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'float' object is not subscriptable"

See original GitHub issue

Ran without modifications, running in the python:3-stretch docker container.

2019-05-06 22:08:10,702 - INFO - no display found. Using non-interactive Agg backend
2019-05-06 22:08:11,899 - WARNING - Configuration file not set (--config), using default: /var/www/HistoQC/config.ini
2019-05-06 22:08:11,902 - INFO - Pipeline will use these steps:
2019-05-06 22:08:11,903 - INFO - 		BasicModule	getBasicStats
2019-05-06 22:08:12,267 - INFO - 		ClassificationModule	byExampleWithFeatures:coverslip_edge
2019-05-06 22:08:12,402 - INFO - 		LightDarkModule	getIntensityThresholdPercent:tissue
2019-05-06 22:08:12,404 - INFO - 		LightDarkModule	getIntensityThresholdPercent:darktissue
2019-05-06 22:08:12,404 - INFO - 		BubbleRegionByRegion	detectSmoothness
2019-05-06 22:08:12,406 - INFO - 		MorphologyModule	removeFatlikeTissue
2019-05-06 22:08:12,408 - INFO - 		MorphologyModule	fillSmallHoles
2019-05-06 22:08:12,408 - INFO - 		MorphologyModule	removeSmallObjects
2019-05-06 22:08:12,409 - INFO - 		BlurDetectionModule	identifyBlurryRegions
2019-05-06 22:08:12,410 - INFO - 		BasicModule	finalProcessingSpur
2019-05-06 22:08:12,411 - INFO - 		BasicModule	finalProcessingArea
2019-05-06 22:08:12,411 - INFO - 		HistogramModule	compareToTemplates
2019-05-06 22:08:12,413 - INFO - 		HistogramModule	getHistogram
2019-05-06 22:08:12,414 - INFO - 		BrightContrastModule	getContrast
2019-05-06 22:08:12,415 - INFO - 		BrightContrastModule	getBrightnessGray
2019-05-06 22:08:12,415 - INFO - 		BrightContrastModule	getBrightnessByChannelinColorSpace:RGB
2019-05-06 22:08:12,416 - INFO - 		BrightContrastModule	getBrightnessByChannelinColorSpace:YUV
2019-05-06 22:08:12,417 - INFO - 		DeconvolutionModule	seperateStains
2019-05-06 22:08:12,418 - INFO - 		SaveModule	saveFinalMask
2019-05-06 22:08:12,419 - INFO - 		SaveModule	saveThumbnails
2019-05-06 22:08:12,420 - INFO - 		BasicModule	finalComputations
2019-05-06 22:08:12,420 - INFO - ----------
2019-05-06 22:08:12,421 - INFO - Number of files detected by pattern:	1
2019-05-06 22:08:12,422 - INFO - -----Working on:	/images/apply.svs		1 of 1
2019-05-06 22:08:12,458 - INFO - apply.svs - 	getMag
2019-05-06 22:08:15,450 - INFO - apply.svs - 	getBasicStats
2019-05-06 22:08:15,450 - INFO - apply.svs - 	ClassificationModule.byExample:	coverslip_edge
2019-05-06 22:08:15,453 - INFO - apply.svs - Training model ClassificationModule.byExample:coverslip_edge
2019-05-06 22:08:15,489 - ERROR - /images/apply.svs - 	 - Error analyzing file (skipping): 	 <class 'TypeError'> Inappropriate argument type. ("'float' object is not subscriptable", '/images/apply.svs', '<code object byExampleWithFeatures at 0x7fdde4d93e40, file "/var/www/HistoQC/ClassificationModule.py", line 143>')
2019-05-06 22:08:15,496 - INFO - ------------Done---------

2019-05-06 22:08:15,496 - INFO - These images failed (available also in error.log), warnings are listed in warnings column in output:
2019-05-06 22:08:15,496 - INFO - /images/apply.svs	<class 'TypeError'> Inappropriate argument type. ("'float' object is not subscriptable", '/images/apply.svs', '<code object byExampleWithFeatures at 0x7fdde4d93e40, file "/var/www/HistoQC/ClassificationModule.py", line 143>')
2019-05-06 22:08:15,497 - INFO - Symlink to output directory created

Issue Analytics

State:
Created 4 years ago
Comments:27 (14 by maintainers)

Top GitHub Comments

1reaction

choosehappycommented, May 11, 2019

error caused by a difference between this version of frangi filter in skimage:

https://scikit-image.org/docs/dev/api/skimage.filters.html#skimage.filters.frangi

and this version:

https://scikit-image.org/docs/0.14.x/api/skimage.filters.html#frangi

requirements now has >=.15 for skimage

0reactions

ragh1975commented, Jul 3, 2019

Thanks

On Wed, Jul 3, 2019 at 12:51 PM choosehappy notifications@github.com wrote:

Coming back to this, added a Dockerfile in a88d190 https://github.com/choosehappy/HistoQC/commit/a88d1902a3a3e282a97b4763c5696e22f267fa3c

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