Pulsar Data Analysis with PSRCHIVE

Use the paper as a workflow map for PSRCHIVE core apps, RFI excision, calibration, TOA extraction, and what still sits outside PSRUI.

This page is a guided companion to the paper Pulsar data analysis with PSRCHIVE.

It does not reproduce the whole paper line by line. Instead, it turns the paper into a practical map for this docs site, so you can jump between the original PSRCHIVE workflow, the concepts behind it, and the subset that PSRUI currently exposes.

Quick entry points

Want the archive-to-TOA mental model first: Archive, DM, and TOA
Want the GUI mapping first: Processing Inspector
Want the command-family overview first: PSRCHIVE Overview
Want RFI and calibration concepts first: RFI and Calibration

Paper structure at a glance

The paper follows a fairly clear progression:

introduce PSRCHIVE as an archive-centric analysis suite
walk through the four core apps: psredit, psrstat, psrsh, and psrplot
use those tools for RFI excision and calibration
prepare a template profile, extract TOAs with pat, and evaluate them with tempo2
finish with more advanced topics such as pcm and psrpca

That makes it especially useful as a workflow paper, not just a command reference.

End-to-end workflow

archive + metadata
-> query / inspect / transform
-> RFI excision
-> calibration
-> template preparation
-> TOA extraction
-> tempo2 residual analysis
-> optional bias correction

For PSRUI users, the important takeaway is that the GUI currently lives mostly in the middle of this chain: preview, archive transforms, zapping, pat preview, and pac preview. The paper helps explain the larger CLI workflow around that middle layer.

Core applications: sections 2 to 5

`psredit`: query and modify metadata

The paper starts with psredit because archive metadata is part of the workflow, not an afterthought. Source name, receiver parameters, observing setup, and data type all influence what comes next.

Use this when you need to:

inspect archive attributes
batch-edit metadata
sort data into pulsar versus calibrator groups

The closest conceptual companion in this docs site is Interface and Data Flow, because PSRUI also treats metadata as part of session materialization rather than a separate export-only concern.

`psrstat`: compute derived quantities

The paper then uses psrstat to answer questions like "what is the S/N?" and "how does that change with channel or sub-integration?"

This is the bridge between raw inspection and decision-making:

quantify profile quality
evaluate expressions over archive data
drive plots or automated thresholds

That pairs naturally with Archive, DM, and TOA, where the physical meaning of those quantities matters more than the exact command syntax.

`psrsh`: apply transformations as scripts

psrsh is where PSRCHIVE stops being just a collection of standalone commands and starts looking like a composable processing language.

In practice, this is the layer that ties together:

zapping
scrunching and other transforms
pre-processing before plotting or statistics
reusable command scripts

This is also the best CLI analogue for PSRUI's non-destructive preview recipe. If you want the GUI equivalent, read Processing Inspector. If you want the command-level summary, read paz / pam.

`psrplot`: make the workflow visible

The paper uses psrplot not just for publication graphics, but as the main diagnostic surface for checking whether a processing choice helped or hurt.

That makes it a good companion to PSRUI's chart area:

phase versus frequency
Stokes views
quality checks before and after transforms

If you are using PSRUI as your first stop and the CLI as your second stop, this is usually the moment where the two views line up most clearly.

RFI excision: section 6

Section 6 is one of the most practical parts of the paper, because it separates several different RFI problems that are easy to blur together.

zap edge: remove known bad band edges
zap median: detect narrow-band interference
zap mow: detect impulsive interference
psrzap: interactively excise time-frequency regions

This maps well onto the surrounding docs:

concepts: RFI and Calibration
current GUI boundary: paz / pam
current GUI behavior: Processing Inspector

PSRUI today: the app currently exposes manual channel zapping in the waterfall view, but not the full family of automated zap median, zap mow, or psrzap workflows described in the paper.

Calibration: section 7

The calibration section is where the paper moves beyond "clean the archive" and into "model the instrument."

The sequence is roughly:

inspect calibrator behavior
derive flux-calibration assets with fluxcal
fix receiver metadata when needed
run first-order calibration with pac
measure cross-coupling with pcm
rerun pac using the MEM solution

This is the right section to read when you need to understand why pac alone is only part of the story.

Recommended jumps:

command summary: pat / pac
concept refresher: RFI and Calibration
broader observing context: Instrumentation for Pulsar Observations

PSRUI today: PSRUI can preview pac-style calibration using existing assets, but it does not yet replace the full calibrator-database and MEM-building workflow shown here.

Arrival time estimation: section 8

Section 8 connects profile preparation, template choice, pat, and tempo2 into a single chain.

The paper emphasizes a few ideas worth keeping together:

template quality matters
scalar and matrix template matching are different choices
calibration quality affects TOA quality
tempo2 is the evaluation stage after TOAs are produced