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Test 4.0.0#54

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r-pascua merged 201 commits intomasterHERA-Team/hera-validation:masterfrom test-4.0.0HERA-Team/hera-validation:test-4.0.0Copy head branch name to clipboardApr 1, 2021

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Commits on Jan 13, 2020

• Update project table

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• Fix project table script

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Commits on Jan 14, 2020

• git-bot: Update table

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Commits on Mar 20, 2020

• github token in home rather than repo

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• Merge branch 'project-table' of github.com:HERA-Team/hera-validation into project-table

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• Add step 4 structure and add_noise function

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• Add notebook scaffolding

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Commits on Mar 21, 2020

• Add a plot_array function to the test-4.0.0 notebook. Quite a bit of experimentation was done in the notebook; it currently houses an example of part of a function to eventually be incorporated int…

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Commits on Mar 27, 2020

• One big commit (oops). Updated add_noise function to automatically find key for autocorrelation (so noise can be added pre-inflation) and allow the user to specify a receiver temperature. Added som…

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• Cleaned up most of the mess that was left in the notebook from experimenting with things. More updates anticipated before ready for handoff.

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• Add error check in _parse_filename_for_cmp to handle when the component can't be inferred from the passed filename. Change docstring to a one-liner.

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Commits on Apr 1, 2020

• Write code for choosing which antennas to keep for simulation preparation.

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• Remove code from test notebook that was used to try to figure out how to perform the antenna matching/selection.

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• Merge branch 'test-4.0.0' of https://github.com/hera-team/hera-validation

  

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• Some formatting changes and comments added. Placeholder functions for adding systematics (gains, reflections, xtalk) written.

  

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Commits on Apr 3, 2020

• Put final touches on tools for making simulation data match observed data as best as possible. Update notebook to show that the resulting files are properly constructed and may be redundantly and a…

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• Merge remote changes and fix conflicts.

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Commits on Apr 4, 2020

• Update comments in sim_prep.add_noise and finish making most of the updates to the function. Note: the beam polynomial still needs to be updated to agree with the beam model used in the RIMEz sim.

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• Write function for adding bandpass gains to a simulation.

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• Write function for simulating cable reflections.

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• Edit some docstrings, start work on xtalk.

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Commits on Apr 6, 2020

• Move apply_gains function and finish writing add_xtalk function. Now need to debug/test.

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• Remove options for performing steps in-place or not and update docstrings.

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Commits on Apr 7, 2020

• Update add_noise function to use the beam model appropriate for the RIMEz simulation.

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• Make data directory in tools module; just for storing beam polynomial appropriate for the RIMEz simulation used. Finish debugging existing tools in sim_prep module. The module should be complete at…

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• Update a line to use np.argmax instead of what it originally did (it's equivalent, but this way is simpler).

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Commits on Apr 8, 2020

• Update file chunking routine. Update lst rephasing function. Make add_noise function somewhat more memory efficient.

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• Add logic for checking if sim files already exist before doing any calculations.

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• Add a message to be issued if chunked sim files exist and are not expected to be overwritten.

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• Update notebook to show: array selection process; chunked simulation files can be redundantly and absolutely calibrated; progression of systematic addition. Cell numbers will be out of order; only …

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• Remove .pyc files and update gitignore to not track these files. Let's hope it works.

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Commits on Apr 9, 2020

• Add comment clarifying the choice of which set of blt indices to use in downselect_antennas function.

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• Simplify logic for choosing autocorrelation in add_noise function as per Steven's solution.

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• Update downselect_antennas function to also update the flag and nsample arrays, so that they aren't messed up if the flag/nsample arrays are not trivial. Also add a comment explaining why the anten…

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• Update chunk_sim_and_save to use capture groups for extracting the jd major/minor components from the reference filename.

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• Simplify logic for choosing unique translations in _build_translations helper function according to Steven's suggestion.

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• Simplify calculation of number of overlapping antennas in _get_optimal_translation helper function according to Steven's suggestion.

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• Simplify arguments of calls to any() and all() wherever the argument is a generator.

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• Update chunk_sim_and_save function to make the filenames end with '.true.uvh5' instead of just '.uvh5'

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• Update notebook and re-run.

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Commits on Apr 11, 2020

• Fix function for checking whether simulation files have already been chunked and saved.

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• Update section detailing how the simulation files are prepared. There's also now code for generating plots for inspecting the visibilities pre/post LST rephasing, but it's all commented out. Some o…

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Commits on Apr 14, 2020

• Add support for seeding the RNG in add_xtalk (in case jitter is added to the crosstalk parameters).

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• Rename adjust_sim_to_data -> prepare_sim_files. Write apply_systematics function to serve as one-stop shop for adding all systematics.

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• Add support for making bandpass gains vary in time.

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• Add check in gain amplitude time variation step to ensure gains aren't changing too much; raise a warning if so.

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• Bit of refactoring; made a function for varying gain amplitudes in time, rather than having a routine written in the add_gains function.

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Commits on Apr 15, 2020

• Flesh out function for adding time variation to gains. Start writing argparsers for file chunking and sim corruption scripts.

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Commits on Apr 16, 2020

• Larger commit than is responsible. Updated docstrings to remove unnecessary whitespace. Fleshed out systematics argparser a bit more, but it's still not done; still on the fence about the best way …

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• Add functionality for writing systematics simulation configuration to disk. Update logic in prepare_sim_files to correctly check whether any new files will be written and skip task if no new files …

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• Write argparser for simulation preparation.

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• Import yaml in sim_prep module.

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• Add option to argparser to skip writing the true visibilities to disk if desired.

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• Write script for running simulation file preparation from the command line.

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Commits on Apr 18, 2020

• Change relative import of sim_prep in prepare_sim_files to absolute import. Let's see if it works...

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• Bugfix

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• Bugfix? Let's see if the problem is actually fixed.

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• Forgot to import argparse before... now it gets imported.

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• Accidentally changed data import from absolute to relative, so I changed it back. (It seems to throw a fit if I do a relative import for some reason; something about not knowing what the parent pac…

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• Hopefully fixed now?

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Commits on Apr 19, 2020

• Make prepare_sim_files function not track individual systematics to save memory.

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• Add functionality for choosing whether to return the systematic being simulated in each add_ function.

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• Fix a bad indent.

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Commits on Apr 20, 2020

• Bugfix.

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• Add verbose option.

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Commits on Apr 22, 2020

• Add functionality for performing simulation file preparation in chunks using the CLI.

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Commits on Apr 23, 2020

• Copy data preparation batch script into git repo.

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• Fix a line to update a change in script name in the batch script.

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• Make script use verbose setting.

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• Update prepare_sim_files script pre-processing to actually update the time variation parameters (for gains) correctly in cases where they need updating.

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• Make reference UVData object downselect to times that had a match in rephase_to_reference function. (Apparently there were cases where one time from the reference wouldn't have a time from the simu…

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• Comment out something put in last commit that allowed us to get away with a time getting missed in the LST rephasing step. It's better to figure out why a time is getting missed in the first place,…

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• Make chunk_sim_and_save a little more flexible. Make argparser for abscal model preparation script.

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• Write script for preparing abscal model. *Does not contain delay filtering step.*

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• Remove unused imports from abscal model preparation script.

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• Rename prepare_abscal_model -> prepare_abscal_model_files.

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• Write batch script for preparing (pre-filtered) abscal model files.

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• Forgot to import UVData from pyuvdata in the abscal file prep script. It's imported now.

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Commits on Apr 24, 2020

• Bugfix; there was a typo where I accidentally used the same variable twice, when I shouldn't have done so.

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• Add verbose option to abscal file prep argparser/script.

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• Make abscal model file preparation batch script make model files for all LSTs, with 60 integrations per file, but prepare files in chunks of 6 hours LST each.

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Commits on Apr 25, 2020

• Modify abscal file prep batch script to do a test for a small LST range. Update downselect_antennas function in sim_prep to (hopefully) be more robust.

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• Update chunk_sim_and_save function to format JD correctly in filename (to ensure the [0-9]{7}.[0-9]{5} regex can be used to find the files).

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• Update abscal model file prep batch script to do all LSTs, processed in chunks of 6 hours each.

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Commits on Apr 26, 2020

• Update abscal preparation script to allow specifying number of chunks to use for performing file preparation.

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• Missed a parenthesis. It's there now.

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• Another bugfix.

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Commits on Apr 27, 2020

• Update some logic for running file preparation in chunks in preparation scripts.

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• Remove a stray 'done' in abscal model preparation batch script.

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• Fix silent bug in chunk_sim_and_save.

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Commits on Apr 28, 2020

• Update rephase_to_reference function.

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• Bugfix in prepare_sim_files function.

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• Fix add_noise to work with wrapped LSTs.

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Commits on Apr 29, 2020

• Bugfix regarding return value for add_noise function.

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• Some bugfixes and some code simplification.

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• Simplify logic for extracting time variation parameters in prepare_sim_files script.

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• Make sure the baseline_array is updated in the antenna downselection step. (It wasn't before, and this ended up causing errors down the line.)

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Commits on Apr 30, 2020

• Fix a silent bug in add_xtalk (was assigning xtalk to data rather than adding in the case ret_cmp == False). Add code to delete temporary data products that are recreated each iteration in a for-lo…

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• Nick added an argparser for the abscal smoothing script.

  

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• Nick wrote a script for smoothing the abscal solutions.

  

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• Merge branch 'test-4.0.0' of https://github.com/hera-team/hera-validation into test-4.0.0

  

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• Update downselect_antennas function to do a better job of updating simulation metadata.

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• Aesthetic changes to prepare_data batch script.

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• Add functionality for specifying LST cuts for file preparation.

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• Update default setting for lst_min and lst_max (was 1-11 before, now it's all LSTs).

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• Import units from astropy in sim_prep module.

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• Apply the LST cut to the obsfile glob rather than the loaded in UVData object to ensure that writing to disk does not break when using obsfiles as a reference for file writing.

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• Forgot to remove lst_min and lst_max from call to adjust_sim_to_data in prepare_sim_files function after the changes made in the last commit. Should be fixed now.

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Commits on May 1, 2020

• Remove application of LST cuts from prepare_sim_files function and move it to the related script instead. Change default lst_min and lst_max parameters to not apply an LST cut when using default se…

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• Update _apply_lst_cut function to have a fast and slow implementation, depending on whether the LST sampling is uniform across files (whether or not this is true is specified by the user).

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• Add argparser option for specifying whether reference files uniformly sample in LST.

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• Update prepare_sim_files script in accordance with last commit. Add a clause so that LST cuts are only applied when they would actually reduce the range of LSTs spanned.

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• Update data preparation batch script in accordance with previous commits.

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• Fix logic in determining whether to apply an LST cut (and -> or).

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• Slight modification to _apply_lst_cut function to ensure that *all* integrations of the files that remain after the cut are within the LST bounds. (The previous version only ensured that the beginn…

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• Update configuration handling to ensure that noise realizations are unique for each chunk when data is processed in chunks.

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• Bugfix.

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• Import UVData in prepare_sim_files script.

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• Explicitly ensure that the time variation parameters determined in prepare_sim_files script are python floats, rather than numpy floats (not 100% sure this will fix the problem, but it's probably g…

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Commits on May 2, 2020

• Make the systematics application step of data preparation more verbose.

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• Change abscal model prep to only do LST 0-12, and process in chunks of 6 hours.

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• Make tolerance for smoothing abscal model files smaller.

  

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• Merge branch 'test-4.0.0' of https://github.com/hera-team/hera-validation into test-4.0.0

  

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• Change number of chunks in abscal file prep from 2 to 4.

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• Merge branch 'test-4.0.0' of https://github.com/hera-team/hera-validation into test-4.0.0

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Commits on May 4, 2020

• Updated notebook, not super clean yet.

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• Make some verbose statements even more verbose.

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Commits on May 5, 2020

• Add documentation to apply_systematics function in sim_prep. Change default setting to *not* return dict of systematics (this is the safer option, since returning the dict has a higher potential of…

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• Remove some redundant code and explicitly set in the call to in in the case that the user wants systematics returned.

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• Change job name in abscal model file prep batch script. Regarding previous commit, the blank spaces in the message are because I didn't know that using backticks causes git to call the bash shell a…

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• Slight modification to notebook; now shows true visibility plot, corrupted visibility plot with systematics addition done in the notebook, and corrupted visibility plot from the pipeline output.

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Commits on May 6, 2020

• Slightly nicer writing

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• Slightly nicer add noise function

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• Extra verbosity

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• Fix slice reference

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Commits on May 7, 2020

• Make add_noise have same outputs as other functions

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• More direct add_noise functio

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• Fix ref to Simulator

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• Fix last ref to sim.data.

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• Fix typo in pol

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• Fix bug in indexing

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• Fix import

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• Fix indexing

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Commits on May 9, 2020

• Remove old verbose statements that were commented out.

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• Make sure that the abscal files are conjugated properly.

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Commits on May 10, 2020

• Make smooth_abscal_model pbs script update read permissions for correct set of files.

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Commits on May 11, 2020

• Make sure that every file has the correct number of integrations (with the exception of the last file).

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• Get the file chunking parameters right.

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Commits on May 12, 2020

• Bugfix in vary_gains_in_time.

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• Make sure that autos remain real-valued after addition of noise. Also ensure that receiver temperature makes it into the autos.

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• Update to make sure abscal model files have noise added.

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• Remove .pyc file from repo.

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• Change upper LST cut to 7 hours (to avoid problem with missing foregrounds at around 8 hours LST).

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Commits on May 14, 2020

• Add function for interpolating to reference (rather than rephasing). Also fix a bug in vary_gains_in_time.

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• Update rephase_to_reference to handle cases where the reference LST range exceeds the simulation LST range. Also have it raise a warning if there is a discontinuity in the rephasing amount.

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• Make adjust_sim_to_data use interpolate_to_reference rather than rephase_to_reference.

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• Fix interpolate_to_reference.

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• Bugfix in interpolate_to_reference.

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• Make sure that simulation Ntimes and Nfreqs parameters get updated in interpolate_to_reference function.

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• Fix abscal_model_argparser to accept Trx as an optional parameter. Also fix interpolate_to_reference to use the correct number of times in the case that the reference visibilities span a larger ran…

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• Bugfix in preparing abscal model files when adding noise.

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• Modify prepare_data batch script to run foregrounds-only file prep for 10 days of data.

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Commits on May 16, 2020

• Update data preparation script to use summed visibility file rather than foreground-only file.

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• Update job name.

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Commits on May 19, 2020

• Adjust data preparation script to just do JD 2458108.

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Commits on May 20, 2020

• Removed some cells from the notebook that were no longer needed. Reran notebook.

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Commits on May 21, 2020

• Merge branch 'master' into test-4.0.0

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• Add captions to figures.

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• Merge branch 'test-4.0.0' of https://github.com/hera-team/hera-validation into test-4.0.0

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• Update some of the text in the notebook to reflect changes to the file preparation pipeline.

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Commits on Jun 2, 2020

• Update prepare_sim_files script to properly handle passing no systematics parameters.

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• Update data preparation batch script to chunk EoR-only files for half an hour's worth of data.

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Commits on Jun 4, 2020

• Update data preparation to run an hour of LST for each day for only the true sum files, and also to *not* update the antenna positions (but rather keep the simulation antenna positions).

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• Use 1d interpolation rather than bivariate.

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• Adjust data preparation script for re-running file preparation.

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• Actually import interp1d from scipy.interpolate

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Commits on Jun 5, 2020

• Bugfix in interpolate_to_reference

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• Change where to write output for file prep

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Commits on Jun 9, 2020

• Update downselect_antennas to update antenna positions appropriately (use the simulation antenna positions, but shifted to produce the maximal overlap).

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Commits on Jun 25, 2020

• Update data preparation script to make one day of chunked EoR files.

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• Update analytic power spectrum calculation to match EoR rescaling used in this test.

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Commits on Jul 19, 2020

• Add support for reflection spectrum.

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• Support varying reflections in time.

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• Add support for multi-reflections.

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• Import itertools.

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• Update preparation batch script.

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• Update time vary params only if config given.

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• Update output log location.

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• Make sure to run data prep with a config.

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• Make reflection_spectrum discoverable in pipeline.

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• Fix reflection shoulder code.

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• Allow more flexibility for multi-reflections.

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• Bugfix in reflection simulation.

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• Improve prepare_data batch script.

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Commits on Jul 30, 2020

• Update batch script to remake sum files.

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Commits on Aug 6, 2020

• Add more plots to end-to-end notebook.

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Commits on Aug 14, 2020

• Update prepare_data for foreground run.

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Commits on Sep 30, 2020

• Subtle bugfix in prepare_sim_files script.

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• Get the bugfix right.

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Commits on Mar 26, 2021

• Update systemtaics sim notebook

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Commits on Apr 1, 2021

• add test criteria for 4.0.0a

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