from ini.trakem2.utils import Utils
from ini.trakem2.display import Display, Patch
from mpicbg.trakem2.align import Align, AlignTask
import fijiCommon as fc
namePlugin = 'init_EM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
EMDataFolder = os.path.join(MagCFolder, 'EMData')
MagCEMFolder = fc.makeNeighborFolder(EMDataFolder, 'MagC_EM')
imageFolders = [
os.path.join(EMDataFolder, sectionFolderName)
for sectionFolderName in fc.naturalSort(os.walk(EMDataFolder).next()[1])
]
nSections = len(imageFolders)
IJ.log('There are ' + str(nSections) + ' EM layers')
# reading EM metadata
EMMetadataPath = os.path.join(MagCEMFolder, 'EM_Metadata.txt')
try: # old Atlas format
mosaicMetadata = os.path.join(
imageFolders[0],
filter(lambda x: 'Mosaic' in x, os.listdir(imageFolders[0]))[0])
root = ET.parse(mosaicMetadata).getroot()
pixelSize = float(root.find('PixelSize').text)
tileinfo = root.find('TileInfo')
exportedEMFolder = fc.findFoldersFromTags(
MagCFolder, ['export_alignedEMForRegistration'])[0]
exportedLMFolder = fc.findFoldersFromTags(
MagCFolder, ['exported_downscaled_1_' + channels[-1]
])[0] # finds the brightfield contrasted channel
temporaryFolder = fc.mkdir_p(
os.path.join(os.path.dirname(projectPath),
'temporary_LMEMRegistration')) # to save contrasted images
registrationFolder = fc.mkdir_p(
os.path.join(os.path.dirname(projectPath),
'LMEMRegistration')) # to save contrasted images
imPaths = {}
imPaths['EM'] = [
os.path.join(exportedEMFolder, imageName)
for i, imageName in enumerate(fc.naturalSort(os.listdir(exportedEMFolder)))
if os.path.splitext(imageName)[1] == '.tif'
]
if BIB:
imPaths['EM'] = [imPaths['EM'][o] for o in ordered_surface_ids]
# surfaceIds = [0,16,32,48,65,81,97,113,129,145,162,179,195,211,227,243,260,276,293,310] # optimal 16-17
# imPaths['EM'] = [imPaths['EM'][i] for i in surfaceIds]
imPaths['LM'] = [
os.path.join(exportedLMFolder, imageName)
for imageName in fc.naturalSort(os.listdir(exportedLMFolder))
if os.path.splitext(imageName)[1] == '.tif'
]
# get the dimensions of the EM layerset by looking at the dimensions of the first EM image, save for next script
exportedEMFolder = fc.findFoldersFromTags(
MagCFolder, ['export_alignedEMForRegistration'])[0]
exportedLMFolder = fc.findFoldersFromTags(
MagCFolder, ['exported_downscaled_1_' + channels[-1]
])[0] # finds the brightfield contrasted channel
temporaryFolder = fc.mkdir_p(
os.path.join(os.path.dirname(projectPath),
'temporary_LMEMRegistration')) # to save contrasted images
registrationFolder = fc.mkdir_p(
os.path.join(os.path.dirname(projectPath),
'LMEMRegistration')) # to save contrasted images
imPaths = {}
imPaths['EM'] = [
os.path.join(exportedEMFolder, imageName)
for imageName in fc.naturalSort(os.listdir(exportedEMFolder))
if os.path.splitext(imageName)[1] == '.tif'
]
imPaths['LM'] = [
os.path.join(exportedLMFolder, imageName)
for imageName in fc.naturalSort(os.listdir(exportedLMFolder))
if os.path.splitext(imageName)[1] == '.tif'
]
# surfaceIds = [0,16,32,48,65,81,97,113,129,145,162,179,195,211,227,243,260,276,293,310] # optimal 16-17
# imPaths['EM'] = [imPaths['EM'][i] for i in surfaceIds]
# get the dimensions of the EM layerset by looking at the dimensions of the first EM image, save for next script
imEM0 = IJ.openImage(imPaths['EM'][0])
widthEM = imEM0.width
heightEM = imEM0.height
nbLayers = EMMetadata['nSections']
IJ.log('There are ' + str(nbLayers) + ' EM layers')
##########################################
# Stitching of the low-res EM project
##########################################
allPatchCoordinates = []
downsampledFolder = os.path.join(MagC_EM_Folder, 'MagC_EM_' + factorString)
IJ.log('downsampledFolder ' + downsampledFolder)
foldersToStitch = [
os.path.join(downsampledFolder, folderName)
for folderName in os.walk(downsampledFolder).next()[1]
]
foldersToStitch = fc.naturalSort(foldersToStitch)
IJ.log('foldersToStitch ------------- ' + str(foldersToStitch))
# stitching should be done in parallel but the stitching plugin does not seem to run in parallel, so fractionCores=0 -> only one core used ...
atom = AtomicInteger(0)
fc.startThreads(parallelStitch,
fractionCores=0,
wait=0,
arguments=(atom, foldersToStitch, allPatchCoordinates))
#for k in range(len(foldersToStitch)):
# sectionFolder = foldersToStitch[k]
# tileConfigurationPath = os.path.join(sectionFolder, 'TileConfiguration_' + str(k).zfill(4) + '.registered.txt')
# stitchCommand = 'type=[Filename defined position] order=[Defined by filename ] grid_size_x=' + str(numTilesX) + ' grid_size_y=' + str(numTilesY) + ' tile_overlap=' + str(100 * (tileOverlapX + tileOverlapY)/2.) + ' first_file_index_x=0 first_file_index_y=0 directory=' + sectionFolder + ' file_names=Tile_{xx}-{yy}_resized_' + factorString + '.tif output_textfile_name=TileConfiguration_' + str(k).zfill(4) +'.txt fusion_method=[Do not fuse images (only write TileConfiguration)] regression_threshold=0.70 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap subpixel_accuracy computation_parameters=[Save computation time (but use more RAM)] image_output=[Write to disk] output_directory=' + sectionFolder
from ini.trakem2 import Project, ControlWindow
from ini.trakem2.display import Patch
from java.util.concurrent.atomic import AtomicInteger
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]
from ini.trakem2.utils import Utils
from ini.trakem2.display import Display, Patch
from mpicbg.trakem2.align import Align, AlignTask
import sys
sys.path.append(IJ.getDirectory('plugins'))
import fijiCommon as fc
namePlugin = 'init_EM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
EMDataFolder = os.path.join(MagCFolder, 'EMData')
MagCEMFolder = fc.makeNeighborFolder(EMDataFolder, 'MagC_EM')
imageFolders = [os.path.join(EMDataFolder, sectionFolderName) for sectionFolderName in fc.naturalSort(os.walk(EMDataFolder).next()[1])]
nSections = len(imageFolders)
IJ.log('There are ' + str(nSections) + ' EM layers')
# reading EM metadata
EMMetadataPath = os.path.join(MagCEMFolder, 'EM_Metadata.txt')
try: # old Atlas format
mosaicMetadata = os.path.join(imageFolders[0] , filter(lambda x: 'Mosaic' in x, os.listdir(imageFolders[0]))[0])
root = ET.parse(mosaicMetadata).getroot()
pixelSize = float(root.find('PixelSize').text)
tileinfo = root.find('TileInfo')
tileWidth = int(tileinfo.find('TileWidth').text)
tileHeight = int(tileinfo.find('TileHeight').text)
tileOverlapX = float(tileinfo.find('TileOverlapXum').text)
from java.awt.geom import AffineTransform
from java.awt import Rectangle
from java.util import HashSet, ArrayList
from ini.trakem2 import Project, ControlWindow
from ini.trakem2.display import Patch
from java.util.concurrent.atomic import AtomicInteger
namePlugin = 'alignRigid_EM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagC_EM_Folder = os.path.join(MagCFolder, 'MagC_EM','')
MagCParameters = fc.readMagCParameters(MagCFolder)
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 = 3 # 1-Rigid, 2-Similarity, 3-Affine
regParams.featuresModelIndex = 3
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
IJ.log('Rigid alignment with register virtual stack')