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imcflibs.imagej.bdv wrappers do not match multiview-reconstruction 9 / BigStitcher 3 #159
Description
The BigStitcher / MVR wrappers build macro strings that partly no longer match the dialogs of
multiview-reconstruction 9.0.11 / BigStitcher 3.0.8 (checked with javap on the jars). ImageJ
ignores unknown keys silently and falls back to the dialog's value, so most of these do not fail but
silently use other settings.
| function | emitted | MVR 9.0.11 / BigStitcher 3.0.8 | effect |
|---|---|---|---|
interest_points_registration |
ransac_iterations=Normal |
choices Fast (1,000), Normal (10,000), ... |
"not a valid choice" error |
interest_points_registration |
inlier_factor=3 |
no such field; Minmal_number_of_inliers (absolute, default 12; typo in MVR) |
ignored, minimum 12 inliers |
interest_points_registration |
search_radius=100 |
only applied with the checkbox limit_search_radius |
ignored |
interest_points_registration, optimize_and_apply_shifts |
- | global optimisation only pre-aligns with the new checkbox pre-align (MVR 7 always did) |
no pre-alignment |
ProcessingOptions |
[Single timepoint (Select from List)], [timepoint N], [Average Timepoints] |
[Single Timepoint (Select from List)], [Timepoint N], [Average TimePoints] |
timepoint selection / grouping ignored |
DefinitionOptions |
multiple_illuminations_directions= |
_____multiple_illumination_directions |
ignored |
fuse_dataset |
create, create_0 |
create_a_bdv/bigstitcher, create_multi-resolution |
no XML / pyramid |
fuse_dataset |
export=HDF5 (default) |
HDF5 export disabled ("currently unavailable due to library incompatibilities with n5 4.0.0-alpha-6") | export stops |
fuse_dataset |
processing selectors not passed | - | single-channel selections lost |
| module import | from ch.epfl.biop... import FuseBigStitcherDatasetIntoOMETiffCommand at module level |
needs the PTBIOP update site | import imcflibs.imagej.bdv fails without it |
In addition, most options of the wrappers are hardcoded (e.g. Affine regularised with Affine,
RELAXED link removal, all groupings, detection downsampling 8x/2x, bounding box "All Views", no
non-rigid fusion), which makes them unusable for other registration setups.
Related: the issue about IJ.run() starting the legacy SPIM_Registration plugin. A pull request
fixing both follows.
Activity
📝 Reference issues imcf#158, imcf#159 and imcf#160
📝 Reference issues imcf#158, imcf#159 and imcf#160