Strauss hack jt

.github/workflows/ci_workflows.yml

@@ -48,7 +48,7 @@ jobs:
             os: ubuntu-latest
             python: '3.11'
             toxenv: py311-test-alldeps-cov
-            toxposargs: --remote-data
+            toxposargs: --remote-data --run-slow
             allow_failure: false
 
           - name: OS X - Python 3.12

.github/workflows/standalone.yml

@@ -9,6 +9,7 @@ on:
     - 'v*'
   workflow_dispatch:
   pull_request:
+    types: [opened, synchronize, labeled, unlabeled]
 
 defaults:
   run:

CHANGES.rst

@@ -5,7 +5,7 @@ New Features
 ------------
 
 - Added flux/surface brightness translation and surface brightness
-  unit conversion in Cubeviz and Specviz. [#2781]
+  unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3113]
 
 - Plugin tray is now open by default. [#2892]
 
@@ -30,6 +30,10 @@ Cubeviz
 Imviz
 ^^^^^
 
+- Added a table with catalog search results. [#2915, #3101]
+
+- "Imviz Line Profiles (XY)" plugin is renamed to "Image Profiles (XY)". [#3121]
+
 Mosviz
 ^^^^^^
 
@@ -67,6 +71,12 @@ Cubeviz
 
 - Spectral Extraction: renamed ``collapse_to_spectrum(...)`` to ``extract(...)``. [#2859]
 
+- Generic FITS parsing now goes through ``specutils`` loaders first, if possible.
+  If a ``specutils`` loader is used, uncertainty is converted to standard deviation type. [#3119]
+
+- Custom Spectrum1D writer format ``jdaviz-cube`` is removed. Use ``wcs1d-fits`` from
+  ``specutils`` instead. [#2094]
+
 Imviz
 ^^^^^
 
@@ -86,6 +96,10 @@ Specviz2d
 Bug Fixes
 ---------
 
+- Markers table can now export to CSV but its columns had to be changed to accomodate this fix:
+  world and pixel (previously containing SkyCoord and pixel location tuples, respectively) are now
+  each two separate columns for world_ra/world_dec and pixel_x/pixel_y, respectively. [#3089]
+
 Cubeviz
 ^^^^^^^
 
@@ -99,6 +113,13 @@ Cubeviz
 - Flux units are now correct for collapsed spectra when using the sum function
   when units are in per steradian. [#2873]
 
+- Mouse over coordinates now responds to the selected surface brightness unit. [#2931]
+
+- Fixed MaNGA cube loading. Uncertainty type is also handled properly now. [#3119]
+
+- Fixed spectral axis value display in Markers plugin. Previously, it failed to display
+  very small values, resulting in zeroes. [#3119]
+
 Imviz
 ^^^^^
 
@@ -181,7 +202,31 @@ Other Changes and Additions
 
 - Max pinned matplotlib to <3.9 due to standalone build problems. [#2917]
 
-3.10.3 (unreleased)
+3.10.4 (unreleased)
+===================
+
+Bug Fixes
+---------
+
+- Fixed the data menu in Model Fitting not being populated if Cube Fit was toggled
+  while a spectral subset was selected. [#3123]
+
+Cubeviz
+^^^^^^^
+
+Imviz
+^^^^^
+
+Mosviz
+^^^^^^
+
+Specviz
+^^^^^^^
+
+Specviz2d
+^^^^^^^^^
+
+3.10.3 (2024-07-22)
 ===================
 
 Bug Fixes
@@ -190,6 +235,14 @@ Bug Fixes
 - Display default filepath in Export plugin, re-enable API exporting, enable relative and absolute
   path exports from the UI. [#2896]
 
+- Fixes exporting the stretch histogram from Plot Options before the Plot Options plugin is ever opened. [#2934]
+
+- Previous zoom tool is optimized to only issue one zoom update to the viewer. [#2949]
+
+- Fixes overwrite behavior for plugin plots, and properly closes overwrite warning overlay after confirmation. [#3094]
+
+- Disable all non-image exporting when the server is not running locally, to avoid confusion with the file being saved on the server. [#3096]
+
 Cubeviz
 ^^^^^^^
 
@@ -201,6 +254,8 @@ Imviz
 - Fix multiple footprints bug that prevented footprint updates on changes to the
   viewer orientation. [#2918]
 
+- Exclude subset layers from the orientation options in the Orientation plugin. [#3097]
+
 Mosviz
 ^^^^^^
 

docs/conf.py

@@ -25,6 +25,7 @@
 # Thus, any C-extensions that are needed to build the documentation will *not*
 # be accessible, and the documentation will not build correctly.
 
+import subprocess
 import sys
 import datetime
 
@@ -145,9 +146,23 @@
 version = '.'.join(release.split('.')[:2])
 
 extensions += ['sphinx.ext.extlinks', 'sphinx_design']  # noqa: F405
-gh_tag = f'v{release}' if '.dev' not in release else 'main'
-extlinks = {'gh-tree': (f'https://github.com/spacetelescope/jdaviz/tree/{gh_tag}/%s', '%s'),
-            'gh-notebook': (f'https://github.com/spacetelescope/jdaviz/blob/{gh_tag}/notebooks/%s.ipynb', '%s notebook')}  # noqa: E501
+
+# get the most recent git commit hash at build time:
+commit_hash = subprocess.run(
+    # git call for the latest commit hash:
+    'git rev-parse HEAD'.split(),
+    capture_output=True
+).stdout.decode().strip()
+
+# inject the most recent commit hash into the github links used in `sample_notebooks.rst`:
+extlinks = {
+    'gh-tree': (
+        f'https://github.com/spacetelescope/jdaviz/tree/{commit_hash}/%s', '%s'
+    ),
+    'gh-notebook': (
+        f'https://github.com/spacetelescope/jdaviz/blob/{commit_hash}/notebooks/%s.ipynb', '%s notebook'
+    )
+}
 
 # -- Options for HTML output --------------------------------------------------
 

docs/cubeviz/export_data.rst

@@ -74,7 +74,7 @@ where the mask (if available) is as defined in
 
 .. code-block:: python
 
-    mydata.write("mydata.fits", format="jdaviz-cube")
+    mydata.write("mydata.fits", format="wcs1d-fits", hdu=1)
 
 
 .. _cubeviz-export-model:

docs/imviz/plugins.rst

@@ -379,7 +379,12 @@ catalog dropdown menu.
     and works best when you only have a single image loaded in a viewer.
 
 To load a catalog from a supported `JWST ECSV catalog file <https://jwst-pipeline.readthedocs.io/en/latest/jwst/source_catalog/main.html#output-products>`_, choose "From File...".
-The file must be able to be parsed by `astropy.table.Table.read` and contain a column labeled 'sky_centroid'.
+The file must be able to be parsed by `astropy.table.Table.read` and contains the following columns:
+
+* ``'sky_centroid'``: Column with `~astropy.coordinates.SkyCoord` sky coordinates of the sources.
+* ``'label'``: Column with string identifiers of the sources. If you have numerical identifiers,
+  they will be recast as string.
+
 Clicking :guilabel:`SEARCH` will show markers for any entry within the filtered zoom window.
 
 If you have multiple viewers open, you will see another dropdown menu to select the active
@@ -397,6 +402,8 @@ are not stored. To save the current result before submitting a new query, you ca
     The table returned from the API above may cover more sources than shown in the currently zoomed-in
     portion of the image. Additional steps will be needed to filter out these points, if necessary.
 
+Performing a search populates a table that contains the
+right ascension, declination, and the object ID of the found sources. 
 
 .. _imviz-footprints:
 

docs/installation.rst

@@ -108,7 +108,7 @@ You also need the up-to-date tags for proper software versioning:
     git rebase upstream/main
 
 For the rest of contributing workflow, it is very similar to
-`how to make a code contribution to astropy <https://docs.astropy.org/en/latest/development/workflow/development_workflow.html>`_,
+`how to make a code contribution to astropy <https://docs.astropy.org/en/latest/development/quickstart.html>`_,
 including setting up virtual environments, git basics, and more.
 
 An exception is the change log; if your patch requires a change log, see ``CHANGES.rst`` for examples.

docs/reference/api_nuts_bolts.rst

@@ -23,6 +23,10 @@ Utilities API
    :no-inheritance-diagram:
    :no-inherited-members:
 
+.. automodapi:: jdaviz.configs.cubeviz.plugins.mixins
+   :no-inheritance-diagram:
+   :no-inherited-members:
+
 .. automodapi:: jdaviz.configs.imviz.wcs_utils
    :no-inheritance-diagram:
    :no-inherited-members:

docs/sample_notebooks.rst

@@ -10,6 +10,6 @@ These tools include three types of example Jupyter notebooks.
 
 1. :gh-tree:`Sample Jdaviz Notebooks <notebooks>` that illustrate how to use Jdaviz and various API calls. These notebooks are located in the ``notebooks`` sub-directory of the git repository.
 
-2. `Sample JDAT notebooks <https://jwst-docs.stsci.edu/jwst-post-pipeline-data-analysis/data-analysis-example-jupyter-notebooks>`_ that illustrate likely science workflows with data obtained from the various JWST instruments. These notebook incorporate ``astropy`` and Jdaviz when possible.
+2. `Sample JDAT notebooks <https://jwst-docs.stsci.edu/jwst-post-pipeline-data-analysis#JWSTPostPipelineDataAnalysis-JWSTdataanalysis(JDAT)notebooks>`_ that illustrate likely science workflows with data obtained from the various JWST instruments. These notebooks incorporate ``astropy`` and Jdaviz when possible.
 
 3. `Sample JWST pipeline notebooks <https://jwst-docs.stsci.edu/jwst-science-calibration-pipeline-overview/example-jupyter-notebooks-running-the-pipeline>`_ that illustrate how to run the JWST science calibration pipeline.

jdaviz/app.py

@@ -76,20 +76,17 @@ def equivalent_units(self, data, cid, units):
                     'Jy', 'mJy', 'uJy', 'MJy',
                     'W / (m2 Hz)', 'W / (Hz m2)',  # Order is different in astropy v5.3
                     'eV / (s m2 Hz)', 'eV / (Hz s m2)',
-                    'erg / (s cm2)',
                     'erg / (s cm2 Angstrom)', 'erg / (s cm2 Angstrom)',
                     'erg / (s cm2 Hz)', 'erg / (Hz s cm2)',
-                    'ph / (s cm2 Angstrom)', 'ph / (s cm2 Angstrom)',
+                    'ph / (Angstrom s cm2)',
                     'ph / (Hz s cm2)', 'ph / (Hz s cm2)', 'bol', 'AB', 'ST'
                 ]
                 + [
                     'Jy / sr', 'mJy / sr', 'uJy / sr', 'MJy / sr',
                     'W / (Hz sr m2)',
-                    'eV / (s m2 Hz sr)',
-                    'erg / (s cm2 sr)',
-                    'erg / (s cm2 Angstrom sr)', 'erg / (s cm2 Hz sr)',
-                    'ph / (s cm2 Angstrom sr)', 'ph / (s cm2 Hz sr)',
-                    'bol / sr', 'AB / sr', 'ST / sr'
+                    'eV / (Hz s sr m2)',
+                    'erg / (s sr cm2)',
+                    'AB / sr'
                 ])
         else:  # spectral axis
             # prefer Hz over Bq and um over micron
@@ -2601,7 +2598,7 @@ def load_configuration(self, path=None, config=None):
         if self.config in ALL_JDAVIZ_CONFIGS:
             self.docs_link = f'https://jdaviz.readthedocs.io/en/{self.vdocs}/{self.config}/index.html'  # noqa
         else:
-            self.docs_link = 'https://jdaviz.readthedocs.io'
+            self.docs_link = f'https://jdaviz.readthedocs.io/en/{self.vdocs}'
 
         self.state.settings.update(config.get('settings'))
 

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -33,6 +33,7 @@ tray:
   - specviz-line-analysis
   - cubeviz-moment-maps
   - imviz-aper-phot-simple
+  - cubeviz-sonify-data
   - export
   - about
 viewer_area:

jdaviz/configs/cubeviz/helper.py

@@ -1,9 +1,3 @@
-import numpy as np
-from astropy.io import fits
-from astropy.io import registry as io_registry
-from specutils import Spectrum1D
-from specutils.io.registers import _astropy_has_priorities
-
 from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.helpers import ImageConfigHelper
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
@@ -166,63 +160,3 @@ def get_aperture_photometry_results(self):
 
         """
         return self.plugins['Aperture Photometry']._obj.export_table()
-
-
-# TODO: We can remove this when specutils supports it, i.e.,
-#       https://github.com/astropy/specutils/issues/592 and
-#       https://github.com/astropy/specutils/pull/1009
-# NOTE: Cannot use custom_write decorator from specutils because
-#       that involves asking user to manually put something in
-#       their ~/.specutils directory.
-
-def jdaviz_cube_fitswriter(spectrum, file_name, **kwargs):
-    """This is a custom writer for Spectrum1D data cube.
-    This writer is specifically targetting data cube
-    generated from Cubeviz plugins (e.g., cube fitting)
-    with FITS WCS. It writes out data in the following format
-    (with MASK only exist when applicable)::
-
-        No.    Name      Ver    Type
-          0  PRIMARY       1 PrimaryHDU
-          1  SCI           1 ImageHDU (float32)
-          2  MASK          1 ImageHDU (uint16)
-
-    The FITS file generated by this writer does not need a
-    custom reader to be read back into Spectrum1D.
-
-    Examples
-    --------
-    To write out a Spectrum1D cube using this writer:
-
-    >>> spec.write("my_output.fits", format="jdaviz-cube", overwrite=True)  # doctest: +SKIP
-
-    """
-    pri_hdu = fits.PrimaryHDU()
-
-    flux = spectrum.flux
-    sci_hdu = fits.ImageHDU(flux.value.astype(np.float32))
-    sci_hdu.name = "SCI"
-    sci_hdu.header.update(spectrum.meta)
-    sci_hdu.header.update(spectrum.wcs.to_header())
-    sci_hdu.header['BUNIT'] = flux.unit.to_string(format='fits')
-
-    hlist = [pri_hdu, sci_hdu]
-
-    # https://specutils.readthedocs.io/en/latest/spectrum1d.html#including-masks
-    # Good: False or 0
-    # Bad: True or non-zero
-    if spectrum.mask is not None:
-        mask_hdu = fits.ImageHDU(spectrum.mask.astype(np.uint16))
-        mask_hdu.name = "MASK"
-        hlist.append(mask_hdu)
-
-    hdulist = fits.HDUList(hlist)
-    hdulist.writeto(file_name, **kwargs)
-
-
-if _astropy_has_priorities():
-    kwargs = {"priority": 0}
-else:  # pragma: no cover
-    kwargs = {}
-io_registry.register_writer(
-    "jdaviz-cube", Spectrum1D, jdaviz_cube_fitswriter, force=False, **kwargs)

jdaviz/configs/cubeviz/plugins/__init__.py

@@ -1,6 +1,8 @@
 from .tools import *  # noqa
+from .mixins import *  # noqa
 from .viewers import *  # noqa
 from .parsers import *  # noqa
 from .moment_maps.moment_maps import *  # noqa
 from .slice.slice import * # noqa
 from .spectral_extraction.spectral_extraction import * # noqa
+from .sonify_data.sonify_data import * # noqa