plantcv.train, naive_bayes, problems generating a PDF

[francisco-franco-86]

Hi, I'm having trouble using naive_bayes to generate a PDF from six 8bitRGB images and their respective binary masks.

I used the following code on google colab to create a PDF, the code ran correctly but the output file is empty.

#import subprocess

imgdir = "/content/drive/MyDrive/..."
maskdir = "/content/drive/MyDrive/..."
outfile = "/content/gdrive/MyDrive/.../naive_bayes_results.txt"

#Command for plantcv-train
command = [
    "plantcv-train", "naive_bayes",
    "--imgdir", imgdir,
    "--maskdir", maskdir,
    "--outfile", outfile,
    "--plots"
    ]

# Run
subprocess.run(command)

print(f"El archivo PDF con los resultados se ha guardado como {outfile}")

[nfahlgren]

Hi @francisco-franco-86, the image and mask directories need to be distinct folders so that the program knows which images are the source images and which are the binary masks.

[francisco-franco-86]

Hi, thanks for your reply.

Sorry, I deleted it in the code, but the images are in separate folders with exactly the same name.

this is my original code:

imgdir = "/content/drive/MyDrive/imagens_paspalum/PDFs/macetas_superiores_imagenes"
maskdir = "/content/drive/MyDrive/imagenes_paspalum/PDFs/macetas_superiores_mask"
outfile = "/content/gdrive/MyDrive/imagenes_paspalum/PDFs/macetas_superiores_imagenes/naive_bayes_results.txt"


# Comando para ejecutar plantcv-train
command = [
    "plantcv-train", "naive_bayes",
    "--imgdir", imgdir,
    "--maskdir", maskdir,
    "--outfile", outfile,
    "--plots"
    ]

# Ejecutar el comando
subprocess.run(command)

print(f"El archivo PDF con los resultados se ha guardado como {outfile}")