diff --git a/CHANGES.rst b/CHANGES.rst index b2f5d5668e..f0410f2be2 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -27,6 +27,8 @@ Cubeviz - Background subtraction support within Spectral Extraction. [#2859] +- Aperture photometry plugin now listens to changes in display unit. [#3118] + Imviz ^^^^^ diff --git a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py index 9d922f6a57..032c9fa2ad 100644 --- a/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py +++ b/jdaviz/configs/cubeviz/plugins/tests/test_cubeviz_aperphot.py @@ -1,13 +1,12 @@ import numpy as np import pytest from astropy import units as u +from astropy.table import Table from astropy.tests.helper import assert_quantity_allclose from astropy.utils.exceptions import AstropyUserWarning from numpy.testing import assert_allclose from regions import RectanglePixelRegion, PixCoord -from jdaviz.configs.cubeviz.plugins.moment_maps.moment_maps import SPECUTILS_LT_1_15_1 - def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_microns): cubeviz_helper.load_data(image_cube_hdu_obj_microns, data_label="test") @@ -82,53 +81,6 @@ def test_cubeviz_aperphot_cube_orig_flux(cubeviz_helper, image_cube_hdu_obj_micr assert np.isnan(row["slice_wave"]) -def test_cubeviz_aperphot_generated_2d_moment(cubeviz_helper, image_cube_hdu_obj_microns): - cubeviz_helper.load_data(image_cube_hdu_obj_microns, data_label="test") - flux_unit = u.Unit("1E-17 erg*s^-1*cm^-2*Angstrom^-1") - - moment_plg = cubeviz_helper.plugins["Moment Maps"] - _ = moment_plg.calculate_moment() - - # Need this to make it available for photometry data drop-down. - cubeviz_helper.app.add_data_to_viewer("uncert-viewer", "test[FLUX] moment 0") - - aper = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=3, height=5) - cubeviz_helper.load_regions(aper) - - plg = cubeviz_helper.plugins["Aperture Photometry"]._obj - plg.dataset_selected = "test[FLUX] moment 0" - plg.aperture_selected = "Subset 1" - plg.vue_do_aper_phot() - row = cubeviz_helper.get_aperture_photometry_results()[0] - - # Basically, we should recover the input rectangle here. - if SPECUTILS_LT_1_15_1: - moment_sum = 540 * flux_unit - moment_mean = 36 * flux_unit - else: - moment_unit = flux_unit * u.um - moment_sum = 0.54 * moment_unit - moment_mean = 0.036 * moment_unit - assert_allclose(row["xcenter"], 1 * u.pix) - assert_allclose(row["ycenter"], 2 * u.pix) - sky = row["sky_center"] - assert_allclose(sky.ra.deg, 205.43985906934287) - assert_allclose(sky.dec.deg, 27.003490103642033) - assert_allclose(row["sum"], moment_sum) # 3 (w) x 5 (h) x 36 (v) - assert_allclose(row["sum_aper_area"], 15 * (u.pix * u.pix)) # 3 (w) x 5 (h) - assert_allclose(row["mean"], moment_mean) - assert np.isnan(row["slice_wave"]) - - # Moment 1 has no compatible unit, so should not be available for photometry. - moment_plg.n_moment = 1 - moment_plg.reference_wavelength = 5 - _ = moment_plg.calculate_moment() - m1_lbl = "test[FLUX] moment 1" - cubeviz_helper.app.add_data_to_viewer("uncert-viewer", m1_lbl) - assert (m1_lbl in cubeviz_helper.app.data_collection.labels and - m1_lbl not in plg.dataset.choices) - - def test_cubeviz_aperphot_generated_3d_gaussian_smooth(cubeviz_helper, image_cube_hdu_obj_microns): cubeviz_helper.load_data(image_cube_hdu_obj_microns, data_label="test") flux_unit = u.Unit("1E-17 erg*s^-1*cm^-2*Angstrom^-1") @@ -192,3 +144,109 @@ def test_cubeviz_aperphot_cube_orig_flux_mjysr(cubeviz_helper, spectrum1d_cube_c assert_allclose(row["mean"], 5 * (u.MJy / u.sr)) # TODO: check if slice plugin has value_unit set correctly assert_quantity_allclose(row["slice_wave"], 0.46236 * u.um) + + +def _compare_table_units(orig_tab, new_tab, orig_flux_unit=None, + new_flux_unit=None): + + # compare two photometry tables with different units and make sure that the + # units are as expected, and that they are equivalent once translated + + for i, row in enumerate(orig_tab): + new_unit = new_tab[i]['unit'] or '-' + orig_unit = row['unit'] or '-' + if new_unit != '-' and orig_unit != '-': + + new_unit = u.Unit(new_unit) + new = float(new_tab[i]['result']) * new_unit + + orig_unit = u.Unit(orig_unit) + orig = float(row['result']) * orig_unit + + # first check that the actual units differ as expected, + # as comparing them would pass if they were the same unit + if orig_flux_unit in orig_unit.bases: + assert new_flux_unit in new_unit.bases + + orig_converted = orig.to(new_unit) + assert_quantity_allclose(orig_converted, new) + + +def test_cubeviz_aperphot_unit_conversion(cubeviz_helper, spectrum1d_cube_custom_fluxunit): + """Make sure outputs of the aperture photometry plugin in Cubeviz + reflect the correct choice of display units from the Unit + Conversion plugin. + """ + + # create cube with units of MJy / sr + mjy_sr_cube = spectrum1d_cube_custom_fluxunit(fluxunit=u.MJy / u.sr, + shape=(5, 5, 4)) + + # create apertures for photometry and background + aper = RectanglePixelRegion(center=PixCoord(x=2, y=3), width=1, height=1) + bg = RectanglePixelRegion(center=PixCoord(x=1, y=2), width=1, height=1) + + cubeviz_helper.load_data(mjy_sr_cube, data_label="test") + cubeviz_helper.load_regions([aper, bg]) + + ap = cubeviz_helper.plugins['Aperture Photometry']._obj + + ap.dataset_selected = "test[FLUX]" + ap.aperture_selected = "Subset 1" + ap.background_selected = "Subset 2" + ap.vue_do_aper_phot() + + uc = cubeviz_helper.plugins['Unit Conversion']._obj + + # check that initial units are synced between plugins + assert uc.flux_unit.selected == 'MJy' + assert uc.angle_unit.selected == 'sr' + assert ap.display_flux_or_sb_unit == 'MJy / sr' + assert ap.flux_scaling_display_unit == 'MJy' + + # and defaults for inputs are in the correct unit + assert_allclose(ap.flux_scaling, 0.003631) + assert_allclose(ap.background_value, 49) + + # output table in original units to compare to + # outputs after converting units + orig_tab = Table(ap.results) + + # change units, which will change the numerator of the current SB unit + uc.flux_unit.selected = 'Jy' + + # make sure inputs were re-computed in new units + # after the unit change + assert_allclose(ap.flux_scaling, 3631) + assert_allclose(ap.background_value, 4.9e7) + + # re-do photometry and make sure table is in new units + # and consists of the same results as before converting units + ap.vue_do_aper_phot() + new_tab = Table(ap.results) + + _compare_table_units(orig_tab, new_tab, orig_flux_unit=u.MJy, + new_flux_unit=u.Jy) + + # test manual background and flux scaling option input in current + # units (Jy / sr) will be used correctly and converted to data units + ap.background_selected == 'Manual' + ap.background_value = 1.0e7 + ap.flux_scaling = 1000 + ap.vue_do_aper_phot() + orig_tab = Table(ap.results) + + # change units back to MJy/sr from Jy/sr + uc.flux_unit.selected = 'MJy' + + # make sure background input in Jy/sr is now in MJy/sr + assert_allclose(ap.background_value, 10) + assert_allclose(ap.flux_scaling, 0.001) + + # and that photometry results match those before unit converson, + # but with units converted + ap.vue_do_aper_phot() + new_tab = Table(ap.results) + + _compare_table_units(orig_tab, new_tab, orig_flux_unit=u.Jy, + new_flux_unit=u.MJy) diff --git a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py index e4b29a2b6e..bf9d63be8e 100644 --- a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py +++ b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py @@ -15,12 +15,14 @@ from traitlets import Any, Bool, Integer, List, Unicode, observe from jdaviz.core.custom_traitlets import FloatHandleEmpty -from jdaviz.core.events import SnackbarMessage, LinkUpdatedMessage, SliceValueUpdatedMessage +from jdaviz.core.events import (GlobalDisplayUnitChanged, SnackbarMessage, + LinkUpdatedMessage, SliceValueUpdatedMessage) from jdaviz.core.region_translators import regions2aperture, _get_region_from_spatial_subset from jdaviz.core.registries import tray_registry from jdaviz.core.template_mixin import (PluginTemplateMixin, DatasetMultiSelectMixin, SubsetSelect, ApertureSubsetSelectMixin, TableMixin, PlotMixin, MultiselectMixin, with_spinner) +from jdaviz.core.validunits import check_if_unit_is_per_solid_angle from jdaviz.utils import PRIHDR_KEY __all__ = ['SimpleAperturePhotometry'] @@ -66,6 +68,8 @@ class SimpleAperturePhotometry(PluginTemplateMixin, ApertureSubsetSelectMixin, # Cubeviz only cube_slice = Unicode("").tag(sync=True) is_cube = Bool(False).tag(sync=True) + display_flux_or_sb_unit = Unicode("").tag(sync=True) + flux_scaling_display_unit = Unicode("").tag(sync=True) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @@ -109,8 +113,7 @@ def valid_cubeviz_datasets(data): acceptable_types = ['spectral flux density wav', 'photon flux density wav', 'spectral flux density', - 'photon flux density', - 'energy flux'] # Moment map 0 + 'photon flux density'] return ((data.ndim in (2, 3)) and ((img_unit == (u.MJy / u.sr)) or (img_unit.physical_type in acceptable_types))) @@ -119,6 +122,9 @@ def valid_cubeviz_datasets(data): self.session.hub.subscribe(self, SliceValueUpdatedMessage, handler=self._on_slice_changed) + self.hub.subscribe(self, GlobalDisplayUnitChanged, + handler=self._on_display_units_changed) + # TODO: expose public API once finalized # @property # def user_api(self): @@ -144,6 +150,87 @@ def _on_dataset_selected_changed(self, event={}): else: self.is_cube = False + def _on_display_units_changed(self, event={}): + + """ + Handle change of display units from Unit Conversion plugin (for now, + cubeviz only). If new display units differ from input data units, input + parameters for ap. phot. (i.e background, flux scaling) are converted + to the new units. Photometry will remain in previous unit until + 'calculate' is pressed again. + """ + + if self.config == 'cubeviz': + + # get previously selected display units + prev_display_flux_or_sb_unit = self.display_flux_or_sb_unit + prev_flux_scale_unit = self.flux_scaling_display_unit + + # update display unit traitlets to new selection + self._set_display_unit_of_selected_dataset() + + # convert the previous background and flux scaling values to new unit so + # re-calculating photometry with the current selections will produce + # the previous output with the new unit. + if prev_display_flux_or_sb_unit != '': + + # convert background to new unit + if self.background_value is not None: + + prev_unit = u.Unit(prev_display_flux_or_sb_unit) + new_unit = u.Unit(self.display_flux_or_sb_unit) + + bg = self.background_value * prev_unit + self.background_value = bg.to_value( + new_unit, u.spectral_density(self._cube_wave)) + + # convert flux scaling to new unit + if self.flux_scaling is not None: + prev_unit = u.Unit(prev_flux_scale_unit) + new_unit = u.Unit(self.flux_scaling_display_unit) + + fs = self.flux_scaling * prev_unit + self.flux_scaling = fs.to_value( + new_unit, u.spectral_density(self._cube_wave)) + + def _set_display_unit_of_selected_dataset(self): + + """ + Set the display_flux_or_sb_unit and flux_scaling_display_unit traitlets, + which depend on if the selected data set is flux or surface brightness, + and the corresponding global display unit for either flux or + surface brightness. + """ + + if not self.dataset_selected or not self.aperture_selected: + self.display_flux_or_sb_unit = '' + self.flux_scaling_display_unit = '' + return + + data = self.dataset.selected_dc_item + comp = data.get_component(data.main_components[0]) + if comp.units: + # if data is something-per-solid-angle, its a SB unit and we should + # use the selected global display unit for SB + if check_if_unit_is_per_solid_angle(comp.units): + flux_or_sb = 'sb' + else: + flux_or_sb = 'flux' + + disp_unit = self.app._get_display_unit(flux_or_sb) + + self.display_flux_or_sb_unit = disp_unit + + # now get display unit for flux_scaling_display_unit. this unit will always + # be in flux, but it will not be derived from the global flux display unit + # note : need to generalize this for non-sr units eventually + fs_unit = u.Unit(disp_unit) * u.sr + self.flux_scaling_display_unit = fs_unit.to_string() + + else: + self.display_flux_or_sb_unit = '' + self.flux_scaling_display_unit = '' + def _get_defaults_from_metadata(self, dataset=None): defaults = {} if dataset is None: @@ -162,6 +249,12 @@ def _get_defaults_from_metadata(self, dataset=None): if telescope == 'JWST': # Hardcode the flux conversion factor from MJy to ABmag mjy2abmag = 0.003631 + + # if display unit is different, translate + if (self.config == 'cubeviz') and (self.display_flux_or_sb_unit != ''): + disp_unit = u.Unit(self.display_flux_or_sb_unit) + mjy2abmag = (mjy2abmag * u.Unit("MJy/sr")).to_value(disp_unit) + if 'photometry' in meta and 'pixelarea_arcsecsq' in meta['photometry']: defaults['pixel_area'] = meta['photometry']['pixelarea_arcsecsq'] if 'bunit_data' in meta and meta['bunit_data'] == u.Unit("MJy/sr"): @@ -242,6 +335,11 @@ def _dataset_selected_changed(self, event={}): f"Failed to extract {self.dataset_selected}: {repr(e)}", color='error', sender=self)) + # get correct display unit for newly selected dataset + if self.config == 'cubeviz': + # set display_flux_or_sb_unit and flux_scaling_display_unit + self._set_display_unit_of_selected_dataset() + # auto-populate background, if applicable. self._aperture_selected_changed() @@ -276,6 +374,10 @@ def _aperture_selected_changed(self, event={}): if self.multiselect: self._background_selected_changed() return + + if self.config == 'cubeviz': + self._set_display_unit_of_selected_dataset() + # NOTE: aperture_selected can be triggered here before aperture_selected_validity is updated # so we'll still allow the snackbar to be raised as a second warning to the user and to # avoid acting on outdated information @@ -331,7 +433,15 @@ def _calc_background_median(self, reg, data=None): img_stat = aper_mask_stat.get_values(comp_data, mask=None) # photutils/background/_utils.py --> nanmedian() - return np.nanmedian(img_stat) # Naturally in data unit + bg_md = np.nanmedian(img_stat) # Naturally in data unit + + # convert to display unit, if necessary (cubeviz only) + + if (self.config == 'cubeviz') and (self.display_flux_or_sb_unit != '') and comp.units: + bg_md = (bg_md * u.Unit(comp.units)).to_value( + u.Unit(self.display_flux_or_sb_unit), u.spectral_density(self._cube_wave)) + + return bg_md @observe('background_selected') def _background_selected_changed(self, event={}): @@ -359,8 +469,13 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, background_value=None, pixel_area=None, counts_factor=None, flux_scaling=None, add_to_table=True, update_plots=True): """ - Calculate aperture photometry given the values set in the plugin or any overrides provided - as arguments here (which will temporarily override plugin values for this calculation only). + Calculate aperture photometry given the values set in the plugin or + any overrides provided as arguments here (which will temporarily + override plugin values for this calculation only). + + Note: Values set in the plugin in Cubeviz are in the selected display unit + from the Unit conversion plugin. Overrides are, as the docstrings note, + assumed to be in the units of the selected dataset. Parameters ---------- @@ -421,6 +536,13 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, del self.app.fitted_models[self._fitted_model_name] comp = data.get_component(data.main_components[0]) + if comp.units: + img_unit = u.Unit(comp.units) + else: + img_unit = None + + if self.config == 'cubeviz': + display_unit = u.Unit(self.display_flux_or_sb_unit) if background is not None and background not in self.background.choices: # pragma: no cover raise ValueError(f"background must be one of {self.background.choices}") @@ -430,14 +552,35 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, raise ValueError("cannot provide background_value with background!='Manual'") elif (background == 'Manual' or (background is None and self.background.selected == 'Manual')): + background_value = self.background_value + + # cubeviz: background_value set in plugin is in display units + # convert temporarily to image units for calculations + if (self.config == 'cubeviz') and (img_unit is not None): + background_value = (background_value * display_unit).to_value( + img_unit, u.spectral_density(self._cube_wave)) + elif background is None and dataset is None: + # use the previously-computed value in the plugin background_value = self.background_value + + # cubeviz: background_value set in plugin is in display units + # convert temporarily to image units for calculations + if (self.config == 'cubeviz') and (img_unit is not None): + background_value = (background_value * display_unit).to_value( + img_unit, u.spectral_density(self._cube_wave)) else: bg_reg = self.aperture._get_spatial_region(subset=background if background is not None else self.background.selected, # noqa dataset=dataset if dataset is not None else self.dataset.selected) # noqa background_value = self._calc_background_median(bg_reg, data=data) + + # cubeviz: computed background median will be in display units, + # convert temporarily back to image units for calculations + if (self.config == 'cubeviz') and (img_unit is not None): + background_value = (background_value * display_unit).to_value( + img_unit, u.spectral_density(self._cube_wave)) try: bg = float(background_value) except ValueError: # Clearer error message @@ -476,11 +619,16 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, include_counts_fac = False include_flux_scale = False if comp.units: - img_unit = u.Unit(comp.units) - bg = bg * img_unit + + # work for now in units of currently selected dataset (which may or + # may not be the desired output units, depending on the display + # units selected in the Unit Conversion plugin. background value + # has already been converted to image units above, and flux scaling + # will be converted from display unit > img_unit comp_data = comp_data << img_unit + bg = bg * img_unit - if u.sr in img_unit.bases: # TODO: Better way to detect surface brightness unit? + if check_if_unit_is_per_solid_angle(img_unit): # if units are surface brightness try: pixarea = float(pixel_area if pixel_area is not None else self.pixel_area) except ValueError: # Clearer error message @@ -494,12 +642,30 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, raise ValueError('Missing or invalid counts conversion factor') if not np.allclose(ctfac, 0): include_counts_fac = True + + # if cubeviz and flux_scaling is provided as override, it is in the data units + # if set in the app, it is in the display units and needs to be converted + # if provided as an override keyword arg, it is assumed to be in the + # data units and does not need to be converted + if ((self.config == 'cubeviz') and (flux_scaling is None) and + (self.flux_scaling is not None)): + # update eventaully to handle non-sr SB units + flux_scaling = (self.flux_scaling * u.Unit(self.flux_scaling_display_unit)).to_value( # noqa: E501 + img_unit * u.sr, u.spectral_density(self._cube_wave)) + try: flux_scale = float(flux_scaling if flux_scaling is not None else self.flux_scaling) except ValueError: # Clearer error message raise ValueError('Missing or invalid flux scaling') if not np.allclose(flux_scale, 0): include_flux_scale = True + + # from now, we will just need the image unit as a string for display + img_unit = img_unit.to_string() + + else: + img_unit = None + phot_aperstats = ApertureStats(comp_data, aperture, wcs=data.coords, local_bkg=bg) phot_table = phot_aperstats.to_table(columns=( 'id', 'sum', 'sum_aper_area', @@ -511,6 +677,8 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, if include_pixarea_fac: pixarea = pixarea * (u.arcsec * u.arcsec / (u.pix * u.pix)) # NOTE: Sum already has npix value encoded, so we simply apply the npix unit here. + + # note: need to generalize this to non-steradian surface brightness units pixarea_fac = (u.pix * u.pix) * pixarea.to(u.sr / (u.pix * u.pix)) phot_table['sum'] = [rawsum * pixarea_fac] else: @@ -548,8 +716,34 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, slice_val = self._cube_wave else: slice_val = u.Quantity(np.nan, self._cube_wave.unit) + phot_table.add_column(slice_val, name="slice_wave", index=29) + if comp.units: # convert phot. results from image unit to display unit + display_unit = u.Unit(self.display_flux_or_sb_unit) + # convert units of certain columns in aperture phot. output table + # to reflect display units (i.e if data units are MJy / sr, but + # Jy / sr is selected in Unit Conversion plugin) + phot_table['background'] = phot_table['background'].to( + display_unit, u.spectral_density(self._cube_wave)) + + if include_pixarea_fac: + phot_table['sum'] = phot_table['sum'].to( + (display_unit * pixarea_fac).unit, u.spectral_density(self._cube_wave)) + else: + phot_table['sum'] = phot_table['sum'].to( + display_unit, u.spectral_density(self._cube_wave)) + for key in ['min', 'max', 'mean', 'median', 'mode', 'std', + 'mad_std', 'biweight_location']: + phot_table[key] = phot_table[key].to( + display_unit, u.spectral_density(self._cube_wave)) + for key in ['var', 'biweight_midvariance']: + try: + phot_table[key] = phot_table[key].to(display_unit**2) + # FIXME: Can fail going between per-wave and per-freq + except u.UnitConversionError: + pass + if add_to_table: try: phot_table['id'][0] = self.table._qtable['id'].max() + 1 @@ -564,14 +758,24 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, # Plots. if update_plots: + + # for cubeviz unit conversion display units + if self.display_flux_or_sb_unit != '': + plot_display_unit = self.display_flux_or_sb_unit + else: + plot_display_unit = None + if self.current_plot_type == "Curve of Growth": if self.config == "cubeviz" and data.ndim > 2: self.plot.figure.title = f'Curve of growth from aperture center at {slice_val:.4e}' # noqa: E501 + eqv = u.spectral_density(self._cube_wave) else: self.plot.figure.title = 'Curve of growth from aperture center' + eqv = [] x_arr, sum_arr, x_label, y_label = _curve_of_growth( comp_data, (xcenter, ycenter), aperture, phot_table['sum'][0], - wcs=data.coords, background=bg, pixarea_fac=pixarea_fac) + wcs=data.coords, background=bg, pixarea_fac=pixarea_fac, + display_unit=plot_display_unit, equivalencies=eqv) self.plot._update_data('profile', x=x_arr, y=sum_arr, reset_lims=True) self.plot.update_style('profile', line_visible=True, color='gray', size=32) self.plot.update_style('fit', visible=False) @@ -580,16 +784,22 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, else: # Radial profile self.plot.figure.axes[0].label = 'pix' - self.plot.figure.axes[1].label = comp.units or 'Value' + if plot_display_unit: + self.plot.figure.axes[1].label = plot_display_unit + else: + self.plot.figure.axes[1].label = img_unit or 'Value' if self.current_plot_type == "Radial Profile": if self.config == "cubeviz" and data.ndim > 2: self.plot.figure.title = f'Radial profile from aperture center at {slice_val:.4e}' # noqa: E501 + eqv = u.spectral_density(self._cube_wave) else: self.plot.figure.title = 'Radial profile from aperture center' + eqv = [] x_data, y_data = _radial_profile( phot_aperstats.data_cutout, phot_aperstats.bbox, (xcenter, ycenter), - raw=False) + raw=False, display_unit=plot_display_unit, image_unit=img_unit, + equivalencies=eqv) self.plot._update_data('profile', x=x_data, y=y_data, reset_lims=True) self.plot.update_style('profile', line_visible=True, color='gray', size=32) @@ -600,7 +810,7 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, self.plot.figure.title = 'Raw radial profile from aperture center' x_data, y_data = _radial_profile( phot_aperstats.data_cutout, phot_aperstats.bbox, (xcenter, ycenter), - raw=True) + raw=True, display_unit=plot_display_unit, image_unit=img_unit) self.plot._update_data('profile', x=x_data, y=y_data, reset_lims=True) self.plot.update_style('profile', line_visible=False, color='gray', size=10) @@ -637,26 +847,40 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None, if key in ('id', 'data_label', 'subset_label', 'background', 'pixarea_tot', 'counts_fac', 'aperture_sum_counts_err', 'flux_scaling', 'timestamp'): continue + x = phot_table[key][0] - if (isinstance(x, (int, float, u.Quantity)) and + + if isinstance(x, u.Quantity): # split up unit and value to put in different cols + unit = x.unit.to_string() + if unit == '': # for eccentricity which is a quantity with an empty unit + unit = '-' + x = x.value + else: + unit = '-' + + if (isinstance(x, (int, float)) and key not in ('xcenter', 'ycenter', 'sky_center', 'sum_aper_area', 'aperture_sum_counts', 'aperture_sum_mag', 'slice_wave')): - tmp.append({'function': key, 'result': f'{x:.4e}'}) + if x == 0: + tmp.append({'function': key, 'result': f'{x:.1f}', 'unit': unit}) + else: + tmp.append({'function': key, 'result': f'{x:.3e}', 'unit': unit}) elif key == 'sky_center' and x is not None: - tmp.append({'function': 'RA center', 'result': f'{x.ra.deg:.6f} deg'}) - tmp.append({'function': 'Dec center', 'result': f'{x.dec.deg:.6f} deg'}) + tmp.append({'function': 'RA center', 'result': f'{x.ra.deg:.6f}', 'unit': 'deg'}) + tmp.append({'function': 'Dec center', 'result': f'{x.dec.deg:.6f}', 'unit': 'deg'}) elif key in ('xcenter', 'ycenter', 'sum_aper_area'): - tmp.append({'function': key, 'result': f'{x:.1f}'}) + tmp.append({'function': key, 'result': f'{x:.1f}', 'unit': unit}) elif key == 'aperture_sum_counts' and x is not None: tmp.append({'function': key, 'result': - f'{x:.4e} ({phot_table["aperture_sum_counts_err"][0]:.4e})'}) + f'{x:.4e} ({phot_table["aperture_sum_counts_err"][0]:.4e})', + 'unit': unit}) elif key == 'aperture_sum_mag' and x is not None: - tmp.append({'function': key, 'result': f'{x:.3f}'}) + tmp.append({'function': key, 'result': f'{x:.3f}', 'unit': unit}) elif key == 'slice_wave': if data.ndim > 2: - tmp.append({'function': key, 'result': f'{slice_val:.4e}'}) + tmp.append({'function': key, 'result': f'{slice_val.value:.4e}', 'unit': slice_val.unit.to_string()}) # noqa: E501 else: - tmp.append({'function': key, 'result': str(x)}) + tmp.append({'function': key, 'result': str(x), 'unit': unit}) if update_plots: # Also display fit results @@ -855,7 +1079,8 @@ def calculate_batch_photometry(self, options=[], add_to_table=True, update_plots # NOTE: These are hidden because the APIs are for internal use only # but we need them as a separate functions for unit testing. -def _radial_profile(radial_cutout, reg_bb, centroid, raw=False): +def _radial_profile(radial_cutout, reg_bb, centroid, raw=False, + image_unit=None, display_unit=None, equivalencies=[]): """Calculate radial profile. Parameters @@ -873,6 +1098,15 @@ def _radial_profile(radial_cutout, reg_bb, centroid, raw=False): If `True`, returns raw data points for scatter plot. Otherwise, use ``imexam`` algorithm for a clean plot. + image_unit : str or None + (For cubeviz only to deal with display unit conversion). Unit of input + 'radial cutout', used with `display_unit` to convert output to desired + display unit. + + display_unit : str or None + (For cubeviz only to deal with display unit conversion). Desired unit + for output. + """ reg_ogrid = np.ogrid[reg_bb.iymin:reg_bb.iymax, reg_bb.ixmin:reg_bb.ixmax] radial_dx = reg_ogrid[1] - centroid[0] @@ -897,11 +1131,16 @@ def _radial_profile(radial_cutout, reg_bb, centroid, raw=False): y_arr = np.bincount(radial_r, radial_img) / np.bincount(radial_r) x_arr = np.arange(y_arr.size) + if display_unit is not None: + if image_unit is None: + raise ValueError('Must provide image_unit with display_unit.') + y_arr = (y_arr * u.Unit(image_unit)).to_value(u.Unit(display_unit), equivalencies) + return x_arr, y_arr -def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0, n_datapoints=10, - pixarea_fac=None): +def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0, + n_datapoints=10, pixarea_fac=None, display_unit=None, equivalencies=[]): """Calculate curve of growth for aperture photometry. Parameters @@ -934,6 +1173,11 @@ def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0 pixarea_fac : float or `None` For ``flux_unit/sr`` to ``flux_unit`` conversion. + display_unit : str or None + (For cubeviz only to deal with display unit conversion). Desired unit + for output. If unit is a surface brightness, a Flux unit will be + returned if pixarea_fac is provided. + Returns ------- x_arr : ndarray @@ -953,6 +1197,18 @@ def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0 """ n_datapoints += 1 # n + 1 + # determined desired unit for output sum array and y label + # cubeviz only to handle unit conversion display unit changes + if display_unit is not None: + sum_unit = u.Unit(display_unit) + else: + if isinstance(data, u.Quantity): + sum_unit = data.unit + else: + sum_unit = None + if sum_unit and pixarea_fac is not None: + sum_unit *= pixarea_fac.unit + if hasattr(aperture, 'to_pixel'): aperture = aperture.to_pixel(wcs) @@ -985,12 +1241,14 @@ def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0 sum_arr = np.array(sum_arr) if pixarea_fac is not None: sum_arr = sum_arr * pixarea_fac + if isinstance(final_sum, u.Quantity): + final_sum = final_sum.to(sum_arr.unit, equivalencies) sum_arr = np.append(sum_arr, final_sum) - if isinstance(sum_arr, u.Quantity): - y_label = sum_arr.unit.to_string() - sum_arr = sum_arr.value # bqplot does not like Quantity - else: + if sum_unit is None: y_label = 'Value' + else: + y_label = sum_unit.to_string() + sum_arr = sum_arr.to_value(sum_unit, equivalencies) # bqplot does not like Quantity return x_arr, sum_arr, x_label, y_label diff --git a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue index 64f18a95a4..c6b673187b 100644 --- a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue +++ b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue @@ -5,7 +5,7 @@ :uses_active_status="uses_active_status" @plugin-ping="plugin_ping($event)" :keep_active.sync="keep_active" - :popout_button="popout_button" + :popout_button="popout_button" :scroll_to.sync="scroll_to"> @@ -99,7 +100,7 @@ label="Pixel area" v-model.number="pixel_area" type="number" - hint="Pixel area in arcsec squared, only used if sr in data unit" + hint="Pixel area in arcsec squared, only used if data is in units of surface brightness." persistent-hint > @@ -129,7 +130,8 @@ label="Flux scaling" v-model.number="flux_scaling" type="number" - hint="Same unit as data, used in -2.5 * log(flux / flux_scaling)" + :suffix="flux_scaling_display_unit" + hint="Used in -2.5 * log(flux / flux_scaling)" persistent-hint > @@ -213,16 +215,16 @@ Result - Value + Value + Unit - - {{ item.function }} - - {{ item.result }} + {{ item.function }} + {{ item.result }} + {{ item.unit }}