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Minor style improvements, updated configuration for documentation, ad…
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…ded reference to Landman et al. (2023)
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@tomasstolker
tomasstolker committed Nov 23, 2023
1 parent 07daa00 commit 789cde9
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -40,7 +40,7 @@ Documentation can be found at `http://pycrires.readthedocs.io <http://pycrires.r
Attribution
-----------

Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and Landman et al. (in prep.) specifically when using the dedicated routines for spatially-resolved sources.
Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://arxiv.org/abs/2311.13527>`_ specifically when using the dedicated routines for spatially-resolved sources.

Contributing
------------
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2 changes: 1 addition & 1 deletion docs/about.rst
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Expand Up @@ -11,7 +11,7 @@ Contact
Attribution
-----------

Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and Landman et al. (in prep.) specifically when using the dedicated routines for spatially-resolved sources.
Please cite `Stolker & Landman (2023) <https://ui.adsabs.harvard.edu/abs/2023ascl.soft07040S/abstract>`_ when *pycrires* is used in a publication and `Landman et al. (2023) <https://arxiv.org/abs/2311.13527>`_ specifically when using the dedicated routines for spatially-resolved sources.

Contributing
------------
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32 changes: 8 additions & 24 deletions docs/conf.py
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Expand Up @@ -14,7 +14,6 @@
import sys
sys.path.insert(0, os.path.abspath('../'))


# -- Project information -----------------------------------------------------

project = 'pycrires'
Expand All @@ -26,6 +25,7 @@
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.

extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.napoleon',
Expand All @@ -36,32 +36,17 @@

numpydoc_show_class_members = False

# Add any paths that contain templates here, relative to this directory.
templates_path = []

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['.ipynb_checkpoints/*']

exclude_patterns = ['_build',
'Thumbs.db',
'.DS_Store',
'.ipynb_checkpoints/*']

# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
# html_theme = 'sphinx_book_theme'
#
# html_theme_options = {
# 'path_to_docs': 'docs',
# 'repository_url': 'https://github.com/tomasstolker/pycrires',
# 'repository_branch': 'main',
# 'use_edit_page_button': True,
# 'use_issues_button': True,
# 'use_repository_button': True,
# 'use_download_button': True,
# }

html_theme = 'pydata_sphinx_theme'

html_theme_options = {
Expand All @@ -76,7 +61,6 @@
"doc_path": "docs",
}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = []
html_static_path = ['_static']

html_search_language = 'en'
103 changes: 48 additions & 55 deletions pycrires/pipeline.py
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Expand Up @@ -4,7 +4,6 @@

import glob
import json
import logging
import os
import shutil
import socket
Expand Down Expand Up @@ -32,17 +31,18 @@
from PyAstronomy.pyasl import fastRotBroad
from scipy import interpolate, ndimage, optimize, signal
from skimage.restoration import inpaint
from typeguard import config as typeguard_config
from typeguard import typechecked, CollectionCheckStrategy
from typeguard import typechecked

# from typeguard import config as typeguard_config
# from typeguard import CollectionCheckStrategy, typechecked

import pycrires
from pycrires import util


PIXEL_SCALE = 0.056 # (arcsec)

log_book = logging.getLogger(__name__)
typeguard_config.collection_check_strategy = CollectionCheckStrategy.ALL_ITEMS
# typeguard_config.collection_check_strategy = CollectionCheckStrategy.ALL_ITEMS


class Pipeline:
Expand All @@ -58,7 +58,7 @@ def __init__(self, path: Optional[str] = None) -> None:
"""
Parameters
----------
path : str
path : str, None
Path of the main reduction folder. The main folder should
contain a subfolder called ``raw`` where the raw data
(both science and calibration) from the ESO archive are
Expand Down Expand Up @@ -174,12 +174,12 @@ def __init__(self, path: Optional[str] = None) -> None:
# Check if there is a new version available

try:
contents = urllib.request.urlopen(
"https://pypi.org/pypi/pycrires/json", timeout=1.0
).read()
pypi_url = "https://pypi.org/pypi/pycrires/json"

data = json.loads(contents)
latest_version = data["info"]["version"]
with urllib.request.urlopen(pypi_url, timeout=1.0) as open_url:
url_content = open_url.read()
url_data = json.loads(url_content)
latest_version = url_data["info"]["version"]

except (urllib.error.URLError, socket.timeout):
latest_version = None
Expand Down Expand Up @@ -1624,9 +1624,7 @@ def cal_flat(self, verbose: bool = True) -> None:

# Update file dictionary with TraceWave table

fits_files = Path(self.path / "calib").glob(
"cr2res_cal_flat_*tw.fits"
)
fits_files = Path(self.path / "calib").glob("cr2res_cal_flat_*tw.fits")

for item in fits_files:
self._update_files("CAL_FLAT_TW", str(item))
Expand Down Expand Up @@ -2534,9 +2532,7 @@ def util_extract(self, calib_type: str, verbose: bool = True) -> None:

print("Creating SOF file:")

sof_file = Path(
self.path / f"calib/util_extract_{calib_type}/files.sof"
)
sof_file = Path(self.path / f"calib/util_extract_{calib_type}/files.sof")

# Find UTIL_CALIB file

Expand Down Expand Up @@ -2875,7 +2871,9 @@ def util_genlines(self, verbose: bool = True) -> None:
file_found = True

if not file_found:
url = f"https://home.strw.leidenuniv.nl/~stolker/pycrires/{file_tag}.fits"
url = (
f"https://home.strw.leidenuniv.nl/~stolker/pycrires/{file_tag}.fits"
)
line_file = output_dir / f"{file_tag}.fits"

if not os.path.exists(line_file):
Expand Down Expand Up @@ -2908,7 +2906,9 @@ def util_genlines(self, verbose: bool = True) -> None:

if line_file.suffix == (".fits"):
line_data = fits.getdata(line_file, hdu=1)
line_data = np.column_stack([line_data['Wavelength'], line_data['Emission']])
line_data = np.column_stack(
[line_data["Wavelength"], line_data["Emission"]]
)

line_file = output_dir / line_file.with_suffix(".dat").name

Expand Down Expand Up @@ -2963,13 +2963,18 @@ def util_genlines(self, verbose: bool = True) -> None:

print("Output files:")

fits_file = output_dir / line_file.with_suffix('.fits').name
fits_file = output_dir / line_file.with_suffix(".fits").name
self._update_files("EMISSION_LINES", str(fits_file))

indices = np.where(self.header_data["DPR.CATG"] == "SCIENCE")[0]
wlen_id = self.header_data["INS.WLEN.ID"][indices[0]]

fits_file = output_dir / line_file.with_name(line_file.stem + f"_{wlen_id}").with_suffix(".fits").name
fits_file = (
output_dir
/ line_file.with_name(line_file.stem + f"_{wlen_id}")
.with_suffix(".fits")
.name
)
self._update_files("EMISSION_LINES", str(fits_file))

# Write updated dictionary to JSON file
Expand Down Expand Up @@ -3940,9 +3945,7 @@ def obs_nodding(
output_dir / f"cr2res_obs_nodding_extractedB_{count_exp:03d}.fits"
)

spec_file = Path(
output_dir / "cr2res_obs_nodding_extracted_combined.fits"
)
spec_file = Path(output_dir / "cr2res_obs_nodding_extracted_combined.fits")
spec_file.rename(
output_dir
/ f"cr2res_obs_nodding_extracted_combined_{count_exp:03d}.fits"
Expand Down Expand Up @@ -3978,16 +3981,12 @@ def obs_nodding(
output_dir / f"cr2res_obs_nodding_slitfuncB_{count_exp:03d}.fits"
)

spec_file = Path(
output_dir / "cr2res_obs_nodding_trace_wave_A.fits"
)
spec_file = Path(output_dir / "cr2res_obs_nodding_trace_wave_A.fits")
spec_file.rename(
output_dir / f"cr2res_obs_nodding_trace_wave_A_{count_exp:03d}.fits"
)

spec_file = Path(
output_dir / "cr2res_obs_nodding_trace_wave_B.fits"
)
spec_file = Path(output_dir / "cr2res_obs_nodding_trace_wave_B.fits")
spec_file.rename(
output_dir / f"cr2res_obs_nodding_trace_wave_B_{count_exp:03d}.fits"
)
Expand Down Expand Up @@ -4120,9 +4119,11 @@ def obs_nodding_irregular(
print(f"Number of exposures at nod B: {nod_b_count}")

if nod_a_count != nod_b_count and unique_pairs is True:
warnings.warn(f"Nodding counts are unequal ({nod_a_count} "
f"A vs {nod_b_count} B). Reverting to "
"unique_pairs = False.")
warnings.warn(
f"Nodding counts are unequal ({nod_a_count} "
f"A vs {nod_b_count} B). Reverting to "
"unique_pairs = False."
)

unique_pairs = False

Expand Down Expand Up @@ -4154,25 +4155,27 @@ def obs_nodding_irregular(
print(f"Already reduced file {output_file}")
else:
print(f"\nCreating SOF file for {output_file}:")
sof_file = Path(
output_dir / f"files_{count_exp:03d}_{nod_ab}.sof"
)
sof_file = Path(output_dir / f"files_{count_exp:03d}_{nod_ab}.sof")

sof_open = open(sof_file, "w", encoding="utf-8")

file_0 = self.header_data["ORIGFILE"][i_row]

if nod_ab == "A":
if not unique_pairs:
closest_i_diffnod = b_i_rows[np.argmin(np.abs(i_row - b_i_rows))]
closest_i_diffnod = b_i_rows[
np.argmin(np.abs(i_row - b_i_rows))
]

else:
closest_i_diffnod = b_i_rows[B_counter]
B_counter += 1

elif nod_ab == "B":
if not unique_pairs:
closest_i_diffnod = a_i_rows[np.argmin(np.abs(i_row - a_i_rows))]
closest_i_diffnod = a_i_rows[
np.argmin(np.abs(i_row - a_i_rows))
]

else:
closest_i_diffnod = a_i_rows[A_counter]
Expand Down Expand Up @@ -4402,9 +4405,7 @@ def obs_nodding_irregular(
/ f"cr2res_obs_nodding_combined{nod_ab}_{count_exp:03d}.fits"
)

spec_file = Path(
output_dir / f"cr2res_obs_nodding_model{nod_ab}.fits"
)
spec_file = Path(output_dir / f"cr2res_obs_nodding_model{nod_ab}.fits")
spec_file.rename(
output_dir
/ f"cr2res_obs_nodding_model{nod_ab}_{count_exp:03d}.fits"
Expand Down Expand Up @@ -4465,11 +4466,11 @@ def obs_nodding_irregular(
json.dump(self.file_dict, json_file, indent=4)

if unique_pairs and verbose:
print('These were the file IDs of the A frames:')
print("These were the file IDs of the A frames:")
print(a_i_rows)
print('\n These were the file IDs of the B frames:')
print("\n These were the file IDs of the B frames:")
print(b_i_rows)
print('\n This is how they were paired in cr2res_obs_nodding:')
print("\n This is how they were paired in cr2res_obs_nodding:")
print(sequence)

@typechecked
Expand Down Expand Up @@ -5449,9 +5450,7 @@ def correct_wavelengths_2d(
# Save corrected wavelengths to all files for this order
for save_file in fits_files:
out_file = output_dir / (
Path(save_file).stem.replace(
"_corr", ""
)
Path(save_file).stem.replace("_corr", "")
+ "_corr.fits"
)
if det_idx == 0 and order_idx == 0:
Expand Down Expand Up @@ -6189,15 +6188,9 @@ def fit_gaussian(
)

input_folder = self.product_folder / extraction_input
fits_files = Path(input_folder).glob(
f"cr2res_combined{nod_ab}_*_extr2d.fits"
)
fits_files = Path(input_folder).glob(f"cr2res_combined{nod_ab}_*_extr2d.fits")
n_exp = len(
list(
Path(input_folder).glob(
f"cr2res_combined{nod_ab}_*_extr2d.fits"
)
)
list(Path(input_folder).glob(f"cr2res_combined{nod_ab}_*_extr2d.fits"))
)

print_msg = ""
Expand Down

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