the rest of that checkin

content/challenge1.md

@@ -1,46 +1,180 @@
 title: Analysis Challenge #1
 slug: challenge1
 
+Welcome to the first ngEHT analysis challenge. The primary objective
+of this first challenge is to set up a framework for the generation of
+synthetic ngEHT data based on theoretical source models, and to
+conduct the organized submission and cross-comparison of
+reconstruction results from multiple teams. This challenge includes
+two static total-intensity source models (SgrA* and M87), and a
+simulated observation using a hypothetical ngEHT array including the
+current EHT and 10 additional stations. Participants are requested to
+submit image reconstructions by June 30th to the ngEHT challenge
+website -- see below for details. Please note that unless otherwise
+specified, all source models and data products should be kept
+proprietary among those currently invited to participate in the
+challenge, which includes all EHT Collaboration members.
+
 ## Schedule
 
-- June 11?, 2021: Synthetic data available
-- June 30?, 2021: Submission deadline
+- June 11, 2021: Synthetic data available
+- June 30, 2021: Submission deadline
 
-## Communicating with the organizers
+## Related links
 
-The primary way to talk to the challenge organizers is the private
-analysis-challenge-1 channel on the ngEHT-2021 Slack.  If you need an
-invite to the Slack or to the channel, please contact Greg at glindahl
-ZAT cfa.harvard.edu.  We're also happy to help people with software
-installation advice.
+[ngEHT Winter meeting challenge files (previous work)](https://drive.google.com/drive/folders/10TrAZbQUzyYQzrK7Ruzt-XCR0T31bySe?usp=sharing)
 
-## Temporary Examples for the people writing content
+ngEHT Simulation group presentations:
+[12/8/2020](https://docs.google.com/presentation/d/1nv3mRWQrk-90J-OzqOQon7R5ZbMEi5OXnxy2p9cjWrk/edit#slide=id.gb228cefa57_7_0),
+[4/23/2021](https://docs.google.com/presentation/d/1fhsno3peFbO5tAXeuIVvdPpNSA_IyVYyCHqVn43Z7Hc/edit#slide=id.gd03baebd48_1_15),
+[6/4/2021](https://docs.google.com/presentation/d/1dsfEtEMKXrhUgC62tT5O1xG1iqWwrZc40X3-WRslykc/edit?pli=1#slide=id.p)
 
-Math can be rendered inline $e = mc^2$ or in its own (centered) block:
+## Source models
 
-$$e = mc^2$$
+### SGRA
 
-You might need to have a shell script:
+![Sgr A* model](../static/sgra_model_challenge1.png)
+Description: Semi-analytic stationary RIAF model for SgrA in the literature (see, e.g. Broderick & Loeb 2006). This model can be used to test the capabilities of next generation arrays in precision modeling of BH parameters. High resolution is needed to capture the unique signature from subring structure. This model does not capture any variability due to turbulence in the system.
 
-    :::bash
-    echo "this is a shell script!"
+Details: The basic model is a=0 (Schwarzschild) at an inclination of i=130 deg and all models include non-thermal particles. The model includes disk height (following Pu et al. 2018), sub-Keplerian flow properties (kappa=0.5, alpha=0.5) following the notation of Tiede et al. 2020 -- e.g. Eq. 10 and 11) and fitted to the observed data of Bower et al. 2015, 2019, Liu et al. 2016 and Zhao et al. 2003.
 
-or a python script:
+Citation: These images are generated for the ngEHT winter science meeting end-to-end simulation studies by Christian Fromm (cfromm@th.physik.uni-frankfurt.de). Please contact C.F. for use outside ngEHT challenge activities.
 
-    :::python
-    print('this is a python script!')
+Parameters:
 
+- GRRT at 230/345/690 GHz at 4096x4096 pixels
+- FOV 128M, d=8.178kpc and m=4.14M_sun (GRAVITY et al. 2019)
 
-## Download data
+### M87
 
-## Submit your results
+Yet to be written
+
+## Array and Data Synthesis
+
+### Station locations
+
+Two arrays were used to generate the synthetic data. They are labeled
+eht_2022 and ngeht_ref1. eht_2022 consists of the 11 stations expected
+to participate in the 2022 EHT observations. In ngeht_ref1, 10
+stations are added to this array. The station locations were chosen
+based on a uv-coverage analysis led by Alex Raymond, investigating
+which combination of sites from Raymond et al. (2021) provided optimal
+uv-coverage, folding in weather dropouts. The LMT, SPT, and KP were
+not included in the 345 GHz observations with eht_2022. The station
+locations are shown in the image below.
+
+![ngEHT ref1](../static/ngeht_ref1.png)
+
+### Data properties
+
+A 24-hour observing track was simulated for each array, source, and
+frequency. Each track consists of 10-minute scans interleaved with
+10-minute gaps. A single frequency channel with a time resolution of
+10 seconds is provided.
+
+Thermal noise expected from the receiver and enhanced by atmospheric
+opacity were added to the complex visibilities. The following
+assumptions were made for all sites:
+
+- Receiver temperature:
+- - 60 K for 230 GHz
+- - 100 K for 345 GHz
+- Aperture efficiency:
+- - 0.68 for 230 GHz
+- - 0.42 for 345 GHz
+- Bandwidth: 8 GHz
+- Quantization efficiency: 0.88
+- Dish diameter: 6 m for new sites, actual diameter for existing sites
+- Opacity: median values in April as extracted from the MERRA-2 data by Raymond et al. (2021), at 30 degrees elevation.
+
+Visibility phases were scrambled, but stabilized across scans. No further systematic errors were added, this will be done in future challenges.
+
+After data generation, data points with a signal-to-noise ratio less than 1 were flagged.
+
+### Summary table
+
+The table below summarizes the station locations and SEFDs resulting
+from the assumptions outlined above. For a more detailed breakdown,
+see [arrays/station_info.csv](../static/ngEHT_Analysis_Challenges/Challenge_1/arrays/station_info.csv)
+
+[jtable]
+Station, Code, X (m), Y (m), Z (m), SEFD_230 (Jy), SEFD_345 (Jy)
+IRAM-30m, PV, 5088968, -301682, 3825016, 809, 4456
+SMT, AZ, -1828796, -5054407, 3427865, 4973, 27410
+SMA, SM, -5464523, -2493147, 2150612, 1500, 5882
+LMT, LM, -768714, -5988542, 2063276, 357, 2710
+ALMA, AA, 2225061, -5440057, -2481681, 63, 231
+SPT, SP, 0, 0, -6359610, 3669, 11552, 
+APEX, AP, 2225040, -5441198, -2479303, 2609, 9261
+JCMT, JC, -5464585, -2493001, 2150654, 2105, 8259
+GLT, GL, 541647, -1388536, 6180829, 2417, 23326
+NOEMA, PB, 4523998, 468045, 4460310, 307, 3022
+KP, KP, -1994314, -5037909, 3357619, 3535, 34109
+BAJA, BA, -2352576, -4940331, 3271508, 11125, 53309
+BAR, BR, -2363000, -4445000, 3907000, 10905, 51219
+CNI, CI, 5311000, -1725000, 3075000, 11813, 74896
+CAT, CT, 1569000, -4559000, -4163000, 15321, 166684
+GAM, GB, 5627890, 1637767, -2512493, 6099, 285727
+GARS, GR, 1538000, -2462000, -5659000, 28480, 949659
+HAY, HA, 1521000, -4417000, 4327000, 1090, 144350
+NZ, NZ, -4540000, 719000, -4409000, 16932, 225001
+OVRO, OV, -2409598, -4478348, 3838607, 23788, 894355
+SGO, SG, 1832000, -5034000, -3455000, 10905, 50204
+[/jtable]
+
+# Submissions
+
+## Images
 
-Please zip up all of your results together
+Please submit your images as FITS files bundled in a zip file. The
+images can be reconstructed with any field of view or pixel
+resolution, as long as this is clear from the FITS header. We will be
+using eht-imaging to load and evaluate the images, so it may be worth
+checking if your image loads properly in eht-imaging.
 
-    :::bash
-    zip -a team_frownie_theme.zip *.
+## Non-imaging results
 
-And then fill out the following form to upload, picking the zip file you just made.
+If you have performed analysis other than imaging (e.g., fit a
+geometric model, measured the black hole mass or spin, or constrained
+plasma parameters), please provide a text file summarizing your method
+and results. These results will not be formally compared or analyzed,
+but could certainly provide us with valuable insights.
+
+## Evaluation
+
+It would be helpful but not required to add a txt file summarizing your experience with this challenge. Think of questions like
+
+- What imaging parameters did you find work best on these datasets?
+- How difficult was it to image ngeht_ref1 versus eht_2022, or 345 GHz versus 230 GHz?
+- Did the reconstruction quality and improvement of different arrays and frequencies meet your expectations?
+- Based on your experience with these datasets, do you think there should be more development of the reconstruction method you used?
+- What source models, data properties, or specific charges would you like to see in future challenges?
+- Do you have any feedback on the infrastructure and organization of the challenges?
+
+## Filename conventions
+
+For the zip files, use the format challenge1_[firstnamelastname].zip. 
+
+Example: challenge1_freekroelofs.zip
+
+For the FITS files, use the format challenge1_[source]_[array]_[frequency]_[method]_[firstnamelastname].fits
+
+- source: SGRA or M87
+- array: eht2022 or ngeht_ref1
+- frequency: 230 or 345
+- method: rml, clean, themage, or other
+
+Example: challenge1_SGRA_eht2022_230_rml_freekroelofs.fits
+
+For non-imaging results, use the format challenge1_[source]_[array]_[frequency]_nonimaging_[firstnamelastname].txt
+
+Example: challenge1_SGRA_eht2022_230_nonimaging_freekroelofs.txt
+
+For the evaluation, use the format challenge1_evaluation_[firstnamelastname].txt. 
+
+Example: challenge1_evaluation_freekroelofs.txt
+
+## Submit your results
 
 <form action="/upload" method="post" accept-charset="utf-8"
       enctype="multipart/form-data">
@@ -57,4 +191,14 @@ And then fill out the following form to upload, picking the zip file you just ma
 
 Our server has a 1 gigabit Internet connection, so uploads shouldn't
 take too long.  The challenge organizers get notified by Slack for
-every failed or successful upload, so we'll probably be in touch
+every failed or successful upload. If you see any problems, we're likely
+to reach out to contact you quickly.
+
+## Communicating with the organizers
+
+The primary way to talk to the challenge organizers is the private
+`analysis-challenge-1` channel on the ngEHT-2021 Slack.  If you need an
+invite to the Slack or to the channel, please contact Greg at glindahl
+ZAT cfa.harvard.edu.  We're also happy to help people with software
+installation advice.
+

content/credits.md

@@ -5,9 +5,7 @@ category: credits
 This analysis challenge is the work of a large community:
 
 - Freek Roelofs and Lindy Blackburn organized the overall challenge.
-- The rest of the committee includes Christian Fromm, Katie Bouman,
-Dom Pesce, Koushik Chatterjee, Daniel Palumbo, Greg Lindahl, Joseph Farah,
-Sandra Bustamante, and Razieh Emami Meibody.
+- The rest of the committee includes: Blackburn, Bouman, Bustamante, Chael, Chatterjee, Doeleman, Emami Meibody, Farah, Fitzpatrick, Fromm, Gomez, Johnson, Levis, Lindahl, Palumbo, Pesce, Gelles, Raymond, Roelofs (coord.), Tiede, Wielgus, Wong, Yoon
 - Thanks are due to Katie Bouman (now at Caltech) for the [previous EHT imaging challenge](http://vlbiimaging.csail.mit.edu/)
 ([also archived here](https://web.archive.org/web/20201205135432/http://vlbiimaging.csail.mit.edu/imagingchallenge)).
 Katie has more information about that previous challenge in

content/index.md

@@ -14,10 +14,7 @@ affect our ability to achieve our science goals.
 
 ## Schedule -- [Challenge 1]({filename}challenge1.md)
 
-- June 11?, 2021: Synthetic data available
-- June 30?, 2021: Submission deadline
-
-
-
+- June 11, 2021: Synthetic data available
+- June 30, 2021: Submission deadline
 
 ![ngEHT](../static/Semifinal_Logo_White_Symbol.jpeg)

pelicanconf.py

@@ -72,7 +72,8 @@
 PATH_METADATA = '(?P<slug>.+).rst'
 
 # pip install pelican-render-math puts this in the right place
-PLUGINS = ["render_math"]
+# ditto for pelican-just-table
+PLUGINS = ["render_math", 'pelican_just_table']
 
 # moved here because I'm not using "make publish"
 GOOGLE_ANALYTICS = "G-WEV8PT1PC9"

requirements.txt

@@ -1,2 +1,8 @@
 pelican[markdown]
 pelican-render-math
+
+#pelican-just-table
+# made a clone of https://github.com/Kristinita/just_table branch KiraPatchAllGenerators
+# which allows tables to be placed in "pages" and not just "articles"
+git+https://github.com/wumpus/just_table.git@KiraPatchAllGenerators
+