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I am working on yielding a confusion matrix with importing an image which is a geotiff format. After classified by a python program, The image has two values (two classifications). However, when I imported the image to ENVI, it warned the ENVI classification type only can be inputted. Before the above progress, I had used ENVI to create the ROI for the validation. I was going to use the ROI and the image to generate a confusion matrix with ENVI. But it was failed.

Is there any method which can produce the confusion matrix using geotiff format image and ROI?

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You can use the semiautomatic classification plugin for qgis, this has many features, but does create error matrix. You can view the documentation here http://semiautomaticclassificationmanual-v5.readthedocs.io/en/latest/remote_sensing.html#accuracy-assessment-definition

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