How to read .pkl files (produced by tapqir) in matlab

[gelles-brandeis]

This is a kludge, maybe someone has a better way?

1. pick a compatible version of python from https://www.mathworks.com/support/requirements/python-compatibility.html 2022b <--> 3.10

2. install that version of python from python.org (if not already installed)

3. make sure that the directories containing the python executable and scripts are at the top of your windows path (in settings/system/about/advanced system settings/environment variables (in my case: C:\Users\gelles\AppData\Local\Programs\Python\Python310 and C:\Users\gelles\AppData\Local\Programs\Python\Python310\Scripts)

4. from a windows terminal run: python -m pip install pandas

5. close and reopen Matlab

6. after I did all that I was able to depickle a tapqir file in matlab (based on https://xcorr.net/2013/06/12/load-pickle-files-in-matlab/) with the following matlab commands:

pyenv % just checking that matlab is connected to python

ans =

PythonEnvironment with properties:

      Version: "3.10"
   Executable: "C:\Users\gelles\AppData\Local\Programs\Python\Python310\python.EXE"
      Library: "C:\Users\gelles\AppData\Local\Programs\Python\Python310\python310.dll"
         Home: "C:\Users\gelles\AppData\Local\Programs\Python\Python310"
       Status: NotLoaded
ExecutionMode: InProcess

fn = "C:\Users\gelles\Downloads\cosmos+hmm_dwelltime-intervals-channel0.pkl"

fn =

"C:\Users\gelles\Downloads\cosmos+hmm_dwelltime-intervals-channel0.pkl"

fid = py.open(fn,'rb');
py.pickle.load(fid)

ans =

Python DataFrame with properties:

      T: [1×1 py.pandas.core.frame.DataFrame]
     at: [1×1 py.pandas.core.indexing._AtIndexer]
  attrs: [1×1 py.dict]
   axes: [1×2 py.list]
columns: [1×1 py.pandas.core.indexes.base.Index]
 dtypes: [1×1 py.pandas.core.series.Series]
  empty: 0
  flags: [1×1 py.pandas.core.flags.Flags]
    iat: [1×1 py.pandas.core.indexing._iAtIndexer]
   iloc: [1×1 py.pandas.core.indexing._iLocIndexer]
  index: [1×1 py.pandas.core.indexes.range.RangeIndex]
    loc: [1×1 py.pandas.core.indexing._LocIndexer]
   ndim: [1×1 py.int]
  shape: [1×2 py.tuple]
   size: [1×1 py.numpy.int32]
 values: [1×1 py.numpy.ndarray]

        posterior_sample  aoi  start_frame  ...  dwell_time  low_or_high  z
0                      0    0            0  ...         944            2  0
1                      0    1            0  ...         289           -2  0
2                      0    1          289  ...           3            1  1
3                      0    1          292  ...         652            2  0
4                      0    2            0  ...         115           -2  0
...                  ...  ...          ...  ...         ...          ... ..
958887               499  262          514  ...          49            0  0
958888               499  262          563  ...          16            1  1
958889               499  262          579  ...          20            0  0
958890               499  262          599  ...           2            1  1
958891               499  262          601  ...         343            2  0

[958892 rows x 7 columns]

a = ans

py.pandas.DataFrame(a).to_csv('csvout.csv') % makes a csv output file that can be read by matlab import data tool or excel

[ordabayevy]

Hi Jeff,

I made it so that dwelltime command would save the dwelltime intervals in matlab format file as well. It is in the latest branch, if you want to test it out you can install it by running:

pip install -U git+https://github.com/gelles-brandeis/tapqir.git@latest

EDIT (02/27/2023): missing git+ was added to the pip command.

[jc-brandeis]

Hi Yerdos,

I tried to install tapqir from the latest branch using the URL provided in your reply, but ran into the following error:

ERROR: HTTP error 404 while getting https://github.com/gelles-brandeis/tapqir/tree/tapqir.git@latest
ERROR: Could not install requirement https://github.com/gelles-brandeis/tapqir/tree/tapqir.git@latest because of HTTP error 404 Client Error: Not Found for url: https://github.com/gelles-brandeis/tapqir/tree/tapqir.git@latest for URL https://github.com/gelles-brandeis/tapqir/tree/tapqir.git@latest

Is the URL the correct? I tried this in tapqir environment.

Johnson

[ordabayevy]

Hi @jc-brandeis ,

Sorry, there was git+ missing in there. Try this:

pip install -U git+https://github.com/gelles-brandeis/tapqir.git@latest

[jc-brandeis]

Hi Yerdos.

 Thanks!  The new command with "git+" works.

Johnson

[gelles-brandeis]

Thanks, Yerdos!  That will be more convenient. -- Jeff

…

On 2/8/2023 11:20 PM, Yerdos Ordabayev wrote: Hi Jeff, I made it so that |dwelltime| command would save the dwelltime intervals in matlab format file as well. It is in the latest branch, if you want to test it out you can install it by running: |pip install -U ***@***.*** | — Reply to this email directly, view it on GitHub <#415 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5AU2MNXJWEZK3RQLALOIDWWRWAVANCNFSM6AAAAAAUV3LXDQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>