Merge branch 'develop' of git.mpi-cbg.de:mosaic/MosaicSuite into develop

doc/source/backgroundSubtraction.rst

@@ -17,8 +17,20 @@ by S.Steinberg (1983).
 
     Background Subtraction in action
 
+
+Running Background Subtractor plugin in ImageJ macro.
+-----------------------------------------------------
+
+Very often there is a need to process multiple TIFF files. This process can be
+simplify by using following macro.
+
+.. literalinclude:: resources/macros/runBgSubtracktor.ijm
+    :language: java
+    :linenos:
+
+
 Algorithm Description
-=====================
+---------------------
 
-For better algorithm understanding please refer to `Histogram-based background subtractor forImageJ <http://mosaic.mpi-cbg.de/Downloads/BGS_manual.pdf>`_ document.
+For better algorithm understanding please refer to `Histogram-based background subtractor forImageJ <http://sbalzarini-lab.org/Downloads/BGS_manual.pdf>`_ document.
 

doc/source/changelog.rst

@@ -23,4 +23,4 @@ Changelog
 
 .. important::
 
-    For information about previous developments not listed here please refere to `old MosaicSuite site <http://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+    For information about previous developments not listed here please refere to `old MosaicSuite site <http://sbalzarini-lab.org/?q=downloads/imageJ>`_.

doc/source/conf.py

@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'MosaicSuite'
-copyright = '2020, MOSAIC Group, Sbalzarini Lab, mosaic.mpi-cbg.de'
+copyright = '2020, MOSAIC Group, Sbalzarini Lab, sbalzarini-lab.org'
 author = 'MOSAIC Group, Sbalzarini Lab'
 
 # The full version, including alpha/beta/rc tags

doc/source/convolutionBesselPSF.rst

@@ -8,5 +8,5 @@ point spread function (PSF).
 Algorithm Description and Manual
 ================================
 
-For better algorithm understanding please refer to `PDF <https://mosaic.mpi-cbg.de/Downloads/BesselPSFConvolver_manual.pdf>`__.
+For better algorithm understanding please refer to `PDF <https://sbalzarini-lab.org/Downloads/BesselPSFConvolver_manual.pdf>`__.
 

doc/source/development.rst

@@ -120,4 +120,50 @@ Running single test within a given test suite:
 
 .. code:: bash
 
-    mvn test -Dtest=CSVTest#testWriteAppend
\ No newline at end of file
+    mvn test -Dtest=CSVTest#testWriteAppend
+
+Documentation
+=============
+
+MosaicSuite documentation is using `Sphinx <https://www.sphinx-doc.org/>`__ documentation generator.
+Documentation is written using reStructuredText markup language (.rxt files) and with Sphinx magic it is easy to convert to HTML or PDF version.
+
+
+Software needed to generate documentation
+-----------------------------------------
+Sphinx requires *make* command, *python* and several libraries. Here are needed steps to install all needed packages using *conda*:
+
+- Create and activate new conda environment:
+
+.. code:: bash
+
+   conda create -n MosaicSuiteDoc
+   conda activate MosaicSuiteDoc
+
+- Install needed libraries:
+
+.. code:: bash
+
+   conda install sphinx
+   conda install recommonmark
+   conda install sphinx_rtd_theme
+
+Generating documentation
+------------------------
+
+Generating documentation is as easy as running *make* command.
+To see all possible targets go to ``doc/`` directory of your cloned MosaicSuite code and run:
+
+.. code:: bash
+
+   make
+
+To generate HTML pages run:
+
+.. code:: bash
+
+   make html
+
+After command is finished in directory ``build/html/`` will be documentation in HTML format ready to deploy server.
+And that's it!
+

doc/source/discreteRegionSampling.rst

@@ -33,7 +33,7 @@ Options specific for DRS
 - **biased proposal**
     enables biased-proposal mode in which in order to propose smoothed shapes
 
-For detail explanation of these parameters please refere to `PHD thesis <http://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__ desribing theory behind DRS.
+For detail explanation of these parameters please refere to `PHD thesis <http://sbalzarini-lab.org/docs/Cardinale2013.pdf>`__ desribing theory behind DRS.
 
 Developer Resources
 ===================
@@ -46,7 +46,7 @@ Citation
 
     | *J. Cardinale*
     | Unsupervised Segmentation and Shape Posterior Estimation under Bayesian Image Models. PhD thesis, Diss. ETH No. 21026, MOSAIC Group, ETH Zurich, 2013.
-    | `PDF <http://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__
+    | `PDF <http://sbalzarini-lab.org/docs/Cardinale2013.pdf>`__
 
 
 *In order to ensure financial support for our project and allow further development of

doc/source/index.rst

@@ -5,11 +5,11 @@ MosaicSuite documentation
 
 .. note ::
    | This documentation is under development. Some parts might be not valid or incomplete.
-   | In a mean time please refere to `old MosaicSuite documentation <http://mosaic.mpi-cbg.de/MosaicToolboxSuite/MosaicToolsuiteTutorials.html>`__.
+   | In a mean time please refere to `old MosaicSuite documentation <http://sbalzarini-lab.org/MosaicToolboxSuite/MosaicToolsuiteTutorials.html>`__.
 
 
 **MosaicSuite** is a plugin for popular image processing software *ImageJ2* and *Fiji*.
-It provides image-processing algorithms developed at the `MOSAIC group <https://mosaic.mpi-cbg.de>`_.
+It provides image-processing algorithms developed at the `MOSAIC group <https://sbalzarini-lab.org>`_.
 The first plugin which is now part of MosaicSuite was a popular 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time. As more plugins have been added, we decided to provide them in a single, coherent package, which will also group them under a common menu point ``Plugins->Mosaic`` in ImageJ2 and Fiji.
 
 

doc/source/install.rst

@@ -28,4 +28,4 @@ Installation of MosaicSuite plugin
 .. important::
 
     If you are using very old Java 6 or because any reason you need to install MosaicSuite manually
-    please refere for detailed instructions `old MosaicSuite site <http://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+    please refere for detailed instructions `old MosaicSuite site <http://sbalzarini-lab.org/?q=downloads/imageJ>`_.

doc/source/interactionAnalysis.rst

@@ -16,7 +16,7 @@ each other, and the absenceof this means they are independent of each other.
 Tutorial
 ========
 
-Nice introduction to Interaction Analysis Plugin can be found in this `PDF <http://mosaic.mpi-cbg.de/Downloads/IAPManual.pdf>`_.
+Nice introduction to Interaction Analysis Plugin can be found in this `PDF <http://sbalzarini-lab.org/Downloads/IAPManual.pdf>`_.
 For better understanding of output please refer to :ref:`ia-citation` papers.
 
 .. _ia-citation:

doc/source/news.rst

@@ -10,7 +10,7 @@ News
 
         | *J. Cardinale*
         | Unsupervised Segmentation and Shape Posterior Estimation under Bayesian Image Models. PhD thesis, Diss. ETH No. 21026, MOSAIC Group, ETH Zurich, 2013.
-        | `PDF <https://mosaic.mpi-cbg.de/docs/Cardinale2013.pdf>`__
+        | `PDF <https://sbalzarini-lab.org/docs/Cardinale2013.pdf>`__
 
     *In order to ensure financial support for our project and allow further development of
     this software, please cite above publications in all your documents and manuscripts that
@@ -28,7 +28,7 @@ News
 
         | *X. Xiao, V. F. Geyer, H. Bowne-Anderson, J. Howard, and I. F. Sbalzarini.*
         | Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets. Med. Image Anal., 32:157–172, 2016.
-        | `PDF <https://mosaic.mpi-cbg.de/docs/Xiao2016.pdf>`__
+        | `PDF <https://sbalzarini-lab.org/docs/Xiao2016.pdf>`__
 
     *In order to ensure financial support for our project and allow further development of
     this software, please cite above publications in all your documents and manuscripts that
@@ -42,7 +42,7 @@ News
     Currently, we implement Gauss curvature, Mean curvature, and Total Variation (TV) filters.
     The only parameters is the number of iterations, i.e., how many passes of the filter should
     be applied to the image. Else the filters are parameter free.
-    A C++ implementation of these filters is also available `here <https://mosaic.mpi-cbg.de/?q=downloads/curvaturefilters>`__.
+    A C++ implementation of these filters is also available `here <https://sbalzarini-lab.org/?q=downloads/curvaturefilters>`__.
 
     The algorithms implemented in this plug-in are described in:
 
@@ -50,7 +50,7 @@ News
 
         | Y. Gong and I. F. Sbalzarini.
         | Curvature filters efficiently reduce certain variational energies. IEEE Trans. Image Process., 26(4):1786–1798, 2017.
-        | `PDF <https://mosaic.mpi-cbg.de/docs/Gong2017.pdf>`__
+        | `PDF <https://sbalzarini-lab.org/docs/Gong2017.pdf>`__
 
     *In order to ensure financial support for our project and allow further development of
     this software, please cite above publications in all your documents and manuscripts that
@@ -72,7 +72,7 @@ News
 
         | Y. Gong and I. F. Sbalzarini.
         | Image enhancement by gradient distribution specification. In Proc. ACCV, 12th Asian Conference on Computer Vision, Workshop on Emerging Topics in Image Enhancement and Restoration, pages w7–p3, Singapore, November 2014.
-        | `PDF <https://mosaic.mpi-cbg.de/docs/Gong2014.pdf>`__
+        | `PDF <https://sbalzarini-lab.org/docs/Gong2014.pdf>`__
 
     *In order to ensure financial support for our project and allow further development of
     this software, please cite above publications in all your documents and manuscripts that
@@ -80,4 +80,4 @@ News
 
 .. important::
 
-    For information about previous news not listed here please refere to `old MosaicSuite site <https://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.
+    For information about previous news not listed here please refere to `old MosaicSuite site <https://sbalzarini-lab.org/?q=downloads/imageJ>`_.

doc/source/particleTracker.rst

@@ -48,7 +48,7 @@ Citation
 
     | *I. F. Sbalzarini and P. Koumoutsakos*
     | Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol., 151(2): 182-195, 2005.
-    | `PDF <http://mosaic.mpi-cbg.de/docs/Sbalzarini2005a.pdf>`__
+    | `PDF <http://sbalzarini-lab.org/docs/Sbalzarini2005a.pdf>`__
 
 *In order to ensure financial support for our project and allow further development of
 this software, please cite above publications in all your documents and manuscripts that

doc/source/poissonNoise.rst

@@ -15,5 +15,5 @@ distribution parameter *λ* is set to the original intensity value.
 Algorithm Description and Manual
 ================================
 
-For better algorithm understanding please refer to `PDF <http://mosaic.mpi-cbg.de/Downloads/PoissonNoise_manual.pdf>`__.
+For better algorithm understanding please refer to `PDF <http://sbalzarini-lab.org/Downloads/PoissonNoise_manual.pdf>`__.
 

doc/source/psfMeasurement.rst

@@ -13,5 +13,5 @@ Algorithm Description and Manual
 
 For better algorithm understanding please refer to:
 
-- **2D** `PDF <https://mosaic.mpi-cbg.de/Downloads/PSFtool.pdf>`__
-- **3D** `PDF <https://mosaic.mpi-cbg.de/Downloads/PSF_measurement_3D.pdf>`__
+- **2D** `PDF <https://sbalzarini-lab.org/Downloads/PSFtool.pdf>`__
+- **3D** `PDF <https://sbalzarini-lab.org/Downloads/PSF_measurement_3D.pdf>`__

doc/source/regionCompetition.rst

@@ -200,7 +200,7 @@ Citation
 
     | *J. Cardinale, G. Paul, and I. F. Sbalzarini*
     | Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012.
-    | `PDF <http://mosaic.mpi-cbg.de/docs/Cardinale2012.pdf>`__
+    | `PDF <http://sbalzarini-lab.org/docs/Cardinale2012.pdf>`__
 
 *In order to ensure financial support for our project and allow further development of
 this software, please cite above publications in all your documents and manuscripts that

doc/source/resources/macros/runBgSubtracktor.ijm

+// This macro run Background Subtractor plugin from MosaicSuite
+
+
+// ----- USER PARAMETERS
+
+// Provide input directory with images and output directory 
+// for saving processed images (if same then input images will be changed!)
+inputDirectory = "/home/gonciarz/1/testImages/"
+outputDirectory="/home/gonciarz/1/results/"
+
+// provide lenght of the sliding window, if set to -1 then plugin will auto-detect
+bgSubtractorSlidingWindowLength=20
+
+// If auto-detection is ON it might happen that plugin is not able to calculate proper length
+// If skipOnFailure is 'false' then popup window will show in such a case (good for interactive operations), 
+// if set to 'true' such a case will be only logged and detected lenght will be set to -1
+//
+// Example of log:
+// 		Macro Options: [length=-1 skipOnFailure ]
+// 		SkipOnFailure = true
+// 		Auto-detected length for image a.tif=201
+// 		Macro Options: [length=-1 skipOnFailure ]
+// 		SkipOnFailure = true
+// 		Auto-detected length for image failingImage.tif=-1
+
+skipOnFailure=false
+
+
+// ----- CODE
+
+// Create output (results) directory, if exist nothing happens
+File.makeDirectory(outputDirectory);
+if (!File.exists(outputDirectory)) {
+    exit("Unable to create directory: " + outputDirectory);
+}
+
+
+// Iterate over all 'tif' images in inputDirectory
+images=getFileList(inputDirectory);
+for (i = 0; i < images.length; i++) {
+
+    // Skip if not 'tif' image
+    if (!endsWith(images[i],".tif")) continue;
+
+    // Open current image
+    fullFileName=inputDirectory + "/" + images[i];
+    print("Processing [" + fullFileName + "]");
+    open(fullFileName);
+    
+
+    // ----- Run background subtractor ------
+    skipCmd = "";
+    if (skipOnFailure) skipCmd = "skipOnFailure";
+    run("Background Subtractor", "length=" + bgSubtractorSlidingWindowLength + " " + skipCmd);	
+
+
+    // Save processed image in output directory and close it
+    save(outputDirectory + "/" + images[i]);
+    close();
+}
+

doc/source/squassh.rst

@@ -24,10 +24,10 @@ Nice introduction to work with Squassh can be found in following documents:
 
 - | *A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini*
   | Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014,
-  | `PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014.pdf>`__
+  | `PDF <http://sbalzarini-lab.org/docs/Rizk2014.pdf>`__
 - | *Aurélien Rizk, Grégory Paul, Pietro Incardona, Milica Bugarski, Maysam Mansouri, Axel Niemann, Urs Ziegler, Philipp Berger, Ivo F. Sbalzarini*
   | An ImageJ/Fiji plugin for segmenting and quantifyingsub-cellular structures in fluorescence microscopy images
-  | `PDF <http://mosaic.mpi-cbg.de/Downloads/SplitBregmanSeg.pdf>`__
+  | `PDF <http://sbalzarini-lab.org/Downloads/SplitBregmanSeg.pdf>`__
 
 Video Tutorial
 --------------
@@ -37,11 +37,11 @@ Video Tutorial
 
      .. raw:: html
 
-        <video controls src="http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v" width="720" height="540"></video>
+        <video controls src="http://sbalzarini-lab.org/Downloads/Squassh_video.m4v" width="720" height="540"></video>
 
 .. only:: latex
 
-    `Squassh video tutorial <http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v>`__
+    `Squassh video tutorial <http://sbalzarini-lab.org/Downloads/Squassh_video.m4v>`__
 
 Developer Resources
 ===================
@@ -54,11 +54,11 @@ Citation
 
     | *G. Paul, J. Cardinale, and I. F. Sbalzarini*
     | Coupling image restoration and segmentation: A generalized linear model/Bregman perspective. Int. J. Comput. Vis., 2013.
-    | `PDF <http://mosaic.mpi-cbg.de/docs/Paul2013a.pdf>`__, `Supplementary Material PDF <http://mosaic.mpi-cbg.de/docs/Paul2013b.pdf>`__, `Matlab Implementation <http://mosaic.mpi-cbg.de/?q=downloads/splitBregman>`__
+    | `PDF <http://sbalzarini-lab.org/docs/Paul2013a.pdf>`__, `Supplementary Material PDF <http://sbalzarini-lab.org/docs/Paul2013b.pdf>`__, `Matlab Implementation <http://sbalzarini-lab.org/?q=downloads/splitBregman>`__
     |
     | *A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini*
     | Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014.
-    | `PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014.pdf>`__, `Supplementary Note PDF <http://mosaic.mpi-cbg.de/docs/Rizk2014a.pdf>`__, `Supplementary Data ZIP <http://mosaic.mpi-cbg.de/docs/Rizk2014_supplement.zip>`__, `Supplementary Video <http://mosaic.mpi-cbg.de/Downloads/Squassh_video.m4v>`__
+    | `PDF <http://sbalzarini-lab.org/docs/Rizk2014.pdf>`__, `Supplementary Note PDF <http://sbalzarini-lab.org/docs/Rizk2014a.pdf>`__, `Supplementary Data ZIP <http://sbalzarini-lab.org/docs/Rizk2014_supplement.zip>`__, `Supplementary Video <http://sbalzarini-lab.org/Downloads/Squassh_video.m4v>`__
 
 
 *In order to ensure financial support for our project and allow further development of