Improved arepo parser #1941
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Improved arepo parser #1941
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Codecov Report
@@ Coverage Diff @@
## master #1941 +/- ##
==========================================
+ Coverage 58.04% 58.13% +0.09%
==========================================
Files 76 75 -1
Lines 8743 8602 -141
==========================================
- Hits 5075 5001 -74
+ Misses 3668 3601 -67
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andrewfullard
approved these changes
Jul 11, 2022
Rodot-
approved these changes
Jul 12, 2022
jayantbhakar
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to jayantbhakar/tardis
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Jul 29, 2022
* Removed line profile as option * Removed mapping to Cartesian grid * Removed automatic plotting after profile creation * Fixed typo in arepo plot * Updated documentation * [build docs] * [build docs] Removed outputs from doc-notebook * Updated tests with new models * Removed deprecated keyword in snapshot loader * Replaced wget with requests for testfile download * Updated file retrieval for testing * Fixed fixture request * Added arepo data to refdata helper * Updated refdata location in docs * Updated paths in tests * Update download_reference_data.sh * Testing areop_parser_tests * Fixed deleted reference file
andrewfullard
pushed a commit
that referenced
this pull request
Aug 3, 2022
* rpacket_tracker returns dataframe * added black formatting * replaced variable i * added rpacket_tracker_df as separate variable * added preallocation step * added non-preallocated-df generator function * tests for df generator function * renamed variables * assert statements corrected * added seed column in df * added documentation for rpacket_tracker_df * added doc str * initial commit * updated documention * moved function to r_packet.py * added block indexing to df Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com> * updated the df function * added multiindexing * shifted the df function call * initial commit * interaction type added * removed unused imports * added tests * initial commit * interaction type added * Created a smart HDF Reader which can re-produce simulation object (#2052) * Added functions to store and load a runner object * Updated hardcode file name in runner_from_hdf * Updated store_runner_to_hdf to append to file * Added name and email to .mailmap * runner hdf functions convert to cgs * store_runner_to_hdf clears group before storing * Storing units for astropy quantities * Formatted code with black * Added functions to store and load model objects * Fixed typo and decoded string from bytes * Fixed typo * Added test for model_to_dict * Formatted previous test code * Added test for store_model_to_hdf * Fixed formatting of model_to_hdf * Fixed issue with test for model_to_dict * Added test for runner_to_dict * Fixed issue with single packet seed storage * Updated test null value of single packet seed * Added test for store_runner_to_hdf * Updated to use isinstance and hasattr * runner_to_dict returns dicts instead of iterators * Reordered imports to match pep8 style * Remove yaml_load_config_file (#2062) * Remove yaml_load_config_file * updated mailmap * Updated __init__.py * Modified Function Name in Config validator according to PEP8 (#2076) Fix function name according pep8 * Added documetation on how to compare environment before update (#2082) * Moved `trace_packet` to tardis tansport (#2083) * Moved the trace_packet function to the transport module, renamed the function to remove continuum reference as it is generic * Formatted to PEP 8 * Reformatted single_packet_loop for PEP 8 * removed old continuum trace packet files * removed references to old files * Added some docstrings * Missed an old function call * Fix broken links in workflow files and goverance md (#2084) * Adding physics introduction to documentation (#2026) * creating files and sections * adding images * writing intro to tardis physics and adding it to sidebar * changing spectra page structure * mostly complete draft of light and matter page * spectrum page * fixing up physics stuff * fixing docstring * Revert "fixing docstring" This reverts commit e24cadd. * andrew's changes * a few more edits * adding note about angstroms * Improved arepo parser (#1941) * Removed line profile as option * Removed mapping to Cartesian grid * Removed automatic plotting after profile creation * Fixed typo in arepo plot * Updated documentation * [build docs] * [build docs] Removed outputs from doc-notebook * Updated tests with new models * Removed deprecated keyword in snapshot loader * Replaced wget with requests for testfile download * Updated file retrieval for testing * Fixed fixture request * Added arepo data to refdata helper * Updated refdata location in docs * Updated paths in tests * Update download_reference_data.sh * Testing areop_parser_tests * Fixed deleted reference file * Arepo docs fix (#2088) * [build-docs] Fixed link in arepo docs * [build-docs] Changed filename in arepo docs * [build-docs] * [build-docs] * [build-docs] * [build docs] * [build-docs] Changed refdata url * [build_docs] * Updated mailmap * [build_docs] Updated url for refdata download * Creating new docs building instructions (#2097) * creating new docs building instructions * typos, grammar, and text in hyperlinks * added tests * added documentation, black formatting Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com> Co-authored-by: Satwik Kambham <satwik.kambham@gmail.com> Co-authored-by: aman kumar <ak584584@gmail.com> Co-authored-by: Rohith Varma Buddaraju <rohith.varma.buddaraju@gmail.com> Co-authored-by: Jaladh Singhal <jaladhsinghal@gmail.com> Co-authored-by: Jack O'Brien <jobrien585@gmail.com> Co-authored-by: Isaac Smith <71480393+smithis7@users.noreply.github.com> Co-authored-by: AlexHls <70367168+AlexHls@users.noreply.github.com>
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Performance improvements to the arepo parser + deprecation of line profiles.
Description
Currently the arepo parser maps snapshots to a Cartesian grid before profile extraction. This is extremely inefficient/ compute time intensive. The mapping is only needed for the line profile. Since line profiles can also be achieved by a very narrow cone, line profiles will be deprecated as well as the mapping to Cartesian grids. Profiles will be extracted directly from the snapshot cells.
Motivation and context
Current implementation is extremely inefficient and contains unneeded mapping procedure.
How has this been tested?
Examples
Type of change
Checklist