Merge pull request #3120 from bmorris3/cube-base-class

Add Rampviz helper, generalize cube config helper and profile viewer

.github/labeler.yml

@@ -60,3 +60,8 @@ specviz2d:
 - changed-files:
   - any-glob-to-any-file:
     - jdaviz/configs/specviz2d/**/*
+
+rampviz:
+- changed-files:
+  - any-glob-to-any-file:
+    - jdaviz/configs/rampviz/**/*

docs/cubeviz/index.rst

@@ -11,7 +11,7 @@
     :alt: Introductory video tour of the Cubeviz configuration and its features
 
 Cubeviz is a visualization and analysis toolbox for data cubes from
-integral field units (IFUs). It is built as part of the
+integral field units (IFUs). It is built on top of the
 `glue visualization <https://glueviz.org>`_ tool. Cubeviz is designed to work
 with data cubes from the NIRSpec and MIRI instruments on JWST, and will work
 with IFU data cubes. It uses

docs/index.rst

@@ -55,6 +55,16 @@ Jdaviz
 
          Jump to Mosviz
 
+   .. grid-item-card::
+      :img-top: logos/cube.svg
+
+      .. button-ref:: rampviz/index
+         :expand:
+         :color: primary
+         :click-parent:
+
+         Jump to Rampviz
+
 ``jdaviz`` is a package of astronomical data analysis visualization
 tools based on the Jupyter platform.  These GUI-based tools link data
 visualization and interactive analysis.  They are designed to work

docs/index_using_jdaviz.rst

@@ -15,6 +15,7 @@ User Guide
   cubeviz/index
   specviz2d/index
   mosviz/index
+  rampviz/index
   plugin_api
   save_state
   display

docs/rampviz/index.rst

@@ -0,0 +1,21 @@
+.. |cubeviz_logo| image:: ../logos/cube.svg
+    :height: 42px
+
+.. _rampviz:
+
+######################
+|cubeviz_logo| Rampviz
+######################
+
+
+Rampviz is a visualization and analysis toolbox for ramp cubes from
+infrared detectors. It is built on top of the
+`glue visualization <https://glueviz.org>`_ tool. Rampviz is designed to work
+with ramp files from the Roman Space Telescope and JWST.
+
+**Using Rampviz**
+
+.. toctree::
+  :maxdepth: 2
+
+  plugins

docs/rampviz/plugins.rst

@@ -0,0 +1,66 @@
+*********************
+Data Analysis Plugins
+*********************
+
+
+
+.. _rampviz-metadata-viewer:
+
+Metadata Viewer
+===============
+
+.. seealso::
+
+    :ref:`Metadata Viewer <imviz_metadata-viewer>`
+        Documentation on using the metadata viewer.
+
+
+.. _rampviz-plot-options:
+
+Plot Options
+============
+
+This plugin gives access to per-viewer and per-layer plotting options.
+To show axes on image viewers, toggle on the "Show axes" option at the bottom of the plugin.
+
+.. seealso::
+
+    :ref:`Image Plot Options <imviz-display-settings>`
+        Documentation on Imviz display settings in the Jdaviz viewers.
+
+.. _rampviz-subset-plugin:
+
+Subset Tools
+============
+
+.. seealso::
+
+    :ref:`Subset Tools <imviz-subset-plugin>`
+        Imviz documentation describing the concept of subsets in Jdaviz.
+
+
+Markers
+=======
+
+.. seealso::
+
+    :ref:`Markers <markers-plugin>`
+        Imviz documentation describing the markers plugin.
+
+.. _rampviz-slice:
+
+Slice
+=====
+
+.. seealso::
+
+    :ref:`Slice <slice>`
+        Documentation on using the Slice plugin.
+
+.. _ramp-extraction:
+
+Ramp Extraction
+===============
+
+
+

docs/reference/api_configs.rst

@@ -20,3 +20,6 @@ Helpers API
 
 .. automodapi:: jdaviz.configs.specviz2d.helper
    :no-inheritance-diagram:
+
+.. automodapi:: jdaviz.configs.rampviz.helper
+   :no-inheritance-diagram:

docs/reference/api_parsers.rst

@@ -17,3 +17,6 @@ Parsers API
 
 .. automodapi:: jdaviz.configs.specviz2d.plugins.parsers
    :no-inheritance-diagram:
+
+.. automodapi:: jdaviz.configs.rampviz.plugins.parsers
+   :no-inheritance-diagram:

docs/reference/api_plugins.rst

@@ -48,6 +48,9 @@ Plugins API
 .. automodapi:: jdaviz.configs.cubeviz.plugins.slice.slice
    :no-inheritance-diagram:
 
+.. automodapi:: jdaviz.configs.cubeviz.plugins.spectral_extraction.spectral_extraction
+   :no-inheritance-diagram:
+
 .. automodapi:: jdaviz.configs.imviz.plugins.aper_phot_simple.aper_phot_simple
    :no-inheritance-diagram:
 
@@ -86,3 +89,6 @@ Plugins API
 
 .. automodapi:: jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction
    :no-inheritance-diagram:
+
+.. automodapi:: jdaviz.configs.rampviz.plugins.ramp_extraction.ramp_extraction
+   :no-inheritance-diagram:

docs/reference/api_viewers.rst

@@ -17,3 +17,6 @@ Viewers API
 
 .. automodapi:: jdaviz.configs.specviz.plugins.viewers
    :no-inheritance-diagram:
+
+.. automodapi:: jdaviz.configs.rampviz.plugins.viewers
+   :no-inheritance-diagram:

jdaviz/__init__.py

@@ -13,11 +13,14 @@
 
 # Top-level API as exposed to users.
 from jdaviz.app import *  # noqa: F401, F403
-from jdaviz.configs.specviz import Specviz  # noqa: F401
-from jdaviz.configs.specviz2d import Specviz2d  # noqa: F401
-from jdaviz.configs.mosviz import Mosviz  # noqa: F401
+
 from jdaviz.configs.cubeviz import Cubeviz  # noqa: F401
 from jdaviz.configs.imviz import Imviz  # noqa: F401
+from jdaviz.configs.mosviz import Mosviz  # noqa: F401
+from jdaviz.configs.rampviz import Rampviz  # noqa: F401
+from jdaviz.configs.specviz import Specviz  # noqa: F401
+from jdaviz.configs.specviz2d import Specviz2d  # noqa: F401
+
 from jdaviz.utils import enable_hot_reloading  # noqa: F401
 from jdaviz.core.launcher import open  # noqa: F401
 

jdaviz/app.py

@@ -99,10 +99,14 @@ def to_unit(self, data, cid, values, original_units, target_units):
         # should return the converted values. Note that original_units
         # gives the units of the values array, which might not be the same
         # as the original native units of the component in the data.
-        if cid.label == "flux":
+
+        if cid.label == 'Pixel Axis 0 [z]' and target_units == '':
+            # handle ramps loaded into Rampviz by avoiding conversion
+            # of the groups axis:
+            return values
+        elif cid.label == "flux":
             try:
                 spec = data.get_object(cls=Spectrum1D)
-
             except RuntimeError:
                 data = data.get_object(cls=NDDataArray)
                 spec = Spectrum1D(flux=data.data * u.Unit(original_units))
@@ -1290,6 +1294,9 @@ def _get_display_unit(self, axis):
                     if check_if_unit_is_per_solid_angle(sv_y_unit):
                         return sv_y_unit
                     return sv_y_unit / u.sr
+            elif axis == 'temporal':
+                # No unit for ramp's time (group/resultant) axis:
+                return None
             else:
                 raise ValueError(f"could not find units for axis='{axis}'")
         uc = self._jdaviz_helper.plugins.get('Unit Conversion')._obj
@@ -1747,7 +1754,8 @@ def _get_first_viewer_reference_name(
             require_spectrum_2d_viewer=False,
             require_table_viewer=False,
             require_flux_viewer=False,
-            require_image_viewer=False
+            require_image_viewer=False,
+            require_profile_viewer=False,
     ):
         """
         Return the viewer reference name of the first available viewer.
@@ -1761,12 +1769,16 @@ def _get_first_viewer_reference_name(
         from jdaviz.configs.mosviz.plugins.viewers import (
             MosvizTableViewer, MosvizProfile2DView
         )
+        from jdaviz.configs.rampviz.plugins.viewers import (
+            RampvizImageView, RampvizProfileView
+        )
 
         spectral_viewers = (SpecvizProfileView, CubevizProfileView)
         spectral_2d_viewers = (MosvizProfile2DView, )
         table_viewers = (MosvizTableViewer, )
-        image_viewers = (ImvizImageView, CubevizImageView)
-        flux_viewers = (CubevizImageView, )
+        image_viewers = (ImvizImageView, CubevizImageView, RampvizImageView)
+        flux_viewers = (CubevizImageView, RampvizImageView)
+        ramp_viewers = (RampvizProfileView, )
 
         for vid in self._viewer_store:
             viewer_item = self._viewer_item_by_id(vid)
@@ -1789,6 +1801,9 @@ def _get_first_viewer_reference_name(
             elif require_flux_viewer:
                 if isinstance(self._viewer_store[vid], flux_viewers) and is_returnable:
                     return viewer_item['reference']
+            elif require_profile_viewer:
+                if isinstance(self._viewer_store[vid], ramp_viewers) and is_returnable:
+                    return viewer_item['reference']
             else:
                 if is_returnable:
                     return viewer_item['reference']

jdaviz/configs/__init__.py

@@ -1,6 +1,7 @@
 from .cubeviz import *  # noqa
-from .specviz import *  # noqa
-from .specviz2d import *  # noqa
 from .default import *  # noqa
-from .mosviz import *  # noqa
 from .imviz import *  # noqa
+from .mosviz import *  # noqa
+from .rampviz import * # noqa
+from .specviz import *  # noqa
+from .specviz2d import *  # noqa

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -23,7 +23,7 @@ tray:
   - g-data-quality
   - g-subset-plugin
   - g-markers
-  - cubeviz-slice
+  - cube-slice
   - g-unit-conversion
   - cubeviz-spectral-extraction
   - g-gaussian-smooth

jdaviz/configs/cubeviz/helper.py

@@ -1,9 +1,8 @@
-from jdaviz.core.events import SnackbarMessage
-from jdaviz.core.helpers import ImageConfigHelper
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
 from jdaviz.configs.specviz import Specviz
-from jdaviz.core.events import (AddDataMessage,
-                                SliceSelectSliceMessage)
+from jdaviz.core.events import AddDataMessage, SnackbarMessage
+from jdaviz.core.helpers import CubeConfigHelper
+from jdaviz.configs.cubeviz.plugins.viewers import CubevizImageView
 
 __all__ = ['Cubeviz']
 
@@ -12,19 +11,22 @@
                         "Wavenumber", "Velocity", "Energy"]
 
 
-class Cubeviz(ImageConfigHelper, LineListMixin):
+class Cubeviz(CubeConfigHelper, LineListMixin):
     """Cubeviz Helper class"""
     _default_configuration = 'cubeviz'
     _default_spectrum_viewer_reference_name = "spectrum-viewer"
     _default_uncert_viewer_reference_name = "uncert-viewer"
     _default_flux_viewer_reference_name = "flux-viewer"
     _default_image_viewer_reference_name = "image-viewer"
+    _cube_viewer_default_label = _default_flux_viewer_reference_name
 
     _loaded_flux_cube = None
     _loaded_uncert_cube = None
+    _cube_viewer_cls = CubevizImageView
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+
         self.app.hub.subscribe(self, AddDataMessage,
                                handler=self._set_spectrum_x_axis)
 
@@ -106,8 +108,7 @@ def select_wavelength(self, wavelength):
         """
         if not isinstance(wavelength, (int, float)):
             raise TypeError("wavelength must be a float or int")
-        msg = SliceSelectSliceMessage(value=wavelength, sender=self)
-        self.app.hub.broadcast(msg)
+        self.select_slice(wavelength)
 
     @property
     def specviz(self):

jdaviz/configs/cubeviz/plugins/__init__.py

@@ -1,7 +1,7 @@
-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 .tools import *  # noqa

jdaviz/configs/cubeviz/plugins/mixins.py

@@ -14,7 +14,7 @@ def slice_component_label(self):
 
     @property
     def slice_display_unit_name(self):
-        return 'spectral'
+        return 'spectral' if self.jdaviz_app.config == 'cubeviz' else 'temporal'
 
     @cached_property
     def slice_indicator(self):
@@ -77,7 +77,7 @@ def slice_component_label(self):
 
     @property
     def slice_display_unit_name(self):
-        return 'spectral'
+        return 'spectral' if self.jdaviz_app.config == 'cubeviz' else 'temporal'
 
     @property
     def slice_values(self):
@@ -91,6 +91,11 @@ def slice_values(self):
         converted_axis = np.array([])
         for layer in self.layers:
             world_comp_ids = layer.layer.data.world_component_ids
+
+            if not len(world_comp_ids):
+                # rampviz uses coordinate components:
+                world_comp_ids = layer.layer.data.coordinate_components
+
             if self.slice_index >= len(world_comp_ids):
                 # Case where 2D image is loaded in image viewer
                 continue

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -10,7 +10,6 @@
 from astropy.wcs import WCS
 from specutils import Spectrum1D
 
-from jdaviz.configs.imviz.plugins.parsers import prep_data_layer_as_dq
 from jdaviz.core.registries import data_parser_registry
 from jdaviz.utils import standardize_metadata, PRIHDR_KEY, download_uri_to_path
 
@@ -342,7 +341,11 @@ def _parse_jwst_s3d(app, hdulist, data_label, ext='SCI',
     app.add_data(data, data_label, parent=parent)
 
     # get glue data and update if DQ:
+
     if ext == 'DQ':
+        # prevent circular import:
+        from jdaviz.configs.imviz.plugins.parsers import prep_data_layer_as_dq
+
         data = app.data_collection[-1]
         prep_data_layer_as_dq(data)