PythonForAivia/PythonEnvForAivia/Recipes/ProcessImages/Boundaries_From_3D_Labeled_Mask.py at master · AiviaCommunity/PythonForAivia · GitHub

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import subprocess
import sys
import os.path
import numpy as np
from skimage.io import imread, imsave
from skimage import segmentation

"""
Detects boundaries of 3D labeled objects and creates measurable objects in Aivia.
Works only when there is no time dimension (yet).

Requirements
------------
numpy (comes with Aivia installer)
scikit-image (comes with Aivia installer)
ctypes

Parameters
----------
Input channel:
    Input channel with labeled mask and touching objects.

Returns
-------
New channel or Object Set in Aivia

Note: replace output with one of the line below to change output type (objects or mask)
# [OUTPUT Name:resultPath Type:string DisplayName:'Labeled Boundaries Mask']
# [OUTPUT Name:resultPath Type:string DisplayName:’Boundaries from labels’ Objects:3D MinSize:0.5 MaxSize:50000.0]
"""


# [INPUT Name:inputImagePath Type:string DisplayName:'Labeled Mask']
# [OUTPUT Name:resultPath Type:string DisplayName:'Labeled Boundaries Mask']
def run(params):
    image_location = params['inputImagePath']
    result_location = params['resultPath']
    tCount = int(params['TCount'])
    if not os.path.exists(image_location):
        print(f"Error: {image_location} does not exist")
        return

    image_data = imread(image_location)
    dims = image_data.shape
    print('-- Input dimensions (expected (Z), Y, X): ', np.asarray(dims), ' --')

    # Checking image is not 2D/2D+t or 3D+t
    if len(dims) == 2 or (len(dims) == 3 and tCount > 1):
        message = 'Error: Cannot be applied to timelapses or 2D images.'
        if not params.get('debugMode', False):
            Mbox('Error', message, 0)
        sys.exit(message)

    output_data = np.empty_like(image_data)

    # Detecting boundaries (mode = ‘thick’, ‘inner’, ‘outer’, ‘subpixel’)
    boundaries = segmentation.find_boundaries(image_data, mode='inner')
    output_data = np.where(boundaries, image_data, 0)

    imsave(result_location, output_data)
    print('Successfully saved output channel')


def Mbox(title, text, style):
    style_tags = ["OkOnly", "OkCancel", "YesNo", "YesNoCancel"]
    cmd = [
        "powershell",
        "-Command",
        "Add-Type -AssemblyName Microsoft.VisualBasic; "
        f"$x=[Microsoft.VisualBasic.Interaction]::MsgBox('{text}', "
        f"[Microsoft.VisualBasic.MsgBoxStyle]::{style_tags[style]}, '{title}');"
        "Write-Output $x"
    ]

    result = subprocess.run(cmd, capture_output=True, text=True)
    try:
        return result.stdout.strip()        # return = "Ok" or "Cancel"
    except:
        return None


if __name__ == '__main__':
    params = {'inputImagePath': r'D:\PythonCode\_tests\3D-image.aivia.tif',
              'resultPath': r'D:\PythonCode\_tests\test.tif',
              'TCount': 1, 'debugMode': True}

    run(params)

# CHANGELOG
#   v1_00: - From Objects_From_3D_Labeled_Mask_1_00.py
#   v1_10: - Mbox with VB for Aivia 16