changing path handling to pathlib

temuller · Jan 25, 2024 · 9c4082d · 9c4082d
1 parent f3a3dbe
commit 9c4082d
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Showing 7 changed files with 67 additions and 61 deletions.
diff --git a/src/hostphot/cutouts.py b/src/hostphot/cutouts.py
@@ -1,4 +1,6 @@
 import os
+from pathlib import Path
+
 import glob
 import copy
 import shutil
@@ -42,7 +44,7 @@
     survey_pixel_scale,
 )
 import hostphot
-hostphot_path = hostphot.__path__[0]
+hostphot_path = Path(hostphot.__path__[0])
 
 import warnings
 from astropy.utils.exceptions import AstropyWarning
@@ -578,7 +580,6 @@ def get_WISE_images(ra, dec, size=3, filters=None):
         size_arcsec = size.to(u.arcsec)
 
     pixel_scale = survey_pixel_scale(survey)
-    # size_pixels = int(size_arcsec.value / pixel_scale)
 
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", AstropyWarning)
@@ -682,7 +683,7 @@ def get_unWISE_images(ra, dec, size=3, filters=None, version="allwise"):
     master_url = base_url + params_url
 
     response = requests.get(master_url, stream=True)
-    target_file = f"unWISE_images_{ra}_{dec}.tar.gz"  # current directory
+    target_file = Path(f"unWISE_images_{ra}_{dec}.tar.gz")  # current directory
     if response.status_code == 200:
         with open(target_file, "wb") as f:
             f.write(response.raw.read())
@@ -1558,7 +1559,7 @@ def get_SPLUS_images(ra, dec, size=3, filters=None):
 
             # add zeropoint
             # file from https://splus.cloud/documentation/dr2_3
-            zps_file = os.path.join(hostphot_path, 'filters', 'SPLUS', 'iDR3_zps.cat')
+            zps_file = hostphot_path.joinpath('filters', 'SPLUS', 'iDR3_zps.cat')
             zps_df = pd.read_csv(zps_file, delim_whitespace=True)
 
             field = hdu[0].header['OBJECT'].replace('_', '-')

diff --git a/src/hostphot/dust.py b/src/hostphot/dust.py
@@ -1,4 +1,6 @@
 import os
+from pathlib import Path
+
 import tarfile
 import requests
 import numpy as np
@@ -18,15 +20,15 @@ def _download_dustmaps():
     """Downloads the dust maps for extinction calculation if they are not found
     locally.
     """
-    mapsdir = hostphot.__path__[0]
+    mapsdir = Path(hostphot.__path__[0])
 
     # check if files already exist locally
     dust_files = [
-        os.path.join(mapsdir, "sfddata-master", f"SFD_dust_4096_{sky}gp.fits")
+        mapsdir.joinpath("sfddata-master", rf"SFD_dust_4096_{sky}gp.fits")
         for sky in ["n", "s"]
     ]
     mask_files = [
-        os.path.join(mapsdir, "sfddata-master", f"SFD_mask_4096_{sky}gp.fits")
+        mapsdir.joinpath("sfddata-master", rf"SFD_mask_4096_{sky}gp.fits")
         for sky in ["n", "s"]
     ]
     maps_files = dust_files + mask_files
@@ -39,7 +41,7 @@ def _download_dustmaps():
         )
         response = requests.get(sfdmaps_url)
 
-        master_tar = "master.tar.gz"
+        master_tar = Path("master.tar.gz")
         with open(master_tar, "wb") as file:
             file.write(response.content)
 
@@ -93,8 +95,8 @@ def deredden(
     """
     _download_dustmaps()
 
-    hostphot_path = hostphot.__path__[0]
-    dustmaps_dir = os.path.join(hostphot_path, "sfddata-master")
+    hostphot_path = Path(hostphot.__path__[0])
+    dustmaps_dir = hostphot_path / "sfddata-master"
 
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", category=DeprecationWarning)

diff --git a/src/hostphot/global_photometry.py b/src/hostphot/global_photometry.py
@@ -14,7 +14,8 @@
 #
 # Some parts of this notebook are based on https://github.com/djones1040/PS1_surface_brightness/blob/master/Surface%20Brightness%20Tutorial.ipynb and codes from Lluís Galbany
 
-import os
+from pathlib import Path
+
 import pickle
 import numpy as np
 import pandas as pd
@@ -239,14 +240,14 @@ def extract_kronparams(
     """
     check_survey_validity(survey)
     check_work_dir(workdir)
-    obj_dir = os.path.join(workdir, name)
+    obj_dir = Path(workdir, name)
     if use_mask:
         suffix = "masked_"
     else:
         suffix = ""
     if isinstance(filt, list):
         filt = "".join(f for f in filt)
-    fits_file = os.path.join(obj_dir, f"{suffix}{survey}_{filt}.fits")
+    fits_file = obj_dir / rf"{suffix}{survey}_{filt}.fits"
 
     hdu = fits.open(fits_file)
     hdu = remove_nan(hdu)
@@ -300,7 +301,7 @@ def extract_kronparams(
         )
 
     if save_plots is True:
-        outfile = os.path.join(obj_dir, f"global_{survey}_{filt}.jpg")
+        outfile = obj_dir / f"global_{survey}_{filt}.jpg"
         title = f"{name}: {survey}-${filt}$"
         plot_detected_objects(
             hdu,
@@ -320,9 +321,7 @@ def extract_kronparams(
         flip = False
 
     if save_aperture_params is True:
-        outfile = os.path.join(
-            obj_dir, f"{survey}_{filt}_aperture_parameters.pickle"
-        )
+        outfile = obj_dir / rf"{survey}_{filt}_aperture_parameters.pickle"
         with open(outfile, "wb") as fp:
             aperture_parameters = gal_obj, img_wcs, kronrad, scale, flip
             pickle.dump(aperture_parameters, fp, protocol=4)
@@ -348,8 +347,7 @@ def load_aperture_params(name, filt, survey):
         Aperture paremeters with the same format as the output of the
         ``extract_kronparams`` function.
     """
-    inputfile = os.path.join(workdir, name, 
-                             f'{survey}_{filt}_aperture_parameters.pickle')
+    inputfile = Path(workdir, name, rf'{survey}_{filt}_aperture_parameters.pickle')
 
     aperture_params = load_pickle(inputfile)
 
@@ -449,12 +447,12 @@ def photometry(
 
     check_survey_validity(survey)
     check_work_dir(workdir)
-    obj_dir = os.path.join(workdir, name)
+    obj_dir = Path(workdir, name)
     if use_mask:
         suffix = "masked_"
     else:
         suffix = ""
-    fits_file = os.path.join(obj_dir, f"{suffix}{survey}_{filt}.fits")
+    fits_file = obj_dir / f"{suffix}{survey}_{filt}.fits"
 
     hdu = fits.open(fits_file)
     hdu = remove_nan(hdu)
@@ -566,7 +564,7 @@ def photometry(
         flux *= 10**(0.4*A_ext)
 
     if save_plots is True:
-        outfile = os.path.join(obj_dir, f"global_{survey}_{filt}.jpg")
+        outfile = obj_dir / f"global_{survey}_{filt}.jpg"
         title = f"{name}: {survey}-${filt}$"
         plot_detected_objects(
             hdu,
@@ -753,7 +751,7 @@ def multi_band_phot(
                 results_dict[f"{filt}_zeropoint"] = np.nan
 
     if save_results is True:
-        outfile = os.path.join(workdir, name, f"{survey}_global.csv")
+        outfile = Path(workdir, name, rf"{survey}_global.csv")
         phot_df = pd.DataFrame(
             {key: [val] for key, val in results_dict.items()}
         )

diff --git a/src/hostphot/image_masking.py b/src/hostphot/image_masking.py
@@ -1,4 +1,5 @@
-import os
+from pathlib import Path
+
 import pickle
 import numpy as np
 from copy import deepcopy
@@ -178,8 +179,8 @@ def create_mask(
     if isinstance(filt, list):
         filt = "".join(f for f in filt)
 
-    obj_dir = os.path.join(workdir, name)
-    fits_file = os.path.join(obj_dir, f"{survey}_{filt}.fits")
+    obj_dir = Path(workdir, name)
+    fits_file = obj_dir / f"{survey}_{filt}.fits"
     hdu = fits.open(fits_file)
     hdu = remove_nan(hdu)
 
@@ -238,7 +239,7 @@ def create_mask(
     masked_data = mask_image(data_sub, nogal_objs, r=r, sigma=sigma)
     masked_hdu = deepcopy(hdu)
     masked_hdu[0].data = masked_data
-    outfile = os.path.join(obj_dir, f"masked_{survey}_{filt}.fits")
+    outfile = obj_dir / f"masked_{survey}_{filt}.fits"
     masked_hdu.writeto(outfile, overwrite=True)
 
     if survey in ["DES", "VISTA", "UKIDSS"]:
@@ -247,15 +248,13 @@ def create_mask(
         flip = False
 
     if save_mask_params is True:
-        outfile = os.path.join(
-            obj_dir, f"{survey}_{filt}_mask_parameters.pickle"
-        )
+        outfile = obj_dir / f"{survey}_{filt}_mask_parameters.pickle"
         with open(outfile, "wb") as fp:
             mask_parameters = gal_obj, nogal_objs, img_wcs, sigma, r, flip
             pickle.dump(mask_parameters, fp, protocol=4)
 
     if save_plots:
-        outfile = os.path.join(obj_dir, f"masked_{survey}_{filt}.jpg")
+        outfile = obj_dir / f"masked_{survey}_{filt}.jpg"
         title = f"{name}: {survey}-${filt}$"
         plot_masked_image(
             hdu,
@@ -293,8 +292,7 @@ def load_mask_params(name, filt, survey):
         Mask paremeters with the same format as the output of the
         ``create_mask`` function.
     """
-    inputfile = os.path.join(workdir, name, 
-                             f'{survey}_{filt}_mask_parameters.pickle')
+    inputfile = Path(workdir, name, rf'{survey}_{filt}_mask_parameters.pickle')
 
     mask_params = load_pickle(inputfile)
 

diff --git a/src/hostphot/local_photometry.py b/src/hostphot/local_photometry.py
@@ -14,7 +14,8 @@
 #
 # Some parts of this notebook are based on https://github.com/djones1040/PS1_surface_brightness/blob/master/Surface%20Brightness%20Tutorial.ipynb and codes from Lluís Galbany
 
-import os
+from pathlib import Path
+
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -244,12 +245,12 @@ def photometry(
 
     check_survey_validity(survey)
     check_work_dir(workdir)
-    obj_dir = os.path.join(workdir, name)
+    obj_dir = Path(workdir, name)
     if use_mask:
         suffix = "masked_"
     else:
         suffix = ""
-    fits_file = os.path.join(obj_dir, f"{suffix}{survey}_{filt}.fits")
+    fits_file = obj_dir / f"{suffix}{survey}_{filt}.fits"
 
     hdu = fits.open(fits_file)
     hdu = remove_nan(hdu)
@@ -337,9 +338,7 @@ def photometry(
         fluxes_err.append(flux_err)
 
         if save_plots:
-            outfile = os.path.join(
-                obj_dir, f"local_{survey}_{filt}_{ap_radius}kpc.jpg"
-            )
+            outfile = obj_dir / rf"local_{survey}_{filt}_{ap_radius}kpc.jpg"
             title = f'{name}: {survey}-${filt}$|r$={ap_radius}$ kpc @ $z={z}$'
             plot_aperture(hdu, px, py, radius_pix, title, outfile)
 
@@ -471,7 +470,7 @@ def multi_band_phot(
                 results_dict[f"{filt}_zeropoint"] = np.nan
 
     if save_results is True:
-        outfile = os.path.join(workdir, name, f"{survey}_local.csv")
+        outfile = Path(workdir, name, rf"{survey}_local.csv")
         phot_df = pd.DataFrame(
             {key: [val] for key, val in results_dict.items()}
         )

diff --git a/src/hostphot/sed_plotting.py b/src/hostphot/sed_plotting.py
@@ -1,4 +1,6 @@
 import os
+from pathlib import Path
+
 import glob
 import numpy as np
 import pandas as pd
@@ -9,8 +11,8 @@
 from hostphot._constants import workdir, font_family
 from hostphot.utils import get_survey_filters
 
-path = hostphot.__path__[0]
-config_file = os.path.join(path, 'filters', 'config.txt')
+path = Path(hostphot.__path__[0])
+config_file = path.joinpath('filters', 'config.txt')
 config_df = pd.read_csv(config_file, delim_whitespace=True)
 
 colours = {'GALEX':'purple', 'PS1':'green', 'SDSS':'blue', 'DES':'lightblue', 
@@ -34,11 +36,11 @@ def get_eff_wave(filt, survey):
     eff_wave: float
         Effective wavelength in angstroms.
     """
-    path = hostphot.__path__[0]
+    path = Path(hostphot.__path__[0])
     if survey=='unWISE':
         survey = 'WISE'
 
-    survey_files = glob.glob(os.path.join(path, 'filters', survey, '*'))
+    survey_files = glob.glob(path.joinpath('filters', survey, '*'))
     filt_file = [file for file in survey_files if file.endswith(f'_{filt}.dat')][0]
 
     wave, trans = np.loadtxt(filt_file).T
@@ -83,7 +85,7 @@ def plot_sed(name, phot_type='global', z=None, radius=None, include=None, exclud
         assert radius is not None, "radius must be given with local photometry"
 
     global colours
-    obj_path = os.path.join(workdir, name, '*')
+    obj_path = Path(workdir, name, '*')
     phot_files = [file for file in glob.glob(obj_path) 
                   if file.endswith(f'_{phot_type}.csv')]
 
@@ -218,9 +220,9 @@ def plot_sed(name, phot_type='global', z=None, radius=None, include=None, exclud
 
     if save_plot is True:
         if outfile is None:
-            obj_dir = os.path.join(workdir, name)
+            obj_dir = Path(workdir, name)
             basename = f'sed_{phot_type}.jpg'
-            outfile = os.path.join(obj_dir, basename)
+            outfile = obj_dir / basename
         plt.savefig(outfile)
 
     plt.show()