Merge pull request #209 from discsim/v1.2.2

v1.2.2

HISTORY.rst

@@ -3,6 +3,32 @@
 Changelog
 +++++++++
 
+v.1.2.2
++++++++
+*One bug fix, some code refactoring, a couple new functionalities, integrates scale-height fits into command-line UI*
+
+- default_parameters.json, parameter_descriptions.json:
+    - Adds parameters: 'convergence_failure', 'I_scale', 'save_figures', 'scale_height'
+- filter.py
+    - Breaks 'spectral_smoothing_matrix' out of 'CriticalFilter'; some restructuring of 'covariance_MAP' and 'log_prior'
+- fit.py
+    - Adds 'get_scale_height' function
+- hankel.py
+    - Adds 'interpolation_coefficients' and 'interpolate' functions
+- io.py
+    - Fixed a bug that was saving incorrect uncertainty for LogNormal brightness profile
+- make_figs.py
+    - Adds non-negative fit to figures
+- radial_fitters.py
+    - Adds 'convergence_failure' arg to FrankFitter
+    - Adds 'log_evidence_laplace' function to FrankFitter
+- statistical_models.py
+    - Adds 'DHT_coefficients' and 'interpolate' functions to 'VisibilityMapping'
+- test.py
+    - Adds tests for non-negative solver ('test_solve_non_negative') and solution object IO ('test_save_load_sol')
+- utilities.py
+    - Adds 'get_fit_stat_uncer' function
+
 v.1.2.1
 +++++++
 *Fixed a bug that caused non-python files to not be installed through pip*

frank/__init__.py

@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>
 #
-__version__ = "1.2.1"
+__version__ = "1.2.2"
 
 from frank import constants
 from frank import geometry

frank/constants.py

@@ -19,7 +19,6 @@
 """This module contains useful conversion constants."""
 
 import numpy as np
-from scipy.constants import c
 
 rad_to_arcsec = 3600 * 180 / np.pi
 sterad_to_arcsec = rad_to_arcsec ** 2

frank/debris_fitters.py

@@ -21,11 +21,6 @@
   of deprojected visibities. Routines in this file assume that the emission is
   optically thin with a Gaussian vertical structure.
 """
-import abc
-from collections import defaultdict
-import logging
-import numpy as np
-
 from frank.radial_fitters import FourierBesselFitter, FrankFitter
 
 class FourierBesselDebrisFitter(FourierBesselFitter):

frank/default_parameters.json

@@ -6,6 +6,7 @@
     "save_profile_fit" : true,
     "save_vis_fit"     : true,
     "save_uvtables"    : true,
+    "save_figures"     : true,
     "iteration_diag"   : false,
     "format"           : null
   },

frank/filter.py

@@ -20,9 +20,6 @@
 import numpy as np
 import scipy.sparse
 
-from frank.constants import rad_to_arcsec
-
-
 def spectral_smoothing_matrix(DHT, weights):
     r"""Compute the spectral smoothing prior matrix, Tij.
     

frank/fit.py

@@ -22,7 +22,6 @@
 """
 
 import os
-import sys
 import time
 import json
 
@@ -38,7 +37,6 @@ def _check_and_warn_if_parallel():
                         "'export OMP_NUM_THREADS=1' to disable this warning.")
 
 import numpy as np
-
 import logging
 
 import frank
@@ -136,6 +134,11 @@ def parse_parameters(*args):
         os.path.join(model['input_output']['save_dir'],
                      os.path.splitext(os.path.basename(uv_path))[0])
 
+    if model['input_output']['save_figures'] is True:
+        model['input_output']['fig_save_prefix'] = save_prefix
+    else:
+        model['input_output']['fig_save_prefix'] = None
+
     log_path = save_prefix + '_frank_fit.log'
     frank.enable_logging(log_path)
 
@@ -550,7 +553,7 @@ def number_to_list(x):
                                                                bin_widths=model['plotting']['bin_widths'],
                                                                dist=model['plotting']['distance'],
                                                                force_style=model['plotting']['force_style'],
-                                                               save_prefix=model['input_output']['save_prefix'],
+                                                               save_prefix=model['input_output']['fig_save_prefix'],
                                                                )
     else:
         logging.info('The multifit figure requires alpha and wsmooth to be lists of length <= 2.'
@@ -628,7 +631,7 @@ def output_results(u, v, vis, weights, sol, geom, model, iteration_diagnostics=N
                                                              geom=geom,
                                                              bin_widths=model['plotting']['bin_widths'],
                                                              force_style=model['plotting']['force_style'],
-                                                             save_prefix=model['input_output']['save_prefix']
+                                                             save_prefix=model['input_output']['fig_save_prefix']
                                                              )
 
             figs.append(deproj_fig)
@@ -641,7 +644,7 @@ def output_results(u, v, vis, weights, sol, geom, model, iteration_diagnostics=N
                                                              dist=model['plotting']['distance'],
                                                              logx=model['plotting']['plot_in_logx'],
                                                              force_style=model['plotting']['force_style'],
-                                                             save_prefix=model['input_output']['save_prefix'],
+                                                             save_prefix=model['input_output']['fig_save_prefix'],
                                                              stretch=model['plotting']['stretch'],
                                                              gamma=model['plotting']['gamma'],
                                                              asinh_a=model['plotting']['asinh_a']
@@ -657,7 +660,7 @@ def output_results(u, v, vis, weights, sol, geom, model, iteration_diagnostics=N
                                                           dist=model['plotting']['distance'],
                                                           logx=model['plotting']['plot_in_logx'],
                                                           force_style=model['plotting']['force_style'],
-                                                          save_prefix=model['input_output']['save_prefix'],
+                                                          save_prefix=model['input_output']['fig_save_prefix'],
                                                           norm_residuals=model['plotting']['norm_residuals'],
                                                           stretch=model['plotting']['stretch'],
                                                           gamma=model['plotting']['gamma'],
@@ -672,7 +675,7 @@ def output_results(u, v, vis, weights, sol, geom, model, iteration_diagnostics=N
                                                              iteration_diagnostics=iteration_diagnostics,
                                                              iter_plot_range=model['plotting']['iter_plot_range'],
                                                              force_style=model['plotting']['force_style'],
-                                                             save_prefix=model['input_output']['save_prefix']
+                                                             save_prefix=model['input_output']['fig_save_prefix']
                                                              )
 
             figs.append(diag_fig)
@@ -716,7 +719,7 @@ def output_results(u, v, vis, weights, sol, geom, model, iteration_diagnostics=N
                                                                         MAP_convolved=MAP_convolved,
                                                                         dist=model['plotting']['distance'],
                                                                         force_style=model['plotting']['force_style'],
-                                                                        save_prefix=model['input_output']['save_prefix']
+                                                                        save_prefix=model['input_output']['fig_save_prefix']
                                                                         )
 
             figs.append(clean_fig)
@@ -788,7 +791,7 @@ def perform_bootstrap(u, v, vis, weights, geom, model):
     boot_fig, boot_axes = make_figs.make_bootstrap_fig(r=sol.r,
                                                        profiles=profiles_bootstrap,
                                                        force_style=model['plotting']['force_style'],
-                                                       save_prefix=model['input_output']['save_prefix']
+                                                       save_prefix=model['input_output']['fig_save_prefix']
                                                        )
 
     return boot_fig, boot_axes

frank/hankel.py

@@ -19,13 +19,9 @@
 """This module contains functions for computing the
 discrete Hankel transform (DHT).
 """
-
 import numpy as np
 from scipy.special import j0, j1, jn_zeros, jv
 
-from frank.constants import rad_to_arcsec
-
-
 class DiscreteHankelTransform(object):
     r"""
     Utilities for computing the discrete Hankel transform.

frank/parameter_descriptions.json

@@ -6,6 +6,7 @@
     "save_profile_fit" : "Whether to save fitted brightness profile",
     "save_vis_fit"     : "Whether to save fitted visibility distribution",
     "save_uvtables"    : "Whether to save fitted and residual UV tables (these are reprojected)",
+    "save_figures"     : "Whether to save generated figures selected in 'plotting'",
     "iteration_diag"   : "Whether to return and save diagnostics of the fit iteration (needed for diag_plot)",
     "format"           : "Output file format. Default is the same as for 'uvtable_filename', else choose from 'npz' or 'txt'"
   },

frank/radial_fitters.py

@@ -25,7 +25,7 @@
 import logging
 import numpy as np
 
-from frank.constants import deg_to_rad, rad_to_arcsec
+from frank.constants import rad_to_arcsec
 from frank.filter import CriticalFilter
 from frank.hankel import DiscreteHankelTransform
 from frank.statistical_models import (

frank/statistical_models.py

@@ -17,18 +17,13 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>
 #
 
-
-import multiprocessing
 import numpy as np
 import scipy.linalg
 import scipy.sparse
 import scipy.optimize
-from collections import defaultdict
 import logging
 
-from frank.hankel import DiscreteHankelTransform
 from frank.constants import rad_to_arcsec, deg_to_rad
-
 from frank.minimizer import LineSearch, MinimizeNewton
 
 class VisibilityMapping:
@@ -278,7 +273,7 @@ def check_hash(self, hash, multi_freq=False, geometry=None):
             if hash[4] is None:
                 return False
             else:
-                return np.alltrue(self._scale_height == hash[4])
+                return np.all(self._scale_height == hash[4])
 
 
     def predict_visibilities(self, I, q, k=None, geometry=None):

frank/tests.py

@@ -528,7 +528,7 @@ def _run_pipeline(geometry='gaussian', fit_phase_offset=True,
         params['plotting']['full_plot'] = True
         params['plotting']['diag_plot'] = True
         params['plotting']['deprojec_plot'] = True
-        params['plotting']['save_figs'] = True
+        params['input_output']['save_figures'] = False
         params['plotting']['distance'] = 121.
         params['plotting']['bin_widths'] = [1e5]
         params['plotting']['iter_plot_range'] = [0, 5]

frank/utilities.py

@@ -21,7 +21,6 @@
 """
 import logging
 import numpy as np
-from scipy.fft import fftfreq
 from scipy.interpolate import interp1d
 
 from frank.constants import deg_to_rad, sterad_to_arcsec, rad_to_arcsec