Why is my script not adding a file into the output folder?

Question

This script should take a file from an input folder, put it through a pretrained model, and put the results in the output folder. I get no errors.

import os
import numpy as np
import imageio.v2 as imageio
from cellpose import models

model_path = r"C:\Users\TomoCube\Desktop\New Testing\trained_model\models\cellpose_residual_on_style_on_concatenation_off_trained_model_2025_05_29_14_15_22.066364"
input_folder = r"C:\Users\TomoCube\Desktop\Input Folder"
output_folder = r"C:\Users\TomoCube\Desktop\Output Folder"
os.makedirs(output_folder, exist_ok=True)

# 🔧 TEST: Write a dummy file to confirm save path works
dummy_test_path = os.path.join(output_folder, "dummy_test.tif")
imageio.imwrite(dummy_test_path, np.zeros((10, 10), dtype='uint16'))
print(f"✅ Dummy test file saved: {dummy_test_path}")

model = models.CellposeModel(pretrained_model=model_path, gpu=False)

image_files = [
    f for f in os.listdir(input_folder)
    if f.lower().endswith(('.png', '.jpg', '.tif')) and '_masks' not in f
]
image_files.sort()

for filename in image_files:
    image_path = os.path.join(input_folder, filename)
    print(f"\n🔍 Processing: {filename}")

    img = imageio.imread(image_path)
    print(f"  ➤ Image shape: {img.shape}, dtype: {img.dtype}")

    masks, flows, styles = model.eval(img, channels=[0, 0])
    print(f"  ➤ masks.max(): {masks.max()}, dtype: {masks.dtype}, shape: {masks.shape}")

    output_filename = f"{os.path.splitext(filename)[0]}_mask.tif"
    output_path = os.path.join(output_folder, output_filename)

    try:
        imageio.imwrite(output_path, masks.astype('uint16'))
        print(f"  ✅ Mask saved: {output_path}")
    except Exception as e:
        print(f"  ❌ Failed to save mask for {filename}: {e}")

print("\n✅ All done! Masks saved to:", output_folder)

I tried updating all possible issues but I was getting nothing.

maybe first check print( image_files ) or print( len(image_files) ) — furas
– furas, Commented May 29 at 20:02
After image_files.sort() add print(image_files) What do you see? — jackal
– jackal, Commented May 30 at 8:00

quantumsurge · Accepted Answer · 2025-05-29 19:02:38Z

The most probable cause is that your image_files list is empty, and as a result, the loop does not get executed.

Try printing out some valuable information to see what's contained in your input folder.

image_files = [
    f for f in os.listdir(input_folder)
    if f.lower().endswith(('.png', '.jpg', '.tif')) and '_masks' not in f
]
image_files.sort()

print("Input folder:", input_folder)
print("Raw contents:", os.listdir(input_folder))
print("Filtered images:", image_files)

If Raw contents is non-empty but Filtered images is [] , then you need to check your filtering logic and make it more flexible.
If Raw contents is indeed empty, then you most likely have the wrong path or input_folder is empty.

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