search

PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
68 stars 15 forks source link

Unable to save multiview deconvolution as TIFF #67

Open ctrueden opened 4 years ago

ctrueden commented 4 years ago

In fiji/SPIM_Registration#136, @Agggy wrote:

So, I have been trying to work on some files in BigStitcher that I get from the Zeiss Z1 SPIM and everything seems to work until the multiview deconvolution step where fiji crushes if I ask it to save the file as TIFF. It works if save it as HDF5... Last time I tried, I got this error message: ![errors_console](https://user-images.githubusercontent.com/56698896/77140502-75cbdd00-6a3f-11ea-8e09-6fd24b16dcbf.png) ![workspace](https://user-images.githubusercontent.com/56698896/77140504-7795a080-6a3f-11ea-82ad-54fbc7a7128c.png) ![errors](https://user-images.githubusercontent.com/56698896/77140515-81b79f00-6a3f-11ea-856f-b7ba802f1e77.png) I am a bit clueless here and hope that someone can give me some helpful tips so that I can finish my image analysis!
StephanPreibisch commented 4 years ago

Can you please post which parameters you chose in the GUI?

StephanPreibisch commented 4 years ago

Just screenshots of the Multiview Deconvolution GUIs, thanks! I think I know what the issue is, but I have to be sure.

StephanPreibisch commented 4 years ago

@Agggy

StephanPreibisch commented 4 years ago

Also, the Log window says that you did a lot after the deconvolution finished. It is not entirely clear what the actual error is @Agggy Please document all steps that lead to a defined error. Thanks so much!

StephanPreibisch commented 4 years ago

Because for me it works just fine, here my log:

(Fri Mar 20 09:23:29 EDT 2020): Blurring input image with sigma = 5.0 to use as input Max intensity in overlapping area of view 0: 255.0 Max intensity in overlapping area of view 1: 255.00002 Max intensity in overlapping area of view 2: 255.00002 Max intensity in overlapping area of view 3: 255.00002 Max intensity in overlapping area of view 4: 254.92769 Max intensity in overlapping area of view 5: 255.00002 Max intensity in overlapping area of view 6: 255.0 iteration: 1 (Fri Mar 20 09:23:32 EDT 2020) iteration: 1, view: 0 [0-0] --- sum change: 9142763.136661887 --- max change per pixel: 47.28997039794922 iteration: 1, view: 1 [0-1] --- sum change: 1993281.3637148738 --- max change per pixel: 65.89476013183594 iteration: 1, view: 2 [0-2] --- sum change: 1.0457211420685768E7 --- max change per pixel: 105.53228759765625 iteration: 1, view: 3 [0-3] --- sum change: -4904594.469871819 --- max change per pixel: 90.79755401611328 iteration: 1, view: 4 [0-4] --- sum change: -1.0755010512727201E7 --- max change per pixel: 103.49136352539062 iteration: 1, view: 5 [0-5] --- sum change: 5715638.240808606 --- max change per pixel: 66.79618835449219 iteration: 1, view: 6 [0-6] --- sum change: 1.3768558119782805E7 --- max change per pixel: 116.74795532226562 DONE (Fri Mar 20 09:41:46 EDT 2020). Fri Mar 20 09:41:46 EDT 2020: Saving file /Users/spreibi/Desktop/fused_tp_0_ch_0.tif Fri Mar 20 09:41:49 EDT 2020: Saved file /Users/spreibi/Desktop/fused_tp_0_ch_0.tif (Fri Mar 20 09:41:49 EDT 2020): DONE.