Point source refactoring

CITATION.rst

@@ -0,0 +1,30 @@
+Citation Guidelines
+===================
+
+|JOSS| |Birrer&Amara|
+
+If you use lenstronomy for work or research presented in a publication (whether
+directly, or as a dependency of another package) we recommend and encourage
+the following acknowledgment:
+
+  This research made use of lenstronomy, a multi-purpose gravitational lens
+  modeling software package (Birrer et. al., 2021, Birrer & Amara, 2018).
+
+where the citations are to our publication in the `Journal of Open Source
+Software`_ and the `Original Publication`_. We also encourage citations within the main text wherever
+appropriate. DOIs and BibTeX keys are available through the links above.
+
+Please also cite `Birrer et al 2015 <http://adsabs.harvard.edu/abs/2015ApJ...813..102B>`_
+when you make use of the lenstronomy work-flow or the Shapelet source reconstruction and make sure to cite also
+the relevant work that was implemented in lenstronomy, as described in the release paper and the documentation.
+Don't hesitate to reach out to the developers if you have questions!
+
+
+.. _Journal of Open Source Software: https://joss.theoj.org/papers/10.21105/joss.03283
+.. _Original Publication: https://ui.adsabs.harvard.edu/abs/2018PDU....22..189B/abstract
+
+.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.03283/status.svg
+    :target: https://joss.theoj.org/papers/10.21105/joss.03283
+
+.. |Birrer&Amara| image:: https://img.shields.io/badge/arXiv-1803.09746%20-yellowgreen.svg
+    :target: https://ui.adsabs.harvard.edu/abs/2018PDU....22..189B/abstract

MAILINGLIST.rst

@@ -1,11 +1,19 @@
-============
-Mailing list
-============
+==============================
+Mailing list and Slack channel
+==============================
 
 You can join the **lenstronomy** mailing list by signing up on the
 `google groups page <https://groups.google.com/forum/#!forum/lenstronomy>`_.
 
 The email list is meant to provide a communication platform between users and developers. You can ask questions,
 and suggest new features. New releases will be announced via this mailing list.
 
-If you encounter errors or problems with **lenstronomy**, please let us know!
+We also have a `Slack channel <https://lenstronomers.slack.com>`_ for the community.
+Please send us an `email <lenstronomy-dev@googlegroups.com>`_ such that we can add you to the channel.
+
+If you encounter errors or problems with **lenstronomy**, please let us know!
+You can open an `issue  <https://github.com/lenstronomy/lenstronomy/issues>`_,
+make a post on the `Slack channel <https://lenstronomers.slack.com>`_ or
+write an `email <lenstronomy-dev@googlegroups.com>`_ to the lenstronomy developers.
+
+We are also encouraging you to reach out with feature requests, general or specific feedback and questions about use cases.

lenstronomy/PointSource/Types/base_ps.py

@@ -13,7 +13,9 @@ def __init__(self, lens_model=None, fixed_magnification=False, additional_image=
 
         :param lens_model: instance of the LensModel() class
         :param fixed_magnification: bool. If True, magnification
-         ratio of point sources is fixed to the one given by the lens model
+         ratio of point sources is fixed to the one given by the lens model.
+         If True, amplitude parameters are passed as 'source_amp'.
+         If False, amplitudes are passed as in the image plane as 'image_amp'.
         :param additional_image: bool. If True, search for additional images of the same source is conducted.
         """
         self._lens_model = lens_model

lenstronomy/PointSource/Types/lensed_position.py

@@ -8,8 +8,8 @@ class LensedPositions(PSBase):
     """
     class of a a lensed point source parameterized as the (multiple) observed image positions
     Name within the PointSource module: 'LENSED_POSITION'
-    parameters: ra_image, dec_image, point_amp
-    If fixed_magnification=True, than 'source_amp' is a parameter instead of 'point_amp'
+    parameters: ra_image, dec_image, source_amp/source_amp
+    If fixed_magnification=True, than 'source_amp' is a parameter instead of 'image_amp'
 
     """
     # def __init__(self, lens_model=None, fixed_magnification=False, additional_image=False):
@@ -82,7 +82,7 @@ def image_amplitude(self, kwargs_ps, kwargs_lens=None, x_pos=None, y_pos=None, m
             mag = self._lens_model.magnification(ra_image, dec_image, kwargs_lens)
             point_amp = kwargs_ps['source_amp'] * np.abs(mag)
         else:
-            point_amp = kwargs_ps['point_amp']
+            point_amp = kwargs_ps['image_amp']
             if x_pos is not None:
                 point_amp = _expand_to_array(point_amp, len(x_pos))
         return np.array(point_amp)
@@ -103,6 +103,6 @@ def source_amplitude(self, kwargs_ps, kwargs_lens=None):
         else:
             ra_image, dec_image = kwargs_ps['ra_image'], kwargs_ps['dec_image']
             mag = self._lens_model.magnification(ra_image, dec_image, kwargs_lens)
-            point_amp = kwargs_ps['point_amp']
+            point_amp = kwargs_ps['image_amp']
             source_amp = np.mean(np.array(point_amp) / np.array(np.abs(mag)))
         return np.array(source_amp)

lenstronomy/PointSource/Types/source_position.py

@@ -11,7 +11,7 @@ class of a single point source defined in the original source coordinate positio
 
     Name within the PointSource module: 'SOURCE_POSITION'
     parameters: ra_source, dec_source, source_amp, mag_pert (optional)
-    If fixed_magnification=True, than 'source_amp' is a parameter instead of 'point_amp'
+    If fixed_magnification=True, than 'source_amp' is a parameter instead of 'image_amp'
     mag_pert is a list of fractional magnification pertubations applied to point source images
 
     """
@@ -76,7 +76,7 @@ def image_amplitude(self, kwargs_ps, kwargs_lens=None, x_pos=None, y_pos=None, m
             mag = self._lens_model.magnification(ra_image, dec_image, kwargs_lens)
             point_amp = kwargs_ps['source_amp'] * np.abs(mag)
         else:
-            point_amp = kwargs_ps['point_amp']
+            point_amp = kwargs_ps['image_amp']
             if x_pos is not None:
                 point_amp = _expand_to_array(point_amp, len(x_pos))
         mag_pert = kwargs_ps.get('mag_pert', 1)
@@ -100,6 +100,6 @@ def source_amplitude(self, kwargs_ps, kwargs_lens=None):
         else:
             ra_image, dec_image = self.image_position(kwargs_ps, kwargs_lens)
             mag = self._lens_model.magnification(ra_image, dec_image, kwargs_lens)
-            point_amp = kwargs_ps['point_amp']
+            point_amp = kwargs_ps['image_amp']
             source_amp = np.mean(np.array(point_amp) / np.array(mag))
         return np.array(source_amp)

lenstronomy/PointSource/Types/unlensed.py

@@ -9,7 +9,7 @@ class Unlensed(PSBase):
     class of a single point source in the image plane, aka star
     Name within the PointSource module: 'UNLENSED'
     This model can deal with arrays of point sources.
-    parameters: ra_image, dec_image, point_amp
+    parameters: ra_image, dec_image, image_amp
 
     """
 
@@ -43,7 +43,7 @@ def image_amplitude(self, kwargs_ps, **kwargs):
         :param kwargs: keyword arguments of function call (which are not used for this object
         :return: numpy array of amplitudes
         """
-        point_amp = kwargs_ps['point_amp']
+        point_amp = kwargs_ps['image_amp']
         return np.array(point_amp)
 
     def source_amplitude(self, kwargs_ps, **kwargs):
@@ -54,5 +54,5 @@ def source_amplitude(self, kwargs_ps, **kwargs):
         :param kwargs: keyword arguments of function call (which are not used for this object
         :return: numpy array of amplitudes
         """
-        point_amp = kwargs_ps['point_amp']
+        point_amp = kwargs_ps['image_amp']
         return np.array(point_amp)

lenstronomy/PointSource/point_source.py

@@ -19,7 +19,7 @@ def __init__(self, point_source_type_list, lensModel=None, fixed_magnification_l
         :param fixed_magnification_list: list of booleans (same length as point_source_type_list).
          If True, magnification ratio of point sources is fixed to the one given by the lens model.
          This option then requires to provide a 'source_amp' amplitude of the source brightness instead of
-         'point_amp' the list of image brightnesses.
+         'image_amp' the list of image brightnesses.
         :param additional_images_list: list of booleans (same length as point_source_type_list). If True, search for
         additional images of the same source is conducted.
         :param flux_from_point_source_list: list of booleans (optional), if set, will only return image positions
@@ -322,7 +322,7 @@ def update_linear(self, param, i, kwargs_ps, kwargs_lens):
                     i += 1
                 else:
                     n_points = len(ra_pos_list[k])
-                    kwargs['point_amp'] = np.array(param[i:i + n_points])
+                    kwargs['image_amp'] = np.array(param[i:i + n_points])
                     i += n_points
         return kwargs_ps, i
 
@@ -361,12 +361,12 @@ def set_amplitudes(self, amp_list, kwargs_ps):
             if self._flux_from_point_source_list[i]:
                 amp = amp_list[i]
                 if model == 'UNLENSED':
-                    kwargs_list[i]['point_amp'] = amp
+                    kwargs_list[i]['image_amp'] = amp
                 elif model in ['LENSED_POSITION', 'SOURCE_POSITION']:
                     if self._fixed_magnification_list[i] is True:
                         kwargs_list[i]['source_amp'] = amp
                     else:
-                        kwargs_list[i]['point_amp'] = amp
+                        kwargs_list[i]['image_amp'] = amp
         return kwargs_list
 
     @classmethod
@@ -375,12 +375,12 @@ def check_positive_flux(cls, kwargs_ps):
         check whether inferred linear parameters are positive
 
         :param kwargs_ps: point source keyword argument list
-        :return: bool, True, if all 'point_amp' parameters are positive semi-definite
+        :return: bool, True, if all 'image_amp' or 'source_amp' parameters are positive semi-definite
         """
         pos_bool = True
         for kwargs in kwargs_ps:
-            if 'point_amp' in kwargs:
-                point_amp = kwargs['point_amp']
+            if 'image_amp' in kwargs:
+                point_amp = kwargs['image_amp']
                 if not np.all(point_amp >= 0):
                     pos_bool = False
                     break

lenstronomy/PointSource/point_source_param.py

@@ -45,7 +45,7 @@ def __init__(self, model_list, kwargs_fixed, num_point_source_list=None, linear_
                 if self._fixed_magnification_list[k] is True and model in ['LENSED_POSITION', 'SOURCE_POSITION']:
                     fixed_low['source_amp'] = 0
                 else:
-                    fixed_low['point_amp'] = np.zeros(num)
+                    fixed_low['image_amp'] = np.zeros(num)
                 kwargs_lower.append(fixed_low)
         if kwargs_upper is None:
             kwargs_upper = []
@@ -60,7 +60,7 @@ def __init__(self, model_list, kwargs_fixed, num_point_source_list=None, linear_
                 if self._fixed_magnification_list[k] is True and model in ['LENSED_POSITION', 'SOURCE_POSITION']:
                     fixed_high['source_amp'] = 100
                 else:
-                    fixed_high['point_amp'] = np.ones(num)*100
+                    fixed_high['image_amp'] = np.ones(num)*100
                 kwargs_upper.append(fixed_high)
         self.lower_limit = kwargs_lower
         self.upper_limit = kwargs_upper
@@ -106,11 +106,11 @@ def get_params(self, args, i):
                 else:
                     kwargs['source_amp'] = kwargs_fixed['source_amp']
             else:
-                if 'point_amp' not in kwargs_fixed:
-                    kwargs['point_amp'] = np.array(args[i:i + self._num_point_sources_list[k]])
+                if 'image_amp' not in kwargs_fixed:
+                    kwargs['image_amp'] = np.array(args[i:i + self._num_point_sources_list[k]])
                     i += self._num_point_sources_list[k]
                 else:
-                    kwargs['point_amp'] = kwargs_fixed['point_amp']
+                    kwargs['image_amp'] = kwargs_fixed['image_amp']
 
             kwargs_list.append(kwargs)
         return kwargs_list, i
@@ -144,8 +144,8 @@ def set_params(self, kwargs_list):
                 if 'source_amp' not in kwargs_fixed:
                     args.append(kwargs['source_amp'])
             else:
-                if 'point_amp' not in kwargs_fixed:
-                    amp = kwargs['point_amp'][0:self._num_point_sources_list[k]]
+                if 'image_amp' not in kwargs_fixed:
+                    amp = kwargs['image_amp'][0:self._num_point_sources_list[k]]
                     for a in amp:
                         args.append(a)
         return args
@@ -182,10 +182,10 @@ def num_param(self):
                     num += 1
                     name_list.append('source_amp')
             else:
-                if 'point_amp' not in kwargs_fixed:
+                if 'image_amp' not in kwargs_fixed:
                     num += self._num_point_sources_list[k]
                     for i in range(self._num_point_sources_list[k]):
-                        name_list.append('point_amp')
+                        name_list.append('image_amp')
         return num, name_list
 
     def add_fix_linear(self, kwargs_fixed):
@@ -199,7 +199,7 @@ def add_fix_linear(self, kwargs_fixed):
             if self._fixed_magnification_list[k] is True and model in ['LENSED_POSITION', 'SOURCE_POSITION']:
                 kwargs_fixed[k]['source_amp'] = 1
             else:
-                kwargs_fixed[k]['point_amp'] = np.ones(self._num_point_sources_list[k])
+                kwargs_fixed[k]['image_amp'] = np.ones(self._num_point_sources_list[k])
         return kwargs_fixed
 
     def num_param_linear(self):

lenstronomy/SimulationAPI/point_source_variability.py

@@ -104,5 +104,5 @@ def point_source_time(self, t):
         for i, dt in enumerate(self._dt_days):
             t_i = -dt + t
             mag[i] = self._variability_func(t_i)
-        kwargs_ps[0]['point_amp'] = self.sim_api_ps.magnitude2cps(mag) * np.abs(self._mag)
+        kwargs_ps[0]['image_amp'] = self.sim_api_ps.magnitude2cps(mag) * np.abs(self._mag)
         return kwargs_ps

test/test_Analysis/test_light_profile.py

@@ -269,7 +269,7 @@ def test_point_source(self):
         kwargs_model = {'lens_model_list': ['SPEMD', 'SHEAR_GAMMA_PSI'], 'point_source_model_list': ['SOURCE_POSITION']}
         lensAnalysis = ProfileAnalysis(kwargs_model=kwargs_model)
         source_x, source_y = 0.02, 0.1
-        kwargs_ps = [{'dec_source': source_y, 'ra_source': source_x, 'point_amp': 75.155}]
+        kwargs_ps = [{'dec_source': source_y, 'ra_source': source_x, 'image_amp': 75.155}]
         kwargs_lens = [{'e2': 0.1, 'center_x': 0, 'theta_E': 1.133, 'e1': 0.1, 'gamma': 2.063, 'center_y': 0}, {'gamma_ext': 0.026, 'psi_ext': 1.793}]
         x_image, y_image = lensAnalysis.PointSource.image_position(kwargs_ps=kwargs_ps, kwargs_lens=kwargs_lens)
         from lenstronomy.LensModel.Solver.lens_equation_solver import LensEquationSolver

test/test_ImSim/test_MultiBand/test_single_band_multi_model.py

@@ -47,7 +47,7 @@ def setup(self):
 
         # Point Source
         point_source_model_list = ['UNLENSED']
-        kwargs_ps = [{'ra_image': [0.4], 'dec_image': [-0.2], 'point_amp': [2]}]
+        kwargs_ps = [{'ra_image': [0.4], 'dec_image': [-0.2], 'image_amp': [2]}]
         point_source_class = PointSource(point_source_type_list=point_source_model_list)
 
         kwargs_numerics = {'supersampling_factor': 1, 'supersampling_convolution': False, 'compute_mode': 'regular'}

test/test_ImSim/test_image_model.py

@@ -173,7 +173,7 @@ def test_point_source_rendering(self):
         ra_pos, dec_pos = makeImage.Data.map_pix2coord(x_pix, y_pix)
         e1, e2 = param_util.phi_q2_ellipticity(0, 0.8)
         kwargs_lens_init = [{'theta_E': 1, 'gamma': 2, 'e1': e1, 'e2': e2, 'center_x': 0, 'center_y': 0}]
-        kwargs_else = [{'ra_image': ra_pos, 'dec_image': dec_pos, 'point_amp': np.ones_like(ra_pos)}]
+        kwargs_else = [{'ra_image': ra_pos, 'dec_image': dec_pos, 'image_amp': np.ones_like(ra_pos)}]
         image = makeImage.image(kwargs_lens_init, kwargs_source={}, kwargs_lens_light={}, kwargs_ps=kwargs_else)
         #print(np.shape(model), 'test')
         #image = makeImage.ImageNumerics.array2image(model)
@@ -186,7 +186,7 @@ def test_point_source_rendering(self):
         phi, q = 0., 0.8
         e1, e2 = param_util.phi_q2_ellipticity(phi, q)
         kwargs_lens_init = [{'theta_E': 1, 'gamma': 2, 'e1': e1, 'e2': e2, 'center_x': 0, 'center_y': 0}]
-        kwargs_else = [{'ra_image': ra_pos, 'dec_image': dec_pos, 'point_amp': np.ones_like(ra_pos)}]
+        kwargs_else = [{'ra_image': ra_pos, 'dec_image': dec_pos, 'image_amp': np.ones_like(ra_pos)}]
         image = makeImage.image(kwargs_lens_init, kwargs_source={}, kwargs_lens_light={}, kwargs_ps=kwargs_else)
         #image = makeImage.ImageNumerics.array2image(model)
         for i in range(len(x_pix)):

test/test_Plots/test_plot_util.py

@@ -31,9 +31,9 @@ def test_source_position_plot(self):
         lensModel = LensModel(lens_model_list=['SIS'])
         ps = PointSource(point_source_type_list=['UNLENSED', 'LENSED_POSITION', 'SOURCE_POSITION'], lensModel=lensModel)
         kwargs_lens = [{'theta_E': 1., 'center_x': 0, 'center_y': 0}]
-        kwargs_ps = [{'ra_image': [1., 1.], 'dec_image': [0, 1], 'point_amp': [1, 1]},
-                          {'ra_image': [1.], 'dec_image': [1.], 'point_amp': [10]},
-                          {'ra_source': 0.1, 'dec_source': 0, 'point_amp': 1.}]
+        kwargs_ps = [{'ra_image': [1., 1.], 'dec_image': [0, 1], 'image_amp': [1, 1]},
+                          {'ra_image': [1.], 'dec_image': [1.], 'image_amp': [10]},
+                          {'ra_source': 0.1, 'dec_source': 0, 'image_amp': 1.}]
         ra_source, dec_source = ps.source_position(kwargs_ps, kwargs_lens)
         from lenstronomy.Data.coord_transforms import Coordinates
         coords_source = Coordinates(transform_pix2angle=np.array([[1, 0], [0, 1]])* 0.1,

test/test_PointSource/test_Types/test_lensed_position.py

@@ -12,7 +12,7 @@ def setup(self):
         self.ps_mag = LensedPositions(lens_model=lens_model, fixed_magnification=True)
         self.ps = LensedPositions(lens_model=lens_model, fixed_magnification=False)
         self.ps_add = LensedPositions(lens_model=lens_model, fixed_magnification=[False], additional_image=True)
-        self.kwargs = {'point_amp': [2, 1], 'ra_image': [0, 1.2], 'dec_image': [0, 0]}
+        self.kwargs = {'image_amp': [2, 1], 'ra_image': [0, 1.2], 'dec_image': [0, 0]}
         self.kwargs_mag = {'source_amp': 2, 'ra_image': [0, 1.2], 'dec_image': [0, 0]}
 
     def test_image_source_position(self):
@@ -37,7 +37,7 @@ def test_image_amplitude(self):
         amp = self.ps.image_amplitude(self.kwargs, kwargs_lens=self.kwargs_lens, x_pos=self.kwargs['ra_image'],
                                       y_pos=self.kwargs['dec_image'], magnification_limit=None,
                                       kwargs_lens_eqn_solver=None)
-        npt.assert_almost_equal(self.kwargs['point_amp'], amp)
+        npt.assert_almost_equal(self.kwargs['image_amp'], amp)
 
         amp = self.ps_mag.image_amplitude(self.kwargs_mag, kwargs_lens=self.kwargs_lens, x_pos=None,
                                           y_pos=None, magnification_limit=None, kwargs_lens_eqn_solver=None)

test/test_PointSource/test_Types/test_source_position.py

@@ -11,7 +11,7 @@ def setup(self):
         self.kwargs_lens = [{'theta_E': 1, 'center_x': 0, 'center_y': 0}]
         self.ps_mag = SourcePositions(lens_model=lens_model, fixed_magnification=True)
         self.ps = SourcePositions(lens_model=lens_model, fixed_magnification=False)
-        self.kwargs = {'point_amp': [2, 1], 'ra_source': 0.1, 'dec_source': 0}
+        self.kwargs = {'image_amp': [2, 1], 'ra_source': 0.1, 'dec_source': 0}
         self.kwargs_mag = {'source_amp': 1, 'ra_source': 0.1, 'dec_source': 0}
 
     def test_image_position(self):
@@ -38,7 +38,7 @@ def test_image_amplitude(self):
         amp = self.ps.image_amplitude(self.kwargs, kwargs_lens=self.kwargs_lens, x_pos=x_img,
                                               y_pos=y_img, magnification_limit=None,
                                               kwargs_lens_eqn_solver=None)
-        npt.assert_almost_equal(amp, self.kwargs['point_amp'])
+        npt.assert_almost_equal(amp, self.kwargs['image_amp'])
 
         #see if works with mag_pert defined
         self.kwargs['mag_pert'] = [0.1,0.1]