Writing network_measures to structure

[JohannesWiesner]

I stumbled upon this thread on google groups because I am facing the same problem. It would be nice if network measures could be exported in a structured form (.mat, .json, etc.). Since the question is already 3 years I wonder if this has been implemented in the meantime?

[frankyeh]

I am sorry that there is still no .mat .jason output. My solution is to write a text reader in MATLAB or python. It seems to only need few lines of code to complete the task.

…

On Wed, Jun 30, 2021 at 8:02 AM JohannesWiesner ***@***.***> wrote: I stumbled upon this thread on google groups <https://groups.google.com/g/dsi-studio/c/rq2FJRvtE6I/m/Pcd9Pc7VAwAJ> because I am facing the same problem. It would be nice if network measures could be exported in a structured form (.mat, .json, etc.). Since the question is already 3 years I wonder if this has been implemented in the meantime? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#61>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACDI4MZG63TSUKFCBV3HWDTVMBTPANCNFSM47SF23XQ> .

[JohannesWiesner]

No worries! :) I just wanted to make sure that I haven't overseen something :) Alright, I will write a python script then to parse the *network_measures.txt into a python dictionary or .json file

[JohannesWiesner]

Just for completeness - here's my code (could probably be optimized but does what it is supposed to do):

def isFloat(string):
    try:
        float(string)
        return True
    except ValueError:
        return False

with open('571144.src.gz.hcp1065.qsdr.1.25.R73.fib.gz.tt.gz.HCP-MMP.ncount.end.network_measures.txt') as f:
    network_measures = [e.split() for e in f.readlines()]
    network_measures = {l[0]:l[1:] for l in network_measures}

    for k,l in network_measures.items():
        if len(l) == 1:
            network_measures[k] = float(l[0])
        elif len(l) > 1:
            network_measures[k] = [float(e) if isFloat(e) else e for e in l]

[frankyeh]

Thanks a lot! I believe many users will find this very helpful. Frank

…

On Wed, Jun 30, 2021 at 10:22 AM JohannesWiesner ***@***.***> wrote: Just for completeness - here's my code (could probably be optimized but does what it is supposed to do): def isFloat(string): try: float(string) return True except ValueError: return False with open('571144.src.gz.hcp1065.qsdr.1.25.R73.fib.gz.tt.gz.HCP-MMP.ncount.end.network_measures.txt') as f: network_measures = [e.split() for e in f.readlines()] network_measures = {l[0]:l[1:] for l in network_measures} for k,l in network_measures.items(): if len(l) == 1: network_measures[k] = float(l[0]) elif len(l) > 1: network_measures[k] = [float(e) if isFloat(e) else e for e in l] — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACDI4K3RA7OND32S5M4TP3TVMSDNANCNFSM47SF23XQ> .

[mattcieslak]

If this would be helpful, here is the function used in qsiprep: https://github.com/PennLINC/qsiprep/blob/master/qsiprep/interfaces/dsi_studio.py#L427

[frankyeh]

Thanks! Wish I have come across this code earlier. I will create a link in the documentation. Frank

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On Wed, Jun 30, 2021 at 11:08 AM Matt Cieslak ***@***.***> wrote: If this would be helpful, here is the function used in qsiprep: https://github.com/PennLINC/qsiprep/blob/master/qsiprep/interfaces/dsi_studio.py#L427 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACDI4JOKYOKX5TMRDDKWGDTVMXOTANCNFSM47SF23XQ> .