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Error in finding contour (find object) for Hyperspectral Image

See original GitHub issue

Description In the pcv.find_objects function. I am constantly getting the same error, even after trying with multiple images. There is a big chance that the error is from my side. But I’ve tried multiple options in my capability. I would like to ask if anyone can solve this for me.

To Reproduce

Installed PlantCV using Anaconda
Python 3.7.12
Conda 4.10.3

The function I am using: id_objects, obj_hierarchy = pcv.find_objects(img=index_array_gdvi.array_data, mask=gdvi_thresh)

Error:

---------------------------------------------------------------------------
error                                     Traceback (most recent call last)
C:\Users\PCADMI~1\AppData\Local\Temp/ipykernel_19112/1019017205.py in <module>
      4    #   img  - RGB or grayscale image data for plotting
      5    #   mask - Binary mask used for detecting contours
----> 6 id_objects, obj_hierarchy = pcv.find_objects(img=index_array_gdvi.array_data, mask=gdvi_thresh)

f:\billy_graham_ram\plantcv\plantcv\plantcv\find_objects.py in find_objects(img, mask)
     32     if len(np.shape(ori_img)) == 2:
     33         ori_img = cv2.cvtColor(ori_img, cv2.COLOR_GRAY2BGR)
---> 34     objects, hierarchy = cv2.findContours(mask1, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)[-2:]
     35     # Cast tuple objects as a list
     36     objects = list(objects)

**error: OpenCV(3.4.16) D:\a\opencv-python\opencv-python\opencv\modules\imgproc\src\contours.cpp:197: error: (-210:Unsupported format or combination of formats) [Start]FindContours supports only CV_8UC1 images when mode != CV_RETR_FLOODFILL otherwise supports CV_32SC1 images only in function 'cvStartFindContours_Impl'**

Local environment: OS: Windows 10 Pro Environment: conda PlantCV Version: 3.13.2

Issue Analytics

State:
Created 2 years ago
Comments:7 (4 by maintainers)

Top GitHub Comments

1reaction

nfahlgrencommented, Dec 1, 2021

Great! We don’t have anything specifically planned at the moment but that is a great idea. We will be doing a workshop at the upcoming NAPPN annual meeting (https://www.plantphenotyping.org/) but I’m not sure what the topic(s) will be yet. We have enjoyed doing virtual workshops through Phenome Force (https://phenome-force.github.io/PhenomeForce/) and I could imagine doing more of those or something similar in the new year.

0reactions

billygrahamramcommented, Dec 1, 2021

@nfahlgren Thank you for your time! It did work. One more request: are there any upcoming workshops on HSI analysis using PlantCV? Thanks.

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