ImageJ_utilities.py

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"""Miscellaneous utilities for python interaction with ImageJ"""
_rcsid="$Id: ImageJ_utilities.py,v 1.3 2003/05/30 13:31:54 mendenhall Release-20030716 $"

def read_ImageJ_measurement_file(file, maxlen=1000000):
    "Read a measurements file from ImageJ, and return a dictionary mapping columns names to numbers, a list of column names, and a table of the data provided"
    f=open(file,"r")
    strings=f.read(maxlen).split("\n")
    f.close()
    columns=[ [i.strip() for i in line.split("\t")] for line in strings if line]
    header=columns[0]
    keys={}
    #extract column names
    for i in range(1,len(header)):
        keys[header[i]]=i
    return keys, columns[0][1:], columns[1:]

def read_ImageJ_roi_file(file):
    "Read a measurements file from ImageJ containing  (at least) the bounding rectangle information for a series of ROIs"
    keys, column_names, data = read_ImageJ_measurement_file(file)
    rois=[]
    column_map=[keys[name] for name in ("BX","BY","Width","Height")] 
    for i in data[1:]:
        x0, y0, width, height= [int(i[c]) for c in column_map] 
        rois.append([x0,y0,x0+width,y0+height])
    return rois
 

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