IMPORTANT NOTE If you install Paintera through conda you will have to use your system Java and JavaFX to be able to run Paintera because there is no JavaFX package on conda at the moment.

TBD

• java (ubuntu):

sudo apt install default-jre default-jdk

• maven (ubuntu):

sudo apt install maven

• javafx (ubuntu):

sudo apt install openjfx

run:

mvn clean install

or, to generate a "fat jar" with all dependencies added, run:

mvn -Pfat clean package

This will include org.slf4j:slf4j-simple as slf4j binding.

conda install -c hanslovsky paintera

paintera [[JRUN ARG...] [JVM ARG...] --] [ARG...]

Jrun/JVM args are separated by --. The default max heap size is half the available system memory. To change the heap size, run

paintera -Xmx<size> -- [ARG...]

or

PAINTERA_MAX_HEAP_SIZE=<size> paintera [ARG...]

By default, org.slf4j:slf4j-simple is used as slf4j binding for logging. This can be replaced by setting the PAINTERA_SLF4J_BINDING environment variable:

PAINTERA_SLF4J_BINDING=groupId:artifactId[:version]

For example, to replace org.slf4j:slf4j-simple with ch.qos.logback:logback-classic, run (on Linux/OSX):

PAINTERA_SLF4J_BINDING=ch.qos.logback:logback-classic paintera

You can also run a compiled fat jar

java <java-opts> -jar target/paintera-0.1.2-SNAPSHOT-shaded.jar

We recommend these Java options:

$ java -jar target/paintera-0.1.1-SNAPSHOT-shaded.jar --help
Usage: Paintera [-h] [--height=HEIGHT] [--width=WIDTH]
                [--label-source=LABEL_SOURCE]... [--raw-source=RAW_SOURCE]...
      --height=HEIGHT   Initial height of viewer. Defaults to 600.
      --label-source=LABEL_SOURCE
                        Open label source at start-up. Has to be [file://]
                          /path/to/<n5-or-hdf5>:path/to/dataset
      --raw-source=RAW_SOURCE
                        Open raw source at start-up. Has to be [file://]
                          /path/to/<n5-or-hdf5>:path/to/dataset
      --width=WIDTH     Initial width of viewer. Defaults to 800.
  -h, --help            Display this help message.

In #61 we introduced a specification for the data format that Paintera can load through the opener dialog (Ctrl O). These restrictions hold only for the graphical user interface. If desired, callers can

• add arbitrary data sets programatically, or
• through the attributes.json project file if an appropriate gson deserializer is supplied.

Accept any of these:

1. any regular (i.e. default mode) three-dimensional N5 dataset that is integer or float. Optional attributes are "resolution": [x,y,z] and "offset": [x,y,z].
2. any multiscale N5 group that has "multiScale" : true attribute and contains three-dimensional multi-scale datasets s0 ... sN. Optional attributes are "resolution": [x,y,z] and "offset: [x,y,z]". In addition to the requirements from (1), all s1 ... sN datasets must contain "downsamplingFactors": [x,y,z] entry (s0 is exempt, will default to [1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored.
3. (preferred) any N5 group with attribute "painteraData : {"type" : "raw"} and a dataset/group data that conforms with (2).

Accept any of these:

1. any regular (i.e. default mode) integer or varlength LabelMultisetType ("isLabelMultiset": true) three-dimensional N5 dataset. Required attributes are "maxId": <id>. Optional attributes are "resolution": [x,y,z], "offset": [x,y,z].
2. any multiscale N5 group that has "multiScale" : true attribute and contains three-dimensional multi-scale datasets s0 ... sN. Required attributes are "maxId": <id>. Optional attributes are "resolution": [x,y,z], "offset": [x,y,z], "maxId": <id>. If "maxId" is not specified, it is determined at start-up and added (this can be expensive). In addition to the requirements from (1), all s1 ... sN datasets must contain "downsamplingFactors": [x,y,z] entry (s0 is exempt, will default to [1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored.
3. (preferred) any N5 group with attribute "painteraData : {"type" : "label"} and a dataset/group data that conforms with (2). Required attributes are "maxId": <id>. Optional sub-groups are:

• fragment-segment-assignment -- Dataset to store fragment-segment lookup table. Can be empty or will be initialized empty if it does not exist.
• label-to-block-mapping -- Multiscale directory tree with one text files per id mapping ids to containing label: label-to-block-mapping/s<scale-level>/<id>. If not present, no meshes will be generated.
• unique-labels -- Multiscale N5 group holding unique label lists per block. If not present (or not using N5FS), meshes will not be updated when commiting canvas.