Commit 11b32456 authored by PENGUEN Julien's avatar PENGUEN Julien

mise à jour README + infos de l'HELP pour les version linux et macos

parent 20b92f89
......@@ -7,8 +7,193 @@ CeSAM (Centre de donnéeS Astrophysique de Marseille) at LAM (Laboratoire d'Astr
# About photos_montage_aladin:
photos_montage_aladin is a SHELL script use to launch [aladin](https://aladin.u-strasbg.fr/aladin-f.gml) with Docker.
This project allow to build a docker image with last `aladin` jar version in order to retrieve automatically images of areas of space (see template_inputs/areas.csv file format) for differents surveys (see template_inputs/surveys.dat file format) and to assemble theses images into one or more mosaics with `imagemagick` tool.
The photos_montage_aladin repository is composed of:
- `conf-montage` folder containing Dockerfile to build the docker image of photos_montage_aladin.
- `template_inputs` folder containing template input files (__areas.csv__ and __surveys.dat__)
- script `photos_montage_aladin.sh` for linux users
- script `photos_montage_aladin_osx.sh` for MAC-OS users
- `.env` file containing environment variables useful for scripts
- `README.md` the readme file
here we have example of template input files format that we must respect imperatively:
-`areas.csv`:
```
id,name,la,ld,ra,dec
878357,HIGALBM348.1809-0.4702,348.180903,0.470223,258.04739,-38.521825
878358,HIGALBM349.1809-0.4802,349.180903,0.480223,258.04739,-38.521825
etc ...
```
-`surveys.dat`:
```
CDS/P/DSS2/red
CDS/P/2MASS/J
CDS/P/2MASS/H
CDS/P/2MASS/K
CDS/P/2MASS/color
CDS/P/allWISE/W1
CDS/P/allWISE/W2
CDS/P/allWISE/W3
CDS/P/allWISE/W4
CDS/P/allWISE/color
CDS/P/SPITZER/IRAC1
CDS/P/SPITZER/IRAC2
CDS/P/SPITZER/IRAC3
CDS/P/SPITZER/IRAC4
CDS/P/SPITZER/color
ESAVO/P/HERSCHEL/PACS70norm
ESAVO/P/HERSCHEL/PACS160norm
ESAVO/P/HERSCHEL/SPIRE250norm
ESAVO/P/HERSCHEL/SPIRE350norm
ESAVO/P/HERSCHEL/SPIRE500norm
CDS/P/ATLASGAL
```
To launch photos_montage_aladin there are two scripts:
- `photos_montage_aladin.sh` for linux users
- `photos_montage_aladin_osx.sh` for MAC-OS users
The photos_montage_aladin script `photos_montage_aladin.sh` (or `photos_montage_aladin_osx.sh` for MAC-OS users) provides output folder `.photos_montage_aladin` on personnal home user folder (__$HOME__ for linux users, __/Users/$USER__ for MAC-OS users ). this output folder contains a folder for each area in areas.csv input file.
For an area folder whe have:
- `images` folder containing images
- `montages` folder containing the mosaic(s)
- `area_[AREA_NAME].ajs` self-generated file containing macro command for aladin
- `[AREA_NAME].log` log of aladin
- `infos_[AREA_NAME].txt` informations about building images and montages
# Requirements
**WARNING**: As photos_montage_aladin scripts use "Bash associative array", you must have bash 4.0+
__*note*__: to see which version of the software you are using:
```
which bash
bash --version
```
1. For Linux users:
* You must have docker on your computer.(see [linux docker installation](https://docs.docker.com/install/))
2. For MAC-OS users:
* You must have docker on your mac.(see [Mac-OS docker installation](https://docs.docker.com/docker-for-mac/install/))
# Installation
1. Clone the photos_montage_aladin repository:
```
git@gitlab.lam.fr:CeSam_TOOLS/photos_montage_aladin.git
```
2. Launch the `photos_montage_aladin.sh` (or `photos_montage_aladin_osx.sh` for MAC-OS users) to create photos_montage_aladin docker image, build and launch photos_montage_aladin docker container :
```
./photos_montage_aladin.sh
```
# How to use photos_montage_aladin
To see all options available for a good use of `photos_montage_aladin.sh` (or `photos_montage_aladin_osx.sh` for MAC-OS users) make:
```
./photos_montage_aladin.sh -h OR --help
```
### Here are the options available in detail:
1. Get photos_montage_aladin script information, options available:
```
./photos_montage_aladin.sh -h OR --help
```
2. Get photos_montage_aladin image version available on Aladin server and on localhost:
```
./photos_montage_aladin.sh -i OR --infos
```
3. Build photos_montage_aladin image with selected VERSION:
```
./photos_montage_aladin.sh -b VERSION OR --build VERSION
```
4. Select a specific photos_montage_aladin image VERSION:
```
./photos_montage_aladin.sh --select VERSION
```
5. force the script to re-run all areas in input csv
```
./photos_montage_aladin.sh --force-all
```
6. force the script to re-run a specific area of the input csv
```
./photos_montage_aladin.sh --force AREA
```
7. Update the current photos_montage_aladin image:
```
./photos_montage_aladin.sh -u OR --update
```
8. Remove photos_montage_aladin image with selected VERSION:
```
./photos_montage_aladin.sh -rm VERSION OR --remove VERSION
```
7. Give script photos_montage_aladin.sh current version number:
```
./photos_montage_aladin.sh -v OR --version
```
### Here are the others options available `only` with :
```
./photos_montage_aladin.sh
or
./photos_montage_aladin.sh --select VERSION
```
in other case the others options have no results or effects
1. run photos_montage_aladin with this survey file (FILE) instead of
the default file define on .env file. the survey file must be on format '.dat' and respect the surveys.dat file format:
```
./photos_montage_aladin.sh --survey FILE
```
2. run photos_montage_aladin with this area file (FILE) instead of
the default file define on .env file. the area file must be on format '.csv' and respect the areas.csv file format:
```
./photos_montage_aladin.sh --area FILE
```
3. run photos_montage_aladin with angular dimension value instead of
the default angular value define on .env file. the angular value must be on second of arc:
```
./photos_montage_aladin.sh --angular NUMBER
```
4. run photos_montage_aladin with this number of pixel by columns for the Image Magick montages instead of the default value define on .env file:
```
./photos_montage_aladin.sh --resolution_col NUMBER
```
5. run photos_montage_aladin with this number of pixel by lines for the Image Magick montages instead of the default value define on .env file:
```
./photos_montage_aladin.sh --resolution_line NUMBER
```
6. run photos_montage_aladin with this number of tiles by columns for the Image Magick montages montages instead of the default value define on .env file:
```
./photos_montage_aladin.sh --nb_tile_col NUMBER
```
7. run photos_montage_aladin with this number of tiles by lines for the Image Magick montages montages instead of the default value define on .env file:
```
./photos_montage_aladin.sh --nb_tile_line NUMBER
```
8. run photos_montage_aladin with a volume mounted on docker container repository /mnt instead of no volume mounted define by default on .env file:
```
./photos_montage_aladin.sh --mount PATH
```
......@@ -158,30 +158,30 @@ function_message()
echo ""
echo "-i, --infos give informations about versions available on aladin server"
echo " and about photos_montage_aladin image present on localhost"
echo "-b version, --build version build photos_montage_aladin image with selected version"
echo "--select version run photos_montage_aladin with selected version number"
echo "-b version, --build VERSION build photos_montage_aladin image with selected version"
echo "--select VERSION run photos_montage_aladin with selected version number"
echo "--force-all re-run all areas in input csv"
echo "--force area re-run for the area, the area must be in input csv"
echo "--force AREA re-run for the area, the area must be in input csv"
echo "-u, --update update photos_montage_aladin image version"
echo "-rm version, --remove version remove photos_montage_aladin image with selected version"
echo "-rm version, --remove VERSION remove photos_montage_aladin image with selected version"
echo "-h, --help show this help message and exit"
echo "-v, --version give photos_montage_aladin.sh current version number"
echo ""
echo ""
echo "OTHERS:"
echo "OTHERS: (available only with no option OR with --select option)"
echo ""
echo "--survey file run photos_montage_aladin with this survey file instead of "
echo "--survey FILE run photos_montage_aladin with this surveys file instead of "
echo "the default file define on .env file. the survey file must be on format '.dat'"
echo "--area file run photos_montage_aladin with this survey file instead of "
echo "--area FILE run photos_montage_aladin with this areas file instead of "
echo "the default file define on .env file. the area file must be on format '.csv'"
echo ""
echo "--angular number run photos_montage_aladin with this angular dimension value instead of "
echo "--angular NUMBER run photos_montage_aladin with this angular dimension value instead of "
echo "the default angular value define on .env file. the angular value must be on second of arc"
echo "--resolution_col number run photos_montage_aladin with this number of pixel by columns for the Image Magick montages"
echo "--resolution_line number run photos_montage_aladin with this number of pixel by lines for the Image Magick montages"
echo "--nb_tile_col number run photos_montage_aladin with this number of tiles by columns for the Image Magick montages"
echo "--nb_tile_line number run photos_montage_aladin with this number of tiles by lines for the Image Magick montages"
echo "--mount path run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo "--resolution_col NUMBER run photos_montage_aladin with this number of pixel by columns for the Image Magick montages"
echo "--resolution_line NUMBER run photos_montage_aladin with this number of pixel by lines for the Image Magick montages"
echo "--nb_tile_col NUMBER run photos_montage_aladin with this number of tiles by columns for the Image Magick montages"
echo "--nb_tile_line NUMBER run photos_montage_aladin with this number of tiles by lines for the Image Magick montages"
echo "--mount PATH run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo ""
fi
......
......@@ -152,37 +152,37 @@ function_message()
echo ""
echo "------------------------------------"
echo ""
echo "use : ./photos_montage_aladin.sh [options] [others]"
echo "use : ./photos_montage_aladin_osx.sh [options] [others]"
echo ""
echo ""
echo "OPTIONS:"
echo ""
echo "-i, --infos give informations about versions available on aladin server"
echo " and about photos_montage_aladin image present on localhost"
echo "-b version, --build version build photos_montage_aladin image with selected version"
echo "--select version run photos_montage_aladin with selected version number"
echo "-b version, --build VERSION build photos_montage_aladin image with selected version"
echo "--select VERSION run photos_montage_aladin with selected version number"
echo "--force-all re-run all areas in input csv"
echo "--force area re-run for the area, the area must be in input csv"
echo "--force AREA re-run for the area, the area must be in input csv"
echo "-u, --update update photos_montage_aladin image version"
echo "-rm version, --remove version remove photos_montage_aladin image with selected version"
echo "-rm version, --remove VERSION remove photos_montage_aladin image with selected version"
echo "-h, --help show this help message and exit"
echo "-v, --version give photos_montage_aladin.sh current version number"
echo ""
echo ""
echo "OTHERS:"
echo "OTHERS: (available only with no option OR with --select option)"
echo ""
echo "--survey file run photos_montage_aladin with this survey file instead of "
echo "--survey FILE run photos_montage_aladin with this surveys file instead of "
echo "the default file define on .env file. the survey file must be on format '.dat'"
echo "--area file run photos_montage_aladin with this survey file instead of "
echo "--area FILE run photos_montage_aladin with this areas file instead of "
echo "the default file define on .env file. the area file must be on format '.csv'"
echo ""
echo "--angular run photos_montage_aladin with this angular dimension value instead of "
echo "--angular NUMBER run photos_montage_aladin with this angular dimension value instead of "
echo "the default angular value define on .env file. the angular value must be on second of arc"
echo "--resolution_col number run photos_montage_aladin with this number of pixel by columns for the Image Magick montages"
echo "--resolution_line number run photos_montage_aladin with this number of pixel by lines for the Image Magick montages"
echo "--nb_tile_col number run photos_montage_aladin with this number of tiles by columns for the Image Magick montages"
echo "--nb_tile_line number run photos_montage_aladin with this number of tiles by lines for the Image Magick montages"
echo "--mount path run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo "--resolution_col NUMBER run photos_montage_aladin with this number of pixel by columns for the Image Magick montages"
echo "--resolution_line NUMBER run photos_montage_aladin with this number of pixel by lines for the Image Magick montages"
echo "--nb_tile_col NUMBER run photos_montage_aladin with this number of tiles by columns for the Image Magick montages"
echo "--nb_tile_line NUMBER run photos_montage_aladin with this number of tiles by lines for the Image Magick montages"
echo "--mount PATH run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo ""
fi
......
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