Move DICOM helper classes to new loci.formats.dicom package

ome · Nov 17, 2021 · 625f8cc · 625f8cc
1 parent fc13799
commit 625f8cc
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Showing 9 changed files with 32 additions and 27 deletions.
diff --git a/components/formats-bsd/build.properties b/components/formats-bsd/build.properties
@@ -15,6 +15,6 @@ component.deprecation    = true
 component.resources-bin  = loci/formats/bio-formats-logo.png \
                            loci/formats/utests/2008-09.ome
 component.resources-text = loci/formats/*.properties \
-                           loci/formats/in/*.txt
+                           loci/formats/dicom/*.txt
 
 component.main-class     = loci.formats.gui.ImageViewer
diff --git a/...d/src/loci/formats/in/DicomAttribute.java → ...rc/loci/formats/dicom/DicomAttribute.java b/...d/src/loci/formats/in/DicomAttribute.java → ...rc/loci/formats/dicom/DicomAttribute.java
@@ -30,7 +30,7 @@
  * #L%
  */
 
-package loci.formats.in;
+package loci.formats.dicom;
 
 import java.io.BufferedReader;
 import java.io.InputStream;
@@ -41,7 +41,7 @@
 
 import loci.common.Constants;
 
-import static loci.formats.in.DicomVR.*;
+import static loci.formats.dicom.DicomVR.*;
 
 /**
  * Describes a DICOM attribute (integer tag, associated description, and expected VR).

diff --git a/...sd/src/loci/formats/in/DicomFileInfo.java → ...src/loci/formats/dicom/DicomFileInfo.java b/...sd/src/loci/formats/in/DicomFileInfo.java → ...src/loci/formats/dicom/DicomFileInfo.java
@@ -30,12 +30,13 @@
  * #L%
  */
 
-package loci.formats.in;
+package loci.formats.dicom;
 
 import java.io.IOException;
 import java.util.List;
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
+import loci.formats.in.DicomReader;
 
 import ome.xml.model.primitives.Timestamp;
 import ome.units.quantity.Length;

diff --git a/...ats-bsd/src/loci/formats/in/DicomTag.java → ...-bsd/src/loci/formats/dicom/DicomTag.java b/...ats-bsd/src/loci/formats/in/DicomTag.java → ...-bsd/src/loci/formats/dicom/DicomTag.java
@@ -30,7 +30,7 @@
  * #L%
  */
 
-package loci.formats.in;
+package loci.formats.dicom;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -40,8 +40,8 @@
 import loci.common.RandomAccessInputStream;
 import loci.formats.FormatException;
 
-import static loci.formats.in.DicomAttribute.*;
-import static loci.formats.in.DicomVR.*;
+import static loci.formats.dicom.DicomAttribute.*;
+import static loci.formats.dicom.DicomVR.*;
 
 /**
  * Represents a complete DICOM tag, including the dictionary attribute,

diff --git a/...ts-bsd/src/loci/formats/in/DicomTile.java → ...bsd/src/loci/formats/dicom/DicomTile.java b/...ts-bsd/src/loci/formats/in/DicomTile.java → ...bsd/src/loci/formats/dicom/DicomTile.java
@@ -30,7 +30,7 @@
  * #L%
  */
 
-package loci.formats.in;
+package loci.formats.dicom;
 
 import loci.common.Region;
 

diff --git a/...mats-bsd/src/loci/formats/in/DicomVR.java → ...s-bsd/src/loci/formats/dicom/DicomVR.java b/...mats-bsd/src/loci/formats/in/DicomVR.java → ...s-bsd/src/loci/formats/dicom/DicomVR.java
@@ -30,7 +30,7 @@
  * #L%
  */
 
-package loci.formats.in;
+package loci.formats.dicom;
 
 import java.util.EnumSet;
 import java.util.HashMap;

diff --git a/.../src/loci/formats/in/dicom-dictionary.txt → ...c/loci/formats/dicom/dicom-dictionary.txt b/.../src/loci/formats/in/dicom-dictionary.txt → ...c/loci/formats/dicom/dicom-dictionary.txt
diff --git a/components/formats-bsd/src/loci/formats/in/DicomReader.java b/components/formats-bsd/src/loci/formats/in/DicomReader.java
@@ -66,8 +66,12 @@
 import ome.units.quantity.Length;
 import ome.units.UNITS;
 
-import static loci.formats.in.DicomAttribute.*;
-import static loci.formats.in.DicomVR.*;
+import loci.formats.dicom.DicomAttribute;
+import loci.formats.dicom.DicomFileInfo;
+import loci.formats.dicom.DicomTag;
+import loci.formats.dicom.DicomTile;
+import static loci.formats.dicom.DicomAttribute.*;
+import static loci.formats.dicom.DicomVR.*;
 
 /**
  * DicomReader is the file format reader for DICOM files.
@@ -1784,73 +1788,73 @@ private void updateCoreMetadata(CoreMetadata ms) {
     }
   }
 
-  protected String getImageType() {
+  public String getImageType() {
     return imageType;
   }
 
-  protected List<DicomTile> getTiles() {
+  public List<DicomTile> getTiles() {
     return tilePositions.get(0);
   }
 
-  protected List<Double> getZOffsets() {
+  public List<Double> getZOffsets() {
     return zOffsets.get(0);
   }
 
-  protected int getConcatenationIndex() {
+  public int getConcatenationIndex() {
     if (concatenationNumber == null) {
       return 0;
     }
     return concatenationNumber.intValue() - 1;
   }
 
-  protected Length getPixelSizeX() {
+  public Length getPixelSizeX() {
     if (pixelSizeX == null) {
       return null;
     }
     return FormatTools.getPhysicalSizeX(new Double(pixelSizeX), UNITS.MILLIMETER);
   }
 
-  protected Length getPixelSizeY() {
+  public Length getPixelSizeY() {
     if (pixelSizeY == null) {
       return null;
     }
     return FormatTools.getPhysicalSizeY(new Double(pixelSizeY), UNITS.MILLIMETER);
   }
 
-  protected Length getPixelSizeZ() {
+  public Length getPixelSizeZ() {
     if (pixelSizeZ == null) {
       return null;
     }
     return FormatTools.getPhysicalSizeZ(new Double(pixelSizeZ), UNITS.MILLIMETER);
   }
 
-  protected List<Double> getPositionX() {
+  public List<Double> getPositionX() {
     List<Double> rtn = new ArrayList<Double>();
     rtn.addAll(positionX);
     return rtn;
   }
 
-  protected List<Double> getPositionY() {
+  public List<Double> getPositionY() {
     List<Double> rtn = new ArrayList<Double>();
     rtn.addAll(positionY);
     return rtn;
   }
 
-  protected List<Double> getPositionZ() {
+  public List<Double> getPositionZ() {
     List<Double> rtn = new ArrayList<Double>();
     rtn.addAll(positionZ);
     return rtn;
   }
 
-  protected List<String> getChannelNames() {
+  public List<String> getChannelNames() {
     return channelNames;
   }
 
-  protected boolean isExtendedDepthOfField() {
+  public boolean isExtendedDepthOfField() {
     return edf;
   }
 
-  protected Timestamp getTimestamp() {
+  public Timestamp getTimestamp() {
     String stamp = null;
 
     if (date != null && time != null) {

diff --git a/components/formats-bsd/src/loci/formats/out/DicomWriter.java b/components/formats-bsd/src/loci/formats/out/DicomWriter.java
@@ -57,7 +57,7 @@
 import loci.formats.codec.JPEG2000Codec;
 import loci.formats.codec.JPEG2000CodecOptions;
 import loci.formats.codec.JPEGCodec;
-import loci.formats.in.DicomTag;
+import loci.formats.dicom.DicomTag;
 import loci.formats.in.DynamicMetadataOptions;
 import loci.formats.in.MetadataOptions;
 import loci.formats.meta.IPyramidStore;
@@ -67,8 +67,8 @@
 import ome.units.UNITS;
 import ome.units.quantity.Length;
 
-import static loci.formats.in.DicomAttribute.*;
-import static loci.formats.in.DicomVR.*;
+import static loci.formats.dicom.DicomAttribute.*;
+import static loci.formats.dicom.DicomVR.*;
 
 /**
  * DicomWriter is the file format writer for DICOM files.
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,7 +30,7 @@ @@
      * #L%
      */
-    package loci.formats.in;
+    package loci.formats.dicom;
     import loci.common.Region;
@@ Expand Down @@