spam issueshttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues2023-02-21T12:14:53+01:00https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/245Latex/math in with matplotlib2023-02-21T12:14:53+01:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frLatex/math in with matplotlibWith new versions of matplotlib use of math/latex seems to break things.
Example here: https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/blob/0e27b371dcc66e319ff7afebea301f5044b62365/tools/label/label.py#L2042
/cc @andoWith new versions of matplotlib use of math/latex seems to break things.
Example here: https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/blob/0e27b371dcc66e319ff7afebea301f5044b62365/tools/label/label.py#L2042
/cc @andohttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/243python 3.10 numpy.float non-existence2023-01-18T15:00:30+01:00Edward Andòpython 3.10 numpy.float non-existencespam-reg didn't work either from pip or git on a clean jammy ubuntu!?spam-reg didn't work either from pip or git on a clean jammy ubuntu!?https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/234spam-pixelSearch with 2D labels doesn't work2022-12-13T20:44:53+01:00Edward Andòspam-pixelSearch with 2D labels doesn't workTrying to run:
`spam-pixelSearch cam_01-bin4/Image_0001_0.tif cam_01-bin4/Image_0003_0.tif -lab1 cam0imLab.tif`
And getting:
> Starting Pixel search (with 20 processes)
> multiprocessing.pool.RemoteTraceback: ...Trying to run:
`spam-pixelSearch cam_01-bin4/Image_0001_0.tif cam_01-bin4/Image_0003_0.tif -lab1 cam0imLab.tif`
And getting:
> Starting Pixel search (with 20 processes)
> multiprocessing.pool.RemoteTraceback: | ETA: --:--:--
> """
> Traceback (most recent call last):
> File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker
> result = (True, func(*args, **kwds))
> File "/home/ed/lab_documents/digital_image_analysis/spam/venv3/bin/spam-pixelSearch", line 212, in pixelSearchOneNode
> imagetteReturns = spam.label.getImagettesLabelled(lab1, nodeNumber,
> File "/home/ed/lab_documents/digital_image_analysis/spam/venv3/lib/python3.10/site-packages/spam/label/label.py", line 701, in getImagettesLabelled
> gottenLabel = getLabel(lab1, label,
> File "/home/ed/lab_documents/digital_image_analysis/spam/venv3/lib/python3.10/site-packages/spam/label/label.py", line 571, in getLabel
> labSubVol = spam.helpers.slicePadded(labelledVolume, [topOfSlice[0], botOfSlice[0], topOfSlice[1], botOfSlice[1], topOfSlice[2], botOfSlice[2]])
> File "/home/ed/lab_documents/digital_image_analysis/spam/venv3/lib/python3.10/site-packages/spam/helpers/imageManipulation.py", line 496, in slicePadded
> stopOffset = numpy.array([min(im.shape[0], stop[0]), min(im.shape[1], stop[1]), min(im.shape[2], stop[2])])
> IndexError: tuple index out of range
> """
>
> The above exception was the direct cause of the following exception:
>
> Traceback (most recent call last):
> File "/home/ed/lab_documents/digital_image_analysis/spam/venv3/bin/spam-pixelSearch", line 271, in <module>
> for returns in pool.imap_unordered(pixelSearchOneNode, range(firstNode, numberOfNodes)):
> File "/usr/lib/python3.10/multiprocessing/pool.py", line 873, in next
> raise value
> IndexError: tuple index out of rangeEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/225spam-reg and spam.DIC.registerMultiscale not terminating upon reaching deltaP...2022-06-03T14:13:02+02:00EXT Ryan Hurleyspam-reg and spam.DIC.registerMultiscale not terminating upon reaching deltaPhiMinIn spam 0.6.0 and 0.6.1: spam-reg and spam.DIC.registerMultiscale do not terminate upon reaching deltaPhiMin, regardless of deltaPhiMin's value (0.01, 0.001, 0.0001). This has been reproduced on registration of 2D and 3D images in comman...In spam 0.6.0 and 0.6.1: spam-reg and spam.DIC.registerMultiscale do not terminate upon reaching deltaPhiMin, regardless of deltaPhiMin's value (0.01, 0.001, 0.0001). This has been reproduced on registration of 2D and 3D images in command-line bash scripts and python scripts. The 2D bash script example and associated images are provided here for easiest replication.
[example.sh](/uploads/a739c80549cbddd087cbc996dddaa298/example.sh)[image1.tif](/uploads/a7740907aaf885a95862100d431610ed/image1.tif)[image2.tif](/uploads/2be60e8b4accc9b618832943fb86cc9e/image2.tif)https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/214spam-mmr-graphical very broken2021-06-22T19:01:08+02:00Edward Andòspam-mmr-graphical very brokenproblems with binning being passed to eregproblems with binning being passed to ereghttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/213crash in pixelSearch on saving when saving VTK files and loaded PhiFile2021-06-23T10:06:54+02:00Edward Andòcrash in pixelSearch on saving when saving VTK files and loaded PhiFilefill in args.NS and nodeDims from FieldDims
copy from ldic which works finefill in args.NS and nodeDims from FieldDims
copy from ldic which works finehttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/211`spam-reg` when mask is passed save the registration .tsv file at the COM of ...2021-06-16T14:58:18+02:00Olga Stamati`spam-reg` when mask is passed save the registration .tsv file at the COM of the maskcurrently it is saved in the centre of the imagecurrently it is saved in the centre of the imagehttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/210`spam-ereg` crashes when pressing ``flip`` button2021-06-22T19:00:37+02:00Olga Stamati`spam-ereg` crashes when pressing ``flip`` button``File "/lib/python3.7/site-packages/spam/visual/visualClass.py", line 1151, in flip
self.images[2] = numpy.flip(self.images[2], 0)
IndexError: list index out of range
Abandon````File "/lib/python3.7/site-packages/spam/visual/visualClass.py", line 1151, in flip
self.images[2] = numpy.flip(self.images[2], 0)
IndexError: list index out of range
Abandon``https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/199getImagettes problmen in branch2021-03-18T15:18:17+01:00Edward AndògetImagettes problmen in branch`spam-ldic -glt 29000 00/00.tif +356g/01.tif -od . -pf 00-01-pixelSearch.tsv -pfd -hws 5 -ns 10 -tif -vtk`
"""
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (Tru...`spam-ldic -glt 29000 00/00.tif +356g/01.tif -od . -pf 00-01-pixelSearch.tsv -pfd -hws 5 -ns 10 -tif -vtk`
"""
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/opt/spam/spam/bin/spam-ldic", line 121, in correlateOneNode
imagetteReturns = spam.DIC.getImagettes(im1, nodePositions[nodeNumber], args.HWS, PhiInit.copy(), im2, margin, im1mask=im1mask, minMaskCoverage=args.MASK_COVERAGE, greyThreshold=[args.GREY_LOW_THRESH, args.GREY_HIGH_THRESH], applyF='no', twoD=twoD)
File "/opt/spam/spam/lib/python3.8/site-packages/spam/DIC/grid.py", line 289, in getImagettes
imagette2 = spam.helpers.slicePadded(im2, startStopIm2)
File "/opt/spam/spam/lib/python3.8/site-packages/spam/helpers/imageManipulation.py", line 486, in slicePadded
assert (startStop[1]>startStop[0]), "spam.helpers.slicePadded(): Zmax should be bigger than Zmin"
AssertionError: spam.helpers.slicePadded(): Zmax should be bigger than Zmin
""Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/198check broken projection tutorial2021-03-18T15:15:55+01:00Olga Stamaticheck broken projection tutorialseems that comes from `projection.py`seems that comes from `projection.py`https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/192spam-ereg-discrete2020-11-16T13:46:03+01:00Edward Andòspam-ereg-discreteif label is missing and getLabel() returns None it crashes :(if label is missing and getLabel() returns None it crashes :(Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/187spam-ereg-discrete2020-11-16T13:46:03+01:00Edward Andòspam-ereg-discrete`mask` option doesn't seem to be respected and so `-nomask` doesn't do anything`mask` option doesn't seem to be respected and so `-nomask` doesn't do anythingEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/186spam-ereg-discrete broke2020-11-16T13:46:03+01:00Edward Andòspam-ereg-discrete brokeCurrently not working likely due to changes in getLabel
REFsubvol[REFgl['subvol'] == 0] = 0
IndexError: boolean index did not match indexed array along dimension 2; dimension is 211 but corresponding boolean dimension is 216Currently not working likely due to changes in getLabel
REFsubvol[REFgl['subvol'] == 0] = 0
IndexError: boolean index did not match indexed array along dimension 2; dimension is 211 but corresponding boolean dimension is 216Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/184Coverage and multiprocessing2020-10-12T12:01:31+02:00Gustavo Pinzongustavo.pinzon@3sr-grenoble.frCoverage and multiprocessingWhen running the test for spam.label.moveLabes(), the test is running but the coverage report is not showing the evaluation of the worker. Adding `--concurrency=multiprocessing && coverage combine` to `python setup.py install && coverage...When running the test for spam.label.moveLabes(), the test is running but the coverage report is not showing the evaluation of the worker. Adding `--concurrency=multiprocessing && coverage combine` to `python setup.py install && coverage run --concurrency=multiprocessing setup.py test && coverage combine && coverage html` solves the issue (the worker is excluded from the coverage), but the file `spam.visual.visualClass.py` is not excluded and tested (under normal operation the file is excluded in the coverage report).
On previous functions with multiprocessing, the worker is excluded in the coverage report.https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/176in spam.label.getLabel() subvol.shape not consistent with returned slice2020-08-21T14:04:18+02:00Edward Andòin spam.label.getLabel() subvol.shape not consistent with returned slicelook into label dilate, but it's not only this
apparently proportional to marginlook into label dilate, but it's not only this
apparently proportional to marginOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/175Allow margin list in registerMultiscale2020-08-21T14:04:18+02:00Edward AndòAllow margin list in registerMultiscaleCopy what's done in register and add testCopy what's done in register and add testOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/163spam-mmr-graphical load TSV2020-06-12T10:02:54+02:00Edward Andòspam-mmr-graphical load TSVLosding TSV from command line works fine, but TSV from first file menu does not work (TSV Phi is not taken into account)Losding TSV from command line works fine, but TSV from first file menu does not work (TSV Phi is not taken into account)https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/151Bad convergence with large `PhiInit` in `register()`2022-12-14T11:23:59+01:00Edward AndòBad convergence with large `PhiInit` in `register()`With very large initial rotations for example, register goes mad.
Apparently swapping back line ~394 in the dot product behaviour is fine but does not
seem mathematically sound.
```
# CASE 7: 3D case with large initial rotation (say 120...With very large initial rotations for example, register goes mad.
Apparently swapping back line ~394 in the dot product behaviour is fine but does not
seem mathematically sound.
```
# CASE 7: 3D case with large initial rotation (say 120 deg)
rot = 120
imDef = spam.DIC.applyPhi(im, Phi=spam.deformation.computePhi({'r': [rot, 0, 0]}))
returns7 = spam.DIC.register(im, imDef, margin=10, PhiInit=spam.deformation.computePhi({'r': [rot+2.5, 0, 0]}))
returns7['transformation'] = spam.deformation.decomposePhi(returns7['Phi'])
# Did you converge? Pas donné...
self.assertEqual(returns7['returnStatus'], 2)
for i in range(3):
self.assertAlmostEqual(numpy.array(returns7['transformation']["t"][i]), 0, places=1)
self.assertAlmostEqual(numpy.array(returns7['transformation']["r"][i]) - [rot, 0, 0][i], 0, places=1)
```Olga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/150spam-ldic KeyError: 'PSCC'2020-04-08T10:26:44+02:00Floriana Anselmuccispam-ldic KeyError: 'PSCC'running a ldic, I have this error
'Traceback (most recent call last):
File "/mnt/ea/users/eroubin/ttk/spam/venv/bin/spam-ldic", line 320, in <module>
PSCC = pixelSearchReturns['PSCC']
KeyError: 'PSCC'
'running a ldic, I have this error
'Traceback (most recent call last):
File "/mnt/ea/users/eroubin/ttk/spam/venv/bin/spam-ldic", line 320, in <module>
PSCC = pixelSearchReturns['PSCC']
KeyError: 'PSCC'
'https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/149with mpi in spam-ddic, np RS=0 grains are skipped for some reason, doesn't ha...2020-04-07T12:31:57+02:00Edward Andòwith mpi in spam-ddic, np RS=0 grains are skipped for some reason, doesn't happen without mpirunThere should only be 1 RS=0 and that is for label 0, however if you run
`mpirun -np X spam-ddic ...`
You'll get X+1 labels with RS=0There should only be 1 RS=0 and that is for label 0, however if you run
`mpirun -np X spam-ddic ...`
You'll get X+1 labels with RS=0Olga StamatiOlga Stamati