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()