JFtp is a graphical Java network and file transfer client.

JFTP is a graphical FTP (File Transfer Protocol) client software for transferring files from one computer to another over TCP/IP networks such as Internet.

JFTP can connect to any system that has a valid Internet address and an FTP server program, allowing you to transfer files between a wide variety of systems, including Windows, UNIX and iSeries (AS/400) systems.

JFTP integrates the most widely used and widely accepted security mechanism, SSL (Secured Sockets Layer), to securely transfer your business critical and sensitive data.

JFTP is written entirely in JavaTM, meaning, it can run on a wide variety of platforms such as Windows, Mac OS X, Linux, Solaris, HP-UX, OS/2, UNIX or any other platform with a compatible JVM (Java Virtual Machine).

It supports FTP using its own FTP API and various other protocols like SMB, SFTP, NFS, HTTP, and file I/O using third party APIs, includes many advanced features such as recursive directory up/download, browsing FTP servers while transferring files, FTP resuming and queueing, browsing the LAN for Windows shares, and more.

You can also have more than one connection open at a time in a mozilla-style tabbed browsing environment.
The FTP API is separated from the GUI and can also be used in third-party applications.

It should ideally be launched in a Web browser via Java Web Start (contained by the Java 1.4 plugin), but can also be started locally.

JFtp is free and distributed under the GNU public license. The API is dual licensed, you may use it under.

You can support JFtp in various ways, first of all please make sure that you fill out bug reports on the SourceForge project page if you find any (Exception data is very important in most cases, so please don't forget including it. You'll find the stacktrace in the console output.).

If you want to help coding, create documentation, link to/distribute/promote JFtp or similar you are always welcome.

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MRIcron is a cross-platform NIfTI format image viewer.

MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcroGL is a variant of MRIcron that uses OpenGL for very fast rendering, but requires a modern NVidia or ATI graphics card.

 I have tried to make the MRIcron main window as useful but simple as possible. While the options may appear confusing at first, I hope over time the software feels intuitive.

A sample window is shown below. You can get a similar view by launching the software, choosing File/OpenTemplates/ch2bet to load the background image (shown as a grayscale brain) and then choosing Overlay/Add and opening the image \Template\attention.

the controls on the tool bar offer quick access to the main tools for brain imaging. The X/Y/Z numbers set the slice to view (X refers to Left/Right, Y to anterior/posterior and Z to superior/inferior). Adjusting these values will change the sagittal, coronal and axial slice displayed. The next item is the zoom-factor. Here images are scaled 'to fit' - e.g. each view of the brain is strecthed to fill its panel optimally. Alternatively, you could choose x1 (100%), x2 (200%) or x3 (300%) zoom factors. The next series of buttons refer to the active layer (more on layers in the next section). In the example below, the currently active layer is image 'attention', and this image is being shown as a red gradient with a minimum value of 1.96 to 4. In this example, attention is a statistical Z-score map that has been placed on top of the background image of a brain. Statistical values less than 1.96 are not shown, with the darkest value set to 4.

Layers

When you use the File menu's Open command (Open, Open recent and Open Templates) you are selecting a background image. What makes MRIcron powerful is its ability to load multiple layers of images. To add additional images on top of your background, simply choose 'Add' from the 'Overlay' menu. For example, launch MRIcron and choose 'File\Open templates\ch2bet', then choose 'Overlay/Add' and select the 'attention.nii.gz' image from the 'Example' folder that (typically, this folder is installed in C:\program files\mricron\examples). Now you should see a brain activation statistical map on top of the background anatomical image. Note that overlay images are scaled to map on top of the background image. You can adjust the appearance of each layer by using the layer panel:

Note that you can click on the leftmost button in the overlay panel to select between the open layers - for example the image above shows settings for the 'Background' image, as well as the overlay image named 'saccades'. Note that the image intensity range for the background is from 45 to 120, using a grayscale color scheme. This means that values of 45 or lower will appear as complete black, and 120 and above will be white, with intermediate intensities appearing as a corresponding gray value. There is also an icon with a color scale and the number zero: this allows you to have the color range set from zero, even if your threshold is greater than zero: for example our statistical map 'saccades' is set to show values from 2.3 to 6: values less than 2.3 will not be shown. However, since the 'color range from zero' button is depressed, a T-score of 2.3 will appear as a dark red (as 2.3 is part way between 0 and 6) instead of a black (if the color range was from 2.3 to 6).

MRIcron allows you to choose different color schemes for each layer. In the example above, the Background image is shown using the 'grayscale' black-and-white colorscheme, while the saccade overlay uses the Red color scheme. You can increase or decrease the colorschemes available by adding or removing files from the 'LUT' folder (this 'look up table' folder is located in the same path as MRIcron). This folder typically contains several *.lut files, with each file storing a different color scheme. For example, the blackbdy.lut' file describes a color scheme that goes from black to orange to yellow and finally white. MRIcron's *.lut files are interchangeable with the *.lut files used by ImageJ, XMedCon, MRIcro. You can copy *.lut files from these programs to MRIcron's LUT folder. Furthermore, you can create your own *.LUT files using ImageJ's LUT panel plugin, ImageJ's LUT Editor or my own LUTmaker.

Note that the 'Overlay' menu also allows you to modify how layers appear. For example, on image 'A' below, I have selected Overlay/TransparencyOnBackground/0%[Opaque], while for image B, I have set the transparency to 50%. Also note that you can load multiple overlays simultaneously. For example, images C and D below show the 'attention'  and  'saccades' files both overlayed on top of ch2bet - with attention shown in green and the saccades shown as red. For image C, I have set the Overlay/TransparencyOnOtherOverlays/50%, while for Figure D this has been set to 'Additive' (so regions with both red and green appear yellow).

Render Window

From MRIcron's main window you can select Window/Render to view a volume rendering of your data. You can change the vieiwing angle of the image by adjusting the Aizmuth and Elevation values. The Background menu allows you to adjust therendering of the background image, while the background menu allows you to determine how overlays will appear. Of critical importance, the Overlay/SearchDepth will adjust whether the rendering shows superficial overlays (e.g. a settings of 4 will only look within the first 4 voxels of the background image [e.g. within the first 4mm if your background image hasa 1mm resoultion), while a setting of 'infinite' will show an overlay regardless of its depth. Also criticial is the Background/BehindOverlay menu item - if checked, the software will only start looking for overlays that exist behind the surface of the background. On the other hand, if this value, overlays will not be constrained by the background image (e.g. you will be able to view an overlay that is closer than the background). You can save your preferred settings by selecting File/SaveSettings. This information will be saved in the 'render' folder, and you will be able to select them by choosing File/OpenSettings.

This image shows a sample rendering. You can view this image by running the fmri.bat file that is included with MRIcron.

Multislice Window
From MRIcron's main window you can select Window/Multislice to see the multislice window. You will then be shown a series of slices of the currently open volumes. Within the Multislice form you can use the View meanu to adjust settings - e.g. to select whether you want to see sagittal, coronal or axial images, and to choose the desired slices and overlap between neighboring slices. You can also choose File/SaveSettings to save your favorite views (previous sets will be listed under File/OpenSettings).

Linux x86 32bit GTK1 Note that it is easier to install the GTK2 version (see below) with recent (>2005) distributions of Linux.

1. Download the software.
2. Unzip the software (for modern Linux systems, right click on the file mricronlx.zip and choose to 'extract here').
3. Open a terminal window.
4. Change to the folder where you installed mricron, e.g. cd ~/mricron
5. Launch mricron by typing ./mricron (note you must be in the same folder as the mricron executable.
6. You can also run the example .bat files, for example ./xfmri.bat shows two statistical maps on top of a high resolution anatomical scan.
1. In case you receive error messages, check if all the dependencies of the program are installed. In particular, you need
1. GTK 1.2 (this is called GTK+ by some distributions, and gtk by others)
2. libgdk_lixbuf2.0
2. You can see a complete list of .so files needed by the software using the command:
     ldd ./mricron
3. In case you cannot run the program and it displays a message saying it cannot find one of these libraries (you must run the program from the command line to see error messages), you need to download and install a package for the necessary library:
   • On RPM-based distributions you can find packages here: http://rpm.pbone.net/
   • On Debian-based distributions you can find packages here: http://www.debian.org/distrib/packages

Linux x86 32bit GTK2 Note that the GTK1 version (above) has been more extensively tested.

1. Download the software.
2. Unzip the software (for modern Linux systems, right click on the file mricronlx2.zip and choose to 'extract here').
3. Double-click on the mricron application icon to launch the program.

Linux x86 64bit GTK1

1. Download the software.
2. Unzip the software (for modern Linux systems, right click on the file mricronx641.zip and choose to 'extract here').
3. Double-click on the mricron application icon to launch the program.

Linux x86 64bit GTK2

1. Download the software.
2. Unzip the software (for modern Linux systems, right click on the file mricronx642.zip and choose to 'extract here').
3. Double-click on the mricron application icon to launch the program.

Linux Debian GTK2

1. MRIcron has been added to the Neuor Debian packages.

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PyMca stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra.

PyMca has been developed by the Software Group of the European Synchrotron Radiation Facility (ESRF).

If you are in doubt about how to pronounce it, just think about how you would spell πMCA.

For the end user, PyMca is a ready to use, and in many aspects state-of-the-art, set of applications implementing most of the needs of X-ray fluorescence data analysis.

For the developer, the PyMca Toolkit is a collection of Python tools for visualization and analysis of energy-dispersive X-ray fluorescence data. It builds its graphic interface and plotting routines on top of the C++ libraries Qt and Qwt through their respective Python bindings PyQt and PyQwt. Nevertheless, the data analysis routines can be used independently of any graphical interface.

In addition to data files, PyMca can also access SPEC shared memory to monitor data acquisitions.

The European Synchrotron Radiation Facility (ESRF) is a joint research facility supported by 19 countries (18 European countries and Israel) situated in Grenoble, France. It has an annual budget of around 80 million euros, employs over 600 people and is host to more than 3500 visiting scientists each year.


Research in the ESRF focuses, in large part, on the use of X-ray radiation in fields as diverse as protein crystallography, earth science, materials science, chemistry and physics. Facilities such as the ESRF offer a flux, energy range and resolution unachievable with conventional (laboratory) radiation sources.


The ESRF physical plant consists of two main buildings: the experiment hall, containing the 844 metre circumference ring and forty tangential beamlines; and a block of laboratories, preparation suites, and offices connected to the ring by a pedestrian bridge. The linear accelerator electron gun and smaller booster ring used to bring the beam to an operating energy of 6 GeV are constructed within the main ring. Until recently bicycles were provided for use indoors in the ring's circumferential corridor. Unfortunately they have got removed after some minor accidents. But even before it was not possible to cycle continuously all the way around, since some of the beamlines exit the hall.

The ESRF site forms part of the "Polygone Scientifique", lying at the confluence of the Drac and Isère rivers about 1.5km from the centre of Grenoble. It is served by local bus and the Lyon airport coach, which stops at the Place de la Résistance just outside the site.


The ESRF shares its site with several other institutions including the Institut Laue-Langevin (ILL) and the European Molecular Biology Laboratory (EMBL). The Centre national de la recherche scientifique (CNRS) has an institute just across the road.

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Sweep is an audio editor and live playback tool for GNU/Linux, BSD and compatible systems.

Sweep is an audio editor and live playback tool for GNU/Linux, BSD and compatible systems.

It supports many music and voice formats including WAV, AIFF, Ogg Vorbis, Speex and MP3, with multichannel editing and LADSPA effects plugins.

It is Free Software, available under the GNU General Public Licence.

Check out the download page for information about downloading source packages and binaries for various operating systems.

Screenshots.

Sweep is a very interactive sound editor which makes heavy use of audio feedback to make your tasks of manually analysing and editing sounds easier. Of course these screenshots cannot capture the interactivity -- you will have to try Sweep out for yourself to experience that. These screenshots show the most common editing windows and dialogs that you will encounter.

	General usage. This section introduces Sweep's main waveform view, extended selections and edit history.
	File dialogs. Sweep supports many file types, including PCM (WAV, AIFF etc.), voice formats including Speex, and the Ogg Vorbis perceptual audio codec. This section displays the options available for loading and saving various different file types, and for creating new files.
	Effects processing. There are over 70 effects plugins freely available for the LADSPA plugin standard, supported by Sweep. This section of the tour provides more information about these, and gives some example screenshots.
	Playback and recording Sweep provides intuitive controls for playback latency and recording.
	Contributed Screenshots . Sweep is used in a wide variety of environments. These screenshots are contributed by users to show some of the different styles and desktop themes available.
	Colour schemes . To finish off the tour, here is a gallery of the various colour schemes available for Sweep's waveform displays

Getting around in Sweep.

Main window

This is the main application window in Sweep. The two waveforms shown represent the left (above) and right (below) channels of a stereo WAV file. The grey regions indicate peaks and the dark regions indicate average values for the audio data. Time offsets in hours, minutes and seconds are shown above the waveforms. This window also includes a standard editing toolbar and playback controls.

 Zoomed in

You can zoom right in to individual PCM data values using the mouse wheel if available, arrow keys or the zoom control located in the top right corner of the window. The number in the dropdown box indicates the duration of sound visible in the window -- in this case 0.003 seconds.

Vertical Zoom

For greater precision, you can zoom the waveform display vertically, either by rolling the mouse wheel over the dB markings on the left side of the window or by pressing Shift and Arrow Up/Down. You can scroll the waveform display up and down by dragging the dB ruler on the left side of the window.

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Gosmore is a program to view, search, and route using openstreetmap data.

Gosmore is a routing and viewer of OSM XML data such as the whole planet.osm or other osm files from Geofabrik (see downloads) or Cloudmade (see downloads).

It includes many features, like acquiring the current location from a GPS receiver, turn-by-turn navigation, and recording of tracklogs in GPX format.

Releases.

The stable 2010.1 version is available for download (see below). 2010.2 is under development. In future it will be easier to customize the user interface and a few other improvements.

Features.

    A 2D map viewing window (Mercator projection), as well as a 3D bird's eye view.
    Incremental search of all tags. Results are ordered from nearest to farthest.
    Routing with basic Relation:restriction support.
    Obtain the current location from a GPS receiver (via gpsd using Linux).
    The ability to add POI's and trace ways which get saved to a .osm format file ready for import into JOSM
    The ability to automatically switch maps on-the-fly, so you can access the whole planet. 

### Example for Ubuntu or Debian ###
sudo apt-get install libxml2-dev libgtk2.0-dev g++ make subversion libcurl4-gnutls-dev libgps-dev
svn co http://svn.openstreetmap.org/applications/rendering/gosmore/
cd gosmore
./configure
make
sudo make install

### Example for Fedora 13 ###
su -c "yum install libxml2-devel gtk2-devel gcc-c++ make subversion libcurl-devel gpsd-devel"
svn co http://svn.openstreetmap.org/applications/rendering/gosmore/
cd gosmore
./configure
make
sudo make install

These instructions are for Ubuntu Lucid.
Create a temporary folder.

1. mkdir ~/temp_gosmore
2. cd ~/temp_gosmore

Download and install CeGCC.

1. wget http://prdownloads.sourceforge.net/project/cegcc/cegcc/0.59.1/mingw32ce-0.59.1.tar.bz2
2. tar xvjf mingw32ce-0.59.1.tar.bz2
3. sudo cp -r ./opt/mingw32ce /opt

Download and extract required 32 bit libraries (required for 64 bit only).

1. wget http://mirrors.kernel.org/ubuntu/pool/main/m/mpfr/libmpfr1ldbl_2.4.2-3ubuntu1_i386.deb
2. wget http://mirrors.kernel.org/ubuntu/pool/main/g/gmp/libgmp3c2_4.3.2+dfsg-1ubuntu1_i386.deb
3. dpkg -x libmpfr1ldbl_2.4.2-3ubuntu1_i386.deb . (don't forget the '.' at the end)
4. dpkg -x libgmp3c2_4.3.2+dfsg-1ubuntu1_i386.deb . (don't forget the '.' at the end)
5. sudo cp usr/lib/* /usr/lib32/

Remove the temp directory

1. cd ../
2. rm -rf temp_gosmore

Add libraries to $PATH

1. export PATH=/opt/mingw32ce/bin/:$PATH
2. export LD_LIBRARY_PATH=/usr/lib32:/usr/lib:$LD_LIBRARY_PATH (required for 64 bit only).

cd to location of source files then

1. make arm-mingw32ce-gosmore.exe

Alternatively install the debian package that may be slightly out of date.

On FreeBSD and MacOSX, you will need to use GNU Make (gmake) to build as the Makefile is in a GNU Make format, rather than the traditional BSD make.

On MacOSX, you will have to install X11, the developer tools and maybe additional packages that are not listed here but are fairly standard when compiling stuff. Feel free to list them if you find any that are not listed here.

After these steps complete, gosmore should appear on your menus. Gosmore will run fairly responsively on a 256 MB machine.

After finding a city or location you are interested in, choose the 'Update Map' function (see the Auto Pak file section below). Downloaded files will be stored in $HOME/.gosmore/

The main window consists of

    the buttons: Options, + zoom in / increase, - zoom out / decrease and 3D.
    the search box
    The main window with 4 modes:
        Map Click or drag to pan.
        Search Results. Direction, distance, type and names are displayed. Click to select.
        Options for selecting icon types, detail level and routing settings. Drag to see all of them. Click to select. See Gosmore/Translations Note that not all options are supported on all platforms.
        Add Object Type List. Select the object you want to add.
        Add Object Name dialog. Set the name.
    the location bar (GTK/Linux only) Copy and paste to / from JOSM or the www.openstreetmap.org permalinks.

The GTK version will look for way points in any selected text in any other application (clipboard mechanism). For example, you can select geocache log and click on the gosmore map window to see where the points are.

When you exit Gosmore it will also save your options and location to gosmore.opt. This file will normally be located in your home directory. Under Windows and Windows Mobile it will be stored in '\My Documents' unless the file was found on in the same directory as gosmore.exe at startup. So most people place an empty gosmore.opt file on their SD card.

At exit it will also create 'YYMMDD-HHMMSS-Vehicle.osm' and 'YYMMDD-HHMMSS.gpx' files that you can open with JOSM:

    Download data to the same layer.
    Edit. To find the pending changes search for 'modified'.
    Upload

    Changing the CommPort and BaudRate settings (Windows Mobile only) requires restarting the application.
    Activate ValidateMode to see unnamed roads.
    Activate FullScreen and restart for more screen space.
    Set Layout (Windows / Windows Mobile only) to 1 to hide the top bar. Set it to 2 on displays that are too narrow for the top bar (width less than 300 pixels).
    Some options like ViewInOSM and UpdateMap is only supported under Linux / Gnome, while others like ZoomIn/OutKey is only supported under Windows or Windows CE.
    LoadGPX is not implemented.
    Activate the 'Exit' option to close the application and write the GPX file, the OSM file and the options.

Bugs.

In order of importance:

    Routing is not calibrated. There are a number of special features, like avoidance of major intersections and turning over oncoming traffic, but the constants can be improved.
    Turn restrictions with complex vias are ignored.
    Verbal instructions do not work well on motorways.
    A number of important platforms aren't supported (OpenTom, Symbian, Android, iphone etc). Note however that the WinCE Core that gosmore requires is cheap [6]. Many of the house brand GPSs are WinCE based.
    32 bit machines can create and use only pak files smaller than 2GB. Rebuild gives segmentation fault on computers with less than 1GB of virtual memory.
    Pak file cannot be dynamically updated e.g. osmosis. However, since the objects we map (roads etc) change infrequently and mappers take very long to resurvey existing data, you will most likely only find the spots where the pak file is out of date if actively go looking for them.
    Pak file cannot be moved to a machine with a different endianness.
    If double decker bridges are drawn with 2 or more nodes on exactly the same latitude and longitude, gosmore may make incorrect routing decisions. (It can be solved at the cost of a 10% larger pak file).
    No way of completely disconnecting from GPS com port. Causes battery drain when internal GPS is activated by just connecting to the proper com port (on WM5 at least).
    When in current direction = up (north upwards=0) mode, stopping at a crossing causes slight precision improvements due to gps averaging which can shift position slightly in any (random) direction, which causes the map to rotate wildly, disorientating the driver (and probably giving wrong instructions if the route is recalculated). Probably a longer (eg 10 m distance, not time) average period should be used to determine direction before rotating the map. 

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