From 267073926ea2aeb7ca08110725d0dc46de5fa023 Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Wed, 22 Jun 2022 15:24:18 -0400 Subject: [PATCH 1/9] Gaussian1D for radial profile --- CHANGES.rst | 3 ++ docs/imviz/plugins.rst | 12 +++++- .../aper_phot_simple/aper_phot_simple.py | 37 +++++++++++++++++-- .../aper_phot_simple/aper_phot_simple.vue | 9 +++++ .../imviz/tests/test_simple_aper_phot.py | 4 ++ .../concepts/imviz_simple_aper_phot.ipynb | 21 ++++++++++- 6 files changed, 80 insertions(+), 6 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index e27820312e..8497e320da 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -27,6 +27,9 @@ Cubeviz Imviz ^^^^^ +- Added the ability to fit Gaussian1D model to radial profile in + Simple Aperture Photometry plugin. [#1409] + Mosviz ^^^^^^ diff --git a/docs/imviz/plugins.rst b/docs/imviz/plugins.rst index b683640810..443ff2ad15 100644 --- a/docs/imviz/plugins.rst +++ b/docs/imviz/plugins.rst @@ -160,7 +160,9 @@ an interactively selected region. A typical workflow is as follows: Caution: having too many data points may cause performance issues with this feature. The exact limitations depend on your hardware. -10. Once all inputs are populated correctly, click on the :guilabel:`CALCULATE` +10. Toggle :guilabel:`Fit Gaussian` on to fit a `~astropy.modeling.functional_models.Gaussian1D` + model to the radial profile data. This is disabled for curve-of-growth. +11. Once all inputs are populated correctly, click on the :guilabel:`CALCULATE` button to perform simple aperture photometry. .. note:: @@ -182,7 +184,7 @@ of the background subtracted data and the photometry results are displayed under Radial profile (raw). -You can also retrieve the results as `~astropy.table.QTable` as follows, +You can also retrieve the photometry results as `~astropy.table.QTable` as follows, assuming ``imviz`` is the instance of your Imviz application:: results = imviz.get_aperture_photometry_results() @@ -258,6 +260,12 @@ The columns are as follow: Once you have the results in a table, you can further manipulated them as documented in :ref:`astropy:astropy-table`. +If you opted to fit a `~astropy.modeling.functional_models.Gaussian1D` +to the radial profile, the last fitted model can be obtained by as follows. +See :ref:`astropy:astropy-modeling` on how to manipulate the model:: + + my_gaussian1d = imviz.app.fitted_models['phot_radial_profile'] + .. _imviz-export-plot: Export Plot 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 2aca9f8c69..37e6d4a067 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 @@ -1,8 +1,12 @@ +import os +import warnings from datetime import datetime import bqplot import numpy as np from astropy import units as u +from astropy.modeling.fitting import LevMarLSQFitter +from astropy.modeling.models import Gaussian1D from astropy.table import QTable from astropy.time import Time from ipywidgets import widget_serialization @@ -41,6 +45,7 @@ class SimpleAperturePhotometry(TemplateMixin, DatasetSelectMixin): current_plot_type = Unicode().tag(sync=True) plot_available = Bool(False).tag(sync=True) radial_plot = Any('').tag(sync=True, **widget_serialization) + fit_radial_profile = Bool(False).tag(sync=True) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @@ -329,6 +334,7 @@ def vue_do_aper_phot(self, *args, **kwargs): bqplot_line = bqplot.Lines(x=x_arr, y=sum_arr, marker='circle', scales={'x': line_x_sc, 'y': line_y_sc}, marker_size=32, colors='gray') + bqplot_marks = [bqplot_line] else: # Radial profile self._fig.axes = [bqplot.Axis(scale=line_x_sc, label='pix'), @@ -344,13 +350,38 @@ def vue_do_aper_phot(self, *args, **kwargs): marker_size=32, colors='gray') else: # Radial Profile (Raw) self._fig.title = 'Raw radial profile from Subset center' - radial_r, radial_img = _radial_profile( + x_data, y_data = _radial_profile( phot_aperstats.data_cutout, phot_aperstats.bbox, aperture, raw=True) - bqplot_line = bqplot.Scatter(x=radial_r, y=radial_img, marker='circle', + bqplot_line = bqplot.Scatter(x=x_data, y=y_data, marker='circle', scales={'x': line_x_sc, 'y': line_y_sc}, default_size=1, colors='gray') - self._fig.marks = [bqplot_line] + # Fit Gaussian1D to radial profile data. + if self.fit_radial_profile: + fitter = LevMarLSQFitter() + y_max = y_data.max() + x_mean = x_data[np.where(y_data == y_max)].mean() + std = 0.5 * (phot_table['semimajor_sigma'][0] + + phot_table['semiminor_sigma'][0]) + if isinstance(std, u.Quantity): + std = std.value + gs = Gaussian1D(amplitude=y_max, mean=x_mean, stddev=std) + with warnings.catch_warnings(record=True) as warns: + fit_model = fitter(gs, x_data, y_data) + if len(warns) > 0: + msg = os.linesep.join([str(w.message) for w in warns]) + self.hub.broadcast(SnackbarMessage( + f"Radial profile fitting: {msg}", color='warning', sender=self)) + y_fit = fit_model(x_data) + self.app.fitted_models['phot_radial_profile'] = fit_model + bqplot_fit = bqplot.Lines(x=x_data, y=y_fit, marker=None, + scales={'x': line_x_sc, 'y': line_y_sc}, + colors='magenta', line_style='dashed') + bqplot_marks = [bqplot_line, bqplot_fit] + else: + bqplot_marks = [bqplot_line] + + self._fig.marks = bqplot_marks except Exception as e: # pragma: no cover self.reset_results() 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 f913d891b8..2aca4f7885 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 @@ -110,6 +110,15 @@ > + + + + + Calculate diff --git a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py index 668efbcdb4..6ab123a073 100644 --- a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py +++ b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py @@ -18,6 +18,10 @@ def test_plugin_wcs_dithered(self): phot_plugin = self.imviz.app.get_tray_item_from_name('imviz-aper-phot-simple') + # Model fitting is already tested in astropy. + # Here, we enable it just to make sure it does not crash. + phot_plugin.fit_radial_profile = True + # Make sure invalid Data/Subset selection does not crash plugin. with pytest.raises(ValueError): phot_plugin.dataset_selected = 'no_such_data' diff --git a/notebooks/concepts/imviz_simple_aper_phot.ipynb b/notebooks/concepts/imviz_simple_aper_phot.ipynb index e0549ed983..2c52adaf24 100644 --- a/notebooks/concepts/imviz_simple_aper_phot.ipynb +++ b/notebooks/concepts/imviz_simple_aper_phot.ipynb @@ -190,10 +190,29 @@ "results" ] }, + { + "cell_type": "markdown", + "id": "b45fcdfe", + "metadata": {}, + "source": [ + "If you fitted Gaussian to radial profile, you can get it back out like this." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bcb594f2", + "metadata": {}, + "outputs": [], + "source": [ + "my_gaussian = imviz.app.fitted_models['phot_radial_profile']\n", + "my_gaussian" + ] + }, { "cell_type": "code", "execution_count": null, - "id": "00435609", + "id": "1e546682", "metadata": {}, "outputs": [], "source": [] From e305ee33774e795ccb375025f74181ad8ca42025 Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Tue, 28 Jun 2022 18:28:35 -0400 Subject: [PATCH 2/9] Sort data for proper raw fit plot --- .../imviz/plugins/aper_phot_simple/aper_phot_simple.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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 37e6d4a067..2879f8d315 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 @@ -446,8 +446,9 @@ def _radial_profile(radial_cutout, reg_bb, aperture, raw=False): radial_img = radial_cutout.compressed() # data unit if raw: - x_arr = radial_r - y_arr = radial_img + i_arr = np.argsort(radial_r) + x_arr = radial_r[i_arr] + y_arr = radial_img[i_arr] else: # This algorithm is from the imexam package, # see licenses/IMEXAM_LICENSE.txt for more details From 530e95213cc9a309e37a9478a51e5272bfbc12f0 Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Tue, 28 Jun 2022 19:15:08 -0400 Subject: [PATCH 3/9] Display Gaussian1D results in GUI and some bug fixes --- docs/imviz/plugins.rst | 4 ++-- .../aper_phot_simple/aper_phot_simple.py | 18 +++++++++++++++++- .../concepts/imviz_simple_aper_phot.ipynb | 6 +++--- 3 files changed, 22 insertions(+), 6 deletions(-) diff --git a/docs/imviz/plugins.rst b/docs/imviz/plugins.rst index 443ff2ad15..7582d8bd00 100644 --- a/docs/imviz/plugins.rst +++ b/docs/imviz/plugins.rst @@ -171,8 +171,8 @@ an interactively selected region. A typical workflow is as follows: However, if NaN exists in data, it will be treated as 0. When calculation is complete, a plot would show the radial profile -of the background subtracted data and the photometry results are displayed under the -:guilabel:`CALCULATE` button. +of the background subtracted data and the photometry and model fitting (if requested) +results are displayed under the :guilabel:`CALCULATE` button. .. figure:: img/imviz_radial_profile.png :alt: Imviz radial profile plot. 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 2879f8d315..57192ddd77 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 @@ -6,6 +6,7 @@ import numpy as np from astropy import units as u from astropy.modeling.fitting import LevMarLSQFitter +from astropy.modeling import Parameter from astropy.modeling.models import Gaussian1D from astropy.table import QTable from astropy.time import Time @@ -68,6 +69,7 @@ def __init__(self, *args, **kwargs): self._fig = bqplot.Figure() self.plot_types = ["Curve of Growth", "Radial Profile", "Radial Profile (Raw)"] self.current_plot_type = self.plot_types[0] + self._fitted_model_name = 'phot_radial_profile' def reset_results(self): self.result_available = False @@ -223,6 +225,11 @@ def vue_do_aper_phot(self, *args, **kwargs): data = self._selected_data reg = self._selected_subset + # Reset last fitted model + fit_model = None + if self._fitted_model_name in self.app.fitted_models: + del self.app.fitted_models[self._fitted_model_name] + try: comp = data.get_component(data.main_components[0]) try: @@ -373,7 +380,7 @@ def vue_do_aper_phot(self, *args, **kwargs): self.hub.broadcast(SnackbarMessage( f"Radial profile fitting: {msg}", color='warning', sender=self)) y_fit = fit_model(x_data) - self.app.fitted_models['phot_radial_profile'] = fit_model + self.app.fitted_models[self._fitted_model_name] = fit_model bqplot_fit = bqplot.Lines(x=x_data, y=y_fit, marker=None, scales={'x': line_x_sc, 'y': line_y_sc}, colors='magenta', line_style='dashed') @@ -410,6 +417,15 @@ def vue_do_aper_phot(self, *args, **kwargs): f'{x:.4e} ({phot_table["aperture_sum_counts_err"][0]:.4e})'}) else: tmp.append({'function': key, 'result': str(x)}) + # Also display fit results + if fit_model is not None and isinstance(fit_model, Gaussian1D): + model_name = fit_model.__class__.__name__ + for param in ('fwhm', 'mean', 'amplitude'): + p_val = getattr(fit_model, param) + if isinstance(p_val, Parameter): + p_val = p_val.value + tmp.append({'function': f'{model_name}_{param}', + 'result': f'{p_val:.4e}'}) self.results = tmp self.result_available = True self.radial_plot = self._fig diff --git a/notebooks/concepts/imviz_simple_aper_phot.ipynb b/notebooks/concepts/imviz_simple_aper_phot.ipynb index 2c52adaf24..55de8717be 100644 --- a/notebooks/concepts/imviz_simple_aper_phot.ipynb +++ b/notebooks/concepts/imviz_simple_aper_phot.ipynb @@ -195,7 +195,7 @@ "id": "b45fcdfe", "metadata": {}, "source": [ - "If you fitted Gaussian to radial profile, you can get it back out like this." + "If you fitted Gaussian to radial profile, you can get it back out like this. If it does not exist, you will get `None`." ] }, { @@ -205,14 +205,14 @@ "metadata": {}, "outputs": [], "source": [ - "my_gaussian = imviz.app.fitted_models['phot_radial_profile']\n", + "my_gaussian = imviz.app.fitted_models.get('phot_radial_profile', None)\n", "my_gaussian" ] }, { "cell_type": "code", "execution_count": null, - "id": "1e546682", + "id": "b7c59fef", "metadata": {}, "outputs": [], "source": [] From 991455f85807d9133eedc0b68f2e69e3c407c28a Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Wed, 29 Jun 2022 13:52:15 -0400 Subject: [PATCH 4/9] Use centroid for radial profile instead of aperture center --- .../plugins/aper_phot_simple/aper_phot_simple.py | 16 +++++++++------- .../configs/imviz/tests/test_simple_aper_phot.py | 9 +++++---- 2 files changed, 14 insertions(+), 11 deletions(-) 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 57192ddd77..bec06736d3 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 @@ -351,14 +351,16 @@ def vue_do_aper_phot(self, *args, **kwargs): if self.current_plot_type == "Radial Profile": self._fig.title = 'Radial profile from Subset center' x_data, y_data = _radial_profile( - phot_aperstats.data_cutout, phot_aperstats.bbox, aperture, raw=False) + phot_aperstats.data_cutout, phot_aperstats.bbox, phot_aperstats.centroid, + raw=False) bqplot_line = bqplot.Lines(x=x_data, y=y_data, marker='circle', scales={'x': line_x_sc, 'y': line_y_sc}, marker_size=32, colors='gray') else: # Radial Profile (Raw) self._fig.title = 'Raw radial profile from Subset center' x_data, y_data = _radial_profile( - phot_aperstats.data_cutout, phot_aperstats.bbox, aperture, raw=True) + phot_aperstats.data_cutout, phot_aperstats.bbox, phot_aperstats.centroid, + raw=True) bqplot_line = bqplot.Scatter(x=x_data, y=y_data, marker='circle', scales={'x': line_x_sc, 'y': line_y_sc}, default_size=1, colors='gray') @@ -436,7 +438,7 @@ def vue_do_aper_phot(self, *args, **kwargs): # 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, aperture, raw=False): +def _radial_profile(radial_cutout, reg_bb, centroid, raw=False): """Calculate radial profile. Parameters @@ -447,8 +449,8 @@ def _radial_profile(radial_cutout, reg_bb, aperture, raw=False): reg_bb : obj Bounding box from ``ApertureStats``. - aperture : obj - ``photutils`` aperture object. + centroid : tuple of int + ``ApertureStats`` centroid or desired center in ``(x, y)``. raw : bool If `True`, returns raw data points for scatter plot. @@ -456,8 +458,8 @@ def _radial_profile(radial_cutout, reg_bb, aperture, raw=False): """ reg_ogrid = np.ogrid[reg_bb.iymin:reg_bb.iymax, reg_bb.ixmin:reg_bb.ixmax] - radial_dx = reg_ogrid[1] - aperture.positions[0] - radial_dy = reg_ogrid[0] - aperture.positions[1] + radial_dx = reg_ogrid[1] - centroid[0] + radial_dy = reg_ogrid[0] - centroid[1] radial_r = np.hypot(radial_dx, radial_dy)[~radial_cutout.mask].ravel() # pix radial_img = radial_cutout.compressed() # data unit diff --git a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py index 6ab123a073..159d6e9d49 100644 --- a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py +++ b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py @@ -259,13 +259,14 @@ def test_annulus_background(imviz_helper): class TestRadialProfile(): def setup_class(self): data = np.ones((51, 51)) * u.nJy - self.aperture = EllipticalAperture((25, 25), 20, 15) - phot_aperstats = ApertureStats(data, self.aperture) + aperture = EllipticalAperture((25, 25), 20, 15) + phot_aperstats = ApertureStats(data, aperture) self.data_cutout = phot_aperstats.data_cutout self.bbox = phot_aperstats.bbox + self.centroid = phot_aperstats.centroid def test_profile_raw(self): - x_arr, y_arr = _radial_profile(self.data_cutout, self.bbox, self.aperture, raw=True) + x_arr, y_arr = _radial_profile(self.data_cutout, self.bbox, self.centroid, raw=True) # Too many data points to compare each one for X. assert x_arr.shape == y_arr.shape == (923, ) assert_allclose(x_arr.min(), 0) @@ -273,7 +274,7 @@ def test_profile_raw(self): assert_allclose(y_arr, 1) def test_profile_imexam(self): - x_arr, y_arr = _radial_profile(self.data_cutout, self.bbox, self.aperture, raw=False) + x_arr, y_arr = _radial_profile(self.data_cutout, self.bbox, self.centroid, raw=False) assert_allclose(x_arr, range(20)) assert_allclose(y_arr, 1) From 3faa064f53a16d2fb62996c34210912884687a6a Mon Sep 17 00:00:00 2001 From: "P. L. Lim" <2090236+pllim@users.noreply.github.com> Date: Wed, 29 Jun 2022 14:38:28 -0400 Subject: [PATCH 5/9] Future-proof Vue.js logic [ci skip] Co-authored-by: Kyle Conroy --- .../imviz/plugins/aper_phot_simple/aper_phot_simple.vue | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 2aca4f7885..b606385bc0 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 @@ -110,7 +110,8 @@ > - + + Date: Wed, 29 Jun 2022 15:52:00 -0400 Subject: [PATCH 6/9] Display fit results in its own section and fix plot titles --- CHANGES.rst | 3 ++- .../aper_phot_simple/aper_phot_simple.py | 13 ++++++++----- .../aper_phot_simple/aper_phot_simple.vue | 19 ++++++++++++++++++- 3 files changed, 28 insertions(+), 7 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 8497e320da..f677898a12 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -28,7 +28,8 @@ Imviz ^^^^^ - Added the ability to fit Gaussian1D model to radial profile in - Simple Aperture Photometry plugin. [#1409] + Simple Aperture Photometry plugin. Radial profile now centers + on source centroid, not Subset center. [#1409] Mosviz ^^^^^^ 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 bec06736d3..fde67ca12a 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 @@ -47,6 +47,7 @@ class SimpleAperturePhotometry(TemplateMixin, DatasetSelectMixin): plot_available = Bool(False).tag(sync=True) radial_plot = Any('').tag(sync=True, **widget_serialization) fit_radial_profile = Bool(False).tag(sync=True) + fit_results = List().tag(sync=True) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @@ -349,7 +350,7 @@ def vue_do_aper_phot(self, *args, **kwargs): label=comp.units or 'Value')] if self.current_plot_type == "Radial Profile": - self._fig.title = 'Radial profile from Subset center' + self._fig.title = 'Radial profile from source centroid' x_data, y_data = _radial_profile( phot_aperstats.data_cutout, phot_aperstats.bbox, phot_aperstats.centroid, raw=False) @@ -357,7 +358,7 @@ def vue_do_aper_phot(self, *args, **kwargs): scales={'x': line_x_sc, 'y': line_y_sc}, marker_size=32, colors='gray') else: # Radial Profile (Raw) - self._fig.title = 'Raw radial profile from Subset center' + self._fig.title = 'Raw radial profile from source centroid' x_data, y_data = _radial_profile( phot_aperstats.data_cutout, phot_aperstats.bbox, phot_aperstats.centroid, raw=True) @@ -419,16 +420,18 @@ def vue_do_aper_phot(self, *args, **kwargs): f'{x:.4e} ({phot_table["aperture_sum_counts_err"][0]:.4e})'}) else: tmp.append({'function': key, 'result': str(x)}) + # Also display fit results + fit_tmp = [] if fit_model is not None and isinstance(fit_model, Gaussian1D): - model_name = fit_model.__class__.__name__ for param in ('fwhm', 'mean', 'amplitude'): p_val = getattr(fit_model, param) if isinstance(p_val, Parameter): p_val = p_val.value - tmp.append({'function': f'{model_name}_{param}', - 'result': f'{p_val:.4e}'}) + fit_tmp.append({'function': param, 'result': f'{p_val:.4e}'}) + self.results = tmp + self.fit_results = fit_tmp self.result_available = True self.radial_plot = self._fig self.bqplot_figs_resize = [self._fig] 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 b606385bc0..a4d285f24b 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 @@ -133,8 +133,25 @@ +
+ Gaussian Fit Results + + Result + Value + + + + {{ item.function }} + + {{ item.result }} + +
+
- Results + Photometry Results Result Value From a48f801da009e5124f99534d6d3ba29de3f0ab9c Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Wed, 29 Jun 2022 15:55:33 -0400 Subject: [PATCH 7/9] Update phot plugin doc --- docs/imviz/plugins.rst | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/imviz/plugins.rst b/docs/imviz/plugins.rst index 7582d8bd00..0571d4a92d 100644 --- a/docs/imviz/plugins.rst +++ b/docs/imviz/plugins.rst @@ -184,6 +184,13 @@ results are displayed under the :guilabel:`CALCULATE` button. Radial profile (raw). +If you opted to fit a `~astropy.modeling.functional_models.Gaussian1D` +to the radial profile, the last fitted model parameters will be displayed +under the radial profile plot. The model itself can be obtained by as follows. +See :ref:`astropy:astropy-modeling` on how to manipulate the model:: + + my_gaussian1d = imviz.app.fitted_models['phot_radial_profile'] + You can also retrieve the photometry results as `~astropy.table.QTable` as follows, assuming ``imviz`` is the instance of your Imviz application:: @@ -260,12 +267,6 @@ The columns are as follow: Once you have the results in a table, you can further manipulated them as documented in :ref:`astropy:astropy-table`. -If you opted to fit a `~astropy.modeling.functional_models.Gaussian1D` -to the radial profile, the last fitted model can be obtained by as follows. -See :ref:`astropy:astropy-modeling` on how to manipulate the model:: - - my_gaussian1d = imviz.app.fitted_models['phot_radial_profile'] - .. _imviz-export-plot: Export Plot From 2da055acc4c41d4d56097aa0702924f7d3d2cbad Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Thu, 30 Jun 2022 18:54:21 -0400 Subject: [PATCH 8/9] Gaussian1D: Fix mean and bind amplitude like imexam PR 241 --- .../imviz/plugins/aper_phot_simple/aper_phot_simple.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) 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 fde67ca12a..a772ac22c2 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 @@ -367,15 +367,17 @@ def vue_do_aper_phot(self, *args, **kwargs): default_size=1, colors='gray') # Fit Gaussian1D to radial profile data. + # mean is fixed at 0 because we recentered to centroid. if self.fit_radial_profile: fitter = LevMarLSQFitter() y_max = y_data.max() - x_mean = x_data[np.where(y_data == y_max)].mean() std = 0.5 * (phot_table['semimajor_sigma'][0] + phot_table['semiminor_sigma'][0]) if isinstance(std, u.Quantity): std = std.value - gs = Gaussian1D(amplitude=y_max, mean=x_mean, stddev=std) + gs = Gaussian1D(amplitude=y_max, mean=0, stddev=std, + fixed={'mean': True, 'amplitude': True}, + bounds={'amplitude': (y_max * 0.5, y_max)}) with warnings.catch_warnings(record=True) as warns: fit_model = fitter(gs, x_data, y_data) if len(warns) > 0: @@ -424,7 +426,7 @@ def vue_do_aper_phot(self, *args, **kwargs): # Also display fit results fit_tmp = [] if fit_model is not None and isinstance(fit_model, Gaussian1D): - for param in ('fwhm', 'mean', 'amplitude'): + for param in ('fwhm', 'amplitude'): # mean is fixed at 0 p_val = getattr(fit_model, param) if isinstance(p_val, Parameter): p_val = p_val.value From 03f0e5f958b88de5e02057940a68a2a2e86d71ca Mon Sep 17 00:00:00 2001 From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com> Date: Fri, 1 Jul 2022 12:42:28 -0400 Subject: [PATCH 9/9] Imviz phot curve of growth also from centroid --- CHANGES.rst | 2 +- .../aper_phot_simple/aper_phot_simple.py | 22 ++++++++++++------- .../imviz/tests/test_simple_aper_phot.py | 9 ++++---- 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index f677898a12..ed8cff47fe 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -28,7 +28,7 @@ Imviz ^^^^^ - Added the ability to fit Gaussian1D model to radial profile in - Simple Aperture Photometry plugin. Radial profile now centers + Simple Aperture Photometry plugin. Radial profile and curve of growth now center on source centroid, not Subset center. [#1409] Mosviz 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 a772ac22c2..a49eba7569 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 @@ -332,10 +332,10 @@ def vue_do_aper_phot(self, *args, **kwargs): line_y_sc = bqplot.LinearScale() if self.current_plot_type == "Curve of Growth": - self._fig.title = 'Curve of growth from Subset center' + self._fig.title = 'Curve of growth from source centroid' x_arr, sum_arr, x_label, y_label = _curve_of_growth( - comp_data, aperture, phot_table['sum'][0], wcs=data.coords, - background=bg, pixarea_fac=pixarea_fac) + comp_data, phot_aperstats.centroid, aperture, phot_table['sum'][0], + wcs=data.coords, background=bg, pixarea_fac=pixarea_fac) self._fig.axes = [bqplot.Axis(scale=line_x_sc, label=x_label), bqplot.Axis(scale=line_y_sc, orientation='vertical', label=y_label)] @@ -482,7 +482,7 @@ def _radial_profile(radial_cutout, reg_bb, centroid, raw=False): return x_arr, y_arr -def _curve_of_growth(data, aperture, final_sum, wcs=None, background=0, n_datapoints=10, +def _curve_of_growth(data, centroid, aperture, final_sum, wcs=None, background=0, n_datapoints=10, pixarea_fac=None): """Calculate curve of growth for aperture photometry. @@ -491,8 +491,14 @@ def _curve_of_growth(data, aperture, final_sum, wcs=None, background=0, n_datapo data : ndarray or `~astropy.units.Quantity` Data for the calculation. + centroid : tuple of int + ``ApertureStats`` centroid or desired center in ``(x, y)``. + aperture : obj - ``photutils`` aperture object. + ``photutils`` aperture to use, except its center will be + changed to the given ``centroid``. This is because the aperture + might be hand-drawn and a more accurate centroid has been + recalculated separately. final_sum : float or `~astropy.units.Quantity` Aperture sum that is already calculated in the @@ -532,20 +538,20 @@ def _curve_of_growth(data, aperture, final_sum, wcs=None, background=0, n_datapo if isinstance(aperture, CircularAperture): x_label = 'Radius (pix)' x_arr = np.linspace(0, aperture.r, num=n_datapoints)[1:] - aper_list = [CircularAperture(aperture.positions, cur_r) for cur_r in x_arr[:-1]] + aper_list = [CircularAperture(centroid, cur_r) for cur_r in x_arr[:-1]] elif isinstance(aperture, EllipticalAperture): x_label = 'Semimajor axis (pix)' x_arr = np.linspace(0, aperture.a, num=n_datapoints)[1:] a_arr = x_arr[:-1] b_arr = aperture.b * a_arr / aperture.a - aper_list = [EllipticalAperture(aperture.positions, cur_a, cur_b, theta=aperture.theta) + aper_list = [EllipticalAperture(centroid, cur_a, cur_b, theta=aperture.theta) for (cur_a, cur_b) in zip(a_arr, b_arr)] elif isinstance(aperture, RectangularAperture): x_label = 'Width (pix)' x_arr = np.linspace(0, aperture.w, num=n_datapoints)[1:] w_arr = x_arr[:-1] h_arr = aperture.h * w_arr / aperture.w - aper_list = [RectangularAperture(aperture.positions, cur_w, cur_h, theta=aperture.theta) + aper_list = [RectangularAperture(centroid, cur_w, cur_h, theta=aperture.theta) for (cur_w, cur_h) in zip(w_arr, h_arr)] else: raise TypeError(f'Unsupported aperture: {aperture}') diff --git a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py index 159d6e9d49..ac602550b4 100644 --- a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py +++ b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py @@ -168,7 +168,7 @@ def test_plugin_wcs_dithered(self): # Curve of growth phot_plugin.current_plot_type = 'Curve of Growth' phot_plugin.vue_do_aper_phot() - assert phot_plugin._fig.title == 'Curve of growth from Subset center' + assert phot_plugin._fig.title == 'Curve of growth from source centroid' class TestSimpleAperPhot_NoWCS(BaseImviz_WCS_NoWCS): @@ -298,11 +298,12 @@ def test_curve_of_growth(with_unit): RectangularAperture(cen, 20, 15)) for aperture in apertures: - final_sum = ApertureStats(data, aperture).sum + astat = ApertureStats(data, aperture) + final_sum = astat.sum if pixarea_fac is not None: final_sum = final_sum * pixarea_fac x_arr, sum_arr, x_label, y_label = _curve_of_growth( - data, aperture, final_sum, background=bg, pixarea_fac=pixarea_fac) + data, astat.centroid, aperture, final_sum, background=bg, pixarea_fac=pixarea_fac) assert_allclose(x_arr, [2, 4, 6, 8, 10, 12, 14, 16, 18, 20]) assert y_label == expected_ylabel @@ -321,5 +322,5 @@ def test_curve_of_growth(with_unit): assert_allclose(sum_arr, [3, 12, 27, 48, 75, 108, 147, 192, 243, 300]) with pytest.raises(TypeError, match='Unsupported aperture'): - _curve_of_growth(data, EllipticalAnnulus(cen, 3, 8, 5), 100, + _curve_of_growth(data, cen, EllipticalAnnulus(cen, 3, 8, 5), 100, pixarea_fac=pixarea_fac)