ACID-code-v2 0.1.2__tar.gz → 0.1.4__tar.gz

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/.gitignore

@@ -27,3 +27,4 @@ wheels/
 .installed.cfg
 *.egg
 unfinished/
+packager/

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/ACID_code_v2/ACID.py

@@ -9,16 +9,7 @@ import multiprocessing as mp
 from functools import partial
 from multiprocessing import Pool
 from math import log10, floor
-
-try:
-    from . import utils
-except Exception:
-    import utils
-
-try:
-    from . import LSD_func_faster as LSD
-except Exception:
-    import LSD_func_faster as LSD
+import LSD, utils
 
 warnings.filterwarnings("ignore")
 importlib.reload(LSD)
@@ -595,9 +586,9 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
     poly_inputs, fluxes1, flux_error_order1, fit = continuumfit(
         fluxes, (wavelengths*a)+b, flux_error_order, poly_ord)
 
-    if verbose:
-        t2 = time.time()
-        print('Set up before LSD %s'%(t2-t0))
+    # if verbose:
+    #     t2 = time.time()
+    #     print('Set up before LSD %s'%(t2-t0))
 
     #### getting the initial profile
     global alpha
@@ -605,9 +596,9 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
         wavelengths, fluxes1, flux_error_order1, linelist, 'False', poly_ord, sn, 30, run_name,
         velocities, verbose=verbose)
 
-    if verbose:
-        t3 = time.time()
-        print('LSD run takes: %s'%(t3-t2))
+    # if verbose:
+    #     t3 = time.time()
+    #     print('LSD run takes: %s'%(t3-t2))
 
     ## Setting the number of points in vgrid (k_max)
     global k_max
@@ -627,14 +618,16 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
     # Masking based off residuals
     global mask_idx
     
+    if verbose:
+        print('Residual masking...')
     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, verbose=verbose)
 
-    if verbose:
-        t4 = time.time()
-        print('residual masking takes: %s' %(t4-t3))
+    # if verbose:
+    #     t4 = time.time()
+    #     print('residual masking takes: %s' %(t4-t3))
 
     ## Setting number of walkers and their start values(pos)
     ndim = len(model_inputs)
@@ -657,7 +650,7 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
 
     if verbose:
         t5 = time.time()
-        print('MCMC set up takes: %s'%(t5-t4))
+        # print('MCMC set up takes: %s'%(t5-t4))
         print('Initialised in %ss'%round((t5-t0), 2))
 
     print('Fitting the continuum using emcee...')
@@ -858,7 +851,9 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
 
     return all_frames
 
-def ACID_HARPS(filelist, line, vgrid, poly_or=3, order_range=np.arange(10,70), save_path = './', file_type = 'e2ds', pix_chunk = 20, dev_perc = 25, n_sig=1, telluric_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]):
+def ACID_HARPS(filelist, line, vgrid, poly_or=3, order_range=np.arange(10,70), save_path = './', file_type = 'e2ds',
+               pix_chunk = 20, dev_perc = 25, n_sig=1, telluric_lines = None, **kwargs):
+
 
     """Accurate Continuum fItting and Deconvolution for HARPS e2ds and s1d spectra (DRS pipeline 3.5)
 
@@ -904,7 +899,8 @@ def ACID_HARPS(filelist, line, vgrid, poly_or=3, order_range=np.arange(10,70), s
 
         frame_wavelengths, frames, frame_errors, sns, telluric_spec = read_in_frames(order, filelist, file_type)
 
-        all_frames = ACID(frame_wavelengths, frames, frame_errors, linelist, sns, velocities, all_frames,  poly_or, pix_chunk, dev_perc, n_sig, telluric_lines, order = order-min(order_range))  
+        all_frames = ACID(frame_wavelengths, frames, frame_errors, linelist, sns, velocities, all_frames, poly_or,
+                          pix_chunk, dev_perc, n_sig, telluric_lines, order = order-min(order_range), **kwargs)
 
     # adding into fits files for each frame
     BJDs = []

acid_code_v2-0.1.2/ACID_code_v2/LSD_func_faster.py → acid_code_v2-0.1.4/ACID_code_v2/LSD.py

@@ -81,8 +81,12 @@ def LSD(wavelengths, flux_obs, rms, linelist, adjust_continuum, poly_ord, sn,
     else:
         block = 512 # after initial testing, this value is a good compromise between memory use and speed
         alpha  = np.zeros((len(blankwaves), len(velocities)), dtype=np.float64)
-        for start_pos in tqdm(range(0, len(wavelengths_expected), block), desc='Calculating alpha matrix'):
-            end_pos = min(start_pos + block, len(wavelengths_expected)) # ensure we don't go out of bounds
+        if verbose:
+            iterable = tqdm(range(0, len(wavelengths_expected), block), desc='Calculating alpha matrix')
+        else:
+            iterable = range(0, len(wavelengths_expected), block)
+        for start_pos in iterable:
+            end_pos = min(start_pos + block, len(wavelengths_expected)) # ensure we don't go out of bounds on last iteration
             wl  = wavelengths_expected[start_pos:end_pos]
             dep = depths_expected[start_pos:end_pos]
 

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/ACID_code_v2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.1.2
+Version: 0.1.4
 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>
@@ -9,7 +9,7 @@ Project-URL: Homepage, https://github.com/Benjamin-Cadell/ACID
 Keywords: lsd,least squares deconvolution,fitting,ACID
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: POSIX
-Requires-Python: >=3.13
+Requires-Python: <3.14,>=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/ACID_code_v2.egg-info/SOURCES.txt

@@ -9,9 +9,8 @@ pyproject.toml
 .other_scripts/5_residual_profiles.py
 .other_scripts/8_master_out_profiles.py
 .vscode/launch.json
-ACID_code_v2/.tutorial_code.py
 ACID_code_v2/ACID.py
-ACID_code_v2/LSD_func_faster.py
+ACID_code_v2/LSD.py
 ACID_code_v2/__init__.py
 ACID_code_v2/utils.py
 ACID_code_v2.egg-info/PKG-INFO
@@ -97,6 +96,7 @@ example/example_linelist.txt
 example/sample_spec_1.fits
 example/sample_spec_2.fits
 example/sample_spec_3.fits
+example/tutorial_code.py
 tests/test.py
 tests/tests.py
 tests/tutorial_test.py

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/ACID_code_v2.egg-info/top_level.txt

@@ -3,4 +3,5 @@ dist
 docs
 downloads
 example
+packager
 tests

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.1.2
+Version: 0.1.4
 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>
@@ -9,7 +9,7 @@ Project-URL: Homepage, https://github.com/Benjamin-Cadell/ACID
 Keywords: lsd,least squares deconvolution,fitting,ACID
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: POSIX
-Requires-Python: >=3.13
+Requires-Python: <3.14,>=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy

acid_code_v2-0.1.2/ACID_code_v2/.tutorial_code.py → acid_code_v2-0.1.4/example/tutorial_code.py

@@ -2,19 +2,22 @@
 from astropy.io import fits
 import importlib, os
 import multiprocessing as mp
-import ACID as acid
-importlib.reload(acid)
 import numpy as np
 import matplotlib.pyplot as plt
+os.chdir(os.path.dirname(__file__))
+os.chdir("../") # ensures we are in the main directory
+import ACID_code_v2 as acid
+importlib.reload(acid)
+os.chdir("example") # change to example directory
 
-spec_file = fits.open('../example/sample_spec_1.fits')
+spec_file = fits.open('sample_spec_1.fits')
 
 wavelength = spec_file[0].data   # Wavelengths in Angstroms
 spectrum = spec_file[1].data     # Spectral Flux
 error = spec_file[2].data        # Spectral Flux Errors
 sn = spec_file[3].data           # SN of Spectrum
 
-linelist = '../example/example_linelist.txt' # Insert path to line list
+linelist = 'example_linelist.txt' # Insert path to line list
 
 # choose a velocity grid for the final profile(s)
 deltav = 0.82   # velocity pixel size must not be smaller than the spectral pixel size

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/pyproject.toml

@@ -4,14 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ACID_code_v2"
-version = "0.1.2"
+version = "0.1.4"
 authors = [
     {name = "Benjamin Cadell", email="bcadell01@qub.ac.uk"},
     {name = "Lucy Dolan"}
 ]
 description = "Returns line profiles from input spectra by fitting the stellar continuum and performing LSD"
 readme = "README.md"
-requires-python = ">=3.13"
+requires-python = "<3.14, >= 3.8"
 license = "MIT"
 keywords = ["lsd", "least squares deconvolution", "fitting", "ACID"]
 license-files = ["LICENSE"]

{acid_code_v2-0.1.2 → acid_code_v2-0.1.4}/tests/tests.py

@@ -1,18 +1,11 @@
 #%%
 from astropy.io import fits
-import os
-
-try:
-    import ACID_code_v2 as acid
-except ImportError:
-    raise ImportError("ACID_code_v2 not found")
-    os.chdir(os.path.dirname(__file__))
-    os.chdir("..")
-    import ACID_code_v2 as acid
-
+import os, glob, importlib
+os.chdir(os.path.dirname(__file__))
+os.chdir("..") # ensures we are in the main directory
+import ACID_code_v2 as acid
 import numpy as np
 import matplotlib.pyplot as plt
-import glob, importlib
 importlib.reload(acid)
 
 def test_run_e2ds():
@@ -21,12 +14,11 @@ def test_run_e2ds():
     linelist = 'example/example_linelist.txt'
     save_path = 'no save'
 
-
     velocities = np.arange(-25, 25, 0.82)
 
     # run ACID on e2ds files
-    ACID_results_e2ds = acid.ACID_HARPS(e2ds_files, linelist, vgrid = velocities, save_path = save_path, order_range = np.arange(41, 43))
-
+    ACID_results_e2ds = acid.ACID_HARPS(e2ds_files, linelist, vgrid = velocities, save_path = save_path,
+                                        order_range = np.arange(41, 43), nsteps=2000)
 
 def test_run_s1d():
 
@@ -37,7 +29,8 @@ def test_run_s1d():
     velocities = np.arange(-25, 25, 0.82)
 
     # run ACID on s1d files
-    ACID_results_s1d = acid.ACID_HARPS(s1d_files, linelist, vgrid = velocities, save_path = save_path, order_range = np.arange(41, 43), file_type = 's1d')
+    ACID_results_s1d = acid.ACID_HARPS(s1d_files, linelist, vgrid = velocities, save_path = save_path,
+                                       order_range = np.arange(41, 43), file_type = 's1d', nsteps=2000)
 
 test_run_e2ds()
 test_run_s1d()