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10 bit tiff support #185

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10 bit tiff support #185

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7bff6c4
Added support for 10-bit tiff grayscale images
evanspa Nov 6, 2022
d1311bc
added defensive check to the read10bitImage() function in the ImageRe…
evanspa Nov 7, 2022
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73 changes: 39 additions & 34 deletions ij/io/FileInfo.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,67 +9,70 @@ public class FileInfo implements Cloneable {

/** 8-bit unsigned integer (0-255). */
public static final int GRAY8 = 0;

/** 16-bit signed integer (-32768-32767). Imported signed images
are converted to unsigned by adding 32768. */
public static final int GRAY16_SIGNED = 1;

/** 16-bit unsigned integer (0-65535). */
public static final int GRAY16_UNSIGNED = 2;

/** 32-bit signed integer. Imported 32-bit integer images are
converted to floating-point. */
public static final int GRAY32_INT = 3;

/** 32-bit floating-point. */
public static final int GRAY32_FLOAT = 4;

/** 8-bit unsigned integer with color lookup table. */
public static final int COLOR8 = 5;

/** 24-bit interleaved RGB. Import/export only. */
public static final int RGB = 6;
public static final int RGB = 6;

/** 24-bit planer RGB. Import only. */
public static final int RGB_PLANAR = 7;

/** 1-bit black and white. Import only. */
public static final int BITMAP = 8;

/** 32-bit interleaved ARGB. Import only. */
public static final int ARGB = 9;

/** 24-bit interleaved BGR. Import only. */
public static final int BGR = 10;

/** 32-bit unsigned integer. Imported 32-bit integer images are
converted to floating-point. */
public static final int GRAY32_UNSIGNED = 11;

/** 48-bit interleaved RGB. */
public static final int RGB48 = 12;
public static final int RGB48 = 12;

/** 12-bit unsigned integer (0-4095). Import only. */
public static final int GRAY12_UNSIGNED = 13;
public static final int GRAY12_UNSIGNED = 13;

/** 24-bit unsigned integer. Import only. */
public static final int GRAY24_UNSIGNED = 14;
public static final int GRAY24_UNSIGNED = 14;

/** 32-bit interleaved BARG (MCID). Import only. */
public static final int BARG = 15;
public static final int BARG = 15;

/** 64-bit floating-point. Import only.*/
public static final int GRAY64_FLOAT = 16;
public static final int GRAY64_FLOAT = 16;

/** 48-bit planar RGB. Import only. */
public static final int RGB48_PLANAR = 17;
public static final int RGB48_PLANAR = 17;

/** 32-bit interleaved ABGR. Import only. */
public static final int ABGR = 18;

/** 32-bit interleaved CMYK. Import only. */
public static final int CMYK = 19;

/** 10-bit unsigned integer (0-1023). Import only. */
public static final int GRAY10_UNSIGNED = 20;

// File formats
public static final int UNKNOWN = 0;
public static final int RAW = 1;
Expand All @@ -91,12 +94,12 @@ public class FileInfo implements Cloneable {
public static final int PACK_BITS = 5;
public static final int ZIP = 6;
public static final int ZIP_WITH_DIFFERENCING = 7;

/* File format (TIFF, GIF_OR_JPG, BMP, etc.). Used by the File/Revert command */
public int fileFormat;

/* File type (GRAY8, GRAY_16_UNSIGNED, RGB, etc.) */
public int fileType;
public int fileType;
public String fileName;
public String directory;
public String url;
Expand All @@ -108,21 +111,21 @@ public class FileInfo implements Cloneable {
public boolean whiteIsZero;
public boolean intelByteOrder;
public int compression;
public int[] stripOffsets;
public int[] stripOffsets;
public int[] stripLengths;
public int rowsPerStrip;
public int lutSize;
public byte[] reds;
public byte[] greens;
public byte[] blues;
public Object pixels;
public Object pixels;
public String debugInfo;
public String[] sliceLabels;
public String info;
public InputStream inputStream;
public VirtualStack virtualStack;
public int sliceNumber; // used by FileInfoVirtualStack

public double pixelWidth=1.0;
public double pixelHeight=1.0;
public double pixelDepth=1.0;
Expand All @@ -148,7 +151,7 @@ public class FileInfo implements Cloneable {
public String openNextDir, openNextName;
public String[] properties; // {key,value,key,value,...}
public boolean imageSaved;

/** Creates a FileInfo object with all of its fields set to their default value. */
public FileInfo() {
// assign default values
Expand All @@ -161,7 +164,7 @@ public FileInfo() {
compression = COMPRESSION_NONE;
samplesPerPixel = 1;
}

/** Returns the file path. */
public String getFilePath() {
String dir = directory;
Expand All @@ -175,7 +178,7 @@ public String getFilePath() {
public final long getOffset() {
return longOffset>0L?longOffset:((long)offset)&0xffffffffL;
}

/** Returns the gap between images as a long. */
public final long getGap() {
return longGap>0L?longGap:((long)gapBetweenImages)&0xffffffffL;
Expand All @@ -185,7 +188,7 @@ public final long getGap() {
public int getBytesPerPixel() {
switch (fileType) {
case GRAY8: case COLOR8: case BITMAP: return 1;
case GRAY16_SIGNED: case GRAY16_UNSIGNED: case GRAY12_UNSIGNED: return 2;
case GRAY16_SIGNED: case GRAY16_UNSIGNED: case GRAY12_UNSIGNED: case GRAY10_UNSIGNED: return 2;
case GRAY32_INT: case GRAY32_UNSIGNED: case GRAY32_FLOAT: case ARGB: case GRAY24_UNSIGNED: case BARG: case ABGR: case CMYK: return 4;
case RGB: case RGB_PLANAR: case BGR: return 3;
case RGB48: case RGB48_PLANAR: return 6;
Expand Down Expand Up @@ -213,7 +216,7 @@ public String toString() {
+ ", ranges=" + (displayRanges!=null?""+displayRanges.length/2:"null")
+ ", samples=" + samplesPerPixel;
}

/** Returns JavaScript code that can be used to recreate this FileInfo. */
public String getCode() {
String code = "fi = new FileInfo();\n";
Expand All @@ -227,15 +230,15 @@ else if (fileType==GRAY32_FLOAT)
else if (fileType==RGB)
type = "RGB";
if (type!=null)
code += "fi.fileType = FileInfo."+type+";\n";
code += "fi.fileType = FileInfo."+type+";\n";
code += "fi.width = "+width+";\n";
code += "fi.height = "+height+";\n";
if (nImages>1)
code += "fi.nImages = "+nImages+";\n";
code += "fi.nImages = "+nImages+";\n";
if (getOffset()>0)
code += "fi.longOffset = "+getOffset()+";\n";
code += "fi.longOffset = "+getOffset()+";\n";
if (intelByteOrder)
code += "fi.intelByteOrder = true;\n";
code += "fi.intelByteOrder = true;\n";
return code;
}

Expand All @@ -244,6 +247,8 @@ private String getType() {
case GRAY8: return "byte";
case GRAY16_SIGNED: return "short";
case GRAY16_UNSIGNED: return "ushort";
case GRAY10_UNSIGNED: return "ushort";
case GRAY12_UNSIGNED: return "ushort";
case GRAY32_INT: return "int";
case GRAY32_UNSIGNED: return "uint";
case GRAY32_FLOAT: return "float";
Expand Down
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