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ChangeLog
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ChangeLog
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4.0.0 (2015/04/01)
------------------
* Core components placed in separate repo licensed under GPLv3
* compact structure for increased capacity (more features with large maps) -
exploit sparseness in spatial distributions
* New method to build corridors!
* user defined kernels with arbitrary shape + single-parameter kernels: threshold, exponential
* core: no more hardcoded limits in landscape identification (in post-processing),
unlimited number of management landscapes (as long as memory is available).
* GUI: new project maker!
* GUI: new tips window
* GUI: New color schemes (spectral, Blue-Yellow-Red diverging, etc.), most of which are
color blind safe (generated with www.colorbrewer2.org)
* GUI: curves are plotted against "proportion of landscape protected" (from 1 to 0)
instead of "proportion lost" (in runtime plots and interactive plots).
* More technical improvements: get rid of the ~2 GB cells limit
dump and reload internal, compact representation of feature distributions (vmat)
* Minimized memory consumption for internal structures, and free memory as soon as possible
(during the prioritization, proportinally to the removal level). Analyses with
~10**9 cells require ~30GB + memory needed to load features and optional layers
* Avoid using temporary disk space for generating rasters (saving of the order of GBs for
large (10**9 cell) layers.
* When using "hierarchical removal mask" ('use mask', 'mask file'), borders between lower
and higher removal levels are added to the edge list. Before, lower level cells could
be removed too late (after higher level cells) if they were enclosed in higher level regions
* bug whereby png images were not created if png specified first in the list of output
formats
3.1.11 (2013/09/23)
-------------------
* core: better error checking and messages for info-gap distributional uncertainty maps.
Also more verbose messages about errors in various raster dimensions.
* core: output.SSI_curves.txt now includes the remaining proportions for every species/feature
(as the normal .curves.txt file). Fixed bug in first column of SSI_curves.txt!
* core: fixed messages for interactions of type 2 (feature numbers and names were missing)
* GUI: don't crash on open raster with null extent or all-missing cells
* core: fixed a bug by which setting an empty list of output image formats
"--image-output-formats" would also set an empty list of output grid formats (and no
grids are generated at all even if several formats have been given in --grid-output-formats)
* core: fixed a lack/order-of-initialization bug in SSI code that could lead to crashes in the
initialization/performance level check stage
3.1.10 (2013/06/05)
-------------------
* core: fixed LSI post-processing analysis - wasn't working because of wrong error checks!
* GUI: fixed an issue with the display of raster maps. Single value rasters were not
correctly shown on the "map view", this did not affect the core and its results.
* GUI: initialize map view settings (background/border) at start
* GUI: fixed links to support/bugs and documentation.
3.1.9 (2013/04/23)
------------------
* Core: New output file: .SSI_features_info.txt similar to .features_info.txt,
shows SSI feature weights and distribution_sum, as well as target violation levels
* Core: in SSI_curves.txt, fixed numerical issues in the the lost_at_fraction field which
could result in fraction 1 wrongly reported as fraction "-1"
* Core: in SSI_curves.txt, increased the Feature/Species field length so that results are
properly displayed when the number of features is >=10001
* Core: in .curves.txt and other output files: properly handle divide-by-zero
exceptions when sum of all feature weights = 0, also miscellaneous changes/updates in
output files and memo messages.
3.1.8 (2013/04/15)
------------------
* In post processing, LSB and LSM: report an error (core text output / text output) if
the extent of the mask does not match the extent of the feature layers.
* Report in the GUI console errors related to 'mask missing areas' and 'area mask file',
and 'use condition layer' and 'condition file'
* Core: clarified in all? messages the ambiguity species/biodiversity feature.
3.1.7 (2013/03/14)
------------------
* Post-processing: new special ("-1 distance") LSM mode to get statistics about
(potentially non-contiguous) units. See the do_ppa.bat example in the tutorial.
Note: you need to use consecutive unit numbers starting from 1.
* nwout#.spp_data.txt files in PPA analyses:
Added spp occurring at >0.001%
fixed these fields: "average proportion remaining over all spp in units", and
"Total proportion and sum remaining for species" (in older versions they used
to be multiplied by 2). Fixed several fields, discard results from older versions!
* Post-processing: report error if the mask file is wrong (LSB or LSM), and don't crash.
* GUI: Fixed bugs with mask layers in post-processing lines
* A bunch of more informative warning/error messages in the core and GUI, (about
memory issues and missing files).
* reload (-l) mode: before starting the removal process, a consistency check is run
to make sure that:
a) all the non-missing cells in the old solution have at least one feature
occurrency (in the potentially new features list)
b) all the cells with occurrencies (in the potentially new features list) are
included in the old solution
If the check fails, Z stops and shows the coordinates of the offending cells.
3.1.6 (2012/12/11)
------------------
* core: ignore "edge removal" and "add edge points" options if running in
re-load (-l) mode (to avoid misleading random failures when reusing settings
files - depending on the (random) edge points)
* Don't print too many SSI x-y-value lines after loading SSI files (for setups
with extremely large numbers of SSI points).
3.1.5 (2012/10/02)
-----------------
* (only affects 64 bits versions) Fixed an issue with FFTW in Sandy Bridge CPUs
(i3/i5/i7) that leads to crashes when using connectivity methods (and if
AVX - Advanced Vector Extensions instructions are supported)
3.1.4 (2012/09/07)
------------------
* core: more informative allocation failure messages - for connectivity matrices
* Bug fix in project window: Z GUI was refusing to open a valid project/setup if the
user had tried before to open it but failed to load because of (now fixed) errors.
3.1.3 (2012/07/30)
------------------
* In 'open raster map': show also .bil files
handle errors gracefully (and don't crash...)
* Bug fix: with many hundreds of columns in the community similarity matrix or the
connectivity matrix, previous versions of the core would fail to load these matrices.
* Bug fix: sometimes only the first line would be written into "projectname".txt,
(issues with redirected output). Now the same output text actually goes into
'.run_info.txt' and '.txt'.
* Bug fix: when loading raster maps, the range of values and # missing cells are
now correctly initialized.
* GUI: Added 'Support / bugs' action in the help menu
3.1.2 (2012/06/11)
------------------
* Added support for transformed layers:
# core:
new settings in a new section '[Transformed layers]':
'output final transformed layers = 1'
'output info-gap transformed layers = 1'
'output distribution smoothing transformed layers = 1'
'output community similarity transformed layers = 1'
'output condition transformed layers = 1'
'output retention transformed layers = 1'
'output matrix connectivity transformed layers = 1'
'output interactions transformed layers = 1'
new output directory: projectname_transf_final_layers/ containing transf. raster files (uses output formats selected in command line)
Other intermediate layers: projectname_transf_info-gap_layers, projectname_transf_distrib_smooth_layers,
projectname_transf_comm_simil_layers, projectname_matrix_conn_layers,
projectname_transf_interactions_layers, projectname_transf_condition_layers,
projectname_transf_retention_layers,
# GUI: in project trees, new 'transformed layers' child under instances, containing transformed layer maps.
* Interactive plots window: in 'histogram of area qualities' features can be 'raw layer' or 'transformed layers'
* Fixed ADMU analysis when using feature sampling ('resample species = n' in settings file)
* Fixed crash in process list (remove + rerun project that has been run before)
* Show green message 'finished ok' at the end of successful runs (notice level)
* Fixed initialization of random numbers for rule '5', now repetitions of random prioritizations will really produce different results.
* Changed sizes of the 'map peek' window so that it can be smaller
* Zoom added to the 4 plots in the 'runtime plot' tab.
3.1.1 (2012/04/04)
------------------
* Interactive plots window: added 'copy to clipboard' and 'save as image/document' actions to every plot.
Supports png, svg, jpg, pdf and ps formats
* Runtime plot:
- same actions as in interactive plots
- horizontal and vertical splitters between plots
* Interactive plots window: maximum curve added to the 'global solution' block
* The removal process is automatically shown on the output tabs for the first process that runs
* Project view: Added 'reload edits' action. Added a checkbox in settings to automatically reload projects before queueing them (default: disabled)
* In 'process view', the last one shown in the output tabs (double-clicked) is highlighted in boldface + icon
* In 'process view', status or progress % is now shown before process name
* New 'always ask for confirmation' checkbox in the exit pop-up (and in the new 'global' tab of the preferences dialog)
* On windows Z preferences are now removed from the registry on uninstall
* Default value for 'override Z executable' is now off
* The installers now honor the 'create desktop icon' checkbox
* 64 bits installer: default installation directory is now "C:\Program Files" (as opposed to 32 bits, "C:\Program Files (x86)")
3.1.0 (2012/03/08)
------------------
Here is a not exhaustive but rather complete change log (of user visible changes) for Zonation 3.1.0:
* New files for the administrative units (admu) analysis:
# per admu curves files
# per admu groups files
# redistributed rank map output (ranks redistributed in [0,1] for every admu, also visible
in the project tree)
* New convenient command line options for zig3: --warp-factor and --removal-rule
* New command line options in zig3: -h, --help, -v, --version
* New error reporting system with several severity levels: notice, warning, error, critical
error. In preferences, you can set different levels of verbosity.
* New "error" state in the process queue. Several fixes for error conditions.
* New interactive plots window (can be opened for every instance). Contains 4 types of plots.
* New "color histogram" dockable window for the merged map
* New "merged map" functionality (additional tab in the visual outputs window).
* New actions to add maps into the merged map from the project view, process view, and map
output.
* New "map peek" dockable window
* Self-installable binaries that will create a desktop icon and entries in the start menu
* Zip packages (and installer also) include a README.txt and a help subdir
* Fully static binaries - no more need to care about dll's!
* In the runtime plot output tab (old Plot view), there's now a black line for the
weighted average values.
* New fields (columns) in .grp_curves.txt files: weighted mean and SA-extinction risk
* .grp_crvs.txt files are now named .grp_curves.txt to be consistent with the manual and other
file names.
* "Clear" action for the console
* Fixed issues with relative and absolute paths in project files
* New kiss random number generator
* .curves.txt file split into .features_info.txt and .curves.txt
* Create full output path if it doesn't exist before zig core generates results
* Additional information goes into the memo: time and date, locale, hard disk space required for
certain files, more information about layers, etc.
* Proper handling of load (-l) mode commands
* Proper handling of missing/unspecified automated post-proc files
* Fixed compressed-tif and compressed-img output formats
* Fixed --use-threads option
* Fixed numeric issues that arised when all the values inside the analysis area mask for a
feature are 0.
* Fixed various issues with NaN values in input layers