TBD
- java (ubuntu):
sudo apt install default-jre default-jdk- maven (ubuntu):
sudo apt install maven- javafx (ubuntu):
sudo apt install openjfxrun:
mvn clean installor, to generate a "fat jar" with all dependencies added, run:
mvn -Pfat clean package(Linux and OSX only)
[PREFIX=</path/to/prefix>] sh install.shSet PREFIX to a path that is on your PATH
If you are on Linux/OSX you can install ctrueden/jrun and the paintera launch script (instructions) and then run:
[VERSION=<version>] [JAVA_OPTS=<java-opts>] paintera [ARG...]If you set VERSION to a SNAPSHOT release you will need to run
mvn clean installfirst.
On any OS, you can also run a compiled fat jar
java <java-opts> -jar target/paintera-0.1.0-SNAPSHOT-shaded.jarWe recommend at these Java options:
| Option | Description |
|---|---|
| -Xmx16G | Maximum Java heap space (replace 16G with desired amount) |
| -XX:+UseConcMarkSweepGC | concurrent garbage collector generally better for UI applications |
$ java -jar target/paintera-0.1.0-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.| Action | Description |
|---|---|
P |
Show Status bar on right side |
(Shift +) Ctrl + Tab |
Cycle current source forward (backward) |
Ctrl + O |
Show open dataset dialog |
M |
Maximize current view |
Shift + M |
Maximize split view of one slicing viewer and 3D scene |
Shift + Z |
Un-rotate but keep scale and translation |
| left click | toggle id under cursor if current source is label source (de-select all others) |
| right click | toggle id under cursor if current source is label source (append to current selection) |
Shift left click |
Merge id under cursor with id that was last toggled active (if any) |
Shift right click |
Split id under cursor from id that was last toggled active (if any) |
Space left click/drag |
Paint with id that was last toggled active (if any) |
Space right click/drag |
Erase within canvas only |
Shift + Space right click/drag |
Paint background label |
Space wheel |
change brush size |
F + left click |
2D Flood-fill in current viewer plane with id that was last toggled active (if any) |
Shift + F + left click |
Flood-fill with id that was last toggled active (if any) |
N |
Select new, previously unused id |
Ctrl + C |
Show dialog to commit canvas and/or assignments |
C |
Increment ARGB stream seed by one |
Shift + C |
Decrement ARGB stream seed by one |
Ctrl + Shift + C |
Show ARGB stream seed spinner |
V |
Toggle visibility of current source |
Shift + V |
Toggle visibility of not-selected ids in current source (if label source) |
R |
Clear mesh caches and refresh meshes (if current source is label source) |
L |
Lock last selected segment (if label source) |
Ctrl + S |
Save current project state |
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.jsonproject file if an appropriate gson deserializer is supplied.
Accept any of these:
- 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]. - any multiscale N5 group that has
"multiScale" : trueattribute and contains three-dimensional multi-scale datasetss0...sN. Optional attributes are"resolution": [x,y,z]and"offset: [x,y,z]". In addition to the requirements from (1), alls1...sNdatasets must contain"downsamplingFactors": [x,y,z]entry (s0is exempt, will default to[1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored. - (preferred) any N5 group with attribute
"painteraData : {"type" : "raw"}and a dataset/groupdatathat conforms with (2).
Accept any of these:
- 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]. - any multiscale N5 group that has
"multiScale" : trueattribute and contains three-dimensional multi-scale datasetss0...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), alls1...sNdatasets must contain"downsamplingFactors": [x,y,z]entry (s0is exempt, will default to[1.0, 1.0, 1.0]). All datasets must have same type. Optional attributes from (1) will be ignored. - (preferred) any N5 group with attribute
"painteraData : {"type" : "label"}and a dataset/groupdatathat 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 usingN5FS), meshes will not be updated when commiting canvas.