def list_scans(experimentFolder, microscopeType): scanList = [] # Makes an empty list # This section screens out text files and other things that might be in the main experimentFolder, and only makes a list of the actual scan directories # For Bruker microscopes, the scan directories are plain, so os.isdir is used to look for them if microscopeType == "Bruker": for File in sorted(os.listdir(experimentFolder)): dirpath = os.path.join(experimentFolder, File) # Makes a complete path to the file if os.path.isdir( dirpath ): # If the dirpath is a directory, print it and add it to scanList. If it's a file, do not add it. print "dirpath is " + dirpath scanList.append(dirpath) return scanList # Returns scanList to run_it() # If the microscope is "Olympus" type, the directories end in .oif.files, so .endswith needs to be used to find them if microscopeType == "Olympus": oifList = [ ] # This doesn't look like it was used, so I should delete it in the future once I have verified this. for File in sorted(os.listdir(experimentFolder)): if File.endswith( ".oif.files" ): # If the item ends with .oif.files, make the complete path and append it to scanList dirpath = os.path.join(experimentFolder, File) #print "dirpath is " + dirpath scanList.append(dirpath) return scanList # Returns scanList to run_it()
def microscope_check(experimentFolder): #If it finds .oif files inside the main folder, it calls the microscope "Olympus" if any(File.endswith(".oif") for File in os.listdir(experimentFolder)): print(".oif files present, running Olympus pipeline") microscopeType = "Olympus" return microscopeType #returns microscopeType to run_it() else: #If there are no .oif files in the main folder, it calls the microscope "Bruker" print("No .oif files present, running Bruker pipeline") microscopeType = "Bruker" return microscopeType #returns microscopeType to run_it()