Component: Fiji

Fiji

Executes a Jython script under Fiji (ImageJ) that generates an image directory from given image directories.

An example script to run a median filter on all input images: "IJ.run(in1, 'Median...', 'radius=2'); out=in1"

Some help on scripting Fiji with Jython can be found on the official site and from this tutorial. See Figuring out what parameters a plugin requires in the tutorial for easy access to ImageJ plugins. The Fiji Javadoc and ImageJ Javadoc may also be of use.

Version	1.0
Bundle	anima
Categories
Authors	Miko Valori (miko.valori@helsinki.fi)
Issue tracker	View/Report issues
Requires	Fiji ; xvfb (DEB) ; download (bash)
Source files	component.xml fijistart.py fijijython.sh
Usage	Example with default values Fiji( //command = TextFile, //table = CSV, //in1 = ImageList, //in2 = ImageList, //in3 = ImageList, //in4 = ImageList, //in5 = ImageList, //inArray = ImageList, //file1 = ImageList, //file2 = ImageList, display = false, extension = ".png", files = 0, javaHeap = 4096, param1 = "", param10 = "", param2 = "", param3 = "", param4 = "", param5 = "", param6 = "", param7 = "", param8 = "", param9 = "", script = "" )

Version

1.0

Bundle

anima

Categories

Authors

Miko Valori (miko.valori@helsinki.fi)

Issue tracker

View/Report issues

Requires

Fiji ; xvfb (DEB) ; download (bash)

Source files

component.xml fijistart.py fijijython.sh

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
command	TextFile	Optional	Jython script file to operate the images with. The string parameter will override this input.
table	CSV	Optional	Optional CSV file to read. Will appear as table.
in1	ImageList	Optional	Source images 1 (in1). The output images will be named after this input folder.
in2	ImageList	Optional	Source images 2 (in2)
in3	ImageList	Optional	Source images 3 (in3)
in4	ImageList	Optional	Source images 4 (in4)
in5	ImageList	Optional	Source images 2 (in5)
inArray	Array<ImageList>	Optional	An array of directories with image files. (ina[0], ina[1], ...)
file1	ImageList	Optional	Source image 1 (file1). This folder should contain only one image. The same image is used in each iteration of dir1.
file2	ImageList	Optional	Source image 2 (file2). See input file1.

Name

Type

Mandatory

Description

command

TextFile

Optional

Jython script file to operate the images with. The string parameter will override this input.

table

CSV

Optional

Optional CSV file to read. Will appear as table.

in1

ImageList

Optional

Source images 1 (in1). The output images will be named after this input folder.

in2

ImageList

Optional

Source images 2 (in2)

in3

ImageList

Optional

Source images 3 (in3)

in4

ImageList

Optional

Source images 4 (in4)

in5

ImageList

Optional

Source images 2 (in5)

inArray

Array<ImageList>

Optional

An array of directories with image files. (ina[0], ina[1], ...)

file1

ImageList

Optional

Source image 1 (file1). This folder should contain only one image. The same image is used in each iteration of dir1.

file2

ImageList

Optional

Source image 2 (file2). See input file1.

Name	Type	Description
out	ImageList	Result images (out)
out2	ImageList	Result images (out2)
tableOut	CSVList	Result tables (tableout)

Name

Type

Description

out

ImageList

Result images (out)

out2

ImageList

Result images (out2)

tableOut

CSVList

Result tables (tableout)

Parameters

Name	Type	Default	Description
display	boolean	false	Set to true to use the current DISPLAY. When false, tries to send screen to Xvfb (if installed). i.e. Set to true for easier debugging.
extension	string	".png"	String to be added after the output filenames. e.g. ".png" to change the image format
files	int	0	If there are no input folders, this number is used as the number of files generated. The resulting files will be named file1[extension], file2[extension], ... Use the variable file in the script to get the file number.
javaHeap	int	4096	JavaHeap for the fiji process
param1	string	""	Value of this parameter will be assigned to param1 variable
param10	string	""	Value of this parameter will be assigned to param10 variable
param2	string	""	Value of this parameter will be assigned to param2 variable
param3	string	""	Value of this parameter will be assigned to param3 variable
param4	string	""	Value of this parameter will be assigned to param4 variable
param5	string	""	Value of this parameter will be assigned to param5 variable
param6	string	""	Value of this parameter will be assigned to param6 variable
param7	string	""	Value of this parameter will be assigned to param7 variable
param8	string	""	Value of this parameter will be assigned to param8 variable
param9	string	""	Value of this parameter will be assigned to param9 variable
script	string	""	Jython script string to operate the images with. This parameter overrides the input script file.

Name

Type

Default

Description

display

boolean

false

Set to true to use the current DISPLAY. When false, tries to send screen to Xvfb (if installed). i.e. Set to true for easier debugging.

extension

string

".png"

String to be added after the output filenames. e.g. ".png" to change the image format

files

int

If there are no input folders, this number is used as the number of files generated. The resulting files will be named file1[extension], file2[extension], ... Use the variable file in the script to get the file number.

javaHeap

int

4096

JavaHeap for the fiji process

param1

string

Value of this parameter will be assigned to param1 variable

param10

string

Value of this parameter will be assigned to param10 variable

param2

string

Value of this parameter will be assigned to param2 variable

param3

string

Value of this parameter will be assigned to param3 variable

param4

string

Value of this parameter will be assigned to param4 variable

param5

string

Value of this parameter will be assigned to param5 variable

param6

string

Value of this parameter will be assigned to param6 variable

param7

string

Value of this parameter will be assigned to param7 variable

param8

string

Value of this parameter will be assigned to param8 variable

param9

string

Value of this parameter will be assigned to param9 variable

script

string

Jython script string to operate the images with. This parameter overrides the input script file.

Test cases

Test case	Parameters▼	IN command	IN table	IN in1	IN in2	IN in3	IN in4	IN in5	IN inArray	IN file1	IN file2	OUT out	OUT out2	OUT tableOut
case1	properties	(missing)	(missing)	in1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	out	(missing)	(missing)
	script=IJ.run(in1, 'Median...', 'radius=' + param1); out=in1, param1=10, metadata.timeout=30
case2	properties	command	(missing)	in1	in2	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	out	(missing)	(missing)
	metadata.timeout=30
case3	properties	(missing)	table	in1	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	(missing)	tableOut
	script=ip=in1.getProcessor(); X=table[0].index('X'); Y=table[0].index('Y'); tableout=[[i, ip.getPixel(int(table[i][X]), int(table[i][Y]))] for i in range(1, len(table))], metadata.timeout=60

Test case

Parameters▼

IN
command

IN
table

IN
in1

IN
in2

IN
in3

IN
in4

IN
in5

IN
inArray

IN
file1

IN
file2

OUT
out

OUT
out2

OUT
tableOut

case1

properties

(missing)

in1

(missing)

out

(missing)

script=IJ.run(in1, 'Median...', 'radius=' + param1); out=in1,
param1=10,
metadata.timeout=30

case2

(missing)

(missing)

(missing)

metadata.timeout=30

case3

(missing)

(missing)

script=ip=in1.getProcessor(); X=table[0].index('X'); Y=table[0].index('Y'); tableout=[[i, ip.getPixel(int(table[i][X]), int(table[i][Y]))] for i in range(1, len(table))],
metadata.timeout=60

Anduril

Fiji

Inputs

Outputs

Parameters

Test cases