[Mne_analysis] Loading ICA solutions saved with mne.preprocessing.ICA.save()

[Geller, Jason]

        External Email - Use Caution        

Hi Daniel, 

You can use the read_ica function to load in your .fif files. 

> On Jul 2, 2019, at 5:17 PM, mne_analysis-request at nmr.mgh.harvard.edu wrote:
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> Today's Topics:
> 
>   1. Applying ICA with No Components Selected out but Signal
>      Changes Using Default Parameters (Rockhill, Alexander P.)
>   2. Re: Applying ICA with No Components Selected out but Signal
>      Changes Using Default Parameters (Rockhill, Alexander P.)
>   3. Loading ICA solutions saved with	mne.preprocessing.ICA.save()
>      (Rivas, Daniel)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 2 Jul 2019 19:25:03 +0000
> From: "Rockhill, Alexander P." <AROCKHILL at mgh.harvard.edu>
> Subject: [Mne_analysis] Applying ICA with No Components Selected out
> 	but Signal Changes Using Default Parameters
> To: "mne_analysis at nmr.mgh.harvard.edu"
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<SN6PR04MB52136FEC2AC2DBB0854F803EE3F80 at SN6PR04MB5213.namprd04.prod.outlook.com>
> 	
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi,
> 
>    In an analysis, I am running:
> 
> ica = ICA(method='fastica', n_components=n_components,  # n_components=None
>          random_state=seed)
> ica.fit(inst2)
> ...
> inst2 = ica.apply(inst2, exclude=ica.exclude)
> 
>    and when I skip all intermediate steps and just fit the ICA and apply it with an empty list for ica.exclude the signal still changes, quite a bit. I thought if no components were selected out and all the max PCA components were used the signal would be unchanged or basically unchanged. Is this a bug or something with my implementation?
> 
> Thanks,
> 
> Alex
> 
> Translational NeuroEngineering Laboratory
> Division of Neurotherapeutics, Department of Psychiatry
> Massachusetts General Hospital, Martinos Center
> 149 13th St Charlestown #2301, Boston, MA 02129
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> ------------------------------
> 
> Message: 2
> Date: Tue, 2 Jul 2019 21:13:41 +0000
> From: "Rockhill, Alexander P." <AROCKHILL at mgh.harvard.edu>
> Subject: Re: [Mne_analysis] Applying ICA with No Components Selected
> 	out but Signal Changes Using Default Parameters
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<SN6PR04MB5213BAF44083E39A2DFBDDF2E3F80 at SN6PR04MB5213.namprd04.prod.outlook.com>
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> Content-Type: text/plain; charset="us-ascii"
> 
> Also, of note the ica scale is off by quite a lot in the plot_sources plot, it is way too zoomed in.
> 
> Alex
> 
> Translational NeuroEngineering Laboratory
> Division of Neurotherapeutics, Department of Psychiatry
> Massachusetts General Hospital, Martinos Center
> 149 13th St Charlestown #2301, Boston, MA 02129
> ________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Rockhill, Alexander P. <AROCKHILL at mgh.harvard.edu>
> Sent: Tuesday, July 2, 2019 3:25 PM
> To: mne_analysis at nmr.mgh.harvard.edu
> Subject: [Mne_analysis] Applying ICA with No Components Selected out but Signal Changes Using Default Parameters
> 
> Hi,
> 
>    In an analysis, I am running:
> 
> ica = ICA(method='fastica', n_components=n_components,  # n_components=None
>          random_state=seed)
> ica.fit(inst2)
> ...
> inst2 = ica.apply(inst2, exclude=ica.exclude)
> 
>    and when I skip all intermediate steps and just fit the ICA and apply it with an empty list for ica.exclude the signal still changes, quite a bit. I thought if no components were selected out and all the max PCA components were used the signal would be unchanged or basically unchanged. Is this a bug or something with my implementation?
> 
> Thanks,
> 
> Alex
> 
> Translational NeuroEngineering Laboratory
> Division of Neurotherapeutics, Department of Psychiatry
> Massachusetts General Hospital, Martinos Center
> 149 13th St Charlestown #2301, Boston, MA 02129
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> ------------------------------
> 
> Message: 3
> Date: Tue, 2 Jul 2019 21:17:24 +0000
> From: "Rivas, Daniel" <rivas.daniel at courrier.uqam.ca>
> Subject: [Mne_analysis] Loading ICA solutions saved with
> 	mne.preprocessing.ICA.save()
> To: "mne_analysis at nmr.mgh.harvard.edu"
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<YQXPR0101MB1751C93CDF3B00AD46EF5184ADF80 at YQXPR0101MB1751.CANPRD01.PROD.OUTLOOK.COM>
> 	
> Content-Type: text/plain; charset="us-ascii"
> 
>        External Email - Use Caution        
> 
> Hi,
> 
> 
> Maybe I've missed something in the documentation, but it seems the current ICA class does not have a "load" function that would allow me to use the .fif file given by ICA.save().  My use case would be to pre-compute a bunch of ICA solutions and then save their removal/visualization/apply() for later, in a batch mode so that it is more efficient for the human operator.
> 
> Any pointers? Thanks!
> 
> 
> Daniel Rivas
> PhD Candidate, Cognitive computing, UQAM
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