Getting Started

Getting Started with `mertisreader`

This page is a Quarto version of the old notebook walkthrough. It keeps the narrative and executable examples together, while the package API remains documented through docstrings.

Quick Install

Use a Python virtual environment or conda environment, then install the package in editable mode while the migration is in progress.

python -m pip install -e ".[docs]"

Import Required Libraries

from pathlib import Path

import rich
import mertisreader as mr

print("Libraries imported successfully.")

Libraries imported successfully.

Initialize `MERTISDataPackReader`

candidate_roots = [Path.cwd().resolve(), Path.cwd().resolve().parent, Path.cwd().resolve().parent.parent]
repo_root = next(root for root in candidate_roots if (root / "data").exists())

input_path = repo_root / "data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal"
output_path = Path("/tmp/")
log_level = "INFO"

if not input_path.exists():
    print(f"Input path {input_path} does not exist.")
else:
    print(f"Reading path {input_path}")

ms_reader = mr.MERTISDataPackReader(input_dir=input_path, output_dir=output_path, log_level=log_level)

print(f"MERTISDataPackReader initialized with input directory: {ms_reader.input_dir}")
print(f"Output directory: {ms_reader.output_dir}")
print(f"Log level: {ms_reader.log_level}")

2026-06-11 11:46:06,627|2181969|INFO|input_dir=PosixPath('/home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal')

Reading path /home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal
MERTISDataPackReader initialized with input directory: /home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal
Output directory: /tmp
Log level: INFO

Inspect the Input Data

ms_reader.show_files()
ms_reader.listfiletypes()

All files in input_dir :

Counter({'.dat': 2, '.lblx': 3, '.fits': 1})

All files in input_dir matching old pattern <v0.2.6 (\d{8}_\d{8}):

Counter()

All files in input_dir matching new pattern >=v0.2.6 (mer_cal_sc_tis_YYYYMMDD_1-...):

Counter({'mer_cal_sc_tis': 1})

{
    'hk_default': ['mer_cal_hk_default_20200409_1-0651130766-12538__0_1.dat'],
    'hk_extended': ['mer_cal_hk_extended_20200409_1-0651130766-12595__0_1.dat'],
    'sc_tis': ['mer_cal_sc_tis_20200409_1-0651130819-21186__0_1.fits'],
    'sc_tir': [],
    'sc_tis_ql': [],
    'sc_tir_ql': []
}

{'hk_default': 1, 'hk_extended': 1, 'sc_tis': 1, 'sc_tir': 0, 'sc_tis_ql': 0, 'sc_tir_ql': 0}

Collect and Assemble Data

ms_reader.data_collector()

print(f"Collected data keys: {ms_reader.collect_data.keys()}")
for key, value in ms_reader.collect_data.items():
    print(f"{key}: {len(value)} files collected")

ms_reader.data_assembler(verbose=True)

Reading filetype: hk_default from mer_cal_hk_default_20200409_1-0651130766-12538__0_1
Processing label: /home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal/mer_cal_hk_default_20200409_1-0651130766-12538__0_1.lblx
Now processing a Table_Delimited structure: MERTIS_CAL_DEFAULT_HOUSEKEEPING_DATA_TABLE
Reading filetype: hk_extended from mer_cal_hk_extended_20200409_1-0651130766-12595__0_1
Processing label: /home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000000_CRE-20240717T132010-ParamEventBootSciHK-short/cal/mer_cal_hk_extended_20200409_1-0651130766-12595__0_1.lblx
Now processing a Table_Delimited structure: MERTIS_CAL_EXTENDED_HOUSEKEEPING_DATA_TABLE
Reading filetype: tis from mer_cal_sc_tis_20200409_1-0651130819-21186__0_1
Collected data keys: dict_keys(['hk_default', 'hk_extended', 'tis'])
hk_default: 1 files collected
hk_extended: 1 files collected
tis: 1 files collected

Reading filetype: tis from
/home/kidpixo/work/esa/mertis_data_management/mertisreader/data/bcmer_tm_all_START-20200409T000000_END-20200410T000
000_CRE-20240717T132010-ParamEventBootSciHK-short/cal/mer_cal_sc_tis_20200409_1-0651130819-21186__0_1.fits

n_wav=40 # generic wavelengths : not precise enough for scientific analysis!
|    | tis_stem                                        |   finite(geo) |   geo.size |
|---:|:------------------------------------------------|--------------:|-----------:|
|  0 | mer_cal_sc_tis_20200409_1-0651130819-21186__0_1 |           672 |      10500 |
Indices of measurements targets (HK_STAT_TIS_DATA_ACQ_TARGET):
space_index_merged.shape=(21,)
bb7_index_merged.shape=(0,)
bb3_index_merged.shape=(0,)
planet_index_merged.shape=(0,)
Collected data statistics:
Number of TIS files: 1
Number of HK files: 2
Number of TIR files: 0
Number of TIS QL files: 0
Number of TIR QL files: 0

Verify the Result

if ms_reader.processing_level != "RAW":
    print(f"Geometry data keys: {ms_reader.geom_ls.keys()}")

print(f"Frames data keys: {ms_reader.frames.keys()}")
print(f"Wavelengths data keys: {ms_reader.wavelengths.keys()}")
print(f"MERTIS TIS metadata keys: {ms_reader.mertis_tis_metadata.keys()}")
print(f"Space index merged shape: {ms_reader.space_index_merged.shape}")
print(f"BB7 index merged shape: {ms_reader.bb7_index_merged.shape}")
print(f"BB3 index merged shape: {ms_reader.bb3_index_merged.shape}")
print(f"Planet index merged shape: {ms_reader.planet_index_merged.shape}")

Geometry data keys: dict_keys(['mer_cal_sc_tis_20200409_1-0651130819-21186__0_1'])
Frames data keys: dict_keys(['mer_cal_sc_tis_20200409_1-0651130819-21186__0_1'])
Wavelengths data keys: dict_keys(['mer_cal_sc_tis_20200409_1-0651130819-21186__0_1'])
MERTIS TIS metadata keys: dict_keys(['mer_cal_sc_tis_20200409_1-0651130819-21186__0_1'])
Space index merged shape: (21,)
BB7 index merged shape: (0,)
BB3 index merged shape: (0,)
Planet index merged shape: (0,)

Next Steps

Once you know which file key you want to explore, you can inspect frames, metadata, and plots exactly as in the notebook version. The API reference on this site comes from quartodoc-generated pages built from docstrings.

Getting Started with mertisreader