![]() ![]() ![]() Print( "Scale Bar Size:", ScaleSize, "Pixel Length:", ScaleBarLength) diff( ScalebarLengthArray)) #Get the indices for the Left and Right scale bar, the difference is the length of the scale bar ScaleBarLength = np. ![]() # y = 721 for the scale bar region print( "Finding Pixel Size of the scale bar") Raise Exception( "There is no scale bar of nm or um size here") ScaleName = "um" elif nm_result != - 1 and um_result = - 1: open( FileList )) # Get the Data String um_result = DataString. ij.py.show(image, cmap='gray') """ for i in range( len( FileList)):ĭataString = pyt. image = ij.py.from_java(jimage) # Display the image (backed by matplotlib). image_url = '' jimage = ij.io().open(image_url) # Convert the image from ImageJ to xarray, a package that adds # labeled datasets to numpy (). import imagej ij = imagej.init() # Load an image. #Defining Macro: macro = """ String FilePath int ScaleSize String ScaleName int PixelLength String FileName print("Opening the File") open(FilePath) run("Set Scale.", "distance="+ PixelLength + " known="+ ScaleSize+ " unit="+ScaleName) //setTool("rectangle") makeRectangle(0, 1, 1022, 673) setAutoThreshold("Default dark") //run("Threshold.") //setThreshold(161, 255) run("Convert to Mask") run("Close") makeRectangle(0, 1, 1022, 673) run("Analyze Particles.", " show=Ellipses display exclude clear summarize in_situ") print("I have done the Analysis") saveAs("Results", FileName +".csv") run("Close All") """ #Now we need to define the Args """ # Create an ImageJ gateway with the newest available version of ImageJ. Nm_string = "nm" um_string = "um" print( "Starting Image J backend") Execute the ImageJ Macro to set the threshold, Do the Watershed analysis, and fit to ellipses """ print( "Did you select a real folder?") crop the image around the scale bar line, find the length of the scale bar using np.diff and np.notzero 4. For each file, do tesseract on the bottom portion, get the scale size of the bar 3. """ ImageJ + Python + Tesseract to automate this shit. Import imagej import numpy as np import os, sys import PIL import pytesseract as pyt from glob import glob import matplotlib. ![]()
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