def run():
gd = GenericDialogPlus("ND2 Conversion Tool")
gd.addMessage("This plugin uses BioFormats to convert ND2 images to JPEG for further processing in ImageJ.")
gd.addDirectoryOrFileField("Input: ", "G:\\Subdir testing\\") #srcDir
gd.addDirectoryOrFileField("Output: ", "G:\\Subdir testing\\") #dstDir
gd.addStringField("File name contains: ", "") #nameContains
gd.addCheckbox("Preserve directory structure?", True) #keepDirs
gd.addCheckbox("Run in headless mode?", True) #anneBoleyn
gd.addCheckbox("Overwrite existing output files?", True)
gd.showDialog()
if gd.wasCanceled():
return
srcDir = gd.getNextString()
dstDir = gd.getNextString()
nameContains = gd.getNextString()
keepDirectories = gd.getNextBoolean()
anneBoleyn = gd.getNextBoolean()
overOut = gd.getNextBoolean()
IJ.run("Input/Output...", "jpeg=100")
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Check for file extension
if not filename.endswith(".nd2"):
continue
# Check for file name pattern
if nameContains not in filename:
continue
process(srcDir, dstDir, nameContains, root, filename, keepDirectories, anneBoleyn, overOut)
from ij import IJ, ImagePlus
from ij.plugin import ImageCalculator
from ij.process import ImageProcessor
from ij.process import FloatProcessor
from fiji.util.gui import GenericDialogPlus
#Input parameters
gd = GenericDialogPlus("Input Parameters")
gd.addDirectoryOrFileField("Select composite color image, 32-bit", "")
gd.addNumericField("Pixel size", 4, 0) # show 3 decimals
gd.addNumericField("Background color", 150, 0) # show 3 decimals
gd.showDialog()
directory_w = gd.getNextString()
px = int(gd.getNextNumber())
bc = int(gd.getNextNumber())
#path to RGB image
IJ.open(str(directory_w))
imp = IJ.getImage()
IJ.run("8-bit")
IJ.run("32-bit")
n_slicesa = imp.getStack().getSize()
L = []
for i in range(1, n_slicesa + 1):
imp.setSlice(i)
n = imp.getProcessor().getPixels()
n2 = [int(val) for val in n]
L.append(n2)
imp.changes = False
#This creates a sparse approximation w of a signal X provided a dictionary D.
#||X-Dw||
#Requires mpv2 package: http://www.ux.uis.no/~karlsk/dle/mpv2-class.zip
#Improvements to come in the next version
from ij import IJ, ImagePlus
from ij.plugin import ImageCalculator
from ij.process import ImageProcessor
from ij.process import FloatProcessor
from fiji.util.gui import GenericDialogPlus
from mpv2 import MatchingPursuit as MP, JamaMatrix as Matrix, SymmetricMatrix as SM
#Input parameters
gd = GenericDialogPlus("Sparse Approximation, Input Parameters")
gd.addDirectoryOrFileField("Select dictionary", "")
gd.addChoice("Greedy algorithm type", ["MP", "OMP", "ORMP"], "OMP")
gd.addNumericField("Number of non-zero elements", 3, 0) # show 3 decimals
gd.showDialog()
directory_w = gd.getNextString()
t_w = int(gd.getNextNumber())
Rt = gd.getNextChoice()
imp2 = IJ.getImage()
IJ.run("32-bit")
imp2 = IJ.getImage()
#path to lighting directions
IJ.run("Text Image... ", "open=" + str(directory_w))
imp = IJ.getImage()
imp.setTitle("Dictionary Atoms")
#@PrefService prefs
#@FormatService fs # to check that the file in the folder are indeed images
from fiji.util.gui import GenericDialogPlus
from ij import IJ
from ij.gui import Roi
from os import listdir
from os.path import join, isfile, isdir
#import time
## Home-Made module
from Template_Matching.MatchTemplate_Module import getHit_Template, CornerToCenter
from Template_Matching.NonMaximaSupression_Py2 import NMS
## Create GUI
Win = GenericDialogPlus("Multiple Template Matching")
Win.addDirectoryOrFileField("Template file or templates folder",
prefs.get("TemplatePath", "template(s)"))
Win.addDirectoryOrFileField("Image file or images folder",
prefs.get("ImagePath", "image(s)"))
Win.addFileField("Rectangular_search_ROI (optional)",
prefs.get("RoiPath", "searchRoi"))
# Template pre-processing
Win.addCheckbox("Flip_template_vertically", prefs.getInt("FlipV", False))
Win.addCheckbox("Flip_template_horizontally", prefs.getInt("FlipH", False))
Win.addStringField("Rotate template by ..(comma-separated)",
prefs.get("Angles", ""))
# Template matchign parameters
Win.addChoice("Matching_method", [
"Normalised Square Difference", "Normalised cross-correlation",
"Normalised 0-mean cross-correlation"
bindir=cmtkgui.install_dir()
print 'bindir is ' + bindir
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger=cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp("http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui")
dirFieldWidth=50
gdMargin=130
gd.addDirectoryField("Registration Folder",None,dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "",dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory",None,dirFieldWidth)
imgdirf = gd.getStringFields().get(2)
gd.setInsets(10,gdMargin,10)
gd.addMessage("Output folders:")
outputf=gd.getMessage()
# what to do: affine/warp/reformat
gd.setInsets(10,200,10)
gd.addCheckboxGroup(3,2,["affine","01","warp","02","reformat","03"],[True,True,True,True,True,True],["Registration Actions","Reformat Channels"])
#gd.addCheckboxGroup(1,3,["01","02","03"],[True,True,True],["Reformat Channels"])
# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual
gd.addChoice("Registration Params",["Jefferis, Potter 2007","Cachero, Ostrovsky 2010"],"Jefferis, Potter 2007")
choicef=gd.getChoices().get(0)
#Set some defaults
IJ.run(
"Set Measurements...",
"area integrated area_fraction limit display scientific redirect=None decimal=3"
)
IJ.setForegroundColor(0, 0, 0)
IJ.setBackgroundColor(255, 255, 255)
#User Input Dialoge
analyses = ["Counts", "ATP"]
yn = ["YES", "NO"]
gdp = GenericDialogPlus("Ex Vivo Granule Analysis")
gdp.addMessage("Choose a UNIQUE directory to save analysis files")
gdp.addDirectoryOrFileField("Output Directory", "D:/Samantha/")
gdp.addMessage("IMPORTANT: Files are tracked based on input order")
gdp.addMessage("Select input files (.tiff)...")
gdp.addFileField("Wildtype", "D:/Samantha/test/VLEwt.tif")
gdp.addFileField("DIC", "D:/Samantha/test/dic.tif")
gdp.addFileField("Mutant", "D:/Samantha/test/ddmut.tif")
gdp.addFileField("Background (DAPI)", "D:/Samantha/test/bg.tif")
gdp.addChoice("Select analysis type", analyses, "Counts")
gdp.addMessage("Choose variable conditions:")
gdp.addNumericField(
"Minimum Threshold. Choose value (0-1) as a percent of maximum threshold",
0.20, 2)
gdp.addNumericField("Minimum granule size (pixel^2)", 20, 0)
gdp.addNumericField(
"Minimum granule circularity/shape. 1.0 = perfect cirlce, 0.5 = ellipse, 0.0 = rod",
0.50, 3)
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger = cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp(
"http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui"
)
dirFieldWidth = 50
gdMargin = 130
gd.addDirectoryField("Registration Folder", None, dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "", dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory", None,
dirFieldWidth)
imgdirf = gd.getStringFields().get(2)
gd.setInsets(10, gdMargin, 10)
gd.addMessage("Output folders:")
outputf = gd.getMessage()
# what to do: affine/warp/reformat
gd.setInsets(10, 200, 10)
gd.addCheckboxGroup(3, 2, ["affine", "01", "warp", "02", "reformat", "03"],
[True, True, True, True, True, True],
["Registration Actions", "Reformat Channels"])
#gd.addCheckboxGroup(1,3,["01","02","03"],[True,True,True],["Reformat Channels"])
# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual