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Commit a63bb0df authored by holukas's avatar holukas
Browse files

Minor modifications

parent 112d13cd
......@@ -2,6 +2,12 @@
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......@@ -65,20 +71,20 @@
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<configuration name="_test" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
<module name="BICO_Binary_Converter" />
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs>
<env name="PYTHONUNBUFFERED" value="1" />
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<option name="SDK_HOME" value="C:\Users\holukas\Anaconda3\envs\BICOFLUXRUN1\python.exe" />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/bico" />
<option name="IS_MODULE_SDK" value="false" />
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<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/bico/bico.py" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/bico/_test.py" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="false" />
<option name="EMULATE_TERMINAL" value="false" />
......@@ -88,17 +94,17 @@
<method v="2" />
</configuration>
<configuration name="bico" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
<module name="BICO_Binary_Converter" />
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<envs>
<env name="PYTHONUNBUFFERED" value="1" />
</envs>
<option name="SDK_HOME" value="C:\Users\holukas\Anaconda3\envs\BICO1\python.exe" />
<option name="SDK_HOME" value="C:\Users\holukas\Anaconda3\envs\BICOFLUXRUN1\python.exe" />
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/bico" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="" />
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<option name="SCRIPT_NAME" value="$PROJECT_DIR$/bico/bico.py" />
<option name="PARAMETERS" value="" />
......@@ -109,20 +115,20 @@
<option name="INPUT_FILE" value="" />
<method v="2" />
</configuration>
<configuration name="example" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
<module name="BICO_Binary_Converter" />
<configuration name="bico" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
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<envs>
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<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/example" />
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<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<module name="" />
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/example/example.py" />
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/bico/bico.py" />
<option name="PARAMETERS" value="" />
<option name="SHOW_COMMAND_LINE" value="false" />
<option name="EMULATE_TERMINAL" value="false" />
......@@ -199,18 +205,18 @@
</configuration>
<list>
<item itemvalue="Python.bico" />
<item itemvalue="Python.example" />
<item itemvalue="Python.gui" />
<item itemvalue="Python.gui (1)" />
<item itemvalue="Python.start_bico" />
<item itemvalue="Python._test" />
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<item itemvalue="Python.gui (1)" />
<item itemvalue="Python.gui" />
<item itemvalue="Python.example" />
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......@@ -324,6 +330,9 @@
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......@@ -332,6 +341,23 @@
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<url>file://$PROJECT_DIR$/bico/ops/bin.py</url>
<line>124</line>
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<line-breakpoint enabled="true" suspend="THREAD" type="python-line">
<url>file://$PROJECT_DIR$/bico/ops/bin.py</url>
<line>151</line>
<option name="timeStamp" value="8" />
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<line-breakpoint enabled="true" suspend="THREAD" type="python-line">
<url>file://$PROJECT_DIR$/bico/ops/bin.py</url>
<line>158</line>
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......@@ -343,13 +369,14 @@
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\ No newline at end of file
import gzip
import datetime as dt
import gzip
import os
import sys
from pathlib import Path
......@@ -13,7 +13,7 @@ from PyQt5 import QtWidgets as qtw
import ops.logger
import ops.setup
from gui.gui import Ui_MainWindow
from ops import bin, format_data, vis, file, stats
from ops import bin, vis, file, stats
from settings import _version
......
,"('U', '[m+1 s-1]', '[R350-A]')","('V', '[m+1 s-1]', '[R350-A]')","('W', '[m+1 s-1]', '[R350-A]')","('T_SONIC', '[K]', '[R350-A]')","('INC_X', '[deg]', '[R350-A]')","('INC_Y', '[deg]', '[R350-A]')","('DATA_SIZE', '[Bytes]', '[IRGA75-A]')","('STATUS_CODE', '[status_code_irga]', '[IRGA75-A]')","('GA_DIAG_CODE', '[bit_map]', '[IRGA75-A]')","('AGC', '[%]', '[IRGA75-A]')","('H2O_CONC', '[mmol+1 m-3]', '[IRGA75-A]')","('CO2_CONC', '[mmol+1 m-3]', '[IRGA75-A]')","('T_BOX', '[degC]', '[IRGA75-A]')","('PRESS_BOX', '[hPa]', '[IRGA75-A]')","('COOLER_V', '[V]', '[IRGA75-A]')","('DATA_SIZE', '[Bytes]', '[QCL-A2]')","('STATUS_CODE', '[bit_map]', '[QCL-A2]')","('STATUS', '[0=OK]', '[QCL-A2]')","('CH4_DRY', '[nmol+1 mol-1]', '[QCL-A2]')","('N2O_DRY', '[nmol+1 mol-1]', '[QCL-A2]')","('CH4', '[nmol+1 mol-1]', '[QCL-A2]')","('T_CELL', '[K]', '[QCL-A2]')","('PRESS_CELL', '[Torr]', '[QCL-A2]')"
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,-0.5,0.32,0.03,284.56,0.0,1.86,16.0,0,255.0,50.0,243.577,5.929,-1.8400000000000034,971.0,1.1365,2.0,104.0,-9999,-9999,-9999,-9999,-9999,-9999
0,-0.49,0.29,0.03,284.58,0.0,1.86,16.0,0,255.0,50.0,243.03,5.9696,-1.8499999999999943,971.0,1.1365,2.0,104.0,,,,,,
1,-0.5,0.27,0.04,284.57,0.0,1.86,16.0,0,255.0,50.0,243.48,5.984,-1.8499999999999943,971.0,1.1375,2.0,104.0,,,,,,
2,-0.49,0.26,0.03,284.58,0.0,1.86,16.0,0,255.0,50.0,243.94799999999998,6.0048,-1.8700000000000043,971.0,1.1385,2.0,104.0,,,,,,
3,-0.5,0.27,0.04,284.57,0.0,1.86,16.0,0,255.0,50.0,243.793,6.0093,-1.8700000000000043,971.0,1.138,2.0,104.0,,,,,,
4,-0.49,0.26,0.06,284.56,0.0,1.86,16.0,0,255.0,50.0,243.977,5.9851,-1.8700000000000043,971.0,1.1375,2.0,104.0,,,,,,
5,-0.51,0.27,0.08,284.56,0.0,1.86,16.0,0,255.0,50.0,244.525,5.9670000000000005,-1.8499999999999943,971.0,1.137,2.0,104.0,,,,,,
6,-0.48,0.25,0.09,284.56,0.0,1.86,16.0,0,255.0,50.0,244.338,5.959,-1.8400000000000036,971.0,1.138,2.0,104.0,,,,,,
7,-0.51,0.28,0.08,284.54,0.0,1.86,16.0,0,255.0,50.0,244.236,5.9803,-1.8599999999999997,971.0,1.138,2.0,104.0,,,,,,
......@@ -138,12 +138,23 @@ class ReadFile:
dblock_vars_read = 0
end_of_data_reached = False
# for var, props in dblock.items():
# if 'DATA_SIZE' in var:
# check=True
for var, props in dblock.items():
if 'bit_pos_start' in props.keys(): # Skip bit map variables, will be extracted later
continue
varbytes = self.open_binary.read(props['bytes']) # Read Bytes for current var
# tic = time.time()
# much=int(10000000)
# for i in range(0, much):
# self.open_binary.read(100)
# print(time.time()-tic)
# Check if end of data
end_of_data_reached = self.check_if_end_of_data(varbytes=varbytes,
required_varbytes=props['bytes'])
......@@ -156,7 +167,14 @@ class ReadFile:
dblock_vars_read += 1
# Get var value
var_val = self.get_var_val(var=var, props=props, varbytes=varbytes)
var_val = self.get_var_val(var=var, varbytes=varbytes,
gain_on_signal=props['gain_on_signal'],
offset_on_signal=props['offset_on_signal'],
apply_gain=props['apply_gain'],
add_offset=props['add_offset'],
conversion_type=props['conversion_type'],
datablock=props['datablock'],
format=props['format'])
# Check if variable gives data block size info
if 'DATA_SIZE' in var:
......@@ -178,7 +196,7 @@ class ReadFile:
# then stop this data block and return.
# Convert to hex or octal if needed
var_val = self.convert_val(props=props, var_val=var_val)
var_val = self.convert_val(units=props['units'], var_val=var_val)
# Add value to data
dblock_data.append(var_val)
......@@ -198,7 +216,7 @@ class ReadFile:
break
# Convert to hex or octal if needed
var_val = self.convert_val(props=props, var_val=var_val)
var_val = self.convert_val(units=props['units'], var_val=var_val)
# Add value to data
dblock_data.append(var_val)
......@@ -206,20 +224,20 @@ class ReadFile:
# Extract variables from bit map
if props['units'] == 'bit_map':
bit_map_vals = self.extract_bit_map(var_val=var_val,
props=props,
num_bytes=props['bytes'],
dblock=dblock)
for bmv in bit_map_vals:
dblock_data.append(bmv)
return dblock_data, end_of_data_reached
def convert_val(self, props, var_val):
def convert_val(self, units, var_val):
"""Convert var value to hex or octal"""
if props['units'] == 'diag_val_hs':
if units == 'diag_val_hs':
var_val = self.convert_val_to_diag_val_hs(var_val=var_val)
if props['units'] == 'status_code_irga':
if units == 'status_code_irga':
var_val = self.convert_val_to_status_code_irga(var_val=var_val)
if props['units'] == 'status_code_lgr':
if units == 'status_code_lgr':
var_val = self.convert_val_to_status_code_lgr(var_val=var_val)
return var_val
......@@ -298,9 +316,9 @@ class ReadFile:
# return var_val_int
return status_code
def extract_bit_map(self, var_val, props, dblock):
def extract_bit_map(self, var_val, num_bytes, dblock):
"""Extract multiple variables from one bit map variable"""
var_binary_string = self.bit_map_var_to_bin(var_val=var_val, num_bytes=props['bytes'])
var_binary_string = self.bit_map_var_to_bin(var_val=var_val, num_bytes=num_bytes)
bit_map_dict = self.bit_map_get_vars(dblock=dblock)
bit_map_vals = self.bit_map_extract_vals(bit_map_dict=bit_map_dict,
var_binary_string=var_binary_string)
......@@ -356,18 +374,20 @@ class ReadFile:
return end_of_data_reached
def get_var_val(self, var, props, varbytes):
dblock_struct = struct.Struct(props['format']) # Define format of read bytes
def get_var_val(self, var, varbytes, gain_on_signal, offset_on_signal,
apply_gain, add_offset, conversion_type, datablock, format):
dblock_struct = struct.Struct(format) # Define format of read bytes
dblock_unpacked = dblock_struct.unpack(varbytes)
var_val = self.convert_bytes_to_value(unpacked_data=dblock_unpacked)
if props['conversion_type'] == 'regular':
var_val = self.remove_gain_offset(var_value=var_val, gain=props['gain_on_signal'],
offset=props['offset_on_signal'])
var_val = self.apply_gain_offset(var_value=var_val, gain=props['apply_gain'], offset=props['add_offset'])
if conversion_type == 'regular':
var_val = self.remove_gain_offset(var_value=var_val,
gain=gain_on_signal,
offset=offset_on_signal)
var_val = self.apply_gain_offset(var_value=var_val, gain=apply_gain, offset=add_offset)
elif props['conversion_type'] == 'exception':
if (props['datablock'] == 'R2-A') & (var == 'T_SONIC'):
elif conversion_type == 'exception':
if (datablock == 'R2-A') & (var == 'T_SONIC'):
var_val = bce.dblock_r2a_t_sonic(var_val=var_val)
else:
......
run_id=BICO-20210112-235248
run_id=BICO-20210113-124047
# INSTRUMENTS
# ===========
# Site
site=CH-CHA
site=CH-DAV
# Data Blocks
header=WECOM3
instrument_1=R350-A
instrument_2=IRGA75-A
instrument_3=QCL-A
instrument_1=HS100-A
instrument_2=IRGA72-A
instrument_3=QCL-C
# RAW DATA
# ========
# Source Folder
dir_source=Y:/CH-CHA_Chamau/20_sonic_ghg/2020/06
dir_source=Y:/CH-DAV_Davos/20_sonic_ghg/2020/09/20_HS_LI72
# Time Range
start_date=2020-06-01 06:00
end_date=2020-06-03 23:00
start_date=2020-09-23 06:00
end_date=2020-09-30 23:00
# File Settings
filename_datetime_format=yyyymmddHH.CMM
file_ext=*.C*
filename_datetime_format=yyyymmddHH.XMM
file_ext=*.X*
file_size_min=900
file_limit=0
file_limit=1
row_limit=0
# Special
......@@ -35,15 +35,15 @@ select_random_files=0
# OUTPUT
# ======
dir_out=A:/FLUXES/x-TEST-OUT
dir_out_run=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248
dir_out_run_log=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248\plots\agg
dir_out_run_raw_data_ascii=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235248\raw_data_ascii
dir_out_run=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047
dir_out_run_log=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots\agg
dir_out_run_raw_data_ascii=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\raw_data_ascii
output_folder_name_prefix=CHA
file_compression=gzip
output_folder_name_prefix=DAV
file_compression=None
plot_file_availability=0
plot_ts_hires=0
......
run_id=BICO-20210112-235241
run_id=BICO-20210113-124047
# INSTRUMENTS
# ===========
# Site
site=CH-CHA
site=CH-DAV
# Data Blocks
header=WECOM3
instrument_1=R350-A
instrument_2=IRGA75-A
instrument_3=QCL-A
instrument_1=HS100-A
instrument_2=IRGA72-A
instrument_3=QCL-C
# RAW DATA
# ========
# Source Folder
dir_source=Y:/CH-CHA_Chamau/20_sonic_ghg/2020/06
dir_source=Y:/CH-DAV_Davos/20_sonic_ghg/2020/09/20_HS_LI72
# Time Range
start_date=2020-06-01 06:00
end_date=2020-06-03 23:00
start_date=2020-09-23 06:00
end_date=2020-09-30 23:00
# File Settings
filename_datetime_format=yyyymmddHH.CMM
file_ext=*.C*
filename_datetime_format=yyyymmddHH.XMM
file_ext=*.X*
file_size_min=900
file_limit=0
file_limit=1
row_limit=0
# Special
......@@ -35,15 +35,15 @@ select_random_files=0
# OUTPUT
# ======
dir_out=A:/FLUXES/x-TEST-OUT
dir_out_run=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241
dir_out_run_log=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241\plots\agg
dir_out_run_raw_data_ascii=A:\FLUXES\x-TEST-OUT\CHA_BICO-20210112-235241\raw_data_ascii
dir_out_run=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047
dir_out_run_log=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\log
dir_out_run_plots=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots
dir_out_run_plots_hires=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots\hires
dir_out_run_plots_agg=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\plots\agg
dir_out_run_raw_data_ascii=A:\FLUXES\x-TEST-OUT\DAV_BICO-20210113-124047\raw_data_ascii
output_folder_name_prefix=CHA
file_compression=gzip
output_folder_name_prefix=DAV
file_compression=None
plot_file_availability=0
plot_ts_hires=0
......
__version__ = "0.2.0"
__version__ = "0.2.1"
__date__ = "13 Jan 2021"
__link_source_code__ = "https://gitlab.ethz.ch/holukas/bico"
__link_releases__ = "https://gitlab.ethz.ch/holukas/bico/-/releases"
......
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