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====== Brewer Python Module ======

We describe here the functions and data structured implemented in brewer.py module. The last version of the python module is available from [[http://rbcce.aemet.es/svn/python/libbrewer/|rbcce subversion repository]].

===== Installation =====

Brewer library can be imported from python code adding the path to brewer.py module to the Python path (list of directories Python goes through to search for modules and files):

  import sys
  sys.path.append("/home/to/module/")

By default the sys.path variable includes the current directory, so if brewer.py is in the same directory as the Python script, the module can be directly imported.

Alternatively, you can download brewer.py file to the standard location for third-party Python modules. This location varies by platform and by how you built/installed Python itself. Typical locations are shown in the following table:

^ Platform ^ Standard installation location ^
^ Windows | C:\PythonXY\Lib\site-packages ^
^ Unix | /usr/local/lib/pythonX.Y/site-packages ^

===== Data structures =====

Functions from //brewer.py// module use four different data structures for both input and output. These structures are python dictionaries: //measure//, //uv//, //hg//, //config// and //bdaily//.

==== measure ====
Dictionary containing values of the DS and SL Brewer measurements. Some of the dictionary fields will be used as input to the calculations of the library functions, and others will be used as the output. The values came from B files or Eubrewnet database through its JSON interface. It contains the following fields:

^ Field ^ Description ^
^ 'gmt' | datetime object ^
^ 'nd_filter_position' | ND filter position of #2 Filterwheel (in steps) ^
^ 'nd_filter' | ND filter position of #2 Filterwheel (index from 0 to 6) ^
^ 'cycles' | # of cycles ^
^ 'raw_counts_w0' | raw counts wavelength #0 ^
^ 'dark_count' | dark count ^
^ 'raw_counts_w0' | raw counts wavelength #0 ^
^ 'raw_counts_w1' | raw counts wavelength #1 ^
^ 'raw_counts_w2' | raw counts wavelength #2 ^
^ 'raw_counts_w3' | raw counts wavelength #3 ^
^ 'raw_counts_w4' | raw counts wavelength #4 ^
^ 'raw_counts_w5' | raw counts wavelength #5 ^
^ 'temp'| Brewer temperature ^
^ 'single_ratio1' | single ratio #1 MS(4) ^
^ 'single_ratio2' | single ratio #2 MS(5) ^
^ 'single_ratio3' | single ratio #3 MS(6) ^
^ 'single_ratio4' | single ratio #4 MS(7) ^
^ 'double_ratio1' | double ratio #1 MS(8) ^
^ 'double_ratio2' | double ratio #2 MS(9) ^
^ 'zenith_angle' | solar zenith angle ^
^ 'apparent_zenith_angle' | solar zenith angle corrected by atmospheric refraction ^
^ 'azimuth_angle' | solar azimuth angle ^
^ 'airmass' | air mass for ozone layer ^
^ 'airmass_rayleigh' | air mass for molecular atmosphere ^
^ 'measure_w0' | counts per second for wavelength #0 corrected by instrument effects^
^ 'measure_w1' | counts per second for wavelength #1 corrected by instrument effects^
^ 'measure_w2' | counts per second for wavelength #2 corrected by instrument effects^
^ 'measure_w3' | counts per second for wavelength #3 corrected by instrument effects^
^ 'measure_w4' | counts per second for wavelength #4 corrected by instrument effects^
^ 'measure_w5' | counts per second for wavelength #5 corrected by instrument effects^
^ 'o3' | ozone ^
^ 'so2' | sulphur dioxide ^
^ 'o3_sl' | ozone corrected by SL ^
^ 'so2_sl' | sulphur dioxide corrected by SL ^
^ 'o3_slcor' | SL correction for ozone ^
^ 'so2_slcor' | SL correction for sulphur dioxide ^
^ 'hg_flag' | Flag from HG measurement ^
^ 'n_summary' | Summary identifier to which the measure belongs ^

==== uv ====

Dictionary containing values of the UV Brewer measurements, including uv, ux, and ua. Some of the dictionary fields will be used as input to the calculations of the library functions, and others will be used as the output. The values came from B files or Eubrewnet database through its JSON interface. It contains the following fields:

^ Field ^ Description ^
^ 'brewerid' | Brewer ID number ^
^ 'scan' | UV scan type ^
^ 'it' | slit sampling time ^
^ 'deadtime' | Dead time (seconds) ^
^ 'cycles' | # of cycles ^
^ 'gmt' | datetime object ^
^ 'mmmm' | Time (GMT) in minutes for 1st wavelength ^
^ 'location' | Site Location ^
^ 'latitude' | Site latitude in decimal degrees (positive latitudes are north of the equator) ^
^ 'longitude' | Site longitude in decimal degrees (positive longitudes are west of the Prime Meridian) ^
^ 'temp'| Brewer temperature in volts^
^ 'press' | Pressure ^
^ 'dark_count' | dark count ^
^ 'time' | list of datetime objects for each measurement ^
^ 'wavelengths' | list of wavelengths ^
^ 'steps' | list of micrometer steps ^
^ 'counts' | list of raw counts ^
^ 'irradiance' | list of irradiance values in W/m²/nm ^
^ 'duv' | Diffey-weighted UV irradiance in mW/m²^
^ 'resdate' | Date of responsivity calibration used to calculate irradiance ^
^ 'straylight' | Stray light used to calculate irradiance ^
==== uvr ====

Dictionary containing values of Brewer responsivity for de UV measurements, determined using a calibrated light source. It contains the following fields:

^ Field ^ Description ^
^ 'brewerid' | Brewer ID number ^
^ 'date' | date of calibration ^
^ 'wavelengths' | list of wavelengths ^
^ 'responsivity' | list of responsivity values (counts/s)/(mW/m²/A)^

==== hg ====
Dictionary containing values of HG Brewer calibration. The values came from B files or Eubrewnet database through its JSON interface. It contains the following fields:

^ Field ^ Description ^
^ 'gmt' | datetime object ^
^ 'step2' | Micrometer set to this step # ^

==== config ====
Dictionary containing values of brewer settings. The values came from B files, ICF or Eubrewnet database through its JSON interface. It contains the following fields:

^ Field ^ Description ^
^ 'latitude' | Site latitude in decimal degrees (positive latitudes are north of the equator) ^
^ 'longitude' | Site longitude in decimal degrees (positive longitudes are west of the Prime Meridian) ^
^ 'press' | Pressure ^
^ 'o3tempcoef' | Ozone temperature coefficient for slit 0 ^
^ 'oslit1' | Ozone temperature coefficient for slit 1 ^
^ 'oslit2' | Ozone temperature coefficient for slit 2 ^
^ 'oslit3' | Ozone temperature coefficient for slit 3 ^
^ 'oslit4' | Ozone temperature coefficient for slit 4 ^
^ 'oslit5' | Ozone temperature coefficient for slit 5 ^
^ 'o3o3rate' | Ozone on ozone ratio ^
^ 'so2so2rate' | SO 2 on SO 2 ratio ^
^ 'o3so2rate' | Ozone on SO 2 ratio ^
^ 'etco3rate' | ETC on ozone ratio ^
^ 'etcso2rate' | ETC on SO 2 ratio ^
^ 'deadtime' | Dead time (seconds) ^
^ 'nfilter0' | Neutral density of filter 0 ^
^ 'nfilter1' | Neutral density of filter 1 ^
^ 'nfilter2' | Neutral density of filter 2 ^
^ 'nfilter3' | Neutral density of filter 3 ^
^ 'nfilter4' | Neutral density of filter 4 ^
^ 'nfilter5' | Neutral density of filter 5 ^
^ 'it' | slit sampling time ^
^ 'be2' | Rayleigh optical depth ( multiplied by 10000*log10(e) ) for wavelength #1 ^
^ 'be3' | Rayleigh optical depth ( multiplied by 10000*log10(e) ) for wavelength #2 ^
^ 'be4' | Rayleigh optical depth ( multiplied by 10000*log10(e) ) for wavelength #3 ^
^ 'be5' | Rayleigh optical depth ( multiplied by 10000*log10(e) ) for wavelength #4 ^
^ 'be6' | Rayleigh optical depth ( multiplied by 10000*log10(e) ) for wavelength #5 ^
^ 'w_so2_0' | weight for double ratio #1 MS(8) calculation, for wavelength #0 ^
^ 'w_so2_2' | weight for double ratio #1 MS(8) calculation, for wavelength #1 ^
^ 'w_so2_3' | weight for double ratio #1 MS(8) calculation, for wavelength #2 ^
^ 'w_so2_4' | weight for double ratio #1 MS(8) calculation, for wavelength #3 ^
^ 'w_so2_5' | weight for double ratio #1 MS(8) calculation, for wavelength #4 ^
^ 'w_so2_6' | weight for double ratio #1 MS(8) calculation, for wavelength #5 ^
^ 'w_o3_0' | weight for double ratio #2 MS(9) calculation, for wavelength #0 ^
^ 'w_o3_2' | weight for double ratio #2 MS(9) calculation, for wavelength #1 ^
^ 'w_o3_3' | weight for double ratio #2 MS(9) calculation, for wavelength #2 ^
^ 'w_o3_4' | weight for double ratio #2 MS(9) calculation, for wavelength #3 ^
^ 'w_o3_5' | weight for double ratio #2 MS(9) calculation, for wavelength #4 ^
^ 'w_o3_6' | weight for double ratio #2 MS(9) calculation, for wavelength #5 ^
^ 'sl_r5' | Calibration reference for double ratio #1 of standard lamp ^
^ 'sl_r6' | Calibration reference for double ratio #2 of standard lamp ^
^ 'wstepn' | Micrometer set on installation to this step #  ^

==== bdaily ====
Dictionary containing daily values calculated from the individual SL measurements. It contains the following fields:

^ Field ^ Description ^
^ 'date' | Date object ^
^ 'sl_r5_median' | R5 daily median of individual SL measurements ^ 
^ 'sl_r6_median' | R6 daily median of individual SL measurements ^
^ 'sl_num' | Number of measures used to calculate the daily median ^
^ 'sl_r5_tma' | Triangular movil average of R5 daily median ^
^ 'sl_r6_tma' | Triangular movil average of R6 daily median ^
^ 'sl_num_tma' | Number of measures used to calculate the Triangular movil average ^


===== Functions =====

The functions of this module are separated into two main sections (Products and Control functions) and four auxiliary sections (Astronomical, Airmass, Data Reduction, and Auxiliary functions). 

==== Products ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#airmass_calc| airmass_calc()]] | Calculates sun position and air mass (rayleigh and ozone) for brewer individual measurements. ^
^ [[devel:brewerpythonmodule#instrumental_cor|instrumental_cor()]] | Applies instrumental corrections (darkcount, deadtime, temperature, filter attenuation) to brewer individual raw measurements. ^
^ [[devel:brewerpythonmodule#rayleigh_cor|rayleigh_cor()]] | Applies Rayleigh corrections to brewer instrumentally corrected individual measurements. ^
^ [[devel:brewerpythonmodule#o3_so2|o3_so2()]] | Calculates $O_3$ and $SO_2$ from the brewer corrected individual measurements. ^
^ [[devel:brewerpythonmodule#o3_so2_sl|o3_so2_sl()]] | Calculates Standard Lamp correction for $O_3$ and $SO_2$. ^
^ [[devel:brewerpythonmodule#uv_cal|uv_cal()]] | Calculates UV Irradiance and DUV. ^

=== airmass_calc() ===

This function calculates sun position and air masses for ozone and molecular atmosphere. To do this, it uses the functions //solar_zenith_angle()//, //solar_azimuth_angle()//, //brewer_airmass()// and //apparent_zenith_angle()//.

**Example**
    import datetime
    import brewer
    
    measure={u'raw_counts_w4': 856609, u'raw_counts_w5': 880063, u'raw_counts_w0': 474, u'raw_counts_w1': 49601, u'raw_counts_w2': 172448, u'raw_counts_w3': 530003, u'airmass': 2.144, u'nd_filter_position': 64, u'mmmm_gmt': 901.63, u'dark_count': 126, u'hg_flag': -1, u'gmt': datetime.datetime(2009, 6, 3, 15, 1, 37), u'double_ratio1': 12021, u'double_ratio2': 5834, u'upper_slit': 6, u'n_summary': 107, u'mmmm': 1010.21452648741, u'date': u'20090603', u'single_ratio4': -291, u'single_ratio1': 11097, u'single_ratio3': 1720, u'single_ratio2': 6196, u'lower_slit': 0, u'temp': 21.0, u'zenith_angle': 62.559, u'filter': 97, u'cycles': 20}
    config={'w_so2_4': 0.0, 'w_so2_5': 4.2, 'w_so2_6': -3.2, 'w_o3_3': -1.0, 'w_so2_2': -1.0, 'w_so2_3': 0.0, 'oslit5': 5.3703, 'it': 0.1147, 'oslit4': 6.738, 'date': datetime.date(2009, 6, 3), 'nfilter2': 10000, 'etcso2rate': 2980.0, 'sl_r6': 1875.0, 'sl_r5': 3405.0, 'latitude': 67.3675, 'be3': 4620, 'be6': 4040, 'be4': 4410, 'be5': 4220, 'be2': 4870, 'press': 990.0, 'w_o3_2': 0.0, 'so2so2rate': 2.35, 'w_o3_6': -1.7, 'w_o3_5': 2.2, 'w_o3_4': 0.5, 'o3so2rate': 1.13903, 'etco3rate': 3101.0, 'oslit1': 7.42, 'nfilter5': 25000, 'oslit3': 7.0417, 'oslit2': 7.2467, 'nfilter0': 0, 'nfilter1': 5000, 'longitude': -26.633, 'nfilter3': 15000, 'nfilter4': 20000, 'o3o3rate': 0.3449, 'deadtime': 3.5e-08}
    
    out=brewer.airmass_calc(measure,config)
    print out['zenith_angle']
    print out['apparent_zenith_angle']
    print out['azimuth_angle']
    print out['airmass']
    print out['airmass_rayleigh']

The field //'gmt'// is used from //measure//, and the fields //'latitude'// and //'longitude'// are used from //config//.

This function returns the input //measure// dictionary, adding the following fields:

  * //'zenith_angle'//. This is calculated as the output of //solar_zenith_angle()// function.
  * //'azimuth_angle'//. This is calculated as the output of //solar_azimuth_angle()// function.
  * //'apparent_zenith_angle'//. This is  calculated as the output of //apparent_zenith_angle()// function, using //'zenith_angle'// as input.
  * //'airmass'//. This is defined as the ozone air mass, and is  calculated as the output of //brewer_airmass()//, using //'zenith_angle'// and a height of 22km as input.
  * //'airmass_rayleigh'//. This is defined as the Rayleigh air mass, and is  calculated as the output of //brewer_airmass()//, using //'zenith_angle'// and a height of 5km as input.


=== instrumental_cor() ===

This function converts raw counts to light intensity, in counts per seconds, while correcting for instrument effects (dark count, dead time, temperature sensitivity and filter attenuation). To do this, it uses the functions //darkcount_cor()//, //deadtime_cor()//, //temp_cor()// and //attenuation_cor()//.

**Example**
    import datetime
    import brewer
    
    measure={u'raw_counts_w4': 856609, u'raw_counts_w5': 880063, u'raw_counts_w0': 474, u'raw_counts_w1': 49601, u'raw_counts_w2': 172448, u'raw_counts_w3': 530003, u'airmass': 2.144, u'nd_filter_position': 64, u'mmmm_gmt': 901.63, u'dark_count': 126, u'hg_flag': -1, u'gmt': datetime.datetime(2009, 6, 3, 15, 1, 37), u'double_ratio1': 12021, u'double_ratio2': 5834, u'upper_slit': 6, u'n_summary': 107, u'mmmm': 1010.21452648741, u'date': u'20090603', u'single_ratio4': -291, u'single_ratio1': 11097, u'single_ratio3': 1720, u'single_ratio2': 6196, u'lower_slit': 0, u'temp': 21.0, u'zenith_angle': 62.559, u'filter': 97, u'cycles': 20}
    config={'w_so2_4': 0.0, 'w_so2_5': 4.2, 'w_so2_6': -3.2, 'w_o3_3': -1.0, 'w_so2_2': -1.0, 'w_so2_3': 0.0, 'oslit5': 5.3703, 'it': 0.1147, 'oslit4': 6.738, 'date': datetime.date(2009, 6, 3), 'nfilter2': 10000, 'etcso2rate': 2980.0, 'sl_r6': 1875.0, 'sl_r5': 3405.0, 'latitude': 67.3675, 'be3': 4620, 'be6': 4040, 'be4': 4410, 'be5': 4220, 'be2': 4870, 'press': 990.0, 'w_o3_2': 0.0, 'so2so2rate': 2.35, 'w_o3_6': -1.7, 'w_o3_5': 2.2, 'w_o3_4': 0.5, 'o3so2rate': 1.13903, 'etco3rate': 3101.0, 'oslit1': 7.42, 'nfilter5': 25000, 'oslit3': 7.0417, 'oslit2': 7.2467, 'nfilter0': 0, 'nfilter1': 5000, 'longitude': -26.633, 'nfilter3': 15000, 'nfilter4': 20000, 'o3o3rate': 0.3449, 'deadtime': 3.5e-08}
    
    out=brewer.instrumental_cor(measure,config)
    print out['double_ratio1']
    print out['double_ratio2']


The fields //'nd_filter_position'//, //'cycles'//, //'raw_counts_w0'//, //'dark_count'//, //'raw_counts_w1'//, //'raw_counts_w2'//, //'raw_counts_w3'//, //'raw_counts_w4'//, //'raw_counts_w5'// and //'temp'// are used from //measure//, and the fields //'deadtime'//, //'it'//, //'nfilter0'//, //'nfilter1'//, //'nfilter2'//, //'nfilter3'//, //'nfilter4'//, //'nfilter5'//, //'oslit1'//, //'oslit2'//, //'oslit3'//, //'oslit4'//, //'oslit5'//, //'w_o3_2'//, //'w_o3_3'//, //'w_o3_4'//, //'w_o3_5'//, //'w_o3_6'//, //'w_so2_2'//, //'w_so2_3'//, //'w_so2_4'//, //'w_so2_5'// and //'w_so2_6'// are used from //config//.

This function returns the input //measure// dictionary, adding the following fields:

  * //'measure_w1'//, //'measure_w2'//, //'measure_w3'//, //'measure_w4'// and //'measure_w5'//. These fields are the output of the consecutive application of //darkcount_cor()//, //deadtime_cor()//, //temp_cor()// and //attenuation_cor()// functions.

  * //'nd_filter'//. This field is calculated as the integer value of:
    * $nd\_filter = nd\_filter\_position / 64$

  * //'single_ratio1'//, //'single_ratio2'//, //'single_ratio3'// and //'single_ratio4'//. These fields are calculates as:
    * $single\_ratio1 = measure\_w4 - measure\_w1$
    * $single\_ratio2 = measure\_w4 - measure\_w2$
    * $single\_ratio3 = measure\_w4 - measure\_w3$
    * $single\_ratio4 = measure\_w5 - measure\_w4$ 

  * //'double_ratio1'// and //'double_ratio2'//. These fields are calculated as:
    * $double\_ratio1 = \sum_{i} measure\_w_i * w\_so2_{i+1} $
    * $double\_ratio2 = \sum_{i} measure\_w_i * w\_o3_{i+1} $


=== rayleigh_cor() ===

This function compensates the absorption of the molecular atmosphere to each channel signal, taking into account the atmospheric pressure:

\begin{displaymath}
measure\_w_i = measure\_w_i + \frac{be_{i+1} * airmass\_rayleigh * press }{1013.0}
\end{displaymath}

where $press$ is the mean Barometric Pressure of the Site in mBar and $be_2$, $be_3$, $be_4$, $be_5$ and $be_6$ are the scaled Rayleigh optical depth:

\begin{displaymath}
be_i= \tau_R(\lambda_i) * 10^4 * log_{10}(e)
\end{displaymath}

Once //'measure_w1'//, //'measure_w2'//, //'measure_w3'//, //'measure_w4'// and //'measure_w5'// fileds are updated, singe and double ratios are also updated.

**Example**
    import datetime
    import brewer
    
    measure={u'raw_counts_w4': 856609, u'raw_counts_w5': 880063, u'raw_counts_w0': 474, u'raw_counts_w1': 49601, u'raw_counts_w2': 172448, u'raw_counts_w3': 530003, u'airmass': 2.144, u'nd_filter_position': 64, u'mmmm_gmt': 901.63, u'dark_count': 126, u'hg_flag': -1, u'gmt': datetime.datetime(2009, 6, 3, 15, 1, 37), u'double_ratio1': 12021, u'double_ratio2': 5834, u'upper_slit': 6, u'n_summary': 107, u'mmmm': 1010.21452648741, u'date': u'20090603', u'single_ratio4': -291, u'single_ratio1': 11097, u'single_ratio3': 1720, u'single_ratio2': 6196, u'lower_slit': 0, u'temp': 21.0, u'zenith_angle': 62.559, u'filter': 97, u'cycles': 20}
    config={'w_so2_4': 0.0, 'w_so2_5': 4.2, 'w_so2_6': -3.2, 'w_o3_3': -1.0, 'w_so2_2': -1.0, 'w_so2_3': 0.0, 'oslit5': 5.3703, 'it': 0.1147, 'oslit4': 6.738, 'date': datetime.date(2009, 6, 3), 'nfilter2': 10000, 'etcso2rate': 2980.0, 'sl_r6': 1875.0, 'sl_r5': 3405.0, 'latitude': 67.3675, 'be3': 4620, 'be6': 4040, 'be4': 4410, 'be5': 4220, 'be2': 4870, 'press': 990.0, 'w_o3_2': 0.0, 'so2so2rate': 2.35, 'w_o3_6': -1.7, 'w_o3_5': 2.2, 'w_o3_4': 0.5, 'o3so2rate': 1.13903, 'etco3rate': 3101.0, 'oslit1': 7.42, 'nfilter5': 25000, 'oslit3': 7.0417, 'oslit2': 7.2467, 'nfilter0': 0, 'nfilter1': 5000, 'longitude': -26.633, 'nfilter3': 15000, 'nfilter4': 20000, 'o3o3rate': 0.3449, 'deadtime': 3.5e-08}
    
    out=brewer.airmass_calc(measure,config)
    out=brewer.instrumental_cor(out,config)
    out=brewer.rayleigh_cor(out,config)
    print out['double_ratio1']
    print out['double_ratio2']

The fields //'measure_w1'//, //'measure_w2'//, //'measure_w3'//, //'measure_w4'//, //'measure_w5'// and //'airmass_rayleigh'// are used from //measure//, and the fields //'press'//, //'be2'//, //'be3'//, //'be4'//, //'be5'//, //'be6'//, //'w_o3_2'//, //'w_o3_3'//, //'w_o3_4'//, //'w_o3_5'//, //'w_o3_6'//, //'w_so2_2'//, //'w_so2_3'//, //'w_so2_4'//, //'w_so2_5'// and //'w_so2_6'// are used from //config//.

This function returns the input //measure// dictionary, updating the following fields as described above: //'measure_w1'//, //'measure_w2'//, //'measure_w3'//, //'measure_w4'//, //'measure_w5'//, //'single_ratio1'//, //'single_ratio2'//, //'single_ratio3'//, //'single_ratio4'//, //'double_ratio1'// and //'double_ratio2'//.

=== o3_so2() ===

This function computes $O_3$ and $SO_2$ amount from Brewer measurements:

\begin{displaymath} 
    O_3 = \frac{double\_ratio2 - etco3rate}{o3o3rate * airmass}
\end{displaymath}
\begin{displaymath} 
    SO_2 = \frac{double\_ratio1 - etcso2rate}{so2so2rate * o3so2rate * airmass} - \frac{O_3}{so2so2rate}
\end{displaymath}

**Example**
    import datetime
    import brewer
    
    measure={u'raw_counts_w4': 856609, u'raw_counts_w5': 880063, u'raw_counts_w0': 474, u'raw_counts_w1': 49601, u'raw_counts_w2': 172448, u'raw_counts_w3': 530003, u'airmass': 2.144, u'nd_filter_position': 64, u'mmmm_gmt': 901.63, u'dark_count': 126, u'hg_flag': -1, u'gmt': datetime.datetime(2009, 6, 3, 15, 1, 37), u'double_ratio1': 12021, u'double_ratio2': 5834, u'upper_slit': 6, u'n_summary': 107, u'mmmm': 1010.21452648741, u'date': u'20090603', u'single_ratio4': -291, u'single_ratio1': 11097, u'single_ratio3': 1720, u'single_ratio2': 6196, u'lower_slit': 0, u'temp': 21.0, u'zenith_angle': 62.559, u'filter': 97, u'cycles': 20}
    config={'w_so2_4': 0.0, 'w_so2_5': 4.2, 'w_so2_6': -3.2, 'w_o3_3': -1.0, 'w_so2_2': -1.0, 'w_so2_3': 0.0, 'oslit5': 5.3703, 'it': 0.1147, 'oslit4': 6.738, 'date': datetime.date(2009, 6, 3), 'nfilter2': 10000, 'etcso2rate': 2980.0, 'sl_r6': 1875.0, 'sl_r5': 3405.0, 'latitude': 67.3675, 'be3': 4620, 'be6': 4040, 'be4': 4410, 'be5': 4220, 'be2': 4870, 'press': 990.0, 'w_o3_2': 0.0, 'so2so2rate': 2.35, 'w_o3_6': -1.7, 'w_o3_5': 2.2, 'w_o3_4': 0.5, 'o3so2rate': 1.13903, 'etco3rate': 3101.0, 'oslit1': 7.42, 'nfilter5': 25000, 'oslit3': 7.0417, 'oslit2': 7.2467, 'nfilter0': 0, 'nfilter1': 5000, 'longitude': -26.633, 'nfilter3': 15000, 'nfilter4': 20000, 'o3o3rate': 0.3449, 'deadtime': 3.5e-08}
    
    out=brewer.airmass_calc(measure,config)
    out=brewer.instrumental_cor(out,config)
    out=brewer.rayleigh_cor(out,config)
    out=brewer.o3_so2(out,config)
    print out['o3']
    print out['so2']


The fields //'double_ratio1'//, //'double_ratio2'// and //'airmass'// are used from //measure//, and the fields //'etco3rate'//, //'etcso2rate'//, //'o3o3rate'//, //'so2so2rate'// and //'o3so2rate'// are used from //config//.

This function returns the input measure structure, adding the following fields, calculated as described above: //'o3'// and //'so2'//

=== o3_so2_sl() ===

This function computes the standard lamp correction for $O_3$ and $SO_2$. It is calculated as the normalized difference between the averaged value of double ratio value from SL measurements and the double ratio value stored during calibration. 

\begin{displaymath}
o3\_slcor = \frac{ sl\_r6\_tma - sl\_r6}{o3o3rate * airmass}
\end{displaymath}
\begin{displaymath} 
so2\_slcor = \frac{ sl\_r5\_tma - sl\_r5}{so2so2rate * o3so2rate * airmass} - \frac{o3\_slcor}{so2so2rate}
\end{displaymath}
\begin{displaymath}
\[ o3\_sl =
  \begin{cases}
    o3             & \quad \text{if } abs(sl\_r6\_tma - sl\_r6) < mindu\\
    o3 + o3\_slcor & \quad \text{if } abs(sl\_r6\_tma - sl\_r6) \geq mindu\\
  \end{cases}
\]
\end{displaymath}
\begin{displaymath}
\[ so2\_sl =
  \begin{cases}
    so2              & \quad \text{if } abs(sl\_r6\_tma - sl\_r6) < mindu\\
    so2 + so2\_slcor & \quad \text{if } abs(sl\_r6\_tma - sl\_r6) \geq mindu\\
  \end{cases}
\]
\end{displaymath}

**Example**
    brewer.o3_so2_sl(measure,config,bdaily,mindu=5)

The fields //'o3'//, //'so2'// and //'airmass'// are used from //measure//, the fields //'o3o3rate'//, //'so2so2rate'//, //'o3so2rate'//, //'sl_r5'// and //'sl_r6'// are used from //config//, and the fields //'sl_r5_tma'// and //'sl_r6_tma'// are used from //bdaily//. The //bdaily// dictionary may be provided by //sl_tma()// function.

The input parameter //'mindu'// determines the minimum d.u. value to apply the correction to $O_3$ and $SO_2$, as shown above. By default this parameter takes a value of 5.

This function returns the input measure structure, adding the following fields, calculated as described above: //'o3_sl'//, //'so2_sl'//, //'o3_slcor'// and //'so2_slcor'//.


=== uv_cal() ===

This function computes the UV irradiance and DUV (Diffey-weighted UV irradiance). UV irradiance is calculated from UV Brewer measurements (including uv, ux, and ua) and the Brewer responsivity determined using a calibrated light source.

DUV is the Diffey-weighted UV irradiance, or erythemal dose rate. 

\begin{displaymath}
DUV = \int_{290}^{400} \mathrm{I(\lambda)\omega(\lambda)}\,\mathrm{d}\lambda
\end{displaymath}

Where $\omega(\lambda)$ is the erythemal action spectrum defined as:

\begin{displaymath}
\[ \omega(\lambda) =
  \begin{cases}
    1             & \quad \text{if } 290 < \lambda \leq 298 \\
    10^{0.094(298-\lambda)} & \quad \text{if } 298 < \lambda \leq 329 \\
    10^{0.015(139-\lambda)} & \quad \text{if } 329 < \lambda \leq 400 \\
    0 & \quad \text{if } \lambda < 400 \\
  \end{cases}
\]
\end{displaymath}

A correction is included in the erythemal action spectrum to account for the interval up to 400nm not measured by the Brewer.

DUV value is typically up to 250 mW/m². It can be arbitrarily divided by 25 mW/m² to generate the UVI (Ultraviolet index), which takes values from 0 to 11, although it can reach higher values. 


**Example**
    brewer.uv_cal(uv,uvr)

This function returns the input //uv// structure, adding the //'irradiance'// and //'duv'// fields.

==== Control ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#check_hg|check_hg()]] | Returns a list with the HG flags. ^
^ [[devel:brewerpythonmodule#sl_dailymedian|sl_dailymedian()]] | Returns the daily median double ratio of SL. ^
^ [[devel:brewerpythonmodule#sl_tma|sl_tma()]] | Returns the triangular moving average double ratio of SL. ^
^ [[devel:brewerpythonmodule#temp_filter|temp_filter()]] | Returns a filtered list of measurements based on the temperature. ^
^ [[devel:brewerpythonmodule#gmt_filter|gmt_filter()]] | Returns a filtered list of measurements based on the time (GMT). ^
^ [[devel:brewerpythonmodule#outliers_filter|outliers_filter()]] | Returns a list of measurements removing outliers. ^
^ [[devel:brewerpythonmodule#measure2summary|measure2summary()]] | Returns the summary everaging in a list of measurements. ^
^ [[devel:brewerpythonmodule#tempfit|tempfit()]] | Finds a linear regression between instrumentally corrected measurements and temperature. ^
^ [[devel:brewerpythonmodule#tempanalysis|tempanalysis()]] | Compares results for old, new and zero temperature coefficientes. ^

=== check_hg() ===

This function computes a list of flags with //True/False// values. The flag will be //True// for a Brewer measurement if the difference between the calculated micrometer step position during mercury-line wavelength calibration and the value saved during the installation is less than //hglimit// steps for the two HG measurements made before and after the Brewer measurement. Otherwise the flag will be //False//.

**Example**
    brewer.check_hg(mesl,hgl,config,hglimit=1)

//mesl// and //hgl// are lists of //measure// and //hg// dictionaries respectively. The field //'gmt'// is used from //measure//, the fields //'gmt'// and //'step2'// are used from //hg//, and the filed //'wstepn'// is used from //config//.

The input parameter //'hglimit'// determine the maximum allowed difference between //'step2'// and //'wstepn'//. By default this parameter take a value of 1.

This function returns the a list of //True/false// values.


=== sl_dailymedian() ===

This function calculates the median value of //'double_ratio1'// and //'double_ratio2'// for a day.

**Example**
    brewer.sl_dailymedian(sll,bdaily)

//sll// is a lists of //measure// dictionaries. The fields //'gmt'//, //'double_ratio1'// and //'double_ratio2'// are used from //measure//. If input //sll// list is void, a //ValueError// is raised. Optionally, a //bdaily// dictionary can also be pass to the function to be used in the output.

This function returns a //bdaily// dictionary with the fields //'date'//, //'sl_r5_median'//, //'sl_r6_median'// and //'sl_num'//.


=== sl_tma() ===

This function applies a triangular moving average over the daily median values of //'double_ratio1'// and //'double_ratio2'//, in a window of $1+2*dint$ days (seven days by default) are used.

**Example**
    brewer.sl_tma(date,bdailyl,dint=3)

The input parameter //date// is a python date object. //bdailyl// is a lists of bdaily dictionaries. The fields //'date'//, //'sl_r5_median'//, //'sl_r6_median'// are used from //bdaily//. If the intersection between the input //bdailyl// list and the window is void, a //ValueError// is raised.

This function returns a //bdaily// dictionary for the //'date'// day with the new fields //'sl_r5_tma'//, //'sl_r6_tma'// and //'sl_num_tma'//. If there is not a //bdaily// dictionary in the //bdailyl// list for //'date'// day, //'sl_num'// filed is set to 0 and //'sl_r5_median'// and //'sl_r6_median'// are set to //None//.

=== temp_filter() ===

This function returns a filtered list of measurements based on the temperature. It accepts two input parameters: //'mlinput'// and //'temp_range'//.

  * //'mlinput'// is a list of measurements ds, sl, etc.

  * //'temp_range'// is a list of 0,1 or 2 temperature values (floats). If //'temp_range'// has zero values nothing is done. If it has one temperature value, the function returns the measurements with //'temp'// values greters or equal to //temp_range[0]//. If it has two temperature values, the function returns the measurements with //'temp'// values betwen //temp_range[0]// and //temp_range[1]//.

**Example**
    import datetime
    import brewer
    import brewerjson
    
    params = {}
    params['brewerid'] = 185
    params['date'] = datetime.date(2012,2,7)
    params['function'] = 'getDS'
    params['user'] = 'user'
    params['password'] = 'password'
    
    ds = brewerjson.getdata(params)
    ds = brewerjson.formatDS(ds)
    
    dsf = brewer.temp_filter(ds,[20])

=== gmt_filter() ===

This function returns a filtered list of measurements based on the time (GMT). It accepts two input parameters: //'mlinput'// and //'gmt_range'//.

  * //'mlinput'// is a list of measurements ds, sl, etc.

  * //'gmt_range'// is a list of 0, 1, 2 or 4 datetime values. If //'gmt_range'// has zero values nothing is done. If it has one value, the function returns the measurements with //'gmt'// values greter or equal to //gmt_range[0]//. If it has two values, the function returns the measurements with //'gmt'// values between //gmt_range[0]// and //gmt_range[1]//. If it has four values, the function returns the measurements with //'gmt'// values between the interval //gmt_range[0]// and //gmt_range[1]// or between the interval //gmt_range[2]// and //gmt_range[3]//. 

**Example**
    import datetime
    import brewer
    import brewerjson
    
    params = {}
    params['brewerid'] = 185
    params['date'] = datetime.date(2012,2,7)
    params['function'] = 'getDS'
    params['user']='user'
    params['password']='password'
    
    ds = brewerjson.getdata(params)
    ds = brewerjson.formatDS(ds)
    
    dsf=brewer.gmt_filter(ds,[datetime.datetime(2012, 2, 7, 12, 0, 0),datetime.datetime(2012, 2, 7, 15, 0, 0)])


=== outliers_filter() ===

This function returns a filtered list of measurements removing outliers. It is considered as outliers all measurement which are more than //alpha// standard deviations away from the mean on either channel (//'raw_counts_w0'//,...,//'raw_counts_w5'//).

The function accepts two input parameters: //'mlinput'// and //'alpha'//, where //'mlinput'// is a list of measurements ds, sl, etc., and //'alpha'// is a float number. By default //'alpha'// value is 3.

**Example**
    import datetime
    import brewer
    import brewerjson
    
    params = {}
    params['brewerid'] = 185
    params['date'] = datetime.date(2012,2,7)
    params['function'] = 'getDS'
    params['user']='user'
    params['password']='password'
    
    ds = brewerjson.getdata(params)
    ds = brewerjson.formatDS(ds)
    
    dsf=brewer.outliers_filter(ds,3)

==== Astronomical ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#solar_ha_dec_et|solar_ha_dec_et()]] | Returns the solar hour angle, declination and equation of time. ^
^ [[devel:brewerpythonmodule#solar_zenith_angle|solar_zenith_angle()]] | Returns the solar zenith angle. ^
^ [[devel:brewerpythonmodule#solar_azimuth_angle|solar_azimuth_angle()]] | Returns the solar azimuth angle. ^
^ [[devel:brewerpythonmodule#moon_ha_dec|moon_ha_dec()]] | Returns the moon hour angle and declination. ^
^ [[devel:brewerpythonmodule#moon_zenith_angle|moon_zenith_angle()]] | Returns the moon zenith angle. ^
^ [[devel:brewerpythonmodule#moon_azimuth_angle|moon_azimuth_angle()]] | Returns the moon azimuth angle. ^
^ [[devel:brewerpythonmodule#min_sza|min_sza()]] | Returns the minimum solar zenith angle (maximum elevation). ^
^ [[devel:brewerpythonmodule#sza_to_time|sza_to_time()]] | Returns the times at wich solar zenith angle is achieved for a specific day. ^
^ [[devel:brewerpythonmodule#apparent_zenith_angle|apparent_zenith_angle()]] | Returns zenith angle of the sun/moon corrected by refraction, also known as apparent zenith angle. ^

=== solar_ha_dec_et() ===

This function returns the solar hour angle, declination and equation of time for a specific day at a specific location. In this case only geographic longitude is required to specify the location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.solar_ha_dec_et(datet, lon)

The input parameter //datet// is a python //datetime// object. //lon// is a //float// that represents the geographic longitude in degrees.

The //solar_ha_dec_et()// function returns a tuple with tree elements: hour angle in radians, solar declination in radians and equation of time in minutes.


=== solar_zenith_angle() ===

This function returns the solar zenith angle for a specific day at a specific location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.solar_zenith_angle(datet, lat, lon)

The input parameter //datet// is a python //datetime// object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //solar_zenith_angle()// function returns a //float// with the value of the solar zenith angle in degrees.


=== solar_azimuth_angle() ===

This function returns the solar azimuth angle for a specific day at a specific location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.solar_azimuth_angle(datet, lat, lon)

The input parameter //datet// is a python //datetime// object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //solar_azimuth_angle()// function returns a //float// with the value of the solar azimuth angle in degrees.


=== moon_ha_dec() ===

This function returns the moon hour angle and declination for a specific day at a specific location. In this case only geographic longitude is required to specify the location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.moon_ha_dec(datet, lon)


The input parameter //datet// is a python //datetime// object. //lon// is a //float// that represents the geographic longitude in degrees.

The //moon_ha_dec()// function returns a tuple with two elements: hour angle in radians and moon declination in radians.


=== moon_zenith_angle() ===

This function returns the moon zenith angle for a specific day at a specific location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.moon_zenith_angle(datet, lat, lon)

The input parameter //datet// is a python //datetime// object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //moon_zenith_angle()// function returns a //float// with the value of the moon zenith angle in degrees.


=== moon_azimuth_angle() ===

This function returns the moon azimuth angle for a specific day at a specific location. The method used to calculate these parameters is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok).

**Example**
    brewer.moon_azimuth_angle(datet, lat, lon)

The input parameter //datet// is a python //datetime// object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //moon_azimuth_angle()// function returns a //float// with the value of the moon azimuth angle in degrees.


=== min_sza() ===
This function returns the minimum solar zenith angle (maximum elevation) for a specific day at a specific location. This is calculated considering the solar hour angle is zero.

**Example**
    brewer.min_sza(d,lat,lon)

The input parameter //datet// is a python //datetime// object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //min_sza()// function returns a //float// with the value of the minimum solar zenith angle in degrees.

=== sza_to_time() ===

This function returns the times at which solar zenith angle (//SZA//) is achieved for a specific day. If the input //SZA// is lower than the //SZA// at noon, the function rise an //ValueError// showing the message "The solar zenith angle is not achieved on the input day.

This function allows us to compute sunrise and sunset times by introducing //SZA//=0. To compute noon time we can use the //SZA// value retrieve by //min_sza()// function.

**Example**_
    brewer.sza_to_time(sza,d,lat,lon)

The input parameter //sza// is a //float// ($sza\geq0$) that represent solar zenith angle in degrees. //d// is a python date object. //lat// and //lon// are //floats// that represents the geographic latitude and longitude in degrees respectively.

The //sza_to_time()// function returns a tuple with two datetime objects, with the times when the sun reaches the input zenith angle during the morning and in the afternoon. If input //sza// is not achieved on the input day, a ValueError is raised.


=== apparent_zenith_angle() ===

This function returns the solar/moon apparent zenith angle, that is, the zenith angle considering atmospheric refraction. The method used to calculate this parameter is the same as that implemented in the Brewer operative software (Tom McElroy / Volodya Savastiok), and is described in //Archer - 1980 - Comments on "Calculating the position of the sun"//. The correction is only applied if $za < 90.5$.

**Example**
    brewer.apparent_zenith_angle(za)

The input parameter //za// is a //float// that represent solar/moon zenith angle in degrees.

The //sza_to_time()// function returns a //float// with the corrected azimuth angle in degrees.


==== Airmass ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#brewer_airmass|brewer_airmass()]]| Returns the air mass calculated for a delta layer at a fixed altitude.  ^


=== brewer_airmass() ===

This function returns the air mass calculated for a delta layer at a fixed altitude, as is described in [[http://www.kippzonen.com/Download/207/Brewer-MkIII-Operator-s-Manual-for-Single-Board|Brewer MkIII - Operator's Manual]]:

\begin{displaymath} 
  airmass=\frac{1}{cos(asin(k * sin(\frac{za * \pi}{180})))}
\end{displaymath}
\begin{displaymath} 
  k=\frac{R_e}{R_e+z}
\end{displaymath}

where $za$ is a the zenith angle, $z$ is the delta layer height, and $R_e$ = 6370 is the radius of earth in km.

This function is typically used considering a layer at an altitude of 22 km for ozone air mass, and a layer at an altitude of 5 km for Rayleigh air mass.

**Example**
    brewer.brewer_airmass(za,z)

The input parameter //'za'// is a //float// with the solar/moon zenith angle in degrees. //'z'// is a //float// that represents the layer height in km.

The //brewer_airmass()// function returns a //float// with the air mass value.


==== Data Reduction ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#darkcount_cor|darkcount_cor()]] | Returns a list with the dark count corrected measurements. ^
^ [[devel:brewerpythonmodule#deadtime_cor|deadtime_cor()]] | Returns a list with the dead time corrected measurements. ^
^ [[devel:brewerpythonmodule#temp_cor|temp_cor()]] | Returns a list with the temperature corrected measurements. ^
^ [[devel:brewerpythonmodule#attenuation_cor|attenuation_cor()]] | Returns a list with the filter attenuation corrected measurements. ^


=== darkcount_cor() ===

This function subtracts the dark count from raw data, then scales the result to produce count rates, in counts per second:

\begin{displaymath} 
    f_{out}[i] = \frac{2*(f[i]- dark )}{cycles*it}
\end{displaymath}

**Example**
    brewer.darkcount_cor(f,dark,cycles,it)

The input parameter //f// is a list of five //integers// with the raw measurements. //dark// is a //float// with the dark count value. //cycles// is an //integer// with the number of cycles for each measurement. //it// is a //float// with the slit sampling time.

The //darkcount_cor()// function returns a list with the dark count corrected measurements in counts per second.


=== deadtime_cor() ===

This function compensates for the dead time, assuming a Poisson distribution function of a paralyzable detection system. The method iterates 9 times the equation:

\begin{displaymath} 
    f_{out}[i] = f[i] * e^{f_{out}[i]*t1}
\end{displaymath}

The deadtime-compensated count rates are normalized by computing the base ten logarithm of e, then scaled by 10000, thus allowing integer arithmetic.

This function is typically applied after dark count correction.

**Example**
    brewer.deadtime_cor(f,t1)

The input parameter //f// is a list of five //floats// with the measurements. //t1// is a //float// with the deadtime of the photon-counting system.

The //deadtime_cor()// function returns a list with the dead time corrected measurements in counts per second.


=== temp_cor() ===

This function compensates for temperature-dependent characteristics of the spectrometer assembly:

\begin{displaymath} 
    f_{out}[i] = f[i] + (tc[i] * t)
\end{displaymath}

This function is typically applied after dead time correction.

**Example**
    brewer.temp_cor(f,t,tc)

The input parameter //f// is a list of five //floats// with the measurements. //tc// is list of five //floats// with the temperature coefficients. //t// is a //float// with the temperature of the system in Celsius degrees.

The //temp_cor()// function returns a list with the temperature corrected measurements in counts per second.


=== attenuation_cor() ===

This function compensates for attenuation of the neutral-density filters used to adjust the light level entering the spectrometer:

\begin{displaymath} 
    f_{out}[i] = f[i] + af[fp]
\end{displaymath}

This function is typically applied after temperature correction.

**Example**
    brewer.attenuation_cor(f,af,fp)

The input parameter //f// is a list of five //floats// with the measurements. //taf// is list of six //floats// with the attenuation values of the neutral-density filters. //fp// is an //integer// with the filter position.

The //attenuation_cor()// function returns a list with the attenuation corrected measurements in counts per second.

==== Auxiliary Functions ====

^ Function ^ Short Description ^
^ [[devel:brewerpythonmodule#wsum|wsum()]] | Returns the weighted sum from all measurements on a list. ^


=== wsum() ===

This function computes the weighted sum from all measurements on a list. Both input lists, measurements and weights, should have the same length:

\begin{displaymath}
wsum=\sum_{i}f[i]*w[i]
\end{displaymath} 

**Example**
    brewer.wsum(f,w)

The input parameter //f// is a list of //floats//. //w// is list of of //floats// of the same length than //f//.

The //wsum()// function returns a //float// with the weighted sum value.
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