Merge pull request #3 from emit-sds/develop

Merge develop into main for v1.3.0

.gitignore

@@ -2,3 +2,4 @@
 emit_sds_l1a.egg-info
 __pycache__
 .coverage
+.DS_Store

CHANGELOG.md

@@ -4,85 +4,97 @@ All notable changes to this project will be documented in this file. Dates are d
 
 Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 
-#### [v1.2.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v1.1.0...v1.2.0)
+#### [v1.3.0](https://github.com/emit-sds/emit-sds-l1a/compare/v1.2.0...v1.3.0)
+
+> 6 June 2022
+
+- J2000 and BAD timing [`#2`](https://github.com/emit-sds/emit-sds-l1a/pull/2)
+- Check number of valid lines and instrument mode [`#1`](https://github.com/emit-sds/emit-sds-l1a/pull/1)
+- Pre ioc ccsds updates [`#21`](https://github.com/emit-sds/emit-sds-l1a/pull/21)
+- update LICENSE and README [`ec26b1e`](https://github.com/emit-sds/emit-sds-l1a/commit/ec26b1ecb48d0601bab1803671cca1deb8a1896f)
+- Check frame instrument modes for consistency and add mode description to report. [`c3244ab`](https://github.com/emit-sds/emit-sds-l1a/commit/c3244ab2132e8786ef162cfd65a7c8581a26e3a9)
+- Add utils to check packet sizes below a threshold and to find all the sync words in a stream. [`975ce53`](https://github.com/emit-sds/emit-sds-l1a/commit/975ce53bc98e4cd7ae8c732e421616c3196d3472)
+
+#### [v1.2.0](https://github.com/emit-sds/emit-sds-l1a/compare/v1.1.0...v1.2.0)
 
 > 18 March 2022
 
-- Add raw waterfall script [`37f5a31`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/37f5a314e622432c0413d84caa0c0fd9183f6cc9)
-- Fix PEP8 [`0ccb1f1`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/0ccb1f1cd9170e560227d7f59302f5640dd1d305)
-- Incrememnt line count by 2 if from processed partition AND coadd is enabled. [`365ac46`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/365ac462f0ae1baa5f9e2f9bb48f449c127937ae)
+- Merge develop to main for v1.2.0 [`#20`](https://github.com/emit-sds/emit-sds-l1a/pull/20)
+- Add raw waterfall script [`37f5a31`](https://github.com/emit-sds/emit-sds-l1a/commit/37f5a314e622432c0413d84caa0c0fd9183f6cc9)
+- Fix PEP8 [`0ccb1f1`](https://github.com/emit-sds/emit-sds-l1a/commit/0ccb1f1cd9170e560227d7f59302f5640dd1d305)
+- Update change log [`b090e59`](https://github.com/emit-sds/emit-sds-l1a/commit/b090e597495bf3d1e5a360a8eaca2d4253ffb7b2)
 
-#### [v1.1.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v1.0.0...v1.1.0)
+#### [v1.1.0](https://github.com/emit-sds/emit-sds-l1a/compare/v1.0.0...v1.1.0)
 
 > 28 February 2022
 
-- Merge develop to main for v1.1.0 [`#19`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/19)
-- CCSDS format change [`#18`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/18)
-- CCSDS format change [`#17`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/17)
-- Add pad_byte_flag and use it to get and set data property to include the garbage pad byte or not. [`eb182c3`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/eb182c36b5f34c70586799cee9d6e9327f67ddcb)
-- Update changelog. [`b037da5`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/b037da57e32452c67848adf196b5181e9ee6d236)
-- Update version to 1.1.0 [`401c442`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/401c4420350206989053e70fc876d693ae458d42)
+- Merge develop to main for v1.1.0 [`#19`](https://github.com/emit-sds/emit-sds-l1a/pull/19)
+- CCSDS format change [`#18`](https://github.com/emit-sds/emit-sds-l1a/pull/18)
+- CCSDS format change [`#17`](https://github.com/emit-sds/emit-sds-l1a/pull/17)
+- Add pad_byte_flag and use it to get and set data property to include the garbage pad byte or not. [`eb182c3`](https://github.com/emit-sds/emit-sds-l1a/commit/eb182c36b5f34c70586799cee9d6e9327f67ddcb)
+- Update changelog. [`b037da5`](https://github.com/emit-sds/emit-sds-l1a/commit/b037da57e32452c67848adf196b5181e9ee6d236)
+- Update version to 1.1.0 [`401c442`](https://github.com/emit-sds/emit-sds-l1a/commit/401c4420350206989053e70fc876d693ae458d42)
 
-### [v1.0.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v0.4.1...v1.0.0)
+### [v1.0.0](https://github.com/emit-sds/emit-sds-l1a/compare/v0.4.1...v1.0.0)
 
 > 9 February 2022
 
-- Merge develop to main for 1.0.0 [`#16`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/16)
-- Add changelog [`b501999`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/b5019998362a6b8cba141073c29e8221544cc8c0)
-- Use the out_arr to lookup the BAD coarse time instead of doing a range from min time to max time. [`c06ed6b`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/c06ed6bbeac405fc788053e2281d4f6f4f788a14)
-- Change version to 1.0.0 [`824959d`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/824959d6dfd11bcb9f1c139701f32e800d39bb06)
+- Merge develop to main for 1.0.0 [`#16`](https://github.com/emit-sds/emit-sds-l1a/pull/16)
+- Add changelog [`b501999`](https://github.com/emit-sds/emit-sds-l1a/commit/b5019998362a6b8cba141073c29e8221544cc8c0)
+- Use the out_arr to lookup the BAD coarse time instead of doing a range from min time to max time. [`c06ed6b`](https://github.com/emit-sds/emit-sds-l1a/commit/c06ed6bbeac405fc788053e2281d4f6f4f788a14)
+- Change version to 1.0.0 [`824959d`](https://github.com/emit-sds/emit-sds-l1a/commit/824959d6dfd11bcb9f1c139701f32e800d39bb06)
 
-#### [v0.4.1](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v0.4.0...v0.4.1)
+#### [v0.4.1](https://github.com/emit-sds/emit-sds-l1a/compare/v0.4.0...v0.4.1)
 
 > 31 January 2022
 
-- Merge develop into main for v0.4.1 [`#15`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/15)
-- Update readme to conform to PGE specification. [`d0e6d52`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/d0e6d5232626f91213223631974c1248bf65dd5b)
-- Update readme [`cb36edd`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/cb36edd188d7e399352cb6fb73d0f23694ebebeb)
-- Update changelog [`7e445ac`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/7e445ac4c5d27d52af2e6190fee7e61761dd6863)
+- Merge develop into main for v0.4.1 [`#15`](https://github.com/emit-sds/emit-sds-l1a/pull/15)
+- Update readme to conform to PGE specification. [`d0e6d52`](https://github.com/emit-sds/emit-sds-l1a/commit/d0e6d5232626f91213223631974c1248bf65dd5b)
+- Update readme [`cb36edd`](https://github.com/emit-sds/emit-sds-l1a/commit/cb36edd188d7e399352cb6fb73d0f23694ebebeb)
+- Update changelog [`7e445ac`](https://github.com/emit-sds/emit-sds-l1a/commit/7e445ac4c5d27d52af2e6190fee7e61761dd6863)
 
-#### [v0.4.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v0.3.0...v0.4.0)
+#### [v0.4.0](https://github.com/emit-sds/emit-sds-l1a/compare/v0.3.0...v0.4.0)
 
 > 20 January 2022
 
-- Merge develop for release 0.4.0 [`#14`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/14)
-- Bad start stop [`#13`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/13)
-- Bad reformatting [`#12`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/12)
-- Line timestamp  [`#11`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/11)
-- Split acquisitions [`#10`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/10)
-- Create initial framework of BAD reformatting. Read in STO file. Start to write out NetCDF file. [`dc47683`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/dc47683868950c6290e98aa55dd30086f4d0ea91)
-- Use start time in frame filename instead of os time. Write report files per acquisition providing details (missing frames, cloudy frames, decompression failures) per acquisition instead of for the entire data collection. [`fa48545`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/fa48545c17f0cad8a2ce083cbb0da4e89524c1a0)
-- Move reassembly code to its own function and iterate over frames using chunksize [`391c4d9`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/391c4d9d02279eb9fb92785933b4e5c6303acfc4)
+- Merge develop for release 0.4.0 [`#14`](https://github.com/emit-sds/emit-sds-l1a/pull/14)
+- Bad start stop [`#13`](https://github.com/emit-sds/emit-sds-l1a/pull/13)
+- Bad reformatting [`#12`](https://github.com/emit-sds/emit-sds-l1a/pull/12)
+- Line timestamp  [`#11`](https://github.com/emit-sds/emit-sds-l1a/pull/11)
+- Split acquisitions [`#10`](https://github.com/emit-sds/emit-sds-l1a/pull/10)
+- Create initial framework of BAD reformatting. Read in STO file. Start to write out NetCDF file. [`dc47683`](https://github.com/emit-sds/emit-sds-l1a/commit/dc47683868950c6290e98aa55dd30086f4d0ea91)
+- Use start time in frame filename instead of os time. Write report files per acquisition providing details (missing frames, cloudy frames, decompression failures) per acquisition instead of for the entire data collection. [`fa48545`](https://github.com/emit-sds/emit-sds-l1a/commit/fa48545c17f0cad8a2ce083cbb0da4e89524c1a0)
+- Move reassembly code to its own function and iterate over frames using chunksize [`391c4d9`](https://github.com/emit-sds/emit-sds-l1a/commit/391c4d9d02279eb9fb92785933b4e5c6303acfc4)
 
-#### [v0.3.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v0.2.0...v0.3.0)
+#### [v0.3.0](https://github.com/emit-sds/emit-sds-l1a/compare/v0.2.0...v0.3.0)
 
 > 25 October 2021
 
-- Merge develop for version 0.3.0 [`#9`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/9)
-- Frame span ccsds [`#8`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/8)
-- Test fpa data [`#7`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/7)
-- Add bytes read since last index into report. [`d1cd9f4`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/d1cd9f42b76e95d3b09b29ed8cd22254bc07269b)
-- Use frame_count_pre and frame_count_post to distinguish those fields. Add a utility to rename a frame with different frame num and expected num of frames. [`3cb1d72`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/3cb1d727fffd25bea8b496f058ebdbf5d7393cac)
-- Change course to coarse. [`8695c04`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/8695c04f22962bb53c296a46317c9dd6e60e8709)
+- Merge develop for version 0.3.0 [`#9`](https://github.com/emit-sds/emit-sds-l1a/pull/9)
+- Frame span ccsds [`#8`](https://github.com/emit-sds/emit-sds-l1a/pull/8)
+- Test fpa data [`#7`](https://github.com/emit-sds/emit-sds-l1a/pull/7)
+- Add bytes read since last index into report. [`d1cd9f4`](https://github.com/emit-sds/emit-sds-l1a/commit/d1cd9f42b76e95d3b09b29ed8cd22254bc07269b)
+- Use frame_count_pre and frame_count_post to distinguish those fields. Add a utility to rename a frame with different frame num and expected num of frames. [`3cb1d72`](https://github.com/emit-sds/emit-sds-l1a/commit/3cb1d727fffd25bea8b496f058ebdbf5d7393cac)
+- Change course to coarse. [`8695c04`](https://github.com/emit-sds/emit-sds-l1a/commit/8695c04f22962bb53c296a46317c9dd6e60e8709)
 
-#### [v0.2.0](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/compare/v0.1.0...v0.2.0)
+#### [v0.2.0](https://github.com/emit-sds/emit-sds-l1a/compare/v0.1.0...v0.2.0)
 
 > 31 August 2021
 
-- Merge develop into main for SDS Release 2 [`#6`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/6)
-- Check Frame Report [`#5`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/5)
-- Rawqa [`#4`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/4)
-- Update ccsds depacketization for engineering and science [`#3`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/3)
-- Frame updates based on latest frame header [`#2`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/2)
-- Integrate decompression [`#1`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/pull/1)
-- Add ccsds code (formerly in emit-l0-sds repo). [`c56bbdd`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/c56bbdd064aa3309a0b9efb6b9c837bf65af5403)
-- Use CCSDSPacket base class ScienceDataPacket sub-class. Incorporate latest CCSDS format (w/ secondary header flags and crc). Update ccsds spoofer to match new format. [`f4dcc3d`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/f4dcc3d378ec86939d0aab845113ad0e956bafb2)
-- When reading next packet, check for already seen packets (to handle overlap) and PSC mismatch. Ignore already seen packets. If there is a mismatch, then save next packet as a partial and raise exception. This has been tested against various ccsds streams to stress edge cases. [`8209902`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/820990223befd4d098aefc3af58ebaac0fa1ef3f)
+- Merge develop into main for SDS Release 2 [`#6`](https://github.com/emit-sds/emit-sds-l1a/pull/6)
+- Check Frame Report [`#5`](https://github.com/emit-sds/emit-sds-l1a/pull/5)
+- Rawqa [`#4`](https://github.com/emit-sds/emit-sds-l1a/pull/4)
+- Update ccsds depacketization for engineering and science [`#3`](https://github.com/emit-sds/emit-sds-l1a/pull/3)
+- Frame updates based on latest frame header [`#2`](https://github.com/emit-sds/emit-sds-l1a/pull/2)
+- Integrate decompression [`#1`](https://github.com/emit-sds/emit-sds-l1a/pull/1)
+- Add ccsds code (formerly in emit-l0-sds repo). [`c56bbdd`](https://github.com/emit-sds/emit-sds-l1a/commit/c56bbdd064aa3309a0b9efb6b9c837bf65af5403)
+- Use CCSDSPacket base class ScienceDataPacket sub-class. Incorporate latest CCSDS format (w/ secondary header flags and crc). Update ccsds spoofer to match new format. [`f4dcc3d`](https://github.com/emit-sds/emit-sds-l1a/commit/f4dcc3d378ec86939d0aab845113ad0e956bafb2)
+- When reading next packet, check for already seen packets (to handle overlap) and PSC mismatch. Ignore already seen packets. If there is a mismatch, then save next packet as a partial and raise exception. This has been tested against various ccsds streams to stress edge cases. [`8209902`](https://github.com/emit-sds/emit-sds-l1a/commit/820990223befd4d098aefc3af58ebaac0fa1ef3f)
 
 #### v0.1.0
 
 > 19 October 2020
 
-- Add initial run script for L1A engineering data [`ea20082`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/ea20082a93a4d7f2086232c009225ca79a8081e2)
-- Update README.md [`0ca6e15`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/0ca6e15a94bf8f4f7e9f823bb3829fe0b12f066d)
-- Initial commit [`6e2c913`](https://github.jpl.nasa.gov/emit-sds/emit-sds-l1a/commit/6e2c913b2dd184a3986fb10702cf3e706776b782)
+- Add initial run script for L1A engineering data [`ea20082`](https://github.com/emit-sds/emit-sds-l1a/commit/ea20082a93a4d7f2086232c009225ca79a8081e2)
+- Update README.md [`0ca6e15`](https://github.com/emit-sds/emit-sds-l1a/commit/0ca6e15a94bf8f4f7e9f823bb3829fe0b12f066d)
+- Initial commit [`6e2c913`](https://github.com/emit-sds/emit-sds-l1a/commit/6e2c913b2dd184a3986fb10702cf3e706776b782)