[Album] Fix a bug causing 32-bit snap-to-album to fail.

This extends a workaround we have for fixing ImageJ display issues with multi-
channel images to also apply for multi-component images. I still have no idea
why this workaround is necessary, nor why it works.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14786 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[Display settings] Don't totally fail to load incomplete display settings.

In particular, if the nominal number of channels doesn't match the length of
the per-channel display settings (e.g. for histogram max or gamma), then we'll
just use the first channel's settings rather than throw an exception and
therefore fail to load the file.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14787 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[MCCDAQ] Allow min/max voltage to be configurable.

Previously, while the adapter would allow you to configure the property
limits for the voltage, when you tried to set a voltage outside of the range
0V-5V, it would throw an error.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14788 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Update CameraLabs.bsh script to work with latest api.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14789 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
TIScam: Fixes to device adapter (Johannes Schindelin)

TIScam: initialize previously unintialized pointers
TIScam: avoid crashes by allocating/releasing the buffer properly

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14790 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
MMCore cannot return a zStageLabel that is null, only an empty one (Johannes Schindelin)

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14791 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Gaussian plugin: Abstracted MMWindow functions

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14792 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[Autofocus] Fix a bug causing getPropertyNames() to fail.

The fix was proposed by Karsten Siller. Thanks, Karsten!

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14793 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Gaussian plugin: added ability to specify window positions that should be analyzed

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14794 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Java API: Added function getTaggedImage(int channel, int slice, int frame, int position) to MMWindow

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14795 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Scripts: Added example script showing how to re-arrange Micro-Manager datasets.  Will soon be superfluous

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14796 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Gaussian plugin: code formatting

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@14797 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Ported Micro-Manager/plugins to Commons Math 3-ish

Ported MicroManager/plugins to Commons Math 3ish

Started porting MicroManager and plugins to commons math 3.

We really need to condense these down to one of two versions, and there's
no sense using version 2 when 3 is available.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>

Finished 'porting' plugins and associated to Commons Math 3.0

By 'porting' I mean 'lobotomizing'. I'm pretty sure I didn't actually
comment out functionality-critical code, though some metadata code won't
work until I find the new functionality analogues and fix them.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>
Apache Commons Math 3.2, Imglib2 Gaussian fitting

Note that these are only changes to mmstudio and SPIMAcquisition.

Fiji's official Apache Commons Math version is now 3.2; due to some API
incompatibilities, SPIMAcquisition has briefly stopped working. I've
upgraded the version used by SPIMAcquisition, mmstudio, and autofocus.

However, I've simultaneously moved away from our dependence on the Vale
Lab's GaussianFit plugin, for two reasons. First, it isn't sensible to
depend on the output of another plugin; this introduces a build order
necessary to correctly compile the plugin. Second, Imglib2 already
provides the necessary fitting routines, and is arguably the more
standardized approach anyhow. (I had planned this move some time ago, but
the recent commons math update rather forced my hand.)

The more cynical reason, though, is that it saves me the trouble of
immediately upgrading GaussianFit to Commons Math 3.2; there are some
complex fitting routines, the use of which I do not yet understand,
involved in i.e. the MLE class. I will doubtless revisit GaussianFit and
upgrade it, but time is short at the moment and I felt it more pressing to
update the plugin.

Signed-off-by: Luke Stuyvenberg <stuyvenberg@wisc.edu>
Ensure necessary paths in bin_Win32 exist

Make sure that bin_Win32\mmplugins and bin_Win32\mm\win32 exist

Noticed by Tobias Pietzsch.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>

Make sure that bin_Win32/plugins/ exists.
FIXUP: Visual Studio projects: copy to bin_Win{32,64}/mm/win{32,64}

To fit the upstream convention of using bin_$(Platform) for build
destinations, all Visual Studio projects' copy-to paths have been changed
from dist/.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
For now, do not try to load the secret device adapters into the workspace

... because Dscho does not have access to them...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a Visual Studio project for mmstudio

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Respect --with-ij-jar when building mmstudio

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Force Ivy to look into the ImageJ Maven repository

Bio-Formats is not available via Maven Central :-(

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>