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='''TrkAna is now obsolete!''' =
As of 2024-10-14, TrkAna has now been replaced by [[EventNtuple]]. This page is just being kept for archival purposes.
== Overview ==
== Overview ==
TrkAna is a track-based ROOT TTree that can be used to help with analysis. Each entry in the TTree corresponds to a single fitted track and contains reconstructed information from the tracker, calorimeter and CRV. There is also the option to write out Monte Carlo truth information and additional information for other track types that might be important to an analysis.
'''Updated: 2024-06-21'''
 
TrkAna is an event-based ROOT TTree that can be used for analysis. Each entry in the TTree corresponds to a single Mu2e event and contains reconstructed information from the tracker, calorimeter and CRV. There is also the option to write out Monte Carlo truth information and hit-level information.


== How to Get Help ==
== How to Get Help ==
Feel free to send any questions to the [https://mu2e.slack.com/archives/C023EVADW2X #trkana Slack channel], or the 'Is It Me Or A Bug?' hypernews forum.
'''Updated: 2024-06-21'''
 
Feel free to send any questions to the [https://mu2e.slack.com/archives/C023EVADW2X #trkana] or #is_it_me_or_a_bug Slack channels


There is a tutorial hosted in the [https://github.com/Mu2e/TrkAna/blob/main/tutorial/README.md GitHub respository].
There is a tutorial hosted in the [https://github.com/Mu2e/TrkAna/blob/main/tutorial/README.md GitHub respository].
Line 9: Line 16:
== For Analyzers ==
== For Analyzers ==
=== How to Analyze a TrkAna Tree ===
=== How to Analyze a TrkAna Tree ===
Each of these contain TTrees that you can use ROOT or python
'''Updated: 2024-06-21'''


==== with ROOT ====
See the tutorials on GitHub here: https://github.com/Mu2e/TrkAna/blob/main/tutorial/README.md for exercises that analyze TrkAna trees with both ROOT and python
You can use the trkana tree like you would any other ROOT TTree: with the ROOT command line for data exploration, with ROOT macros to make plots etc.


==== with Python ====
=== How To Create a TrkAna Tree ===
*Note: the below is for the latest version of uproot4
'''Updated: 2024-06-21'''
 
The best way to open ROOT files in Python is to use the [https://uproot.readthedocs.io/en/latest/ uproot] package. It does not require a working installation of ROOT, so it allows to read a ROOT file on basically any platform that supports Python (e.g. [https://colab.research.google.com/ Colaboratory]). It also provides a more ''pythonic'' bridge between ROOT and Numpy/pandas.
 
In order to open a ROOT TTree with uproot it's sufficient to write:
 
<pre>
import uproot
trkananeg = uproot.open("trkana.root:TrkAnaNeg/trkana") # opens the 'trkana' tree in the 'TrkAnaNeg' folder
</pre>
 
Now, if we want to store, for example, the <code>deent</code> branch in the dataframe:


<code>
df = tree.arrays(filter_name=['deent*'],library="pd")
</code>
Once your data is stored in a pandas dataframe or in a numpy array you can plot it with the many plotting libraries available ([https://matplotlib.org matplotlib], [https://plot.ly/python/ plot.ly], etc.). This example shows how to plot an histogram with matplotlib:
<pre>
import uproot
import matplotlib.pyplot as plt
trkananeg = uproot.open("trkana.root:TrkAnaNeg/trkana")
df = trkananeg(filter_name=['deent*'],library="pd")
plt.hist(df["deent.mom"], bins=60, range=(95,110))
</pre>
A class that allows you to query the dataframe and plot manipulated variables can be found at https://github.com/soleti/mu2e_plotter.
=== How To Create a TrkAna Tree ===
You can use the TrkAna Musing like so:
You can use the TrkAna Musing like so:
<pre>
<pre>
setup mu2e
mu2einit
muse setup TrkAna
muse setup TrkAna
mu2e -c TrkAna/fcl/TrkAnaReco.fcl -s mcs.art --TFileName trkana.root
mu2e -c TrkAna/fcl/TrkAnaReco.fcl -s mcs.art --TFileName trkana.root
Line 56: Line 32:
where mcs.art contains the result of the Mu2e reconstruction.
where mcs.art contains the result of the Mu2e reconstruction.


In the trkana.root file, you will see two different TrkAna-related folders:
In the trkana.root file, you will find the TrkAna TTree in <pre>TrkAna/trkana</pre>.
* TrkAnaNeg contains the results of the negatively-charged tracks, and
* TrkAnaPos contains the results of the positively-charged tracks.


TrkAna is designed to be flexibile so if this does not produce the type of tree you want, then there are fcl parameters that can be changed. A few examples are available here: https://github.com/Mu2e/TrkAna/tree/main/fcl and are given in the table below in [[#TrkAna Fcl Examples]]. Also, you can always ask for help on the #trkana channel on Slack
TrkAna is designed to have some flexibility. There are fcl parameters that can be changed and there are a few examples available here: https://github.com/Mu2e/TrkAna/tree/main/fcl and are given in the table below in [[#TrkAna Fcl Examples]]. Also, you can always ask for help on the #trkana channel on Slack


== For Developers ==
== For Developers ==
If you will be contributing to the development of TrkAna, then you can fork TrkAna on GitHub and build it within [[Muse]] Like so:  
'''Updated: 2024-06-17'''
 
If you will be contributing to the development of TrkAna, then you should fork TrkAna on GitHub into your GitHub account, and then set up your development area like so:


Once you log in:
Once you log in:
<pre>
<pre>
setup mu2e
mu2einit
cd /your/working/directory
cd /your/working/directory
git clone git@github.com:<Your GitHub Username>/Offline.git (or muse backing Offline vXX_YY_ZZ)
muse backing HEAD
git clone git@github.com:<Your GitHub Username>/TrkAna.git
git clone git@github.com:<Your GitHub Username>/TrkAna.git
cd TrkAna
git remote -f add mu2e https://github.com/Mu2e/TrkAna # add the main Mu2e/TrkAna repository as a remote
git fetch mu2e main # grab the current HEAD of Mu2e/TrkAna
git checkout --no-track -b <name-of-your-dev-branch> mu2e/main # create a branch from the HEAD of Mu2e/TrkAna
muse setup
muse setup
muse build -j4 --mu2eCompactPrint
muse build -j4 --mu2eCompactPrint
</pre>
</pre>


Then you can make your developments and put in a pull request.
Then you can make your developments (git commit, git push etc.) and then put in a pull request on GitHub.


== Version History / TrkAna Musings ==
== Version History / TrkAna Musings ==
'''Updated: 2024-08-09'''


This is the list of TrkAna Musings. The top row corresponds to the "current" version.
This is the list of TrkAna Musings. The top row corresponds to the "current" version.
Line 89: Line 73:
! scope="col"| notes
! scope="col"| notes
|-
|-
| v05_02_00
| v05_05_00
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_05_00 v05_05_00]
| SimJob MDC2020ah --> Production v00_24_00, mu2e_trig_config v3_04_00 --> Offline v10_32_00
| al9-prof-e28-p057
|
|-
| v05_04_00
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_04_00 v05_04_00]
| SimJob MDC2020ag --> Production v00_23_00, mu2e_trig_config v3_03_00 --> Offline v10_31_00
| al9-e28-prof-p057
|
|-
| v05_03_00
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_03_00 v05_03_00]
| SimJob MDC2020af --> Production v00_22_00, mu2e_trig_config v3_02_00 --> Offline v10_30_00
| al9-e28-prof-p057
|
|-
| (not built)
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_02_00 v05_02_00]
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_02_00 v05_02_00]
| TBD
| N/A
| TBD
| N/A
| use with datasets that are from MDC2020ae and later
| use with datasets that are from MDC2020ae and later
| v05_01_00
|-
| (not built)
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_01_00 v05_01_00]
| [https://github.com/Mu2e/TrkAna/releases/tag/v05_01_00 v05_01_00]
| TBD
| N/A
| TBD
| N/A
| use with datasets earlier than MDC2020ae
| use with datasets earlier than MDC2020ae
|-
|-

Latest revision as of 16:35, 14 October 2024

TrkAna is now obsolete!

As of 2024-10-14, TrkAna has now been replaced by EventNtuple. This page is just being kept for archival purposes.

Overview

Updated: 2024-06-21

TrkAna is an event-based ROOT TTree that can be used for analysis. Each entry in the TTree corresponds to a single Mu2e event and contains reconstructed information from the tracker, calorimeter and CRV. There is also the option to write out Monte Carlo truth information and hit-level information.

How to Get Help

Updated: 2024-06-21

Feel free to send any questions to the #trkana or #is_it_me_or_a_bug Slack channels

There is a tutorial hosted in the GitHub respository.

For Analyzers

How to Analyze a TrkAna Tree

Updated: 2024-06-21

See the tutorials on GitHub here: https://github.com/Mu2e/TrkAna/blob/main/tutorial/README.md for exercises that analyze TrkAna trees with both ROOT and python

How To Create a TrkAna Tree

Updated: 2024-06-21

You can use the TrkAna Musing like so: 

mu2einit
muse setup TrkAna
mu2e -c TrkAna/fcl/TrkAnaReco.fcl -s mcs.art --TFileName trkana.root

where mcs.art contains the result of the Mu2e reconstruction.

In the trkana.root file, you will find the TrkAna TTree in 

TrkAna/trkana

.

TrkAna is designed to have some flexibility. There are fcl parameters that can be changed and there are a few examples available here: https://github.com/Mu2e/TrkAna/tree/main/fcl and are given in the table below in #TrkAna Fcl Examples. Also, you can always ask for help on the #trkana channel on Slack

For Developers

Updated: 2024-06-17

If you will be contributing to the development of TrkAna, then you should fork TrkAna on GitHub into your GitHub account, and then set up your development area like so:

Once you log in: 

mu2einit
cd /your/working/directory
muse backing HEAD
git clone git@github.com:<Your GitHub Username>/TrkAna.git

cd TrkAna
git remote -f add mu2e https://github.com/Mu2e/TrkAna # add the main Mu2e/TrkAna repository as a remote
git fetch mu2e main # grab the current HEAD of Mu2e/TrkAna
git checkout --no-track -b <name-of-your-dev-branch> mu2e/main # create a branch from the HEAD of Mu2e/TrkAna

muse setup
muse build -j4 --mu2eCompactPrint

Then you can make your developments (git commit, git push etc.) and then put in a pull request on GitHub.

Version History / TrkAna Musings

Updated: 2024-08-09

This is the list of TrkAna Musings. The top row corresponds to the "current" version.

TrkAna Musing TrkAna tag muse backings muse stub notes
v05_05_00 v05_05_00 SimJob MDC2020ah --> Production v00_24_00, mu2e_trig_config v3_04_00 --> Offline v10_32_00 al9-prof-e28-p057
v05_04_00 v05_04_00 SimJob MDC2020ag --> Production v00_23_00, mu2e_trig_config v3_03_00 --> Offline v10_31_00 al9-e28-prof-p057
v05_03_00 v05_03_00 SimJob MDC2020af --> Production v00_22_00, mu2e_trig_config v3_02_00 --> Offline v10_30_00 al9-e28-prof-p057
(not built) v05_02_00 N/A N/A use with datasets that are from MDC2020ae and later
(not built) v05_01_00 N/A N/A use with datasets earlier than MDC2020ae
v05_00_00 v05_00_00 SimJob MDC2020ac --> Production v00_19_00, mu2e_trig_config v1_1_0 --> Offline v10_28_00 sl7-prof-e28-p055 new major version
(not built) v04_04_00 N/A N/A final tag before v05 release
(not built) v04_03_00 N/A N/A for TutorialBacking test
v04_02_00 v04_02_00 SimJob MDC2020ab --> Offline v10_26_00 sl7-prof-e28-p051
v04_01_00 v04_01_00 SimJob MDC2020z1 --> Offline v10_23_02 sl7-prof-e28-p049 CRV branch filling moved from Offline to TrkAna
v04_00_00 v04_00_00 SimJob MDC2020z --> Offline v10_23_01 sl7-prof-e28-p049 breaking changes: demfit[] branch, new genealogy branches
(not built) v03_00_01 N/A N/A tag before major breaking change, just code tidying so no associated musing
v03_00_00 v03_00_00 SimJob MDC2020y --> Offline v10_22_01 sl7-prof-e20-p040 breaking changes: branch names now three characters; uses KinKal fits
v02_03_00 v02_03_00 SimJob MDC2020w --> Offline v10_21_00 sl7-prof-e20-p039
v02_02_00 v02_02_00 SimJob MDC2020v --> Offline v10_20_00 sl7-prof-e20-p035
v02_01_00 v02_01_00 SimJob MDC2020u --> Production v00_10_00 --> Offline v10_18_00 sl7-prof-e20-p033
v02_00_01 v02_00_01 SimJob MDC2020t --> Production v00_09_11 --> Offline v10_17_00 sl7-prof-e20-p026
(not built) v02_00_00 N/A N/A failed build due to incompatible KinKal version
v01_01_00 v01_01_00 SimJob MDC2020r --> Production v00_09_02 --> Offline v10_15_01 sl7-prof-e20-p023 adds TrkAnaUtils
(not built) v01_00_01 N/A N/A resolves MDC2020r incompatibility
v01_00_00a v01_00_00 Production v00_07_00 --> Offline v10_11_00 sl7-prof-e20-p021 updated for muse 1-path/2-path change
v01_00_00 v01_00_00 Production v00_06_00 --> Offline v10_10_01 sl7-prof-e20-p018 uses deprecated "muse link"

Tree Structure

The TrkAna tree structure is documented in google sheet (spreadsheet). There are separate sheets for different major version numbers. Links to the existing sheets are below. These are viewable by anyone; if you would like to comment or edit these sheets please send a message to the #TrkAna slack channel. Note that the sheets have multiple tabs, at the bottom of the page. The main tab lists the branches, while the other tabs list the detailed content (leafs) of the individual branches, by name.

Hit Level Information

By setting the diagLevel to 2 when running TrkAna, you will fill hit level information branches. If you are processing Monte Carlo information, hit level Monte Carlo truth branches will also be added. Adding these increases the size of the output file by an order of magnitude.

Future Developments

We're always looking for input from developers and analyzers to keep TrkAna up-to-date! Get in touch on the #trkana Slack channel, or with Andy Edmonds directly with any thoughts / comments you have

TrkAna Fcl Examples

fcl file module label candidate supplements notes
TrkAnaReco.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
CrvExpert.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus adds crvinfo, crvinfomc, crvsummary, crvsummarymc, and crvinfomcplane branches
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
TrkAnaReco_Upstream.fcl TrkAnaNeg upstream e-minus downstream e-minus, upstream mu-minus
TrkAnaPos upstream e-plus downstream e-plus, upstream mu-plus
TrkAnaReco_ceSimReco.fcl TrkAnaNeg downstream e-minus none for use with reco files generated with ceSimReco.fcl
fcl files below are flagged for updating / removal
TrkAnaRecoEnsemble-MC.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus for use with MDC2018 Ensemble datasets
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
TrkAnaRecoEnsemble-Data.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus for use with MDC2018 Ensemble datasets, no MC information
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
TrkAnaReco_wTrkQualFilter.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus an art filter module is run before creating the TrkAna tree
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
TrkAnaReco_MultipleTrkQual.fcl TrkAnaNeg downstream e-minus upstream e-minus, downstream mu-minus an additional TrkQual algorithm is used for each track
TrkAnaPos downstream e-plus upstream e-plus, downstream mu-plus
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