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 ...@@ -7,8 +7,193 @@ CeSAM (Centre de donnéeS Astrophysique de Marseille) at LAM (Laboratoire d'Astr
# About photos_montage_aladin: # 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 # 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 # 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 # 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() ...@@ -158,30 +158,30 @@ function_message()
echo "" echo ""
echo "-i, --infos give informations about versions available on aladin server" echo "-i, --infos give informations about versions available on aladin server"
echo " and about photos_montage_aladin image present on localhost" echo " and about photos_montage_aladin image present on localhost"
echo "-b version, --build version build photos_montage_aladin image with selected version" 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 "--select VERSION run photos_montage_aladin with selected version number"
echo "--force-all re-run all areas in input csv" 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 "-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 "-h, --help show this help message and exit"
echo "-v, --version give photos_montage_aladin.sh current version number" echo "-v, --version give photos_montage_aladin.sh current version number"
echo "" echo ""
echo "" echo ""
echo "OTHERS:" echo "OTHERS: (available only with no option OR with --select option)"
echo "" 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 "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 "the default file define on .env file. the area file must be on format '.csv'"
echo "" 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 "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_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 "--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_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 "--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 "--mount PATH run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo "" echo ""
fi fi
......
...@@ -152,37 +152,37 @@ function_message() ...@@ -152,37 +152,37 @@ function_message()
echo "" echo ""
echo "------------------------------------" echo "------------------------------------"
echo "" echo ""
echo "use : ./photos_montage_aladin.sh [options] [others]" echo "use : ./photos_montage_aladin_osx.sh [options] [others]"
echo "" echo ""
echo "" echo ""
echo "OPTIONS:" echo "OPTIONS:"
echo "" echo ""
echo "-i, --infos give informations about versions available on aladin server" echo "-i, --infos give informations about versions available on aladin server"
echo " and about photos_montage_aladin image present on localhost" echo " and about photos_montage_aladin image present on localhost"
echo "-b version, --build version build photos_montage_aladin image with selected version" 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 "--select VERSION run photos_montage_aladin with selected version number"
echo "--force-all re-run all areas in input csv" 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 "-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 "-h, --help show this help message and exit"
echo "-v, --version give photos_montage_aladin.sh current version number" echo "-v, --version give photos_montage_aladin.sh current version number"
echo "" echo ""
echo "" echo ""
echo "OTHERS:" echo "OTHERS: (available only with no option OR with --select option)"
echo "" 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 "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 "the default file define on .env file. the area file must be on format '.csv'"
echo "" 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 "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_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 "--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_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 "--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 "--mount PATH run photos_montage_aladin with a volume mounted on docker container repository /mnt"
echo "" echo ""
fi fi
......
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