def main(argv):
"""Register the slices in a stack."""
source_dir = 'SOURCE_DIR/'
target_dir = 'TARGET_DIR/'
transf_dir = 'TARGET_DIR/trans/'
reference_name = 'REFNAME'
use_shrinking_constraint = 0
p = Register_Virtual_Stack_MT.Param()
p.sift.maxOctaveSize = 1024
p.minInlierRatio = 0.05
Register_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir,
reference_name, p, use_shrinking_constraint)
def Composite_Aligner(channels, dirs, parameters):
""" Aligns composite images, saves to directory. """
# Reference image name (must be within source directory)
reference_name = "Timepoint000.tif"
# Shrinkage option (False = 0)
if parameters["shrinkage"] == "True":
use_shrinking_constraint = 1
print "shrink"
else:
use_shrinking_constraint = 0
print "noshrink"
# Parameters method, RVSS
p = Register_Virtual_Stack_MT.Param()
# SIFT parameters:
# python cannot coerce string "floats" to int directly,
# hence int(float("1.0")) (RVSS wants ints..).
p.sift.maxOctaveSize = int(float(parameters["max_oct"]))
p.sift.fdSize = int(float(parameters["fd_size"]))
p.sift.initialSigma = int(float(parameters["sigma"]))
p.maxEpsilon = int(float(parameters["max_eps"]))
p.sift.steps = int(float(parameters["steps"]))
p.minInlierRatio = int(float(parameters["min_inlier"]))
# 1 = RIGID, 3 = AFFINE
p.featuresModelIndex = int(float(parameters["feat_model"]))
p.registrationModelIndex = int(float(parameters["reg_model"]))
# Opens a dialog to set transformation options, comment out to run in default mode
#IJ.beep()
#p.showDialog()
# Executes alignment.
print ("Registering stack...")
reference_name = "Timepoint000.tif"
Register_Virtual_Stack_MT.exec(dirs["Composites"] + os.sep,
dirs["Composites_Aligned"] + os.sep,
dirs["Transformations"] + os.sep,
reference_name, p, use_shrinking_constraint)
print ("Registration completed.")
# Close alignment window.
imp = WindowManager.getCurrentImage()
imp.close()
def rigidAlignment(projectPath, params, name = '', boxFactor = 1):
# rigid alignment outside trakem2 with register virtual stack plugin because bug in trakem2
projectFolder = os.path.dirname(projectPath)
projectName = os.path.splitext(os.path.basename(projectPath))[0]
project, loader, layerset, nLayers = openTrakemProject(projectPath)
exportForRigidAlignmentFolder = mkdir_p(os.path.join(projectFolder, 'exportForRigidAlignment'))
resultRigidAlignmentFolder = mkdir_p(os.path.join(projectFolder, 'resultRigidAlignment'))
bb = layerset.get2DBounds()
roi = Rectangle(int(bb.width/2 * (1 - boxFactor)), int(bb.height/2 * (1 - boxFactor)), int(bb.width*boxFactor), int(bb.height*boxFactor))
boxPath = os.path.join(resultRigidAlignmentFolder, 'alignmentBox.txt')
writeRectangle(roi, boxPath)
exportFlat(project, exportForRigidAlignmentFolder, 1, baseName = 'exportForRigidAlignment', roi = roi)
referenceName = naturalSort(os.listdir(exportForRigidAlignmentFolder))[0]
use_shrinking_constraint = 0
IJ.log('Rigid alignment with register virtual stack')
Register_Virtual_Stack_MT.exec(exportForRigidAlignmentFolder, resultRigidAlignmentFolder, resultRigidAlignmentFolder, referenceName, params, use_shrinking_constraint)
time.sleep(2)
IJ.log('Warning: rigidAlignment closing all existing windows')
WindowManager.closeAllWindows() # problematic because it also closes the log window
# IJ.getImage().close()
for l, layer in enumerate(layerset.getLayers()):
imagePath = os.path.join(exportForRigidAlignmentFolder, 'exportForRigidAlignment_' + str(l).zfill(4) + '.tif')
transformPath = os.path.join(resultRigidAlignmentFolder, 'exportForRigidAlignment_' + str(l).zfill(4) + '.xml')
aff = getAffFromRVSTransformPath(transformPath)
for patch in layer.getDisplayables(Patch):
patch.setLocation(patch.getX()-roi.x, patch.getY()-roi.y) # compensate for the extracted bounding box
# patch.setLocation(roi.x, roi.y) # compensate for the extracted bounding box
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
patch.setAffineTransform(currentAff)
resizeDisplay(layerset)
project.save()
closeProject(project)
IJ.log('All LM layers have been aligned in: ' + projectPath)
def runVirtualAlignment(self):
IJ.log("Function runVirtualAlignment on " + self.inputFolder)
refImage = None
for (DAPIFile, fluoFiles) in self.imageFiles:
copyfile(DAPIFile,
self.inputDAPIFolder + os.path.basename(DAPIFile))
for fluoFile in fluoFiles:
copyfile(fluoFile,
self.inputFluoFolder + os.path.basename(fluoFile))
if refImage is None:
refImage = os.path.basename(self.inputDAPIFolder +
os.path.basename(DAPIFile))
p = Register_Virtual_Stack_MT.Param()
use_shrinking_constraint = self.useShrinking
IJ.log("Registering DAPI")
Register_Virtual_Stack_MT.exec(self.inputDAPIFolder,
self.outputDAPIFolder,
self.outputDAPIFolder, refImage, p,
use_shrinking_constraint)
IJ.log("Copying DAPI transformation matrices to Fluo folder")
for (DAPIFile, fluoFiles) in self.imageFiles:
for fluoFile in fluoFiles:
copyfile(
self.outputDAPIFolder +
os.path.basename(DAPIFile).replace(".tif", ".xml"),
self.outputFluoFolder +
os.path.basename(fluoFile).replace(".tif", ".xml"))
use_interpolate = self.useInterpolate
IJ.log("Registering Fluo based on DAPI transformations")
Transform_Virtual_Stack_MT.exec(self.inputFluoFolder,
self.outputFluoFolder,
self.outputFluoFolder, use_interpolate)
self.displayStack()
from register_virtual_stack import Register_Virtual_Stack_MT namePlugin = 'alignRigid_LM' MagCFolder = fc.startPlugin(namePlugin) ControlWindow.setGUIEnabled(False) # get mosaic size MagCParameters = fc.readMagCParameters(MagCFolder) executeAlignment = MagCParameters[namePlugin]['executeAlignment'] boxFactor = MagCParameters[namePlugin]['boxFactor'] # e.g. 0.5, use only the center part of the layer to compute alignment: 0.5 divides the x and y dimensions by 2 projectPath = fc.findFilesFromTags(MagCFolder,['LMProject'])[0] # alignment parameters regParams = Register_Virtual_Stack_MT.Param() regParams.minInlierRatio = 0 regParams.registrationModelIndex = 1 regParams.featuresModelIndex = 1 regParams.sift.fdBins = 8 regParams.sift.fdSize = 4 regParams.sift.initialSigma = 1.6 regParams.sift.maxOctaveSize = 1024 regParams.sift.minOctaveSize = 64 regParams.sift.steps = 6 regParams.interpolate = True regParams.maxEpsilon = 25 regParams.minInlierRatio = 0 regParams.rod = 0.92
for c in range(1,(xdim+1)):
cs= str(c)
# source directory
source_dir = ISanalysisfolder + "%04d" % i + "/aligned/conv_561adj/c_" + cs + "/"
# output directory
# transforms directory
transf_dir = ISanalysisfolder + "%04d" % i + "/aligned/conv_561adj/c_" + cs + "/"
# reference image
file = (glob.glob(source_dir + "*" + ".tif"))
print >>f1, os.path.basename(file[0])
reference_name = os.path.basename(file[0])
# shrinkage option (false)
use_shrinking_constraint = 0
p = Register_Virtual_Stack_MT.Param()
p.featuresModelIndex = 0
p.registrationModelIndex = 0
p.interpolate = 1
p.maxEpsilon = 25
# The "maximum image size":
p.sift.maxOctaveSize = 400
p.sift.fdBins = 8
p.sift.fdSize = 8
p.sift.initialSigma = 1.0
p.sift.steps = 6
p.sift.minOctaveSize = 64
# The "inlier ratio":
p.minInlierRatio = 0.03
iterat = 0
## script to run Register_Virtual_Stack as CLI based on http://imagej.net/Register_Virtual_Stack_Slices#Scripting_.2F_PlugIn import sys # to get command line args # import argparse # fiji's jython does not have argparse: https://ilovesymposia.com/2014/02/26/fiji-jython/ from register_virtual_stack import Register_Virtual_Stack_MT argv = sys.argv # shrinkage option (false) use_shrinking_constraint = 0 ## http://javadoc.imagej.net/Fiji/register_virtual_stack/Register_Virtual_Stack_MT.html p = Register_Virtual_Stack_MT.Param() # p.sift.maxOctaveSize = 1024 # The "maximum image size" # p.minInlierRatio = 0.05 # The "inlier ratio" p.featuresModelIndex = Register_Virtual_Stack_MT.RIGID # 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE p.registrationModelIndex = Register_Virtual_Stack_MT.RIGID # 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE, 4=ELASTIC, 5=MOVING_LEAST_SQUARES Register_Virtual_Stack_MT.save_transforms= True Register_Virtual_Stack_MT.exec(argv[1], argv[2], argv[3], argv[4], p, use_shrinking_constraint)
format='tiff')
featuremodelindex = ["Translation", "Rigid", "Similarity", "Affine"]
regmodelindex = [
"Translation", "Rigid", "Similarity", "Affine", "Elastic",
"Moving Least Squares"
]
fmi = featuremodelindex.index(fmodelstring)
rmi = regmodelindex.index(rmodelstring)
# shrinkage option (false)
use_shrinking_constraint = False
p = Register_Virtual_Stack_MT.Param()
# inlier ratio
p.minInlierRatio = 0.05
# implemented transformation models for choice 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE
#p.featuresModelIndex = 3
p.featuresModelIndex = fmi
# maximal allowed alignment error in pixels
p.maxEpsilon = 10
# Implemented transformation models for choice 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE, 4=ELASTIC, 5=MOVING_LEAST_SQUARES
#p.registrationModelIndex = 3
p.registrationModelIndex = rmi
# Closest/next neighbor distance ratio
p.rod = 0.9
############# bunwarpJ Parameters #########
namePlugin = 'alignRigid_EM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagC_EM_Folder = os.path.join(MagCFolder, 'MagC_EM', '')
MagCParameters = fc.readMagCParameters(MagCFolder)
regModel = MagCParameters[namePlugin]['regModel']
inputFolder = fc.findFoldersFromTags(MagCFolder,
['export_stitchedEMForAlignment'])[0]
imagePaths = filter(
lambda x: os.path.splitext(x)[1] == '.tif',
fc.naturalSort(
[os.path.join(inputFolder, x) for x in os.listdir(inputFolder)]))
regParams = Register_Virtual_Stack_MT.Param()
regParams.minInlierRatio = 0
regParams.registrationModelIndex = regModel # 1-Rigid, 2-Similarity, 3-Affine
regParams.featuresModelIndex = regModel
exportForRigidAlignmentFolder = inputFolder
resultRigidAlignmentFolder = fc.mkdir_p(
os.path.join(MagC_EM_Folder, 'resultRigidAlignment'))
################################################
# rigid alignment outside trakem2 with register virtual stack plugin because bug in trakem2
transformsPath = os.path.join(
MagC_EM_Folder, 'rigidAlignmentTransforms_' + namePlugin + '.txt')
referenceName = fc.naturalSort(os.listdir(exportForRigidAlignmentFolder))[0]
use_shrinking_constraint = 0
from register_virtual_stack import Register_Virtual_Stack_MT # source directory source_dir = "C:\\Users\\stoeter\\Documents\\Temp\\sequence_GreinerGlassPlate_GSP_500nm_beads_H12_T0001F001_raw_xx_plane6\\" # output directory target_dir = "C:\\Users\\stoeter\\Documents\\Temp\\result\\" # transforms directory transf_dir = "C:\\Users\\stoeter\\Documents\\Temp\\transform\\" # reference image reference_name = "GreinerGlassPlate_GSP_500nm_beads_H12_T0001F001_raw_01_plane6.tif" # shrinkage option (false) use_shrinking_constraint = 0 p = Register_Virtual_Stack_MT.Param() # The "maximum image size": p.sift.maxOctaveSize = 2800 # The "inlier ratio": p.minInlierRatio = 0.05 # Implemented transformation models for choice # 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE, 4=ELASTIC, 5=MOVING_LEAST_SQUARES p.registrationModelIndex = 3 # Implemented transformation models for choice # 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE p.featuresModelIndex = 3 Register_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir, reference_name, p, use_shrinking_constraint)