To reproduce:
crop the area in the AM curator, then revert the change, then choose a better spanning square and crop again. You'll get this:
(6149.36, 2997.46) --> (10338.57, 7113.60)
(6246.78, 2997.46) --> (10435.99, 7113.60)
The post maldi cropped image is saved at /home/renat/EMBL/Sharaz_images/rhodamin/Analysis/gridFit/AM_cropped.tif
cropPMimage finished
Ablation mark finding and filtering started
Traceback (most recent call last):
File "/home/renat/Downloads/programs/pycharm-2018.1.4/helpers/pydev/_pydev_bundle/pydev_monkey_qt.py", line 180, in _new_run
return self._original_run()
File "/home/renat/EMBL/spaceM_Luca/linux/1c_gui_complete/__main__.py", line 31, in run
find_am.step2()
File "/home/renat/EMBL/spaceM_Luca/linux/1c_gui_complete/pipelinecontroller.py", line 74, in step2
self.FLUO_POSTMIMAGE, self.UDP_FILE, self.MALDI_METADATA, window=0)
File "/home/renat/EMBL/spaceM_Luca/linux/1c_gui_complete/pipelineMethods.py", line 30, in ablation_mark_filter
spaceM.Registration.AblationMarkFinder.GridFit(MF, postMaldiImgPath, UDPpath=UDPpath, maldiMetadataPath=maldiMetadataPath)
File "/home/renat/EMBL/spaceM_Luca/linux/spaceM/Registration/AblationMarkFinder.py", line 616, in GridFit
show_results=False) # TODO provide option to swtch to DAN at higher level
File "/home/renat/EMBL/spaceM_Luca/linux/spaceM/Registration/AblationMarkFinder.py", line 40, in spotFinder
img_i = DHB_prep(MF, path1, path2)
File "/home/renat/EMBL/spaceM_Luca/linux/spaceM/Registration/AblationMarkFinder.py", line 29, in DHB_prep
im3 = scale(contrast(scale(scale(im2) * scale(im1) * -1), 0.9, 1))* 65535
ValueError: operands could not be broadcast together with shapes (8951,5607) (4117,4189)```
To reproduce: crop the area in the AM curator, then revert the change, then choose a better spanning square and crop again. You'll get this: