while l.get() < min(nLayers, currentWrittenLayer + nLayersAtATime + 1) :
k = l.getAndIncrement()
if k < min(nLayers, currentWrittenLayer + nLayersAtATime):
IJ.log('Start montaging elastically layer ' + str(k))
if layerset.getLayers().get(k).getNDisplayables() > 1: # some EM projects have a single large tile
AlignTask().montageLayers(params, layerset.getLayers(k, k))
namePlugin = 'montage_ElasticEM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
nLayersAtATime = MagCParams[namePlugin]['nLayersAtATime']
nThreads = MagCParams[namePlugin]['nThreads']
projectPath = fc.cleanLinuxPath(fc.findFilesFromTags(MagCFolder,['EM', 'Project'])[0])
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
IJ.log('Sleeping in case the opening of the large project takes some time ...')
time.sleep(20)
# parameters for elastic montage
params = ElasticMontage.Param().clone()
params.bmScale = 0.5
params.bmSearchRadius = 50
params.bmBlockRadius = 50
params.bmMinR = 0.1
params.bmMaxCurvatureR = 100
params.bmRodR = 1
import sys
sys.path.append(IJ.getDirectory('plugins'))
import fijiCommon as fc
from mpicbg.trakem2.align import RegularizedAffineLayerAlignment
from java.awt.geom import AffineTransform
from java.awt import Rectangle
from java.util import HashSet
from ini.trakem2.display import Patch
from ini.trakem2.imaging import Blending
from ini.trakem2 import Project, ControlWindow
namePlugin = 'export_LMChannels'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
transformsPath = fc.findFilesFromTags(MagCFolder, ['LM', 'transforms'])[0]
with (open(transformsPath, 'r')) as f:
transforms = f.readlines()
nLayers = max([int(transforms[i]) for i in range(1, len(transforms), 8)]) + 1
IJ.log('nLayers = ' + str(nLayers))
width, height, nChannels, xGrid, yGrid, scaleX, scaleY, channels = fc.readSessionMetadata(
MagCFolder)
MagCParameters = fc.readMagCParameters(MagCFolder)
scaleFactors = MagCParameters[namePlugin][
'scaleFactors'] # scale factor for export, typically 1 and 0.1
flipX = MagCParameters[namePlugin]['flipX']
IJ.log('Iterating over the LM channels')
for channel in channels:
from java.util import HashSet from ini.trakem2 import Project, ControlWindow from ini.trakem2.display import Patch 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
from distutils.dir_util import copy_tree
namePlugin = 'export_TransformedCroppedLM'
MagCFolder = fc.startPlugin(namePlugin)
# MagCFolder = r'E:\Users\Thomas\MixturesClean\MinimalPipelineTest5Sections_OneMoreTest04_07_17'
ControlWindow.setGUIEnabled(False)
width, height, nChannels, xGrid, yGrid, scaleX, scaleY, channels = fc.readSessionMetadata(
MagCFolder)
# channels = ['Brightfield', 'GFP', 'DsRed', 'contrastedBrightfield']
LMFolder = os.path.join(MagCFolder, 'MagC_LM')
projectPath = fc.findFilesFromTags(
MagCFolder,
['EM', 'Project'
])[0] # should I make 2 projects ? One for rigid, one for warped ?
exportedEMFolder = fc.findFoldersFromTags(
MagCFolder, ['export_alignedEMForRegistration'])[0]
nLayers = len(os.listdir(exportedEMFolder))
registrationFolder = os.path.join(os.path.dirname(projectPath),
'LMEMRegistration')
f = open(os.path.join(registrationFolder, 'lowResEMBounds'), 'r')
widthEM, heightEM = pickle.load(f)
f.close()
pZ, loaderZ, layersetZ, nLayersZ = fc.getProjectUtils(
fc.initTrakem(registrationFolder, 1))
[l, distance, len(inliers)])
namePlugin = 'compute_RegistrationMovingLeastSquares'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
matchingThreshold = MagCParams[namePlugin][
'matchingThreshold'] # rejection threshold for the mean displacement of the transforms for the low and high resolution steps, respectively
nOctaves = MagCParams[namePlugin]['nOctaves']
width, height, nChannels, xGrid, yGrid, scaleX, scaleY, channels = fc.readSessionMetadata(
MagCFolder)
EMMetadataPath = fc.findFilesFromTags(MagCFolder, ['EM', 'Metadata'])[0]
nSections = fc.readParameters(EMMetadataPath)['nSections']
# nSections = 20
BIB = False
ordered_surface_ids_path = [
os.path.join(MagCFolder, n) for n in os.listdir(MagCFolder)
if 'ordered_surface_ids' in n
]
if len(ordered_surface_ids_path) != 0:
ordered_surface_ids_path = ordered_surface_ids_path[0]
ordered_surface_ids = readIds(ordered_surface_ids_path)
BIB = True
projectPath = fc.findFilesFromTags(MagCFolder, ['EM', 'Project'])[0]
if not os.path.isfile(resizedFilePath):
im = fc.resize(im, scaleFactor)
FileSaver(im).saveAsTiff(resizedFilePath)
IJ.log('Image resized to ' + resizedFilePath)
im.close()
namePlugin = 'downsample_EM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParameters = fc.readMagCParameters(MagCFolder)
EMDataFolder = os.path.join(MagCFolder, 'EMData')
MagCEMFolder = os.path.join(MagCFolder, 'MagC_EM')
# read metadata
EMMetadataPath = fc.findFilesFromTags(MagCFolder,['EM_Metadata'])[0]
EMMetadata = fc.readParameters(EMMetadataPath)
tileWidth = int(EMMetadata['tileWidth'])
tileHeight = int(EMMetadata['tileHeight'])
IJ.log('TileWidth ' + str(tileWidth))
IJ.log('TileHeight ' + str(tileHeight))
cropRoi = Roi(100, 20, tileWidth - 2*100, tileHeight-20) # remove first lines because the Zeiss API
# read downsampling factor
downsamplingFactor = MagCParameters[namePlugin]['downsamplingFactor']
scaleFactor = 1./downsamplingFactor
factorString = str(int(1000000*downsamplingFactor)).zfill(8)
filePathsPath = os.path.join(MagCEMFolder, 'imagePathsForDownsampling' + factorString + '.txt')
nTilesAtATime = MagCParameters[namePlugin]['nTilesAtATime']
IJ.log('Start montaging elastically layer ' + str(k))
if layerset.getLayers().get(k).getNDisplayables(
) > 1: # some EM projects have a single large tile
AlignTask().montageLayers(params, layerset.getLayers(k, k))
namePlugin = 'montage_ElasticEM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
nLayersAtATime = MagCParams[namePlugin]['nLayersAtATime']
nThreads = MagCParams[namePlugin]['nThreads']
projectPath = fc.cleanLinuxPath(
fc.findFilesFromTags(MagCFolder, ['EM', 'Project'])[0])
projectPath = os.sep + projectPath
IJ.log('projectPath ----------' + str(projectPath))
IJ.log('os.path.isfile(projectPath)------- ' +
str(os.path.isfile(projectPath)))
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
IJ.log('Sleeping in case the opening of the large project takes some time ...')
time.sleep(20)
# parameters for elastic montage
params = ElasticMontage.Param().clone()
params.bmScale = 0.5
params.bmSearchRadius = 50
params.bmBlockRadius = 50
resultRigidAlignmentFolder,
resultRigidAlignmentFolder, referenceName,
regParams, use_shrinking_constraint)
time.sleep(2)
# IJ.getImage().close()
WindowManager.closeAllWindows()
IJ.log('Rigid Alignment done')
else:
IJ.log('Rigid alignment already performed - skipping')
################################################
###########################################
IJ.log('Aligning the lowEM with the new rigid transforms')
projectPath = fc.cleanLinuxPath(
fc.findFilesFromTags(MagCFolder,
['EMProject_'])[0]) # this is the low res EM
project, loader, layerset, nLayers = fc.openTrakemProject(
projectPath) # the low res EM
for l, layer in enumerate(layerset.getLayers()):
transformPath = os.path.join(
resultRigidAlignmentFolder,
'stitchedDownsampledEM_' + str(l).zfill(4) + '.xml')
theList = ArrayList(HashSet())
aff = fc.getAffFromRVSTransformPath(transformPath)
for patch in layer.getDisplayables(Patch):
patch.setLocation(
patch.getX(),
patch.getY()) # compensate for the extracted bounding box
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
if os.path.isfile(orderPath):
newOrder = fc.readOrder(orderPath)
else:
newOrder = range(10000)
# Reorder both the low EM and the EM projects
## low EM
# downsamplingFactor
downsamplingFactor = MagCParameters['downsample_EM']['downsamplingFactor']
factorString = str(int(1000000 * downsamplingFactor)).zfill(8)
MagCEMFolder = os.path.dirname(
fc.cleanLinuxPath(
fc.findFilesFromTags(MagCFolder,
['montage_ElasticEM_Transforms.txt'])[0]))
projectPath = fc.cleanLinuxPath(
os.path.join(MagCEMFolder, 'EMProject_' + factorString +
'.xml')) # this is the low res EM project
unorderedProjectPath = fc.cleanLinuxPath(
os.path.join(MagCEMFolder, 'LowEMProjectUnordered.xml'))
# if a reordering had already been made, reinitialize the unordered project
if os.path.isfile(unorderedProjectPath):
if os.path.isfile(projectPath):
os.remove(projectPath)
shutil.copyfile(unorderedProjectPath, projectPath)
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
project.saveAs(projectPath, True)
fc.closeProject(project)
################################################
# 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
IJ.log('Rigid alignment with register virtual stack')
Register_Virtual_Stack_MT.exec(exportForRigidAlignmentFolder, resultRigidAlignmentFolder, resultRigidAlignmentFolder, referenceName, regParams, use_shrinking_constraint)
time.sleep(2)
# IJ.getImage().close()
WindowManager.closeAllWindows()
IJ.log('Rigid Alignment done')
################################################
###########################################
IJ.log('Aligning the lowEM with the new rigid transforms')
projectPath = fc.cleanLinuxPath(fc.findFilesFromTags(MagCFolder,['EMProject_'])[0]) # this is the low res EM
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath) # the low res EM
for l, layer in enumerate(layerset.getLayers()):
transformPath = os.path.join(resultRigidAlignmentFolder, 'stitchedDownsampledEM_' + str(l).zfill(4) + '.xml')
theList = ArrayList(HashSet())
aff = fc.getAffFromRVSTransformPath(transformPath)
for patch in layer.getDisplayables(Patch):
patch.setLocation(patch.getX(), patch.getY()) # compensate for the extracted bounding box
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
patch.setAffineTransform(currentAff)
fc.resizeDisplay(layerset)
project.save()
fc.closeProject(project)
