#!/usr/bin/env python #----------------------------------------------------------------------- # General script to setup standard Xmipp protocols # - Preprocessing of micrographs # - Manual particle picking # - Preprocessing of extracted particles # - 2D image alignment and classification (by ML2D, CL2D & kerdenSOM) # - 2D image analysis by classification of rotational spectra # - 3D classification by ml3D # - 3D projection matching refinement # # Example use: # ./setup_protocols.py # # {please cite} The Xmipp team (2007) Nature Protocols, 3, 977-990 # # Author: Sjors Scheres, March 2007 #------------------------------------------------------------------------ # Choose the protocol(s) you want to setup: #------------------------------------------------------------------------ # {setup-} This is need to recognize this script as setup #------------------------------------------------------------------------ # {section} Global Parameters #------------------------------------------------------------------------ # Absolute path to the root directory name for this project: ProjectDir='/media/usbdisk/Experiments/TestProtocols/Protocol_Small' # System flavour for parallelization SystemFlavour='' # Directory name for logfiles: LogDir='Logs' # #------------------------------------------------------------------------------------------------ #------------------------------------------------------------------------------------------------ # {end-of-header} USUALLY YOU DO NOT NEED TO MODIFY ANYTHING BELOW THIS LINE ... #------------------------------------------------------------------------------------------------ #------------------------------------------------------------------------------------------------ # class setup_protocols_class: #init variables def __init__(self, ProjectDir, SystemFlavour, LogDir, AutoLaunch): import os,sys self.ProjectDir=ProjectDir self.SystemFlavour=SystemFlavour self.LogDir=LogDir self.AutoLaunch=AutoLaunch scriptdir = os.path.split(os.path.dirname(os.popen('which xmipp_protocols','r').read()))[0]+'/protocols' sys.path.append(scriptdir) # add default search path self.SYSTEMSCRIPTDIR=scriptdir # Which protocols will appears in main windows self.LaunchSections = ["Preprocessing", "2D Analysis", "3D Analysis"] self.LaunchButtons = {}; ####### Preprocessing self.LaunchButtons['SetupPreProcessMicrographs'] = {'title': 'Preprocess micrographs', 'script': 'xmipp_protocol_preprocess_micrographs.py', 'section': 'Preprocessing'} self.LaunchButtons['SetupParticlePick'] = {'title': 'Particle selection', 'script': 'xmipp_protocol_particle_pick.py', 'section': 'Preprocessing'} self.LaunchButtons['SetupPreProcessParticles'] = {'title': 'Preprocess particles', 'script': 'xmipp_protocol_preprocess_particles.py', 'section': 'Preprocessing'} ######## 2D Analysis self.LaunchButtons['SetupAlign'] = {'title': 'Align', 'section': '2D Analysis', 'childs': 'SetupML2D, SetupCL2D'} self.LaunchButtons['SetupAlignClassify'] = {'title': 'Align + Classify', 'section': '2D Analysis', 'childs': 'SetupML2D, SetupCL2D'} self.LaunchButtons['SetupClassify'] = {'title': 'Classify', 'section': '2D Analysis', 'childs': 'SetupKerDenSOM, SetupRotSpectra'} self.LaunchButtons['SetupML2D'] = {'title': 'ML2D', 'script': 'xmipp_protocol_ml2d.py'} self.LaunchButtons['SetupCL2D'] = {'title': 'CL2D', 'script': 'xmipp_protocol_cl2d.py'} self.LaunchButtons['SetupKerDenSOM'] = {'title': 'KerDenSOM', 'script': 'xmipp_protocol_kerdensom.py'} self.LaunchButtons['SetupRotSpectra'] = {'title': 'Rotational Spectra', 'script': 'xmipp_protocol_rotspectra.py'} ####### 3D Analysis self.LaunchButtons['SetupInitialModel'] = {'title': 'Initial Model', 'section': '3D Analysis', 'childs': 'SetupCommonLines, SetupRCT'} self.LaunchButtons['SetupCommonLines'] = {'title': 'Common lines', 'script': 'xmipp_protocol_commonlines.py'} self.LaunchButtons['SetupRCT'] = {'title': 'Random Conical Tilt', 'script': 'xmipp_protocol_rct.py'} self.LaunchButtons['Setup3DClassify'] = {'title': 'ML3D Classification', 'section': '3D Analysis', 'script': 'xmipp_protocol_ml3d.py'} self.LaunchButtons['SetupModelRefine'] = {'title': 'Model refinement', 'section': '3D Analysis', 'script': 'xmipp_protocol_projmatch.py'} # For automated editing of default directories in protocols self.DEFAULTDIRS={"ProjectDir":self.ProjectDir, "LogDir":self.LogDir, "SystemFlavour":self.SystemFlavour } # Perform the actual setup: if (self.AutoLaunch != ""): # A. Setup from GUI (Autolaunch) # This will copy the (modified) protocol script to the corresponding directory # and will automatically launch the GUI for this protocol self.setup_protocol(self.AutoLaunch) else: # B. Setup from this script: # This will only copy the (modified) protocol script to the corresponding directory for buttonData in self.LaunchButtons: if 'script' in buttonData: self.setup_protocol(buttonData['script']) def modify_script_header(self,src): import sys # Read script header and body fh=open(src,'r') header_lines=[] body_lines=[] isheader=False while (isheader!=True): line=fh.readline() if line=="": print "Error, this file does not have a {end-of-header} label" sys.exit() header_lines.append(line) if (line.find('{end-of-header}') > -1): isheader=True body_lines=fh.readlines() fh.close() # Loop over all project-related directories and preset default directories for dir in self.DEFAULTDIRS: # Only change DEFAULTDIRS if entry is not empty in the setup protocol if (len(self.DEFAULTDIRS[dir]) > 0): newheader_lines=[] for line in header_lines: if ( (not line[0]=="#" and not line[0]==" " and not line[0]=="\t" and not line[0]=="\n" and not line[0]=="\"") and (line.find(dir) > -1) ): args=line.split("=") lineb=str(args[0])+'=\"'+self.DEFAULTDIRS[dir]+'\"\n' else: lineb=line newheader_lines.append(lineb) header_lines=newheader_lines return header_lines+body_lines def setup_protocol(self,protocol): import os import shutil os.chdir(self.ProjectDir) visualize=protocol.replace('xmipp_protocol','visualize') myscripts=[protocol, visualize] for script in myscripts: src=str(self.SYSTEMSCRIPTDIR)+"/"+str(script) dst=str(script) if os.path.exists(dst): src=dst print "* File "+dst+" already existed (now updated)" elif (not os.path.exists(src)): src=str(self.SYSTEMSCRIPTDIR)+"/not_implemented.py" text=self.modify_script_header(src) fh=open(dst,'w') fh.writelines(text) fh.close() os.chmod(dst,0755) # Only auto-launch the first script if (self.AutoLaunch!=""): command='python '+str(self.SYSTEMSCRIPTDIR)+'/xmipp_protocol_gui.py '+str(protocol)+' &' os.system(command) # # Main # if __name__ == '__main__': import sys if (len(sys.argv) < 2): AutoLaunch="" else: AutoLaunch=sys.argv[1] setup = setup_protocols_class(ProjectDir, SystemFlavour, LogDir, AutoLaunch)