-
Notifications
You must be signed in to change notification settings - Fork 0
/
Color_Merger_+_Zprojector_batch.py
37 lines (29 loc) · 1.17 KB
/
Color_Merger_+_Zprojector_batch.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
# Color_Merger_batch.py
# Dev: Igor Bonacossa Pereira.
# Email: i.bonacossapereira@uq.edu.au
#@File (label="Images folder", style="directory") img_folder
#@File (label="Save folder", style="directory") save_folder
#@String (label="Images extension", value=".jpg") ext
# Bootstrap to extend modules search path #
from sys import path
import os
from java.lang.System import getProperty
jython_scripts = os.path.join(getProperty('user.home'), 'Jython_scripts')
path.append(jython_scripts)
#=========================================#
# GUI for getting parameters to run ColorMerger in batch mode.
from IBPlib.ij.ColorMerger import ColorMerger
from IBPlib.ij.Projector import Projector
savefolder = save_folder.getPath()
imgfolder = img_folder.getPath()
save_folders = [os.path.join(savefolder, folder) for folder in ["colormeged", "z-projections"]]
for directory in save_folders:
if not os.path.isdir(directory):
try:
os.makedirs(directory)
except Exception as e:
print(e.args[0])
projector = Projector(save_folders[1], imgfolder, ext)
postProcessingMethod = projector.doprojection
cm = ColorMerger(save_folders[0], imgfolder, ext,)
cm.run(postProcessingMethod=postProcessingMethod)