DOC: update markdown

README.md

@@ -29,7 +29,7 @@ ClearCutsDetection in an OTBApplication.
 It can be used as any OTB application (gui, command line, python, c++, ...).
 
 ```
-This is the ClearCutsDetection (ClearCutsDetection) application, version 6.1.0
+This is the ClearCutsDetection (ClearCutsDetection) application, version 6.2.0
 
 This application performs cuts detection, from two input images and an optional forest mask
 Parameters: 
@@ -63,9 +63,58 @@ Clear cuts detection are computed from a stack or multiple images (typicaly LS o
 
 ### How to use it
 
-ClearCutsMultitemporalDetection in an OTBApplication.
+ClearCutsMultitemporalDetection is an OTBApplication.
 It can be used as any OTB application (gui, command line, python, c++, ...).
 
+```
+This is the ClearCutsMultitemporalDetection application, version 6.2.0
+Performs clear cuts detection from NDVI time series
+
+Parameters: 
+        -progress              <boolean>        Report progress 
+MISSING -il                    <string list>    Input time series  (mandatory)
+MISSING -dates                 <string>         Input time series dates ASCII file (Must be YYYYMMDD format)  (mandatory)
+        -masksdir              <string>         Vegetation masks directory  (optional, off by default)
+        -backward.tmax         <int32>          Limit, in number of days, to look backward  (optional, on by default, default value is 730)
+        -backward.nmin         <int32>          Minimum number of valid pixel inside backward range  (optional, on by default, default value is 5)
+        -forward.tmax          <int32>          Limit, in number of days, to look forward  (optional, on by default, default value is 62)
+        -forward.nmin          <int32>          Minimum number of valid pixel inside forward range  (optional, on by default, default value is 2)
+        -clouds.threshold      <float>          Clouds drop threshold  (optional, on by default, default value is 0.4)
+        -clouds.tmax           <int32>          Limit, in number of days, for rejecting NDVI drop due to clouds.  (optional, on by default, default value is 40)
+        -veg.threshold         <float>          Vegetation threshold  (optional, on by default, default value is 0.4)
+        -range.start.day       <int32>          Detection range start (day)  (optional, on by default, default value is 1)
+        -range.start.month     <int32>          Detection range start (month)  (optional, on by default, default value is 5)
+        -range.end.day         <int32>          Detection range end (day)  (optional, on by default, default value is 31)
+        -range.end.month       <int32>          Detection range end (month)  (optional, on by default, default value is 8)
+        -sfilter               <string>         Spatial filtering method [none/connect/morpho] (mandatory, default value is none)
+        -sfilter.connect.size  <int32>          Minimum number of pixels  (mandatory, default value is 5)
+        -sfilter.morpho.radius <int32>          Radius of the spatial filter  (optional, on by default, default value is 1)
+        -sfilter.morpho.struct <string>         Structuring element type [ball/cross] (mandatory, default value is ball)
+        -sfilter.morpho.op     <string>         Operation type [open] (mandatory, default value is open)
+        -thresholds            <string list>    NDVI drop thresholds (defaults: 0.0 0.3 0.4 1.0)  (optional, off by default)
+        -nodata                <float>          Input NDVI no-data value  (optional, on by default, default value is -2)
+        -inputscale            <float>          Input scale  (optional, on by default, default value is 1)
+        -outvec                <string>         Output vector layer  (optional, off by default)
+        -outlabel              <string> [pixel] Output label image  [pixel=uint8/uint16/int16/uint32/int32/float/double] (default value is uint8) (optional, off by default)
+        -ram                   <int32>          Available RAM (Mb)  (optional, off by default, default value is 128)
+        -inxml                 <string>         Load otb application from xml file  (optional, off by default)
+
+Examples: 
+otbcli_ClearCutsMultitemporalDetection -il im1.tif im2.tif ... imN.tif -dates dates.txt -outlabel cuts.shp -thresholds 0.0 0.3 0.4 0.5 1.0
+
+```
+
+### Additional scripts
+
+In the _scripts_ folder, there is some bash scripts which enables the large scale processing of the multitemporal clear cuts detection application.
+Here is some description of the files:
+* _LoadEnvironmentVariables.sh_ contains every environment variables (paths, parameters) to deploy the framework: its the only script you need to modify,
+* _DownloadTheiaProducts.sh_ once executed, this script goes to THEIA and retrieve tiles. NDVI images are then computed and stored then the entire downloaded archive is remove to save disk space,
+* _ProcessTimeSeries.sh_ once executed, this script process the detection of clear cuts over the available NDVI tiles,
+* _BashUtils.sh_ is a set of low level bash functions,
+* _ProcessArchive.sh_ is called by _DownloadTheiaProducts.sh_ to process one downloaded archive.
+Basically, the only script you need to modify is _LoadEnvironmentVariables.sh_ to set up the system. The only thing you need to do then, is to execute _DownloadTheiaProducts.sh_ then _ProcessTimeSeries.sh_.
+
 Licence
 =======
 
@@ -76,7 +125,7 @@ Contact
 
 For any issues regarding this module please contact Rémi Cresson.
 
-remi.cresson@teledetection.fr
+remi.cresson at irstea.fr
 
 Irstea ((French) National Research Institute of Science and Technology for Environment and Agriculture)
 www.irstea.fr