Tested single channel tif with LOCI bioformats

Automatic reading of calibration from .tif files

Now recongnizes only first .czi file and fixes first job bug

This reverts commit fe74d067.

Conflicts:

	spim_registration/timelapse/Snakefile

Rule registration depends on the output of hdf5_xml and resave_hdf5
Protects it against too early deletion.

This approach assumes that the processing itself runs without error.
When Fiji fails in on process then the whole workflow needs to restart.
Because the dummy files are now gone.

Now uses sysconfcpus and cluster.jason is adjusted for these parameters

* added new function that replaces occurrences of a defined set of parameters
  (required to handle brackets inside filenames)
* using glob_and_escape in Snakefile now

Pipeline tested and works with single channel data

the output rule now references to the correct xml filename

Log files are ordered

hdf5_xml_output rule does again touch the output
Tested and works

compute_on is not present in Snakefile

compute_on, directory_cuda and cudafourierconvolution System.getProperty
now correct

For registration:
New added downsampling
New added Difference of Gaussian Detection
Difference of Gaussian with GPU or CPU

Switching between Difference of Mean and Gaussian is possible

Switching between GPU and CPU deconvolution is possible

Allows to process dual channel datasets were only one channel
contains beads

Added a switch in .yaml file for selecting dublication of transformation
Added a part in the snakefile for dublication of the transformation
in the pipeline

BUG: "Single Channel" is not a valid choice for "Process_channel"
When choosing Single channel in reg_process_channel then
this is not a valid input for the macro.
Now reg_process_channel is set to All Channel for Single
Channel processing

External transformation has a bug it breaks the .xml file
External tranformation is disabled for now.

Added new cluster settings for resave_hdf5_output in cluster.json

BUG in export_output.bsh: took subsampling and chunk sizes from
resave hdf5. But these were not good.
Added new chunck size and subsampling option

Started to update fusion

Added dual channel processing for these parts
updated .bsh file