Important

For MIRI MRS stripe correction: When spec3.cube_build.coord_system = 'ifualign': the pipeline aligns in the FOV of the IFU in the y direction. This may result in the 'horizontal' stripes still appearing diagonal. To make the stripes actually be horizontal (required for calibration) the IFU should be aligned in the x direction. To do this, replace ifu_cube.py under the directory path of form:

/opt/anaconda3/envs/jwst/lib/python3.10/site-packages/jwst/cube_build

with the script calibration_pipeline/ifu_align.py

MIRI-Toolkit

Repository for MIRI visualisation and analysis tools

Available Codes

!!!! Note that all codes here are experimental, use at your own risk !!!!

• MIRIClean_FFT.ipynb - Attempt to clean IFU-aligned MIRI frames by inspecting and filtering their 2D FFTs - this doesn't currently work as implemented, we're exploring other techniques.

Known Challenges

• MIRI/MRS Wavelength solution currently insufficient, leading to striping in images associated with narrow emission lines. The wavelengths must be shifted spaxel by spaxel to a uniform solution.
• MRS Saturation for Jupiter beyond 11 µm - this was expected, but workarounds are needed to access the unsaturated frames in the 4/5-group integrations.

Details of available code

For the JWST calibration pipeline:

• Use calibration_pipeline/jwstpipeline_v4.py to combine the dither positions in stage 3
• Use calibration_pipeline/jwstpipeline_singledither_v2.py to leave these dither positions seperate

To map the data using Pat Fry's code, use:

• navigation/navigation2.py
• navigation/jupkerns.tm
• navigation/jwst_kernels

To plot spectra from a lat/lon point in the resulting band cubes use:

• plot_pixseperate_v3.py

To save each spaxel in a band as a spectral txt file (useful for retrievals) use:

• retrieval_map.py This will also save latitude, longitude and emission angle (mu) in fits files in the same directory

To visulise the data as a RGB image (using 3 different RGB wavelengths) use:

• mosaic_generation/plot_pixseperate_v3.py
• mosaic_generation/visulise_single.py
• mosaic_generation/build_mosaic_1.py
• mosaic_generation/build_mosaic_2.py
• mosaic_generation/visulise_mosaic.py

To generate spx files (for NEMESIS) using a txt file input (like the ones generated by retrieval_map.py) use:

• gen_spx.py

To generate contribution functions using the results of a NEMESIS forward model use:

• plot_contribution.py

Post-pipeline calibration

To calibrate wave-cal offsets and generate and apply flat-fields, refer to the post_pipeline directory and the instructions:

• wavelength_calibration/wave_cal_offset_instructions.docx