Using PLANTCV together with other packages

[JSCG95]

I'm trying to use PLANTCV in one of my image analyses scripts but I just need to use just a few functionalities from the package. However, when I'm importing the whole library (import plantcv) I'm unable to include specific attributes into my code. This is the error message I'm receiving.

"AttributeError: module 'plantcv' has no attribute 'find_objects'".

Same error message is displaying with almost all functionalities of PLANTCV.

Do you have any idea what am I doing wrong? I apologize if is something obvious I'm just getting familiarized with the package

[HaleySchuhl]

Hi @JSCG95 ,

Thanks for opening a discussion! One slightly unusual trait of the PlantCV software package is that there's a namespace with all image analysis functionality within the software package name. In practice, this means you should use from plantcv import plantcv.find_objects rather than import plantcv.find_objects.

[JSCG95]

That is not the only function that I'm trying to use. Let me try to explain it properly. I would like to import the whole package by using

import plantcv as pcv

and then access each function by calling the package and the function (eg. pcv.find_objects). However, I'm not able to do that. The suggestions spyder was giving me is to use pcv.plantcv.find_objects(), but the missing atttribute error is still there.

I tried to do what you suggested but spyder is considering an invalid syntax.

I've been using PLANTCV in my jupyter files without any issue, however when I start a new .py script from the scratch using spyder I'm unable to use PLANTCV functions. I'm sure the package is installed in my environment because when writing down "pcv." spyder displays recommendations with a few modules (learn,parallel,plantcv) but not the functions I'm trying to use.

Here I share a simplified version of my code

`import os
import cv2
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import pyplot as plt
import plantcv as pcv

raw = cv2.imread("./pic_1.bmp")
plt.imshow(raw)

Crop image to see the plants crearly

crop = raw[625:975, 850:1225]
plt.imshow(crop)

#Convert to grayscale
img_gray = cv2.cvtColor(crop, cv2.COLOR_BGR2GRAY)
plt.imshow(img_gray)

Apply binary thresholding

ret, thresh = cv2.threshold(img_gray, 10, 255, cv2.THRESH_BINARY)
plt.imshow(thresh)

Detect objects using Plant CV module

obj, obj_hierarchy = pcv.plantcv.find_objects(crop, mask=thresh)`

[nfahlgren]

Hi @JSCG95, if you change import plantcv as pcv to from plantcv import plantcv as pcv then you can access the functions via pcv.find_objects, etc.

[JSCG95]

Thanks Noah. That worked.