From 34e3b5fdb2b5877960b65765411ea7f7d1620b5e Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 26 Mar 2012 21:29:17 +0000
Subject: [PATCH] Add methods getCamera, getEmissionTag, getExitationTag,
getExpCam, getFilterRef, getLightSRef, getWaveLength, getChannelDescription
from Matt.
SVN: 24786
---
.../imagereaders/bioformats/FlexHelper.java | 126 ++++++++++++++++--
.../bioformats/FlexHelperTest.java | 17 ++-
2 files changed, 129 insertions(+), 14 deletions(-)
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelper.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelper.java
index d1ef872d845..c03cc4d713a 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelper.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelper.java
@@ -13,7 +13,6 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-
package ch.systemsx.cisd.imagereaders.bioformats;
import java.io.StringReader;
@@ -44,9 +43,9 @@ import ch.systemsx.cisd.common.geometry.SpatialPoint;
/**
* A helper class with utility methods that parse metadata from FLEX files.
* <p>
- * Clients can implement their own utility methods on the top of FlexHelper, by parsing the
- * metadata XML as returned by {@link #getMetadata()} or by directly executing XPath query
- * via {@link #selectByXpathQuery(String)}.
+ * Clients can implement their own utility methods on the top of FlexHelper, by parsing the metadata
+ * XML as returned by {@link #getMetadata()} or by directly executing XPath query via
+ * {@link #selectByXpathQuery(String)}.
*
* @author Kaloyan Enimanev
*/
@@ -61,6 +60,21 @@ public class FlexHelper
private static final String SELECT_TILE_FOR_IMAGE =
"//Images/Image[@BufferNo='%s']/Sublayout/text()";
+ private static final String SELECT_FILTER_REF_FOR_IMAGE =
+ "//Images/Image[@BufferNo='%s']/FilterCombinationRef/text()";
+
+ private static final String SELECT_LIGHTS_REF_FOR_IMAGE =
+ "//Images/Image[@BufferNo='%s']/LightSourceCombinationRef/text()";
+
+ private static final String SELECT_EMISSION_FOR_IMAGE =
+ "//FilterCombinations/FilterCombination[@ID='%s']/SliderRef[@ID='%s']";
+
+ private static final String SELECT_LASER_FOR_IMAGE =
+ "//LightSourceCombinations/LightSourceCombination[@ID='%s']/LightSourceRef/@ID";
+
+ private static final String SELECT_EXCITATION_FOR_IMAGE =
+ "//LightSources/LightSource[@ID='%s']/Wavelength/text()";
+
private static final String SELECT_TILE_XCOORDS = "//Sublayouts/Sublayout/Field/OffsetX/text()";
private static final String SELECT_TILE_YCOORDS = "//Sublayouts/Sublayout/Field/OffsetY/text()";
@@ -95,7 +109,7 @@ public class FlexHelper
String tile = nodeList.item(0).getNodeValue();
return Integer.parseInt(tile.trim());
}
-
+
public String getChannelCode(int imageIdx)
{
NodeList nodeList = selectByXpathQuery(SELECT_CHANNELS);
@@ -106,6 +120,100 @@ public class FlexHelper
return nodeList.item(imageIdx).getNodeValue();
}
+ public String getChannelDescription(int imageIdx)
+ {
+ String out =
+ getChannelCode(imageIdx) + " - Ex:" + getExcitationTag(imageIdx) + "nm Em:"
+ + getEmissionTag(imageIdx) + "nm";
+ return out;
+ }
+
+ public String getExpCam(int imageIdx)
+ {
+ NodeList nodeList = selectByXpathQuery(SELECT_CHANNELS);
+ if (imageIdx < 0 || nodeList.getLength() <= imageIdx)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + imageIdx);
+ }
+ return nodeList.item(imageIdx).getNodeValue();
+ }
+
+ public String getFilterRef(int imageIdx)
+ {
+ String query = String.format(SELECT_FILTER_REF_FOR_IMAGE, imageIdx);
+ NodeList nodeList = selectByXpathQuery(query);
+ if (nodeList.getLength() == 0)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + imageIdx);
+ }
+ String filterRef = nodeList.item(0).getNodeValue();
+ return filterRef.trim();
+ }
+
+ public String getLightSRef(int imageIdx)
+ {
+ String query = String.format(SELECT_LIGHTS_REF_FOR_IMAGE, imageIdx);
+ NodeList nodeList = selectByXpathQuery(query);
+ if (nodeList.getLength() == 0)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + imageIdx);
+ }
+ String filterRef = nodeList.item(0).getNodeValue();
+ return filterRef.trim();
+ }
+
+ public String getCamera(int imageIdx)
+ {
+ String expCam = getExpCam(imageIdx);
+ String cam = "Camera" + expCam.split("Cam")[1];
+ return cam.trim();
+ }
+
+ public String getEmissionTag(int imageIdx)
+ {
+ String query =
+ String.format(SELECT_EMISSION_FOR_IMAGE, getFilterRef(imageIdx),
+ getCamera(imageIdx));
+ NodeList nodeList = selectByXpathQuery(query);
+ if (nodeList.getLength() == 0)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + imageIdx);
+ }
+ String emissionTag = nodeList.item(0).getAttributes().getNamedItem("Filter").getNodeValue();
+ return emissionTag.trim();
+
+ }
+
+ public String getExcitationTag(int imageIdx)
+ {
+ String query = String.format(SELECT_LASER_FOR_IMAGE, getLightSRef(imageIdx));
+ NodeList nodeList = selectByXpathQuery(query);
+ if (nodeList.getLength() == 0)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + imageIdx);
+ }
+ String out = "";
+ for (int i = 0; i < nodeList.getLength(); i++)
+ {
+ out = out + getWaveLength(nodeList.item(i).getNodeValue()) + ",";
+ }
+ out = out.substring(0, out.length() - 1);
+ return out;
+
+ }
+
+ public String getWaveLength(String laser)
+ {
+ String query = String.format(SELECT_EXCITATION_FOR_IMAGE, laser);
+ NodeList nodeList = selectByXpathQuery(query);
+ if (nodeList.getLength() == 0)
+ {
+ throw new IllegalArgumentException("No image can be matched to idx=" + laser);
+ }
+ String waveLength = nodeList.item(0).getNodeValue();
+ return waveLength.trim();
+ }
+
public Map<Integer, SpatialPoint> getTileCoordinates()
{
Map<Integer, SpatialPoint> points = new HashMap<Integer, SpatialPoint>();
@@ -193,11 +301,11 @@ public class FlexHelper
return dBF.newDocumentBuilder().parse(is);
} catch (Exception e)
{
- final String errorMessage = String.format(
- "Failed to parse FLEX metadata :\n\n%s\n\nisn't a well formed XML document. %s",
- value, e.getMessage());
+ final String errorMessage =
+ String.format(
+ "Failed to parse FLEX metadata :\n\n%s\n\nisn't a well formed XML document. %s",
+ value, e.getMessage());
throw new IllegalArgumentException(errorMessage);
}
}
-
}
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelperTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelperTest.java
index 6722a621ad4..1fcb3fb6a9d 100644
--- a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelperTest.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/FlexHelperTest.java
@@ -39,6 +39,8 @@ public class FlexHelperTest extends ImageReaderTestCase
assertEquals(1, helper.getTileNumber(0));
assertEquals("Exp1Cam1", helper.getChannelCode(0));
+ assertEquals("488", helper.getExcitationTag(0));
+ assertEquals("565/40", helper.getEmissionTag(0));
Map<Integer, SpatialPoint> tileCoordinates = helper.getTileCoordinates();
assertEquals(1, tileCoordinates.size());
@@ -59,16 +61,21 @@ public class FlexHelperTest extends ImageReaderTestCase
{ "Exp1", "Exp1", "Exp2" };
final String[] CAMS = new String[]
{ "Cam1", "Cam3", "Cam2" };
-
+ final String[] EXCITATION = new String[]
+ { "561,405", "561,405", "488" };
+ final String[] EMISSION = new String[]
+ { "450/50", "690/70", "565/40" };
+
for (int i = 0; i < 12; i++)
{
int parsedTile = helper.getTileNumber(i);
- String parsedChannelName = helper.getChannelCode(i);
assertEquals((i / 3) + 1, parsedTile);
- String channelName = EXPOSURES[ i % 3 ] + CAMS[ i % 3 ];
- assertEquals(channelName, parsedChannelName);
+ String channelName = EXPOSURES[i % 3] + CAMS[i % 3];
+ assertEquals(channelName, helper.getChannelCode(i));
+ assertEquals(EXCITATION[i % 3], helper.getExcitationTag(i));
+ assertEquals(EMISSION[i % 3], helper.getEmissionTag(i));
}
-
+
Map<Integer, SpatialPoint> tileCoordinates = helper.getTileCoordinates();
assertEquals(4, tileCoordinates.size());
assertEquals(new SpatialPoint(4.44E-4, 6.61E-4), tileCoordinates.get(1));
--
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