Map configuration examples in JSON

This page is linked from Sample Codes for web API use

If you replace the JSON objects ( between two "JSON") in seg2 of example.pl in this page with the following examples, the content of result.png file will change accordingly.
You may also read Map API specification which is another expression of similar content.

To check the syntax of map configuration in JSON, Pasete you JSON object ( {...} in Seg2 )next to the ? of the following URL.

http://lifesciencedb.jp/bp3d/API/image?JSONSeg2
http://lifesciencedb.jp/bp3d/API/animate?JSONSeg2

Map API specification: a table of parameter types and allowed values

1 Examples of map configuration in JSON format
2 Make your data into choropleth map configuration
- 2.1 Preparation of tabular data (scalardata.txt)
- 2.2 A Script Seg2 to generate Map configuration (JSON object) from a data table

Examples of map configuration in JSON format

+The Image of excel sheets below will soon become in copy-able forms.

1. The common parameters specifying kit version

"PartName" in config is looked up in specified tree ("isa" for example) and then another tree ("partof") is searched automatically. (tree parameter affects only when data in two trees confricts)
If you do not specify data "Version", your map may change as version goes, because the data for a concept may change as version goes.
As of March 2014、there are three versions of kit data you may specify :"2.0"、"3.0"、"4.0".

Common parameters

Parameter type	Default value	parameter meaning	allowed values, range
"Common":{			Array of key value pairs in JSON
"Model":	"bp3d"	Kit name	"bp3d"
"Version":	"4.0"	Kit version	"2.0"\|"3.0"\|"4.0"\|"4.1"
"AnatomogramVersion":	"20110318"	Configuration syntax version	"20110318" at this moment
"ScalarMaximum":	65535	Maximum value for heatmap	any integer
"ScalarMinimum":	-65535	Minimum value for heatmap	any integer smaller than max
"ColorbarFlag":	false	Insert color progression chart in image	false \| true
"ScalarColorFlag":	false	Use backcloth of flagged parts as Choropleth map	false \| true
"TreeName":	"isa"	Logical tree for parts aggregation	"isa"\|"partof"
"DateTime":	none	Time stamp of configuration	"yyyymmddhhmmss"
"CoordinateSystemName":	"bp3d"	Rendering space	"bp3d"
"CopyrightType":	""	Copyright insert on the image	"large"\|"medium"\|"small"
"PinDescriptionDrawFlag"	false	Show notes for pins on the image	false \| true
"PinIndicationLineDrawFlag"	0	Draw lines between pins and pin note 1; tail, 2; head	0 \| 1 \| 2
}

map configuration as JSON object

URL for map image

result.png

Skip common parameters = latest (4.1) and isa

{

"Part":[

{

"PartName":"anatomical entity",

"PartColor":"F0D2A0",

"PartOpacity":0.1

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Part":[{"PartName":"anatomical entity","PartColor":"F0D2A0","PartOpacity":0.1},{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}]}

Specify kit version and FMA tree you may use

{

"Common":{

"Version":"4.0",

"TreeName":"partof"

"Part":[

{

"PartName":"anatomical entity",

"PartColor":"F0D2A0",

"PartOpacity":0.1

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"partof"},"Part":[{"PartName":"anatomical entity","PartColor":"F0D2A0","PartOpacity":0.1},{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}]}

Cange FMA tree to 3.0 where "region of wall of heart"is not contained.

{

"Common":{

"Version":"3.0",

"TreeName":"isa"

"Part":[

{

"PartName":"anatomical entity",

"PartColor":"F0D2A0",

"PartOpacity":0.1

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"3.0","TreeName":"isa"},"Part":[{"PartName":"anatomical entity","PartColor":"F0D2A0","PartOpacity":0.1},{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}]}

2. Adding parts

You can add parts from the kit listed in here:
- Partonomy tree:ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/20130619/partof_parts_list_e.txt
- Taxonomy tree: ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/20130619/isa_parts_list_e.txt
- In RDB:
  - http://togodb.biosciencedbc.jp/togodb/view/bodyparts3d_partof_parts_list_e
  - http://togodb.biosciencedbc.jp/togodb/view/bodyparts3d_isa_parts_list_e
- otherwise you can find it in map editor: http://lifesciencedb.jp/bp3d/
You can specify colors and opacities for each part in hexadecimal code[1] and zero (invisible) to 1(opaque) value by 0.1 pitch
When "PartName" in config is not found in specified tree ("isa" for example) another tree ("partof") is searched automatically.

Part parameters

Parameter type	Default value	parameter meaning	allowed values, range
"Part":[			repeat for all parts with comma separation
{			Array of key value pairs in JSON
"PartID":	""	concept ID for body parts in FMA
"PartName":	""	common concept names (effective when no ID specified)
"PartColor":	"FFFFFF"	hexadecimal color code
"PartScalar":	0	Data value mapped to the Part
"ScalarColorFlag"	false	Use surface as a part of Choropleth map	true \| false
"PartOpacity":	1	Opacity of the surface 1=opaque	actual number 0 to 1
"PartRepresentation":	"surface"	object representation	"surface"\|"wireframe"\|"point"
"UseForBoudingBoxFlag":	true	included in bounding box for zoom	true \| false
"PartDeleteFlag":	false	Do not shown this part	true \| false
}
]

Alteration in map config.

use API from browser (URL)

content of "result.png" = return from URL request

origin(ORI)

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

]

}

Add stomach (FMA7148) in yellow (FFFF00) and 50% opaque to ORI (STO)

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

{

"PartName":"stomach",

"PartOpacity":0.5,

"PartColor":"FFFF00"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"},{"PartName":"stomach","PartOpacity":0.5,"PartColor":"FFFF00"}]}

same as above but use "FMA ID" to specify the part

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

{

"PartID":"FMA7148",

"PartOpacity":0.5,

"PartColor":"FFFF00"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"},{"PartID":"FMA7148","PartOpacity":0.5,"PartColor":"FFFF00"}]}

3. Region of interest

By default, image is generated by making framing of the image identical to bounding box--a smallest cuboid containing all kit parts.
If you explicitly deny to use a part in making bounding box, image is zoomed into the rest of the part.

Alteration in map config.

use API from browser (URL)

content of "result.png" = return from URL request

Ignore bone in framing for ORI

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF",

"UseForBoundingBoxFlag":false

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

]

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF","UseForBoundingBoxFlag":false},{"PartName":"region of wall of heart","PartColor":"FF0000"}]}

Ignore bone in framing for STO

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF",

"UseForBoundingBoxFlag":false

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

{

"PartName":"FMA7148",

"PartOpacity":0.5,

"PartColor":"FFFF00"

}

]

}

4. Background and window

Window specification put the image of bounding box in a window with specified size.

Window parameters

Parameter type	Default value	parameter meaning	allowed values, range
"Window":{			Array of key value pairs in JSON
"ImageWidth":	500	Output image width in pixcel	integer less than 5000 (1000 for animation)
"ImageHeight":	500	Height of the output image in pixcel	integer less than 5000 (1000 for animation)
"BackgroundColor":	"FFFFFF"	Background color in hexadecimal code	"000000" to "FFFFFF"
"BackgroundOpacity":	100	Background opacity（0～100）	integer 0 to 100
"GridFlag":	FALSE	Draw grid pattern on the image	false \| true
"GridTickInterval":	100	Unit of the grid（mm）	non negative integer
"GridColor":	"FFFFFF"	Grid line color in Hexadecimal code	"000000" to "FFFFFF"
}

Alteration in map config.

use API from browser (URL)

content of "result.png" = return from URL request

deny bone bounding and specify window

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF",

"UseForBoundingBoxFlag":false

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

"Window" : {

"ImageWidth":200,

"ImageHeight":300,

"BackgroundColor":"00A4AC"

}

with bone as a bounding box and specify window

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

"Window" : {

"ImageWidth":200,

"ImageHeight":300,

"BackgroundColor":"00A4AC"

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}],"Window":{"ImageWidth":200,"ImageHeight":300,"BackgroundColor":"00A4AC"}}

overlay a white grid with 50mm tick on the window.

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

"Window" : {

"ImageWidth":200,

"ImageHeight":300,

"BackgroundColor":"00A4AC",

"GridFlag":true,

"GridTickInterval":50,

"GridColor":"FFFFFF",

"BackgroundOpacity":10

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}],"Window":{"ImageWidth":200,"ImageHeight":300,"BackgroundColor":"00A4AC","GridFlag":true,"GridTickInterval":50,"GridColor":"FFFFFF","BackgroundOpacity":10}}

5. Camera positioning=

Camera parameters

Parameter type	Default value	parameter meaning	allowed values, range
"Camera":{			Array of key value pairs in JSON
"CameraMode":	"front"	camera mode, either movable or fixed	"camera"\|"front"\|"back"\|"left"\|"right"\|"top"\|"bottom"
"CameraX":	0	camera X-coordinate, when mode=camera	Double precision
"CameraY":	0	camera Y-coordinate, when mode=camera	Double precision
"CameraZ":	0	camera Z-coordinate, when mode=camera	Double precision
"TargetX":	0	Camera direction X coordinate of target point	Double precision
"TargetY":	0	Camera direction Y coordinate of target point	Double precision
"TargetZ":	0	Camera direction Z coordinate of target point	Double precision
"CameraUpVectorX":	0	Camera up vector X (upside of camera device)	Double precision (usually unit vector)
"CameraUpVectorY":	0	Camera up vector Y	Double precision (usually unit vector)
"CameraUpVectorZ":	0	Camera up vector Z	Double precision (usually unit vector)
"Zoom":	0	Arbitrary zooming power	0 to 19.8
"AddLatitudeDegree":	0	Rotate latitudinary	0 to 360
"AddLongitudeDegree":	0	Rotate longitudinary	0 to 360
}

Alteration in map config.

use API from browser (URL)

content of "result.png" = return from URL request

camera locates left to the manikin

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

"Camera":{

"CameraMode":"left"

}

Move the camera +30degree North and +30 degree East on the orbit

{

"Common":{

"Version":"4.0",

"TreeName":"isa"

"Part":[

{

"PartName":"bone organ",

"PartColor":"FFFFFF"

{

"PartName":"region of wall of heart",

"PartColor":"FF0000"

}

"Camera":{

"CameraMode":"left",

"AddLatitudeDegree":30,

"AddLongitudeDegree":30

}

http://lifesciencedb.jp/bp3d/API/image?{"Common":{"Version":"4.0","TreeName":"isa"},"Part":[{"PartName":"bone organ","PartColor":"FFFFFF"},{"PartName":"region of wall of heart","PartColor":"FF0000"}],"Camera":{"CameraMode":"left","AddLatitudeDegree":30,"AddLongitudeDegree":30}}

Make your data into choropleth map configuration

"PartColor" may be used to visualize quantitative or qualitative value given in your data.
Anatomography supports transformation of scalar into color code according to rainbow color progression( red---toward--purple)

Preparation of tabular data (scalardata.txt)

Put your data in a tab delimited table "scalardata.txt" as below .
Anatomical entity must be represented in FMA_ID or preferred name for it which is listed as a kit component in the link below.
- Partonomy tree:ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/20130619/partof_parts_list_e.txt
- Taxonomy tree: ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/20130619/isa_parts_list_e.txt

esophagus	 9405
stomach	32851
rectum	8530
liver	         23421
gallbladder	7476
pancreas	11933
trachea	43921
prostate	8840
urinary bladder	3817

Place this table in the same directory as the example.pl

A Script Seg2 to generate Map configuration (JSON object) from a data table

This section describes making Seg2 according to your scalar data.
Joining Seg1,Seg2,Seg3,Seg4 (see Sample_Codes_for_web_API_use) into one file example.pl and execute it will result in result.png of choroplethmap.
Use Common parameters to declare that scalar value is used to specify "PartsColor".
The color range is the range of scalar in scalar.txt by default.

Base configuration: setting values instead of "null" in "Scalar maximum" and "ScalarMinimum" fix the scalar values for both extremes. Use "human body" as frame of the map.

my $json = <<JSON;
{
 "Common":{
  "Model":"bp3d",
  "Version":"4.0",
  "TreeName":"partof",
  "ColorbarFlag":true,
  "ScalarColorFlag":true,
  "ScalarMaximum":null,
  "ScalarMinimum":null
 },
 "Part":[
  {
   "PartName":"human body",
   "PartOpacity":0.1
  }
JSON

Appending Parts parameters by extracting data from scalar.txt

open LIST,"scalardata.txt";
while (<LIST>) {
 my ($organ, $value) = split("\t", $_);
 $json .= <<JSON;
  ,{
   "PartName":"$organ",
   "PartScalar":$value,
   "ScalarColorFlag":true
  }
JSON
}
close LIST;
$json .= <<JSON;
 ]
}
JSON

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Map configuration examples in JSON

Contents

Examples of map configuration in JSON format

1. The common parameters specifying kit version

2. Adding parts

3. Region of interest

4. Background and window

5. Camera positioning=

Make your data into choropleth map configuration

Preparation of tabular data (scalardata.txt)

A Script Seg2 to generate Map configuration (JSON object) from a data table