# The list of files.
#imFileNames = ["test_file.nrrd", "test_file2.nrrd", "test_file3.nrrd"]
# The list of roi files (Needs to have same number of entries as .im files above).
#roiFileNames = ["test_file.rois.zip", "test_file2.rois.zip", "test_file3.rois.zip"]
# List of statistics.
# Others: "mean", "stddev", "median", "N/D",
# "min", "max", "sum", "mode", "area",
# "group", "roix", "roiy",
# "roiwidth", "roiheight"
stats = ["group", "area", "mean", "stddev", "N/D"]
#////////////////////////////
# Initialize stuff.
#////////////////////////////
ui = UI()
ui.show()
#////////////////////////////
# Loop over files.
#////////////////////////////
for i in range(len(imFileNames)):
imFile = File(imFileNames[i])
roiFile = File(roiFileNames[i])
#IJ.log("Opening: "+imFileNames[i])
ui.openFile(imFile)
#IJ.log("Opening: "+roiFileNames[i])
ui.openFile(roiFile)
#////////////////////////////
imFileName = ["test_file.nrrd", "test_file2.nrrd", "test_file3.nrrd"]
# The list of roi files (Needs to have same number of entries as .im files above).
roiFileName = ["test_file.rois.zip", "test_file2.rois.zip", "test_file3.rois.zip"]
# List of statistics.
# Others: "mean", "stddev", "median", "N/D",
# "min", "max", "sum", "mode", "area",
# "group (table only)", "roix", "roiy",
# "roiwidth", "roiheight"
stats = ["mean", "stddev"]
#////////////////////////////
# Initialize stuff.
#////////////////////////////
ui = UI()
ui.show()
#////////////////////////////
# Loop over files.
#////////////////////////////
for i in range(len(imFileName)):
#where is this going?
#print "Opening: " #+ imFileName[i] + ", " roiFileName[i]
imFile = File(imDirName, imFileName[i])
roiFile = File(imDirName, roiFileName[i])
IJ.log("Opening: "+imFileName[i])
ui.openFile(imFile)
IJ.log("Opening: "+roiFileName[i])
ui.openFile(roiFile)
import com.nrims.data as nrimsData
import com.nrims.UI as nrimsUI
import java.io.File as File
import java.lang as lang
import java.util.ArrayList as ArrayList
import java.lang.Integer as Integer
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/")
import os
import jarray
IJ.log("Starting auto Turbo reg")
ui = nrimsUI.getInstance()
if ui == None:
IJ.log("No instance of OpenMims window")
else:
openSum = ui.getOpenSumImages()
if len(openSum) != 0:
#copy sum and source image
#setting sum image to first one for testing's sake
sumImage = openSum[0]
target = sumImage.duplicate()
source = IJ.getImage().duplicate()
#scale image
targetProcessor = target.getProcessor()
import java.io.File as File
import java.lang as lang
import java.util.ArrayList as ArrayList
import java.lang.Integer as Integer
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/")
import os
import jarray
#////////////////////////////
# Get existing instance of OpenMims
#////////////////////////////
IJ.log("Starting auto Turbo reg")
ui = nrimsUI.getInstance()
if ui == None:
IJ.log("No instance of OpenMims window")
else:
openSum = ui.getOpenSumImages()
if len(openSum) != 0:
#////////////////////////////
# copy sum and source image
# source = image we want to modify through turboreg
# target = image that we are fitting source to
# note: setting sum image to first one for testing's sake, ideally we'll find another solution
#////////////////////////////
sumImage = openSum[0]
target = sumImage.duplicate()
source = IJ.getImage().duplicate()
from org.jfree.data.xy import DefaultXYDataset
from java.awt import Color, Rectangle
print "\nStarting 'QSA-ScatterPlot'."
print "Grab images."
#imgA = WindowManager.getImage("25.90:test_file")
#imgB = WindowManager.getImage("26.93/25.90:test_file")
imgA = WindowManager.getImage("12.12:test_file")
imgB = WindowManager.getImage("13.01/12.12:test_file")
ui = UI.getInstance()
rois = ui.getRoiManager().getAllROIs()
print "Create empty dataset"
dataset = DefaultXYDataset()
print "Create ScatterPlot"
chart = ChartFactory.createScatterPlot(
"Scatter Plot", imgA.getTitle(), imgB.getTitle(),
dataset, PlotOrientation.VERTICAL,
True, False, False);
# random test data
#
#print "Add series to dataset"
# The list of files.
#imFileNames = ["test_file.nrrd", "test_file2.nrrd", "test_file3.nrrd"]
# The list of roi files (Needs to have same number of entries as .im files above).
#roiFileNames = ["test_file.rois.zip", "test_file2.rois.zip", "test_file3.rois.zip"]
# List of statistics.
# Others: "mean", "stddev", "median", "N/D",
# "min", "max", "sum", "mode", "area",
# "group", "roix", "roiy",
# "roiwidth", "roiheight"
stats = ["group", "area", "mean", "stddev", "N/D"]
#////////////////////////////
# Initialize stuff.
#////////////////////////////
ui = UI()
ui.show()
#////////////////////////////
# Loop over files.
#////////////////////////////
for i in range(len(imFileNames)):
imFile = File(imFileNames[i])
roiFile = File(roiFileNames[i])
#IJ.log("Opening: "+imFileNames[i])
ui.openFile(imFile)
#IJ.log("Opening: "+roiFileNames[i])
ui.openFile(roiFile)
#////////////////////////////