MIEN FAQ
Do I actually have to use a Terminal (aka command prompt, CLI) in order to run MIEN!!??
DataViewer says there are "No numerical elements to display".
Many traceback errors on startup
If MIEN reports a lot of errors (in the form of Python error tracebacks) on startup, but still starts, it is probable that these are extension block import errors. If the tracebacks are preceded by a message "error loading block FOO", and contain something like "blocks.py", line 68, in tryLoad, then you definitely have a block import error.
These are extremely common. They occur because the various extension blocks have more dependancies than the core MIEN package. Many of them require other third party libraries, or their own compiled C extensions. If these are not installed on your machine, or are not compiled for your machines architecture, then the extension will not load.
The good news is, this is not usually a fatal error. MIEN should run normally, after printing the errors. Features provided by the failed extension will simply be omitted. If you are looking for a command that used to be offered in an Extensions, Spatial, or DSP menu, and is now missing, this is because it was provided by a block that didn't load. If you don't need these commands, you can go on with your work.
If you don't like seeing the errors print, you can disable the failed blocks. Go to the blocks directory (usually $HOME/mienblocks or PYTHONLIB/site-packages/mienblocks, where HOME is your home directory, and PYTHONLIB is wherever python put its libraries, for example /usr/local/lib/python2.5/lib on many types of Linux). Once in the block directory, locate the package that didn't load. This will be a directory with the same name as the block, so if you saw "error loading module fibr", you want a directory named "fibr". Now you have two choices: delete it, or disable it. To delete it, just remove the directory. To disable it, add a file in the mienblocks directory named "disabled_blocks.txt" (if this file already exists, just edit it). Add a line to the file with the name of the block. Now instead of an error, MIEN should report "ignoring disabled block fibr" on startup.
If you need the block, you will have to install or compile the required dependencies for that block. This can be arduous. Look for documentation for the particular block, since there is no way to document every possible extension as part of the main MIEN documentation.
Menu buttons missing on Macintosh
Some versions of the Mac/Carbon/wx GUI now identify themselves with a different name. Since Mac doesn't support one menu bar per window, the menu buttons on MIEN windows in Mac OS have to be specially implemented. If MIEN does not recognize the reported GUI type as Mac OS, this isn't done, the menus end up at the top of the screen, Mac style, and if more than one MIEN window is open, only one menu bar is available. As far as I know, this is corrected in recent revisions of MIEN, so an update should fix the problem.
I see an error that there is no module "mien"
Make sure that your PYTHONPATH variable includes where you put mien. If you installed in Python's site packages directory, make sure you are actually calling the version of Python that you installed MIEN for. Some systems have several versions of Python installed. You need to set things up so that "env python" will run the Python you installed MIEN on. Alternately, you can call Python, and mien, by full path names.
Errors on exit in Python 2.6
This seems to be caused within the SciPy extension, rather than in MIEN, so I can't fix it. The core MIEN package doesn't require scipy, but the module mien.image.simple imports it if it is available (in order to use "convolve2d" for image blurring). If you don't have scipy, you shouldn't get any errors. If you do, you can edit the mentioned module to not import scipy, or just live with the errors on exit. As far as I know they don't cause any real problems. Presumably the reference handling within scipy will become "Python 2.6 safe" some day soon.
Do I have to use a Terminal?
Trust me, terminals are your friends. Once you get used to one, you will never look back to Finder, Windows Explorer, Nautilus, or whatever slow and imprecise interface you are currently using :)
But to answer the question: No, you don't have to, but there are some problems you might encounter if you don't.
There are several access points to the MIEN GUIs that don't require a command prompt. The Macintosh package installer provides extensive support for mouse-click launching of MIEN apps. Check out your options on the mac platform page. The Windows binary installer provides a Windows exe file that can be launched by double-click. In Linux you don't have any click-to-launch options "out of the box", but it is easy to set them up. See the linux page for help with this.
That said, you probably don't want to use a mouse-click launch method for the following reasons:
MIEN uses the controlling terminal to print status messages, the results of some computations, and notifications of errors. Terminal programs are very good at displaying text. They remember many lines of output and provide nice scroll-back features. If MIEN is launched without a terminal, it makes its own status report window, but this window takes screen space away from the other graphical display windows, and it isn't nearly as good at displaying lengthy messages as a terminal.
GUI methods of opening files, including drag-and-drop and the File->load dialog, can only open locally stored files. Arguments passed to the command line can be local files or URLs, which may be local or remote. This allows you to open a data file stored at an http or ftp address using the mien command.
If you launch a Python interactive session from within MIEN, the controlling terminal is used for that session. If you don't have a terminal, MIEN uses a PyCrust graphical Python shell instead. I deeply respect the brilliant coders associated to the WxPython project, but they were not just making a pun when they named PyCrust "The Flakiest Python Shell". It is unstable and can be hard to navigate. A terminal-based Python shell will be more stable and more powerful.
The CLI launch method allows you to open input files automatically. If you close MIEN, you can re-open the same file by pressing up-arrow in the shell and re-executing the mien command, with the input files included. If you open MIEN by clicking an icon, you have to find your input files with a graphical browser, and if you reopen mien, you will have to repeat the file opening procedure from scratch.
Why does the DataViewer say there are "No numerical elements to display". I know I loaded numerical data!
The usual reason is because there actually aren't any numerical elements. Anatomical point data, for example, can't be displayed by the Data Viewer, even though they may seem to be "numerical" data. Make sure that you have actually loaded data elements. Try opening the XML Editor using Edit->Data Editor. In the XML Editor, look for elements that are called "Data" elements.
Assuming that you do have some Data elements, there are a few reasons why Data Viewer might not display them. First, they could be nested inside other non-numerical elements. If this is the case, browse down to the Data elements in the XML editor and right click on one. Select "Send to Viewer" from the context menu. If this results in correct display, then you can also get DV to display these elements on file open by moving them to the top level of the documents (in the XML Editor), or by using File->Append Subset in DV to open only selected elements from a file, and selecting these elements.
If you can't see the Data element even when it is sent directly to DV, try examining the element in the XML Editor. In particular, make sure that the shape of the associated data array is non-zero, and check the SampleType attribute. DV won't show data of certain SampleTypes (such as locus). If your data are a 2D array, you can try setting the attribute "SamplesPerSecond" to some value (for example 1.0), and changing the SampleType to "timeseries" using the XML editor. This should cause DV to display the data, although it may not be the display you want. If this works and data are displayed, but in the wrong way, read the "Data" API documentation to find an appropriate SampleType.