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insert aeroprofile and atmosprofile to tutorial #17

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40 changes: 31 additions & 9 deletions doc/source/tutorials.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,3 @@



Tutorial
============

Expand Down Expand Up @@ -63,6 +60,7 @@ To use ARCSI to generate a surface reflectance product (alongside top of atmosph
.. code-block:: bash

arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.25 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 -o ./Outputs \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

Expand All @@ -73,13 +71,11 @@ To use ARCSI to generate a surface reflectance product (alongside top of atmosph

``--stats``: specifies that the output images should be populate with statistics and pyramids, makes data display much faster

``-p RAD TOA SREF``: specifies the output products to be generated. You only need to specify what you want, e.g., SREF but if other products (e.g., RAD) are required then these will also be produced even if they are not
specified.
``-p RAD TOA SREF``: specifies the output products to be generated. You only need to specify what you want, e.g., SREF but if other products (e.g., RAD) are required then these will also be produced even if they are not specified.

``--aeropro Maritime``: specifies that the 'Maritime' aerosol profile should be used.

``--atmospro MidlatitudeSummer``: specifies that the 'MidlatitudeSummer' atmosphere profile should be
used.
``--atmospro MidlatitudeSummer``: specifies that the 'MidlatitudeSummer' atmosphere profile should be used.

``--aot 0.25``: specifies that an AOT value of 0.25 will be used for the correction.

Expand Down Expand Up @@ -123,21 +119,25 @@ For example,

# AOT 0.05
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.05 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 -o ./OutputsAOT005 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

# AOT 0.1
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.1 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 -o ./OutputsAOT01 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

# AOT 0.5
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.5 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 -o ./OutputsAOT05 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

# AOT 0.95
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.95 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 -o ./OutputsAOT95 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

Expand Down Expand Up @@ -173,16 +173,19 @@ For example,

# Water Content 0.5
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.25 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 --atmoswater 0.5 --atmosozone 0.9 -o ./OutputsWater05 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

# Water Content 3
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.25 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 --atmoswater 3 --atmosozone 0.9 -o ./OutputsWater3 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

# Water Content 9
arcsi.py -s lstm -f KEA --stats -p RAD TOA SREF --aot 0.25 \
--aeropro Maritime --atmospro MidlatitudeSummer \
--surfacealtitude 0.4 --atmoswater 9 --atmosozone 0.9 -o ./OutputsWater9 \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

Expand All @@ -200,6 +203,7 @@ ARCSI provides a method of doing this using a dark object subtraction (DOS) to e
.. code-block:: bash

arcsi.py -s lstm -f KEA --stats -p RAD DOSAOTSGL SREF METADATA \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsAOTInv --dem ./UKSRTM_90m.kea --tmpath ./tmp \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

Expand All @@ -224,6 +228,7 @@ ARCSI has a number of other products and options which can be applied. However,
.. code-block:: bash

arcsi.py -s lstm -p CLOUDS DOSAOTSGL STDSREF METADATA -o ./OutputsStdSREF/ \
--aeropro Maritime --atmospro MidlatitudeSummer \
--stats --format KEA --tmpath ./tmp \
--dem ./UKSRTM_90m.kea --cloudmethods LSMSK \
--keepfileends stdsref.kea clouds.kea meta.json \
Expand All @@ -236,6 +241,10 @@ Where:

``-o ./OutputsStdSREF/``: directory where outputs will be outputted.

``--aeropro Maritime``: specifies that the 'Maritime' aerosol profile should be used.

``--atmospro MidlatitudeSummer``: specifies that the 'MidlatitudeSummer' atmosphere profile should be used.

``--stats``: statistics and pyramids (overviews) should be created for visualisation.

``--format KEA``: output file formation (i.e., KEA)
Expand Down Expand Up @@ -263,6 +272,7 @@ Depending on your use case you may want to keep more outputs, in this case the t
.. code-block:: bash

arcsi.py -s lstm -p CLOUDS DOSAOTSGL STDSREF SATURATE TOPOSHADOW FOOTPRINT \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsStdSREF2/ --stats --format KEA --tmpath ./tmp \
--dem ./UKSRTM_90m.kea --cloudmethods LSMSK \
--k clouds.kea meta.json sat.kea toposhad.kea valid.kea stdsref.kea \
Expand All @@ -277,6 +287,7 @@ By default the masks generated by ARCSI are applied to the image being processed
.. code-block:: bash

arcsi.py -s lstm -p CLOUDS DOSAOTSGL STDSREF SATURATE TOPOSHADOW FOOTPRINT \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsStdSREFFull/ --stats --format KEA --tmpath ./tmp \
--dem ./UKSRTM_90m.kea --cloudmethods LSMSK \
--fullimgouts --k clouds.kea meta.json sat.kea toposhad.kea valid.kea stdsref.kea \
Expand Down Expand Up @@ -324,6 +335,7 @@ The following command will undertake the same analysis as above but the output w
.. code-block:: bash

arcsi.py -s lstm -p CLOUDS DOSAOTSGL STDSREF SATURATE TOPOSHADOW FOOTPRINT \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsStdSREFOSGB/ --stats --format KEA --tmpath ./tmp --dem ./UKSRTM_90m.kea \
--cloudmethods LSMSK --projabbv osgb --outwkt BritishNationalGrid.wkt \
--k clouds.kea meta.json sat.kea toposhad.kea valid.kea stdsref.kea \
Expand All @@ -342,6 +354,7 @@ The 'clear-sky' product can produced by simply adding ``CLEARSKY`` to the list o
.. code-block:: bash

arcsi.py -s lstm -p CLOUDS DOSAOTSGL STDSREF SATURATE TOPOSHADOW FOOTPRINT CLEARSKY \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsStdSREFClearSky/ --stats --format KEA --tmpath ./tmp \
--dem ./UKSRTM_90m.kea --cloudmethods LSMSK \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt
Expand All @@ -355,6 +368,7 @@ Some sensors (e.g., Landsat) have thermal channels and ARCSI can process these a
.. code-block:: bash

arcsi.py -s lstm -p DOSAOTSGL SREF THERMAL \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsThermal/ --stats --format KEA --tmpath ./tmp --dem ./UKSRTM_90m.kea \
-i LT05_L1TP_203024_19950815_20180217_01_T1/LT05_L1TP_203024_19950815_20180217_01_T1_MTL.txt

Expand All @@ -376,6 +390,7 @@ I have provided a sample Sentinel-2 scene over North Wales, just cutting off Nor
.. code-block:: bash

arcsi.py -s sen2 -f KEA --stats -p DOSAOTSGL SREF METADATA \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsSen2_10m --dem ./UKSRTM_90m.kea --tmpath ./tmp \
-i S2A_MSIL1C_20170617T113321_N0205_R080_T30UVD_20170617T113319.SAFE/MTD_MSIL1C.xml

Expand All @@ -385,6 +400,7 @@ The following command produces a 20 m resolution output:
.. code-block:: bash

arcsi.py -s sen2 -f KEA --stats -p DOSAOTSGL SREF METADATA \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsSen2_20m --dem ./UKSRTM_90m.kea --tmpath ./tmp --resample2lowres \
-i S2A_MSIL1C_20170617T113321_N0205_R080_T30UVD_20170617T113319.SAFE/MTD_MSIL1C.xml

Expand All @@ -394,6 +410,7 @@ Finally, the following command produces a 10 m resolution product where the 20 m
.. code-block:: bash

arcsi.py -s sen2 -f KEA --stats -p DOSAOTSGL SREF METADATA SHARP \
--aeropro Maritime --atmospro MidlatitudeSummer \
-o ./OutputsSen2_10mSharp --dem ./UKSRTM_90m.kea --tmpath ./tmp \
-i S2A_MSIL1C_20170617T113321_N0205_R080_T30UVD_20170617T113319.SAFE/MTD_MSIL1C.xml

Expand All @@ -406,6 +423,7 @@ When running through Sentinel-2 to create an Analysis Ready Data (ARD) product t
.. code-block:: bash

arcsi.py -s sen2 -p CLOUDS DOSAOTSGL STDSREF SHARP METADATA -o ./OutputsSen2ARD/ \
--aeropro Maritime --atmospro MidlatitudeSummer \
--stats --format KEA --tmpath ./tmp --dem ./UKSRTM_90m.kea \
--cloudmethods S2LESSFMSK --keepfileends stdsref.kea clouds.kea meta.json \
-i S2A_MSIL1C_20170617T113321_N0205_R080_T30UVD_20170617T113319.SAFE/MTD_MSIL1C.xml
Expand Down Expand Up @@ -480,6 +498,7 @@ Notice that these are very similar to the individual commands that you previousl
.. code-block:: bash

arcsibuildcmdslist.py -s lstm -f KEA --stats -p CLOUDS DOSAOTSGL STDSREF \
--aeropro Maritime --atmospro MidlatitudeSummer \
--outpath ./Outputs --dem ../UKSRTM_90m.kea --cloudmethods LSMSK \
--keepfileends stdsref.kea clouds.kea \
--tmpath ./tmp -i ./Inputs -e "*MTL.txt" -o LSARCSICmds.sh
Expand All @@ -492,6 +511,7 @@ If you have a selection of landsat scenes from different versions of the sensor
.. code-block:: bash

arcsibuildcmdslist.py -s LANDSAT -f KEA --stats -p CLOUDS DOSAOTSGL STDSREF \
--aeropro Maritime --atmospro MidlatitudeSummer \
--outpath ./Outputs --dem ../UKSRTM_90m.kea --cloudmethods LSMSK \
--keepfileends stdsref.kea clouds.kea \
--tmpath ./tmp -i ./Inputs -e "*MTL.txt" -o LSARCSICmds.sh
Expand Down Expand Up @@ -528,10 +548,11 @@ As an example, the following command was used to process several thousand Sentin
.. code-block:: bash

arcsibuildcmdslist.py -i ./Inputs -o ./Sen2ARCSICmds.sh \
--aeropro Maritime --atmospro MidlatitudeSummer \
-e "*MTD*.xml" -d 1 -f KEA --stats --outpath ./Outputs --cloudmethods LSMSK \
-p RAD SATURATE TOPOSHADOW TOA CLOUDS DOSAOTSGL SREF STDSREF SHARP FOOTPRINT METADATA \
-s sen2 --checkouts --fullimgouts --outproj4 ./osgb_proj4.prj \
--projabbv osgb --tmpath ./tmp --dem ./SRTM_1arc_UK.kea
--projabbv osgb --tmpath ./tmp --dem ./UKSRTM_90m.kea


Downloading Landsat and Sentinel-2 Data
Expand Down Expand Up @@ -602,7 +623,8 @@ To download image for the French Guiana coast to assess mangrove change then the

Note. the ``--lstcmds`` switch requests that the full commands are outputted rather than just the urls and ``--multi`` specifies that multiple connections are used for the download.

### Perform Download
Perform Download
~~~~~~~~~~~~~~~~~~~~

To perform the download requires that the Google Cloud tools are downloaded and set up on your machine such that the ``gsutils`` commands is available on your system.

Expand Down