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Topp-Roots-Lab / 3d-root-crown-analysis-pipeline

A pipeline to process 3-D volumes (.raw) of maize root crowns. Also known as XRCAP.
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Reshaping Error for KDE-based Traits #25

Closed tparkerd closed 3 years ago

tparkerd commented 3 years ago

Describe the bug Unable to process 20200617ZmStd_CSU19_RPFT2_18 with rootCrownImageAnalysis3D. Unsure what caused the error. Reported by Gabriella Pflederer.

To Reproduce Steps to reproduce the behavior:

  1. Run raw2img with default settings
  2. Run batch-segmentation with default settings
  3. Run rootCrownImageAnalysis3D (see error below)
2020-11-28 18:27:12,722 - [DEBUG] - rootCrownImageAnalysis3D.py 242 - ['kde-traits /shares/ctopp_share/private/gpflederer/xrt/CSU19/20200617ZmStd_CSU19_RPFT2_18_thresholded_images/2125_109um 0.109 2' exited with 0]
2020-11-28 18:27:12,723 - [DEBUG] - rootCrownImageAnalysis3D.py 255 - ['0.0013636236246', '0.0015167888774', '0.0016299138523', '0.0020165573017', '0.0026962257563', '0.0030969819841', '0.0022275460463', '0.0017024163284', '0.0013149573703', '0.0009184131309', '0.0007296307010', '0.0006032803528', '0.0005437122773', '0.0004407968359', '0.0003839237656', '0.0002550785697', '0.0000249220121', '0.0000000271583', '0.0000000000000', '0.0000000000000']
2020-11-28 18:27:12,723 - [DEBUG] - rootCrownImageAnalysis3D.py 256 - ['0.0002860121771', '0.0004946607146', '0.0006422812869', '0.0007602985597', '0.0009527013381', '0.0011878500506', '0.0018045605634', '0.0022497657791', '0.0022538893259', '0.0021745868894', '0.0019952153276', '0.0017939908099', '0.0016201031786', '0.0014259281296', '0.0012451474441', '0.0007896376529', '0.0000835927664', '0.0000001123407', '0.0000000000000', '0.0000000000000']
2020-11-28 18:27:15,534 - [ERROR] - rootCrownImageAnalysis3D.py 360 - (AttributeError("'NoneType' object has no attribute 'shape'"),)
2020-11-28 18:27:15,781 - [DEBUG] - rootCrownImageAnalysis3D.py 162 - maximum_number_of_points=620821392
2020-11-28 18:27:15,781 - [DEBUG] - rootCrownImageAnalysis3D.py 163 - chunksize=41388092
2020-11-28 18:27:17,741 - [DEBUG] - rootCrownImageAnalysis3D.py 162 - maximum_number_of_points=620821392¾±%trø+±¢L%

Expected behavior Should reshape the results produced by Matlab code into csv format.

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tparkerd commented 3 years ago

Related to #23, possibly duplicate.