Skip to content

Commit 7b7d83b

Browse files
elevanselevans
committed
Refactor SACATest to use setup helper method
This commit refactors the SACA test to use a setup helper method create the resources needed for the tests just once.
1 parent 12ca5f8 commit 7b7d83b

File tree

1 file changed

+20
-26
lines changed
  • scijava-ops-image/src/test/java/org/scijava/ops/image/coloc/saca

1 file changed

+20
-26
lines changed

‎scijava-ops-image/src/test/java/org/scijava/ops/image/coloc/saca/SACATest.java‎

Lines changed: 20 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -29,19 +29,17 @@
2929

3030
package org.scijava.ops.image.coloc.saca;
3131

32-
import io.scif.img.ImgOpener;
3332
import net.imglib2.RandomAccess;
3433
import net.imglib2.img.Img;
3534
import net.imglib2.type.logic.BitType;
36-
import net.imglib2.type.numeric.real.FloatType;
3735
import net.imglib2.type.numeric.real.DoubleType;
3836
import net.imglib2.type.numeric.integer.UnsignedByteType;
3937

40-
import org.scijava.io.location.FileLocation;
4138
import org.scijava.types.Nil;
4239
import org.scijava.ops.image.AbstractColocalisationTest;
4340

4441
import org.junit.jupiter.api.Test;
42+
import org.junit.jupiter.api.BeforeAll;
4543
import static org.junit.jupiter.api.Assertions.assertEquals;
4644

4745
/**
@@ -58,27 +56,33 @@ public class SACATest extends AbstractColocalisationTest {
5856
private final static int[] yPositions = { 30, 36, 80, 79, 139, 102, 77, 41,
5957
142, 118 };
6058

61-
// green and red colocalization images
62-
private Img<UnsignedByteType> green = getPositiveCorrelationImageCh1();
63-
private Img<UnsignedByteType> red = getPositiveCorrelationImageCh2();
59+
// image containers
60+
private static Img<DoubleType> zscore;
6461

65-
@Test
66-
public void testSACAHeatmapZScore() {
67-
final double[] zscoreExpected = { 0.0, 6.117364936585281, 0.0,
68-
-1.282447034877343, 0.0, 6.642396454955293, 0.0, -1.6567255788972388, 0.0,
69-
3.5385003044434877 };
62+
@BeforeAll
63+
public static void setUpTest() {
64+
// green and red colocalization images
65+
Img<UnsignedByteType> green = getPositiveCorrelationImageCh1();
66+
Img<UnsignedByteType> red = getPositiveCorrelationImageCh2();
7067

7168
// get slice 15 from colocalization data
7269
var gs = ops.op("transform.hyperSliceView").input(green, 2, 15).apply();
7370
var rs = ops.op("transform.hyperSliceView").input(red, 2, 15).apply();
7471

7572
// create image container
76-
Img<DoubleType> zscore = ops.op("create.img").input(gs, new DoubleType())
77-
.outType(new Nil<Img<DoubleType>>()
73+
zscore = ops.op("create.img").input(gs, new DoubleType()).outType(
74+
new Nil<Img<DoubleType>>()
7875
{}).apply();
7976

8077
// run SACA heatmap Z score op
8178
ops.op("coloc.saca.heatmapZScore").input(gs, rs).output(zscore).compute();
79+
}
80+
81+
@Test
82+
public void testSACAHeatmapZScore() {
83+
final double[] zscoreExpected = { 0.0, 6.117364936585281, 0.0,
84+
-1.282447034877343, 0.0, 6.642396454955293, 0.0, -1.6567255788972388, 0.0,
85+
3.5385003044434877 };
8286

8387
// get random access and assert results are equal
8488
final RandomAccess<DoubleType> zRA = zscore.randomAccess();
@@ -92,17 +96,15 @@ public void testSACAHeatmapZScore() {
9296
@Test
9397
public void testSACASigMask() {
9498
final double[] sigExpected = { 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
95-
1.0 };
96-
97-
Img<FloatType> zscore_ref = openFloatImg("stats/zscore_test_data.tif");
99+
0.0 };
98100

99101
// create image container
100-
Img<BitType> sigMask = ops.op("create.img").input(zscore_ref, new BitType())
102+
Img<BitType> sigMask = ops.op("create.img").input(zscore, new BitType())
101103
.outType(new Nil<Img<BitType>>()
102104
{}).apply();
103105

104106
// run SACA significant pixel mask op
105-
ops.op("coloc.saca.sigMask").input(zscore_ref).output(sigMask).compute();
107+
ops.op("coloc.saca.sigMask").input(zscore).output(sigMask).compute();
106108

107109
// get random access and assert results are equal
108110
final RandomAccess<BitType> sRA = sigMask.randomAccess();
@@ -112,12 +114,4 @@ public void testSACASigMask() {
112114
assertEquals(sigExpected[i], sRA.get().getRealDouble());
113115
}
114116
}
115-
116-
@SuppressWarnings("unchecked")
117-
public Img<FloatType> openFloatImg(final String relPath) {
118-
final ImgOpener opener = new ImgOpener();
119-
String source = "src/test/resources/org/scijava/ops/image/" + relPath;
120-
FileLocation loc = new FileLocation(source);
121-
return (Img) opener.openImgs(loc).get(0);
122-
}
123117
}

0 commit comments

Comments
 (0)