Update documentation

_sources/tutorials.rst.txt

@@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
 Using Singularity
 *****************
 
-'Singularity <https://sylabs.io/>'_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud...
-A container is a single file without anything else to install
+[Singularity](https://sylabs.io/) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources.
+A container is a single file without anything else to install.
 
 Downloading image
 =================
 Singularity can use ODM Docker container after their download. It creates .sif images
 
-For latest ODM Docker image
+For latest ODM Docker image (Recommended)
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:latest
+   singularity pull --disable-cache  docker://opendronemap/odm:latest
 
 For latest ODM GPU Docker image
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:gpu
+   singularity pull --disable-cache  docker://opendronemap/odm:gpu
 
 Using Singularity SIF image
 ===========================
 
-As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories. 
-Here is a linux example for ODM ::
+Once you have used one of the above commands to download and create the `odm_latest.sif` image, it can be ran using singularity. 
+Place your images in a directory named “images” (for example /my/project/images) , then simply run
 
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
-
-
-Here is a linux example for the ODM with GPU ::
-
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
+..code:: bash
 
+   singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets
 
+Like with docker, additional Options and Flags can be added to the command.
 
 *************************************
 Using ODM from low-bandwidth location

cs/_sources/tutorials.rst.txt

@@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
 Using Singularity
 *****************
 
-'Singularity <https://sylabs.io/>'_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud...
-A container is a single file without anything else to install
+[Singularity](https://sylabs.io/) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources.
+A container is a single file without anything else to install.
 
 Downloading image
 =================
 Singularity can use ODM Docker container after their download. It creates .sif images
 
-For latest ODM Docker image
+For latest ODM Docker image (Recommended)
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:latest
+   singularity pull --disable-cache  docker://opendronemap/odm:latest
 
 For latest ODM GPU Docker image
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:gpu
+   singularity pull --disable-cache  docker://opendronemap/odm:gpu
 
 Using Singularity SIF image
 ===========================
 
-As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories. 
-Here is a linux example for ODM ::
+Once you have used one of the above commands to download and create the `odm_latest.sif` image, it can be ran using singularity. 
+Place your images in a directory named “images” (for example /my/project/images) , then simply run
 
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
-
-
-Here is a linux example for the ODM with GPU ::
-
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
+..code:: bash
 
+   singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets
 
+Like with docker, additional Options and Flags can be added to the command.
 
 *************************************
 Using ODM from low-bandwidth location

cs/flowchart/index.html

@@ -24,7 +24,7 @@
         <script src="https://unpkg.com/d3/dist/d3.min.js"></script>
         <script>
                 window.addEventListener("load", function () {
-                  var svgs = d3.selectAll(".mermaid#id-dc547208-7dbe-419c-ba88-117a7403453f svg");
+                  var svgs = d3.selectAll(".mermaid#id-4f9d4b40-c51b-4635-bea3-66a3880d2bfa svg");
                   svgs.each(function() {
                     var svg = d3.select(this);
                     svg.html("<g>" + svg.html() + "</g>");
@@ -442,7 +442,7 @@
 
   <section id="flowchart-with-options">
 <h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
-<div id="id-dc547208-7dbe-419c-ba88-117a7403453f" class="mermaid">
+<div id="id-4f9d4b40-c51b-4635-bea3-66a3880d2bfa" class="mermaid">
              flowchart  TB
 
 

cs/tutorials/index.html

@@ -641,55 +641,23 @@ <h3>Úklid po Dockeru<a class="headerlink" href="#cleaning-up-after-docker" titl
 </section>
 <section id="using-singularity">
 <h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
-<p>‚Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;‘_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud…
-A container is a single file without anything else to install</p>
+<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources.
+A container is a single file without anything else to install.</p>
 <section id="downloading-image">
 <h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
 <p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
-<p>For latest ODM Docker image</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w">  </span>docker://opendronemap/odm:latest
-</pre></div>
-</div>
+<p>For latest ODM Docker image (Recommended)</p>
 <p>For latest ODM GPU Docker image</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w">  </span>docker://opendronemap/odm:gpu
-</pre></div>
-</div>
 </section>
 <section id="using-singularity-sif-image">
 <h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
-<p>As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories.
-Here is a linux example for ODM</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>images_dir=/path_to_image_dir/
-name=`basename $images_dir`
-output_dir=/path_to_output_directories/$name
-mkdir -p $output_dir
-
-singularity run
---bind $images_dir:/$output_dir/code/images,\
---writable-tmpfs odm_latest.sif  \
---orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
---smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
---ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
---use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
---project-path $output_dir
-</pre></div>
-</div>
-<p>Here is a linux example for the ODM with GPU</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>images_dir=/path_to_image_dir/
-name=`basename $images_dir`
-output_dir=/path_to_output_directories/$name
-mkdir -p $output_dir
-
-singularity run
---bind $images_dir:/$output_dir/code/images,\
---writable-tmpfs odm_latest.sif  \
---orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
---smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
---ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
---use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
---project-path $output_dir
-</pre></div>
-</div>
+<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
+Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
+<p>..code:: bash</p>
+<blockquote>
+<div><p>singularity run –bind /my/project:datasets/code odm_latest.sif –project-path /datasets</p>
+</div></blockquote>
+<p>Like with docker, additional Options and Flags can be added to the command.</p>
 </section>
 </section>
 <section id="using-odm-from-low-bandwidth-location">

es/_sources/tutorials.rst.txt

@@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
 Using Singularity
 *****************
 
-'Singularity <https://sylabs.io/>'_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud...
-A container is a single file without anything else to install
+[Singularity](https://sylabs.io/) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources.
+A container is a single file without anything else to install.
 
 Downloading image
 =================
 Singularity can use ODM Docker container after their download. It creates .sif images
 
-For latest ODM Docker image
+For latest ODM Docker image (Recommended)
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:latest
+   singularity pull --disable-cache  docker://opendronemap/odm:latest
 
 For latest ODM GPU Docker image
 
 .. code:: bash
-  
-  > singularity pull --disable-cache  docker://opendronemap/odm:gpu
+   singularity pull --disable-cache  docker://opendronemap/odm:gpu
 
 Using Singularity SIF image
 ===========================
 
-As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories. 
-Here is a linux example for ODM ::
+Once you have used one of the above commands to download and create the `odm_latest.sif` image, it can be ran using singularity. 
+Place your images in a directory named “images” (for example /my/project/images) , then simply run
 
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
-
-
-Here is a linux example for the ODM with GPU ::
-
-   images_dir=/path_to_image_dir/
-   name=`basename $images_dir`
-   output_dir=/path_to_output_directories/$name
-   mkdir -p $output_dir 
-
-   singularity run
-   --bind $images_dir:/$output_dir/code/images,\
-   --writable-tmpfs odm_latest.sif  \
-   --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \
-   --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \
-   --ignore-gsd  --matcher-type flann --feature-quality ultra --max-concurrency 16 \
-   --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \
-   --project-path $output_dir
+..code:: bash
 
+   singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets
 
+Like with docker, additional Options and Flags can be added to the command.
 
 *************************************
 Using ODM from low-bandwidth location

es/flowchart/index.html

@@ -24,7 +24,7 @@
         <script src="https://unpkg.com/d3/dist/d3.min.js"></script>
         <script>
                 window.addEventListener("load", function () {
-                  var svgs = d3.selectAll(".mermaid#id-0ca248c5-781d-4a82-9e25-b7b1299a76c3 svg");
+                  var svgs = d3.selectAll(".mermaid#id-147597ca-9f3d-49db-a833-53384613f7a8 svg");
                   svgs.each(function() {
                     var svg = d3.select(this);
                     svg.html("<g>" + svg.html() + "</g>");
@@ -442,7 +442,7 @@
 
   <section id="flowchart-with-options">
 <h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Enlace permanente a este encabezado"></a></h1>
-<div id="id-0ca248c5-781d-4a82-9e25-b7b1299a76c3" class="mermaid">
+<div id="id-147597ca-9f3d-49db-a833-53384613f7a8" class="mermaid">
              flowchart  TB