Hello,
I want to get X coordinate and Y coordinate from Roi(.roi file).
I could find a couple of posts related to this.
This article wrote about how to get X coordinate and Y coordinate, but I want to get this directly by RoiFile(Roi Path) or “ij.plugin.frame.RoiManager”
Is there any way to get the X and Y coordinates directly from this ROI folder that I attached?
Apologies in advance if this is covered elsewhere, can’t find it easily. Thanks,
RoiSet.zip (13.7 KB)
Sorry, this post is solution for me.
Hello,
I have something similar but as a jython script, I only tested when there was just one zip file in a directory and it shows the result as a results table. Maybe this helps too and also if you want to extend and try it on a directory containing a bunch of zip files it could work for that case as well.
#@ File(label='Choose Roi directory', style='directory') roidir
#@ String(label='File types', value='zip') file_type_Roi
#@ String(label='Filter', value='._') filter_Roi
#@ Boolean(label='Recursive search', value=False) do_recursive
import os
from java.io import File
from ij.measure import ResultsTable
from ij import IJ
from ij.plugin.frame import RoiManager
from ij import WindowManager as wm
def batch_open_Rois(pathRoi, file_typeRoi=None, name_filterRoi=None, recursive=False):
'''Open all files in the given folder.
:param path: The path from were to open the Rois. String and java.io.File are allowed.
:param file_type: Only accept files with the given extension (default: None).
:param name_filter: Reject files that contain the given string (default: wild characters).
:param recursive: Process directories recursively (default: False).
'''
# Converting a File object to a string.
if isinstance(pathRoi, File):
pathRoi = pathRoi.getAbsolutePath()
def check_type(string):
'''This function is used to check the file type.
It is possible to use a single string or a list/tuple of strings as filter.
This function can access the variables of the surrounding function.
:param string: The filename to perform the check on.
'''
if file_typeRoi:
# The first branch is used if file_type is a list or a tuple.
if isinstance(file_typeRoi, (list, tuple)):
for file_type_ in file_typeRoi:
if string.endswith(file_type_):
# Exit the function with True.
return True
else:
# Next iteration of the for loop.
continue
# The second branch is used if file_type is a string.
elif isinstance(file_typeRoi, string):
if string.endswith(file_typeRoi):
return True
else:
return False
return False
# Accept all files if file_type is None.
else:
return True
# We collect all files to open in a list.
path_to_Roi = []
# Replacing some abbreviations (e.g. $HOME on Linux).
path = os.path.expanduser(pathRoi)
# If we don't want a recursive search, we can use os.listdir().
if not recursive:
for file_name in os.listdir(pathRoi):
full_path = os.path.join(pathRoi, file_name)
if os.path.isfile(full_path):
if check_type(file_name):
path_to_Roi.append(full_path)
# For a recursive search os.walk() is used.
else:
# os.walk() is iterable.
# Each iteration of the for loop processes a different directory.
# the first return value represents the current directory.
# The second return value is a list of included directories.
# The third return value is a list of included files.
for directory, dir_names, file_names in os.walk(pathRoi):
# We are only interested in files.
for file_name in file_names:
# The list contains only the file names.
# The full path needs to be reconstructed.
full_path = os.path.join(directory, file_name)
# Both checks are performed to filter the files.
if check_type(file_name):
# Add the file to the list of Rois to open.
path_to_Roi.append([full_path, os.path.basename(os.path.splitext(full_path)[0])])
# Create the list that will be returned by this function.
RoisX = []
RoisY = []
print('path',path_to_Roi)
for roi_path in path_to_Roi:
print('path',roi_path)
# An object equals True and None equals False.
rm = RoiManager.getInstance()
if (rm==None):
rm = RoiManager()
Roi = IJ.open(roi_path)
roi_points = rm.getRoisAsArray()
table = ResultsTable()
for Roi in roi_points:
xpoints = Roi.getPolygon().xpoints
ypoints = Roi.getPolygon().ypoints
for i in range(len(xpoints)):
table.incrementCounter()
table.addValue("Index", i)
table.addValue("X", xpoints[i])
table.addValue("Y", ypoints[i])
table.show("XY-Coordinates")
return roi_points
def split_string(input_string):
'''Split a string to a list and strip it
:param input_string: A string that contains semicolons as separators.
'''
string_splitted = input_string.split(';')
# Remove whitespace at the beginning and end of each string
strings_striped = [string.strip() for string in string_splitted]
return strings_striped
if __name__ in ['__builtin__','__main__']:
# Run the batch_open_Rois() function using the Scripting Parameters.
Rois = batch_open_Rois(roidir ,
split_string(file_type_Roi),
split_string(filter_Roi),
do_recursive
)
Good Morning from Japan.
I’ve read your code. I’m a beginner at programming, but I’d like to finally write code that can be published in my lab or outside.
Your code is very informative.
Thanks, Dan
Morning from Paris!
There are lots of code out here and on Github, I have some macros IJMacros that have ijm and jython examples. I like to keep one template and change the function inside it to do different things, that makes things easier and consistent for me. Hope this helps 
Cheers, Varun