Patch/11bit

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.ndtiffstorage</groupId>
     <artifactId>NDTiffStorage</artifactId>
-    <version>2.9.34</version>
+    <version>2.10.0</version>
     <packaging>jar</packaging>
     <name>NDTiff Storage file format</name>
     <description>Java-based writer and reader used for NDTiffStorage format</description>

java/src/main/java/org/micromanager/ndtiffstorage/IndexEntryData.java

@@ -26,6 +26,7 @@ public class IndexEntryData {
    public static final int TEN_BIT = 3;
    public static final int TWELVE_BIT = 4;
    public static final int FOURTEEN_BIT = 5;
+   public static final int ELEVEN_BIT = 6;
 
    public static final int UNCOMPRESSED = 0;
 
@@ -137,7 +138,7 @@ public boolean isRGB() {
 
    public int getByteDepth() {
       if (pixelType_ == SIXTEEN_BIT || pixelType_ == FOURTEEN_BIT || pixelType_ == TWELVE_BIT ||
-          pixelType_ == TEN_BIT) {
+          pixelType_ == TEN_BIT || pixelType_ == ELEVEN_BIT) {
          return 2;
       }
       return 1;
@@ -156,6 +157,8 @@ public int getBitDepth() {
          return 16;
       } else if (pixelType_ == EIGHT_BIT_RGB) {
          return 8;
+      } else if (pixelType_ == ELEVEN_BIT) {
+         return 11;
       } else {
          throw  new RuntimeException("Unknown pixel type");
       }

java/src/main/java/org/micromanager/ndtiffstorage/NDTiffReader.java

@@ -288,6 +288,9 @@ private TaggedImage readTaggedImage(IndexEntryData data) throws IOException {
       } else if (data.pixelType_ == IndexEntryData.EIGHT_BIT_RGB) {
          bytesPerPixelOnDisk = 3;
          bytesPerPixelReturned = 4;
+      } else if (data.pixelType_ == IndexEntryData.ELEVEN_BIT) {
+         bytesPerPixelOnDisk = 2;
+         bytesPerPixelReturned = 2;
       } else {
          throw new RuntimeException("Unknown pixel type");
       }

java/src/main/java/org/micromanager/ndtiffstorage/NDTiffWriter.java

@@ -400,6 +400,8 @@ private IndexEntryData writeIFD(String indexKey, Object pixels, byte[] metadata,
          pixelType = IndexEntryData.FOURTEEN_BIT;
       } else if (bitDepth == 16) {
          pixelType = IndexEntryData.SIXTEEN_BIT;
+      } else if (bitDepth == 11) {
+         pixelType = IndexEntryData.ELEVEN_BIT;
       } else {
          throw new RuntimeException("Unknown pixel type");
       }

python/ndtiff/_version.py

@@ -1,2 +1,2 @@
-version_info = (1, 10, 0)
+version_info = (1, 11, 0)
 __version__ = ".".join(map(str, version_info))

python/ndtiff/nd_tiff_current.py

@@ -48,6 +48,7 @@ class _SingleNDTiffReader:
     TEN_BIT_MONOCHROME = 3
     TWELVE_BIT_MONOCHROME = 4
     FOURTEEN_BIT_MONOCHROME = 5
+    ELEVEN_BIT_MONOCHROME = 6
 
     UNCOMPRESSED = 0
 
@@ -126,7 +127,8 @@ def read_image(self, index):
         elif index["pixel_type"] == self.SIXTEEN_BIT_MONOCHROME or \
                 index["pixel_type"] == self.TEN_BIT_MONOCHROME or \
                 index["pixel_type"] == self.TWELVE_BIT_MONOCHROME or \
-                index["pixel_type"] == self.FOURTEEN_BIT_MONOCHROME:
+                index["pixel_type"] == self.FOURTEEN_BIT_MONOCHROME or \
+                index["pixel_type"] == self.ELEVEN_BIT_MONOCHROME:
             bytes_per_pixel = 2
             dtype = np.uint16
         else:
@@ -509,7 +511,8 @@ def _parse_first_index(self, first_index):
         elif first_index["pixel_type"] == _SingleNDTiffReader.SIXTEEN_BIT_MONOCHROME or \
                 first_index["pixel_type"] == _SingleNDTiffReader.FOURTEEN_BIT_MONOCHROME or \
                 first_index["pixel_type"] == _SingleNDTiffReader.TWELVE_BIT_MONOCHROME or \
-                first_index["pixel_type"] == _SingleNDTiffReader.TEN_BIT_MONOCHROME:
+                first_index["pixel_type"] == _SingleNDTiffReader.TEN_BIT_MONOCHROME or \
+                first_index["pixel_type"] == _SingleNDTiffReader.ELEVEN_BIT_MONOCHROME:
             self.bytes_per_pixel = 2
             self.dtype = np.uint16
 

python/ndtiff/test/data_loading_test.py

@@ -83,3 +83,9 @@ def test_v3_2_12bit_pycromanager_data(test_data_path):
     data_path = os.path.join(test_data_path, 'v3', '12_bit_pycromanager_mda')
     dataset = Dataset(data_path)
     assert(dataset.read_image(time=0, channel='DAPI').dtype == np.uint16)
+
+def test_v3_2_11bit_data(test_data_path):
+    data_path = os.path.join(test_data_path, 'v3', 'ndtiff3.2_11bit_1')
+    dataset = Dataset(data_path)
+    assert(dataset.read_metadata(time=0)['BitDepth'] == 11)
+    assert(dataset.read_image(time=0).dtype == np.uint16)