diff --git a/docs/source/available_notebooks.rst b/docs/source/available_notebooks.rst
index c2c883e17f7e3747d45c862452668b874b98f443..a984d547b8e62f6aa90c0ec475ac7182c46d9c83 100644
--- a/docs/source/available_notebooks.rst
+++ b/docs/source/available_notebooks.rst
@@ -8,7 +8,7 @@ Offline Calibration tool chain.
LPD
----
+----
Dark Images Evaluation
~~~~~~~~~~~~~~~~~~~~~~
@@ -19,67 +19,7 @@ dark images for one capacitor setting.
.. code::
% python calibrate_nbc.py LPD dark --help
- usage: calibrate_nbc.py [-h] [--cluster-profile str] --in-folder str
- --out-folder str [--sequences int [int ...]]
- --capacitor-setting int --run-high int --run-med int
- --run-low int [--mem-cells int] [--local-output]
- [--db-output] [--bias-voltage int]
- [--cal-db-interface str]
- [--thresholds-offset-sigma float]
- [--thresholds-offset-hard int [int ...]]
- [--thresholds-noise-sigma float]
- [--thresholds-noise-hard int [int ...]]
- [--skip-first-ntrains int] [--use-dir-creation-date]
- [--instrument str] [--ntrains int]
- [--high-res-badpix-3d]
- DETECTOR TYPE
-
- Main entry point for offline calibration
-
- positional arguments:
- DETECTOR The detector to calibrate
- TYPE Type of calibration: AGIPD,LPD
-
- optional arguments:
- -h, --help show this help message and exit
- --cluster-profile str
- The ipcluster profile to use. Default: noDB
- --in-folder str path to input data, required. Default: None
- --out-folder str path to output to, required. Default: None
- --sequences int [int ...]
- sequence files to evaluate.. Default: [0]
- --capacitor-setting int
- capacitor_setting for which data was taken, required.
- Default: None
- --run-high int run number in which high gain data was recorded,
- required. Default: None
- --run-med int run number in which medium gain data was recorded,
- required. Default: None
- --run-low int run number in which low gain data was recorded,
- required. Default: None
- --mem-cells int number of memory cells used. Default: 128
- --local-output output constants locally. Default: True
- --db-output output constants to database. Default: True
- --bias-voltage int detector bias voltage. Default: 500
- --cal-db-interface str
- the database interface to use. Default: tcp://max-
- exfl015:5005
- --thresholds-offset-sigma float
- Default: 3.0
- --thresholds-offset-hard int [int ...]
- Default: [400, 1500]
- --thresholds-noise-sigma float
- Default: 7.0
- --thresholds-noise-hard int [int ...]
- Default: [1, 35]
- --skip-first-ntrains int
- Default: 10
- --use-dir-creation-date
- use the creation date of the directory for database
- time derivation. Default: True
- --instrument str Default: FXE
- --ntrains int Default: 300
- --high-res-badpix-3d Default: False
+
Pulse Capacitor Evaluation
@@ -92,49 +32,7 @@ It requires offset maps as input.
.. code::
% python calibrate_nbc.py LPD PC --help
- usage: calibrate_nbc.py [-h] [--cluster-profile str] --in-folder str
- --out-folder str [--offset-store str]
- [--modules int [int ...]] --capacitor-setting int
- [--mem-cells int] [--local-output] [--db-output]
- [--db-input] [--bias-voltage int]
- [--cal-db-interface str] [--use-dir-creation-date]
- [--instrument str] [--high-res-badpix-3d]
- DETECTOR TYPE
-
- Main entry point for offline calibration
-
- positional arguments:
- DETECTOR The detector to calibrate
- TYPE Type of calibration: AGIPD,LPD
-
- optional arguments:
- -h, --help show this help message and exit
- --cluster-profile str
- The ipcluster profile to use. Default: noDB555
- --in-folder str path to input data, required. Default: None
- --out-folder str path to output to, required. Default: None
- --offset-store str path to offset store, overwrite use_db_input. Default:
- /gpfs/exfel/exp/FXE/201830/p900020/proc/calibration/da
- rk/lpd_offset_store_r0206_r0207_r0208_5pf.h5
- --modules int [int ...]
- Default: None
- --capacitor-setting int
- capacitor_setting for which data was taken, required.
- Default: None
- --mem-cells int number of memory cells used. Default: 128
- --local-output output constants locally. Default: True
- --db-output output constants to database. Default: False
- --db-input Default: True
- --bias-voltage int detector bias voltage. Default: 500
- --cal-db-interface str
- the database interface to use. Default: tcp://max-
- exfl015:5005
- --use-dir-creation-date
- use the creation date of the directory for database
- time derivation. Default: True
- --instrument str Default: FXE
- --high-res-badpix-3d Default: False
-
+
Correction
~~~~~~~~~~
@@ -144,61 +42,62 @@ Corrects an LPD run with calibration constants from the database and/or files.
.. code::
% python calibrate_nbc.py LPD correct --help
- usage: calibrate_nbc.py [-h] --in-folder str --run int --out-folder str
- [--relgain-store str] --offset-store str
- [--ff-store str] [--sequences str [str ...]]
- [--mem-cells int] [--overwrite] [--no-relative-gain]
- [--no-flat-fields] [--cluster-profile str]
- [--max-pulses int] [--use-dir-creation-date]
- [--max-cells-db int] [--rawversion int]
- [--instrument str] [--local-input] [--db-input]
- [--bias-voltage int] [--cal-db-interface str]
- [--geometry-file str]
- [--beam-center-offset float [float ...]]
- DETECTOR TYPE
-
- Main entry point for offline calibration
-
- positional arguments:
- DETECTOR The detector to calibrate
- TYPE Type of calibration: LPD,AGIPD
-
- optional arguments:
- -h, --help show this help message and exit
- --in-folder str the folder to read data from, required. Default: None
- --run int runs to process, required. Default: None
- --out-folder str the folder to output to, required. Default: None
- --relgain-store str path to base constant store. Default: /gpfs/exfel/exp/
- FXE/201830/p900020/proc/calibration/CI5pf_pp/lpd_ci_st
- ore_CHANID_16_5pf.h5
- --offset-store str path to offset constant store, required. Default: None
- --ff-store str path to flat fields. Default: /gpfs/exfel/exp/FXE/2018
- 30/p900020/proc/calibration/flat_field_ci_pp/lpd_flatf
- ield_store_r0230.h5
- --sequences str [str ...]
- sequences to correct, set to -1 for all, range
- allowed. Default: [-1]
- --mem-cells int memory cells in data. Default: 512
- --overwrite set to True if existing data should be overwritten.
- Default: False
- --no-relative-gain do not do relative gain correction. Default: False
- --no-flat-fields do not do flat field correction. Default: False
- --cluster-profile str
- Default: noDB
- --max-pulses int Default: 128
- --use-dir-creation-date
- Default: False
- --max-cells-db int Default: 128
- --rawversion int Default: 2
- --instrument str Default: FXE
- --local-input output constants locally. Default: True
- --db-input output constants to database. Default: True
- --bias-voltage int detector bias voltage. Default: 500
- --cal-db-interface str
- the database interface to use. Default: tcp://max-
- exfl014:5005
- --geometry-file str the geometry file to use, MAR 2018. Default:
- /gpfs/exfel/d/cal/exchange/lpdMF_00.h5
- --beam-center-offset float [float ...]
- offset from the beam center, MAR 2018. Default: [1.5,
- 1]
+
+
+AGIPD
+-----
+
+Dark Images Evaluation
+~~~~~~~~~~~~~~~~~~~~~~
+
+This notebook produces offset, noise and derived bad pixel data from AGIPD
+dark images.
+
+.. code::
+
+ % python calibrate_nbc.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_nbc.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_nbc.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_nbc.py AGIPD combine --help
+
+
+Correction
+~~~~~~~~~~
+
+Corrects an AGIPD run with calibration constants from the database and/or files.
+
+.. code::
+
+ % python calibrate_nbc.py AGIPD correct --help
+
diff --git a/docs/source/how_it_works.rst b/docs/source/how_it_works.rst
index 0b125cddfc2ecc20a6315e8108c5b6956bc31a6c..fe1f3640d3398244e7c8f8acba14d32adc0b749c 100644
--- a/docs/source/how_it_works.rst
+++ b/docs/source/how_it_works.rst
@@ -7,7 +7,9 @@ to expose Jupyter_ notebooks to a command line interface.
Additionally, it leverages the DESY/XFEL Maxwell cluster to run these jobs in parallel
via SLURM_.
-Here is a list of `Available Notebooks`_.
+Here is a list of :ref:`_available_notebooks`_.
+
+If you would like to integrate additional notebooks please see the :ref:`development_workflow`_.
.. _nbparameterise: https://github.com/takluyver/nbparameterise
.. _nbconver: https://github.com/jupyter/nbconvert
diff --git a/docs/source/workflow.rst b/docs/source/workflow.rst
index 07536255fd92a7786aebce7c7b5be1001d35c6a8..06957509973ff54e69793b37b101b65c5ecee03c 100644
--- a/docs/source/workflow.rst
+++ b/docs/source/workflow.rst
@@ -1,3 +1,5 @@
+.. _development_workflow:
+
Development Workflow
====================
@@ -307,6 +309,12 @@ is generated at the end.
Finally, you should verify that the report contains the information you'd like to convey and
is intelegable to people other than you.
+Documenting
+-----------
+
+Most documentation should be done in the notebook itself. However, please add new notebooks
+to the `available_notebooks.rst` file in the `docs` folder.
+
.. _nbparameterise: https://github.com/takluyver/nbparameterise
.. _ipcluster: https://ipyparallel.readthedocs.io/en/latest/