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& \textbf {\vhdatename } - & \textbf {\vhauthorname } - & \textbf {\vhchangename }\\\hline -0.0 - & 22.08.2019 - & \listset {Samuel Hunt, Agnieszka Bia\l {}ek, Niall Origo} - & Initial draft\\\hline -\end {longtable} diff --git a/docs/atbd/~$pernets-NPL-Algorithm_Theoretical_Basis_Document-v0.0.docx b/docs/atbd/~$pernets-NPL-Algorithm_Theoretical_Basis_Document-v0.0.docx deleted file mode 100755 index 26e1d62b..00000000 Binary files a/docs/atbd/~$pernets-NPL-Algorithm_Theoretical_Basis_Document-v0.0.docx and /dev/null differ diff --git a/docs/file_formats/Fileformat_L1_SHunt.png b/docs/file_formats/Fileformat_L1_SHunt.png deleted file mode 100755 index f3fb528a..00000000 Binary files a/docs/file_formats/Fileformat_L1_SHunt.png and /dev/null differ diff --git a/docs/file_formats/Fileformat_L2_CGoyens.png b/docs/file_formats/Fileformat_L2_CGoyens.png deleted file mode 100755 index 51c44617..00000000 Binary files a/docs/file_formats/Fileformat_L2_CGoyens.png and /dev/null differ diff --git a/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.0.docx b/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.0.docx deleted file mode 100755 index 9b3122ec..00000000 Binary files a/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.0.docx and /dev/null differ diff --git a/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.5.docx b/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.5.docx deleted file mode 100755 index d63a0dd8..00000000 Binary files a/docs/file_formats/Hypernets-Product_Data_Format_Specification-v0.5.docx and /dev/null differ diff --git a/docs/file_formats/waterhypernet_datametadata.pdf b/docs/file_formats/waterhypernet_datametadata.pdf deleted file mode 100755 index cf6f6b27..00000000 Binary files a/docs/file_formats/waterhypernet_datametadata.pdf and /dev/null differ diff --git a/docs/file_formats/waterhypernet_datametadata.yml b/docs/file_formats/waterhypernet_datametadata.yml deleted file mode 100755 index b0dbce4e..00000000 --- a/docs/file_formats/waterhypernet_datametadata.yml +++ /dev/null @@ -1,106 +0,0 @@ -# data model segments - -- segment: &dmd Data metadata -- segment: &imd Instrument metadata -- segment: &smd System metadata -- segment: &simd Site metadata -- segment: &comd Components metadata -- segment: &camd Calibration metadata - -# Tables and columns - -- table: Global atrtributes - segment: *dmd - display: accent5 - columns: - system_id: {key: yes} - instrument_id: {key: yes} - site_id: {key: yes} - rad_vnir_id: {key: yes} - irrad_vnir_id: {key: yes} - latitude_average: - latitude_minimum: - latitude_maximum: - longitude_average: - longitude_minimum: - longitude_maximum: - -- table: sequence_cycle - segment: *dmd - display: accent5 - columns: - sequence_id: {key: yes} - subsequence_id: {key: yes} - measurement_configuration_file: - measurement_sequence_file: - relative_azimuth_angle: - timestamp: - solar_zenith_angle: - lu_datetime_average: - lu_datetime_start: - lu_datetime_finish: - ld_datetime_average: - ld_datetime_start: - ld_datetime_finish: - ed_datetime_average: - ed_datetime_start: - ed_datetime_finish: - lu_units: - ld_units: - ed_units: - lw_units: - rhow_units: - rhow_nosc_units: - -- table: Processing - segment: *dmd - display: accent5 - columns: - processor_name: - processor_version: - processor_configuration_file: - processor_atbd: - processor_input: - processor_output: - processor_data_level: - file_created: - inputfile: - fresnel_rhof: - fresnel_type: - fresnel_wind: - fresnel_sza: - fresnel_vza: - fresnel_raa: - rad_inclination: - irr_inclination: - lu_scans_total: - lu_scans_temporalvsincomplete: - lu_scans_good: - ld_scans_total: - ld_scans_temporalvsincomplete: - ld_scans_good: - ed_scans_total: - ed_scans_temporalvsincomplete: - ed_scans_good: - wavelen1: - wavelen2: - epsave: - epsmin: - epsmax: - epsstd: - -- table: Calibration - segment: *dmd - display: accent5 - columns: - rad_vnir_radcal_filename_1: - rad_vnir_radcal_filename_2: - rad_vnir_radcal_date_1: - rad_vnir_radcal_date_2: - rad_vnir_radcal_interp: - irr_vnir_radcal_filename_1: - irr_vnir_radcal_filename_2: - irr_vnir_radcal_date_1: - irr_vnir_radcal_date_2: - irr_vnir_radcal_interp: - diff --git a/docs/file_formats/waterhypernet_metadata.pdf b/docs/file_formats/waterhypernet_metadata.pdf deleted file mode 100755 index 33419137..00000000 Binary files a/docs/file_formats/waterhypernet_metadata.pdf and /dev/null differ diff --git a/docs/file_formats/waterhypernet_metadata_keysonly.pdf b/docs/file_formats/waterhypernet_metadata_keysonly.pdf deleted file mode 100755 index 0ac65d57..00000000 Binary files a/docs/file_formats/waterhypernet_metadata_keysonly.pdf and /dev/null differ diff --git a/docs/images/design-class_interations.png b/docs/images/design-class_interations.png deleted file mode 100755 index ead30376..00000000 Binary files a/docs/images/design-class_interations.png and /dev/null differ diff --git a/docs/images/design-flowchart.png b/docs/images/design-flowchart.png deleted file mode 100755 index eb5d7f31..00000000 Binary files a/docs/images/design-flowchart.png and /dev/null differ diff --git a/docs/sphinx/conf.py b/docs/sphinx/conf.py index 85807a88..cda4aa2a 100755 --- a/docs/sphinx/conf.py +++ b/docs/sphinx/conf.py @@ -18,7 +18,8 @@ import os import sys -sys.path.insert(0, os.path.abspath('sphinx')) + +sys.path.insert(0, os.path.abspath("sphinx")) def run_apidoc(_): @@ -37,15 +38,19 @@ def run_apidoc(_): try: # Sphinx 1.7+ from sphinx.ext import apidoc + apidoc.main(argv) except ImportError: # Sphinx 1.6 (and earlier) from sphinx import apidoc + argv.insert(0, apidoc.__file__) apidoc.main(argv) + def setup(app): - app.connect('builder-inited', run_apidoc) + app.connect("builder-inited", run_apidoc) + # -- General configuration ------------------------------------------------ @@ -57,41 +62,41 @@ def setup(app): # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.mathjax', + "sphinx.ext.autodoc", + "sphinx.ext.mathjax", ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] -source_suffix = '.rst' +source_suffix = ".rst" # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' -atbd = 'atbd' -userguide = 'userguide' +master_doc = "index" +atbd = "atbd" +userguide = "userguide" # General information about the project. -project = u'hypernets_processor' -copyright = u'2020, Hypernets Project Team' -author = u'Hypernets Project Team' +project = "hypernets_processor" +copyright = "2020, Hypernets Project Team" +author = "Hypernets Project Team" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -version = u'2.0' +version = "2.0" # The full version, including alpha/beta/rc tags. -release = u'2.0' +release = "2.0" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -134,7 +139,7 @@ def setup(app): # show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] @@ -151,7 +156,7 @@ def setup(app): # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -185,7 +190,7 @@ def setup(app): # 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 = ['_static'] +html_static_path = ["_static"] # html_context = { # 'css_files': [ @@ -271,36 +276,43 @@ def setup(app): # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = 'hypernets_processordocs' +htmlhelp_basename = "hypernets_processordocs" # -- Options for LaTeX output --------------------------------------------- latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (atbd, 'hypernets_processor_atbd.tex', u'Hypernets Processor Algorithm Theoretical Basis Document', - u'Hypernets Project Team', 'manual'), - (userguide, 'hypernets_processor_userguide.tex', u'Hypernets Processor User Guide', - u'Hypernets Project Team', 'manual'), + ( + atbd, + "hypernets_processor_atbd.tex", + "Hypernets Processor Algorithm Theoretical Basis Document", + "Hypernets Project Team", + "manual", + ), + ( + userguide, + "hypernets_processor_userguide.tex", + "Hypernets Processor User Guide", + "Hypernets Project Team", + "manual", + ), ] # The name of an image file (relative to this directory) to place at the top of @@ -341,8 +353,13 @@ def setup(app): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'hypernets_processor', u'hypernets_processor Documentation', - [author], 1) + ( + master_doc, + "hypernets_processor", + "hypernets_processor Documentation", + [author], + 1, + ) ] # If true, show URL addresses after external links. @@ -356,9 +373,15 @@ def setup(app): # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'hypernets_processor', u'Hypernets Processor User Guide', - author, 'hypernets_processor', 'One line description of project.', - 'Miscellaneous'), + ( + master_doc, + "hypernets_processor", + "Hypernets Processor User Guide", + author, + "hypernets_processor", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. diff --git a/docs/sphinx/content/atbd/figures/plot_clearskycheck_irradiance_HYPERNETS_L_GHNA_L1B_IRR_20220804T1000_20231227T1443_v2.0.jpeg b/docs/sphinx/content/atbd/figures/plot_clearskycheck_irradiance_HYPERNETS_L_GHNA_L1B_IRR_20220804T1000_20231227T1443_v2.0.jpeg new file mode 100644 index 00000000..b4619707 Binary files /dev/null and b/docs/sphinx/content/atbd/figures/plot_clearskycheck_irradiance_HYPERNETS_L_GHNA_L1B_IRR_20220804T1000_20231227T1443_v2.0.jpeg differ diff --git a/docs/sphinx/content/atbd/processing/CLEAR_SKY_JSIT.png b/docs/sphinx/content/atbd/processing/CLEAR_SKY_JSIT.png new file mode 100644 index 00000000..14be843b Binary files /dev/null and b/docs/sphinx/content/atbd/processing/CLEAR_SKY_JSIT.png differ diff --git a/docs/sphinx/content/atbd/processing/CLOUDY_SCENE_LOBE.png b/docs/sphinx/content/atbd/processing/CLOUDY_SCENE_LOBE.png new file mode 100644 index 00000000..9f25eb65 Binary files /dev/null and b/docs/sphinx/content/atbd/processing/CLOUDY_SCENE_LOBE.png differ diff --git a/docs/sphinx/content/atbd/processing/MISALIGNMENT_MODEL.png b/docs/sphinx/content/atbd/processing/MISALIGNMENT_MODEL.png new file mode 100644 index 00000000..d22aca2d Binary files /dev/null and b/docs/sphinx/content/atbd/processing/MISALIGNMENT_MODEL.png differ diff --git a/docs/sphinx/content/atbd/processing/NDVI_JSIT.png b/docs/sphinx/content/atbd/processing/NDVI_JSIT.png new file mode 100644 index 00000000..761a9863 Binary files /dev/null and b/docs/sphinx/content/atbd/processing/NDVI_JSIT.png differ diff --git a/docs/sphinx/content/atbd/processing/NDVI_LOBE.png b/docs/sphinx/content/atbd/processing/NDVI_LOBE.png new file mode 100644 index 00000000..fb8cc643 Binary files /dev/null and b/docs/sphinx/content/atbd/processing/NDVI_LOBE.png differ diff --git a/docs/sphinx/content/atbd/processing/REFLECTANCE_BOUNDS_GHNA.png b/docs/sphinx/content/atbd/processing/REFLECTANCE_BOUNDS_GHNA.png new file mode 100644 index 00000000..5d71df87 Binary files /dev/null and b/docs/sphinx/content/atbd/processing/REFLECTANCE_BOUNDS_GHNA.png differ diff --git a/docs/sphinx/content/atbd/processing/post_processing.rst b/docs/sphinx/content/atbd/processing/post_processing.rst index 579d1225..fffec201 100644 --- a/docs/sphinx/content/atbd/processing/post_processing.rst +++ b/docs/sphinx/content/atbd/processing/post_processing.rst @@ -5,13 +5,136 @@ .. _post_processing: +Post Processing - Site-specific Quality Checks +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Post Processing - Site-specific Quality checks -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Once the L2A datasets have been produced, a final set of site-specific quality checks and masks are -applied. The site-specific quality checks and masks are determined after inspection of the first months of -data in consultation of the site owners. The resulting masks are applied to the L2A -dataset and stored as L2B. The same masks are also applied to the L1B datasets and stored as L1D. Only -the L1D and L2B data will be distributed to satellite validation users. +The LANDHYPERNET L2A data still contains erroneous sequences which are not +suitable for Cal/Val, and thus not suitable for public distribution. +The standard L2A processing as described in the previous sections applies general quality checks to the +data. However, no site-specific QC has been applied in the processing to L2A. -These post-processing quality checks are still under development and will be detailed here in the future. \ No newline at end of file +To ensure the highest quality of the L2A data over the Cal/Val sites, additional +quality checks are applied to the data. This is done in two stages: + +1. An offline analysis is performed for each deployment period at each site, to identify + periods with known issues (e.g. due to site heterogeneity, bad deployment conditions, + unsuitable viewing or solar angles, etc). Based on this offline analysis, a range of config + values are determined for each site and deployment period, which are then stored in the job.config file (see :ref:`config`). + +2. During processing to L2B, the site-specific quality checks are applied to the data, + using the config values determined in the offline analysis. Only data suitable for Cal/Val + are retained in the L2B data. + +Flags Set in the L2A Data +------------------------- + +Data flagged with a critical issue in L2A and L1B data are removed. Specifically, the following flags are removed (see also :ref:`using_hypernets`):: + + bad_flags=["pt_ref_invalid", "half_of_scans_masked", "not_enough_dark_scans", "not_enough_rad_scans", + "not_enough_irr_scans", "no_clear_sky_irradiance", "variable_irradiance", + "half_of_uncertainties_too_big", "discontinuity_VNIR_SWIR", "single_irradiance_used"] + +See :ref:`flags` for more information on these flags. + +Sequences Outside Any Valid Deployment Date Ranges +-------------------------------------------------- + +The datetime of the sequence being processed is simply checked against the valid deployment ranges +(see https://www.landhypernet.org.uk/site_descriptions for these date ranges for each site). + +Periods with Bad Deployment Conditions +-------------------------------------- + +Such date/time/datetime periods can be revealed as part of the offline analysis, or can be known by the site owner +due to expert knowledge about the site, knowledge about the deployment, etc. + +Periods with Site Heterogeneity +------------------------------- + +Homogeneous periods are defined using NDVI at vegetated sites. We first define a reference period through manual analysis +of images from sites and conversations with site owners and calculate the standard deviation of the NDVI in this period. +The homogeneous periods are then defined as periods where a rolling standard deviation of NDVI is below 1.5 times the reference standard deviation. +Any measurements outside these homogeneous periods are removed. + +.. figure:: NDVI_LOBE.png + :width: 600px + :align: center + :alt: NDVI timeseries for LOBE April 2025 – August 2025 + + (Top) NDVI timeseries for LOBE April 2025 – August 2025. Green dots show NDVI of a measurement; blue line shows rolling average of 100 measurements with rolling standard deviation as shaded region. (Bottom) Rolling standard deviation of NDVI timeseries; red, orange, and yellow lines show 1, 2, and 3 times the reference standard deviation, respectively, where the reference is defined as the standard deviation of a known homogeneous period (here July 2025). + +Unsuitable Viewing Zenith & Azimuth Angle +----------------------------------------- + +Such angles with tolerances can be revealed as part of the offline analysis (e.g. see Figure below), or can be known by the site owner due to expert site knowledge, knowledge about the deployment, etc. +To mask out shadows, there is also the option to specify the relative azimuth angle (shadows typically at 0 degrees) and to select all zenith angles smaller than the solar zenith angle. + +.. figure:: NDVI_JSIT.png + :width: 600px + :align: center + :alt: NDVI Timeseries for JSIT Jan – Jul 2025 coloured by viewing zenith angle + + NDVI Timeseries for JSIT Jan – Jul 2025 coloured by viewing zenith angle, lower NDVI can be seen close to nadir (0 and 5 degrees). Close to nadir the sensor is looking at bare soil next to the mast and this data is removed in L2B. + +Unsuitable Sun Zenith Angle +-------------------------- + +Any measurements with a solar zenith angle above 60 degrees are removed. This value is changed for some high-latitude sites where very low solar zeniths occur; these are defined in offline analysis. + +Poorly Performing Wavelength Ranges +----------------------------------- + +Wavelength ranges with known issues (such as calibration failures) are masked. + +.. figure:: CLEAR_SKY_JSIT.png + :width: 600px + :align: center + :alt: Clear sky check plot for JSIT irradiance measurements + + Clear sky check plot for JSIT irradiance measurements on 2024-05-17 at 9:00 UTC. There is an erroneous peak in the measured irradiance around 585 nm. + +A Note on Clear-Sky Modelling +----------------------------- + +Site-specific clear sky models are generated using the LibRadtran Radiative Transfer software. The surface was set to be Lambertian with reflectance equal to the mean L2A spectral reflectance for the specific site at a viewing zenith angle of 20 degrees. Atmospheric properties were taken from ERA5 reanalysis data averaged over 2023. One set of models was run with no aerosols, and one set of models was run with the median aerosol optical depth taken from CAMS reanalysis data over the site in 2023. BOA irradiance calculations (including direct and diffuse contributions) were then performed using RT for a range of different solar zenith angles (0 to 80 in steps of 10). The altitude for each simulation was also set specifically from the Copernicus DEM, extracted at each site. During analysis, models are interpolated to the solar zenith angle of the measurements. + +Misalignment of the HYPSTAR Sensor +---------------------------------- + +Sequences with erroneous irradiances were spotted with the likely cause being a slight misalignment of the HYPSTAR sensor to the vertical during the irradiance measurements, causing a trend in the ratio between a clear sky model and the irradiance measurements throughout the day. The observed ratio between the clear sky model with median aerosols (described above) and the irradiance measurements is used to fit a modelled ratio. The modelled ratio has the following free parameters: misalignment viewing zenith angle (the tilt from the vertical); misalignment viewing azimuth angle (the azimuthal direction of the tilt with 0 as North); offset (to account for errors in the clear sky model and drift in the calibration). These free parameters are fit using a Markov Chain Monte Carlo (MCMC) process. The data is then normalised using a correction factor so that the average irradiance is the same as prior to the misalignment correction. + +.. figure:: MISALIGNMENT_MODEL.png + :width: 600px + :align: center + :alt: Illustration of the misalignment modelling results + + Illustration of the misalignment modelling results. Data points show data from JAES May-Sep 2023 in bins of time-of-day. Errorbars show standard deviation within the bin. Top: observed ratio of clear sky model and irradiance measurements, which shows some unexpected variability during the day. 2nd panel: modelled ratio, allowing for viewing zenith and azimuth angle to be pointed not exactly at nadir (also includes an offset to account for mismatches between model and observations). 3rd panel: residual between observations and models. 4th panel: normalised corrected ratios (by using the modelled misalignment, but not applying offset). Bottom: solar zenith angle in each bin. + +More Stringent Clear Sky Check +------------------------------ + +The improved clear sky consists of discarding any sequences where the measured irradiances (after correction for misalignment) are either more than 5% higher than the model without aerosols at 550 nm, or more than 10% smaller than the clear sky model with median aerosols. Note that various thresholds and aerosol loads were experimented with, and this combination was found to hold the best trade-off between masking erroneous sequences and wrongfully masking valid sequences. + +.. figure:: CLOUDY_SCENE_LOBE.png + :width: 600px + :align: center + :alt: Example of cloudy scene from LOBE + + Example of cloudy scene from LOBE which passed L2A QC. More stringent L2B site-specific cloud checks correctly identify this as a cloudy scene. + +Unsuitable Reflectances for Specific Site +----------------------------------------- + +Based on offline analysis, realistic upper and lower bounds on the reflectance values are provided in bins along multiple dimensions (typically solar zenith angle, viewing zenith angle, relative azimuth angle, and optionally temporal bins), to allow for angular variability due to BRDF effects (and optionally seasonal effects). The bounds themselves come from binning the data within these bins, and then iteratively removing outliers (as compared to other values in the bin, as well as fits to the overall angular and temporal variability). + +.. figure:: REFLECTANCE_BOUNDS_GHNA.png + :width: 600px + :align: center + :alt: Illustration of the reflectance bounds for GHNA May 2022 – Oct 2023 + + Illustration of the reflectance bounds for GHNA May 2022 – Oct 2023. The bounds are shown in blue, data which pass in green, and data which are removed in red. + +Other Unusual Conditions +------------------------ + +Any remaining issues, due to unusual conditions that occur occasionally, can be omitted by manually specifying the sequence ID. diff --git a/docs/sphinx/content/atbd/processing/processing_config.rst b/docs/sphinx/content/atbd/processing/processing_config.rst index 9e4ff66e..686572d8 100755 --- a/docs/sphinx/content/atbd/processing/processing_config.rst +++ b/docs/sphinx/content/atbd/processing/processing_config.rst @@ -61,7 +61,7 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro - system longitude - longitude of site * - angle2use - - Ange used to compute the viewing geometry (i.e. pt_ref is the pan and tilt angles with the HYPSTAR as reference - use offset pan and tilt to retrieve viewing geometry with true North) + - Angle used to compute the viewing geometry (i.e. pt_ref is the pan and tilt angles with the HYPSTAR as reference - use offset pan and tilt to retrieve viewing geometry with true North) - pt_ref, pt_ask or pt_abs **Table 2: Processor** @@ -84,19 +84,25 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro - 0 no uncertainties, suggested > 100 when uncertainties * - max_level - maximum level of processing - - Default: L2A + - Default: L2B * - uncertainty_l1a - uncertainty computation of the level L1A - Default: False - * - bad_wavelenth_ranges + * - bad_wavelength_ranges - wavelength ranges for which uncertainties are expected to be high and ignored when triggering flags and anomalies - Default: 757.5-767.5, 1350-1390 + * - delay_hours + - minimum delay between sequence acquisition and processing (e.g. to allow time for ancillary data download) + - Default: 48 * - verbose - printing warnings and errors in terminal - Default: False * - archive_directory - directory where products will be saved when running automated processing - + * - reprocess_from + - Optional processing level from which to restart reprocessing (overrides defaults if set) + - e.g. L1B **Table 3: Databases** @@ -217,6 +223,12 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - measurement_function_calibrate - measurement function used for the calibration of the radiance and irradiance scans - e.g. StandardMeasurementFunction + * - calibration_interpolation_method + - interpolation method for interpolating between pre-deployment and post-deployment calibration + - e.g. previous or linear + * - calibration_file_version + - version of the calibration file to be used + - e.g. 2.4 **Table 8: Interpolate** @@ -526,7 +538,7 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - uncertainty_l1a - uncertainty computation of the level L1A - Default: False - * - bad_wavelenth_ranges + * - bad_wavelength_ranges - wavelength ranges for which uncertainties are expected to be high and ignored when triggering flags and anomalies - Default: 757.5-767.5, 1350-1390 * - verbose @@ -535,6 +547,12 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - archive_directory - directory where products will be saved when running automated processing - + * - delay_hours + - minimum delay between sequence acquisition and processing (e.g. to allow time for ancillary data download) + - e.g. 1 + * - reprocess_from + - Optional processing level from which to restart reprocessing (overrides defaults if set) + - e.g. L1B **Table 3: Databases** @@ -732,6 +750,12 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - write_l2a - Write output file L2A - Default: True + * - write_l2b + - Write output file L2B + - Default: True + * - write_l1d + - Write output file L1D + - Default: True **Table 12: Plotting** @@ -769,6 +793,12 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - plot_l2a - Plotting L2A data - Default: True + * - plot_l2b + - Plotting L2B data + - Default: True + * - plot_l1d + - Plotting L1D data + - Default: True * - plot_uncertainty - Plotting uncertainties - Default: True @@ -787,4 +817,74 @@ Default configuration files can be changed in `hypernets_processor/hypernets_pro * - plot_polar_max - macimum reflectace in the colourscale for polar plot showing the angular variation in reflectance - + * - plot_polar_ndvi + - Plot NDVI in polar plots + - Default: True + +**Table 13: Site_specific_QC** + +.. list-table:: + :widths: 20 60 20 + :header-rows: 1 + + * - Configuration parameter + - Definition + - Options/example + * - deployment_periods + - List of deployment periods with start/stop dates, instrument serial number, validity, and comments. + - e.g [{"start_date": "2022-05-17", "stop_date": "2023-10-17", "HYPSTAR_SN": 220261, "valid": True, "comments": "v1 instrument"}, ...] + * - bad_dates_period + - List of date ranges to exclude for each period. + - e.g. [None, None, ...] + * - limit_tod_period + - List of time-of-day limits for each period. + - e.g. [["08:30","19:00"], ...] + * - bad_sequences_period + - List of sequence IDs to exclude for each period. + - e.g. [[], [], ...] + * - max_sza_period + - Maximum solar zenith angle allowed for each period. + - e.g. [60, 60, ...] + * - bad_viewing_angles_period + - List of viewing zenith/azimuth angle pairs to mask for each period. + - e.g. [[(0, "all"), (5, "all")], ...] + * - bad_solar_angles_period + - List of solar angle pairs to mask for each period. + - e.g. [[], [], ...] + * - bad_relative_angles_period + - List of relative angles to mask for each period. + - e.g. [[("sza", 0), ("sza", 360)], ...] + * - angle_tolerance + - Tolerance for angle matching for bad angle masking (degrees). + - e.g. 1 + * - raa_angle_tolerance + - Tolerance for relative azimuth angle matching for bad angle masking (degrees). + - e.g. 10 + * - bad_wavelengths_period + - List of wavelength ranges to exclude for each period. + - e.g. [[], [], ...] + * - postprocessing_qc_file_period + - List of filenames for post-processing QC bounds for each period. + - e.g. ["GHNA_2022May_2023Oct_bounds.nc", ...] + * - misalignment_vza + - Misalignment viewing zenith angle for each period. + - e.g. [1.01, 1.96, ...] + * - misalignment_vza_unc + - Uncertainty for misalignment viewing zenith angle. + - e.g. [0.07, 0.06, ...] + * - misalignment_vaa + - Misalignment viewing azimuth angle for each period. + - e.g. [97, -72, ...] + * - misalignment_vaa_unc + - Uncertainty for misalignment viewing azimuth angle. + - e.g. [6, 3, ...] + * - misalignment_corr + - Correction factor for misalignment. + - e.g. [0.99, 1.01, ...] + * - misalignment_corr_unc + - Uncertainty for correction factor. + - e.g. [0.01, 0.02, ...] + * - apply_site_specific_cloud_check + - Enable/disable site-specific cloud checks. + - True/False diff --git a/docs/sphinx/content/atbd/products/product_files.rst b/docs/sphinx/content/atbd/products/product_files.rst index cfd49f32..fdf2c7dc 100755 --- a/docs/sphinx/content/atbd/products/product_files.rst +++ b/docs/sphinx/content/atbd/products/product_files.rst @@ -16,14 +16,6 @@ The naming convention is intended to allow the unique identification of all prod *SYSTEM_NETWORK_SITEID_LEVEL_TYPE_ACQUISITIONDATETIME_PROCESSINGDATETIME_version.nc* -For the HYPSTAR calibration data, the file name is similar except that it includes the system_id and the date and time of the calibration. - -*SYSTEM_NETWORK_SYSTEMID_TYPE_CALIBRATIONDATETIME_version.nc* - -For the RGB images taken during the measurements, the file name is similar except that it also includes the series ID, viewing and azimuth angle. - -*SYSTEM_NETWORK_SITEID_TYPE_ACQUISITIONDATETIME_PROCESSINGDATETIME_SERIESID_ZENITH_AZIMUTH_version.nc* - The files are stored in the NetCDF data format and so have the extension “.nc” (except for the RGB images taken during the measurements by the instrument). The definition of the data fields and their allowed contents is described as follows: **Table 1: File name conventions** @@ -80,6 +72,15 @@ Table 2 defines the abbreviated name convention applicable to the individual Hyp | VEIT | Aqua Alta Oceanographic Tower, Venice, Italy | +---------+----------------------------------------------------------+ +For the HYPSTAR calibration data, the file name is similar except that it includes the system_id and the date and time of the calibration. + +*SYSTEM_NETWORK_SYSTEMID_TYPE_CALIBRATIONDATETIME_version.nc* + +For the RGB images taken during the measurements, the file name is similar except that it also includes the series ID, viewing and azimuth angle. + +*SYSTEM_NETWORK_SITEID_TYPE_ACQUISITIONDATETIME_PROCESSINGDATETIME_SERIESID_ZENITH_AZIMUTH_version.nc* + + Data level ---------- The end-to-end prototype processor takes the data from acquisition (raw data) to application of calibration and quality controls, computation of correction factors (e.g. Fresnel correction for water processing), temporal interpolation to coincident timestamps, processing to surface reflectance and averaging per series. To account for all these steps different data levels have been defined (see Table 3). See :ref:`data_structure` for a detailed explanantion of the terminology used. diff --git a/docs/sphinx/content/atbd/products/table_anomalies.csv b/docs/sphinx/content/atbd/products/table_anomalies.csv index 16acfa42..a46a70a3 100755 --- a/docs/sphinx/content/atbd/products/table_anomalies.csv +++ b/docs/sphinx/content/atbd/products/table_anomalies.csv @@ -9,10 +9,19 @@ ms, series_missing , L & W , L1B , Check if there are any missing series (either u, negative_unc , L & W , L1B , There are negative uncertainties, True , o, half_of_unc_too_big , L & W , L1B , More than 50\% of data has random error above 100\% (likely corrupted or dark data), False , 17 nu, check_valid_irradiance , L & W , L1C , Halt processing if `variable_irradiance' flag was triggered at previous level, True , -in, check_valid_sequence , L & W , L1C , Halt processing if there are no valid series (flagged by `not_enough_dark_scans'; `not_enough_irr_scans'; `not_enough_rad_scans' or `vza_irradiance')., True , +in, check_valid_sequence , L & W , L1C , Halt processing if there are no valid series (not present or flagged by `not_enough_dark_scans'; `not_enough_irr_scans'; `not_enough_rad_scans' or `vza_irradiance')., True , cl, no_clear_sky_sequence , L & W , L1C , If all irradiance series are flagged with the `no_clear_sky_irradiance' flag, False , 19 d, discontinuity_VNIR_SWIR , L , L1B , Checks if the VNIR and SWIR are different by more than 25\%, False, 20 nd, variable_radiance, W , L1C , More than 10\% difference between start and end $L_d$ at 550~nm, True , l, ld_missing, W , L1C , Ld missing for sky reflectance correction, True, -x, unexpected_error, L & W , , unexpected error during processing; catches all errors, True, - +per, not_deploy_period, L , L2B , Sequence not within deployment periods, True, +val, not_valid_period, L , L2B ,sequence within deployment periods that is not valid for satellite validation, True, +tod, bad_time_of_day, L , L2B , Sequence not within selected time of day, True, +hsn, hypstar_not_deploy_period, L , L2B , HYPSTAR_SN does not match deployment periods, True, +scl, no_clear_sky_site_specific, L , L2B , Site-specific clear sky check has failed (irr not within 10% of model), True, +npr, no_pre_files, L , L2B , No pre-existing files available, while config is set up to reprocess from pre-existing files, True, +man, manual_discard, L , L2B , This sequences was manually discarded as unreliable in the config file, True, +wns, wrong_number_series, L2B , Wrong number of series (l2a and l1b rad do not match in number of series). No L1d file is produced, False, +nos, no_series_site_specific, L , L2B , No series was present in the sequences after applying all site-specific QC, True, +hos, half_of_series_site_specific, L, L2B, More than half series were removed by site-specific QC checks (excluding bad viewing angles and bad dates), True, +x, unexpected_error, L & W , , unexpected error during processing; catches all errors, True, \ No newline at end of file diff --git a/docs/sphinx/content/atbd/products/table_flags_common.csv b/docs/sphinx/content/atbd/products/table_flags_common.csv index 829aa512..63bbc10f 100644 --- a/docs/sphinx/content/atbd/products/table_flags_common.csv +++ b/docs/sphinx/content/atbd/products/table_flags_common.csv @@ -1,20 +1,20 @@ Bit #,name,network,level,Description,anomaly raised -1, lon_default, L & W , L0A , Default longitude as given in the configuration file is used (missing Lon in metadata) , -2, lat_default, L & W , L0A , same as `lon_default' but for latitude , -3, pt_ref_invalid , L & W , L0A , No effective pan/tilt is returned and the requested pan/tilt was used instead , -4, bad_pointing , L & W , L0A , Difference between requested and effective pan/tilt angle is >= 3° , `a' -5, outliers, L & W , L1A , If the spectrally integrated signal of the scan is more than 3 sigma or more than 25\% (whichever is largest) removed from the mean; it is masked and will not be used when averaging the series. This process is repeated until convergence and applied to the measured (ir)radiances and to the darks. , -6, L0_threshold, L & W , L1A , Check if any of the spectral pixels are saturated; i.e. digital number DN>=64000 , -7, L0_discontinuity, L & W , L1A , Check if there are missing values in the spectrum; or significant discontinuities (\Delta DN>10^4) , -8, dark_masked, L & W , L1A , If any of the darks have been masked by `outliers'; `L0_threshold'; and/or; `L0_discontinuity' , -9, half_of_scans_masked, L & W , L0B , Less than half of the scans for a series passed quality checks `bad_pointing'; `outliers'; `L0_threshold'; and; `L0_discontinuity' , -10, not_enough_dark_scans, L & W , L0B , Not enough valid dark scans for this series (# valid dark scans < n_valid_dark from the config file) , `nld' -11, not_enough_rad_scans, L & W , L0B , Not enough valid radiance scans for this series (# valid radiance scans < n_valid_rad from the config file) ,`nlu' -12, not_enough_irr_scans, L & W , L0B , Not enough valid irradiance scans for this series (# valid irradiance scans < n_valid_irr from the config file) , `ned' -13, series_missing , L & W , L1B , Check if there are any missing series (either not present or flagged by `not_enough_dark_scans'; `not_enough_irr_scans'; `not_enough_rad_scans' or `vza_irradiance') , `ms' -14, vza_irradiance , L & W , L1B , One of the irradiance measurements did not have theta_v=180° (within 2° tolerance) so has been masked , -15, no_clear_sky_irradiance, L & W , L1B , More than 10% of the wavelength bands have a difference of more than 50% with the clear-sky model , -16, variable_irradiance, L & W , L1B , More than 10\% difference between start and end E_d at 550~nm , -17, half_of_unc_too_big , L & W , L1B , More than 50\% of data has random error above 100% (likely corrupted or dark data) , `o' -18, single_irradiance_used, L & W , L1C , If only one series of irradiance is used for the computation of the reflectance , -19, no_clear_sky_sequence , L & W , L1C , If all irradiance series are flagged with the `no_clear_sky_irradiance' flag , `cl' \ No newline at end of file +0, lon_default, L & W , L0A , Default longitude as given in the configuration file is used (missing Lon in metadata) , +1, lat_default, L & W , L0A , same as `lon_default' but for latitude , +2, pt_ref_invalid , L & W , L0A , No effective pan/tilt is returned and the requested pan/tilt was used instead , +3, bad_pointing , L & W , L0A , Difference between requested and effective pan/tilt angle is >= 3° , `a' +4, outliers, L & W , L1A , If the spectrally integrated signal of the scan is more than 3 sigma or more than 25\% (whichever is largest) removed from the mean; it is masked and will not be used when averaging the series. This process is repeated until convergence and applied to the measured (ir)radiances and to the darks. , +5, L0_threshold, L & W , L1A , Check if any of the spectral pixels are saturated; i.e. digital number DN>=64000 , +6, L0_discontinuity, L & W , L1A , Check if there are missing values in the spectrum; or significant discontinuities (\Delta DN>10^4) , +7, dark_masked, L & W , L1A , If any of the darks have been masked by `outliers'; `L0_threshold'; and/or; `L0_discontinuity' , +8, half_of_scans_masked, L & W , L0B , Less than half of the scans for a series passed quality checks `bad_pointing'; `outliers'; `L0_threshold'; and; `L0_discontinuity' , +9, not_enough_dark_scans, L & W , L0B , Not enough valid dark scans for this series (# valid dark scans < n_valid_dark from the config file) , `nld' +10, not_enough_rad_scans, L & W , L0B , Not enough valid radiance scans for this series (# valid radiance scans < n_valid_rad from the config file) ,`nlu' +11, not_enough_irr_scans, L & W , L0B , Not enough valid irradiance scans for this series (# valid irradiance scans < n_valid_irr from the config file) , `ned' +12, series_missing , L & W , L1B , Check if there are any missing series (either not present or flagged by `not_enough_dark_scans'; `not_enough_irr_scans'; `not_enough_rad_scans' or `vza_irradiance') , `ms' +13, vza_irradiance , L & W , L1B , One of the irradiance measurements did not have theta_v=180° (within 2° tolerance) so has been masked , +14, no_clear_sky_irradiance, L & W , L1B , More than 10% of the wavelength bands have a difference of more than 50% with the clear-sky model , +15, variable_irradiance, L & W , L1B , More than 10\% difference between start and end E_d at 550~nm , +16, half_of_unc_too_big , L & W , L1B , More than 50\% of data has random error above 100% (likely corrupted or dark data) , `o' +17, single_irradiance_used, L & W , L1C , If only one series of irradiance is used for the computation of the reflectance , +18, no_clear_sky_sequence , L & W , L1C , If all irradiance series are flagged with the `no_clear_sky_irradiance' flag , `cl' \ No newline at end of file diff --git a/docs/sphinx/content/atbd/products/table_flags_land.csv b/docs/sphinx/content/atbd/products/table_flags_land.csv index bd201588..a82338f1 100644 --- a/docs/sphinx/content/atbd/products/table_flags_land.csv +++ b/docs/sphinx/content/atbd/products/table_flags_land.csv @@ -1,2 +1,2 @@ Bit #,name,network,level,Description,anomaly raised -20, discontinuity_VNIR_SWIR , L , L1B , Checks if the VNIR and SWIR are different by more than 25% ,`d' \ No newline at end of file +19, discontinuity_VNIR_SWIR , L , L1B , Checks if the VNIR and SWIR are different by more than 25% ,`d' \ No newline at end of file diff --git a/docs/sphinx/content/atbd/products/table_flags_water.csv b/docs/sphinx/content/atbd/products/table_flags_water.csv index a366b83d..9f3d7d2d 100644 --- a/docs/sphinx/content/atbd/products/table_flags_water.csv +++ b/docs/sphinx/content/atbd/products/table_flags_water.csv @@ -1,12 +1,12 @@ Bit #,name,network,level,Description,anomaly raised -20, single_skyradiance_used, W , L1C , If only one series of downwelling radiance is used for the computation of the reflectance , -21, lu_eq_missing, W , L1C , If there is no upwelling and downwelling radiance pair with similar pointing azimuth angles (within 1° tolerance) , `l' -22, rhof_angle_missing, W , L1C , If there is no downwelling radiance scans at the appropriate viewing zenith angle (i.e. 180°-theta_v; within 1° tolerance), `l' -23, rhof_default, W , L1C , If the viewing geometry of the upwelling and downwelling radiance measurements are outside the viewing geometry range of the selected LUT for the `rhof_option' (e.g. Delta \phi > 180° when using the LUT from Mobley et al 1999 a default rho_F is used for the air-water interface correction factor (default: rho_F=0.0256) , -24, temp_variability_irr, W , L1C , If the difference in E_d scans does not exceed a given threshold between two neighbouring scans (default: threshold = 25% for wavelength = 550nm; see also Ruddick et al. (2006)) , -25, temp_variability_rad, W , L1C , If the difference in L_d or L_u scans does not exceed a given threshold between two neighbouring scans (default: threshold = 25% for wavelength = 550nm; Ruddick et al. (2006)) , -26, min_nbred, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `ned' -27, min_nbrlu, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `nlu' -28, min_nblsky, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `nld' -29, def_wind_flag, W , L1C , If a default wind speed is used (by default: wind speed = 2m/s) , -30, simil_fail, W , L1C , If the quality check applied on the NIR similarity spectrum is not verified as suggested by Ruddick et al. (2005) (see Section 3.2 and Fig. 4 in Ruddick et al. (2005)) with default values for the computation of the NIR Similarity being 780 and 870~nm; the reference wavelength 670~nm and the threshold 5% , +19, single_skyradiance_used, W , L1C , If only one series of downwelling radiance is used for the computation of the reflectance , +20, lu_eq_missing, W , L1C , If there is no upwelling and downwelling radiance pair with similar pointing azimuth angles (within 1° tolerance) , `l' +21, rhof_angle_missing, W , L1C , If there is no downwelling radiance scans at the appropriate viewing zenith angle (i.e. 180°-theta_v; within 1° tolerance), `l' +22, rhof_default, W , L1C , If the viewing geometry of the upwelling and downwelling radiance measurements are outside the viewing geometry range of the selected LUT for the `rhof_option' (e.g. Delta \phi > 180° when using the LUT from Mobley et al 1999 a default rho_F is used for the air-water interface correction factor (default: rho_F=0.0256) , +23, temp_variability_irr, W , L1C , If the difference in E_d scans does not exceed a given threshold between two neighbouring scans (default: threshold = 25% for wavelength = 550nm; see also Ruddick et al. (2006)) , +24, temp_variability_rad, W , L1C , If the difference in L_d or L_u scans does not exceed a given threshold between two neighbouring scans (default: threshold = 25% for wavelength = 550nm; Ruddick et al. (2006)) , +25, min_nbred, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `ned' +26, min_nbrlu, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `nlu' +27, min_nblsky, W , L1C , If the total number of scans not flagged by either `L0_threshold'; `bad_pointing' or `outliers' is less than a given threshold (default: 3) , `nld' +28, def_wind_flag, W , L1C , If a default wind speed is used (by default: wind speed = 2m/s) , +29, simil_fail, W , L1C , If the quality check applied on the NIR similarity spectrum is not verified as suggested by Ruddick et al. (2005) (see Section 3.2 and Fig. 4 in Ruddick et al. (2005)) with default values for the computation of the NIR Similarity being 780 and 870~nm; the reference wavelength 670~nm and the threshold 5% , diff --git a/hypernets_processor/anomaly_handler.py b/hypernets_processor/anomaly_handler.py index 3d1bb26e..194d7a95 100755 --- a/hypernets_processor/anomaly_handler.py +++ b/hypernets_processor/anomaly_handler.py @@ -43,6 +43,7 @@ def __init__( self.anomalies_dict = anomalies_dict self.anomalies_added = [] + self.anomalies_SEQ = [] def add_anomaly(self, anomaly_id, ds=None): """ @@ -53,7 +54,7 @@ def add_anomaly(self, anomaly_id, ds=None): :type ds: xarray.Dataset :param ds: producgt that was being processed when anomaly was raised """ - + print(f"Adding anomaly: {anomaly_id}") # Check anomaly defined if anomaly_id not in self.get_anomaly_ids(): self.context.logger.info( @@ -64,6 +65,9 @@ def add_anomaly(self, anomaly_id, ds=None): # Add anomaly to list of anomalies added during current processing self.anomalies_added.append(anomaly_id) + # Add anomaly to list of anomalies for current sequence + self.anomalies_SEQ.append(anomaly_id) + # Add anomaly to db if self.anomaly_db is not None: self.anomaly_db.add_anomaly(anomaly_id, ds) @@ -87,7 +91,9 @@ def add_x_anomaly(self): if self.get_sequence_crashing_anomalies() == []: self.add_anomaly("x") - + else: + print("Not adding x anomaly as other crashing anomalies already present (%s)" % ",".join(self.get_sequence_crashing_anomalies())) + def get_anomaly_ids(self): """ Returns available anomaly ids @@ -136,10 +142,10 @@ def get_crashing_anomaly_ids(self): :return: crashing anomaly ids """ - crashing_anomalies = [] + crashing_anomalies = ["x"] for anomaly_id in self.get_anomaly_ids(): - if self.get_anomaly_error(anomaly_id) is not None: + if self.get_anomaly_error(anomaly_id) is not None and anomaly_id != "m": crashing_anomalies.append(anomaly_id) return crashing_anomalies diff --git a/hypernets_processor/calibration/calibrate.py b/hypernets_processor/calibration/calibrate.py index b8d75747..9c3204c8 100755 --- a/hypernets_processor/calibration/calibrate.py +++ b/hypernets_processor/calibration/calibrate.py @@ -1,6 +1,7 @@ """ Calibration class """ + import datetime from hypernets_processor.version import __version__ @@ -92,9 +93,9 @@ def calibrate_l1a( store_unc_percent=True, ) - if self.context.get_config_value("bad_wavelenth_ranges"): + if self.context.get_config_value("bad_wavelength_ranges"): for maskrange in self.context.get_config_value( - "bad_wavelenth_ranges" + "bad_wavelength_ranges" ).split(","): start_mask = float(maskrange.split("-")[0]) end_mask = float(maskrange.split("-")[1]) @@ -107,18 +108,10 @@ def calibrate_l1a( ] += 50 else: - measurand = calibrate_function.run(dataset_l0_masked, calibration_data) - dataset_l1a[measurandstring].values = measurand - dataset_l1a[measurandstring].attrs["unc_comps"] = [] - dataset_l1a = dataset_l1a.drop( - [ - "u_rel_random_" + measurandstring, - "u_rel_systematic_indep_" + measurandstring, - "u_rel_systematic_corr_rad_irr_" + measurandstring, - "err_corr_systematic_indep_" + measurandstring, - "err_corr_systematic_corr_rad_irr_" + measurandstring, - ] + measurand = calibrate_function.run_meas_function( + dataset_l0_masked, calibration_data ) + dataset_l1a[measurandstring].values = measurand if self.context.get_config_value("write_l1a"): self.writer.write( @@ -176,26 +169,17 @@ def calibrate_l1b( store_unc_percent=True, ) else: - measurand = calibrate_function.run(dataset_l0b, calibration_data) - dataset_l1b[measurandstring].values = measurand - dataset_l1b[measurandstring].attrs["unc_comps"] = [] - dataset_l1b = dataset_l1b.drop( - [ - "u_rel_random_" + measurandstring, - "u_rel_systematic_indep_" + measurandstring, - "u_rel_systematic_corr_rad_irr_" + measurandstring, - "err_corr_systematic_indep_" + measurandstring, - "err_corr_systematic_corr_rad_irr_" + measurandstring, - ] + measurand = calibrate_function.run_meas_function( + dataset_l0b, calibration_data ) - + dataset_l1b[measurandstring].values = measurand if self.context.get_config_value("mcsteps") > 0: self.qual.perform_quality_check_rand_unc(dataset_l1b, measurandstring) - if self.context.get_config_value("bad_wavelenth_ranges"): + if self.context.get_config_value("bad_wavelength_ranges"): for maskrange in self.context.get_config_value( - "bad_wavelenth_ranges" + "bad_wavelength_ranges" ).split(","): start_mask = float(maskrange.split("-")[0]) end_mask = float(maskrange.split("-")[1]) @@ -397,11 +381,11 @@ def preprocess_l0(self, datasetl0, datasetl0_bla, dataset_calib): datasetl0masked, mask = self.qual.perform_quality_check_L0A( datasetl0masked, series_ids ) - datasetl0masked["quality_flag"][ - np.where(dark_outlier_rad == 1) - ] = DatasetUtil.set_flag( - datasetl0masked["quality_flag"][np.where(dark_outlier_rad == 1)], - "dark_masked", + datasetl0masked["quality_flag"][np.where(dark_outliers_radscans == 1)] = ( + DatasetUtil.set_flag( + datasetl0masked["quality_flag"][np.where(dark_outliers_radscans == 1)], + "dark_masked", + ) ) # for i in range(len(mask))] # calculate and store random uncertainties on radiance/irradiance diff --git a/hypernets_processor/calibration/calibration_converter.py b/hypernets_processor/calibration/calibration_converter.py index 43ee1221..2e4f1706 100755 --- a/hypernets_processor/calibration/calibration_converter.py +++ b/hypernets_processor/calibration/calibration_converter.py @@ -1,3 +1,5 @@ +import warnings + from hypernets_processor.version import __version__ from hypernets_processor.data_io.data_templates import DataTemplates from hypernets_processor.test.test_functions import ( @@ -39,12 +41,53 @@ def __init__(self, context): self.templ = DataTemplates(context) self.writer = HypernetsWriter(context) self.context = context - self.version = self.context.get_config_value("version") - if self.version == 0.0: + self.version = self.context.get_config_value("calibration_file_version") + if self.version is None or self.version == 0.0: self.version = input( "Enter hypernets_processor version for which you are generating calib files:" ) + def convert_coordinates_dt64(self, ds): + ds = ds.assign_coords( + calibrationdates=[ + datetime.strptime(date, "%y%m%dT%H%M%S") + for date in ds["calibrationdates"].values + ] + ) + ds = ds.assign_coords( + nonlineardates=[ + datetime.strptime(date, "%y%m%dT%H%M%S") + for date in ds["nonlineardates"].values + ] + ) + ds = ds.assign_coords( + wavdates=[ + datetime.strptime(date, "%y%m%dT%H%M%S") + for date in ds["wavdates"].values + ] + ) + return ds + + def interpolate_calibration_ds(self, ds, sequence_dt64): + ds = self.convert_coordinates_dt64(ds) + for coord in ["calibrationdates", "nonlineardates", "wavdates"]: + dt64s = ds[coord].values + if self.context.get_config_value( + "calibration_interpolation_method" + ) == "previous" or sequence_dt64 > np.max(dt64s): + i = [x for x, date in enumerate(dt64s) if date < sequence_dt64][-1] + ds = ds.isel(indexers={coord: i}) + elif sequence_dt64 <= np.max(dt64s) and sequence_dt64 >= np.min(dt64s): + ds = ds.interp( + coords={coord: sequence_dt64}, + method=self.context.get_config_value( + "calibration_interpolation_method" + ), + ) + else: + raise NotImplementedError + return ds + def read_calib_files(self, sequence_path): metadata = ConfigParser() @@ -91,89 +134,13 @@ def read_calib_files(self, sequence_path): os.path.join(hypstar_path, name) + " calibration file does not exist" ) - sequence_datetime = parse_sequence_path(sequence_path)["datetime"] - - calibration_data_times = calibration_data_rad["calibrationdates"].values - nonlin_times = calibration_data_rad["nonlineardates"].values - wav_times = calibration_data_rad["wavdates"].values + sequence_dt64 = np.datetime64(parse_sequence_path(sequence_path)["datetime"]) - # print(nonlin_times) - # - # - # calib_i=[x for x, date in enumerate(calibration_data_times) - # if datetime.strptime(date,"%y%m%dT%H%M%S") < sequence_datetime][-1] - # - # if len(nonlin_times)==1: - # nlin_i=0 - # else: - # nlin_i=[x for x, date in enumerate(nonlin_times) if datetime.strptime(date,"%y%m%dT%H%M%S") < sequence_datetime][-1] - - calib_i = [ - x - for x, date in enumerate(calibration_data_times) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - if len(nonlin_times) == 1: - nlin_i = 0 - else: - nlin_i = [ - x - for x, date in enumerate(nonlin_times) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - - wav_i = [ - x - for x, date in enumerate(wav_times) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - - calibration_data_rad = calibration_data_rad.sel( - calibrationdates=calibration_data_times[calib_i] + calibration_data_rad = self.interpolate_calibration_ds( + calibration_data_rad, sequence_dt64 ) - calibration_data_rad = calibration_data_rad.sel( - nonlineardates=nonlin_times[nlin_i] - ) - calibration_data_rad = calibration_data_rad.sel(wavdates=wav_times[wav_i]) - - calibration_data_times_irr = calibration_data_irr["calibrationdates"].values - nonlin_times_irr = calibration_data_irr["nonlineardates"].values - wav_times_irr = calibration_data_irr["wavdates"].values - - calib_i_irr = [ - x - for x, date in enumerate(calibration_data_times_irr) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - - # if len(nonlin_times)==1: - # nlin_i_irr=0 - # else: - # nlin_i_irr=[x for x, date in enumerate(nonlin_times) if datetime.strptime(date,"%y%m%dT%H%M%S") < sequence_datetime][-1] - # - if len(nonlin_times) == 1: - nlin_i_irr = 0 - else: - nlin_i_irr = [ - x - for x, date in enumerate(nonlin_times_irr) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - - wav_i_irr = [ - x - for x, date in enumerate(wav_times_irr) - if datetime.strptime(date, "%y%m%dT%H%M%S") < sequence_datetime - ][-1] - - calibration_data_irr = calibration_data_irr.sel( - calibrationdates=calibration_data_times_irr[calib_i_irr] - ) - calibration_data_irr = calibration_data_irr.sel( - nonlineardates=nonlin_times_irr[nlin_i_irr] - ) - calibration_data_irr = calibration_data_irr.sel( - wavdates=wav_times_irr[wav_i_irr] + calibration_data_irr = self.interpolate_calibration_ds( + calibration_data_irr, sequence_dt64 ) if self.context.get_config_value("network") == "l": @@ -211,29 +178,140 @@ def read_calib_files(self, sequence_path): + " calibration file does not exist" ) - calibration_data_times = calibration_data_rad_swir[ - "calibrationdates" - ].values - nonlin_times = calibration_data_rad_swir["nonlineardates"].values - calibration_data_rad_swir = calibration_data_rad_swir.sel( - calibrationdates=calibration_data_times[calib_i] - ) - calibration_data_rad_swir = calibration_data_rad_swir.sel( - nonlineardates=nonlin_times[nlin_i] - ) - calibration_data_rad_swir = calibration_data_rad_swir.sel( - wavdates=wav_times[wav_i] + calibration_data_rad_swir = self.interpolate_calibration_ds( + calibration_data_rad_swir, sequence_dt64 ) - calibration_data_irr_swir = calibration_data_irr_swir.sel( - calibrationdates=calibration_data_times_irr[calib_i_irr] - ) - calibration_data_irr_swir = calibration_data_irr_swir.sel( - nonlineardates=nonlin_times_irr[nlin_i_irr] - ) - calibration_data_irr_swir = calibration_data_irr_swir.sel( - wavdates=wav_times_irr[wav_i_irr] + calibration_data_irr_swir = self.interpolate_calibration_ds( + calibration_data_irr_swir, sequence_dt64 ) + # + # if self.context.get_config_value("calibration_interpolation_method")=="previous" or sequence_datetime>np.max(calibration_data_times): + # calib_i = [ + # x + # for x, date in enumerate(calibration_data_times) + # if date < sequence_datetime + # ][-1] + # if len(nonlin_times) == 1: + # nlin_i = 0 + # else: + # nlin_i = [ + # x + # for x, date in enumerate(nonlin_times) + # if date < sequence_datetime + # ][-1] + # + # wav_i = [ + # x + # for x, date in enumerate(wav_times) + # if date < sequence_datetime + # ][-1] + # + # calibration_data_rad = calibration_data_rad.sel( + # calibrationdates=calibration_data_times[calib_i] + # ) + # calibration_data_rad = calibration_data_rad.sel( + # nonlineardates=nonlin_times[nlin_i] + # ) + # calibration_data_rad = calibration_data_rad.sel(wavdates=wav_times[wav_i]) + # + # + # + # calib_i_irr = [ + # x + # for x, date in enumerate(calibration_data_times_irr) + # if date < sequence_datetime + # ][-1] + # + # if len(nonlin_times) == 1: + # nlin_i_irr = 0 + # else: + # nlin_i_irr = [ + # x + # for x, date in enumerate(nonlin_times_irr) + # if date < sequence_datetime + # ][-1] + # + # wav_i_irr = [ + # x + # for x, date in enumerate(wav_times_irr) + # if date < sequence_datetime + # ][-1] + # + # calibration_data_irr = calibration_data_irr.sel( + # calibrationdates=calibration_data_times_irr[calib_i_irr] + # ) + # calibration_data_irr = calibration_data_irr.sel( + # nonlineardates=nonlin_times_irr[nlin_i_irr] + # ) + # calibration_data_irr = calibration_data_irr.sel( + # wavdates=wav_times_irr[wav_i_irr] + # ) + # + # if self.context.get_config_value("network") == "l": + # + # calibration_data_rad_swir = calibration_data_rad_swir.sel( + # calibrationdates=calibration_data_times_swir[calib_i] + # ) + # calibration_data_rad_swir = calibration_data_rad_swir.sel( + # nonlineardates=nonlin_times_swir[nlin_i] + # ) + # calibration_data_rad_swir = calibration_data_rad_swir.sel( + # wavdates=wav_times_swir[wav_i] + # ) + # calibration_data_irr_swir = calibration_data_irr_swir.sel( + # calibrationdates=calibration_data_times_irr_swir[calib_i_irr] + # ) + # calibration_data_irr_swir = calibration_data_irr_swir.sel( + # nonlineardates=nonlin_times_irr_swir[nlin_i_irr] + # ) + # calibration_data_irr_swir = calibration_data_irr_swir.sel( + # wavdates=wav_times_irr_swir[wav_i_irr] + # ) + # + # else: + # calibration_data_rad = calibration_data_rad.interp(calibrationdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_rad = calibration_data_rad.interp(nonlineardates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_rad = calibration_data_rad.interp(wavdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # + # calibration_data_irr = calibration_data_irr.interp(calibrationdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_irr = calibration_data_irr.interp(nonlineardates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_irr = calibration_data_irr.interp(wavdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # if self.context.get_config_value("network") == "l": + # + # calibration_data_rad_swir = calibration_data_rad_swir.interp(calibrationdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_rad_swir = calibration_data_rad_swir.interp(nonlineardates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_rad_swir = calibration_data_rad_swir.interp(wavdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # + # calibration_data_irr_swir = calibration_data_irr_swir.interp(calibrationdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_irr_swir = calibration_data_irr_swir.interp(nonlineardates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + # calibration_data_irr_swir = calibration_data_irr_swir.interp(wavdates=[sequence_datetime], + # method=self.context.get_config_value( + # "calibration_interpolation_method")) + + if self.context.get_config_value("network") == "l": return ( calibration_data_rad, calibration_data_irr, @@ -312,40 +390,69 @@ def prepare_calibration_data(self, measurandstring, hypstar, swir=False): minwav = 350 for caldatepath in caldatepaths: if measurandstring == "radiance": - calpath = glob.glob( + filelist = glob.glob( os.path.join( caldatepath, "hypstar_" + str(hypstar) + "_radcal_L_*_%s.dat" % (sensortag), ) - )[0] - caldate = calpath[-15:-9] - print(os.path.basename(caldatepath)) - if ("b" in os.path.basename(caldatepath)) or ( - "10C" in os.path.basename(caldatepath) - ): - caldate += "T235959" - elif "a" in os.path.basename(caldatepath): - caldate += "T000000" + ) + if len(filelist) == 1: + calpath = filelist[0] + caldate = calpath[-15:-9] + print(os.path.basename(caldatepath)) + if ("b" in os.path.basename(caldatepath)) or ( + "10C" in os.path.basename(caldatepath) + ): + caldate += "T235959" + elif "a" in os.path.basename(caldatepath): + caldate += "T000000" + else: + caldate += "T120000" + print(caldate) else: - caldate += "T120000" - print(caldate) + warnings.warn( + "the number of files matching %s is not equal to 1: %s" + % ( + os.path.join( + caldatepath, + "hypstar_" + + str(hypstar) + + "_radcal_L_*_%s.dat" % (sensortag), + ), + filelist, + ) + ) else: - calpath = glob.glob( + filelist = glob.glob( os.path.join( caldatepath, "hypstar_" + str(hypstar) + "_radcal_E_*_%s.dat" % (sensortag), ) - )[0] - caldate = calpath[-15:-9] - if ("b" in os.path.basename(caldatepath)) or ( - "10C" in os.path.basename(caldatepath) - ): - caldate += "T235959" - elif "a" in os.path.basename(caldatepath): - caldate += "T000000" + ) + if len(filelist) == 1: + calpath = filelist[0] + caldate = calpath[-15:-9] + if ("b" in os.path.basename(caldatepath)) or ( + "10C" in os.path.basename(caldatepath) + ): + caldate += "T235959" + elif "a" in os.path.basename(caldatepath): + caldate += "T000000" + else: + caldate += "T120000" else: - caldate += "T120000" - + warnings.warn( + "the number of files matching %s is not equal to 1: %s" + % ( + os.path.join( + caldatepath, + "hypstar_" + + str(hypstar) + + "_radcal_E_*_%s.dat" % (sensortag), + ), + filelist, + ) + ) if os.path.exists(calpath): caldates = np.append(caldates, caldate) gains_temp = np.genfromtxt(calpath) @@ -360,44 +467,59 @@ def prepare_calibration_data(self, measurandstring, hypstar, swir=False): for path in glob.glob( os.path.join(directory, "hypstar_" + str(hypstar), "linearity", "*") ) + if ".pdf" not in path ] - if len(lincaldatepaths) == 0: - lincaldatepaths = [ - path - for path in glob.glob( - os.path.join( - directory, "hypstar_" + str(hypstar), "radiometric", "*" - ) + lincaldatepaths += [ + path + for path in glob.glob( + os.path.join( + directory, "hypstar_" + str(hypstar), "radiometric", "*" ) - if len( - glob.glob( - os.path.join( - path, - "hypstar_" + str(hypstar) + "_nonlin_corr_coefs_*.dat", - ) + ) + if len( + glob.glob( + os.path.join( + path, + "hypstar_" + str(hypstar) + "_nonlin_corr_coefs_*.dat", ) ) - > 0 - ] + ) + > 0 + ] nonlindates = [] for lincaldatepath in lincaldatepaths: - nonlinpath = glob.glob( + filelist = glob.glob( os.path.join( lincaldatepath, "hypstar_" + str(hypstar) + "_nonlin_corr_coefs_*.dat", ) - )[0] - lincaldate = nonlinpath[-10:-4] - if ("b" in os.path.basename(lincaldatepath)) or ( - "10C" in os.path.basename(lincaldatepath) - ): - lincaldate += "T235959" - elif "a" in os.path.basename(lincaldatepath): - lincaldate += "T000000" + ) + if len(filelist) == 1: + nonlinpath = filelist[0] + lincaldate = nonlinpath[-10:-4] + if ("b" in os.path.basename(lincaldatepath)) or ( + "10C" in os.path.basename(lincaldatepath) + ): + lincaldate += "T235959" + elif "a" in os.path.basename(lincaldatepath): + lincaldate += "T000000" + else: + lincaldate += "T120000" else: - lincaldate += "T120000" + warnings.warn( + "the number of files matching %s is not equal to 1: %s" + % ( + os.path.join( + caldatepath, + "hypstar_" + + str(hypstar) + + "_radcal_E_*_%s.dat" % (sensortag), + ), + filelist, + ) + ) if os.path.exists(nonlinpath): nonlindates = np.append(nonlindates, lincaldate) @@ -442,12 +564,15 @@ def prepare_calibration_data(self, measurandstring, hypstar, swir=False): i_nonlin = 0 # todo remove [-1] and use all calibrations and interpolate? for lincaldatepath in lincaldatepaths: - nonlinpath = glob.glob( - os.path.join( - lincaldatepath, - "hypstar_" + str(hypstar) + "_nonlin_corr_coefs_*.dat", - ) - )[0] + try: + nonlinpath = glob.glob( + os.path.join( + lincaldatepath, + "hypstar_" + str(hypstar) + "_nonlin_corr_coefs_*.dat", + ) + )[0] + except: + stop if os.path.exists(nonlinpath): if swir: non_linear_cals = np.genfromtxt(nonlinpath)[:, 1] @@ -466,13 +591,13 @@ def prepare_calibration_data(self, measurandstring, hypstar, swir=False): float(line.strip()[8::]) / 2 ) # reading in from comments in non_lin files, and convert to k=1 - calibration_data["non_linearity_coefficients"].values[ - i_nonlin - ] = np.pad( - non_linear_cals, - (0, 13 - len(non_linear_cals)), - "constant", - constant_values=(0, 0), + calibration_data["non_linearity_coefficients"].values[i_nonlin] = ( + np.pad( + non_linear_cals, + (0, 13 - len(non_linear_cals)), + "constant", + constant_values=(0, 0), + ) ) i_nonlin += 1 @@ -502,130 +627,137 @@ def prepare_calibration_data(self, measurandstring, hypstar, swir=False): for caldatepath in caldatepaths: # print(caldatepath,) if measurandstring == "radiance": - calpath = glob.glob( + filelist = glob.glob( os.path.join( caldatepath, "hypstar_" + str(hypstar) + "_radcal_L_*_%s.dat" % (sensortag), ) - )[0] + ) + else: - calpath = glob.glob( + filelist = glob.glob( os.path.join( caldatepath, "hypstar_" + str(hypstar) + "_radcal_E_*_%s.dat" % (sensortag), ) - )[0] + ) - if os.path.exists(calpath): - caldates = np.append(caldates, caldate) - gains = np.genfromtxt(calpath) - wavs = gains[:, 1] - gains = gains[np.where(wavs > 350)[0]] - wavs = wavs[np.where(wavs > 350)[0]] - placeholder_unc = 2 - gainlen = len(calibration_data["wavpix"].values[i_cal, :]) - if True: - # calibration_data["wavelength"].values = gains[:, 1] - calibration_data["wavpix"].values[i_cal, :] = gains[:gainlen, 0] - calibration_data["gains"].values[i_cal, :] = gains[:gainlen, 2] - # calibration_data["u_rel_random_gains"].values = None - - calibration_data["u_rel_systematic_indep_gains"].values[ - i_cal, : - ] = ( - ( - gains[:, 6] ** 2 - + gains[:, 7] ** 2 - + gains[:, 8] ** 2 - + gains[:, 9] ** 2 - + gains[:, 10] ** 2 - + gains[:, 11] ** 2 - + gains[:, 12] ** 2 - + gains[:, 13] ** 2 - + gains[:, 14] ** 2 - + gains[:, 15] ** 2 - + gains[:, 16] ** 2 - + gains[:, 17] ** 2 - + gains[:, 19] ** 2 - + nonlin_unc**2 - + placeholder_unc**2 - ) - ** 0.5 - )[ - :gainlen - ] + if len(filelist) == 1: + calpath = filelist[0] - cov_diag = cm.convert_corr_to_cov( - np.eye(len(gains[:, 2])), gains[:, 2] * (gains[:, 19]) - ) + if os.path.exists(calpath): + caldates = np.append(caldates, caldate) + gains = np.genfromtxt(calpath) + wavs = gains[:, 1] + gains = gains[np.where(wavs > 350)[0]] + wavs = wavs[np.where(wavs > 350)[0]] + placeholder_unc = 2 + gainlen = len(calibration_data["wavpix"].values[i_cal, :]) + if True: + # calibration_data["wavelength"].values = gains[:, 1] + calibration_data["wavpix"].values[i_cal, :] = gains[:gainlen, 0] + calibration_data["gains"].values[i_cal, :] = gains[:gainlen, 2] + # calibration_data["u_rel_random_gains"].values = None + + calibration_data["u_rel_systematic_indep_gains"].values[ + i_cal, : + ] = ( + ( + gains[:, 6] ** 2 + + gains[:, 7] ** 2 + + gains[:, 8] ** 2 + + gains[:, 9] ** 2 + + gains[:, 10] ** 2 + + gains[:, 11] ** 2 + + gains[:, 12] ** 2 + + gains[:, 13] ** 2 + + gains[:, 14] ** 2 + + gains[:, 15] ** 2 + + gains[:, 16] ** 2 + + gains[:, 17] ** 2 + + gains[:, 19] ** 2 + + nonlin_unc**2 + + placeholder_unc**2 + ) + ** 0.5 + )[ + :gainlen + ] + + cov_diag = cm.convert_corr_to_cov( + np.eye(len(gains[:, 2])), gains[:, 2] * (gains[:, 19]) + ) - cov_other = cm.convert_corr_to_cov( - np.eye(len(gains[:, 2])), - gains[:, 2] - * ( - gains[:, 8] ** 2 - + gains[:, 10] ** 2 - + gains[:, 11] ** 2 - + gains[:, 16] ** 2 - + gains[:, 17] ** 2 - + nonlin_unc**2 + cov_other = cm.convert_corr_to_cov( + np.eye(len(gains[:, 2])), + gains[:, 2] + * ( + gains[:, 8] ** 2 + + gains[:, 10] ** 2 + + gains[:, 11] ** 2 + + gains[:, 16] ** 2 + + gains[:, 17] ** 2 + + nonlin_unc**2 + ) + ** 0.5, ) - ** 0.5, - ) - cov_full = cm.convert_corr_to_cov( - np.ones((len(gains[:, 2]), len(gains[:, 2]))), - gains[:, 2] - * ( - gains[:, 7] ** 2 - + gains[:, 9] ** 2 - + gains[:, 12] ** 2 - + gains[:, 13] ** 2 - + gains[:, 14] ** 2 - + gains[:, 15] ** 2 - + placeholder_unc**2 + cov_full = cm.convert_corr_to_cov( + np.ones((len(gains[:, 2]), len(gains[:, 2]))), + gains[:, 2] + * ( + gains[:, 7] ** 2 + + gains[:, 9] ** 2 + + gains[:, 12] ** 2 + + gains[:, 13] ** 2 + + gains[:, 14] ** 2 + + gains[:, 15] ** 2 + + placeholder_unc**2 + ) + ** 0.5, ) - ** 0.5, - ) - cov_filament = cm.convert_corr_to_cov( - np.ones((len(gains[:, 2]), len(gains[:, 2]))), - gains[:, 2] * (gains[:, 6] ** 2) ** 0.5, - ) + cov_filament = cm.convert_corr_to_cov( + np.ones((len(gains[:, 2]), len(gains[:, 2]))), + gains[:, 2] * (gains[:, 6] ** 2) ** 0.5, + ) - calibration_data["err_corr_systematic_indep_gains"].values[ - i_cal, :, : - ] = cm.correlation_from_covariance( - cov_diag + cov_other + cov_full + cov_filament - )[ - :gainlen, :gainlen - ] - - calibration_data["u_rel_systematic_corr_rad_irr_gains"].values[ - i_cal, : - ] = ( - (gains[:, 4] ** 2 + gains[:, 5] ** 2 + gains[:, 18] ** 2) ** 0.5 - )[ - :gainlen - ] - - cov_other = cm.convert_corr_to_cov( - np.eye(len(gains[:, 2])), - gains[:, 2] * (gains[:, 4] ** 2 + gains[:, 18] ** 2) ** 0.5, - ) + calibration_data["err_corr_systematic_indep_gains"].values[ + i_cal, :, : + ] = cm.correlation_from_covariance( + cov_diag + cov_other + cov_full + cov_filament + )[ + :gainlen, :gainlen + ] + + calibration_data["u_rel_systematic_corr_rad_irr_gains"].values[ + i_cal, : + ] = ( + (gains[:, 4] ** 2 + gains[:, 5] ** 2 + gains[:, 18] ** 2) + ** 0.5 + )[ + :gainlen + ] + + cov_other = cm.convert_corr_to_cov( + np.eye(len(gains[:, 2])), + gains[:, 2] * (gains[:, 4] ** 2 + gains[:, 18] ** 2) ** 0.5, + ) - cov_filament = cm.convert_corr_to_cov( - np.ones((len(gains[:, 2]), len(gains[:, 2]))), - gains[:, 2] * (gains[:, 5] ** 2) ** 0.5, - ) + cov_filament = cm.convert_corr_to_cov( + np.ones((len(gains[:, 2]), len(gains[:, 2]))), + gains[:, 2] * (gains[:, 5] ** 2) ** 0.5, + ) - calibration_data["err_corr_systematic_corr_rad_irr_gains"].values[ - i_cal, :, : - ] = cm.correlation_from_covariance(cov_other + cov_filament)[ - :gainlen, :gainlen - ] - # except: - # print(caldatepath, " failed") + calibration_data[ + "err_corr_systematic_corr_rad_irr_gains" + ].values[i_cal, :, :] = cm.correlation_from_covariance( + cov_other + cov_filament + )[ + :gainlen, :gainlen + ] + # except: + # print(caldatepath, " failed") i_cal += 1 return calibration_data diff --git a/hypernets_processor/calibration/calibration_files/HYPSTAR_cal/hypstar_120241/HYPERNETS_CAL_HYPSTAR_120241_IRR_v2.0.nc b/hypernets_processor/calibration/calibration_files/HYPSTAR_cal/hypstar_120241/HYPERNETS_CAL_HYPSTAR_120241_IRR_v2.1.nc similarity index 97% rename from hypernets_processor/calibration/calibration_files/HYPSTAR_cal/hypstar_120241/HYPERNETS_CAL_HYPSTAR_120241_IRR_v2.0.nc rename to hypernets_processor/calibration/calibration_files/HYPSTAR_cal/hypstar_120241/HYPERNETS_CAL_HYPSTAR_120241_IRR_v2.1.nc index 48fe7422..7cbfa385 100644 Binary files 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