diff --git a/.gitignore b/.gitignore
index f0359b27ed236ac40fded5393ee7b091da3a9aed..2cfd63149241e0a8f1fbf0bd41a61ac369f25bfb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,3 +24,6 @@ Test
slurm_tmp*
./temp
*egg*
+docs/source/available_notebooks.rst
+docs/build
+
diff --git a/docs/source/available_notebooks.rst b/docs/source/available_notebooks.rst
deleted file mode 100644
index aa390841fdb3122337b998d74a741a1180584d27..0000000000000000000000000000000000000000
--- a/docs/source/available_notebooks.rst
+++ /dev/null
@@ -1,103 +0,0 @@
-.. _available_notebooks:
-
-Available Notebooks
-===================
-
-The following notebooks are currently integrated into the European XFEL
-Offline Calibration tool chain.
-
-
-LPD
-----
-
-Dark Images Evaluation
-~~~~~~~~~~~~~~~~~~~~~~
-
-This notebook produces offset, noise and derived bad pixel data from LPD
-dark images for one capacitor setting.
-
-.. code::
-
- % python calibrate.py LPD dark --help
-
-
-
-Pulse Capacitor Evaluation
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This notebook produces per-pixel relative gain, normalizing all memory cells
-for a given pixel w.r.t. the three gain stages for a given capacitor setting.
-It requires offset maps as input.
-
-.. code::
-
- % python calibrate.py LPD PC --help
-
-
-Correction
-~~~~~~~~~~
-
-Corrects an LPD run with calibration constants from the database and/or files.
-
-.. code::
-
- % python calibrate.py LPD correct --help
-
-
-AGIPD
------
-
-Dark Images Evaluation
-~~~~~~~~~~~~~~~~~~~~~~
-
-This notebook produces offset, noise and derived bad pixel data from AGIPD
-dark images.
-
-.. code::
-
- % python calibrate.py AGIPD dark --help
-
-
-
-Pulse Capacitor Evaluation
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This notebook produces per-pixel relative gain, normalizing all memory cells
-for a given pixel w.r.t. the three gain stages.
-
-.. code::
-
- % python calibrate.py AGIPD PC --help
-
-
-Flat Field Evaluation
-~~~~~~~~~~~~~~~~~~~~~
-
-This notebook produces flat field deduced correction constants, which are used
-to normalize the pulse capacitor data.
-
-.. code::
-
- % python calibrate.py AGIPD FF --help
-
-
-Combine
-~~~~~~~
-
-This notebook combines inputs from the other characterization notebooks into
-a consolidated, normalized set of correction constants.
-
-.. code::
-
- % python calibrate.py AGIPD combine --help
-
-
-Correction
-~~~~~~~~~~
-
-Corrects an AGIPD run with calibration constants from the database and/or files.
-
-.. code::
-
- % python calibrate.py AGIPD correct --help
-
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 64f9fe1f2a88b7b461bbbda48467ac00c954f216..31b968bf21f7f5a1202e531ac03f1582609b9328 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -346,3 +346,64 @@ texinfo_documents = [
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'https://docs.python.org/': None}
+
+# generate the list of available notebooks
+from xfel_calibrate import notebooks
+from subprocess import check_output
+from textwrap import dedent, indent
+from nbconvert import RSTExporter
+import os
+import nbformat
+rst_exporter = RSTExporter()
+with open("available_notebooks.rst", "w") as f:
+ f.write(dedent("""
+ .. _available_notebooks:
+
+ Available Notebooks
+ ===================
+
+ The following notebooks are currently integrated into the European XFEL
+ Offline Calibration tool chain.
+
+
+ """))
+
+ for detector in sorted(notebooks.notebooks.keys()):
+ values = notebooks.notebooks[detector]
+ f.write("{}\n".format(detector))
+ f.write("{}\n".format("-"*len(detector)))
+ f.write("\n")
+
+ for caltype in sorted(values.keys()):
+ data = values[caltype]
+
+ nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"]))
+ with open(nbpath, "r") as nf:
+ nb = nbformat.read(nf, as_version=4)
+ def first_markdown_cell(nb):
+ for cell in nb.cells:
+ if cell.cell_type == 'markdown':
+ return cell
+ mdcell = first_markdown_cell(nb)
+ nb.cells = [mdcell] # we only want this single cell
+ body, _ = rst_exporter.from_notebook_node(nb)
+ adjusted = []
+ # adjust titles
+ for line in body.split("\n"):
+ if line.startswith("=="):
+ line = line.replace("=", "+")
+ if line.startswith("--"):
+ line = line.replace("-", "~")
+ adjusted.append(line)
+ f.write("\n".join(adjusted))
+ f.write("\n")
+
+ f.write("To invoke this notebook and display help use:\n\n")
+ f.write(".. code-block:: bash\n\n")
+ f.write(" xfel-calibrate {} {} --help\n\n".format(detector, caltype))
+ f.write("The full parameter list of this notebook (with defaults is): \n\n")
+ f.write(".. code-block:: bash\n\n")
+ nb_help = ["xfel-calibrate", detector, caltype, "--help"]
+ output = check_output(nb_help).decode('utf8')
+ f.write(indent(output.replace("DETECTOR", detector).replace("TYPE", caltype), " "*4))
+ f.write("\n\n")
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index 4f9f3e6a6ca01ddd9c47eb740d912462f7b3a967..40c2e276c92af715870ce13d476c3b6c54a1d732 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -161,7 +161,8 @@ if len(sys.argv) == 3 and "-h" in sys.argv[2]:
# The information is extracted from the first markdown cell of
# the notebook.
for caltype, notebook in det_notebooks.items():
- with open(os.path.abspath(notebook["notebook"]), "r") as f:
+ nbpath = os.path.abspath("{}/../../{}".format(__file__, notebook["notebook"]))
+ with open(nbpath, "r") as f:
nb = nbformat.read(f, as_version=4)
msg += make_epilog(nb, caltype=caltype)
@@ -176,7 +177,7 @@ elif len(sys.argv) >= 3:
detector = sys.argv[1].upper()
caltype = sys.argv[2].upper()
try:
- notebook = os.path.abspath(notebooks[detector][caltype]["notebook"])
+ notebook = os.path.abspath("{}/../../{}".format(__file__, notebooks[detector][caltype]["notebook"]))
cvar = notebooks[detector][caltype].get("concurrency",
{"parameter": None,
"default concurrency": None,