From 2af230ce69703e6f41bf04c8d299e7ef737fedbd Mon Sep 17 00:00:00 2001 From: AarynnCarter <23636747+AarynnCarter@users.noreply.github.com> Date: Wed, 7 Aug 2024 12:44:06 -0400 Subject: [PATCH 1/4] Update installation instructions, and remove instructions from README --- README.rst | 141 ------------------ docs/source/Installation-and-dependencies.rst | 10 +- 2 files changed, 5 insertions(+), 146 deletions(-) diff --git a/README.rst b/README.rst index da93c9af..15873b56 100644 --- a/README.rst +++ b/README.rst @@ -10,144 +10,3 @@ Compatible test data: `here `_ -Installation -************ - -At this stage it is recommended that you clone the Git repository directory for installation: - -:: - - git clone https://github.com/kammerje/spaceKLIP.git - -If you would like to install a specific branch: - -:: - - git clone https://github.com/kammerje/spaceKLIP.git@branch - -From here, it is **highly** recommended that you create a unique Anaconda environment to hold all of the spaceKLIP dependencies: - -:: - - conda create -n spaceklip python=3.11 - conda activate spaceklip - -With the Anaconda environment created, move to the cloned directory and install the dependencies and spaceKLIP itself: - -:: - - cd where/you/saved/the/git/repo - conda install conda-forge::git-lfs - pip install -r requirements.txt - pip install -e . - -Note that installing git-lfs from pip does not work as of 25 June 2024. - -Finally, and very importantly, you will need to download the reference files and set the environment variables supporting the functioning of :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF `_, `WebbPSF_ext `_). Ensure that if you edit your .bashrc file, close and reopen your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work). - -SpaceKLIP also makes use of the JWST Calibration Reference Data System (CRDS) and you will need to set the corresponding environment variables. Follow the instructions here for bash or zsh: https://jwst-crds.stsci.edu/docs/cmdline_bestrefs/. Note that you do not have to install AstroConda, just set the environment variables (making sure that the CRDS path you set actually exists, i.e., you may need to create the directory). - -Code status -*********** - -The current capabilities of the code are summarized below. - -:: - - database.py - -- ``read_jwst_s012_data``: working -- ``read_jwst_s3_data``: working -- ``read_jwst_s4_data``: working -- ``print_obs``: working -- ``print_red``: working -- ``print_src``: working -- ``update_obs``: working -- ``update_src``: working -- ``summarize``: working - -:: - - plotting.py - -- ``display_coron_image``: working -- ``display_coron_dataset``: working - -:: - - utils.py - -- ``read_obs``: working -- ``write_obs``: working -- ``read_red``: working - -:: - - coron1pipeline.py - -- ``run_obs``: working -- custom saturation step: working -- custom reference pixel step: needs updating (side reference pixels not working for subarrays) - -:: - - coron2pipeline.py - -- ``run_obs``: working -- additional outlier detection step: working - -:: - - coron3pipeline.py - -- ``make_asn_file``: working -- ``run_obs``: working - -:: - - pyklippipeline.py - -- ``run_obs``: working -- no absolute PSF alignment, this is now done using the ``ImageTools`` library -- no relative frame alignment, this is now done using the ``ImageTools`` library -- the old ``JWST.py`` is now implemented here -- save individual rolls with ``save_rolls = True`` keyword - -:: - - classpsfsubpipeline.py - -- ``run_obs``: working, under development -- save individual rolls with ``save_rolls = True`` keyword - -:: - - imagetools.py - -- ``remove_frames``: working -- ``crop_frames``: working -- ``pad_frames``: working -- ``coadd_frames``: working -- ``subtract_median``: working -- ``subtract_background``: working -- ``fix_bad_pixels``: working -- ``replace_nans``: working -- ``blur_frames``: working -- ``update_nircam_centers``: working with filter-dependent shifts -- ``recenter_frames``: working (absolute PSF alignment) -- ``align_frames``: working (relative frame alignment) - -:: - - analysistools.py - -- ``raw_contrast``: working with ``pyklippipeline`` products, not working with ``coron3pipeline`` products since PSF center not being tracked -- ``extract_companions``: working with ``pyklippipeline`` products, not working with ``coron3pipeline`` products since PSF center not being tracked -- combined coronagraphic throughput map: working -- `` calibrated_contrast`` working with ``pyklippipeline`` products - -:: - - mast.py - -- ``query_coron_datasets``: working diff --git a/docs/source/Installation-and-dependencies.rst b/docs/source/Installation-and-dependencies.rst index 7c96bfb6..547eab5a 100644 --- a/docs/source/Installation-and-dependencies.rst +++ b/docs/source/Installation-and-dependencies.rst @@ -18,8 +18,8 @@ dependencies. spaceKLIP is not currently compatible with python 3.12 :: - conda create -n sklip python=3.11 - conda activate sklip + conda create -n spaceklip python=3.11 + conda activate spaceklip With the anaconda environment created, move to the cloned directory and install most of the dependencies: @@ -28,8 +28,8 @@ With the anaconda environment created, move to the cloned directory and install cd where/you/installed/the/git/repo pip install -r requirements.txt pip install -e . - cd spaceKLIP/ - python make_psfmasks.py - Finally, and very importantly, you will need to download reference files to support the functioning of the :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF `_, `webbpsf_ext `_). Ensure that if you edit your .bashrc file that you reopen and close your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work) + + +SpaceKLIP also makes use of the JWST Calibration Reference Data System (CRDS) and you will need to set the corresponding environment variables. Follow the instructions here for bash or zsh: https://jwst-crds.stsci.edu/docs/cmdline_bestrefs/. Note that you do not have to install AstroConda, just set the environment variables (making sure that the CRDS path you set actually exists, i.e., you may need to create the directory). \ No newline at end of file From 16b64942ec62078b34d119d45a33c57423da1db4 Mon Sep 17 00:00:00 2001 From: AarynnCarter <23636747+AarynnCarter@users.noreply.github.com> Date: Wed, 7 Aug 2024 13:59:40 -0400 Subject: [PATCH 2/4] Add installation instructions to README --- README.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 15873b56..8f6a718e 100644 --- a/README.rst +++ b/README.rst @@ -6,7 +6,10 @@ SpaceKLIP 🚀🪐 SpaceKLIP is a data reduction pipeline for JWST high-contrast imaging. The current release has been tested with NIRCam and MIRI coronagraphy data. -Compatible test data: `here `_ +Installation Instructions: `here `_ Documentation: `here `_ +Compatible test data: `here `_ + + From 1ae6f4c5314d060ea3a24190f0ee83a284455692 Mon Sep 17 00:00:00 2001 From: AarynnCarter <23636747+AarynnCarter@users.noreply.github.com> Date: Wed, 7 Aug 2024 14:34:50 -0400 Subject: [PATCH 3/4] Adjust description for CRDS variables --- docs/source/Installation-and-dependencies.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/Installation-and-dependencies.rst b/docs/source/Installation-and-dependencies.rst index 547eab5a..ae59a6e0 100644 --- a/docs/source/Installation-and-dependencies.rst +++ b/docs/source/Installation-and-dependencies.rst @@ -31,5 +31,4 @@ With the anaconda environment created, move to the cloned directory and install Finally, and very importantly, you will need to download reference files to support the functioning of the :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF `_, `webbpsf_ext `_). Ensure that if you edit your .bashrc file that you reopen and close your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work) - -SpaceKLIP also makes use of the JWST Calibration Reference Data System (CRDS) and you will need to set the corresponding environment variables. Follow the instructions here for bash or zsh: https://jwst-crds.stsci.edu/docs/cmdline_bestrefs/. Note that you do not have to install AstroConda, just set the environment variables (making sure that the CRDS path you set actually exists, i.e., you may need to create the directory). \ No newline at end of file +spaceKLIP makes use of the JWST data reduction pipeline (:code:`jwst` package) and its dependencies, including the JWST Calibration Reference Data System (CRDS).You will need to set environment variables for CRDS. Instructions are available here in the JWST pipeline docs: https://jwst-pipeline.readthedocs.io/en/latest/getting_started/quickstart.html (Section 3). If you already have a working copy of the JWST data pipeline on your computer, then this is probably already taken care of. From c1e1bdd6bc4560f017789996b4be098f58392888 Mon Sep 17 00:00:00 2001 From: AarynnCarter <23636747+AarynnCarter@users.noreply.github.com> Date: Wed, 7 Aug 2024 14:35:14 -0400 Subject: [PATCH 4/4] Adjust description for CRDS variables --- docs/source/Installation-and-dependencies.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/Installation-and-dependencies.rst b/docs/source/Installation-and-dependencies.rst index ae59a6e0..f13996a7 100644 --- a/docs/source/Installation-and-dependencies.rst +++ b/docs/source/Installation-and-dependencies.rst @@ -29,6 +29,6 @@ With the anaconda environment created, move to the cloned directory and install pip install -r requirements.txt pip install -e . -Finally, and very importantly, you will need to download reference files to support the functioning of the :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF `_, `webbpsf_ext `_). Ensure that if you edit your .bashrc file that you reopen and close your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work) +Very importantly, you will need to download reference files to support the functioning of the :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF `_, `webbpsf_ext `_). Ensure that if you edit your .bashrc file that you reopen and close your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work) -spaceKLIP makes use of the JWST data reduction pipeline (:code:`jwst` package) and its dependencies, including the JWST Calibration Reference Data System (CRDS).You will need to set environment variables for CRDS. Instructions are available here in the JWST pipeline docs: https://jwst-pipeline.readthedocs.io/en/latest/getting_started/quickstart.html (Section 3). If you already have a working copy of the JWST data pipeline on your computer, then this is probably already taken care of. +Finally, spaceKLIP makes use of the JWST data reduction pipeline (:code:`jwst` package) and its dependencies, including the JWST Calibration Reference Data System (CRDS).You will need to set environment variables for CRDS. Instructions are available here in the JWST pipeline docs: https://jwst-pipeline.readthedocs.io/en/latest/getting_started/quickstart.html (Section 3). If you already have a working copy of the JWST data pipeline on your computer, then this is probably already taken care of.