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OpenSMFS / FRETBursts

Burst analysis software for single and multi-spot single-molecule FRET (smFRET) data.
https://opensmfs.github.io/FRETBursts/
GNU General Public License v2.0
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merging multiple .ptu files to a single hdf5 #34

Open Mattyboi123 opened 4 years ago

Mattyboi123 commented 4 years ago

Apologies if this is an already answered question or I've missed something obvious but how does one combine multiple .ptu files into a single hdf5 file prior to further analysis withe pycorrelate or fretbursts?

Best Matt

mayeshh commented 4 years ago

I suggest keeping your files separate and loading the data into one large DataFrame. For example bursts_all = pd.concat(dataframe_list, ignore_index=True) .

Mattyboi123 commented 3 years ago

hi thanks for the suggestion but will that preserve all of the nanotimes and still be navigable using the normal fretbursts commands?

Mattyboi123 commented 3 years ago

by the by did you sole the issue you were having with no module named phrates_c? I now have the same issue trying to import FRETbursts on a new clean anaconda install on a new machine perhaps it is a python 3.8 issue as when Itried to install fretbursts through conda-forge it said something about that and didn't install so Icloned my version that was working on another machine (python 3.7) then this issue on the new machine

mayeshh commented 3 years ago

hi thanks for the suggestion but will that preserve all of the nanotimes and still be navigable using the normal fretbursts commands?

Yes, each data object will have the same fields and FRETBursts will work on them in the same way.

mayeshh commented 3 years ago

by the by did you sole the issue you were having with no module named phrates_c? I now have the same issue trying to import FRETbursts on a new clean anaconda install on a new machine perhaps it is a python 3.8 issue as when Itried to install fretbursts through conda-forge it said something about that and didn't install so Icloned my version that was working on another machine (python 3.7) then this issue on the new machine

I haven't upgraded to python 3.8, so I don't have experience with the compatibility. I would not expect this to be the issue, rather updates in the dependencies could cause issues (e.g. deprecations in numpy).

Please try an “editable” installation:

git clone https://github.com/OpenSMFS/FRETBursts.git
cd FRETBursts
pip install -e .
Mattyboi123 commented 3 years ago

Ye I did try installing like that, it didn't help. In the end I just checked commented out the line in phrates.py that called for phrates_c. Then another line about normpdf in matplot lib bad something else which I forget now and it works fine on 3.8.

On Sat, 12 Dec 2020, 17:39 mayeshh, notifications@github.com wrote:

by the by did you sole the issue you were having with no module named phrates_c? I now have the same issue trying to import FRETbursts on a new clean anaconda install on a new machine perhaps it is a python 3.8 issue as when Itried to install fretbursts through conda-forge it said something about that and didn't install so Icloned my version that was working on another machine (python 3.7) then this issue on the new machine

I haven't upgraded to python 3.8, so I don't have experience with the compatibility. I would not expect this to be the issue, rather updates in the dependencies could cause issues (e.g. deprecations in numpy).

Please try installing as suggested in phconvert issue #50 https://github.com/Photon-HDF5/phconvert/issues/50:

pip install git+https://github.com/Photon-HDF5/phconvert

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenSMFS/FRETBursts/issues/34#issuecomment-743789651, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM2MFHTAFGYVTUFU5D2YF5LSUOTG3ANCNFSM4JPWA24Q .

mayeshh commented 3 years ago

Ye I did try installing like that, it didn't help. In the end I just checked commented out the line in phrates.py that called for phrates_c. Then another line about normpdf in matplot lib bad something else which I forget now and it works fine on 3.8.

Yes, the phrates_c module is a C optimized version of phrates, so it is faster but not necessary for FRETBursts to work.

For the deprecation warning in matplotlib, I have submitted a PR for the normpdf issue but I haven't been able to figure out why it fails the CI checks so it has not been merged to the master branch.

Could you print a list of your dependencies and versions for reference?

Mattyboi123 commented 3 years ago

unfortunately, phrates_c is also required for the alex2cde filter script to run as it uses it to implement a laplace kernel, apparently. Perhaps its a windows not compiling things issue. I've installed visual studio and trying with code to compile from an issue that someone else had with cython modules not being imported into spyder

https://stackoverflow.com/questions/49837155/spyder-does-not-recognise-cython-modules-when-importing-in-a-script

On Sat, Dec 12, 2020 at 6:04 PM mayeshh notifications@github.com wrote:

Ye I did try installing like that, it didn't help. In the end I just checked commented out the line in phrates.py that called for phrates_c. Then another line about normpdf in matplot lib bad something else which I forget now and it works fine on 3.8.

Yes, the phrates_c module is a C optimized version of phrates, so it is faster but not necessary for FRETBursts to work.

For the deprecation warning in matplotlib, I have submitted a PR https://github.com/OpenSMFS/FRETBursts/pull/33 for the normpdf issue but I haven't been able to figure out why it fails the CI checks so it has not been merged to the master branch.

Could you print a list of your dependencies and versions for reference?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenSMFS/FRETBursts/issues/34#issuecomment-743793450, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM2MFHX3V7FJDOGK6TOT6Q3SUOWDZANCNFSM4JPWA24Q .

Mattyboi123 commented 3 years ago

Hello, I still have this issue with cython scritpts not being found when runing FRETbursts even in the dedicated envoronment you suggested and after installing build tools for virtual studio. It just says 'no module named phrates_c' Can you tell me if you are running on a windows machine, how your cython extension scripts/modules are being compiled?

Mattyboi123 commented 3 years ago

I was able to get it to work now in the manner you suggetsed - there was a path issue becuasue I was opening scripts from Spyder that were in a different folder. creating local copies within the FRETbursts dedicated environment and opening those worked perfectly with the only caveat I've yet found being that the normPPDF from matplotlib needed to be commented out - whihc as Iunderstand it hads been worked around easily.

Thanks