97 lines
4.2 KiB
Python
97 lines
4.2 KiB
Python
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import os
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import pickle
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from distutils.dir_util import copy_tree
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from shutil import copyfile
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from stack3d.study.components import StudyData, MouseData, TimepointData
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def setup_study_collection_from_remote(path):
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"""Scan the remote directory structure. Remote needs to be mounted first
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with Samba etc."""
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study_collection = []
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study_dirs = next(os.walk(path))[1]
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for study_dir in study_dirs:
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new_study = StudyData()
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new_study.raw_data_path = study_dir
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print "Set up study: ", study_dir
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mouse_dirs = next(os.walk(path + "/" + study_dir))[1]
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for mouse_dir in mouse_dirs:
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new_mouse = MouseData()
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new_mouse.raw_data_path = mouse_dir
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print "Set up mouse: ", mouse_dir
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cumulative_path = path + "/" + study_dir + "/" + mouse_dir
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if os.path.isdir(cumulative_path + "/Outputs_new_model"):
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new_mouse.extra_path = "/Outputs_new_model/"
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elif os.path.isdir(cumulative_path + "/Outputs"):
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new_mouse.extra_path = "/Outputs/"
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timepoint_dirs = next(os.walk(cumulative_path + new_mouse.extra_path))[1]
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for timepoint_dir in timepoint_dirs:
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if "TIF" not in timepoint_dir:
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new_timepoint = TimepointData()
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new_timepoint.raw_data_path = timepoint_dir
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new_mouse.timepoints.append(new_timepoint)
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new_study.mice.append(new_mouse)
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study_collection.append(new_study)
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return study_collection
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def setup_local_study_directory_structure(path, study_collection):
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for eachStudy in study_collection:
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study_dir = path + "/" + eachStudy.raw_data_path
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if not os.path.exists(study_dir):
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os.makedirs(study_dir)
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for eachMouse in eachStudy.mice:
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mouse_dir = study_dir + "/" + eachMouse.raw_data_path
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if not os.path.exists(mouse_dir):
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os.makedirs(mouse_dir)
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for eachTimePoint in eachMouse.timepoints:
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time_dir = mouse_dir + "/" + eachTimePoint.raw_data_path
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if not os.path.exists(time_dir):
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os.makedirs(time_dir)
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def copy_files(remote_path, local_path, study_collection):
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for eachStudy in study_collection:
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print "Copying Study: ", eachStudy.raw_data_path
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remote_study_dir = remote_path + "/" + eachStudy.raw_data_path
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local_study_dir = local_path + "/" + eachStudy.raw_data_path
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for eachMouse in eachStudy.mice:
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print "Copying Mouse: ", eachMouse.raw_data_path
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remote_mouse_dir = remote_study_dir + "/" + eachMouse.raw_data_path
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local_mouse_dir = local_study_dir + "/" + eachMouse.raw_data_path
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for eachTimePoint in eachMouse.timepoints:
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remote_time_dir = remote_mouse_dir + eachMouse.extra_path + "/" + eachTimePoint.raw_data_path
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local_time_dir = local_mouse_dir + "/" + eachTimePoint.raw_data_path
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if os.path.isdir(remote_time_dir + "/analysis_analysis"):
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groups = ["csv", "histograms", "plots"]
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for group in groups:
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if os.path.isdir(remote_time_dir + "/analysis_analysis/" + group):
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copy_tree(remote_time_dir + "/analysis_analysis/" + group,
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local_time_dir + "/analysis_analysis/" + group)
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if os.path.isfile(remote_time_dir + "/analysis_analysis/skeleton.pkl"):
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copyfile(remote_time_dir + "/analysis_analysis/skeleton.pkl",
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local_time_dir + "/analysis_analysis/skeleton.pkl")
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#
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work_dir = "/scratch/jgrogan/stack-working/study/"
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samba_path = os.environ["XDG_RUNTIME_DIR"] + "/gvfs/"
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raw_data_path = samba_path + "smb-share:server=imcore1.rob.ox.ac.uk,share=maths"
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raw_data_path += "/Window Experiments/James/Network analysis/"
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# study_collection = setup_study_collection_from_remote(raw_data_path)
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# f = open(work_dir + "/study_collection.p", "wb")
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# pickle.dump(study_collection, f)
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f = open(work_dir + "/study_collection.p", 'r')
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study_collection = pickle.load(f)
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#setup_local_study_directory_structure(work_dir, study_collection)
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copy_files(raw_data_path, work_dir, study_collection)
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