Context Navigation

← Previous Change
Next Change →

Changeset 1596 for branches/3.0-Beta2

Timestamp:

06/05/07 20:08:58 (17 months ago)

Author:

david

Message:

DeltaVision? pixelbuffer testing unfinished

Location:

branches/3.0-Beta2/components/romio

Files:

: 2 added
: 2 modified

src/ome/io/nio/DeltaVision.java (modified) (29 diffs)
src/ome/io/nio/DeltaVisionHeader.java (modified) (6 diffs)
test/ome/io/nio/utests/DeltaVisionTest.java (added)
test/ome/io/nio/utests/tinyTest.d3d.dv (added)

Legend:

: Unmodified
: Added
: Removed

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVision.java

r1578	r1596
20	20	* image file.
21	21	* <p>
22		* Copyright 2007 Glencoe Software Inc. All rights reserved.
23		* Use is subject to license terms supplied in LICENSE.txt
24		* <p/>
25		*
	22	* Copyright 2007 Glencoe Software Inc. All rights reserved. Use is subject to
	23	* license terms supplied in LICENSE.txt <p/>
	24	*
26	25	* @author David L. Whitehurst      <a
27	26	* href="mailto:david@glencoesoftware.com">david@glencoesoftware.com</a>
…	…
55	54
56	55	public boolean little = false;
57
	56
58	57	public DeltaVisionHeader header;
59	58
…	…
83	82	"Original file not available, Critical Error!");
84	83	} catch (RuntimeException rtex) {
	84	rtex.printStackTrace();
85	85	throw new RuntimeException(
86	86	"The binary file is not a valid DeltaVision file!");
…	…
90	90	}
91	91
92		/* (non-Javadoc)
	92	/*
	93	* (non-Javadoc)
	94	*
93	95	* @see ome.io.nio.PixelBuffer#calculateMessageDigest()
94	96	*/
95	97	public byte[] calculateMessageDigest() throws IOException {
96
	98	// TODO - test
97	99	MessageDigest md;
98	100
…	…
116	118	}
117	119
118		/* (non-Javadoc)
	120	/*
	121	* (non-Javadoc)
	122	*
119	123	* @see ome.io.nio.PixelBuffer#close()
120	124	*/
…	…
126	130	}
127	131
128		/* (non-Javadoc)
129		* @see ome.io.nio.PixelBuffer#getPlane(java.lang.Integer, java.lang.Integer, java.lang.Integer)
	132	/*
	133	* (non-Javadoc)
	134	*
	135	* @see ome.io.nio.PixelBuffer#getPlane(java.lang.Integer,
	136	* java.lang.Integer, java.lang.Integer)
130	137	*/
131	138	public MappedByteBuffer getPlane(Integer z, Integer c, Integer t)
132	139	throws IOException, DimensionsOutOfBoundsException {
	140	// TODO - test
133	141	Long offset = getPlaneOffset(z, c, t);
134	142	Integer size = getPlaneSize();
135
	143
136	144	MappedByteBuffer region = getRegion(size, offset);
137	145
…	…
148	156	}
149	157
150		/* (non-Javadoc)
151		* @see ome.io.nio.PixelBuffer#getPlaneOffset(java.lang.Integer, java.lang.Integer, java.lang.Integer)
	158	/*
	159	* (non-Javadoc)
	160	*
	161	* @see ome.io.nio.PixelBuffer#getPlaneOffset(java.lang.Integer,
	162	* java.lang.Integer, java.lang.Integer)
152	163	*/
153	164	public Long getPlaneOffset(Integer z, Integer c, Integer t)
…	…
155	166
156	167	checkBounds(null, z, c, t);
157
158		Integer timepointSize = getTimepointSize();
159		Integer stackSize = getStackSize();
160		Integer planeSize = getPlaneSize();
161
162		return (long) timepointSize * t + (long) stackSize * c
163		+ (long) planeSize * z;
164
165		}
166
167		/* (non-Javadoc)
	168	int planeNo = getAbsolutePlaneOffset(z, c, t);
	169
	170	return (long) getPlaneSize() * planeNo;
	171
	172	}
	173
	174	/**
	175	* Privately returns the absolute plane number index in the set of X-Y
	176	* planes (planes start with 1)
	177	*
	178	* @param z
	179	* @param c
	180	* @param t
	181	* @return
	182	*/
	183	private int getAbsolutePlaneOffset(Integer z, Integer c, Integer t) {
	184
	185	int result = 0;
	186
	187	switch (getHeader().getSequence()) {
	188
	189	case 0: // ZTC
	190	result = ((c * getSizeT() * getSizeZ()) + (t * getSizeZ()) + z);
	191	break;
	192
	193	case 1: // CZT
	194	result = ((t * getSizeC() * getSizeZ()) + (z * getSizeC()) + c);
	195	break;
	196
	197	case 2: // ZCT
	198	result = ((t * getSizeC() * getSizeZ()) + (c * getSizeZ()) + z);
	199	break;
	200
	201	default:
	202	result = -1;
	203	}
	204
	205	return result;
	206	}
	207
	208	/*
	209	* (non-Javadoc)
	210	*
168	211	* @see ome.io.nio.PixelBuffer#getPlaneSize()
169	212	*/
…	…
175	218	}
176	219
177		/* (non-Javadoc)
	220	/*
	221	* (non-Javadoc)
	222	*
178	223	* @see ome.io.nio.PixelBuffer#getRegion(java.lang.Integer, java.lang.Long)
179	224	*/
…	…
187	232	}
188	233
189		/* (non-Javadoc)
190		* @see ome.io.nio.PixelBuffer#getRow(java.lang.Integer, java.lang.Integer, java.lang.Integer, java.lang.Integer)
	234	/*
	235	* (non-Javadoc)
	236	*
	237	* @see ome.io.nio.PixelBuffer#getRow(java.lang.Integer, java.lang.Integer,
	238	* java.lang.Integer, java.lang.Integer)
191	239	*/
192	240	public MappedByteBuffer getRow(Integer y, Integer z, Integer c, Integer t)
…	…
199	247	}
200	248
201		/* (non-Javadoc)
202		* @see ome.io.nio.PixelBuffer#getRowOffset(java.lang.Integer, java.lang.Integer, java.lang.Integer, java.lang.Integer)
	249	/*
	250	* (non-Javadoc)
	251	*
	252	* @see ome.io.nio.PixelBuffer#getRowOffset(java.lang.Integer,
	253	* java.lang.Integer, java.lang.Integer, java.lang.Integer)
203	254	*/
204	255	public Long getRowOffset(Integer y, Integer z, Integer c, Integer t)
…	…
216	267	}
217	268
218		/* (non-Javadoc)
	269	/*
	270	* (non-Javadoc)
	271	*
219	272	* @see ome.io.nio.PixelBuffer#getRowSize()
220	273	*/
…	…
228	281	}
229	282
230		/* (non-Javadoc)
	283	/*
	284	* (non-Javadoc)
	285	*
231	286	* @see ome.io.nio.PixelBuffer#getSizeC()
232	287	*/
…	…
235	290	}
236	291
237		/* (non-Javadoc)
	292	/*
	293	* (non-Javadoc)
	294	*
238	295	* @see ome.io.nio.PixelBuffer#getSizeT()
239	296	*/
…	…
242	299	}
243	300
244		/* (non-Javadoc)
	301	/*
	302	* (non-Javadoc)
	303	*
245	304	* @see ome.io.nio.PixelBuffer#getSizeX()
246	305	*/
…	…
249	308	}
250	309
251		/* (non-Javadoc)
	310	/*
	311	* (non-Javadoc)
	312	*
252	313	* @see ome.io.nio.PixelBuffer#getSizeY()
253	314	*/
…	…
256	317	}
257	318
258		/* (non-Javadoc)
	319	/*
	320	* (non-Javadoc)
	321	*
259	322	* @see ome.io.nio.PixelBuffer#getSizeZ()
260	323	*/
…	…
263	326	}
264	327
265		/* (non-Javadoc)
266		* @see ome.io.nio.PixelBuffer#getStack(java.lang.Integer, java.lang.Integer)
	328	/*
	329	* (non-Javadoc)
	330	*
	331	* @see ome.io.nio.PixelBuffer#getStack(java.lang.Integer,
	332	* java.lang.Integer)
267	333	*/
268	334	public MappedByteBuffer getStack(Integer c, Integer t) throws IOException,
…	…
275	341	}
276	342
277		/* (non-Javadoc)
278		* @see ome.io.nio.PixelBuffer#getStackOffset(java.lang.Integer, java.lang.Integer)
	343	/**
	344	* Privately returns the absolute stack number. Starts with 1
	345	*
	346	* @param c
	347	* @param t
	348	* @return
	349	*/
	350	private int getAbsoluteStackOffset(Integer c, Integer t) {
	351	int result = 0;
	352
	353	switch (getHeader().getSequence()) {
	354
	355	case 0: // ZTC
	356	result = ((c * getSizeT()) + t);
	357	break;
	358
	359	case 1: // CZT
	360	// TODO - tricky one
	361	break;
	362
	363	case 2: // ZCT
	364	result = ((t * getSizeC()) + c);
	365	break;
	366
	367	default:
	368	result = -1;
	369	}
	370
	371	return result;
	372	}
	373
	374	/*
	375	* (non-Javadoc)
	376	*
	377	* @see ome.io.nio.PixelBuffer#getStackOffset(java.lang.Integer,
	378	* java.lang.Integer)
279	379	*/
280	380	public Long getStackOffset(Integer c, Integer t)
281	381	throws DimensionsOutOfBoundsException {
282		// TODO - affected by ZCT ordering
	382
283	383	checkBounds(null, null, c, t);
284	384
285		Integer timepointSize = getTimepointSize();
286		Integer stackSize = getStackSize();
287
288		return (long) timepointSize * t + (long) stackSize * c;
289		}
290
291		/* (non-Javadoc)
	385	int stackNo = getAbsoluteStackOffset(c, t);
	386	return (long) stackNo * stackSize;
	387
	388	}
	389
	390	/*
	391	* (non-Javadoc)
	392	*
292	393	* @see ome.io.nio.PixelBuffer#getStackSize()
293	394	*/
294	395	public Integer getStackSize() {
295		// stack is X-Y (plane) by Z (focalpoints)
296		if (stackSize == null) {
297		stackSize = getPlaneSize() * getSizeZ();
	396
	397	// stack is X-Y (plane) by Z (focalpoints) ... Z first
	398	if (getHeader().getSequence() == 0 \|\| getHeader().getSequence() == 2) {
	399	if (stackSize == null) {
	400	stackSize = getPlaneSize() * getSizeZ();
	401	}
	402	} else {
	403	// TODO - we need some new code
298	404	}
299	405
…	…
301	407	}
302	408
303		/* (non-Javadoc)
	409	/*
	410	* (non-Javadoc)
	411	*
304	412	* @see ome.io.nio.PixelBuffer#getTimepoint(java.lang.Integer)
305	413	*/
…	…
313	421	}
314	422
315		/* (non-Javadoc)
	423	/*
	424	* (non-Javadoc)
	425	*
316	426	* @see ome.io.nio.PixelBuffer#getTimepointOffset(java.lang.Integer)
317	427	*/
…	…
326	436	}
327	437
328		/* (non-Javadoc)
	438	/*
	439	* (non-Javadoc)
	440	*
329	441	* @see ome.io.nio.PixelBuffer#getTimepointSize()
330	442	*/
…	…
337	449	}
338	450
339		/* (non-Javadoc)
	451	/*
	452	* (non-Javadoc)
	453	*
340	454	* @see ome.io.nio.PixelBuffer#getTotalSize()
341	455	*/
…	…
348	462	}
349	463
350
351		/* (non-Javadoc)
352		* @see ome.io.nio.PixelBuffer#checkBounds(java.lang.Integer, java.lang.Integer, java.lang.Integer, java.lang.Integer)
	464	/*
	465	* (non-Javadoc)
	466	*
	467	* @see ome.io.nio.PixelBuffer#checkBounds(java.lang.Integer,
	468	* java.lang.Integer, java.lang.Integer, java.lang.Integer)
353	469	*/
354	470	public void checkBounds(Integer y, Integer z, Integer c, Integer t)
…	…
374	490	}
375	491	}
376
377		/* (non-Javadoc)
	492
	493	/*
	494	* (non-Javadoc)
	495	*
378	496	* @see ome.io.nio.PixelBuffer#getId()
379	497	*/
…	…
382	500	}
383	501
	502	/**
	503	* Getter for Header
	504	*
	505	* @return
	506	*/
384	507	public DeltaVisionHeader getHeader() {
385	508	return header;
386	509	}
387	510
	511	/*
	512	* (non-Javadoc)
	513	*
	514	* @see ome.io.nio.PixelBuffer#getPath()
	515	*/
	516	public String getPath() {
	517	return originalFile.getPath();
	518	}
	519
	520	/**
	521	* Setter for Header
	522	*
	523	* @param header
	524	*/
388	525	public void setHeader(DeltaVisionHeader header) {
389	526	this.header = header;
390	527	}
391
	528
392	529	// ---------- set or write methods ----------
393	530	/**
…	…
468	605	}
469	606
470		~~/* (non-Javadoc)~~
471		* @see ome.io.nio.PixelBuffer#getPath()
472		*/
473		~~public String getPath() {~~
474		~~return originalFile.getPath();~~
475		}
476
477	607	// ---------- private methods ----------------------
478	608
…	…
483	613	return header.getBytesPerPixel();
484	614	}
485
	615
486	616	/**
487	617	* This method is used to establish most of the DeltaVision data that the
…	…
495	625	File file = new File(originalFile.getPath());
496	626	RandomAccessFile randomAccessFile = new RandomAccessFile(file, "rw");
497
	627
498	628	channel = randomAccessFile.getChannel();
499
	629
500	630	buf = channel.map(FileChannel.MapMode.READ_ONLY, 0, 1024);
501	631

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVisionHeader.java

r1578	r1596
2	2
3	3	import java.nio.ByteOrder;
	4	import java.nio.CharBuffer;
4	5	import java.nio.MappedByteBuffer;
	6
	7	import ome.io.nio.utests.DeltaVisionTest;
	8
	9	import org.apache.commons.logging.Log;
	10	import org.apache.commons.logging.LogFactory;
5	11
6	12	/**
…	…
53	59	private String imageType;
54	60
	61	private transient static Log log = LogFactory.getLog(DeltaVisionHeader.class);
	62
55	63	/**
56	64	* Constructor
…	…
61	69	public DeltaVisionHeader(MappedByteBuffer data, boolean endian) {
62	70
	71
63	72	// make sure this is a header
64	73	if (data.capacity() != IMAGE_HEADER_SIZE) {
…	…
67	76	}
68	77
	78	// set our data
	79	this.data = data;
	80
69	81	// endianness
70	82	if (isNative()) {
	83	data.order(ByteOrder.BIG_ENDIAN);
	84	} else {
71	85	data.order(ByteOrder.LITTLE_ENDIAN);
72		} else {
73		data.order(ByteOrder.BIG_ENDIAN);
74		}
75
76		// set our data
77		this.data = data;
	86	}
	87
78	88	}
79	89
…	…
91	101	*/
92	102	public int getImageCount() {
93		return data.get~~Shor~~t(IMAGE_COUNT_OFFSET);
	103	return data.getInt(IMAGE_COUNT_OFFSET);
94	104	}
95	105
…	…
163	173	*/
164	174	public int getSizeZ() {
165		return getImageCount() / getSizeC() * getSizeT();
	175
	176	int result = 0;
	177	if (getSizeC() == 0) {
	178	result = getImageCount() / getSizeT();
	179	} else if (getSizeT() == 0) {
	180	result = getImageCount() / getSizeC();
	181	} else {
	182	result = getImageCount()/(getSizeT() * getSizeC());
	183	}
	184
	185	return result;
166	186	}
167	187

Context Navigation

Changeset 1596 for branches/3.0-Beta2

Legend:

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVision.java

branches/3.0-Beta2/components/romio/src/ome/io/nio/DeltaVisionHeader.java

Download in other formats: