From 4744bf3a694869bf49d23f3877b700b26baf5e9c Mon Sep 17 00:00:00 2001 From: Tomas Stolker Date: Fri, 31 Mar 2023 14:24:26 +0200 Subject: [PATCH] Updated README, minor bug fix with dark_item in for loop --- README.rst | 10 ++++++++-- docs/running.rst | 2 +- pycrires/pipeline.py | 9 +++++++-- 3 files changed, 16 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 734eb73..eca7e85 100644 --- a/README.rst +++ b/README.rst @@ -24,7 +24,13 @@ Data reduction pipeline for VLT/CRIRES+ .. image:: https://img.shields.io/github/license/tomasstolker/pycrires :target: https://github.com/tomasstolker/pycrires/blob/main/LICENSE -*pycrires* is a Python wrapper for running the CRIRES+ recipes of *EsoRex*. The pipeline organizes the raw data, creates SOF and configuration files for *EsoRex*, runs the calibration and science recipes, applies a telluric correction with *Molecfit*, and creates plots of the images and extracted spectra. +*pycrires* is a Python wrapper for running the CRIRES+ recipes of *EsoRex*. + +The pipeline organizes the raw data, creates SOF and configuration files for *EsoRex*, runs the calibration and science recipes, improves the wavelength solution, and creates plots of the images and extracted spectra. + +Additionally, there are dedicated routines for the extraction, calibration, and detection of spatially-resolved objects such as directly imaged planets. + +For spatially resolved objects, the telluric lines can typically be corrected with the stellar spectrum. Otherwise, it is possible to use an empirical modeling approach with the recipes of *MolecFit*. The pipeline interface of *pycrires* provides functionalities for both cases. Documentation ------------- @@ -34,7 +40,7 @@ Documentation can be found at `http://pycrires.readthedocs.io `_ when *pycrires* is used in a publication. +Please cite `Stolker & Landman, 2023, ascl: 3541 `_ when *pycrires* is used in a publication and Landman et al. (in prep.) specifically when using the dedicated routines for spatially-resolved sources. Contributing ------------ diff --git a/docs/running.rst b/docs/running.rst index f75fca5..a98d58a 100644 --- a/docs/running.rst +++ b/docs/running.rst @@ -80,7 +80,7 @@ Next, for spatially-resolved targets (e.g. directly imaged exoplanets), there ar collapse_spatially=True, collapse_exposures=True, accuracy=0.001) pipeline.remove_starlight(nod_ab, input_folder='correct_wavelengths_2d', - telluric_mask=[0.6, 1.6], svd_broadening_kernel=True) + telluric_mask=(0.6, 1.6), svd_broadening_kernel=True) pipeline.remove_systematics(nod_ab, n_modes=5, input_folder='remove_starlight') diff --git a/pycrires/pipeline.py b/pycrires/pipeline.py index ed12c6a..68e76c7 100644 --- a/pycrires/pipeline.py +++ b/pycrires/pipeline.py @@ -396,10 +396,11 @@ def _update_files(self, sof_tag: str, file_name: str) -> None: decimal = len(file_tmp.split(".")[-1]) if decimal == 5: - for dark_item in self.file_dict["DARK"]: + for dark_item in self.file_dict["DARK"].values(): if float(file_tmp) == round(dark_item["DIT"], 5): file_dict["DIT"] = dark_item["DIT"] break + else: file_dict["DIT"] = float(file_tmp) @@ -6519,7 +6520,11 @@ def detection_map( for which the cross-correlation map will be calculated. For each value of :math:`v\\sin\\,i`, a subplot will be created that shows the cross-correlation as function - of radial velocity and separation from the star.") + of radial velocity and separation from the star. When + using this parameter, make sure that the template of + ``model_flux`` has not been broadened and make sure + that the wavelengths of ``model_wavel`` are evenly + spaced. nod_ab : str Nod position which will be cross-correlated. input_folder : str