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Aliaksandr Halavatyi
AutoMicTools
Commits
d99d11ff
Commit
d99d11ff
authored
Aug 22, 2021
by
Aliaksandr Halavatyi
Browse files
additional util functions
parent
5af6741f
Changes
4
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pom.xml
View file @
d99d11ff
...
...
@@ -8,7 +8,7 @@
<version>5.0</version> <relativePath /> </parent> -->
<groupId>
embl.almf
</groupId>
<artifactId>
AutoMicTools_
</artifactId>
<version>
1.1.
29
-SNAPSHOT
</version>
<version>
1.1.
30
-SNAPSHOT
</version>
<name>
plugins/AutoMicTools_.jar
</name>
<description>
Collection of tools for automated (feedback) microscopy data acquisition and analysis
</description>
...
...
src/main/java/automic/geom/Point3D.java
View file @
d99d11ff
...
...
@@ -11,6 +11,14 @@ public class Point3D {
z
=
_z
;
}
public
Point3D
(
Integer
_xInt
,
Integer
_yInt
,
Integer
_zInt
)
{
x
=(
_xInt
==
null
)?
null
:
Double
.
valueOf
(
_xInt
);
y
=(
_yInt
==
null
)?
null
:
Double
.
valueOf
(
_yInt
);
z
=(
_zInt
==
null
)?
null
:
Double
.
valueOf
(
_zInt
);
}
public
Double
getX
(){
return
x
;
}
...
...
@@ -23,6 +31,25 @@ public class Point3D {
return
z
;
}
public
Integer
getXInteger
(){
if
(
x
==
null
)
return
null
;
return
x
.
intValue
();
}
public
Integer
getYInteger
(){
if
(
y
==
null
)
return
null
;
return
y
.
intValue
();
}
public
Integer
getZInteger
(){
if
(
z
==
null
)
return
null
;
return
z
.
intValue
();
}
public
void
setX
(
Double
_x
)
{
x
=
_x
;
}
...
...
src/main/java/automic/online/microscope/ZenBlueCommander.java
View file @
d99d11ff
...
...
@@ -179,11 +179,4 @@ public class ZenBlueCommander implements MicroscopeCommanderInterface{
_jObject
.
add
(
_key
,
_value
);
}
private
static
Double
getValueFromNonNullArray
(
double
[]
_array
,
int
_index
)
{
if
(
_array
==
null
)
return
null
;
return
_array
[
_index
];
}
}
src/main/java/automic/utils/imagefiles/ImageOpenerWithBioformats.java
View file @
d99d11ff
...
...
@@ -16,6 +16,8 @@ import loci.plugins.in.ImporterOptions;
import
java.lang.Exception
;
import
automic.geom.Point3D
;
import
java.io.File
;
import
java.io.IOException
;
...
...
@@ -197,5 +199,44 @@ public class ImageOpenerWithBioformats {
return
imgs
[
0
];
}
public
static
Point3D
getVoxelSizeUm
(
String
_imageFilePath
)
throws
Exception
{
ImageReader
reader
=
new
ImageReader
();
IMetadata
omeMeta
=
MetadataTools
.
createOMEXMLMetadata
();
reader
.
setMetadataStore
(
omeMeta
);
reader
.
setId
(
_imageFilePath
);
double
xSize
=
omeMeta
.
getPixelsPhysicalSizeX
(
0
).
value
().
doubleValue
();
double
ySize
=
omeMeta
.
getPixelsPhysicalSizeY
(
0
).
value
().
doubleValue
();
double
zSize
=
omeMeta
.
getPixelsPhysicalSizeZ
(
0
).
value
().
doubleValue
();
reader
.
close
();
return
new
Point3D
(
xSize
,
ySize
,
zSize
);
}
public
static
Point3D
getVoxelSizeNm
(
String
_imageFilePath
)
throws
Exception
{
Point3D
voxelSizeInUm
=
getVoxelSizeUm
(
_imageFilePath
);
return
new
Point3D
(
voxelSizeInUm
.
getX
()*
1000
,
voxelSizeInUm
.
getY
()*
1000
,
voxelSizeInUm
.
getZ
()*
1000
);
}
public
static
Point3D
getImageSizePx
(
String
_imageFilePath
)
throws
Exception
{
ImageReader
reader
=
new
ImageReader
();
IMetadata
omeMeta
=
MetadataTools
.
createOMEXMLMetadata
();
reader
.
setMetadataStore
(
omeMeta
);
reader
.
setId
(
_imageFilePath
);
double
xSize
=
omeMeta
.
getPixelsSizeX
(
0
).
getValue
();
double
ySize
=
omeMeta
.
getPixelsSizeY
(
0
).
getValue
();
double
zSize
=
omeMeta
.
getPixelsSizeZ
(
0
).
getValue
();
reader
.
close
();
return
new
Point3D
(
xSize
,
ySize
,
zSize
);
}
}
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