7/2/2013

C-CARGO

RESEARCH WORK USER MANUAL

Contents
Step 1-Installation steps for MiniDOAS ....................................................................................... 3
Step 2-Ocean Optics and DOASIS Configuration ......................................................................... 4
Step 3-Spectral Calibration using WINDOAS ............................................................................... 8
Step 4-Convolution using WINDOAS ......................................................................................... 17
Step 5-Ring spectrum determination using DOASIS.................................................................. 19
Step 6-DOAS analysis using WINDOAS ...................................................................................... 21
Step 7- VCD Extraction .............................................................................................................. 36
Step 8-Querries for SQL Database ............................................................................................. 39
Step 9-Using QGIS and pg-Admin III .......................................................................................... 40
Step 10- Interpolation using IDW Tool in ArcGIS ...................................................................... 53

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Step 1-Installation steps for MiniDOAS

1. Install the ocean optics:
Installation\1_OceanOptics_Intall_before_connecting_USB\ooibase32setup.exe
(Restart computer)
2. Install HMTUSBDriver:
Installation\2_Install_before_USB_Connection_InstallerHMTUSBDriver\Setup.Exe
3. Install HMTUSBActiveXControl:
Installation\3_stepper\ Setup.Exe
4. Install DOASIS:
Installation\4_InstallerDOASIS3.0.1569.zip

5. Connect the USB cables to the computer (ocean optics and HMT), install both
drivers like follows:

Select not this time

Select install the software automatically

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Select continue anyway, then finish

6. Start DOASIS, select: Device, MiniDOAS; the MiniDOAS should be automatically
detected.

Close DOASIS and start minimax.exe

Step 2-Ocean Optics and DOASIS Configuration

Open OOIBase32 by double clicking on the icon on Desktop
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In Spectrometer menu click configuration

In the Wavelength Calibration Tab add Spectrometer Serial Number

USB2+H02435
Click OK

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If that would not work select Open Configuration in Spectrometer menu and select
Default.spec and click open. Repeat the previous step once again

Adjust elevation angle

-Start Minimax.exe
-Press Init to move the motor to the end switch. This needs to be done once after
startup of the program
-select configure, motor calibration
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-after a few seconds, the instrument has turned into the horizontal position. Move the
motor up or down until the true horizontal position is reached. This has to be tested
using the water level.
-press OK
(if the instrument position was not changed, this step can be omitted for restart of
measurements)
Manual acquisition of spectra
Manual spectra are needed to characterise the electronic offset and dark current.
Manual operations are performed by selecting fixed (acquisition) in the main menu.
Press Acquire; the spectrum is displayed and automatically saved to
Disk.
For offset spectra, chose a small integration time (per scan), e.g. 3 msec and a high
scan number, e.g. 1000.
For dark current spectra, chose a moderate integration time (per scan), e.g. 10000
msec and a small scan number, e.g. 1. If saturation is reached, select a smaller
integration time.
Attention:
a) always close the telescope with a black paper or something similar
b) the dark current and offset spectra are only useful if the set detector temperature
was actually reached. This might take some minutes. The best option is to measure
several subsequent offset and dark current spectra

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Step 3-Spectral Calibration using WINDOAS

Example and description for ground based observations, Thomas Wagner, 24.07.2008
The spectral calibration is performed by fitting a measured spectrum to a convoluted
solar spectrum. During the fitting process, the wavelength from the solar spectrum
will be assigned to the individual detector pixels of the own measurements. In
addition, also the spectral resolution of the own measurement is determined (as
function of wavelength)
Often the calibration fit is referred to as Kurucz-fit because usually a high resolution
spectrum from the Kurucz solar atlas is used as input.
Start WinDOAS
Open .wds file from File menu

In the Project Window your measured spectra will be opened entitled as Raw Spectra

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Right Click Calibra properties and input Offset and Dark Current measured by
DOASIS in Instrumental Tab

In the Calibration Tab give path of High resolution Solar Spectrum

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Calibration 1
Browse to a noon spectrum by next button on the toolbar

min/max: indicates the wavelength range used for the calibration

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-Number of sub-windows: the whole wavelength range (as defined by min/max) is

sub-divided into several sub-windows. The actual fit is performed separately in each
of these sub-windows.
-Shift/SFP: indicates the polynomial degree used for interpolating the results of the
individual sub-windows.
-fit parameters: a new menu appears:

-here, additional spectra (e.g. ozone cross section) can be added.

The chosen entries have the following meaning:

-continuous function: defines the degree of the fitted polynomial

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-Offset (const, order 1/2): allows to fit an intensity offset (polynomial of different
degree)
-sol: allows a fit coefficient of the solar spectrum to vary freely

-the spectra included here will be shifted (and squeezed). In our case, the own
measurement is shifted until it matches the wavelength calibration of the solar
spectrum

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-here, gaps in the wavelength range can be added

The Fit is performed by clicking with the right mouse button at the measured
spectrum.
-select run calibration. Now the spectrum appears.
-by clicking at the arrow button in the menu line

the fit is started.

As result, the following graph appears:

-The first window shows the result of the fit (in red the measured spectrum; in black
the convoluted solar spectrum)
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-The second window shows the residual of the fit (the difference between the
measured spectrum and the fit result)
-the third window shows the determined shift (individual points for the different subwindows) with respect to the pre-calibration.
-the fourth window shows the determined spectral resolution (FWHM) for the
different sub-windows.
All small figures can be enlarged by clicking on them. Then, they can be saved as
figures or as ascii files.
It is recommended to save the following results:
A) first window as ascii-file. This is used as calibration file for the convolution of
reference spectra

B) fourth window as bmp-file. The FWHM is also used as input for the convolution.

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Calibration 2
Repeat all the steps from calibration 1 expect replacing the high resolution spectrum
with your saved calibrated spectrum from calibration 1

The residual will now decrease as shown in figure

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Step 4-Convolution using WINDOAS

Note: Various cross sections to be used as input will be given only ring spectrum
needs to be calculated using DOASIS that is explained in the next step.
-click in the top menu tools, select convolution/filtering
the following menu appears:

Here, three paths have to be specified.

-The calibration file is that derived from the kurucz-fit as calibration 2
-the output path specifies the directory in which the convoluted (or interpolated) cross
sections are stored
-the input path describes the file with the high-resolution cross section to be
convoluted
-convolution type has to be standard (for convolution) or none (for interpolation)
a second menu appears if slit function is selected:

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Here a slit function has to be selected, e.g. a Gaussian shape. Then a line with
(FWHM) has to be defined. Here the value determined from the calibration (see
calibration.doc) has to be used. In the case of NO2, which is analysed around 440nm,
a FWHM of 0.5 nm is chosen.
Alternatively to a Gaussian function, also a Voigt function, or a measured slit function
(provided from an ascii-file) can be used.

The result of the spectral convolution is mapped to the wavelength calibration of the
own measurement (as provided in calibration.txt).
Note:
Usually all literature cross sections are convoluted with the instrument function.
However, in some cases (e.g. for O4), the original measurement was taken at a broad
spectral resolution, usually broader than the own measurement. Then, instead of a
convolution (standard), an interpolation (none) has to be selected.

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Step 5-Ring spectrum determination using DOASIS

First, measured spectrum has to be selected and prepared:
-Usually, a measurement with good signal to noise ratio taken around noon at 90
elevation angle is used for the Ring spectrum calculation.
-usually, the same spectrum is chosen as was used for the spectral calibration and for
the Fraunhofer spectrum in the DOAS analysis.
You might select a measurement for the Ring calculation in the following way:
-browse the spectra of your measurements (click right mouse button at the folder with
your measurements).
-In the graphs window, the spectrum is displayed. In the data window, the properties
of the spectrum is displayed (see below).
In the data window, the elevation angle is indicated in the field Record name (see
red circles below). Browse the subsequent spectra by using the arrow button in the top
menu. If you find a spectrum of good quality (as shown in the graphs window) and
with elevation angle 90 (as in the data window), then click with the right mouse
button at the spectrum and select save as ascii file.
Save the spectrum at a file name and path of your choice.

Calculation of the Ring spectrum:

-Start DOASIS
-select file, open in the top menu
-load a measurement (as ascii file, two columns, see above)
-the spectrum must be displayed as a function of wavelength, see below:

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Note: if instead of wavelength, the pixel number is displayed, you must load the
correct file.
Without correct wavelength, no Ring spectrum can be calculated
-select in the top menu math, Ring spectrum. The following spectrum will appear:

-Save the Ring spectrum by selecting file, save as in the top menu. Make sure that
you save the file as ascii file, and chose the directory, where you want to store the file.
-The Ring spectrum calculated in this way has the correct file format to be used in the
DOAS analysis.
-you must, however, change the file name to match the naming convention required
by WINDOAS. A useful file name would e.g. be: Ring_date_time.txt

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Step 6-DOAS analysis using WINDOAS

Short description for MAXDOAS measurements, Thomas Wagner, 27.07.2008
-Start Windoas
-open analysis.wds
The screen will appear like the example below (left). After clicking on the small
plus signs, additional items appear (below, right)

Insert the path to the folder with the measured spectra:

-click right mouse button at Raw spectra, select insert path
-browse paths and chose the folder with the measured spectra
-if all sub folders should be considered, select include subfolders (see below).

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load the file with the wavelength calibration:

-click right mouse button at Calibra, select properties, select instrumental.
The following menu appears:

-use the button calibration file and load the file with the wavelength calibration (e.g.
calibration_260708.txt)
-in addition, make sure that as Format it is selected MFC (Heidelberg). If this
format is chosen, then the binary data format (MFC format) of the measured spectra
can be used.
-insert the offset and dark current spectra using the buttons Dark current and
Offset. Also these files have to be in the MFC format.
-the 1st wavelength must be the same as for the measured spectrum (this is not
necessarily the true first wavelength, but is the wavelength stored together with the
spectra).
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Now, the spectra can be displayed:

-click with right mouse button on the path with the measured spectra, select browse
spectra. Now the first spectrum is displayed; also the properties of the spectra are
displayed in the data screen.
-by clicking the right arrow button in the top menu, the following spectra are
displayed subsequentially.
-make sure that the spectra is displayed as function of wavelength (see below):

-If the calibration file was not loaded correctly, then the spectra are displayed as
function of the pixel number (see below):

In that case, make sure that the correct calibration file is loaded.
Define the fitting parameters:
-click right mouse button on the item below analysis window (in our case, the item
is NO2); select properties. The following menu appears:

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the following entries should be made:

-minand max define the wavelength interval used for the fit. For the NO2 analysis,
420 and 450 are good values.
-insert the path and filename of the Fraunhofer reference spectrum (Reference 1);
this file should be an ascii file with two columns (1st column: wavelength; second
column: counts). For more details of the Fraunhofer reference spectrum, see below.
-delete, change or insert cross sections by clicking the right mouse button on the list
below cross sections. For the format of the cross sections, see below. If you want to
change the properties of the existing cross sections, select properties. For inserting
or deleting, select insert or remove.
-Please note that cross sections can only be removed (or changed) if they are not
linked to other cross sections (see below).
Select the degree of the polynomial for the DOAS fit:
-chose continuous function. The following menu appears:

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-select the degree by clicking the different degrees x0, x1,x5

(in the example shown above, a polynomial of degree 3 is selected)
Chose the degree of the additional polynomial (often also referred to as
intensity offset)
-chose predefined parameters. The following menu appears:

-select Offset (constant), or Offset (order 1) or Offset (order 2). An intensity

offset of degree 0 (constant), 1 (linear) or 2 (parabolic) is chosen.
Select shift and stretch, and linking of different cross sections:
-chose shift and stretch. The following menu appears:

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-click the right mouse button at the location marked by the red oval, select insert.
The following menu appears:

In the left window, all cross sections inserted, as well as Ref and spectrum
appears. Ref indicates the Fraunhofer reference spectrum, Spectrum indicates the
measured spectrum.
-by marking a cross section in the left window and pressing the arrow button, the
cross section is transferred in the right window. For a typical DOAS analysis, all
items, except Spectrum are transferred into the right window. Then the menu looks
like below:

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-after pressing OK, the shift and stretch menu looks like:

-now, the selected cross sections and spectra are shifted during the fit procedure until
they match the wavelength calibration of the measured spectrum (Spectrum). All
selected cross sections and spectra are shifted together by the same amount.
-in addition to shift fit also a stretch fit of order 1 or 2 can be selected. For typical
analyses, however, a shift fit is sufficient.
-Usually, the Gaps and Output menu is not changed.
-After pressing OK, the fit parameters are stored.

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You might check if all cross sections are correctly loaded, by clicking with the right
mouse button at NO2 (below analysis) and selecting view cross sections. Then
the cross sections are displayed:

Format and selection of the Fraunhofer Reference spectrum

As mentioned above, the Fraunhofer reference spectrum must be an ascii file with two
columns. The first column contains the wavelength (from the spectral calibration); the
second column contains the spectrum (counts).
As Fraunhofer spectrum, usually the spectrum which was used for the calibration, is
chosen. Alternatively, also a spectrum close in time to the spectrum chosen for the
calibration can be used. The Fraunhofer reference spectrum should ideally fulfil two
requirements:
a) it should be measured at 90 elevation
b) it should have a good signal to noise ratio
Usually, a spectrum measured around noon is chosen as Fraunhofer reference
spectrum.
You might select a Fraunhofer reference spectrum in the following way:
-browse the spectra of your measurements (click right mouse button at the folder with
your measurements).
-In the graphs window, the spectrum is displayed. In the data window, the properties
of the spectrum is displayed (see below).
In the data window, the elevation angle is indicated in the field Record name (see
red circles below). Browse the subsequent spectra by using the arrow button in the top
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menu. If you find a spectrum of good quality (as shown in the graphs window) and
with elevation angle 90 (as in the data window), then click with the right mouse
button at the spectrum and select save as ascii file.
Save the spectrum at a file name and path of your choice. The file will be stored as
needed for the DOAS fit.

Format of the cross sections

The windoas program allows only to load cross section files (and Ring spectrum file)
with strictly defined file names.
First, cross section names have to be defined:
-For that purpose, click with right mouse button at user defined symbols, select
insert item
-give a name to this item, e.g. NO2, press return. A new menu symbol properties
appear. Just press OK.
-Follow this procedure until you have inserted names for all the cross sections (and
Ring spectrum) of the selected DOAS analysis.
Naming convention for the cross section files:
The file names of the cross sections have to start with the names given above. After
the name, a _ has to appear; then additional information (e.g. the temperature) can
be added. A typical example will be:
NO2_vandaele97_294_vac.txt_std
Content of the cross section (and Ring spectrum) files:
Like the Frunhofer reference spectrum, the cross sections have to be ascii files with
two columns. The first column contains the wavelength, the second column contains
the cross section.
The files created in the convolution process have the correct format and can be
directly used for the DOAS fit.

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Performing the DOAS fit

Before the DOAS fit is performed, several properties have to be specified:
-click right mouse button at Calibra, select properties, select spectra. The
following menu will appear:

Here you can chose which information should be displayed at the screen after the
DOAS fit of the each individual spectrum.
Normally you should select Spectra, Fits, and Data. You should also select
pause; then the analysis automatically stops after each spectrum and the results can
be looked at.
Chose ASCII results, and the following menu appears:

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Here you should select a path and file name (Output path or file) for the file
containing the fit results.
After pressing OK the program is ready for the analysis.
To start the DOAS fit, click with the right mouse button at the folder which contains
your spectra, select run analysis.
A screen with the first spectrum appears:

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Also the spectrum properties are displayed at the data screen:

-to start the DOAS fit, press the arrow button in the top menu. The fit results are then
displayed. Typical fit results are like the following example:

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-The first window shows the measured spectrum and the Fraunhofer reference
spectrum.
-the second window shows the fit residual
-the following windows show the results for the different cross sections (and Ring
spectrum)
-the last window shows the fitted polynomial
All small windows can be enlarged by clicking on them.
The above example shows a typical result for a NO2 analysis. Besides the NO2
absorption features (center plot), also the H2Oabsorptions are clearly visible.
Processing large data sets:
After it is checked that the fit works well (looking at individual fit results, like above),
large quantities of spectra (e.g. a whole day, or week) can be processed automatically.
For that purpose, the following parameters should be selected:
-click right mouse button at Calibra, select properties, select spectra. The
following menu will appear:

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Here the markers at spectra, fits, pause, and data are removed (see above).
This enables a higher processing speed of the data analysis.
Result files:
The data are stored in result files in the structure shown below. After loading the
result file into EXCEL, the following entries appear:

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-column 1: spectrum number

-column 2: (record) name. In our case, here the elevation angle is stored.
-columns 3-5: date and time
-column 6: number of scans
-column 7: the total integration time
-column 8: the solar zenith angle
-column 9: shift
-columns 10,11: latitude and longitude
-column 12: RMS of the fit
-remaining columns: fit results of the cross sections: first column: SCD, second
column: fit error of the SCD

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Step 7- VCD Extraction

Short description for the extraction of tropospheric NO2 VCDs from Car MAXDOAS measurements

T. Wagner, 02.12.2012

The different steps are described for the example of the car MAX-DOAS
measurements made in Islamabad and Rawalpindi on 16.11.2012 (see xls-file:
Description_16Nov2012.xls).

A) Selection of good measurements

Plot the NO2 DSCDs as function of time
(sheet NO2 in Description_16Nov2012.xls)
Plot the RMS as function of time
(sheet rms in Description_16Nov2012.xls)
Delete all measurements with large rms value (here a threshold of 3.5e-3 was chosen;
the remaining measurements are copied into new table (RMS_below_3.5e-3)
Remark 1: Note that at the end of the measurements on 16.11.2012 the rms values are
higher than earlier on that day. This is caused by much shorter integration times of the
later spectra on that day (the reason for the shorter integration times is, however, not
clear and should be checked).
Remark 2: On some days (not on 16. Nov. 2012) measurements are performed until
the evening. On such days, the last measurements at high SZA usually have enhanced
rms because of the low signal to noise ratio. For these late measurements a higher
threshold for the rms might be used.

B) Determination of the DSCDref and the stratospheric background

The Determination of the DSCDref and the stratospheric background is performed as
decsribed in Wagner et al., 2010.
1) For each elevation sequence, pairs of 90 elevation and low elevation angles (here
30) have to be selected. In our case, the 90 and the directly following 30 spectra
are selected; the other 30 spectra are ignored (deleted).
The selected 90/30 pairs is copied in sheet 30_90_all.
For each of these pairs the following value is calculated:
offset = [AMF(90) * DSCD(30) - AMF(30) * DSCD(90)] / [AMF(30) AMF(90)]
(see equation 14 in Wagner et al., 2010)

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For the selected elevation angles, and using the geometric approximation, the AMFs
become:
AMF(30) = 2
AMF(90) = 1
Thus the above equation reduces to:
offset = DSCD(30) 2 * DSCD(90)
These values are calculated in column D in sheet 30_90_all.

2) The stratospheric AMF is estimated: The stratospheric AMF is calculated from the
SZA according to the geometric approximation:
AMFstrat = 1 / cos(SZA)
The stratospheric AMF is calculated in column L in sheet 30_90_all.
3) The stratospheric SCD is estimated assuming a typical stratospheric VCD (for mid
latitudes in autumn a typical value is 2e15 molec/cm).
The stratospheric SCD is calculated in column m in sheet 30_90_all.
4) The stratospheric SCD is added to the offset (from step 1, see above).
According to equation 12 in Wagner et al., 2010, this yields the DSCDref.
The sum of offset and stratospheric SCD is calculated in column E in the sheet
30_90_all.
This value is plotted in the sheet offset.
5) Unrealistic values have to be removed. Especially close to strong emission sources,
usually not the same air masses are observed at both elevation angles. This leads to
strong negative or positive deviations. (see sheet offset).
These outliers have to be removed. The remaining good values are copied into the
table in sheet 30_90.
Now the average of all values in column E is calculated. This is then our best
estimate for the DSCDref. In our case it is 1.07e16 molec/cm, see bottom of column
E).
C) Calculation sequence of the tropospheric NO2 VCDs from all 30 elevation
spectra
From the sheet RMS_below_3.5e-3, all 30 elevation spectra are selected and
copied into new table (sheet 30).
The tropospheric VCD is calculated according to:
VCDtrop = SCD(30) / AMF(30)
with
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SCD(30) = DSCD(30) + DSCDref - SCDstrat

The DSCDref was calculated in step B5 above
The SCDstrat was calculated in step B3 above
SCD(30) is calculated in column K in sheet 30.

With AMF(30) = 2, the VCDtrop is calculated in column L in sheet 30.

The tropospheric VCD is plotted in sheet NO2_VCDtrop.

Remark: For car MAX-DOAS measurements made at rather low SZA (as for 16. Nov.
2012), the variation of the SCDstrat with time is small. Thus this variation can be
neglected and the offset could be determined in a simplified way (without adding the
SCDstrat, see column D in sheet 30_90). The respective average value for 16. Nov.
2012 is 6.4e15 molec/cm, see bottom of column D in sheet 30_90.
This (new) offset has to be added to the DSCD(30) (but without subtracting the
SCDstrat). This simplified determination of the VCDtrop is shown in column M in
sheet 30. It is very similar to the one calculated before (column L).
For days with measurements made at high SZA (>75) the simplified method can
not be used.

Reference:
Wagner, T., Ibrahim, O., Shaiganfar, R., and Platt, U.: Mobile MAX-DOAS
observations of tropospheric trace gases, Atmos. Meas. Tech., 3, 129-140,
doi:10.5194/amt-3-129-2010, 2010.

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Step 8-Querries for SQL Database

Querries to be used in pg-Admin (SQL Database) to patch time
To create table with name time_calss and 3 cloumn of type time and integer
create table time_class (t1 time, t2 time, id integer);
Copy csv with three cloumns to database table time_class
COPY time_class (t1, t2, id) FROM E'D:\\time_class.csv'
WITH CSV HEADER delimiter as ',';
Add colum of time_id type integer in tables gps and no2
There are two ways of doing this
1 is from graphical interface "Right click on table gps/ n02, click on create new
object, then click on add column. A form will open. In this form type colum name
time_id and in select integer type for this colum, Click on okay"
2 way is through qurey..................
Update gps time_id from time class table using this query
update gps g
set time_id= t.id
from time_class t
where g."utc time"::time>= t.t1 and g."utc time"::time<= t.t2

Update no2 time_id from time class table using this query
update no2 n
set time_id= t.id
from time_class t
where n."time (hh_m"::time>= t.t1 and n."time (hh_m"::time<= t.t2

Update the lat log of no2 table from gps table based on time_class
update no2 n
set longitude= g.longitude
from gps g
where n.time_id=g.time_id
update no2 n
set latitude= g.latitude
from gps g
where n.time_id=g.time_id
Copy no2 table into csv
COPY (SELECT * FROM no2)

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Step 9-Using QGIS and pg-Admin III

User name= postgres

Password = postgresql

Add new Database

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Make a shape file on qgis and save as ESRI shape file

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Now go to pgadmin III and from plugin icon add a postGIS shapefile
and DBF loader (add the saved shape file here)

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Execute query

Go to qgis and add postGIS layers

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Make a new connection if not already made

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Add the newly saved csv file

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Composer window opens

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Step 10- Interpolation using IDW Tool in ArcGIS

Firstly convert all abnormal values of NO2 VCDs to Zero by REPLACE option in MS
EXCEL

For interpolation it is better to crop data from the satellite swath over Pakistan.

Pakistan Longitude range from 61 77 degrees E

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Same exercise is to be done for latitude 23 37 N

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Copy the selection and paste in a new excel sheet and save as csv file for satellite data
over Pakistan only

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Open ArcGIS and add the csv file to it

Display XY Data by Right clicking at the file in Table of Contents

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You have to add no2 as Z-value

Your point data of no2 VCDs via satellite data will be displayed as following:

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Save it as a shapefile, by right clicking at the file in TOC, go to Data, and then Export
Data

Specify the path of you file and click OK

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ArcGIS will ask you add exported to the map as layer, click yes.

The shapefile is added to the map

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Click on Arc Toolbox Window

Arc Toolbox will open

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Go to Spatial Analyst Tool, Select Interpolation and then select IDW

Double Click on IDW Tool, a popup window will open

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Input your shapefile, specify Z-value as no2 and output path, Input cell size as
0.0090440444966989, click OK

The interpolated raster image will be prepared in a while; you should give a suitable
color ramp to present your pollution levels more conveniently

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You can add you project area shapefile to represent your pollution levels at different
locations

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