Ticket #171: lsm700

File lsm700, 19.5 KB (added by faim, 10 years ago)
Line 
1Enabled logging to 'C:/Program Files/xuvtools-1.8.0-beta3-r3506-win32/lsm700'.
2current number of tiles: 1
3current number of tiles: 2
4current number of tiles: 3
5current number of tiles: 4
6Thumbnail calculation started.
7done 25%
8done 50%
9done 75%
10done 100%
11Thumbnail calculation finished.
12GridPositionsDialog, nTiles is 4
13done 0%
14Detected input type is 'unsigned char', using that for template worker.
15done 0%
16Started.
17_xuvstitch() parameters:
18movingWinRadius = (16,16,16)
19fixedWinRadius = (32,16,16)
20projectFileName =
21importanceSamplingSteps = 20
22phase_sampling_steps = 1
23phase_sampling_abort_value = 0.7
24smoothRawData = 0
25verbose = 8
26numThreads = 1
27enabled tiles = tile0001, tile0002, tile0003, tile0004
28done 0%
29Stitcher started.
30movingWindowRadius has been decreased from (16,16,16) to the minimum occurring radius (6,16,16)
31fixedWindowRadius has been decreased from (32,16,16) to the maximum occurring radius (6,16,16)
32movingWinRadius is >= fixedWinRadius, decreasing it further to '(5,15,15)'.
33will parse sizes from configMap.
34stack0001_size_um (11,320.087,320.087) = stackSize (11,512,512) * element_size_um (1,0.62517,0.62517)
35stack0002_size_um (7,320.087,320.087) = stackSize (7,512,512) * element_size_um (1,0.62517,0.62517)
36stack0003_size_um (8,320.087,320.087) = stackSize (8,512,512) * element_size_um (1,0.62517,0.62517)
37stack0004_size_um (10,320.087,320.087) = stackSize (10,512,512) * element_size_um (1,0.62517,0.62517)
38Found initial tile positions for all stacks.
39parsed size attributes for all stacks.
40inspecting sizes of all tiles / stacks.
41tile tile0001 has um-size (11,320.087,320.087) / max_element_size (1,0.62517,0.62517) = normsize: (11,512,512)
42tile tile0002 has um-size (7,320.087,320.087) / max_element_size (1,0.62517,0.62517) = normsize: (7,512,512)
43tile tile0003 has um-size (8,320.087,320.087) / max_element_size (1,0.62517,0.62517) = normsize: (8,512,512)
44tile tile0004 has um-size (10,320.087,320.087) / max_element_size (1,0.62517,0.62517) = normsize: (10,512,512)
45XuvStitch found factor '0.829' to downscale the stacks for phase-only correlation.
46The stacks will be scaled from (11,512,512) to (10,432,432).
47finding max stack sizes recommends (10,432,432) for a maxNormSize of (11,512,512), scaleFac = (0.909091,0.84375,0.84375)
48done 1%
49sampledSizes[0]: (10,432,432)
50sampledSizes[1]: (6,432,432)
51sampledSizes[2]: (6,432,432)
52sampledSizes[3]: (8,432,432)
53Will now inspect your Computer. This can take some time.
54starting (one-time) FFTW planning. This can take longer, but is done only the first time you use a new fft size. The result is saved to disk.
55forward plan done
56done 1%
57backward plan done
58Saved Wisdom
59done 2%
60done 5%
61Will now inspect the list of enabled tiles, which ones need to be checked against each other.
62new findNextTestTiles() start
63findNextTestTiles() first time called, should use absolute positions, will construct a new set of test-pairs and re-set all positions to one long list.
64find_overlapping_tiles: checking 0 vs 1 of 3: overlap size = 181983
65find_overlapping_tiles: checking 0 vs 2 of 3: overlap size = 15662
66find_overlapping_tiles: checking 0 vs 3 of 3: overlap size = 64600
67find_overlapping_tiles: checking 1 vs 2 of 3: overlap size = 52733
68find_overlapping_tiles: checking 1 vs 3 of 3: overlap size = 20487
69find_overlapping_tiles: checking 2 vs 3 of 3: overlap size = 323676
70find_overlapping_tiles recommends testing the following tuples:
71(0, 1); (0, 2); (0, 3); (1, 2); (1, 3); (2, 3);
72update_connected_components(): new connComp map is:
731, 1, 2, 3,
74update_connected_components(): new connComps list is:
750:
761: 0, 1,
772: 2,
783: 3,
79update_connected_components(): new connComp map is:
801, 1, 1, 3,
81update_connected_components(): new connComps list is:
820:
831: 0, 1, 2,
842:
853: 3,
86update_connected_components(): new connComp map is:
871, 1, 1, 1,
88update_connected_components(): new connComps list is:
890:
901: 0, 1, 2, 3,
912:
923:
93update_connected_components(): new connComp map is:
941, 1, 1, 1,
95update_connected_components(): new connComps list is:
960:
971: 0, 1, 2, 3,
982:
993:
100update_connected_components(): new connComp map is:
1011, 1, 1, 1,
102update_connected_components(): new connComps list is:
1030:
1041: 0, 1, 2, 3,
1052:
1063:
107update_connected_components(): new connComp map is:
1081, 1, 1, 1,
109update_connected_components(): new connComps list is:
1100:
1111: 0, 1, 2, 3,
1122:
1133:
114find_connected_components_from_overlap(): connected components-test found:
115 0  1  2  3
116 1  1  1  1
117findNextTestTiles() first time init using absolute positions done.
118findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
119The next pair of tiles is (tile0001, tile0002).
120took best phaseonly displacement
121maxTest 0 between tiles tile0001 and tile0002 is: (0,-0.94723,-238.625) um)
122moving in um: start (-5.5,-160.044,-160.044) size (11,320.087,320.087), fixed in um: start (-3.5,-159.096,78.5818) size (7,320.087,320.087)
123The tiles overlap in um from (-3.5,-159.096,78.5818) to (3.5,160.044,160.044) and in movingArrPixels from (2,2,382) to (8,511,511), that is 3
124[ 6 509 129 ] pixels.
125The tiles tile0001 and tile0002 don't overlap enough.
126stitcher set KeyValueMap::asString(tile0001_tile0002_displacement) = 0,-0.94723,-238.625
127correlated (another) stack
128new findNextTestTiles() start
129findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
130Inspecting the list of test-tiles if there are pairs where both stacks are loaded
131Could not find an already loaded pair to correlate next.
132done 21%
133The next pair of tiles is (tile0001, tile0003).
134took best phaseonly displacement
135maxTest 0 between tiles tile0001 and tile0003 is: (0,295.459,-240.595) um)
136moving in um: start (-5.5,-160.044,-160.044) size (11,320.087,320.087), fixed in um: start (-4,-455.502,80.5518) size (8,320.087,320.087)
137The tiles overlap in um from (-4,-160.044,80.5518) to (4,-135.415,160.044) and in movingArrPixels from (2,0,385) to (9,38,511), that is 3
138[ 7 38 126 ] pixels.
139The tiles tile0001 and tile0003 don't overlap enough.
140stitcher set KeyValueMap::asString(tile0001_tile0003_displacement) = 0,295.459,-240.595
141correlated (another) stack
142new findNextTestTiles() start
143findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
144Inspecting the list of test-tiles if there are pairs where both stacks are loaded
145Could not find an already loaded pair to correlate next.
146done 37%
147The next pair of tiles is (tile0001, tile0004).
148took best phaseonly displacement
149maxTest 0 between tiles tile0001 and tile0004 is: (0,296.407,-47.2853) um)
150moving in um: start (-5.5,-160.044,-160.044) size (11,320.087,320.087), fixed in um: start (-5,-456.45,-112.758) size (10,320.087,320.087)
151The tiles overlap in um from (-5,-160.044,-112.758) to (5,-136.363,160.044) and in movingArrPixels from (1,0,76) to (10,37,511), that is 3
152[ 9 37 435 ] pixels.
153_xuvstitch_loadarray_genfft():
154temp memory 'tmpLoadArrPtr' exists, has size (0,0,0)
155temp memory 'tmpSmoothArrPtr' exists, has size (0,0,0)
156temp memory 'tmpSampledArrPtr' exists, has size (0,0,0)
157temp memory 'tmpPaddedArrPtr' exists, has size (0,0,0)
158Will load and process stack '0-11,0' from file '//faimstore/faim/Testimages/XuvTools_Testimages/Test_stitch_LSM700/SteveB/test_stack.lsm'.
159loaded stack 'stack0001'.
160_xuvstitch_loadarray_genfft():
161temp memory 'tmpLoadArrPtr' exists, has size (0,0,0)
162temp memory 'tmpSmoothArrPtr' exists, has size (0,0,0)
163temp memory 'tmpSampledArrPtr' exists, has size (0,0,0)
164temp memory 'tmpPaddedArrPtr' exists, has size (0,0,0)
165Will load and process stack '0-10,0' from file '//faimstore/faim/Testimages/XuvTools_Testimages/Test_stitch_LSM700/SteveB/test_stack_3.lsm'.
166loaded stack 'stack0004'.
167findCorrPosImportance() start
168computed normalized correlation positions
169normcrosscorr: next position
1700: pos = (5,23,293) ((0,-145.665,70.4166)um) => movingPosition (6,23,369), fixedPosition (5,497,293)
171CrossCorrelation::resize(): will resize fixedWin temporary memory
172CrossCorrelation::resize(): resized temporary memory
173CrossCorrelation::normCorrelate(): no need to copy fixedWin.
174CrossCorrelation::normCorrelate(): need to copy movingWin.
175computed normalized cross-correlation
176added coefficients to normCrossCorrSum
177normcrosscorr: next position
1781: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
179CrossCorrelation::normCorrelate(): no need to copy fixedWin.
180CrossCorrelation::normCorrelate(): need to copy movingWin.
181computed normalized cross-correlation
182added coefficients to normCrossCorrSum
183normcrosscorr: next position
1842: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
185CrossCorrelation::normCorrelate(): no need to copy fixedWin.
186CrossCorrelation::normCorrelate(): need to copy movingWin.
187computed normalized cross-correlation
188added coefficients to normCrossCorrSum
189normcrosscorr: next position
1903: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
191CrossCorrelation::normCorrelate(): no need to copy fixedWin.
192CrossCorrelation::normCorrelate(): need to copy movingWin.
193computed normalized cross-correlation
194added coefficients to normCrossCorrSum
195normcrosscorr: next position
1964: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
197CrossCorrelation::normCorrelate(): no need to copy fixedWin.
198CrossCorrelation::normCorrelate(): need to copy movingWin.
199computed normalized cross-correlation
200added coefficients to normCrossCorrSum
201normcrosscorr: next position
2025: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
203CrossCorrelation::normCorrelate(): no need to copy fixedWin.
204CrossCorrelation::normCorrelate(): need to copy movingWin.
205computed normalized cross-correlation
206added coefficients to normCrossCorrSum
207normcrosscorr: next position
2086: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
209CrossCorrelation::normCorrelate(): no need to copy fixedWin.
210CrossCorrelation::normCorrelate(): need to copy movingWin.
211computed normalized cross-correlation
212added coefficients to normCrossCorrSum
213normcrosscorr: next position
2147: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
215CrossCorrelation::normCorrelate(): no need to copy fixedWin.
216CrossCorrelation::normCorrelate(): need to copy movingWin.
217computed normalized cross-correlation
218added coefficients to normCrossCorrSum
219normcrosscorr: next position
2208: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
221CrossCorrelation::normCorrelate(): no need to copy fixedWin.
222CrossCorrelation::normCorrelate(): need to copy movingWin.
223computed normalized cross-correlation
224added coefficients to normCrossCorrSum
225normcrosscorr: next position
2269: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
227CrossCorrelation::normCorrelate(): no need to copy fixedWin.
228CrossCorrelation::normCorrelate(): need to copy movingWin.
229computed normalized cross-correlation
230added coefficients to normCrossCorrSum
231normcrosscorr: next position
23210: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
233CrossCorrelation::normCorrelate(): no need to copy fixedWin.
234CrossCorrelation::normCorrelate(): need to copy movingWin.
235computed normalized cross-correlation
236added coefficients to normCrossCorrSum
237normcrosscorr: next position
23811: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
239CrossCorrelation::normCorrelate(): no need to copy fixedWin.
240CrossCorrelation::normCorrelate(): need to copy movingWin.
241computed normalized cross-correlation
242added coefficients to normCrossCorrSum
243normcrosscorr: next position
24412: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
245CrossCorrelation::normCorrelate(): no need to copy fixedWin.
246CrossCorrelation::normCorrelate(): need to copy movingWin.
247computed normalized cross-correlation
248added coefficients to normCrossCorrSum
249normcrosscorr: next position
25013: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
251CrossCorrelation::normCorrelate(): no need to copy fixedWin.
252CrossCorrelation::normCorrelate(): need to copy movingWin.
253computed normalized cross-correlation
254added coefficients to normCrossCorrSum
255normcrosscorr: next position
25614: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
257CrossCorrelation::normCorrelate(): no need to copy fixedWin.
258CrossCorrelation::normCorrelate(): need to copy movingWin.
259computed normalized cross-correlation
260added coefficients to normCrossCorrSum
261normcrosscorr: next position
26215: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
263CrossCorrelation::normCorrelate(): no need to copy fixedWin.
264CrossCorrelation::normCorrelate(): need to copy movingWin.
265computed normalized cross-correlation
266added coefficients to normCrossCorrSum
267normcrosscorr: next position
26816: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
269CrossCorrelation::normCorrelate(): no need to copy fixedWin.
270CrossCorrelation::normCorrelate(): need to copy movingWin.
271computed normalized cross-correlation
272added coefficients to normCrossCorrSum
273normcrosscorr: next position
27417: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
275CrossCorrelation::normCorrelate(): no need to copy fixedWin.
276CrossCorrelation::normCorrelate(): need to copy movingWin.
277computed normalized cross-correlation
278added coefficients to normCrossCorrSum
279normcrosscorr: next position
28018: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
281CrossCorrelation::normCorrelate(): no need to copy fixedWin.
282CrossCorrelation::normCorrelate(): need to copy movingWin.
283computed normalized cross-correlation
284added coefficients to normCrossCorrSum
285normcrosscorr: next position
28619: pos = (5,19,401) ((0,-148.165,137.935)um) => movingPosition (6,19,477), fixedPosition (5,493,401)
287CrossCorrelation::normCorrelate(): no need to copy fixedWin.
288CrossCorrelation::normCorrelate(): need to copy movingWin.
289computed normalized cross-correlation
290added coefficients to normCrossCorrSum
291fineDisplacement for tiles   0,   3, phase-test  0 is (  0,   0,   0) = (  0.00,   0.00,   0.00) um with score 0.6792, total (   0.00,  296.41,  -47.29)
292stitcher set KeyValueMap::asString(tile0001_tile0004_displacement) = 0,296.407,-47.2853
293correlated (another) stack
294new findNextTestTiles() start
295findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
296Tile tile0001 is not used in the future, will be purged from cache.
297Inspecting the list of test-tiles if there are pairs where both stacks are loaded
298Could not find an already loaded pair to correlate next.
299done 53%
300The next pair of tiles is (tile0002, tile0003).
301took best phaseonly displacement
302maxTest 0 between tiles tile0002 and tile0003 is: (0.00,296.41,-1.97) um)
303moving in um: start (-3.50,-160.04,-160.04) size (7.00,320.09,320.09), fixed in um: start (-4.00,-456.45,-158.07) size (8.00,320.09,320.09)
304The tiles overlap in um from (-3.50,-160.04,-158.07) to (3.50,-136.36,160.04) and in movingArrPixels from (0,0,3) to (6,37,511), that is 3
305[ 6 37 508 ] pixels.
306The tiles tile0002 and tile0003 don't overlap enough.
307stitcher set KeyValueMap::asString(tile0002_tile0003_displacement) = 0,296.406,-1.97
308correlated (another) stack
309new findNextTestTiles() start
310findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
311Inspecting the list of test-tiles if there are pairs where both stacks are loaded
312Could not find an already loaded pair to correlate next.
313done 68%
314The next pair of tiles is (tile0002, tile0004).
315took best phaseonly displacement
316maxTest 0 between tiles tile0002 and tile0004 is: (0.00,297.35,191.34) um)
317moving in um: start (-3.50,-160.04,-160.04) size (7.00,320.09,320.09), fixed in um: start (-5.00,-457.40,-351.38) size (10.00,320.09,320.09)
318The tiles overlap in um from (-3.50,-160.04,-160.04) to (3.50,-137.31,-31.30) and in movingArrPixels from (0,0,0) to (6,35,205), that is 3
319[ 6 35 205 ] pixels.
320The tiles tile0002 and tile0004 don't overlap enough.
321stitcher set KeyValueMap::asString(tile0002_tile0004_displacement) = 0,297.354,191.34
322correlated (another) stack
323new findNextTestTiles() start
324findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
325Tile tile0002 is not used in the future, will be purged from cache.
326Inspecting the list of test-tiles if there are pairs where both stacks are loaded
327Could not find an already loaded pair to correlate next.
328done 84%
329The next pair of tiles is (tile0003, tile0004).
330took best phaseonly displacement
331maxTest 0 between tiles tile0003 and tile0004 is: (0.00,0.95,193.31) um)
332moving in um: start (-4.00,-160.04,-160.04) size (8.00,320.09,320.09), fixed in um: start (-5.00,-160.99,-353.35) size (10.00,320.09,320.09)
333The tiles overlap in um from (-4.00,-160.04,-160.04) to (4.00,159.10,-33.27) and in movingArrPixels from (0,0,0) to (7,509,202), that is 3
334[ 7 509 202 ] pixels.
335The tiles tile0003 and tile0004 don't overlap enough.
336stitcher set KeyValueMap::asString(tile0003_tile0004_displacement) = 0,0.947998,193.31
337correlated (another) stack
338new findNextTestTiles() start
339findNextTestTiles() uses absolute positions, so it should not update the list of test-pairs. Will return now.
340Tile tile0003 is not used in the future, will be purged from cache.
341Tile tile0004 is not used in the future, will be purged from cache.
342Inspecting the list of test-tiles if there are pairs where both stacks are loaded
343Could not find an already loaded pair to correlate next.
344done 100%
345starting detection of connected components for threshold 0.23.
346pairwiseScore is (starting from 1, not 0):
347  0.000  -0.100  -0.100   0.679
348  0.000   0.000  -0.100  -0.100
349  0.000   0.000   0.000  -0.100
350  0.000   0.000   0.000   0.000
351update_connected_components(): new connComp map is:
3523, 1, 2, 3,
353update_connected_components(): new connComps list is:
3540:
3551: 1,
3562: 2,
3573: 0, 3,
358connected components-test found for thresh 0.23:
359(0,3) x (0,3)
360[ 0 -0.1 -0.1 0.679153
361  0 0 -0.1 -0.1
362  0 0 0 -0.1
363  0 0 0 0 ]
364 0  1  2  3
365 3  1  2  3
366component is empty
367component has single element 1, placing it at 0/0/0.
368component has single element 2, placing it at 0/0/0.
369Finding positions of (next) connected component, size 2, 1 equations.
370starting singular value decomposition for 2 images, 1 equations
371chiSquare = 0chiSquare = 0chiSquare = 0starting singular value decomposition for 2 images, 1 equations
372stack[0]: (0,0,0)
373stack[1]: (0,-296.407,47.2853)
374computed svdPositions
375_estimate_absolute_positions done, will call place_tiles_using_absolute_positions to write results to the map.
376component 0 ( 0 elements):
377component 1 ( 1 elements): (0,0,0),
378component 2 ( 1 elements): (0,0,330.087),
379component 3 ( 2 elements): (0,296.407,660.174), (0,0,707.459),
380could not place all tiles in a single connected component.
381Estimation of positions is finished.
382freeing temporary memory.
383automatic stitching finished.
384~CrossCorrelation(): not freeing fftw, as you requested
385done 100%
386Stitcher finished.
387done 0%