="", cluster_cores=8,
sequential=False, priority=2):
@@ -377,6 +405,7 @@ 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)
+ set_figure_format(new_nb, args["vector_figs"])
base_name = nbname.replace(".ipynb", "")
new_name = "{}__{}__{}.ipynb".format(
os.path.basename(base_name), cparm, suffix)