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))
layersetZ.setDimensions(0, 0, widthEM * 5, heightEM * 5)
layerZ = layersetZ.getLayers().get(0)
# create the folders
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]
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'
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)
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'))
################################################