Package: vipersci
vipersciThis vipersci package is software to support the activities of the
Volatiles Investigating Polar Exploration Rover (VIPER) Science Team.This software will implement scientific models to convert instrument
raw data to useful derived data (but not including any proprietary
instrument details). This includes functionality for running the
models “in reverse” in order to simulate instrument data for tests
and mission simulations. This software will enable and support the
creation of various geospatial data sets (maps) to help visualize
and understand data from the spacecraft. It will also support the
creation of PDS4 archive labels and structures for eventual data
delivery to the Planetary Data System (PDS).At the moment, this repo is under significant development and change as we
attempt to craft various pieces of code.  It is definitely a work-in-progress.The VIPER Science Team is developing this software “in the open”
in order to adhere to the newNASA Science Information Policy for
the Science Mission Directorate (SPD-41)as much as is possible.Free software: Apache 2 LicenseInstallationThe vipersci package is available on PyPI and pip-installable.Installation via Conda will be forthcoming.For the moment, follow the “Get Started!” directions in the CONTRIBUTING.rst document.ContributingFeedback, issues, and contributions are always gratefully welcomed. See the
contributing guide for details on how to help and setup a development
environment.Creditsvipersci was developed in the open at NASA’s Ames Research Center.See theAUTHORSfile for a complete list of developers.LicenseSee LICENSE file for the full text of the license that applies to vipersci.Copyright (c) 2022-2023, United States Government as represented by
the Administrator of the National Aeronautics and Space
Administration. All rights reserved.The “vipersci” software is licensed under the Apache License, Version 2.0
(the “License”); you may not use this file except in compliance with the
License.  You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an “AS IS” BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied. See the License for the specific language governing
permissions and limitations under the License.ChangelogAll notable changes to this project will be documented in this file.The format is based onKeep a Changelog,
and this project adheres toSemantic Versioning.When updating this file, please add an entry for your change underUnreleasedand one of the following headings:Added - for new features.Changed - for changes in existing functionality.Deprecated - for soon-to-be removed features.Removed - for now removed features.Fixed - for any bug fixes.Security - in case of vulnerabilities.If the heading does not yet exist underUnreleased, then add it
as a 3rd level heading, underlined with pluses (see examples below).When preparing for a public release add a new 2nd level heading,
underlined with dashes underUnreleasedwith the version number
and the release date, in year-month-day format (see examples below).Unreleased0.8.0 (2024-02-21)ChangedThe instrument_name() function in pid.py now can deal with alias names that are
within a given string, not just an exact match.Now that pid.instrument_name() is more robust, ImageRecord.__init__() can handle a
wider variety of Yamcs parameter names, should they change in the future.create_mmgis_pano.py - create() now takes a thumbsize int or tuple of ints that
will control the creation and size of an output thumbnail JPG file, with naming
convention set by Yamcs/OpenMCT.image_records.py - Added icer_byte_quota and icer_minloss parameters to ImageRecord,
as well as a variety of improved handling related to this change and in pid.py.pid.py - Changed handling of the compression value to match the kinds of data we’ll
get from telemetry, so that the letters are assigned to cover an interval of possible
compression ratios, and to reflect the new default byte quota value for driving
images.0.7.0 (2024-02-05)ChangedThe light_records.py table now just records state changes (from ‘on’ to ‘off’ or
vice-versa).create_image.py’s create() method now has an imgtype argument that default to TIFF
(but can be PNG).junc_image_req_ldst.py got some additional columns to manage the Science Team
evaluation of images acquired from Image Requests.create_pano.py’s make_pano_product() function renamed to make_pano_record().nss_simulator.py - nodata defaults for ideal detector count maps updated to more
realistic values for dry terrain.image_statistics.py - Added additional stats in the compute() function, and added
a pprint() function to format the info nicely.Addedpds.Purpose now provides names and explanations for the PDS-allowable values
for “purpose.”yamcs_reception_time column added to the image_records.py table.Association table junc_image_pano created which provides a many-to-many
connection between ImageRecords and PanoRecords and added bidirectional
relationship entries to each table.pano_records table now has pan and tilt angle min/max values to indicate
angular range of panorama coverage.ImageRecord objects will now extract an ImageRequest ID from the provided capture_id
if it is larger than the 16 bit range.image_requests.py - “Acquired,” “Not Acquired,” “Not Planned,” and “Not Obtainable”
statuses added to enum.  Also added asdict() method.ptu_records.py - Tables to record the pan and tilt of the rover’s pan-tilt-unit (PTU).create_browse.py - For making browse products from existing image products.create_mmgis_pano.py - For making pano products for use in MMGIS.create_pano.py - updated to correctly add PanoRecord associations, can now query
database for ImageRecords.create_pano_product.py - takes PanoRecords and makes a PDS Pano Product.get_position.py - Gets position and yaw from a REST-based service.create_vis_dbs.py - Now also supports spatialite databases, primarily for testing.create_raw.py - Added components for adding observational intent and data quality
to the XML label.labelmaker - A program to help build PDS4 bundle and collection labels.bundle_install - A program to copy just the files related to a PDS4 bundle into a
new location.  Fundamentally allowing a “make install” for PDS4 bundles.Removedldst_verification.py because the evaluation activity reflected here was on a per-image
basis, but it has been revised to be on a per-Image-Request basis.0.6.1 (2023-09-25)Fixedvalidators.validate_dateimte_asutc now properly raises a ValueError if the provided
tz-aware datetime has a non-UTC tz offset (before any tz-aware datetime would pass
the validator).image_records.ImageRecord object now has pgaGain instead of ppaGain (which was surely
a typo in the early upstream data.create_image.py now correctly imports all of the tables that have a relation to the
image_records table so that SQLAlchemy can properly resolve them, and downstream
users of the create_image.create() function don’t need to worry about sorting that
out.nss_simulator.py, when asked to produce an output set of maps, uses a zero nodata value
rather than whatever nodata value was present in the input burial depth map.anaglyph.py needed some minor changes to align with upcoming changes in the
scikit-image architecture.0.6.0 (2023-09-25)Changed the concept of primarily recording PDS-like “products” in the database and data
structures, and changed the concept to capture “records” of various kinds (ImageRecords,
LightRecords, and derived things like PanoRecords) in the database and as the primary
data unit for use and interaction.  And then PDS “products” will be made at a later
time via a process that sources one or many records.Addedimage_records.py (this replaces the concept of raw_products.py)create_image.py (this replaces most of the functionality of the previous
create_raw.py)image_tags.py which contains image tag information.image_requests.py defines the table for holding image requests.Junction tables to connect LDST information to ImageRequests and ImageTags
to ImageRecords.ldst.py table which contains LDST information.light_records.py which handles information about luminaire state.anaglyph.pypano_check.py to sort through image records and figure out what would be a good
panorama set.Changedheader.pga_gain_dict structure now has values that are always floats, which helps
to determine whether this transformation needs to be applied.image_stats.py is the new raw_stats.py, supporting ImageRecord objects.pano_products.py is now pano_records.py, supporting ImageRecord objects.create_pano.py now supports ImageRecords and PanoRecords.create_raw.py rearchitected to gather information from “records” to build XML PDS
labels.create_vis_dbs entry point changed to vis_create_dbs to conform with other vis-related
entry points.pid.VISID now properly sorts the uncompressed “z” state lower (better) than the
lossless compressed “a” state.pid.VISID now has a best_compression() function to sort out the best compression state
from an iterable containing may compression states from a single observation.0.5.0 (2023-07-26)AddedPanoID class added to pds.pidpano_products and create_pano added, still very preliminary, mostly just mock-ups.colorforge program for managing colormaps.mypy is now in the development dependencies to support type checking.lint/mypy target added to Makefile.tri2gpkg now has a –remove_facets option to remove facets with a particular value.ChangedExplicit in documentation about developing in Python 3.8 (although earlier versions
should still be supported).Many changes to improve type checking.Added numeric instrument aliases and checking for them.Added information for procesingInfo and outputMask from Yamcs.Upgrade to SQLAlchemy >=2.Moved definition of Base class up to vis.db.heatmaps.py will now accept value data lists or arrays with np.nan or None values
which will be appropriate ignored in the density heatmap calculation.Fixedtri2gpkg - if the provided polygons have zero area, issue an error rather than
making a confusing GeoPackage file.0.4.0 (2023-03-01)Addedcarto.bounds module added to unify functionality for both heatmaps and dotmaps.carto.dotmap module for creating simple heatmap-like visualizations from 2d scalar data.Makefile now has a “lint/twine” option to hopefully help me remember to test that.VIS image_statistics.py and raw_stats.py modules.A variety of unit tests.mypy configuration arguments.ChangedUpdated templates and modules for PDS information model 21.Flattened test directory structure.tri2gpkg -v is no longer an alias for –value-names, as it now determines verbosity
since logging has been added.GitHub workflows have been re-arranged.  Black and flake8 are now run under the “Lint”
action, and the flake8 tests are removed from the Python testing matrix.RemovedThe pinned versions requirements_dev.txtFixedCHANGELOG.rst had an unescaped underbar which caused trouble with twine upload.setup.cfg arrangement in install_requires passed local testing, but not GitHub testing,
have now fixed.heatmap’s generate_density_heatmap() function now properly returns values of zero
in the returned out_count numpy array when there are no counts in those grid cells
instead of the provided nodata value.raw-template.xml can only have one Image_Filter object.tri2gpkg now works correctly if –keep_z is specifiedtri2gpkg now uses the correct srs if a pre-defined site is selected.0.3.0 (2022-11-15)Addedpds.datetime.fromisozformat() function.pds.pid.VISID.compression_class() function.pds.xml.py added, very minimal, functionality may be moved.vis.db.raw_products.RawProduct.from_xml() function.vis.db.raw_products.RawProduct.asdict() function.vis.pds.create_raw.check_bit_depth() function.vis.db.create_vis_dbs convenience program to add empty tables to database.ChangedUpdated templates and modules for PDS information model 18.vis.db.raw_products.RawProduct has some improved error-checking in __init__() and
validate_datetime_asutc().vis.db.raw_products.RawProduct product_id column is now unique in database.vis.db.raw_products.RawProduct md5_checksum changed to file_md4_checksum to
clearly associate it with the other properties that begin with “file_”.vis.pds.create_raw.tiff_info() no longer raises an error if a bit depth other than 16
is provided.vis.pds.create_raw now creates .JSON output files by default instead of XML PDS4
labels, but XML files can still be made.carto.heatmap.write_geotiff_rasterio now supports compressed output and defaults to “deflate”Fixedcarto.tri2gpkg.replace_with() now correctly returns a float value in all circumstances.pds.pid.VIPERID.datetime() now properly returns datetimes with a UTC timezone.vis.db.raw_products.RawProduct.label_dict() now correctly sets sample_bits and
sample_bit_mask if the image is a SLoG image.Added __init__.py files to all modules (some modules did not get incorporated into the
PyPI package because they did not have __init__.py files.The setup.cfg now properly includes requirements that vipersci needs.RemovedMany modules still had if __name__ == “__main__” constructs from early development
which are now not needed with the entry points in setup.cfg.0.2.0 (2022-11-07)AddedData Simulators for NSS, NIRVSS, and MSoloLots of material to enaable PDS archiving of VIS data.Added GitHub workflow to perform Black format checkingChangedMany updates to heatmap.pyApplied Black formatting to all code in the repo.Modified Python testing workflow to actually work.0.1.0 (2022-10-05)Initial release.