Imviz: Add a different radial profile approach

docs/imviz/plugins.rst

@@ -56,8 +56,8 @@ an interactively selected region. A typical workflow is as follows:
 
 1. Load image(s) in Imviz (see :ref:`imviz-import-data`).
 2. Draw a region over the object of interest (see :ref:`imviz_defining_spatial_regions`).
-3. Select the desired image using :guilabel:`Data` drop-down menu.
-4. Select the desired region using :guilabel:`Subset` drop-down menu.
+3. Select the desired image using the :guilabel:`Data` drop-down menu.
+4. Select the desired region using the :guilabel:`Subset` drop-down menu.
 5. If you want to subtract background before performing photometry, enter
    the background value in the :guilabel:`Background value` field. This value
    must be in the same unit as display data, if applicable.
@@ -82,8 +82,9 @@ an interactively selected region. A typical workflow is as follows:
    display data unit is already in linear flux unit. Setting this to 1 is equivalent
    to not applying any scaling. If this field is not applicable for you, leave it at 0.
    **This field resets every time Data selection changes.**
-9. Once all inputs are populated correctly, click on the :guilabel:`CALCULATE`
-   button to perform simple aperture photometry.
+9. Select the desired plot type using the :guilabel:`Plot Type` drop-down menu.
+10. Once all inputs are populated correctly, click on the :guilabel:`CALCULATE`
+    button to perform simple aperture photometry.
 
 .. note::
 

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py

@@ -8,7 +8,7 @@
 from glue.core.message import SubsetCreateMessage, SubsetDeleteMessage, SubsetUpdateMessage
 from ipywidgets import widget_serialization
 from regions.shapes.rectangle import RectanglePixelRegion
-from traitlets import Any, Bool, List
+from traitlets import Any, Bool, List, Unicode
 
 from jdaviz.configs.imviz.helper import layer_is_image_data
 from jdaviz.core.events import AddDataMessage, RemoveDataMessage, SnackbarMessage
@@ -29,6 +29,8 @@ class SimpleAperturePhotometry(TemplateMixin):
     flux_scaling = Any(0).tag(sync=True)
     result_available = Bool(False).tag(sync=True)
     results = List().tag(sync=True)
+    plot_types = List([]).tag(sync=True)
+    current_plot_type = Unicode().tag(sync=True)
     plot_available = Bool(False).tag(sync=True)
     radial_plot = Any('').tag(sync=True, **widget_serialization)
 
@@ -43,12 +45,15 @@ def __init__(self, *args, **kwargs):
 
         self._selected_data = None
         self._selected_subset = None
+        self.plot_types = ["Radial Profile", "Radial Profile (Raw)"]
+        self.current_plot_type = self.plot_types[0]
 
     def reset_results(self):
         self.result_available = False
         self.results = []
         self.plot_available = False
         self.radial_plot = ''
+        bqplt.clear()
 
     def _on_viewer_data_changed(self, msg=None):
         # To support multiple viewers, we allow the entire data collection.
@@ -241,25 +246,38 @@ def vue_do_aper_phot(self, *args, **kwargs):
                     d['id'] = 1
                     self.app._aper_phot_results = _qtable_from_dict(d)
 
-            # Radial profile
+            # Radial profile (Raw)
             reg_bb = reg.bounding_box
             reg_ogrid = np.ogrid[reg_bb.iymin:reg_bb.iymax, reg_bb.ixmin:reg_bb.ixmax]
             radial_dx = reg_ogrid[1] - reg.center.x
             radial_dy = reg_ogrid[0] - reg.center.y
             radial_r = np.hypot(radial_dx, radial_dy).ravel()  # pix
             radial_img = comp_no_bg_cutout.ravel()
+
             if comp.units:
                 y_data = radial_img.value
                 y_label = radial_img.unit.to_string()
             else:
                 y_data = radial_img
                 y_label = 'Value'
+
+            # Radial profile
+            if self.current_plot_type == "Radial Profile":
+                # This algorithm is from the imexam package,
+                # see licenses/IMEXAM_LICENSE.txt for more details
+                radial_r = list(radial_r)
+                y_data = np.bincount(radial_r, y_data) / np.bincount(radial_r)
+                radial_r = np.arange(len(y_data))
+                markerstyle = 'g--o'
+            else:
+                markerstyle = 'go'
+
             bqplt.clear()
             # NOTE: default margin in bqplot is 60 in all directions
             fig = bqplt.figure(1, title='Radial profile from Subset center',
                                fig_margin={'top': 60, 'bottom': 60, 'left': 40, 'right': 10},
                                title_style={'font-size': '12px'})  # TODO: Jenn wants title at bottom. # noqa
-            bqplt.plot(radial_r, y_data, 'go', figure=fig, default_size=1)
+            bqplt.plot(radial_r, y_data, markerstyle, figure=fig, default_size=1)
             bqplt.xlabel(label='pix', mark=fig.marks[-1], figure=fig)
             bqplt.ylabel(label=y_label, mark=fig.marks[-1], figure=fig)
 

jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue

@@ -66,6 +66,16 @@
       </v-text-field>
     </v-row>
 
+    <v-row>
+      <v-select
+        :items="plot_types"
+        v-model="current_plot_type"
+        label="Plot Type"
+        hint="Aperture photometry plot type"
+        persistent-hint
+      ></v-select>
+    </v-row>
+
     <v-row justify="end">
       <v-btn color="primary" text @click="do_aper_phot">Calculate</v-btn>
     </v-row>

jdaviz/configs/imviz/tests/test_simple_aper_phot.py

@@ -27,12 +27,14 @@ def test_plugin_wcs_dithered(self):
         assert self.imviz.get_aperture_photometry_results() is None
         assert not phot_plugin.plot_available
         assert phot_plugin.radial_plot == ''
+        assert phot_plugin.current_plot_type == 'Radial Profile'  # Software default
 
         # Perform photometry on both images using same Subset.
         phot_plugin.vue_data_selected('has_wcs_1[SCI,1]')
         phot_plugin.vue_subset_selected('Subset 1')
         phot_plugin.vue_do_aper_phot()
         phot_plugin.vue_data_selected('has_wcs_2[SCI,1]')
+        phot_plugin.current_plot_type = 'Radial Profile (Raw)'
         phot_plugin.vue_do_aper_phot()
         assert_allclose(phot_plugin.background_value, 0)
         assert_allclose(phot_plugin.counts_factor, 0)
@@ -82,6 +84,7 @@ def test_plugin_wcs_dithered(self):
         phot_plugin._on_viewer_data_changed()
         phot_plugin.vue_data_selected('has_wcs_1[SCI,1]')
         phot_plugin.vue_subset_selected('Subset 2')
+        phot_plugin.current_plot_type = 'Radial Profile'
         phot_plugin.vue_do_aper_phot()
         tbl = self.imviz.get_aperture_photometry_results()
         assert len(tbl) == 3  # New result is appended

licenses/IMEXAM_LICENSE.txt

@@ -0,0 +1,28 @@
+Copyright (c) 2011-2021, Imexam developers
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimer in the
+  documentation and/or other materials provided with the distribution.
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.