Fix rcr indexing

.circleci/config.yml

@@ -18,6 +18,10 @@ merge-check: &merge-check
       git checkout -qf pr/$CIRCLE_PR_NUMBER/merge
     fi
 
+submodules: &submodules
+  name: Update submodules
+  command: git submodule update --init --recursive
+
 apt-run: &apt-install
   name: Install apt packages
   command: |
@@ -47,9 +51,13 @@ jobs:
       - run: *no-backports
       - run: *skip-check
       - run: *merge-check
+      - run: *submodules
       - run: *apt-install
       - run: pip install -U tox
-      - run: tox -e build_docs
+      - run:
+          name: Build docs
+          command: tox -e build_docs
+          no_output_timeout: 30m
       - run:
           name: Prepare for upload
           command: |

.coveragerc

@@ -4,6 +4,8 @@ omit =
   stixpy/*setup_package*
   stixpy/extern/*
   stixpy/version*
+  stixpy/_dev/*
+  */stixpy/_dev/*
   */stixpy/conftest.py
   */stixpy/*setup_package*
   */stixpy/extern/*

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "6436220cebd96b3638682023e7149eb78e012fdc",
+  "commit": "0c0f34c2ccd536ba8320fcda29c4d8e0f8f9adc5",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -33,7 +33,7 @@
         ".github/workflows/sub_package_update.yml"
       ],
       "_template": "https://github.com/sunpy/package-template",
-      "_commit": "6436220cebd96b3638682023e7149eb78e012fdc"
+      "_commit": "0c0f34c2ccd536ba8320fcda29c4d8e0f8f9adc5"
     }
   },
   "directory": null

.github/dependabot.yml

@@ -6,3 +6,7 @@ updates:
       interval: "monthly"
     cooldown:
       default-days: 7
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/sub_package_update.yml

@@ -104,7 +104,7 @@ jobs:
       issues: write
     steps:
       - name: Open an issue if workflow fails
-        uses: actions/github-script@v8  # zizmor: ignore[unpinned-uses]
+        uses: actions/github-script@v9  # zizmor: ignore[unpinned-uses]
         with:
           github-token: ${{ github.token }}
           # This script is adapted from https://github.com/scientific-python/issue-from-pytest-log-action

.mailmap

@@ -4,3 +4,7 @@ Shane Maloney <shane.maloney@dias.ie> Shane Maloney <shane@spacemacs.local>
 Laura Hayes <hayesla@tcd.ie> hayesla <hayesla@tcd.ie>
 Daniel F. Ryan <ryand5@tcd.ie> Dan Ryan <ryand5@tcd.ie>
 Daniel F. Ryan <ryand5@tcd.ie> DanRyanIrish <ryand5@tcd.ie>
+Thomas Long <thomaslong491@gmail.com> tlong491 <thomaslong491@gmail.com>
+Hannah Collier <collierh@tcd.ie> Hannah Collier <76849369+hannahc243@users.noreply.github.com>
+Hannah Collier <76849369+hannahc243@users.noreply.github.com> hannahc243 <76849369+hannahc243@users.noreply.github.com>
+Rachel Hubbard <rachel.hubbard.25@ucl.ac.uk> rh2082 <rachel.hubbard.25@ucl.ac.uk>

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 repos:
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.23.1
+    rev: v1.25.2
     hooks:
       - id: zizmor
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.9"
+    rev: "v0.15.15"
     hooks:
       - id: ruff-check
         args: ["--fix"]

.zenodo.json

@@ -24,31 +24,42 @@
             "orcid": "0000-0001-8661-3825",
             "affiliation": "University College London, Mullard Space Science Laboratory (UCL/MSSL)"
         },
+        {
+            "name": "Nicky Hochmuth",
+            "orcid": "",
+            "affiliation": "Ateleris>"
+        },
         {
             "name": "Paolo Massa",
             "orcid": "0000-0002-0993-1974",
             "affiliation": "University of Applied Sciences and Arts Northwestern Switzerland (FHNW)"
         },
         {
             "name": "Alasdair Wilson",
-            "orcid": "",
-            "affiliation": ""
+            "orcid": "0000-0003-0820-8159",
+            "affiliation": "Oxford Research Software Engineering Team, University of Oxford"
         },
         {
-            "name": "Nicky Hochmuth",
-            "orcid": "",
-            "affiliation": ""
+            "name": "Hannah Collier",
+            "orcid": "0000-0001-5592-8023",
+            "affiliation": "University of Applied Sciences and Arts Northwestern Switzerland (FHNW)"
+        },
+        {
+            "name": "MHerrmann06"
+        },
+        {
+            "name": "Mashhoor Ahdal"
+        },
+        {
+            "name": "Rachel Hubbard",
+            "orcid": "0009-0003-8548-5691",
+            "affiliation": "University College London, Mullard Space Science Laboratory (UCL/MSSL)"
         },
         {
             "name": "Steven Christe",
             "orcid": "0000-0001-6127-795X",
             "affiliation": "NASA Goddard Space Flight Center"
         },
-        {
-            "name": "Hannah Collier",
-            "orcid": "0000-0001-5592-8023",
-            "affiliation": "University of Applied Sciences and Arts Northwestern Switzerland (FHNW)"
-        },
         {
             "name": "Thomas Long",
             "orcid": "",

CHANGELOG.rst

@@ -0,0 +1,158 @@
+0.3.0 (2026-06-05)
+==================
+
+Breaking Changes
+----------------
+
+- The `~stixpy.product.sources.science.ScienceData` method :meth:`~stixpy.product.sources.science.ScienceData.get_data` is now keyword only. (`#196 <https://github.com/TCDSolar/stixpy/pull/196>`__)
+- Increased minimum versions for these dependencies:
+
+  - Python >= 3.12
+  - astropy >= 6.1.0
+  - matplotlib >= 3.8.0
+  - sunpy >= 7.0
+  - xrayvisim >= 0.2.1 (`#212 <https://github.com/TCDSolar/stixpy/pull/212>`__)
+
+
+Removals
+--------
+
+- Remove deprecated ``stixpy.science`` module use `stixpy.product.Product` instead. (`#196 <https://github.com/TCDSolar/stixpy/pull/196>`__)
+
+
+New Features
+------------
+
+- Add ability to control the data normalisation to `~stixpy.product.sources.science.ScienceData.get_data` via the `vtype` keyword:
+
+  - 'c' - count [c]
+  - 'cr' - count rate [c/s]
+  - 'dcr' - differential count rate [c/(s keV)] (`#196 <https://github.com/TCDSolar/stixpy/pull/196>`__)
+
+
+Bug Fixes
+---------
+
+- Fixed version attributes not being exported in stixpy.net.attrs module. All version attributes (Version, VersionU, MinVersion, MinVersionU, MaxVersion, MaxVersionU) are now properly included in the module's ``__all__`` list and can be imported directly from ``stixpy.net.attrs``. (`#209 <https://github.com/TCDSolar/stixpy/pull/209>`__)
+- Fix :ref:`sphx_glr_generated_gallery_imaging_demo.py` to correctly use center of STIX field of view for initial grid correction and flare position estimation. (`#216 <https://github.com/TCDSolar/stixpy/pull/216>`__)
+
+
+Internal Changes
+----------------
+
+- Update `~stixpy.net.client.STIXClient` Fido client to use format keyword and ``parse`` syntax, internal changes only. (`#177 <https://github.com/TCDSolar/stixpy/pull/177>`__)
+- Update package with sunpy template and enable updates. (`#219 <https://github.com/TCDSolar/stixpy/pull/219>`__)
+
+
+Stixpy 0.2.1 (2026-03-10)
+=========================
+
+Bug Fixes
+---------
+
+- Update sunpy dependency to <7.0 as code not updated for new Fido client API. (`#211 <https://github.com/TCDSolar/stixpy/pull/211>`__)
+
+
+Stixpy 0.2.0 (2026-01-18)
+=========================
+
+Backwards Incompatible Changes
+------------------------------
+
+- Update minimum dependencies of Python 3.11 and sunpy to 6.0.0 inline with `SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_. (`#174 <https://github.com/TCDSolar/stixpy/pull/174>`__)
+
+
+Features
+--------
+
+- Update `Fido` client to optionally take root path or url. Also add attributes to enable searching for specific versions for example latest version available. (`#143 <https://github.com/TCDSolar/stixpy/pull/143>`__)
+- Enable `stixpy.calibration.visibility.create_meta_pixels` to include only top or bottom row of big pixels. (`#148 <https://github.com/TCDSolar/stixpy/pull/148>`__)
+- Update `Fido` client for change in aspect/ephemeris file name and path. (`#153 <https://github.com/TCDSolar/stixpy/pull/153>`__)
+- Add the pixel area normalisation from `~stixpy.calibration.visibility.create_meta_pixels` to dictionary returned. (`#162 <https://github.com/TCDSolar/stixpy/pull/162>`__)
+- Add new timeseries source for STIX ANC aspect data `~stixpy.timeseries.anc.ANCAspect`. (`#169 <https://github.com/TCDSolar/stixpy/pull/169>`__)
+- Add a instrument configuration constant `~stixpy.config.instrument.STIX_INSTRUMENT` to bundle instrument constants like grid configurations, pixel sizes .... (`#171 <https://github.com/TCDSolar/stixpy/pull/171>`__)
+- Update imaging demo to use Sun center as location for making initial full disk back projection to determine flare location. (`#173 <https://github.com/TCDSolar/stixpy/pull/173>`__)
+- Add enhanced pixel plot ~`stixpy.product.sources.science.PixelPlotMixin` improved layout now shows detector quadrant and labels. Pixel plots now support three options a normal bar plot an error bar plot and configuration plot. (`#178 <https://github.com/TCDSolar/stixpy/pull/178>`__)
+- Created new `stixpy.visualisation.plotters.PixelPlotter` class to create pixel plots by moving and refactored code from current mixin so current API is maintained. This new approach simplifies the `~stixpy.product.sources.science` module and programmatic access to the plot controls enabling animations. (`#181 <https://github.com/TCDSolar/stixpy/pull/181>`__)
+
+
+Bug Fixes
+---------
+
+- Fixed a bug in stixpy.calibration.visibility.create_meta_pixels to correctly determine which time bins to include in the sum based on their overlap with the specified time range. (`#138 <https://github.com/TCDSolar/stixpy/pull/138>`__)
+- Fix bug in orientation of grids for internal shadowing. (`#146 <https://github.com/TCDSolar/stixpy/pull/146>`__)
+- Fix bug where pointing information could be improperly interpolated in `~stixpy.coordinates.transforms.get_hpc_info`. (`#152 <https://github.com/TCDSolar/stixpy/pull/152>`__)
+- Fix typo in `~stixpy.calibration.visibility.create_meta_pixels` which cased error if grid shadow correction was enabled. Also update grid calculations to use `Skycoord` objects. (`#156 <https://github.com/TCDSolar/stixpy/pull/156>`__)
+- Fix error in `~stixpy.net.client.StixQueryResponse.filter_for_latest_version` if the result table was empty. (`#160 <https://github.com/TCDSolar/stixpy/pull/160>`__)
+- Fix bug in STIX Fido client which caused data that spanned midnight to be missed. (`#176 <https://github.com/TCDSolar/stixpy/pull/176>`__)
+- Fix apparent bug in `~stixpy.calibration.visibility.create_meta_pixels` by improving naming and docstrings. (`#194 <https://github.com/TCDSolar/stixpy/pull/194>`__)
+- Fix incomplete conversion of `~stixpy.calibration.visibility.calibrate_visibility` to use `~astropy.coordinates.SkyCoord`. (`#194 <https://github.com/TCDSolar/stixpy/pull/194>`__)
+- Fix ELUT reader `~stixpy.io.readers.read_elut` for column name change in upstream files. (`#194 <https://github.com/TCDSolar/stixpy/pull/194>`__)
+- Restore mistakenly dropped updateds to the energies used in `~stixpy.calibration.transmission.generate_transmission_tables`.: (`#197 <https://github.com/TCDSolar/stixpy/pull/197>`__)
+- Fix bug in `~stixpy.product.sources.science.ScienceData.get_data` when specifying `pixel_indices` with data containing less than 12 pixels. (`#200 <https://github.com/TCDSolar/stixpy/pull/200>`__)
+
+
+Improved Documentation
+----------------------
+
+- Convert reconstructions to proper sunpy maps in ref`:ref:`sphx_glr_generated_gallery_imaging_demo.py`. (`#141 <https://github.com/TCDSolar/stixpy/pull/141>`__)
+- Added instructions for initializing and updating git submodules and fixed broken links. (`#157 <https://github.com/TCDSolar/stixpy/pull/157>`__)
+
+
+Trivial/Internal Changes
+------------------------
+
+- Update project configuration move to `project.toml` and individual config files for each tool (isort, ruff, pytest, etc) and add zenodo config file and mailmap. (`#158 <https://github.com/TCDSolar/stixpy/pull/158>`__)
+
+
+Stixpy 0.1.2 (2024-07-16)
+==================================================
+
+Features
+--------
+
+- Add a custom coordinate frame :class:`stixpy.coordinate.frames.STIXImaging` and the associated transformations (`~stixpy.coordinates.transforms.stixim_to_hpc`, `~stixpy.coordinates.transforms.hpc_to_stixim`) to and from `~sunpy.coordinates.frames.Helioprojective`.
+  Also add a `stixpy.map.stix.STIXMap` for `~sunpy.map.Map` source which properly displays the :class:`stixpy.coordinate.frames.STIXImaging` coordinate frame. (`#90 <https://github.com/TCDSolar/stixpy/pull/90>`__)
+- Merged `stixpy.calibration.get_visibility_info_giordano` and `stixpy.calibration.get_visibility_info` into `stixpy.calibration.get_uv_points_data` and removed `stixpy.calibration.correct_phase_projection`. (`#98 <https://github.com/TCDSolar/stixpy/pull/98>`__)
+- Update livetime correction parameter `eta`, `tau` and  add code to calculate pileup 'beta' :func:`stixpy.calibration.livetime.pileup_correction_factor`. (`#100 <https://github.com/TCDSolar/stixpy/pull/100>`__)
+- Add background subtraction step to imaging demo, update `EnergyEdgeMasks`. (`#106 <https://github.com/TCDSolar/stixpy/pull/106>`__)
+- Update imaging demo to use images and construct `~sunpy.map.Map` using `~stixpy.coordinates.frames.STIXImaging` and `~sunpy.map.header_helper.make_fitswcs_header`. (`#107 <https://github.com/TCDSolar/stixpy/pull/107>`__)
+- Update :func:`~stixpy.coordinates.transforms.get_hpc_info` to use mean or interpolate pointing and location data based on number of data points in given timerange. Add function cache for aux data frequenly needed during coordinate transforms. (`#111 <https://github.com/TCDSolar/stixpy/pull/111>`__)
+- Make the imaging demo compatible with :class:`~xrayvision.visibility.Visibilities` (`#123 <https://github.com/TCDSolar/stixpy/pull/123>`__)
+- Update code and examples to use new :class:`~xrayvision.visibility.Visibilities`, tidy API of `~stixpy.imaging.em.em`. (`#124 <https://github.com/TCDSolar/stixpy/pull/124>`__)
+- Add missing QL products `~stixpy.product.sources.quicklook.QLVariance`, `~stixpy.product.sources.quicklook.QLFlareFlag`, and `~stixpy.product.sources.quicklook.QLTMStatusFlareList` to Product. Also added some useful properties to the for status words. (`#125 <https://github.com/TCDSolar/stixpy/pull/125>`__)
+
+
+Bug Fixes
+---------
+
+- Fix ELUT correction when the requested data has less then than 32 energy channels. (`#106 <https://github.com/TCDSolar/stixpy/pull/106>`__)
+- Update `~stixpy.calibration.energy.get_elut` to use correct science energy channels for given date. (`#107 <https://github.com/TCDSolar/stixpy/pull/107>`__)
+- Fix a bug where the incorrect unit was set on :class:`~stixpy.timeseries.quicklook.QLLightCurve`, :class:`~stixpy.timeseries.quicklook.QLBackground` and :class:`~stixpy.timeseries.quicklook.QLVariance`. (`#118 <https://github.com/TCDSolar/stixpy/pull/118>`__)
+- Fix bug where coordinate transforms did not support arrays of coordinates or times. To so support both integrated (e.g. images) and instantaneous (e.g. coarse flare flag) a new property `obstime_end` was added to `~stixpy.coordinates.frames.STIXImaging` when set if possible mean pointing and position information are use for transformations other wise they are interpolated between the two nearest data points. (`#128 <https://github.com/TCDSolar/stixpy/pull/128>`__)
+- Fix typo in `~stixpy.product.sources.science.ScienceData` 'durtaion' -> 'duration'. (`#132 <https://github.com/TCDSolar/stixpy/pull/132>`__)
+- Fix some inconsistencies on the data units in plots, also return handle to the image from `~stixpy.product.sources.science.SpectrogramPlotMixin.plot_spectrogram`. (`#134 <https://github.com/TCDSolar/stixpy/pull/134>`__)
+
+
+Improved Documentation
+----------------------
+
+- Update README, fix graphviz RTD configuration, configure theme logo text. (`#89 <https://github.com/TCDSolar/stixpy/pull/89>`__)
+- Correct calculation of the HPC coordinate of the center of the STIX pointing in the imaging demo. (`#112 <https://github.com/TCDSolar/stixpy/pull/112>`__)
+- Update imaging demo for latest changes in `xrayvision <https://github.com/TCDSolar/xrayvision>`_. (`#115 <https://github.com/TCDSolar/stixpy/pull/115>`__)
+
+
+Trivial/Internal Changes
+------------------------
+
+- Format code with ruff and turn on ruff format in pre-commit. (`#116 <https://github.com/TCDSolar/stixpy/pull/116>`__)
+
+
+Stixpy 0.1.3 (2024-07-16)
+==================================================
+
+Bug Fixes
+---------
+
+- Fix some inconsistencies on the data units in plots, also return handle to the image from `~stixpy.product.sources.science.SpectrogramPlotMixin.plot_spectrogram`. (`#134 <https://github.com/TCDSolar/stixpy/pull/134>`__)
+- Fix bug reintroduce by last fix in `~stixpy.imaging.em.em`, update code in `~stixpy.calibration.visibility.calibrate_visibility` and imaging demo to use Tx, Ty rather than Ty, Tx as before. (`#137 <https://github.com/TCDSolar/stixpy/pull/137>`__)

CITATION.cff

@@ -0,0 +1,71 @@
+cff-version: 1.2.0
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+
+# Project information
+title: STIXpy
+abstract: >-
+  An open-source Python analysis library for the Spectrometer
+  Telescope for Imaging X-rays (STIX) instrument on Solar Orbiter.
+authors:
+  - family-names: Maloney
+    given-names: Shane
+    orcid: https://orcid.org/0000-0002-4715-1805
+    affiliation: Dublin Institute for Advanced Studies
+  - family-names: Clarke
+    given-names: Brendan
+    affiliation: >-
+      Trinity College Dublin / Dublin Institute for Advanced Studies
+  - family-names: Hayes
+    given-names: Laura
+    orcid: https://orcid.org/0000-0002-6835-2390
+    affiliation: Dublin Institute for Advanced Studies
+  - family-names: Ryan
+    given-names: Daniel F.
+    orcid: https://orcid.org/0000-0001-8661-3825
+    affiliation: >-
+      University College London, Mullard Space Science Laboratory
+      (UCL/MSSL)
+  - family-names: Massa
+    given-names: Paolo
+    orcid: https://orcid.org/0000-0002-0993-1974
+    affiliation: >-
+      University of Applied Sciences and Arts Northwestern Switzerland
+      (FHNW)
+  - family-names: Wilson
+    given-names: Alasdair
+  - family-names: Hochmuth
+    given-names: Nicky
+  - family-names: Christe
+    given-names: Steven
+    orcid: https://orcid.org/0000-0001-6127-795X
+    affiliation: NASA Goddard Space Flight Center
+  - family-names: Collier
+    given-names: Hannah
+    orcid: https://orcid.org/0000-0001-5592-8023
+    affiliation: >-
+      University of Applied Sciences and Arts Northwestern Switzerland
+      (FHNW)
+  - family-names: Long
+    given-names: Thomas
+
+repository-code: https://github.com/TCDSolar/stixpy
+url: https://stixpy.readthedocs.io
+license: BSD-3-Clause
+
+identifiers:
+  - type: doi
+    description: Zenodo concept DOI (all versions)
+    value: "10.5281/zenodo.8086101"
+  - type: url
+    description: PyPI package
+    value: https://pypi.org/project/stixpy/
+
+keywords:
+  - solar physics
+  - x-ray astronomy
+  - Solar Orbiter
+  - STIX
+  - Python
+  - astronomy

CITATION.rst

@@ -0,0 +1 @@
+stixpy/CITATION.rst