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Commit 348c3582 authored by holukas's avatar holukas
Browse files

More data blocks

parent 41214867
......@@ -2,9 +2,15 @@
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<change afterPath="$PROJECT_DIR$/bico/settings/data_blocks/IRGA75-A-GN1.md" afterDir="false" />
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<change beforePath="$PROJECT_DIR$/bico/ops/setup.py" beforeDir="false" afterPath="$PROJECT_DIR$/bico/ops/setup.py" afterDir="false" />
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<change beforePath="$PROJECT_DIR$/bico/settings/Bico.settings" beforeDir="false" afterPath="$PROJECT_DIR$/bico/settings/Bico.settings" afterDir="false" />
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<change beforePath="$PROJECT_DIR$/bico/settings/_version.py" beforeDir="false" afterPath="$PROJECT_DIR$/bico/settings/_version.py" afterDir="false" />
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<option name="HIGHLIGHT_CONFLICTS" value="true" />
......@@ -44,7 +50,7 @@
<property name="RunOnceActivity.OpenProjectViewOnStart" value="true" />
<property name="SHARE_PROJECT_CONFIGURATION_FILES" value="true" />
<property name="WebServerToolWindowFactoryState" value="false" />
<property name="last_opened_file_path" value="$PROJECT_DIR$/bico/settings/data_blocks/infrared_gas_analyzers" />
<property name="last_opened_file_path" value="$PROJECT_DIR$/bico/settings/data_blocks" />
<property name="nodejs_interpreter_path.stuck_in_default_project" value="undefined stuck path" />
<property name="nodejs_npm_path_reset_for_default_project" value="true" />
<property name="restartRequiresConfirmation" value="false" />
......@@ -52,11 +58,11 @@
</component>
<component name="RecentsManager">
<key name="CopyFile.RECENT_KEYS">
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks" />
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks\infrared_gas_analyzers" />
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks\sonic_anemometers" />
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks\laser_gas_analyzers" />
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks\header" />
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\ops" />
</key>
<key name="MoveFile.RECENT_KEYS">
<recent name="L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings\data_blocks" />
......@@ -287,7 +293,14 @@
<workItem from="1607812206779" duration="8920000" />
<workItem from="1607939225501" duration="15331000" />
<workItem from="1607988216099" duration="18000" />
<workItem from="1607988810219" duration="607000" />
<workItem from="1607988810219" duration="1298000" />
<workItem from="1608126300896" duration="803000" />
<workItem from="1608566771229" duration="18000" />
<workItem from="1608929398045" duration="123000" />
<workItem from="1608929567337" duration="2985000" />
<workItem from="1609065970989" duration="8000" />
<workItem from="1609110762183" duration="1238000" />
<workItem from="1609331721109" duration="6020000" />
</task>
<servers />
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......@@ -296,23 +309,6 @@
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<component name="XDebuggerManager">
<breakpoint-manager>
<breakpoints>
<line-breakpoint enabled="true" suspend="THREAD" type="python-line">
<url>file://$PROJECT_DIR$/bico/ops/vis.py</url>
<line>10</line>
<option name="timeStamp" value="1" />
</line-breakpoint>
<line-breakpoint enabled="true" suspend="THREAD" type="python-line">
<url>file://$PROJECT_DIR$/bico/bico.py</url>
<line>369</line>
<option name="timeStamp" value="2" />
</line-breakpoint>
<line-breakpoint enabled="true" suspend="THREAD" type="python-line">
<url>file://$PROJECT_DIR$/bico/ops/vis.py</url>
<line>175</line>
<option name="timeStamp" value="4" />
</line-breakpoint>
</breakpoints>
<default-breakpoints>
<breakpoint type="python-exception">
<properties notifyOnTerminate="true" exception="BaseException">
......@@ -330,7 +326,7 @@
<SUITE FILE_PATH="coverage/BICO$main.coverage" NAME="bico Coverage Results" MODIFIED="1598258463691" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/bico" />
<SUITE FILE_PATH="coverage/BICO_Binary_Converter$gui.coverage" NAME="gui Coverage Results" MODIFIED="1606435918815" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/bico" />
<SUITE FILE_PATH="coverage/BICO_Binary_Converter$main.coverage" NAME="main Coverage Results" MODIFIED="1596498134562" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/bico" />
<SUITE FILE_PATH="coverage/BICO_Binary_Converter$start_bico.coverage" NAME="start_bico Coverage Results" MODIFIED="1607989420103" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/bico" />
<SUITE FILE_PATH="coverage/BICO_Binary_Converter$start_bico.coverage" NAME="start_bico Coverage Results" MODIFIED="1609334088654" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/bico" />
<SUITE FILE_PATH="coverage/BICO_Binary_Converter$example.coverage" NAME="example Coverage Results" MODIFIED="1606348759035" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/example" />
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\ No newline at end of file
......@@ -169,7 +169,7 @@ class Ui_MainWindow(object):
# Data Blocks
sonic_anemometers = ['HS50-A', 'HS50-B', 'HS100-A','R350-A', '-None-']
gas_analyzers = ['IRGA72-A', 'IRGA72-B', 'IRGA75-A', 'LGR-A', 'QCL-C', '-None-']
gas_analyzers = ['IRGA72-A', 'IRGA72-B', 'IRGA75-A', 'IRGA75-A-GN1', 'LGR-A', 'QCL-C', '-None-']
header_instr_data_blocks = qtw.QLabel('Data Blocks')
header_instr_data_blocks.setProperty('labelClass', 'header_2')
......
......@@ -28,7 +28,7 @@ def make_run_outdirs(settings_dict):
"""Set output paths and create output folders"""
# Run output folder
# settings_dict['dir_out_run'] = Path(settings_dict['dir_out']) / "TEST_OUT"
# settings_dict['dir_out_run'] = Path(settings_dict['dir_out']) / "BICO_TEST_OUT"
settings_dict['dir_out_run'] = Path(settings_dict['dir_out']) / settings_dict['run_id'] # todo act
if not Path.is_dir(settings_dict['dir_out_run']):
print(f"Creating folder {settings_dict['dir_out_run']} ...")
......
......@@ -167,7 +167,7 @@ def high_res_histogram(df, outfile, outdir, logger):
size=8, color='black', backgroundcolor='none', zorder=100)
col_idx = -1
for col in dblock_df.columns:
print(f"HIST {col}")
# print(f"HIST {col}")
col_idx += 1
ax = axes[col_idx]
......@@ -261,6 +261,7 @@ def high_res_ts(df, outfile, outdir, logger):
fig.savefig(f"{dblock_outfile}.png", format='png', bbox_inches='tight', facecolor='w',
transparent=True, dpi=150)
def check_plot_data(ax, df, col):
dataok = False
isnumeric = False if df[col].dtypes == object else True
......@@ -303,6 +304,7 @@ def check_plot_data(ax, df, col):
size=14, color='white', backgroundcolor=facecolor)
return dataok
def _format_spines(ax, color, lw):
spines = ['top', 'bottom', 'left', 'right']
for spine in spines:
......
run_id=BICO-20201228-001616
# INSTRUMENTS
# ===========
# Site
site=CH-AES
# Data Blocks
header=WECOM3
instrument_1=R350-A
instrument_2=IRGA75-A
instrument_3=LGR-A
# RAW DATA
# ========
# Source Folder
dir_source=Y:/CH-INO_InnoFarm/20_sonic_ghg/2020/06
# Time Range
start_date=2020-06-01 00:00
end_date=2020-06-02 00:00
# File Settings
filename_datetime_format=yyyymmddHH.XMM
file_ext=*.X*
file_size_min=900
file_limit=0
row_limit=0
# Special
select_random_files=0
# OUTPUT
# ======
dir_out=A:/FLUXES/x-TEST-OUT
dir_out_run=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608
dir_out_run_log=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\log
dir_out_run_plots=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots
dir_out_run_plots_hires=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots\hires
dir_out_run_plots_agg=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots\agg
dir_out_run_raw_data_csv=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\raw_data_csv
file_compression=gzip
plot_file_availability=1
plot_ts_hires=1
plot_histogram_hires=1
plot_ts_agg=1
# DIRECTORIES
# ===================
dir_bico=L:\Dropbox\luhk_work\programming\BICO_Binary_Converter
dir_script=L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico
dir_settings=L:\Dropbox\luhk_work\programming\BICO_Binary_Converter\bico\settings
dir_root=L:\Dropbox\luhk_work\programming
dir_server_CH-AES=
dir_server_CH-AWS=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-AWS_CrapAlv\20_sonic_ghg
dir_server_CH-CHA=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-CHA_Chamau\20_sonic_ghg
dir_server_CH-DAE=
dir_server_CH-DAV=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-DAV_Davos\20_sonic_ghg
dir_server_CH-FRU=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-FRU_Fruebuel\20_sonic_ghg
dir_server_CH-INO=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-INO_InnoFarm\20_sonic_ghg
dir_server_CH-LAE=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-LAE_Laegeren\20_sonic_ghg
dir_server_CH-LAS=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-LAS_Lae-Subcanopy\20_sonic_ghg
dir_server_CH-OE2=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\CH-OE2_Oensingen\20_sonic_ghg
dir_server_CH-TWE=\\green.ethz.ch\share-green-gl-archive-1-$\FluxData\US-TWE_ToolikWetland\20_sonic_ghg
run_id=BICO-20201215-004608
run_id=BICO-20201230-141449
# INSTRUMENTS
# ===========
......@@ -9,40 +9,40 @@ site=CH-AES
# Data Blocks
header=WECOM3
instrument_1=R350-A
instrument_2=IRGA75-A
instrument_2=IRGA75-A-GN1
instrument_3=LGR-A
# RAW DATA
# ========
# Source Folder
dir_source=Y:/CH-INO_InnoFarm/20_sonic_ghg/2020/08
dir_source=Y:/CH-INO_InnoFarm/20_sonic_ghg/2020/06
# Time Range
start_date=2020-06-01 13:00
end_date=2020-12-31 00:00
start_date=2020-06-01 00:00
end_date=2020-06-02 00:00
# File Settings
filename_datetime_format=yyyymmddHH.XMM
file_ext=*.X*
file_size_min=900
file_limit=1
row_limit=10000
row_limit=0
# Special
select_random_files=0
# OUTPUT
# ======
dir_out=P:/Flux/RDS_calculations/INO/AES/BICO
dir_out_run=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608
dir_out_run_log=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\log
dir_out_run_plots=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots
dir_out_run_plots_hires=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots\hires
dir_out_run_plots_agg=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\plots\agg
dir_out_run_raw_data_csv=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004608\raw_data_csv
dir_out=A:/FLUXES/x-TEST-OUT
dir_out_run=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449
dir_out_run_log=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449\plots\agg
dir_out_run_raw_data_csv=A:\FLUXES\x-TEST-OUT\BICO-20201230-141449\raw_data_csv
file_compression=None
file_compression=gzip
plot_file_availability=1
plot_ts_hires=1
......
run_id=BICO-20201215-004342
run_id=BICO-20201230-141143
# INSTRUMENTS
# ===========
......@@ -16,33 +16,33 @@ instrument_3=LGR-A
# ========
# Source Folder
dir_source=Y:/CH-INO_InnoFarm/20_sonic_ghg/2020/08
dir_source=Y:/CH-INO_InnoFarm/20_sonic_ghg/2020/06
# Time Range
start_date=2020-06-01 13:00
end_date=2020-12-31 00:00
start_date=2020-06-01 00:00
end_date=2020-06-02 00:00
# File Settings
filename_datetime_format=yyyymmddHH.XMM
file_ext=*.X*
file_size_min=900
file_limit=1
row_limit=10000
row_limit=0
# Special
select_random_files=0
# OUTPUT
# ======
dir_out=P:/Flux/RDS_calculations/INO/AES/BICO
dir_out_run=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342
dir_out_run_log=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342\log
dir_out_run_plots=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342\plots
dir_out_run_plots_hires=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342\plots\hires
dir_out_run_plots_agg=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342\plots\agg
dir_out_run_raw_data_csv=P:\Flux\RDS_calculations\INO\AES\BICO\BICO-20201215-004342\raw_data_csv
dir_out=A:/FLUXES/x-TEST-OUT
dir_out_run=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143
dir_out_run_log=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143\plots\agg
dir_out_run_raw_data_csv=A:\FLUXES\x-TEST-OUT\BICO-20201230-141143\raw_data_csv
file_compression=None
file_compression=gzip
plot_file_availability=1
plot_ts_hires=1
......
__version__ = "0.0.2"
__date__ = "15 Dec 2020"
__date__ = "31 Dec 2020"
__link_source_code__ = "https://gitlab.ethz.ch/holukas/bico"
__link_releases__ = "https://gitlab.ethz.ch/holukas/bico/-/releases"
__link_wiki__ = "https://gitlab.ethz.ch/holukas/bico/-/wikis/home"
......
# ====================================
# IRGA75-A-GN1 - INFRARED GAS ANALYZER
# ====================================
DATA_SIZE == {'order': 1, 'bytes': 1, 'format': 'B', 'gain_on_signal': 1, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'Bytes', 'datablock': 'IRGA75-A'}
STATUS_CODE == {'order': 2, 'bytes': 1, 'format': 'B', 'gain_on_signal': 1, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'octal', 'datablock': 'IRGA75-A'}
DIAG_VAL == {'order': 3, 'bytes': 1, 'format': 'B', 'gain_on_signal': 1, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'bit_map', 'datablock': 'IRGA75-A'}
H2O_CONC == {'order': 4, 'bytes': 3, 'format': 'B B B', 'gain_on_signal': 1000, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'mmol+1 m-3', 'datablock': 'IRGA75-A'}
CO2_CONC == {'order': 5, 'bytes': 3, 'format': 'B B B', 'gain_on_signal': 10000, 'offset_on_signal': 0, 'apply_gain': 0.974, 'add_offset': 0, 'units': 'mmol+1 m-3', 'datablock': 'IRGA75-A'}
T_BOX == {'order': 6, 'bytes': 2, 'format': 'B B', 'gain_on_signal': 100, 'offset_on_signal': 100, 'apply_gain': 1, 'add_offset': 0, 'units': 'degC', 'datablock': 'IRGA75-A'}
PRESS_BOX == {'order': 7, 'bytes': 2, 'format': 'B B', 'gain_on_signal': 10, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'hPa', 'datablock': 'IRGA75-A'}
COOLER_V == {'order': 8, 'bytes': 3, 'format': 'B B B', 'gain_on_signal': 10000, 'offset_on_signal': 0, 'apply_gain': 1, 'add_offset': 0, 'units': 'V', 'datablock': 'IRGA75-A'}
# Values extracted from DIAG_VAL:
# --------------------------------------
AGC == {'order': 3.04, 'bit_pos_start': 0, 'bit_pos_end': 3, 'apply_gain': 6.25, 'add_offset': 6.25, 'units': '%', 'output': 1, 'datablock': 'IRGA75-A'}
SYNC == {'order': 3.05, 'bit_pos_start': 4, 'bit_pos_end': 5, 'apply_gain': 1, 'add_offset': 0, 'units': '1=OK', 'output': 0, 'datablock': 'IRGA75-A'}
PLL == {'order': 3.06, 'bit_pos_start': 5, 'bit_pos_end': 6, 'apply_gain': 1, 'add_offset': 0, 'units': '1=OK', 'output': 0, 'datablock': 'IRGA75-A'}
DETECTOR == {'order': 3.07, 'bit_pos_start': 6, 'bit_pos_end': 7, 'apply_gain': 1, 'add_offset': 0, 'units': '1=OK', 'output': 0, 'datablock': 'IRGA75-A'}
CHOPPER == {'order': 3.08, 'bit_pos_start': 7, 'bit_pos_end': 8, 'apply_gain': 1, 'add_offset': 0, 'units': '1=OK', 'output': 0, 'datablock': 'IRGA75-A'}
# IRGA75-A-GN1
Based on IRGA75-A but with a different gain on CO2_CONC.
## Variables
- DATA_SIZE ... Data size of current data block, number of bytes in Licor 7500 record
(2 = missing, 16 = available)
- STATUS_CODE ... Status of IRGA data aquisition, see Table 7 in WE's sonicread.pdf
- octal value converted to integer yields:
- 0 .. Status OK, no problems (octal 0000)
- 20 .. IRGA did not respond (0020)
- 40 .. Status OK, old data used (0040)
- 200 .. not OK, IRGA data are missing (0200)
- GA_DIAG_CODE ... IRGA diagnostic value
- The cell diagnostic value is a 1 byte unsigned integer (value between 0 and 255) with the following bit map (in order of how the code reads it, orig bit position in brackets):
- (7) CHOPPER: 1 = OK
- (6) DETECTOR: 1 = OK
- (5) PLL: 1 = OK
- (4) SYNC: 1 = OK
- (3,2,1,0) AGC: 100% = bad (generally true, but check data files for exceptions), automatic gain control, window dirtiness, signal strength
- 'output': 1 means that the var is written to the output stream of this data block, i.e. included in the
output file.
- H2O_CONC ... H2O concentration density, molar density
- CO2_CONC ... CO2 concentration density, molar density
**A GAIN of 0.974 is applied to this signal to correct for the usage of a wrong calibration gas.
For more info, see here: https://www.swissfluxnet.ethz.ch/index.php/knowledge-base/wrong-calibration-gas-2017/**
- T_BOX ... Ambient temperature measured in the control box
- P_BOX ... Atmospheric pressure measured in the control box
- COOLER_V ... Cooler voltage
## BICO Settings
- 'order' ... Order in the data block variable sequence
- 'bytes' ... Number of bytes in the binary data
- 'format' ... Format to convert from binary to integers, floats, etc.
- 'gain_on_signal' ... Gain that was applied to the raw data signal, to get to units *divide* by this gain
- 'offset_on_signal' ... Offset that was added to the raw data signal, to get to units *subtract* this offset
- 'apply_gain' ... Gain that is applied during conversion, e.g. to convert to different units if needed
- 'add_offset' ... Offset that is added during conversion, e.g. to convert to different units if needed
- 'units' ... Units
- 'datablock' ... Data block ID
*Before BICO, the binary conversion was done in FCT FluxCalcTool:*
- Old ID in FCT: li-7500_co2_gain0974
- Old data block in FCT: data_block_irga_li7500_co2_gain0974
- FCT Source code: --> https://gitlab.ethz.ch/holukas/fct-flux-calculation-tool
## Details
Please see IRGA75-A.md for more info on the LI-7500.
## Binary info
- B...unsigned char, integer, 1 Byte
- h...short integer, 2 Bytes
- ">"...big-endian, MSB most-significant Byte at lowest address
Big-endian systems store the most significant byte of a word in the smallest address
- --> https://docs.python.org/3/library/struct.html
- --> https://docs.python.org/3.1/library/struct.html#format-characters
\ No newline at end of file
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