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)