ACID-code-v2 0.2.0a1__tar.gz → 0.2.2__tar.gz

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/.github/workflows/publish.yml

@@ -5,7 +5,7 @@ on:
       - 'v*'
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.2.0a1
+Version: 0.2.2
 Summary: Returns line profiles from input spectra by fitting the stellar continuum and performing LSD
 Author: Lucy Dolan
 Author-email: Benjamin Cadell <bcadell01@qub.ac.uk>

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/src/ACID_code_v2/ACID.py

@@ -8,7 +8,6 @@ from functools import partial
 from multiprocessing import Pool
 from . import utils
 from . import LSD
-from . import mcmc_utils
 
 warnings.filterwarnings("ignore")
 importlib.reload(LSD)
@@ -233,11 +232,57 @@ def model_func(inputs, x):
    
     return mdl
 
+def log_likelihood(theta, x, y, yerr):
+    ## maximum likelihood estimation for the mcmc model.
+    model = model_func(theta, x)
+
+    lnlike = -0.5 * np.sum(((y) - (model)) ** 2 / yerr**2 + np.log(yerr**2)+ np.log(2*np.pi))
+
+    return lnlike
+
+def log_prior(theta):
+    ## imposes the prior restrictions on the inputs - rejects if profile point is less than -10 or greater than 0.5.
+    check = 0
+    z = theta[:k_max]
+
+    for i in range(len(theta)):
+        if i < k_max: ## must lie in z
+            if -10 <= theta[i] <= 0.5:
+                pass
+            else:
+                check = 1
+
+    if check == 0:
+
+        # excluding the continuum points in the profile (in flux)
+        z_cont = []
+        v_cont = []
+        for i in range(0, 5):
+                z_cont.append(np.exp(z[len(z)-i-1])-1)
+                v_cont.append(velocities[len(velocities)-i-1])
+                z_cont.append(np.exp(z[i])-1)
+                v_cont.append(velocities[i])
+
+        z_cont = np.array(z_cont)
+        v_cont = np.array(v_cont)
+
+        p_pent = np.sum((np.log((1/np.sqrt(2*np.pi*0.01**2)))-0.5*(z_cont/0.01)**2))
+
+        return p_pent
+
+    return -np.inf
+
+def log_probability(theta):
+    ## calculates log probability - used for mcmc
+    lp = log_prior(theta)
+    if not np.isfinite(lp):
+        return -np.inf
+    final = lp + log_likelihood(theta, x, y, yerr)
+    return final
+
 def residual_mask(wavelengths, data_spec_in, data_err, initial_inputs, poly_ord, linelist,
                   velocities=np.arange(-25, 25, 0.82), pix_chunk=20, dev_perc=25, 
-                  tell_lines=[3820.33, 3933.66, 3968.47, 4327.74, 4307.90, 4383.55,
-                              4861.34, 5183.62, 5270.39, 5889.95, 5895.92, 6562.81,
-                              7593.70, 8226.96], n_sig=1):
+                  tell_lines=None, n_sig=1, alpha=None):
     ## iterative residual masking - mask continuous areas first - then possibly progress to masking the narrow lines
 
     forward = model_func(initial_inputs, wavelengths)
@@ -568,7 +613,7 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
     yerr, model_inputs_resi, mask_idx = residual_mask(x, y, yerr, model_inputs, poly_ord,
                                                       linelist, pix_chunk=pix_chunk,
                                                       dev_perc=dev_perc, tell_lines=telluric_lines,
-                                                      n_sig=n_sig)
+                                                      n_sig=n_sig, alpha=alpha)
 
     # if verbose:
     #     t4 = time.time()
@@ -593,9 +638,6 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
     pos = np.array(pos)
     pos = np.transpose(pos)
 
-    # Inistialise MCMC class:
-    mcmc_class = mcmc_utils.Model(model_func, x, y, yerr, velocities, k_max)
-
     if verbose:
         t5 = time.time()
         # print('MCMC set up takes: %s'%(t5-t4))
@@ -619,7 +661,7 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
         if sys.platform != "win32":
             ctx = mp.get_context("fork")
             with ctx.Pool(processes = cores) as pool:
-                sampler = emcee.EnsembleSampler(nwalkers, ndim, mcmc_class.log_probability, pool=pool)
+                sampler = emcee.EnsembleSampler(nwalkers, ndim, log_probability, pool=pool)
                 sampler.run_mcmc(pos, nsteps, progress=True, store=True)
 
             # with Pool() as pool: # Original code
@@ -633,7 +675,7 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
 
 
     else:
-        sampler = emcee.EnsembleSampler(nwalkers, ndim, mcmc_class.log_probability)
+        sampler = emcee.EnsembleSampler(nwalkers, ndim, log_probability)
         sampler.run_mcmc(pos, nsteps, progress=True)
 
     print('MCMC run takes: %s'%(time.time()-t5))
@@ -799,8 +841,16 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
 
     return all_frames
 
-def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './', file_type = 'e2ds', **kwargs):
-    """_summary_
+def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './',
+               file_type = 'e2ds', name="test", **kwargs):
+    """Accurate Continuum fItting and Deconvolution for HARPS e2ds and s1d spectra (DRS pipeline 3.5)
+
+    Fits the continuum of the given spectra and performs LSD on the continuum corrected spectra,
+    returning an LSD profile for each file given. Files must all be kept in the same folder as well
+    as their corresponding blaze files. If 's1d' are being used their e2ds equivalents must also be
+    in this folder. Result files containing profiles and associated errors for each order (or
+    corresponding wavelength range in the case of 's1d' files) will be created and saved to a
+    specified folder. It is recommended that this folder is seperate to the input files.
 
     Parameters
     ----------
@@ -843,6 +893,8 @@ def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './', file_t
     global frame_wavelengths
     global frame_errors
     global sns
+    global run_name
+    run_name = name
 
     if order_range is None:
         order_range = np.arange(10, 70)
@@ -886,5 +938,3 @@ def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './', file_t
         errors.append(result2)
 
     return BJDs, profiles, errors
-
-

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/src/ACID_code_v2/LSD.py

@@ -1,13 +1,12 @@
 import numpy as np
 from scipy import linalg
 from astropy.io import  fits
-import glob, time, warnings, sys, psutil
+import glob, time, warnings, sys, psutil, os
 import scipy.constants as const
 import matplotlib.pyplot as plt
 from scipy.signal import find_peaks
 from scipy.interpolate import interp1d, LSQUnivariateSpline
 from tqdm import tqdm
-import os
 ckms = float(const.c/1e3)  # speed of light in km/s
 
 def LSD(wavelengths, flux_obs, rms, linelist, adjust_continuum, poly_ord, sn, 
@@ -199,9 +198,9 @@ def continuumfit(wavelengths1, fluxes1, poly_ord):
         
         return flux_obs
 
-# from MM-LSD code - give credit if needed
 def upper_envelope(x, y):
-    #used to compute the tapas continuum. find peaks then fit spline to it.
+    # from MM-LSD code - give credit if needed
+    # used to compute the tapas continuum. find peaks then fit spline to it.
     peaks = find_peaks(y, height=0.2, distance=len(x) // 500)[0]
     # t= knot positions
     spl = LSQUnivariateSpline(x=x[peaks], y=y[peaks], t=x[peaks][5::10])

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/src/ACID_code_v2/utils.py

@@ -21,7 +21,6 @@ def ensure_list(x, allow_none=False):
     else:
         raise TypeError("Input must be a list or numpy array")
 
-
 def round_sig(x1, sig):
     return round(x1, sig-int(floor(log10(abs(x1))))-1)
 

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/src/ACID_code_v2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.2.0a1
+Version: 0.2.2
 Summary: Returns line profiles from input spectra by fitting the stellar continuum and performing LSD
 Author: Lucy Dolan
 Author-email: Benjamin Cadell <bcadell01@qub.ac.uk>

{acid_code_v2-0.2.0a1 → acid_code_v2-0.2.2}/src/ACID_code_v2.egg-info/SOURCES.txt

@@ -6,7 +6,6 @@ README.md
 acid.yml
 pyproject.toml
 .github/workflows/publish.yml
-.github/workflows/python-app.yml
 .other_scripts/5_residual_profiles.py
 .other_scripts/8_master_out_profiles.py
 .vscode/launch.json
@@ -26,7 +25,6 @@ example/tutorial_code.py
 src/ACID_code_v2/ACID.py
 src/ACID_code_v2/LSD.py
 src/ACID_code_v2/__init__.py
-src/ACID_code_v2/mcmc_utils.py
 src/ACID_code_v2/utils.py
 src/ACID_code_v2.egg-info/PKG-INFO
 src/ACID_code_v2.egg-info/SOURCES.txt

acid_code_v2-0.2.0a1/.github/workflows/python-app.yml

@@ -1,35 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-
-    runs-on: macos-latest
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.7"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest
-        git clone https://github.com/ldolan05/ACID.git
-        cd ACID
-        python -m pip install -e .
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
-    - name: Test with pytest
-      run: |
-        pytest tests/*

acid_code_v2-0.2.0a1/src/ACID_code_v2/mcmc_utils.py

@@ -1,60 +0,0 @@
-import numpy as np
-from ACID_code_v2.ACID import model_func
-
-
-class Model:
-    def __init__(self, model_func, x, y, yerr, velocities, k_max):
-        self.model_func = model_func
-        self.x = x
-        self.y = y
-        self.yerr = yerr
-        self.velocities = velocities
-        self.k_max = k_max
-
-    def log_likelihood(self, theta, x, y, yerr):
-        ## maximum likelihood estimation for the mcmc model.
-        model = model_func(theta, x)
-
-        lnlike = -0.5 * np.sum(((y) - (model)) ** 2 / yerr**2 + np.log(yerr**2)+ np.log(2*np.pi))
-
-        return lnlike
-
-    def log_prior(self, theta):
-        ## imposes the prior restrictions on the inputs - rejects if profile point is less than -10 or greater than 0.5.
-        check = 0
-        z = theta[:self.k_max]
-
-        for i in range(len(theta)):
-            if i < self.k_max: ## must lie in z
-                if -10 <= theta[i] <= 0.5:
-                    pass
-                else:
-                    check = 1
-
-        if check == 0:
-
-            # excluding the continuum points in the profile (in flux)
-            z_cont = []
-            v_cont = []
-            for i in range(0, 5):
-                    z_cont.append(np.exp(z[len(z)-i-1])-1)
-                    v_cont.append(self.velocities[len(self.velocities)-i-1])
-                    z_cont.append(np.exp(z[i])-1)
-                    v_cont.append(self.velocities[i])
-
-            z_cont = np.array(z_cont)
-            v_cont = np.array(v_cont)
-
-            p_pent = np.sum((np.log((1/np.sqrt(2*np.pi*0.01**2)))-0.5*(z_cont/0.01)**2))
-
-            return p_pent
-
-        return -np.inf
-
-    def log_probability(self, theta):
-        ## calculates log probability - used for mcmc
-        lp = self.log_prior(theta)
-        if not np.isfinite(lp):
-            return -np.inf
-        final = lp + self.log_likelihood(theta, self.x, self.y, self.yerr)
-        return final