Quicklook viewer by MNBrod · Pull Request #2090 · pypeit/PypeIt

MNBrod · 2026-03-14T01:19:18Z

Adds a Quicklook GUI to PypeIt.

The changes are mostly isolated to /pypeit/display/ with a few exceptions:

pypeit/logger was changed to fix a bug where repeated invocations of pypeit's logger from the same process would not carry through a user's requested log file. This was a simple "move that block of code up a but" fix.

pypeit/scripts/ql.py was changed to accept manual extraction info as a command line argument, and pass that along appropriately.

pyproject.toml was changed to add the HTTP packages needed to handle a remote backend as optional dependencies (i.e. they are not installed by default).

The overall architecture of the plugin is described in the docstrings of qlview.py and at the bottom of the readthedocs page. Quick overview:

ui.py has all the widget stuff
state.py has a small struct-like class for keeping GUI state neat
file_browser.py has the logic for file sorting/display
slit_overlay.py draws slits over raw images and helps with clicking callbacks and the like. It's mostly stolen from show2dspec, but adapted to use Ginga slightly differently.
backend.py provides an "abstract" interface for talking to a filesystem and pypeit. There are currently two implementation, a local backend that passes through to whatever machine Ginga is running on, and an HTTP backend that allows PypeIt and the science files to be running on another machine on the network (which will be what Keck uses operationally, eventually). I have not tested the HTTP server much at all, that's on the to-do list.
servers has the HTTP server itself in it. This isn't really related to "display" per se, but there's no where else that it seemed to fit in PypeIt.
qlview.py has the meat of the plugin
display.py was updated to add this plugin. I went for Eric's show1dspec implementation approach

A readthedocs page has been started at pypeit/doc/quicklook_viewer.rst, I will be adding to it over the next few days (filling out sections and providing screenshots). This page was added to the end of the "Reference" section for now, it can be moved somewhere more fitting if someone has a better idea. I tried to be thorough with docstrings, many are Claude generated, but most are mine (Claude's are probably better...).

Items on my to-do list:

I am still making changes to this, but the core of the plugin is basically done and I can get feedback while adding more instruments/fixing minor stuff.

Finish the sphinx page
Thoroughly test each instrument. So far, I have only extensively used the GUI with longslit and multislit MOSFIRE data, and some DEIMOS. The code for HIRES, NIRES, LRIS R/B, and NIRSPEC is totally AI generated and I have not reviewed it.
Remove the Keck specific stuff. All I know about so far is using a "INSTRUME" FITS header to identify what instrument a file came from, that should be an easy enough fix
Figure out what tests look like for this. There are no pytest tests at the moment, nor am I sure what the right way to handle that is (especially for testing things like the HTTP server - I can write tests for that easily, but it shouldn't be part of the dev suite, right?)
Test the HTTP backend
Improve dithering support, right now it handles AB (in a clunky way) and can do a 2dcoadd of two science files, but you can't do more than 2, and it takes forever (fixing that is a bigger pypeit task, but there's some low hanging parallelization stuff there).
Better feedback on what's happening behind the scenes. Either a subwindow that lets you tail the log, or watching the log for more keywords and bodging a progress bar out of that.
I have some calibration scripts I can add to pypeit, they take the default ql.py and inst ql params and parallelizes it out from there (runs all setups at the same time, and all detectors/mosaics at the same time).

What Feedback I Need:

Generally, if people who are already familiar with PypeIt would be most helpful right now (so that I don't have to disentangle "I wish pypeit did ____" from "I wish the GUI did ____" myself) could play around with the GUI and report bugs/wanted features, that would be great. I would use a multislit dataset from DEIMOS for now - it has the highest density of slits (i.e. most places for it to go wrong) and also yields cleaner outputs than a single IR AB pair will. MOSFIRE is also a reasonable choice.

I have been using this GUI with Keck SAs and observers for a while, so the general shape of things seems OK at the moment.

There was a substantial refactor in February '26, so the commit history beyond that is a bit cluttered, apologies.

… fixes

…what's there

…endered in different coordinates

…nto quicklook_viewer pulling rebase back in

allow slitwavelength.py to display rms buffer if have

profxj

Thanks max!

I think my comments/requests are pretty bening
so holler if you think otherwise.

profxj · 2026-04-06T23:14:42Z

+#. The Plugin is launched on the right-hand side of the screen. Select your
+   instrument from the dropdown at the top.
+#. In the "Raw Data" table, navigate to where the raw science files are stored.
+#. In the "Reduced Calibrations" table, navigate to where the pre-processed


As we discussed, this needs some massaging. Or, I should say, the code doesn't work if the user chooses Calibrations directly.

profxj · 2026-04-06T23:15:15Z

+#. Pick your calibrations. If PypeIt was able to detect a matching configuration
+   amongst the calibrations in the directory you selected, it will pre-select it for
+   you. Then, press "Render Slits" to draw the slits on top of the raw image. Press
+   "Show Wavelengths" to display wavelength information on top of the raw image (as


This never enabled for me

profxj · 2026-04-06T23:15:41Z

+   you hover over the image, the wavelength will be shown in the lower left of the
+   screen).
+#. Select the slit you would like to process either by clicking directly on it,
+   or selecting it from the drop-down menu next to "Reduce Slit."


Comment on what one should see. I saw one orange trace. It then turned cyan

profxj · 2026-04-06T23:16:50Z

+    [DEFAULT]
+    redux_path = /data/redux
+    raw_path = /data/raw
+    reduced_path = /data/reduced


I realized (late in the game) to set this manually.

If that is the standard move, add that to the HOWTO steps above.

Related: should the path be exposed in the
"Reduction Control" section?

profxj · 2026-04-06T23:18:50Z

+==================
+
+[PIC HERE: Annotated screenshot labelling the four main UI sections:
+instrument selector, Raw Data frame, Reduced Calibrations frame, and


Can the fonts for each section be Bold or a different color or something to distinguish them as Section headings?

profxj · 2026-04-06T23:36:09Z

+class LRISBlue(Instrument):
+    """Keck LRIS Blue channel — multi-slit, 2-detector mosaic.
+
+    Untested!


not reviewed! :)

profxj · 2026-04-06T23:45:11Z

@@ -0,0 +1,2608 @@
+"""


I scanned through the entire module but didn't comment; largely because I'm not Ginga plug-in savvy

I will make one plea - in any try/except clause, try to make sure to log the failure in some depth. I'll also note my logging didn't seem to work (it generated 0kb file). But I'm rather sure that was user error

profxj · 2026-04-06T23:46:05Z

@@ -0,0 +1,303 @@
+from __future__ import annotations


comment on what this module is for

profxj · 2026-04-06T23:46:40Z

+        -------
+        None
+        """
+        top = Widgets.VBox()


Kindly sprinkle in a number of Inline comments
thanks!

profxj · 2026-04-06T23:49:49Z

    "scikit-learn>=1.2",
    "IPython>=8.0.0",
-    "ginga>=5.5.1",
+    "ginga==5.5.1",


is this the only ginga allowed?

MNBrod added 30 commits October 24, 2024 19:55

enable selected slit showing in blue

8cf0901

register plugin with ginga

dba1271

copy setup.cfg from naoj branch

c036af9

add spec1dview

a93a538

implement reduce_slit

76dabbf

try to use show1dspec in ginga

28bfc33

add ability to show slits from within the plugin

eeefc98

add options to hide file trees

2b243e9

quick fix to pass not having opt extraction

5790d35

update redux path to use widget

f15e189

shift text box location

3cf455c

fix vbox bug

311fa4d

fix show spec

e9e2f42

fix spec1d id bug

0af8303

fix order of spec1d invvocation

fd2e1c2

try this?

b83dc14

add SNR threshold as configurable

7afd416

who knows anymore

1dc5536

add log to spectra show

9cb31d6

add config file for defaults

48276a3

auto browse to default locations

6f83192

handle case where defaults are bad

d8f31bc

fix raw button calling reduced cals

5e39841

auto load defaults into treeview

e0e8e85

logging slit re-rendering

c513c11

more logging

106dd78

and more logging

d812f8f

filepath to str

fafa319

watch for files, too

6b808db

in print statements we trust

929087d

MNBrod added 23 commits March 13, 2026 09:36

revise state docs

3a071d1

revise qlview docs, add lots more details

8b73939

add tooltips

44fb62a

add pypeit script interface

1f09c94

refactor instruments to explicitly define all columns, no bases

2ce41c4

fix bug where compressed fits files were assigned the wrong icon

58fd50e

scale the slit drawing sampling dynamically to support small slits

eecca7e

remove stale development path from redux_path

c9cc7cf

clean up imports, add stricter regex to path checking, assorted small…

79f41dd

… fixes

add a skip to avoid needing to instantiate instruments just to check …

4a619ae

…what's there

catch missing requests when using remote backend

c6d0eee

Start of readthedocs page

a69d242

only enable DEIMOS and MOSFIRE for now

1b5f65d

check to see if mask design exists before it's accessed

7190e86

fix handling and reporting of threaded reduction exceptions

2d2c82e

fix stacking show callbacks

978e7a2

add logging to passed exceptions

3870ca9

various race condition fixes

62a7e3f

fix visual bug with mosaic detectors where slits and raw image were r…

75346cd

…endered in different coordinates

Propogate the fix to trace overlaying and manual extraction

f8f1b16

Merge branch 'develop' into quicklook_viewer

483ce1b

remove pre-refactor version of the plugin

397528e

move waveimg construction into dedicated file

ccf1369

profxj requested review from ejeschke and profxj March 19, 2026 23:10

tbowers7 added the enhancement label Mar 24, 2026

MNBrod added 3 commits March 25, 2026 10:21

Merge remote-tracking branch 'refs/remotes/origin/quicklook_viewer' i…

531892d

…nto quicklook_viewer pulling rebase back in

allow slitwavelength.py to display rms buffer if have

4652ae2

Merge pull request #2 from MNBrod/add_rms_to_slitwavelength

a6680fb

allow slitwavelength.py to display rms buffer if have

profxj requested changes Apr 6, 2026

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Quicklook viewer#2090

Quicklook viewer#2090
MNBrod wants to merge 104 commits intopypeit:developfrom
MNBrod:quicklook_viewer

MNBrod commented Mar 14, 2026 •

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MNBrod commented Mar 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Adds a Quicklook GUI to PypeIt.

Items on my to-do list:

What Feedback I Need:

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MNBrod commented Mar 14, 2026 •

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