paths = []
locations = []
layers = []
for i in range(0, len(transforms), 8):
alignedPatchPath = transforms[i]
alignedPatchName = os.path.basename(alignedPatchPath)
toAlignPatchName = alignedPatchName.replace('_' + factorString, '').replace('_resized', '')
toAlignPatchPath = os.path.join(MagCFolder, 'EMData', os.path.basename(os.path.dirname(alignedPatchPath)), toAlignPatchName)
toAlignPatchPath = fc.cleanLinuxPath(toAlignPatchPath[:-1]) # mysterious trailing character ...
IJ.log('toAlignPatchPath ' + toAlignPatchPath)
l = int(transforms[i+1])
paths.append(toAlignPatchPath)
locations.append([0,0])
layers.append(l)
importFilePath = fc.createImportFile(MagC_EM_Folder, paths, locations, layers = layers, name = namePlugin)
# insert the tiles in the project
IJ.log('I am going to insert many files at factor ' + str(downsamplingFactor) + ' ...')
task = loader.importImages(layerset.getLayers().get(0), importFilePath, '\t', 1, 1, False, 1, 0)
task.join()
# apply the transforms
for i in range(0, len(transforms), 8):
alignedPatchPath = transforms[i]
alignedPatchName = os.path.basename(alignedPatchPath)
toAlignPatchName = alignedPatchName.replace('_' + factorString, '').replace('_resized', '')
toAlignPatchPath = os.path.join(MagCFolder, 'EMData', os.path.basename(os.path.dirname(alignedPatchPath)), toAlignPatchName)
toAlignPatchPath = toAlignPatchPath[:-1] # why is there a trailing something !?
if toAlignPatchPath[:2] == os.sep + os.sep:
toAlignPatchPath = toAlignPatchPath[1:]
IJ.log('Assembling LM sections from all layers')
for l in range(nLayers):
IJ.log('Each section consists of ' + str(xGrid) + ' x ' + str(yGrid) +
' patches')
for y in range(yGrid):
for x in range(xGrid):
sectionFolder = os.path.join(LMDataFolder,
'section_' + str(l).zfill(4))
patchName = 'section_' + str(l).zfill(
4) + '_channel_' + channel + '_tileId_' + str(x).zfill(
2) + '-' + str(y).zfill(2) + '-tissue.tif'
patchPath = os.path.join(sectionFolder, patchName)
paths.append(patchPath)
locations.append([x * widthEffective, y * heightEffective])
layers.append(l)
# import all tiles
importFile = fc.createImportFile(LMFolder, paths, locations, layers=layers)
task = loader.importImages(layerset.getLayers().get(0), importFile, '\t', 1, 1,
False, 1, 0)
task.join()
# resize display and save
fc.resizeDisplay(layerset)
time.sleep(5)
project.save()
time.sleep(1)
fc.closeProject(project)
IJ.log('Assembling the LM project done and saved into ' + projectPath)
fc.terminatePlugin(namePlugin, MagCFolder)