plotastrodata 1.1.2.post1__tar.gz → 1.1.3__tar.gz

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: plotastrodata
-Version: 1.1.2.post1
+Version: 1.1.3
 Summary: plotastrodata is a tool for astronomers to create figures from FITS files and perform fundamental data analyses with ease.
 Home-page: https://github.com/yusukeaso-astron/plotastrodata
 Download-URL: https://github.com/yusukeaso-astron/plotastrodata
@@ -13,6 +13,7 @@ License-File: LICENSE
 Requires-Dist: astropy
 Requires-Dist: corner
 Requires-Dist: dynesty
+Requires-Dist: emcee
 Requires-Dist: matplotlib
 Requires-Dist: multiprocess
 Requires-Dist: numpy
@@ -79,6 +80,7 @@ plotastrodata can do the following things.
 * astropy
 * corner (only for fitting)
 * dynesty (only for fitting)
+* emcee (only for fitting)
 * ffmpeg (only for movie)
 * matplotlib
 * multiprocess (only for fitting)

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/README.md

@@ -54,6 +54,7 @@ plotastrodata can do the following things.
 * astropy
 * corner (only for fitting)
 * dynesty (only for fitting)
+* emcee (only for fitting)
 * ffmpeg (only for movie)
 * matplotlib
 * multiprocess (only for fitting)

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', UserWarning)
-__version__ = '1.1.2-1'
+__version__ = '1.1.3'

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/plotastrodata/analysis_utils.py

@@ -8,7 +8,7 @@ from plotastrodata.other_utils import (coord2xy, rel2abs, estimate_rms, trim,
                                        Mfac, Mrot, dot2d, gaussian2d)
 from plotastrodata.fits_utils import FitsData, data2fits, Jy2K
 from plotastrodata import const_utils as cu
-from plotastrodata.fitting_utils import PTEmceeCorner
+from plotastrodata.fitting_utils import EmceeCorner
 
 
 def to4dim(data: np.ndarray) -> np.ndarray:
@@ -316,10 +316,10 @@ class AstroData():
 
         Args:
             model (function): The model function in the form of f(par, x, y).
-            bounds (np.ndarray): bounds for fitting_utils.PTEmceeCorner.
-            progressbar (bool, optional): progressbar for fitting_utils.PTEmceeCorner. Defaults to False.
-            kwargs_fit (dict, optional): Arguments for fitting_utils.PTEmceeCorner.fit.
-            kwargs_plotcorner (dict, optional): Arguments for fitting_utils.PTEmceeCorner.plotcorner.
+            bounds (np.ndarray): bounds for fitting_utils.EmceeCorner.
+            progressbar (bool, optional): progressbar for fitting_utils.EmceeCorner. Defaults to False.
+            kwargs_fit (dict, optional): Arguments for fitting_utils.EmceeCorner.fit.
+            kwargs_plotcorner (dict, optional): Arguments for fitting_utils.EmceeCorner.plotcorner.
             chan (int, optional): The channel number where the 2D model is fitted. Defaults to None.
 
         Returns:
@@ -338,8 +338,8 @@ class AstroData():
         def logl(p):
             rss = np.nansum((model(p, x, y) - d)**2)
             return -0.5 * rss / self.sigma**2 / pixelperbeam
-        
-        mcmc = PTEmceeCorner(bounds=bounds, logl=logl, progressbar=progressbar)
+
+        mcmc = EmceeCorner(bounds=bounds, logl=logl, progressbar=progressbar)
         kwargs_fit0 = {}
         kwargs_fit0.update(kwargs_fit)
         mcmc.fit(**kwargs_fit0)

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/plotastrodata/fitting_utils.py

@@ -1,5 +1,6 @@
 import numpy as np
 import matplotlib.pyplot as plt
+import emcee
 import ptemcee
 import corner
 from dynesty import DynamicNestedSampler as DNS
@@ -30,7 +31,7 @@ def logp(x: np.ndarray) -> float:
         return -np.inf
 
 
-class PTEmceeCorner():
+class EmceeCorner():
     warnings.simplefilter('ignore', RuntimeWarning)
 
     def __init__(self, bounds: np.ndarray, logl: object | None = None,
@@ -65,8 +66,8 @@ class PTEmceeCorner():
 
     def fit(self, nwalkersperdim: int = 2, ntemps: int = 1, nsteps: int = 1000,
             nburnin: int = 500, ntry: int = 1, pos0: np.ndarray | None = None,
-            savechain: str | None = None, ncores: int = 1, grcheck: bool = False
-            ) -> None:
+            savechain: str | None = None, ncores: int = 1, grcheck: bool = False,
+            pt: bool = False) -> None:
         """Perform a Markov Chain Monte Carlo (MCMC) fitting process using the ptemcee library, which is a parallel tempering version of the emcee package, and make a corner plot of the samples using the corner package.
 
         Args:
@@ -79,11 +80,15 @@ class PTEmceeCorner():
             savechain (str, optional): File name of the chain in format of .npy. Defaults to None.
             ncores (int, optional): Number of cores for multiprocessing.Pool. ncores=1 does not use multiprocessing. Defaults to 1.
             grcheck (bool, optional): Whether to check Gelman-Rubin statistics. Defaults to False.
+            pt (bool, optional): Whether to use ptemcee; otherwise, emcee is used. Defaults to False.
         """
         global bar
         if nwalkersperdim < 2:
             print(f'nwalkersperdim < 2 is not allowed. Use 2 instead of {nwalkersperdim:d}.')
         nwalkers = max(nwalkersperdim, 2) * self.dim  # must be even and >= 2 * dim
+        if ntemps > 1 and not pt:
+            print('ntemps>1 is supported only with pt=True. Set pt=True.')
+            pt = True
         if global_progressbar:
             bar = tqdm(total=ntry * ntemps * nwalkers * (nsteps + 1) // ncores)
             bar.set_description('Within the ranges')
@@ -95,16 +100,37 @@ class PTEmceeCorner():
             if pos0 is None:
                 pos0 = np.random.rand(ntemps, nwalkers, self.dim) \
                        * (self.bounds[1] - self.bounds[0]) + self.bounds[0]
-            pars = {'ntemps': ntemps, 'nwalkers': nwalkers, 'dim': self.dim,
-                    'logl': self.logl, 'logp': self.logp}
-            if ncores > 1:
-                with Pool(ncores) as pool:
-                    sampler = ptemcee.Sampler(**pars, pool=pool)
+                if not pt:
+                    pos0 = pos0[0]
+            if pt:
+                pars = {'ntemps': ntemps, 'nwalkers': nwalkers, 'dim': self.dim,
+                        'logl': self.logl, 'logp': self.logp}
+                if ncores > 1:
+                    with Pool(ncores) as pool:
+                        sampler = ptemcee.Sampler(**pars, pool=pool)
+                        sampler.run_mcmc(pos0, nsteps)
+                else:
+                    sampler = ptemcee.Sampler(**pars)
                     sampler.run_mcmc(pos0, nsteps)
+                samples = sampler.chain[0, :, nburnin:, :]  # temperature, walker, step, dim
             else:
-                sampler = ptemcee.Sampler(**pars)
-                sampler.run_mcmc(pos0, nsteps)
-            samples = sampler.chain[0, :, nburnin:, :]  # temperature, walker, step, dim
+                if ncores > 1:
+                    print('Use logl as log_prob_fn to avoid function-in-function.')
+                    log_prob_fn = self.logl
+                else:
+                    def log_prob_fn(x):
+                        return self.logp(x) + self.logl(x)
+
+                pars = {'nwalkers': nwalkers, 'ndim': self.dim,
+                        'log_prob_fn': log_prob_fn}
+                if ncores > 1:
+                    with Pool(ncores) as pool:
+                        sampler = emcee.EnsembleSampler(**pars, pool=pool)
+                        sampler.run_mcmc(pos0, nsteps)
+                else:
+                    sampler = emcee.EnsembleSampler(**pars)
+                    sampler.run_mcmc(pos0, nsteps)
+                samples = sampler.chain[:, nburnin:, :]  # walker, step, dim
             if grcheck:
                 # Gelman-Rubin statistics #
                 B = np.std(np.mean(samples, axis=1), axis=0)
@@ -122,9 +148,14 @@ class PTEmceeCorner():
         self.samples = samples
         if savechain is not None:
             np.save(savechain.replace('.npy', '') + '.npy', samples)
-        lnps = sampler.logprobability[0]  # [0] is in the temperature axis.
-        idx_best = np.unravel_index(np.argmax(lnps), lnps.shape)
-        self.popt = sampler.chain[0][idx_best]
+        if pt:
+            lnps = sampler.logprobability[0]  # [0] is in the temperature axis.
+            idx_best = np.unravel_index(np.argmax(lnps), lnps.shape)
+            self.popt = sampler.chain[0][idx_best]  # [0] is in the temperature axis.
+        else:
+            lnps = sampler.lnprobability
+            idx_best = np.unravel_index(np.argmax(lnps), lnps.shape)
+            self.popt = sampler.chain[idx_best]
         self.lnps = lnps[:, nburnin:]
         s = samples.reshape((-1, self.dim))
         self.plow = np.percentile(s, self.percent[0], axis=0)
@@ -199,7 +230,8 @@ class PTEmceeCorner():
             plt.show()
         plt.close()
 
-    def posteriorongrid(self, ngrid: list = 100, log: list[bool] = False, pcut: float = 0):
+    def posteriorongrid(self, ngrid: list[int] | int = 100,
+                        log: list[bool] | bool = False, pcut: float = 0):
         """Calculate the posterior on a grid of ngrid x ngrid x ... x ngrid.
 
         Args:

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/plotastrodata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: plotastrodata
-Version: 1.1.2.post1
+Version: 1.1.3
 Summary: plotastrodata is a tool for astronomers to create figures from FITS files and perform fundamental data analyses with ease.
 Home-page: https://github.com/yusukeaso-astron/plotastrodata
 Download-URL: https://github.com/yusukeaso-astron/plotastrodata
@@ -13,6 +13,7 @@ License-File: LICENSE
 Requires-Dist: astropy
 Requires-Dist: corner
 Requires-Dist: dynesty
+Requires-Dist: emcee
 Requires-Dist: matplotlib
 Requires-Dist: multiprocess
 Requires-Dist: numpy
@@ -79,6 +80,7 @@ plotastrodata can do the following things.
 * astropy
 * corner (only for fitting)
 * dynesty (only for fitting)
+* emcee (only for fitting)
 * ffmpeg (only for movie)
 * matplotlib
 * multiprocess (only for fitting)

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/plotastrodata.egg-info/requires.txt

@@ -1,6 +1,7 @@
 astropy
 corner
 dynesty
+emcee
 matplotlib
 multiprocess
 numpy

{plotastrodata-1.1.2.post1 → plotastrodata-1.1.3}/setup.cfg

@@ -19,6 +19,7 @@ install_requires =
 	astropy
 	corner
 	dynesty
+	emcee
 	matplotlib
 	multiprocess
 	numpy