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IREA-CNR-MI · Jun 8, 2020 · 00e59bd · 00e59bd
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diff --git a/README.md b/README.md
@@ -23,147 +23,27 @@ Italy (CNR-IREA)*
 
 # Installation
 
-You can install the development version from
-[GitHub](https://github.com/) with:
+You can install the last stable version of `prismaread` from
+[GitHub](https://github.com/) using:
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("lbusett/prismaread")
+remotes::install_github("lbusett/prismaread", ref = "v0.2.0")
 library(prismaread)
 ```
 
-# Importing Level 1 Data
-
-The function to be used is `convert_prisma`. It takes as input the full
-path of a PRISMA L1 hdf5 image, an output file name and format, and a
-series of switches allowing to decide which datasets should be saved.
-
-In particular, the `FULL` argument allows deciding if a complete
-VNIR+SWIR cube has to be created alongside the “single” VNIR and SWIR
-ones. In that case, the ‘join\_priority’ keyword is used to decide if
-keeping bands from the “VNIR” or the “SWIR” data cube in the wavelength
-were they overlap.
-
-A “base” georeferincing in Lat/Lon WGS-84 based on the “GLT and Bowtie
-Correction” technique used in ENVI, and described in
-<https://www.harrisgeospatial.com/docs/backgroundgltbowtiecorrection.html>,
-unless the `base_georef` argument is set to FALSE.
-
-For example the following code:
+, or the last development version using:
 
 ``` r
-in_file  = "/home/lb/tmp/test/PRS_L1_STD_OFFL_20190825103112_20190825103117_0001.he5"
-out_file = "/home/lb/tmp/test/test_1"
-out_format = "ENVI"
-
-# Save a full image, prioritizing the VNIR spectrometer and save in EVI format
-convert_prisma(in_file    = in_file,
-               out_file   = out_file,
-               out_format = out_format,
-               join_priority = "VNIR", 
-               FULL = TRUE,
-               PAN  = TRUE,
-               CLOUD  = TRUE)
+# install.packages("remotes")
+remotes::install_github("lbusett/prismaread")
+library(prismaread)
 ```
 
-accesses the input file and saves both the VNIR and SWIR cubes, as well
-as a full hyperspectral cube and the PAN and CLOUD images. **See
-[documentation](reference/convert_prisma.html) of the convert\_prisma()
-function for info on available arguments**.
-
-The function also saves ancillary data related to wavelengths and fwhms
-of the different images, and to hour and sun geometry at acquisition in
-ancillary txt files.
-
-### Creation of ATCOR files
-
-Starting `v0.02` the function also allows automatic creation of text
-files required to run an ATCOR atmospheric correction. Those files are
-saved in the `ATCOR` subfolder of the main output folder.
-
-In “standard” behaviour, only the three “standard” ATCOR files (`.wvl`,
-`.dat` and `.cal`) are created, with the `.wvl` file containing nominal
-wavelengths and FWHMs derived from the `cw` and `fwhm` attributes of the
-*.he5* file- The user can however also choose to generate additional
-ATCOR files, containing data about wavelengths and FWHMs related to
-different “columns” of the data cube, as derived from the
-`KDP_AUX/Cw_Vnir_Matrix`, `KDP_AUX/Cw_Swir_Matrix`,
-`KDP_AUX/Cw_Fwhm_Matrix`, `KDP_AUX/Cw_Fwhm_Matrix` HDF layers. This
-could allow running different atmospheric corrections for different
-columns of the data, potentially allowing compensating “smile” effects
-on the retrieved surface reflectances. For example:
-
-``` r
-in_file  = "/home/lb/tmp/test/PRS_L1_STD_OFFL_20190825103112_20190825103117_0001.he5"
-out_file = "/home/lb/tmp/test/test_1"
-out_format = "ENVI"
-
-# Save a full image, prioritizing the VNIR spectrometer and save in EVI format
-convert_prisma(in_file    = in_file,
-               out_file   = out_file,
-               out_format = out_format,
-               join_priority = "VNIR", 
-               ATCOR = TRUE, 
-               ATCOR_wls = c(200,800), 
-               FULL = TRUE,
-               PAN  = TRUE,
-               CLOUD  = TRUE)
-```
+# Usage
 
-**IMPORTANT NOTE**
-
-The latter functionality may be only appliable to “HRC” L1 data cubes.
-We are currently investigating this - proceed with caution\!
-
-# Work on Level 2 Data
-
-The function to be used is still `convert_prisma`, with similar syntax.
-Only differences are:
-
-1.  The “PAN”, “CLOUD”, “LC” and “GLINT” arguments are ignored, because
-    they are not available in L2 files;
-2.  The “ATCOR” and “ATCOR\_wls” arguments are ignored, because they are
-    useless in this case;
-3.  The output imagery is properly georeferenced, **if level is 2D**.
-    Otherwise, the same “ballpark” georeferencing as for L1 data is
-    applied.
-
-# Output Formats
-
-  - Outputs are provided as rasters in **ENVI** or **GEOTIFF** format
-    according to user’s choice.
-
-  - Filenames are built starting from the output file name provided by
-    the user, by adding appropriate suffixes. For example, if the user
-    specified `out_file = "D:/myoutfolder/myoutfil"`, and `source =
-    "HCO"`, the output file for the VNIR cube will be
-    `D:/myoutfolder/myoutfil_HCO_VNIR.envi` (or
-    `D:/myoutfolder/myoutfil_HCO_VNIR.tif`).
-
-  - Measure units of the output hyperspectral data are as follows:
-
-    | LEVEL |  Variable   |    Measure Units    |
-    | :---: | :---------: | :-----------------: |
-    |  L1   |  Radiance   | W / m^2 \* sr \* um |
-    |  L2B  |  Radiance   | W / m^2 \* sr \* um |
-    |  L2C  | Reflectance |  unitless (ratio)   |
-    |  L2D  | Reflectance |  unitless (ratio)   |
-
-
-  - If output format is “ENVI”, the wavelengths of the different bands
-    for the hyperspectral cubes are properly written in the appropriate
-    header (.hdr) file.
-
-  - Irrespective from output format, info about wavelengths and fwhms of
-    the hyperspectral cubes are saved in appropriate txt files. For
-    example, if the output file is
-    `D:/myoutfolder/myoutfil_HCO_VNIR.envi`, info about the wavelengths
-    is saved in `D:/myoutfolder/myoutfil_HCO_VNIR_meta.txt`
-
-  - Info about acquisition date and angles is saved in a dedicated txt
-    file. For example, if output file is
-    `D:/myoutfolder/myoutfil_VNIR.envi`, info about the angles is saved
-    in `D:/myoutfolder/myoutfil_HCO_VNIR_meta.txt`
+See `prismaread` [website](https://lbusett.github.io/prismaread/) for
+further instructions and info on output formats.
 
 # Future Work
 

diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/index.md b/index.md
@@ -38,17 +38,14 @@ See the **Articles** section of the website for detailed info on usage.
 
   - Instructions for importing PRISMA
     [**L1**](articles/Importing-Level-1-Data.html) and
-    [**L2**](docs/articles/Importing-Level-2-Data.html)
+    [**L2**](articles/Importing-Level-2-Data.html)
 
   - Info about [Output format and Naming
     Conventions](articles/Output-Format-and-Naming.html)
 
-  - Info about [Creation of ATCOR input
-    files](articles/Creation-of-ATCOR-files.html)
-
   - Instructions for extracting PRISMA data over features of a vector
     dataset [Extracting Data from PRISMA
-    images](articles/Extract-Data.html)
+    images](articles/Extracting-data-over-vector.html)
 
 # Future Work