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Commit f23025fa authored by Steffen Hauf's avatar Steffen Hauf
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docs/source/available_notebooks.rst
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...@@ -8,7 +8,7 @@ Offline Calibration tool chain. ...@@ -8,7 +8,7 @@ Offline Calibration tool chain.
LPD LPD
--- ----
Dark Images Evaluation Dark Images Evaluation
~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~
...@@ -19,67 +19,7 @@ dark images for one capacitor setting. ...@@ -19,67 +19,7 @@ dark images for one capacitor setting.
.. code:: .. code::
% python calibrate_nbc.py LPD dark --help % 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 Pulse Capacitor Evaluation
...@@ -92,49 +32,7 @@ It requires offset maps as input. ...@@ -92,49 +32,7 @@ It requires offset maps as input.
.. code:: .. code::
% python calibrate_nbc.py LPD PC --help % 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 Correction
~~~~~~~~~~ ~~~~~~~~~~
...@@ -144,61 +42,62 @@ Corrects an LPD run with calibration constants from the database and/or files. ...@@ -144,61 +42,62 @@ Corrects an LPD run with calibration constants from the database and/or files.
.. code:: .. code::
% python calibrate_nbc.py LPD correct --help % 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 ...]] AGIPD
[--mem-cells int] [--overwrite] [--no-relative-gain] -----
[--no-flat-fields] [--cluster-profile str]
[--max-pulses int] [--use-dir-creation-date] Dark Images Evaluation
[--max-cells-db int] [--rawversion int] ~~~~~~~~~~~~~~~~~~~~~~
[--instrument str] [--local-input] [--db-input]
[--bias-voltage int] [--cal-db-interface str] This notebook produces offset, noise and derived bad pixel data from AGIPD
[--geometry-file str] dark images.
[--beam-center-offset float [float ...]]
DETECTOR TYPE .. code::
Main entry point for offline calibration % python calibrate_nbc.py AGIPD dark --help
positional arguments:
DETECTOR The detector to calibrate
TYPE Type of calibration: LPD,AGIPD Pulse Capacitor Evaluation
~~~~~~~~~~~~~~~~~~~~~~~~~~
optional arguments:
-h, --help show this help message and exit This notebook produces per-pixel relative gain, normalizing all memory cells
--in-folder str the folder to read data from, required. Default: None for a given pixel w.r.t. the three gain stages.
--run int runs to process, required. Default: None
--out-folder str the folder to output to, required. Default: None .. code::
--relgain-store str path to base constant store. Default: /gpfs/exfel/exp/
FXE/201830/p900020/proc/calibration/CI5pf_pp/lpd_ci_st % python calibrate_nbc.py AGIPD PC --help
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 Flat Field Evaluation
30/p900020/proc/calibration/flat_field_ci_pp/lpd_flatf ~~~~~~~~~~~~~~~~~~~~~
ield_store_r0230.h5
--sequences str [str ...] This notebook produces flat field deduced correction constants, which are used
sequences to correct, set to -1 for all, range to normalize the pulse capacitor data.
allowed. Default: [-1]
--mem-cells int memory cells in data. Default: 512 .. code::
--overwrite set to True if existing data should be overwritten.
Default: False % python calibrate_nbc.py AGIPD FF --help
--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 Combine
Default: noDB ~~~~~~~
--max-pulses int Default: 128
--use-dir-creation-date This notebook combines inputs from the other characterization notebooks into
Default: False a consolidated, normalized set of correction constants.
--max-cells-db int Default: 128
--rawversion int Default: 2 .. code::
--instrument str Default: FXE
--local-input output constants locally. Default: True % python calibrate_nbc.py AGIPD combine --help
--db-input output constants to database. Default: True
--bias-voltage int detector bias voltage. Default: 500
--cal-db-interface str Correction
the database interface to use. Default: tcp://max- ~~~~~~~~~~
exfl014:5005
--geometry-file str the geometry file to use, MAR 2018. Default: Corrects an AGIPD run with calibration constants from the database and/or files.
/gpfs/exfel/d/cal/exchange/lpdMF_00.h5
--beam-center-offset float [float ...] .. code::
offset from the beam center, MAR 2018. Default: [1.5,
1] % python calibrate_nbc.py AGIPD correct --help
docs/source/how_it_works.rst
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...@@ -7,7 +7,9 @@ to expose Jupyter_ notebooks to a command line interface. ...@@ -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 Additionally, it leverages the DESY/XFEL Maxwell cluster to run these jobs in parallel
via SLURM_. 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 .. _nbparameterise: https://github.com/takluyver/nbparameterise
.. _nbconver: https://github.com/jupyter/nbconvert .. _nbconver: https://github.com/jupyter/nbconvert
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docs/source/workflow.rst
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.. _development_workflow:
Development Workflow Development Workflow
==================== ====================
...@@ -307,6 +309,12 @@ is generated at the end. ...@@ -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 Finally, you should verify that the report contains the information you'd like to convey and
is intelegable to people other than you. 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 .. _nbparameterise: https://github.com/takluyver/nbparameterise
.. _ipcluster: https://ipyparallel.readthedocs.io/en/latest/ .. _ipcluster: https://ipyparallel.readthedocs.io/en/latest/
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