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From: Dave B. <db...@Co...> - 2014-04-29 20:04:42
|
I will be very interested in trying out the MOOSE Python implemention of hsolved when it is fully ready. In GENESIS 2, hsolve performs both the functions of a Hines method compartmental solver, and of a Discrete Event Solver for the efficient delivery of spike messages. Ideally, these should be in separate solvers, as they are in GENESIS 3 (unfortunately still under development). How is this being handled in MOOSE? Can networks of hsolved cells in MOOSE benefit from equivalent optimizations in spike delivery that GENESIS hsolve gives? Or is a separate mechanism used for spike delivery? On Tue, 29 Apr 2014, Dilawar Singh wrote: > Hi Saeed, > > We are in process of integrating 'hsolve' into async13 branch. Only today, I > got some sanity check of hsolve working. I am not sure how long it will take > to get hsolve properly integrated with python. > > For time being -- if you want to use async13 branch -- you can change the > solver to 'ee' from 'hsolve'. > > I'll let you know as soon as hsolve is ready. > > Dilawar |
|
From: Saeed <sa...@gn...> - 2014-04-29 18:17:01
|
Hi Dilawar,
Thank you for importing hsolve. I thought it might be not related
to HSolve because it happened before defining HSovle and for example at
Hopfield I got the same error.
Thank you again. Therefore, I wont change anything now and will
wait for the code to be stable.
Saeed
On 29-04-2014 15:02, Dilawar Singh wrote:
> Hi Saeed,
>
> We are in process of integrating 'hsolve' into async13 branch. Only today, I
> got some sanity check of hsolve working. I am not sure how long it will take
> to get hsolve properly integrated with python.
>
> For time being -- if you want to use async13 branch -- you can change the
> solver to 'ee' from 'hsolve'.
>
> I'll let you know as soon as hsolve is ready.
>
> Dilawar
>
> On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
>> Sure, Sorry for the lack of information.
>> As I found it happens in many of Demo files, for example at "async13/Demos/snippets/testHsolve.py" the below error produces:
>>
>> =====================================
>> on node 0, numNodes = 1, numCores = 12
>> Info: Time to define moose classes:0
>> Info: Time to initialize module:0.05
>> Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
>> Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
>> Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
>> Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
>> Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
>> Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
>> Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
>> Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
>> Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
>> 0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
>> Traceback (most recent call last):
>> File "testHsolve.py", line 297, in <module>
>> main()
>> File "testHsolve.py", line 294, in main
>> test_elec_alone()
>> File "testHsolve.py", line 265, in test_elec_alone
>> make_spiny_compt()
>> File "testHsolve.py", line 243, in make_spiny_compt
>> moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
>> NameError: check field names and type compatibility.
>>
>> ======================================
>>
>> It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all object names.
>>
>>
>>
>>> Upi
>>> Dear Saeed,
>>> Please give script snippet where this happens. Also you might wish
>>> to look in Demos/snippets for examples of the correct use of the function.
>>> Best,
>>> Upi
>>> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>>>> Hi,
>>>>
>>>> At async13 branch, when it tries to use connect method, the below error
>>>> throws away:
>>>>
>>>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>>>
>>>> It would be my please if you have a look at this.
>>>>
>>>> Bests,
>>>> Saeed
>>>> ------------------------------------------------------------------------------
>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>> unparalleled scalability from the best Selenium testing platform available.
>>>> Simple to use. Nothing to install. Get started now for free."
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>>>> _______________________________________________
>>>> moose-devel mailing list
>>>> moose-devel@...
>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
>
|
|
From: Dilawar S. <dil...@nc...> - 2014-04-29 18:03:50
|
Hi Saeed,
We are in process of integrating 'hsolve' into async13 branch. Only today, I
got some sanity check of hsolve working. I am not sure how long it will take
to get hsolve properly integrated with python.
For time being -- if you want to use async13 branch -- you can change the
solver to 'ee' from 'hsolve'.
I'll let you know as soon as hsolve is ready.
Dilawar
On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
>Sure, Sorry for the lack of information.
>As I found it happens in many of Demo files, for example at "async13/Demos/snippets/testHsolve.py" the below error produces:
>
>=====================================
>on node 0, numNodes = 1, numCores = 12
>Info: Time to define moose classes:0
>Info: Time to initialize module:0.05
>Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
>Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
>Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
>Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
>Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
>Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
>Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
>Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
>Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
>0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
>Traceback (most recent call last):
> File "testHsolve.py", line 297, in <module>
> main()
> File "testHsolve.py", line 294, in main
> test_elec_alone()
> File "testHsolve.py", line 265, in test_elec_alone
> make_spiny_compt()
> File "testHsolve.py", line 243, in make_spiny_compt
> moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
>NameError: check field names and type compatibility.
>
>======================================
>
>It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all object names.
>
>
>
>>Upi
>> Dear Saeed,
>> Please give script snippet where this happens. Also you might wish
>> to look in Demos/snippets for examples of the correct use of the function.
>> Best,
>> Upi
>> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>>> Hi,
>>>
>>> At async13 branch, when it tries to use connect method, the below error
>>> throws away:
>>>
>>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>>
>>> It would be my please if you have a look at this.
>>>
>>> Bests,
>>> Saeed
>>> ------------------------------------------------------------------------------
>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>> unparalleled scalability from the best Selenium testing platform available.
>>> Simple to use. Nothing to install. Get started now for free."
>>>http://p.sf.net/sfu/SauceLabs
>>> _______________________________________________
>>> moose-devel mailing list
>>> moose-devel@...
>>>https://lists.sourceforge.net/lists/listinfo/moose-devel
>
>
>------------------------------------------------------------------------------
>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>unparalleled scalability from the best Selenium testing platform available.
>Simple to use. Nothing to install. Get started now for free."
>http://p.sf.net/sfu/SauceLabs
>_______________________________________________
>moose-devel mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Saeed <sa...@gn...> - 2014-04-29 17:58:37
|
Sure, Sorry for the lack of information.
As I found it happens in many of Demo files, for example at "async13/Demos/snippets/testHsolve.py" the below error produces:
=====================================
on node 0, numNodes = 1, numCores = 12
Info: Time to define moose classes:0
Info: Time to initialize module:0.05
Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
Traceback (most recent call last):
File "testHsolve.py", line 297, in <module>
main()
File "testHsolve.py", line 294, in main
test_elec_alone()
File "testHsolve.py", line 265, in test_elec_alone
make_spiny_compt()
File "testHsolve.py", line 243, in make_spiny_compt
moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
NameError: check field names and type compatibility.
======================================
It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all object names.
>Upi
> Dear Saeed,
> Please give script snippet where this happens. Also you might wish
> to look in Demos/snippets for examples of the correct use of the function.
> Best,
> Upi
> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>> Hi,
>>
>> At async13 branch, when it tries to use connect method, the below error
>> throws away:
>>
>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>
>> It would be my please if you have a look at this.
>>
>> Bests,
>> Saeed
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>>http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moose-devel@...
>>https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: U.S.Bhalla <bh...@nc...> - 2014-04-29 15:55:10
|
Dear Saeed,
Please give script snippet where this happens. Also you might wish
to look in Demos/snippets for examples of the correct use of the function.
Best,
Upi
On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
> Hi,
>
> At async13 branch, when it tries to use connect method, the below error
> throws away:
>
> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>
> It would be my please if you have a look at this.
>
> Bests,
> Saeed
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Saeed S. <sd....@gm...> - 2014-04-29 15:34:45
|
Hi, At async13 branch, when it tries to use connect method, the below error throws away: 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0 It would be my please if you have a look at this. Bests, Saeed |
|
From: U.S.Bhalla <bh...@nc...> - 2014-04-23 04:01:39
|
Hi, Vivek,
This is good to know. Let's get going on the implementation now!
Best,
Upi
On Tuesday 22 April 2014 11:11 PM, vivek sagar wrote:
> Hey everyone!
>
> Just wanted to let the group know that I have been selected for this year's
> Google Summer of Code, and will be working on the project "Optimization of
> parallel computation in MOOSE" with Upinder sir.
>
> To all those who were involved in the GSoC selection procedure, thank you.
> I am really excited to be working with you all!
>
> Here is the link to my proposal:
> http://www.google-melange.com/gsoc/proposal/review/student/google/gsoc2014/sharkash/5668600916475904
>
> Vivek
> ------------------------------------------------------------------------------
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> moose-devel mailing list
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> https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: vivek s. <viv...@gm...> - 2014-04-22 17:46:51
|
Oops, looks like the link above is only for those who are signed in. Please use this link instead: http://www.google-melange.com/gsoc/proposal/public/google/gsoc2014/sharkash/5668600916475904 Sorry for the inconvenience, Vivek On Tue, Apr 22, 2014 at 11:11 PM, vivek sagar <viv...@gm...>wrote: > Hey everyone! > > Just wanted to let the group know that I have been selected for this > year's Google Summer of Code, and will be working on the project "Optimization > of parallel computation in MOOSE" with Upinder sir. > > To all those who were involved in the GSoC selection procedure, thank you. > I am really excited to be working with you all! > > Here is the link to my proposal: > http://www.google-melange.com/gsoc/proposal/review/student/google/gsoc2014/sharkash/5668600916475904 > > Vivek > |
|
From: vivek s. <viv...@gm...> - 2014-04-22 17:41:57
|
Hey everyone! Just wanted to let the group know that I have been selected for this year's Google Summer of Code, and will be working on the project "Optimization of parallel computation in MOOSE" with Upinder sir. To all those who were involved in the GSoC selection procedure, thank you. I am really excited to be working with you all! Here is the link to my proposal: http://www.google-melange.com/gsoc/proposal/review/student/google/gsoc2014/sharkash/5668600916475904 Vivek |
|
From: Zbigniew Jędrzejewski-S. <zje...@gm...> - 2014-04-09 21:32:51
|
On 04/02/2014 11:44 PM, Subhasis Ray wrote: >> On Wed, Apr 02, 2014 at 11:55:29AM +0530, Subhasis Ray wrote: >>> Hi, >>> Thanks for your contribution to the project. I should point out that >>> (1) the buildQ branch is outdated and it will be better to put your >> efforts >>> on async13 branch which is the current one. >> Oh, OK. The buildQ branch is advertised in the documentation, so that's >> why I started with it. I'll move to async13. >> >>> (2) rather than sending patches, create your own branch on sourceforge >> repo >>> and do the modifications there and once tested ok, merge it to the common >>> branch. Hi, I pushed one trivial spelling fix to 'async13', and also created branch 'zbigniew_py3k', and pushed my other commits there. What kind of testing should be performed? I see various regression tests and examples, but I'm don't know how to run them... Thanks, Zbyszek |
|
From: Subhasis R. <ray...@gm...> - 2014-04-07 09:13:33
|
Hi, A hacker's approach to this (when there is a known correct implementation, but do not have a tutor to correct you) is to step through the correct implementation of the algorithm and compare against what you get manually. Tedious, but the best method if all you have is a debugger. Though a still better approach exists : "The most effective debugging tool is still careful thought, coupled with judiciously placed print statements." - Brian Kernighan [Unix for Beginners (1979)] :) Best, - Subhasis ( ʃʊbʱaːʃɪʃ ) On Wed, Apr 2, 2014 at 10:22 AM, vivek sagar <viv...@gm...>wrote: > Hello all, > > I have been trying for the past few days to understand how the Hines' > Solver works using the paper written by Hines and some other resources from > the internet. At this point, I have generated the Hines matrix for a small > network of compartments and have used gaussian elimination to calculate the > new Voltage vector using this matrix. However, I am not sure how I should > proceed. I am not even entirely sure if what I have done until now is > correct. > > I have attached images of how I worked out the Hines matrix and did the > gaussian elimination. Could you please give me some pointers as to what I > have to do next? > > Thanks > > Vivek > > > ------------------------------------------------------------------------------ > Put Bad Developers to Shame > Dominate Development with Jenkins Continuous Integration > Continuously Automate Build, Test & Deployment > Start a new project now. Try Jenkins in the cloud. > http://p.sf.net/sfu/13600_Cloudbees_APR > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > > |
|
From: Subhasis R. <ray...@gm...> - 2014-04-03 03:44:42
|
Added. Best, - Subhasis ( ʃʊbʱaːʃɪʃ ) On Wed, Apr 2, 2014 at 6:46 PM, Zbigniew Jędrzejewski-Szmek < zb...@in...> wrote: > On Wed, Apr 02, 2014 at 11:55:29AM +0530, Subhasis Ray wrote: > > Hi, > > Thanks for your contribution to the project. I should point out that > > (1) the buildQ branch is outdated and it will be better to put your > efforts > > on async13 branch which is the current one. > Oh, OK. The buildQ branch is advertised in the documentation, so that's > why I started with it. I'll move to async13. > > > (2) rather than sending patches, create your own branch on sourceforge > repo > > and do the modifications there and once tested ok, merge it to the common > > branch. > > Please let me know your sourceforge id and I shall add you to the > > developer's list. > "zbigniew_szmek" > > Thanks, > Zbyszek > |
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-02 13:16:21
|
On Wed, Apr 02, 2014 at 11:55:29AM +0530, Subhasis Ray wrote: > Hi, > Thanks for your contribution to the project. I should point out that > (1) the buildQ branch is outdated and it will be better to put your efforts > on async13 branch which is the current one. Oh, OK. The buildQ branch is advertised in the documentation, so that's why I started with it. I'll move to async13. > (2) rather than sending patches, create your own branch on sourceforge repo > and do the modifications there and once tested ok, merge it to the common > branch. > Please let me know your sourceforge id and I shall add you to the > developer's list. "zbigniew_szmek" Thanks, Zbyszek |
|
From: Subhasis R. <ray...@gm...> - 2014-04-02 06:25:57
|
Hi, Thanks for your contribution to the project. I should point out that (1) the buildQ branch is outdated and it will be better to put your efforts on async13 branch which is the current one. (2) rather than sending patches, create your own branch on sourceforge repo and do the modifications there and once tested ok, merge it to the common branch. Please let me know your sourceforge id and I shall add you to the developer's list. Best, - Subhasis ( ʃʊbʱaːʃɪʃ ) On Wed, Apr 2, 2014 at 2:20 AM, Zbigniew Jędrzejewski-Szmek < zb...@in...> wrote: > Hi, > > Since this is my first post to the list, let me start with an > introduction: I work in the Computational and Experimental > Neuroplasticity Laboratory directed by dr. Avrama Blackwell. > > We are currently using a MOOSE model created in Python to fit model > parameters to experimental data registered in the lab, with promising > results. Following patches allow the MOOSE module to be used from > Python 3. They are based on the buildQ branch. > > Just the module is modified, the GUI parts are still Python 2 only. > > The following approach is taken: code is tweaked to use a common > subset of Python 2 and 3. More specifically, it is made compatible > with Python 2.7 and Python 3.3 or later. In a few unavoidable places, > like the module initialization in the C++ code, separate branches in > #ifdefs are used. In the Python part, some compatiblity imports (in > _compat.py) are used to "wrap" the remaining differences. This (using > the exact same code under both Python 2 and 3) seems to be nicest way > to do the conversion. > > I haven't done very extensive testing, but at least our model seems to > return identical results under Python 2 and 3. > > I hope posting patches to the mailing list the proper way to submit > changes... If no, please let me know. > > Regards, > Zbigniew Jędrzejewski-Szmek > > > Zbigniew Jędrzejewski-Szmek (19): > Add gitignore > Declare that deprecated Numpy API will not be used > Fix warnings about deprecated cast to char* > Use pkg-config for Python compliation flags > Makefile: simplify detection of python flags > Fix compilation under Python 3 > Convert to print() > Apply has_key fixer > Convert to modern raise syntax > Apply except fixer > Remove some unnecessary .keys() and list() calls > Convert to incremental zip, map, filter > Add compatiblity layer for basestr and unicode > Remove unused import > Apply imports fixer > Convert to relative imports > Remove old separate Python 3 code > Make sure classes have __module__ set > Add missing space in output > > .gitignore | 7 + > Makefile | 31 +-- > gui/shell.py | 2 +- > pymoose/ematrix.cpp | 18 +- > pymoose/melement.cpp | 2 + > pymoose/mfield.cpp | 2 + > pymoose/moosemodule.cpp | 38 +++- > pymoose/moosemodule.h | 2 + > python/moose/_compat.py | 5 + > python/moose/alternate.py | 31 +-- > python/moose/graphutil.py | 4 +- > python/moose/hdfutil.py | 45 ++-- > python/moose/moose.py | 38 ++-- > python/moose/moose_py3k.py | 249 > --------------------- > python/moose/mtypes.py | 5 +- > python/moose/multiscale/core/mumbl.py | 14 +- > python/moose/multiscale/core/simulator.py | 6 +- > python/moose/multiscale/core/stimulus.py | 4 +- > python/moose/multiscale/core/types.py | 9 +- > python/moose/multiscale/helper/graph_methods.py | 4 +- > python/moose/multiscale/helper/moose_methods.py | 9 +- > .../neuroml/v1.8/GranuleCell/FvsI_Granule98.py | 5 +- > .../models/neuroml/v1.8/GranuleCell/Granule98.py | 7 +- > .../neuroml/v1.8/GranuleCell/Granule98_hsolve.py | 9 +- > .../moose/multiscale/multi_bhalla/diffusionOnly.py | 21 +- > python/moose/multiscale/multi_bhalla/lm2.py | 7 +- > python/moose/multiscale/multi_bhalla/loadMulti.py | 53 ++--- > python/moose/multiscale/multi_bhalla/minimal.py | 3 +- > python/moose/multiscale/multi_bhalla/runcell18.py | 16 +- > python/moose/multiscale/multi_bhalla/x_compt.py | 3 +- > python/moose/multiscale/parser/ChannelML.py | 12 +- > python/moose/multiscale/parser/MorphML.py | 6 +- > python/moose/multiscale/parser/NetworkML.py | 9 +- > python/moose/multiscale/parser/NeuroML.py | 6 +- > python/moose/multiscale/parser/parser.py | 2 +- > python/moose/multiscale/parser/utils.py | 3 +- > python/moose/neuroml/ChannelML.py | 27 +-- > python/moose/neuroml/MorphML.py | 33 +-- > python/moose/neuroml/NetworkML.py | 23 +- > python/moose/neuroml/NeuroML.py | 13 +- > python/moose/neuroml/utils.py | 13 +- > python/moose/neuroml2/converter.py | 3 +- > python/moose/neuroml2/generated_neuroml.py | 160 ++++++------- > python/moose/neuroml2/hhfit.py | 2 +- > python/moose/neuroml2/reader.py | 26 ++- > python/moose/neuroml2/test_converter.py | 5 +- > python/moose/neuroml2/test_hhfit.py | 19 +- > python/moose/neuroml2/test_reader.py | 3 +- > python/moose/neuroml2/units.py | 5 +- > python/moose/recording.py | 10 +- > python/moose/utils.py | 58 ++--- > python/moose/xmls_to_network/.noweb/main.nw | 6 +- > python/moose/xmls_to_network/core/hhfit.py | 2 +- > python/moose/xmls_to_network/core/load_multi.py | 49 ++-- > python/moose/xmls_to_network/core/multiscale.py | 7 +- > .../moose/xmls_to_network/core/neuroml2_parser.py | 174 +++++++------- > .../moose/xmls_to_network/core/neuroml_to_moose.py | 31 ++- > .../moose/xmls_to_network/helper/graph_methods.py | 4 +- > python/moose/xmls_to_network/parser/nml_parser.py | 170 +++++++------- > .../generatedNEURON/NEURONUtils/NEURONSimUtils.py | 2 +- > .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- > .../generatedNEURON/NeuroMLUtils/NetworkMLNet.py | 5 +- > .../NeuroMLUtils/NetworkMLSaxHandler.py | 91 ++++---- > .../twoNeurons/generatedNEURON/twoNeurons.hoc | 4 +- > .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- > .../generatedPyNN/NeuroMLUtils/NetworkMLNet.py | 5 +- > .../NeuroMLUtils/NetworkMLSaxHandler.py | 85 +++---- > .../twoNeurons/generatedPyNN/PyNNUtils/Pop.py | 13 +- > .../generatedPyNN/PyNNUtils/PyNNUtils.py | 11 +- > 69 files changed, 791 insertions(+), 971 deletions(-) > create mode 100644 .gitignore > create mode 100644 python/moose/_compat.py > delete mode 100644 python/moose/moose_py3k.py > > -- > 1.8.5.3 > > > > ------------------------------------------------------------------------------ > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > |
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From: vivek s. <viv...@gm...> - 2014-04-02 04:53:17
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Hello all, I have been trying for the past few days to understand how the Hines' Solver works using the paper written by Hines and some other resources from the internet. At this point, I have generated the Hines matrix for a small network of compartments and have used gaussian elimination to calculate the new Voltage vector using this matrix. However, I am not sure how I should proceed. I am not even entirely sure if what I have done until now is correct. I have attached images of how I worked out the Hines matrix and did the gaussian elimination. Could you please give me some pointers as to what I have to do next? Thanks Vivek |
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From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:12:23
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---
pymoose/ematrix.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pymoose/ematrix.cpp b/pymoose/ematrix.cpp
index 72d9558..503e7fc 100644
--- a/pymoose/ematrix.cpp
+++ b/pymoose/ematrix.cpp
@@ -473,7 +473,7 @@ extern "C" {
ostringstream repr;
repr << "<moose.ematrix: class="
<< Field<string>::get(self->id_, "className") << ", "
- << "id=" << self->id_.value() << ","
+ << "id=" << self->id_.value() << ", "
<< "path=" << self->id_.path() << ">";
return PyString_FromString(repr.str().c_str());
} // ! moose_Id_repr
--
1.8.5.3
|
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From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:12:16
|
Using the print function, instead of the print statement, is the first step to making the code simultaneously Python 2 and Python 3 compatible. print() also has slightly nicer semantics and is more readable, when end=..., sep=... are used, and when arguments span more than one line. --- gui/shell.py | 2 +- python/moose/alternate.py | 17 +++---- python/moose/hdfutil.py | 15 +++--- python/moose/moose.py | 25 +++++----- python/moose/moose_py3k.py | 1 + python/moose/mtypes.py | 3 +- python/moose/multiscale/core/mumbl.py | 2 + python/moose/multiscale/core/simulator.py | 2 + python/moose/multiscale/core/stimulus.py | 4 +- python/moose/multiscale/core/types.py | 2 +- python/moose/multiscale/helper/moose_methods.py | 4 +- .../neuroml/v1.8/GranuleCell/FvsI_Granule98.py | 5 +- .../models/neuroml/v1.8/GranuleCell/Granule98.py | 7 +-- .../neuroml/v1.8/GranuleCell/Granule98_hsolve.py | 9 ++-- .../moose/multiscale/multi_bhalla/diffusionOnly.py | 21 +++++---- python/moose/multiscale/multi_bhalla/lm2.py | 7 +-- python/moose/multiscale/multi_bhalla/loadMulti.py | 53 +++++++++++----------- python/moose/multiscale/multi_bhalla/minimal.py | 3 +- python/moose/multiscale/multi_bhalla/runcell18.py | 16 ++++--- python/moose/multiscale/multi_bhalla/x_compt.py | 3 +- python/moose/multiscale/parser/NetworkML.py | 3 +- python/moose/multiscale/parser/utils.py | 1 + python/moose/neuroml/ChannelML.py | 19 ++++---- python/moose/neuroml/MorphML.py | 23 +++++----- python/moose/neuroml/NetworkML.py | 17 +++---- python/moose/neuroml/NeuroML.py | 7 +-- python/moose/neuroml/utils.py | 11 +++-- python/moose/neuroml2/generated_neuroml.py | 3 +- python/moose/neuroml2/reader.py | 14 +++--- python/moose/neuroml2/test_converter.py | 5 +- python/moose/neuroml2/test_hhfit.py | 19 ++++---- python/moose/neuroml2/test_reader.py | 3 +- python/moose/neuroml2/units.py | 3 +- python/moose/recording.py | 5 +- python/moose/utils.py | 52 +++++++++++---------- python/moose/xmls_to_network/core/load_multi.py | 47 +++++++++---------- python/moose/xmls_to_network/core/multiscale.py | 5 +- .../moose/xmls_to_network/core/neuroml2_parser.py | 3 +- .../moose/xmls_to_network/core/neuroml_to_moose.py | 12 +++-- python/moose/xmls_to_network/parser/nml_parser.py | 3 +- .../generatedNEURON/NeuroMLUtils/NetworkMLNet.py | 5 +- .../NeuroMLUtils/NetworkMLSaxHandler.py | 3 +- .../generatedPyNN/NeuroMLUtils/NetworkMLNet.py | 5 +- .../NeuroMLUtils/NetworkMLSaxHandler.py | 3 +- .../twoNeurons/generatedPyNN/PyNNUtils/Pop.py | 13 +++--- .../generatedPyNN/PyNNUtils/PyNNUtils.py | 5 +- 46 files changed, 271 insertions(+), 219 deletions(-) diff --git a/gui/shell.py b/gui/shell.py index 2eeafb5..5790447 100644 --- a/gui/shell.py +++ b/gui/shell.py @@ -17,7 +17,7 @@ # http://obswww.unige.ch/~revaz/git/old.glups-4.0/glups/shell.py - # Subhasis Ray -__doc__=""" +""" This module implements a QT4 python interpreter widget. It is inspired bu PyCute : http://gerard.vermeulen.free.fr """ diff --git a/python/moose/alternate.py b/python/moose/alternate.py index e54b57f..24a0d41 100644 --- a/python/moose/alternate.py +++ b/python/moose/alternate.py @@ -280,6 +280,7 @@ le(obj) -- list element under object, if no parameter specified, list elements under current working element """ +from __future__ import print_function from functools import partial import warnings from collections import defaultdict @@ -825,7 +826,7 @@ def getCwe(): def pwe(): """Print present working element. Convenience function for GENESIS users.""" - print _moose.getCwe().getPath() + print(_moose.getCwe().getPath()) def connect(src, srcMsg, dest, destMsg, msgType='Single'): """Connect src object's source field specified by srcMsg to @@ -842,9 +843,9 @@ def le(element=None): element = getCwe()[0] elif isinstance(element, str): element = Neutral(element) - print 'Elements under', element.path + print('Elements under', element.path) for ch in element.children: - print ch + print(ch) ce = setCwe @@ -886,18 +887,18 @@ def showfield(element, field='*', showtype=False): value_field_dict = getFieldDict(element.className, 'valueFinfo') max_type_len = max([len(dtype) for dtype in value_field_dict.values()]) max_field_len = max([len(dtype) for dtype in value_field_dict.keys()]) - print - print '[', element.path, ']' + print() + print('[', element.path, ']') for key, dtype in value_field_dict.items(): if dtype == 'bad' or key == 'this' or key == 'dummy' or key == 'me' or dtype.startswith('vector') or 'ObjId' in dtype: continue value = element.oid_.getField(key) if showtype: - print dtype.ljust(max_type_len + 4), - print key.ljust(max_field_len + 4), '=', value + print(dtype.ljust(max_type_len + 4), end=' ') + print(key.ljust(max_field_len + 4), '=', value) else: try: - print field, '=', element.getField(field) + print(field, '=', element.getField(field)) except AttributeError: pass # Genesis silently ignores non existent fields diff --git a/python/moose/hdfutil.py b/python/moose/hdfutil.py index 0f114c3..a17ff5a 100644 --- a/python/moose/hdfutil.py +++ b/python/moose/hdfutil.py @@ -84,6 +84,7 @@ # Code: +from __future__ import print_function import moose as moose__ import numpy as np import h5py as h5 @@ -118,9 +119,9 @@ def get_rec_dtype(em): if em.className in dtype_table: dtype = dtype_table[em.className] else: - print 'Creating entries for class:', obj.className + print('Creating entries for class:', obj.className) fielddict = moose__.getFieldDict(obj.className, 'valueFinfo') - print fielddict + print(fielddict) keys = sorted(list(fielddict.keys())) fields = [] # [('path', 'S1024')] for fieldname in keys: @@ -244,7 +245,7 @@ def savestate(filename=None): for obj in moose__.wildcardFind("/##"): if obj.path.startswith('/Msg') or obj.path.startswith('/class') or obj.className == 'Table' or obj.className == 'TableEntry': continue - print 'Processing:', obj.path, obj.className + print('Processing:', obj.path, obj.className) typeinfo.append((obj.path, obj.className, str(obj.shape), obj[0].parent.path)) objcount += 1 if len(typeinfo) == size_step: @@ -253,9 +254,9 @@ def savestate(filename=None): typeinfo = [] # If we do not yet have dataset for this class, create one and keep it in dict if obj.className not in class_dataset_dict: - print 'Creating entries for class:', obj.className + print('Creating entries for class:', obj.className) fielddict = moose__.getFieldDict(obj.className, 'valueFinfo') - print fielddict + print(fielddict) keys = sorted(list(fielddict.keys())) fields = [] # [('path', 'S1024')] for fieldname in keys: @@ -273,9 +274,9 @@ def savestate(filename=None): ds = class_dataset_dict[obj.className] for entry in obj: fields = [] - print entry.path, + print(entry.path, end=' ') for f in ds.dtype.names: - print 'getting field:', f + print('getting field:', f) entry.getField(f) fields = [f.path if isinstance(f, moose__.ematrix) or isinstance(f, moose__.element) else f for f in fields] class_array_dict[obj.className].append(fields) diff --git a/python/moose/moose.py b/python/moose/moose.py index 92e87d5..af62d19 100644 --- a/python/moose/moose.py +++ b/python/moose/moose.py @@ -31,6 +31,7 @@ # Code: +from __future__ import print_function import cStringIO import warnings import platform @@ -76,7 +77,7 @@ def pwe(): """ pwe_ = _moose.getCwe() - print pwe_.getPath() + print(pwe_.getPath()) return pwe_ def le(el=None): @@ -102,9 +103,9 @@ def le(el=None): el = element(el) elif isinstance(el, ematrix): el = el[0] - print 'Elements under', el.path + print('Elements under', el.path) for ch in el.children: - print ch.path + print(ch.path) ce = setCwe # ce is a GENESIS shorthand for change element. @@ -163,7 +164,7 @@ def showfield(el, field='*', showtype=False): value_field_dict = getFieldDict(el.className, 'valueFinfo') max_type_len = max([len(dtype) for dtype in list(value_field_dict.values())]) max_field_len = max([len(dtype) for dtype in list(value_field_dict.keys())]) - print '\n[', el.path, ']' + print('\n[', el.path, ']') for key, dtype in list(value_field_dict.items()): if dtype == 'bad' or key == 'this' or key == 'dummy' or key == 'me' or dtype.startswith('vector') or 'ObjId' in dtype: continue @@ -173,11 +174,11 @@ def showfield(el, field='*', showtype=False): # The following hack is for handling both Python 2 and # 3. Directly putting the print command in the if/else # clause causes syntax error in both systems. - print typestr, - print key.ljust(max_field_len + 4), '=', value + print(typestr, end=' ') + print(key.ljust(max_field_len + 4), '=', value) else: try: - print field, '=', el.getField(field) + print(field, '=', el.getField(field)) except AttributeError: pass # Genesis silently ignores non existent fields @@ -233,12 +234,12 @@ def showmsg(el): """ obj = element(el) - print 'INCOMING:' + print('INCOMING:') for msg in obj.msgIn: - print msg.e2.path, msg.destFieldsOnE2, '<---', msg.e1.path, msg.srcFieldsOnE1 - print 'OUTGOING:' + print(msg.e2.path, msg.destFieldsOnE2, '<---', msg.e1.path, msg.srcFieldsOnE1) + print('OUTGOING:') for msg in obj.msgOut: - print msg.e1.path, msg.srcFieldsOnE1, '--->', msg.e2.path, msg.destFieldsOnE2 + print(msg.e1.path, msg.srcFieldsOnE1, '--->', msg.e2.path, msg.destFieldsOnE2) def getfielddoc(tokens, indent=''): """Return the documentation for field specified by `tokens`. @@ -390,7 +391,7 @@ def doc(arg, paged=False): if pager: pager(text) else: - print text + print(text) # diff --git a/python/moose/moose_py3k.py b/python/moose/moose_py3k.py index 43dd80b..f4c5302 100644 --- a/python/moose/moose_py3k.py +++ b/python/moose/moose_py3k.py @@ -30,6 +30,7 @@ # Code: +from __future__ import print_function import warnings import platform from collections import defaultdict diff --git a/python/moose/mtypes.py b/python/moose/mtypes.py index 6a3ae57..2f520ad 100644 --- a/python/moose/mtypes.py +++ b/python/moose/mtypes.py @@ -45,6 +45,7 @@ # Code: +from __future__ import print_function import re import moose @@ -142,7 +143,7 @@ def isNeuroML(filename): """ doc = md.parse(filename) for child in doc.childNodes: - print child.nodeName, child.nodeType == child.ELEMENT_NODE + print(child.nodeName, child.nodeType == child.ELEMENT_NODE) if child.nodeType == child.ELEMENT_NODE and \ (child.nodeName == 'networkml' or \ child.nodeName == 'morphml' or \ diff --git a/python/moose/multiscale/core/mumbl.py b/python/moose/multiscale/core/mumbl.py index e6ec650..32e5ca1 100644 --- a/python/moose/multiscale/core/mumbl.py +++ b/python/moose/multiscale/core/mumbl.py @@ -8,6 +8,8 @@ Last modified: Fri Jan 24, 2014 05:27PM """ +from __future__ import print_function + __author__ = "Dilawar Singh" __copyright__ = "Copyright 2013, NCBS Bangalore" __credits__ = ["NCBS Bangalore", "Bhalla Lab"] diff --git a/python/moose/multiscale/core/simulator.py b/python/moose/multiscale/core/simulator.py index bffb2cf..03f519b 100644 --- a/python/moose/multiscale/core/simulator.py +++ b/python/moose/multiscale/core/simulator.py @@ -7,6 +7,8 @@ Last modified: Sat Feb 01, 2014 04:01AM """ +from __future__ import print_function + __author__ = "Dilawar Singh" __copyright__ = "Copyright 2013, NCBS Bangalore" diff --git a/python/moose/multiscale/core/stimulus.py b/python/moose/multiscale/core/stimulus.py index 1cc63db..f144259 100644 --- a/python/moose/multiscale/core/stimulus.py +++ b/python/moose/multiscale/core/stimulus.py @@ -5,6 +5,8 @@ Created on: 2013-11-25 Description: generates stimuous """ +from __future__ import print_function + import random import numpy as np @@ -139,7 +141,7 @@ def timetable_file(filename='timetable.txt', simtime=100): def timetable_demo(): tt_array, sp_array = timetable_nparray() - print sp_array + print(sp_array) tt_file, sp_file = timetable_file() # Create a synchan inside a compartment to demonstrate how to use # TimeTable to send artificial spike events to a synapse. diff --git a/python/moose/multiscale/core/types.py b/python/moose/multiscale/core/types.py index ca3d31e..4ae60c1 100644 --- a/python/moose/multiscale/core/types.py +++ b/python/moose/multiscale/core/types.py @@ -75,4 +75,4 @@ if __name__ == "__main__": for s in b: a.insertUniqueVal(s) - print a + print(a) diff --git a/python/moose/multiscale/helper/moose_methods.py b/python/moose/multiscale/helper/moose_methods.py index f51e4e1..b99b4bd 100644 --- a/python/moose/multiscale/helper/moose_methods.py +++ b/python/moose/multiscale/helper/moose_methods.py @@ -7,6 +7,8 @@ Last modified: Tue Jan 28, 2014 10:31PM """ +from __future__ import print_function + __author__ = "Dilawar Singh" __copyright__ = "Copyright 2013, NCBS Bangalore" __credits__ = ["NCBS Bangalore", "Bhalla Lab"] @@ -135,7 +137,7 @@ def dumpMatchingPaths(path, pat='/##'): def dumpFieldName(path, whichInfo='valueF'): - print path.getFieldNames(whichInfo+'info') + print(path.getFieldNames(whichInfo+'info')) def writeGraphviz(pat='/##', filename=None, filterList=[]): '''This is a generic function. It takes the the pattern, search for paths diff --git a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/FvsI_Granule98.py b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/FvsI_Granule98.py index 8544793..5c0d2a4 100755 --- a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/FvsI_Granule98.py +++ b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/FvsI_Granule98.py @@ -8,6 +8,7 @@ ## Modification Date: 2012-07-12 ######################################################################################## +from __future__ import print_function import os os.environ['NUMPTHREADS'] = '1' import sys @@ -56,8 +57,8 @@ for currenti in currentvec: spikesList = spikesList[where(spikesList>0.0)[0]] spikesNow = len(spikesList) else: spikesNow = 0.0 - print "For injected current =",currenti,\ - "number of spikes in",RUNTIME,"seconds =",spikesNow + print("For injected current =", currenti, + "number of spikes in", RUNTIME, "seconds =", spikesNow) freqList.append( spikesNow/float(RUNTIME) ) ## plot the F vs I curve of the neuron diff --git a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98.py b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98.py index 6f4215d..4d3bb4b 100755 --- a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98.py +++ b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98.py @@ -6,6 +6,7 @@ python testNeuroML_Gran98.py (other channels and morph xml files are already present in this same directory). The soma name below is hard coded for gran98, else any other file can be used by modifying this script. """ +from __future__ import print_function import os os.environ['NUMPTHREADS'] = '1' import sys @@ -31,9 +32,9 @@ def loadGran98NeuroML_L123(filename): somaIKCa = setupTable('somaIKCa',moose.HHChannel(soma_path+'/Gran_KCa_98'),'Gk') #KDrX = setupTable('ChanX',moose.HHChannel(soma_path+'/Gran_KDr_98'),'X') soma = moose.Compartment(soma_path) - print "Reinit MOOSE ... " + print("Reinit MOOSE ... ") resetSim(['/elec','/cells'],simdt,plotdt,simmethod='ee') # from moose.utils - print "Running ... " + print("Running ... ") moose.start(runtime) tvec = arange(0.0,runtime,plotdt) plot(tvec,somaVm.vec[1:]) @@ -50,7 +51,7 @@ def loadGran98NeuroML_L123(filename): title('KCa current (A)') xlabel('time (s)') ylabel('') - print "Showing plots ..." + print("Showing plots ...") show() filename = "GranuleCell.net.xml" diff --git a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98_hsolve.py b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98_hsolve.py index c9b2172..3fae9ad 100755 --- a/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98_hsolve.py +++ b/python/moose/multiscale/models/neuroml/v1.8/GranuleCell/Granule98_hsolve.py @@ -7,6 +7,7 @@ python testNeuroML_Gran98.py The soma name below is hard coded for gran98, else any other file can be used by modifying this script. """ +from __future__ import print_function import os os.environ['NUMPTHREADS'] = '1' import sys @@ -34,11 +35,11 @@ def loadGran98NeuroML_L123(filename): ## Am not able to plot KDr gating variable X when running under hsolve #KDrX = setupTable('ChanX',moose.HHChannel(soma_path+'/Gran_KDr_98'),'X') - print "Reinit MOOSE ... " - print cells_path + print("Reinit MOOSE ... ") + print(cells_path) resetSim(['/elec',cells_path], simdt, plotdt, simmethod='hsolve') - print "Running ... " + print("Running ... ") moose.start(runtime) tvec = arange(0.0,runtime*2.0,plotdt) tvec = tvec[ : somaVm.vec.size ] @@ -56,7 +57,7 @@ def loadGran98NeuroML_L123(filename): title('soma KCa current') xlabel('time (s)') ylabel('KCa current (A)') - print "Showing plots ..." + print("Showing plots ...") show() filename = "GranuleCell.net.xml" diff --git a/python/moose/multiscale/multi_bhalla/diffusionOnly.py b/python/moose/multiscale/multi_bhalla/diffusionOnly.py index 9965ce2..636f9de 100644 --- a/python/moose/multiscale/multi_bhalla/diffusionOnly.py +++ b/python/moose/multiscale/multi_bhalla/diffusionOnly.py @@ -30,6 +30,7 @@ # Code: +from __future__ import print_function import sys sys.path.append('../../python') import os @@ -95,7 +96,7 @@ def loadChem( neuroCompt, spineCompt, psdCompt ): assert( spineCompt.volume == 1.0 ) assert( psdCompt.volume == 1.0 ) assert( neuroCompt.mesh.num == 1 ) - print 'volume = ', neuroCompt.mesh[0].volume + print('volume = ', neuroCompt.mesh[0].volume) #assert( neuroCompt.mesh[0].volume == 1.0 ) #an unfortunate mismatch # So we'll have to resize the volumes of the current compartments to the @@ -114,7 +115,7 @@ def loadChem( neuroCompt, spineCompt, psdCompt ): pCaCaM.concInit = 0.001 dCaCaM = moose.element( '/model/model/kinetics/PSD/Ca_CaM' ) sCaCaM = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' ) - print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit + print("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit) #moose.delete( moose.ematrix( '/model/model/kinetics/SPINE/Ca_CaM' ) ) #CaCaM2 = moose.element( '/model/model/kinetics/SPINE/Ca_CaM' ) #CaCaM2.concInit = 0.001 @@ -123,20 +124,20 @@ def loadChem( neuroCompt, spineCompt, psdCompt ): oldS = moose.element( '/model/chem/compartment_1' ) oldP = moose.element( '/model/chem/compartment_2' ) oldN = moose.element( '/model/chem/kinetics' ) - print 'oldvols[p,s,d] = ', oldP.volume, oldS.volume, oldN.volume - print 'newvols[p,s,d] = ', psdCompt.mesh[0].volume, spineCompt.mesh[0].volume, neuroCompt.mesh[0].volume + print('oldvols[p,s,d] = ', oldP.volume, oldS.volume, oldN.volume) + print('newvols[p,s,d] = ', psdCompt.mesh[0].volume, spineCompt.mesh[0].volume, neuroCompt.mesh[0].volume) oldN.volume = neuroCompt.mesh[0].volume oldS.volume = spineCompt.mesh[0].volume oldP.volume = psdCompt.mesh[0].volume - print 'after redoing vols' - print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit + print('after redoing vols') + print("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit) moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt ) moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt ) # Need to do the DEND last because the oldN is /kinetics, # and it will be deleted. moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt ) - print 'after moving to new compts' - print "CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit + print('after moving to new compts') + print("CaCaM.concInit[p,s,d] = ", pCaCaM.concInit, sCaCaM.concInit, dCaCaM.concInit) def makeNeuroMeshModel(): diffLength = 20e-6 # But we only want diffusion over part of the model. @@ -198,7 +199,7 @@ def makeNeuroMeshModel(): moose.connect( pm, 'remesh', pmksolve, 'remesh' ) #print "psd: nv=", pmksolve.numLocalVoxels, ", nav=", pmksolve.numAllVoxels, pmksolve.numVarPools, pmksolve.numAllPools # - print 'neuroMeshvolume = ', neuroCompt.mesh[0].volume + print('neuroMeshvolume = ', neuroCompt.mesh[0].volume) #print 'Assigning the cell model' # Now to set up the model. @@ -423,7 +424,7 @@ def testNeuroMeshMultiscale(): moose.start( 0.5 ) dumpPlots( plotName ) - print 'All done' + print('All done') def main(): diff --git a/python/moose/multiscale/multi_bhalla/lm2.py b/python/moose/multiscale/multi_bhalla/lm2.py index f27640e..d290d1b 100644 --- a/python/moose/multiscale/multi_bhalla/lm2.py +++ b/python/moose/multiscale/multi_bhalla/lm2.py @@ -25,6 +25,7 @@ # Code: +from __future__ import print_function import sys import os os.environ['NUMPTHREADS'] = '1' @@ -66,13 +67,13 @@ def addPlot( objpath, field, plot ): tab = moose.Table( '/graphs/' + plot ) obj = moose.element( objpath ) if obj.className == 'Neutral': - print "addPlot failed: object is a Neutral: ", objpath + print("addPlot failed: object is a Neutral: ", objpath) return moose.element( '/' ) else: moose.connect( tab, 'requestData', obj, field ) return tab else: - print "addPlot failed: object not found: ", objpath + print("addPlot failed: object not found: ", objpath) return moose.element( '/' ) def dumpPlots( fname ): @@ -298,7 +299,7 @@ def testNeuroMeshMultiscale(): moose.start( 0.5 ) dumpPlots( plotName ) - print 'All done' + print('All done') def main(): diff --git a/python/moose/multiscale/multi_bhalla/loadMulti.py b/python/moose/multiscale/multi_bhalla/loadMulti.py index 10a26cd..6b4a563 100644 --- a/python/moose/multiscale/multi_bhalla/loadMulti.py +++ b/python/moose/multiscale/multi_bhalla/loadMulti.py @@ -24,6 +24,7 @@ # Code: +from __future__ import print_function import sys sys.path.append('../../python') import os @@ -66,14 +67,14 @@ def addPlot( objpath, field, plot ): tab = moose.Table( '/graphs/' + plot ) obj = moose.element( objpath ) if obj.className == 'Neutral': - print "addPlot failed: object is a Neutral: ", objpath + print("addPlot failed: object is a Neutral: ", objpath) return moose.element( '/' ) else: #print "object was found: ", objpath, obj.className moose.connect( tab, 'requestData', obj, field ) return tab else: - print "addPlot failed: object not found: ", objpath + print("addPlot failed: object not found: ", objpath) return moose.element( '/' ) def dumpPlots( fname ): @@ -102,7 +103,7 @@ def loadChem( neuroCompt, spineCompt, psdCompt ): assert( spineCompt.volume == 1.0 ) assert( psdCompt.volume == 1.0 ) assert( neuroCompt.mesh.num == 1 ) - print 'volume = ', neuroCompt.mesh[0].volume + print('volume = ', neuroCompt.mesh[0].volume) #assert( neuroCompt.mesh[0].volume == 1.0 ) #an unfortunate mismatch # So we'll have to resize the volumes of the current compartments to the @@ -114,33 +115,33 @@ def loadChem( neuroCompt, spineCompt, psdCompt ): oldN = moose.element( '/model/chem/kinetics' ) oldS = moose.element( '/model/chem/compartment_1' ) oldP = moose.element( '/model/chem/compartment_2' ) - print 'old NSP vols = ', oldN.volume, oldS.volume, oldP.volume - print 'old NSP.mesh vols = ', oldN.mesh[0].volume, oldS.mesh[0].volume, oldP.mesh[0].volume - print 'new NSP vols = ', neuroCompt.volume, spineCompt.volume, psdCompt.volume - print 'new NSP.mesh vols = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume + print('old NSP vols = ', oldN.volume, oldS.volume, oldP.volume) + print('old NSP.mesh vols = ', oldN.mesh[0].volume, oldS.mesh[0].volume, oldP.mesh[0].volume) + print('new NSP vols = ', neuroCompt.volume, spineCompt.volume, psdCompt.volume) + print('new NSP.mesh vols = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume) for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ): - print i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb + print(i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb) tr0 = moose.element( '/model/chem/kinetics/SPINE/CaMKII_BULK/tr0[6]' ) - print "tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb + print("tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb) oldN.volume = neuroCompt.mesh[0].volume oldS.volume = spineCompt.mesh[0].volume oldP.volume = psdCompt.mesh[0].volume #oldN.volume = neuroCompt.volume #oldS.volume = spineCompt.volume #oldP.volume = psdCompt.volume - print 'old NSP vols = ', oldN.volume, oldS.volume, oldP.volume - print 'old NSP.mesh vols = ', oldN.mesh[0].volume, oldS.mesh[0].volume, oldP.mesh[0].volume - print 'new NSP vols = ', neuroCompt.volume, spineCompt.volume, psdCompt.volume - print 'new NSP.mesh vols = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume - print "tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb + print('old NSP vols = ', oldN.volume, oldS.volume, oldP.volume) + print('old NSP.mesh vols = ', oldN.mesh[0].volume, oldS.mesh[0].volume, oldP.mesh[0].volume) + print('new NSP vols = ', neuroCompt.volume, spineCompt.volume, psdCompt.volume) + print('new NSP.mesh vols = ', neuroCompt.mesh[0].volume, spineCompt.mesh[0].volume, psdCompt.mesh[0].volume) + print("tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb) for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ): - print i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb + print(i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb) moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt ) moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt ) moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt ) - print "aftermove tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb + print("aftermove tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb) for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ): - print i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb + print(i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb) def makeNeuroMeshModel(): diffLength = 20e-6 # But we only want diffusion over part of the model. @@ -256,14 +257,14 @@ def makeNeuroMeshModel(): path = '/model/elec/spine_head_14_' + str( i + 1 ) + '/NMDA_Ca_conc' elecCa = moose.element( path ) moose.connect( elecCa, 'concOut', adaptCa[i], 'input', 'Single' ) - print path + print(path) moose.connect( adaptCa, 'outputSrc', chemCa, 'set_conc', 'OneToOne' ) adaptCa.inputOffset = 0.0 # adaptCa.outputOffset = 0.00008 # 80 nM offset in chem. adaptCa.scale = 1e-5 # 520 to 0.0052 mM - print adaptCa.inputOffset - print adaptCa.outputOffset - print adaptCa.scale + print(adaptCa.inputOffset) + print(adaptCa.outputOffset) + print(adaptCa.scale) #print adaptCa.outputOffset #print adaptCa.scale @@ -348,9 +349,9 @@ def makeChemPlots(): addPlot( '/model/chem/spineMesh/SPINE/CaMKII_BULK/foo[6]', 'get_conc', 'spine_foo' ) bar = moose.element( '/model/chem/psdMesh/PSD/CaMKII_PSD/bar[6]' ) foo = moose.element( '/model/chem/spineMesh/SPINE/CaMKII_BULK/foo[6]' ) - print "bar,foo vols = ", bar.volume, foo.volume, bar.concInit, foo.concInit + print("bar,foo vols = ", bar.volume, foo.volume, bar.concInit, foo.concInit) tr0 = moose.element( '/model/chem/spineMesh/SPINE/CaMKII_BULK/tr0[6]' ) - print "tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb + print("tr0 rates = ", tr0.Kf, tr0.Kb, tr0.kf, tr0.kb) signal.signal( signal.SIGUSR1, do_nothing) @@ -361,9 +362,9 @@ def testNeuroMeshMultiscale(): plotName = 'nm.plot' makeNeuroMeshModel() - print "after model is completely done" + print("after model is completely done") for i in moose.wildcardFind( '/model/chem/#/#/#/transloc#' ): - print i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb + print(i[0].name, i[0].Kf, i[0].Kb, i[0].kf, i[0].kb) """ for i in moose.wildcardFind( '/model/chem/##[ISA=PoolBase]' ): @@ -427,7 +428,7 @@ def testNeuroMeshMultiscale(): moose.start( 0.5 ) dumpPlots( plotName ) - print 'All done' + print('All done') def main(): diff --git a/python/moose/multiscale/multi_bhalla/minimal.py b/python/moose/multiscale/multi_bhalla/minimal.py index 278bc11..7eb1a7a 100644 --- a/python/moose/multiscale/multi_bhalla/minimal.py +++ b/python/moose/multiscale/multi_bhalla/minimal.py @@ -27,6 +27,7 @@ # Code: +from __future__ import print_function import sys sys.path.append('../../python') import os @@ -350,7 +351,7 @@ def testNeuroMeshMultiscale(): moose.start( 0.5 ) dumpPlots( plotName ) - print 'All done' + print('All done') def main(): diff --git a/python/moose/multiscale/multi_bhalla/runcell18.py b/python/moose/multiscale/multi_bhalla/runcell18.py index 3387680..387f2b3 100644 --- a/python/moose/multiscale/multi_bhalla/runcell18.py +++ b/python/moose/multiscale/multi_bhalla/runcell18.py @@ -1,3 +1,5 @@ +from __future__ import print_function + # First pass at loading and running a cell model import os os.environ['NUMPTHREADS'] = '1' @@ -38,7 +40,7 @@ soma.inject = 2e-10 moose.connect( tab, 'requestData', soma, 'get_Vm' ) capool = moose.element( '/cell/soma/Ca_conc' ) moose.connect( catab, 'requestData', capool, 'get_Ca' ) -print 1 +print(1) dt = 50e-6 moose.setClock( 0, dt ) moose.setClock( 1, dt ) @@ -49,12 +51,12 @@ moose.useClock( 1, '/cell/##[ISA=Compartment]', 'process' ) moose.useClock( 2, '/cell/##[ISA!=Compartment]', 'process' ) moose.useClock( 3, '/graphs/soma,/graphs/ca', 'process' ) -print 2 +print(2) moose.reinit() -print 3 +print(3) moose.start( 0.1 ) dumpPlots( '50usec.plot' ) -print 4 +print(4) moose.reinit() hsolve = moose.HSolve( '/cell/hsolve' ) moose.useClock( 1, '/cell/hsolve', 'process' ) @@ -62,10 +64,10 @@ hsolve.dt = dt hsolve.target = '/cell/soma' moose.reinit() moose.reinit() -print 5 +print(5) moose.start( 0.1 ) -print 6 +print(6) dumpPlots( 'h50usec.plot' ) -print 7 +print(7) diff --git a/python/moose/multiscale/multi_bhalla/x_compt.py b/python/moose/multiscale/multi_bhalla/x_compt.py index bd46996..a108545 100644 --- a/python/moose/multiscale/multi_bhalla/x_compt.py +++ b/python/moose/multiscale/multi_bhalla/x_compt.py @@ -31,6 +31,7 @@ # Code: +from __future__ import print_function import sys sys.path.append('../../python') import os @@ -362,7 +363,7 @@ def testNeuroMeshMultiscale(): moose.start( 0.5 ) dumpPlots( plotName ) - print 'All done' + print('All done') def main(): diff --git a/python/moose/multiscale/parser/NetworkML.py b/python/moose/multiscale/parser/NetworkML.py index eb60e28..9ec1562 100644 --- a/python/moose/multiscale/parser/NetworkML.py +++ b/python/moose/multiscale/parser/NetworkML.py @@ -22,6 +22,7 @@ """ +from __future__ import print_function from xml.etree import cElementTree as ET import string import os @@ -527,7 +528,7 @@ class NetworkML(object): except KeyError as e: debug.printDebug("ERR", "Failed find key {0}".format(e) , frame = inspect.currentframe()) - print self.projectionDict.keys() + print(self.projectionDict.keys()) sys.exit(0) properties = connection.findall('./{'+nmu.nml_ns+'}properties') diff --git a/python/moose/multiscale/parser/utils.py b/python/moose/multiscale/parser/utils.py index ad9f051..18e2ae2 100644 --- a/python/moose/multiscale/parser/utils.py +++ b/python/moose/multiscale/parser/utils.py @@ -11,6 +11,7 @@ while still including certain others. indent(...) is an in-place prettyprint formatter copied from http://effbot.org/zone/element-lib.htm """ +from __future__ import print_function from xml.etree import cElementTree as ET from xml.etree import ElementTree as slowET from math import * diff --git a/python/moose/neuroml/ChannelML.py b/python/moose/neuroml/ChannelML.py index c560aa3..79ca6f9 100644 --- a/python/moose/neuroml/ChannelML.py +++ b/python/moose/neuroml/ChannelML.py @@ -11,6 +11,7 @@ readChannelMLFromFile(...) to load a standalone ChannelML file (synapse/channel) readChannelML(...) / readSynapseML to load from an xml.etree xml element (could be part of a larger NeuroML file). """ +from __future__ import print_function from xml.etree import cElementTree as ET import string import os, sys @@ -49,10 +50,10 @@ class ChannelML(): Tfactor = 1.0 Gfactor = 1.0 else: - print "wrong units", units,": exiting ..." + print("wrong units", units,": exiting ...") sys.exit(1) moose.Neutral('/library') # creates /library in MOOSE tree; elif present, wraps - if utils.neuroml_debug: print "loading synapse :",synapseElement.attrib['name'],"into /library ." + if utils.neuroml_debug: print("loading synapse :",synapseElement.attrib['name'],"into /library .") moosesynapse = moose.SynChan('/library/'+synapseElement.attrib['name']) doub_exp_syn = synapseElement.find('./{'+self.cml+'}doub_exp_syn') moosesynapse.Ek = float(doub_exp_syn.attrib['reversal_potential'])*Vfactor @@ -81,11 +82,11 @@ class ChannelML(): Gfactor = 1.0 concfactor = 1.0 else: - print "wrong units", units,": exiting ..." + print("wrong units", units,": exiting ...") sys.exit(1) moose.Neutral('/library') # creates /library in MOOSE tree; elif present, wraps channel_name = channelElement.attrib['name'] - if utils.neuroml_debug: print "loading channel :", channel_name,"into /library ." + if utils.neuroml_debug: print("loading channel :", channel_name,"into /library .") IVrelation = channelElement.find('./{'+self.cml+'}current_voltage_relation') concdep = IVrelation.find('./{'+self.cml+'}conc_dependence') if concdep is None: @@ -113,7 +114,7 @@ class ChannelML(): gates = IVrelation.findall('./{'+self.cml+'}gate') if len(gates)>3: - print "Sorry! Maximum x, y, and z (three) gates are possible in MOOSE/Genesis" + print("Sorry! Maximum x, y, and z (three) gates are possible in MOOSE/Genesis") sys.exit() gate_full_name = [ 'gateX', 'gateY', 'gateZ' ] # These are the names that MOOSE uses to create gates. ## if impl_prefs tag is present change VMIN, VMAX and NDIVS @@ -195,7 +196,7 @@ class ChannelML(): if fn_name in ['alpha','beta']: self.make_cml_function(transition, fn_name, concdep) else: - print "Unsupported transition ", name + print("Unsupported transition ", name) sys.exit() time_course = gate.find('./{'+self.cml+'}time_course') @@ -326,10 +327,10 @@ class ChannelML(): ionSpecies = ionConcElement.find('./{'+self.cml+'}ion_species') if ionSpecies is not None: if not 'ca' in ionSpecies.attrib['name']: - print "Sorry, I cannot handle non-Ca-ion pools. Exiting ..." + print("Sorry, I cannot handle non-Ca-ion pools. Exiting ...") sys.exit(1) capoolName = ionConcElement.attrib['name'] - print "loading Ca pool :",capoolName,"into /library ." + print("loading Ca pool :",capoolName,"into /library .") caPool = moose.CaConc('/library/'+capoolName) poolModel = ionConcElement.find('./{'+self.cml+'}decaying_pool_model') caPool.CaBasal = float(poolModel.attrib['resting_conc']) * concfactor @@ -370,7 +371,7 @@ class ChannelML(): expr_string = self.replace(expr_string, 'beta', 'self.beta(v'+ca_name+')') fn = self.make_function( fn_name, fn_type, expr_string=expr_string, concdep=concdep ) else: - print "Unsupported function type ", fn_type + print("Unsupported function type ", fn_type) sys.exit() def make_function(self, fn_name, fn_type, **kwargs): diff --git a/python/moose/neuroml/MorphML.py b/python/moose/neuroml/MorphML.py index 14282c9..6982c87 100644 --- a/python/moose/neuroml/MorphML.py +++ b/python/moose/neuroml/MorphML.py @@ -13,6 +13,7 @@ It is assumed that any channels and synapses referred to by above MorphML have already been loaded under that same name in /library in MOOSE (use ChannelML loader). """ +from __future__ import print_function from xml.etree import cElementTree as ET # cELementTree is mostly API-compatible but faster than ElementTree import string import sys @@ -43,7 +44,7 @@ class MorphML(): returns { cellname1 : segDict, ... } see readMorphML(...) for segDict """ - print filename + print(filename) tree = ET.parse(filename) neuroml_element = tree.getroot() cellsDict = {} @@ -66,7 +67,7 @@ class MorphML(): self.length_factor = 1.0 cellname = cell.attrib["name"] moose.Neutral('/library') # creates /library in MOOSE tree; elif present, wraps - print "loading cell :", cellname,"into /library ." + print("loading cell :", cellname,"into /library .") if 'IF' in cellname: # if integrate & fire -- hackjob -- rectify moosecell = moose.LeakyIaF('/library/'+cellname) @@ -186,7 +187,7 @@ class MorphML(): ## with the potential synapses on this segment, in function set_compartment_param(..) self.segDict[running_segid] = [running_comp.name,(running_comp.x0,running_comp.y0,running_comp.z0),\ (running_comp.x,running_comp.y,running_comp.z),running_comp.diameter,running_comp.length,[]] - if neuroml_utils.neuroml_debug: print 'Set up compartment/section', running_comp.name + if neuroml_utils.neuroml_debug: print('Set up compartment/section', running_comp.name) ############################################### #### load cablegroups into a dictionary @@ -284,7 +285,7 @@ class MorphML(): if mechanism.attrib.has_key("passive_conductance"): if mechanism.attrib['passive_conductance'] in ["true",'True','TRUE']: passive = True - print "Loading mechanism ", mechanismname + print("Loading mechanism ", mechanismname) ## ONLY creates channel if at least one parameter (like gmax) is specified in the xml ## Neuroml does not allow you to specify all default values. ## However, granule cell example in neuroconstruct has Ca ion pool without @@ -308,8 +309,8 @@ class MorphML(): self.set_group_compartment_param(cell, cellname, parameter,\ 'inject', Ifactor*float(parameter.attrib["value"]), self.bio) else: - print "WARNING: Yo programmer of MorphML! You didn't implement parameter ",\ - parametername, " in mechanism ",mechanismname + print("WARNING: Yo programmer of MorphML! You didn't implement parameter ",\ + parametername, " in mechanism ",mechanismname) else: if parametername in ['gmax']: gmaxval = float(eval(parameter.attrib["value"],{"__builtins__":None},{})) @@ -323,8 +324,8 @@ class MorphML(): 'thick', self.length_factor*float(parameter.attrib["value"]),\ self.bio, mechanismname) else: - print "WARNING: Yo programmer of MorphML import! You didn't implement parameter ",\ - parametername, " in mechanism ",mechanismname + print("WARNING: Yo programmer of MorphML import! You didn't implement parameter ",\ + parametername, " in mechanism ",mechanismname) #### Connect the Ca pools and channels #### Am connecting these at the very end so that all channels and pools have been created #### Note: this function is in moose.utils not moose.neuroml.utils ! @@ -344,7 +345,7 @@ class MorphML(): self.set_group_compartment_param(cell, cellname, potential_syn_loc,\ 'spikegen_type', potential_syn_loc.attrib['synapse_type'], self.nml, mechanismname='spikegen') - print "Finished loading into library, cell: ",cellname + print("Finished loading into library, cell: ",cellname) return {cellname:self.segDict} def set_group_compartment_param(self, cell, cellname, parameter, name, value, grouptype, mechanismname=None): @@ -375,7 +376,7 @@ class MorphML(): elif name == 'initVm': compartment.initVm = value elif name == 'inject': - print compartment.name, 'inject', value, 'A.' + print(compartment.name, 'inject', value, 'A.') compartment.inject = value elif mechanismname is 'synapse': # synapse being added to the compartment ## these are potential locations, we do not actually make synapses. @@ -465,4 +466,4 @@ class MorphML(): ## Later, when calling connect_CaConc, ## B is set for caconc based on thickness of Ca shell and compartment l and dia. ## OR based on the Mstring phi under CaConc path. - if neuroml_utils.neuroml_debug: print "Setting ",name," for ",compartment.path," value ",value + if neuroml_utils.neuroml_debug: print("Setting ",name," for ",compartment.path," value ",value) diff --git a/python/moose/neuroml/NetworkML.py b/python/moose/neuroml/NetworkML.py index ccce65a..a521ed9 100644 --- a/python/moose/neuroml/NetworkML.py +++ b/python/moose/neuroml/NetworkML.py @@ -11,6 +11,7 @@ readNetworkMLFromFile(...) to load a standalone NetworkML file, OR readNetworkML(...) to load from an xml.etree xml element (could be part of a larger NeuroML file). """ +from __future__ import print_function from xml.etree import cElementTree as ET import string import os @@ -47,12 +48,12 @@ class NetworkML(): these synapses receive file based pre-synaptic events, not presynaptically connected to a cell. """ - print "reading file ... ", filename + print("reading file ... ", filename) tree = ET.parse(filename) root_element = tree.getroot() - print "Tweaking model ... " + print("Tweaking model ... ") tweak_model(root_element, params) - print "Loading model into MOOSE ... " + print("Loading model into MOOSE ... ") return self.readNetworkML(root_element,cellSegmentDict,params,root_element.attrib['lengthUnits']) def readNetworkML(self,network,cellSegmentDict,params={},lengthUnits="micrometer"): @@ -67,11 +68,11 @@ class NetworkML(): self.network = network self.cellSegmentDict = cellSegmentDict self.params = params - print "creating populations ... " + print("creating populations ... ") self.createPopulations() # create cells - print "creating connections ... " + print("creating connections ... ") self.createProjections() # create connections - print "creating inputs in /elec ... " + print("creating inputs in /elec ... ") self.createInputs() # create inputs (only current pulse supported) return (self.populationDict,self.projectionDict) @@ -132,7 +133,7 @@ class NetworkML(): for population in self.network.findall(".//{"+nml_ns+"}population"): cellname = population.attrib["cell_type"] populationname = population.attrib["name"] - print "loading", populationname + print("loading", populationname) ## if cell does not exist in library load it from xml file if not moose.exists('/library/'+cellname): mmlR = MorphML(self.nml_params) @@ -218,7 +219,7 @@ class NetworkML(): Tfactor = 1.0 for projection in self.network.findall(".//{"+nml_ns+"}projection"): projectionname = projection.attrib["name"] - print "setting",projectionname + print("setting",projectionname) source = projection.attrib["source"] target = projection.attrib["target"] self.projectionDict[projectionname] = (source,target,[]) diff --git a/python/moose/neuroml/NeuroML.py b/python/moose/neuroml/NeuroML.py index 3712c9b..4594c0a 100644 --- a/python/moose/neuroml/NeuroML.py +++ b/python/moose/neuroml/NeuroML.py @@ -21,6 +21,7 @@ use the separate Channel, Morph and NetworkML loaders in moose.neuroml.<...> . For testing, you can also call this from the command line with a neuroML file as argument. """ +from __future__ import print_function import moose from moose.utils import * from xml.etree import cElementTree as ET @@ -44,7 +45,7 @@ class NeuroML(): Returns (populationDict,projectionDict), see doc string of NetworkML.readNetworkML() for details. """ - print "Loading neuroml file ... ", filename + print("Loading neuroml file ... ", filename) moose.Neutral('/library') # creates /library in MOOSE tree; elif present, wraps tree = ET.parse(filename) root_element = tree.getroot() @@ -58,7 +59,7 @@ class NeuroML(): self.temperature = float(meta_property.attrib['value']) self.temperature_default = False if self.temperature_default: - print "Using default temperature of", self.temperature,"degrees Celsius." + print("Using default temperature of", self.temperature,"degrees Celsius.") self.nml_params = { 'temperature':self.temperature, 'model_dir':self.model_dir, @@ -96,7 +97,7 @@ def loadNeuroML_L123(filename): if __name__ == "__main__": if len(sys.argv)<2: - print "You need to specify the neuroml filename." + print("You need to specify the neuroml filename.") sys.exit(1) loadNeuroML_L123(sys.argv[1]) diff --git a/python/moose/neuroml/utils.py b/python/moose/neuroml/utils.py index 39ab789..3a1e3c0 100644 --- a/python/moose/neuroml/utils.py +++ b/python/moose/neuroml/utils.py @@ -11,6 +11,7 @@ while still including certain others. indent(...) is an in-place prettyprint formatter copied from http://effbot.org/zone/element-lib.htm """ +from __future__ import print_function from xml.etree import cElementTree as ET from xml.etree import ElementTree as slowET from math import * @@ -139,7 +140,7 @@ def keepOnlyInclude(network, onlyInclude): includeCellsDict = {includepopname:includecellids} ## projections 'includeProjs' will be pruned later, keeping connections to second order cells. includeProjs = [] - print "removing obviously extra connections in ... " + print("removing obviously extra connections in ... ") for projection in network.findall(".//{"+nml_ns+"}projection"): projname = projection.attrib['name'] includeProj = False @@ -153,7 +154,7 @@ def keepOnlyInclude(network, onlyInclude): includeProjs.append(projection) source = projection.attrib["source"] target = projection.attrib["target"] - print projname, source, target + print(projname, source, target) connections = projection.find(".//{"+nml_ns+"}connections") if connections is not None: for connection in connections.findall(".//{"+nml_ns+"}connection"): @@ -190,7 +191,7 @@ def keepOnlyInclude(network, onlyInclude): for key in includeCellsDict: includeCellsDict[key] = set(includeCellsDict[key]) - print "removing extra cells ... " + print("removing extra cells ... ") ### remove the cells that are not in includeCellsDict populations = network.find(".//{"+nml_ns+"}populations") for population in network.findall(".//{"+nml_ns+"}population"): @@ -208,8 +209,8 @@ def keepOnlyInclude(network, onlyInclude): ### Prune the 'includeProjections' that we skipped pruning before, ### while keeping connections to second order cells! for projection in includeProjs: - print "removing projection",projection.attrib['name'],\ - "keeping second-order connections." + print("removing projection",projection.attrib['name'],\ + "keeping second-order connections.") source = projection.attrib["source"] target = projection.attrib["target"] ## boolean: True if includeCellsDict has key source diff --git a/python/moose/neuroml2/generated_neuroml.py b/python/moose/neuroml2/generated_neuroml.py index b319f6c..f03fa42 100644 --- a/python/moose/neuroml2/generated_neuroml.py +++ b/python/moose/neuroml2/generated_neuroml.py @@ -5,6 +5,7 @@ # Generated Sun Jul 28 10:18:38 2013 by generateDS.py version 2.10a. # +from __future__ import print_function import sys import getopt import re as re_ @@ -14143,7 +14144,7 @@ Usage: python <Parser>.py [ -s ] <in_xml_file> def usage(): - print USAGE_TEXT + print(USAGE_TEXT) sys.exit(1) diff --git a/python/moose/neuroml2/reader.py b/python/moose/neuroml2/reader.py index fa0596e..28d7d5e 100644 --- a/python/moose/neuroml2/reader.py +++ b/python/moose/neuroml2/reader.py @@ -51,6 +51,8 @@ TODO: handle include statements (start with simple ion channel prototype includes. """ + +from __future__ import print_function import sys, os from itertools import izip from urllib2 import urlopen @@ -235,7 +237,7 @@ class NML2Reader(object): according to NeuroML2 cell `nmlcell`.""" bp = nmlcell.biophysicalProperties if bp is None: - print 'Warning: %s in %s has no biophysical properties' % (nmlcell.id, self.filename) + print('Warning: %s in %s has no biophysical properties' % (nmlcell.id, self.filename)) return self.importMembraneProperties(nmlcell, moosecell, bp.membraneProperties) self.importIntracellularProperties(nmlcell, moosecell, bp.intracellularProperties) @@ -302,7 +304,7 @@ class NML2Reader(object): try: ionChannel = self.id_to_ionChannel[chdens.ionChannel] except KeyError: - print 'No channel with id', chdens.ionChannel + print('No channel with id', chdens.ionChannel) continue if ionChannel.type_ == 'ionChannelPassive': for seg in segments: @@ -351,7 +353,7 @@ class NML2Reader(object): error = None break if error: - print 'Last exception:', error + print('Last exception:', error) raise IOError('Could not read any of the locations: %s' % (paths)) def importIonChannels(self, doc, vmin=-120e-3, vmax=40e-3, vdivs=3000): @@ -411,9 +413,9 @@ class NML2Reader(object): else: name = concModel.id ca = moose.CaConc('%s/%s' % (self.lib.path, id)) - print '11111', concModel.restingConc - print '2222', concModel.decayConstant - print '33333', concModel.shellThickness + print('11111', concModel.restingConc) + print('2222', concModel.decayConstant) + print('33333', concModel.shellThickness) ca.CaBasal = SI(concModel.restingConc) ca.tau = SI(concModel.decayConstant) diff --git a/python/moose/neuroml2/test_converter.py b/python/moose/neuroml2/test_converter.py index 4a56dcb..3145551 100644 --- a/python/moose/neuroml2/test_converter.py +++ b/python/moose/neuroml2/test_converter.py @@ -47,6 +47,7 @@ # Code: +from __future__ import print_function import os import numpy as np import uuid @@ -59,7 +60,7 @@ from neuroml.writers import NeuroMLWriter outdir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'tmp') if not os.access(outdir, os.F_OK): - print 'Creating output directory', outdir + print('Creating output directory', outdir) os.mkdir(outdir) class TestConvertMorphology(unittest.TestCase): @@ -91,7 +92,7 @@ class TestConvertMorphology(unittest.TestCase): doc.id = 'TestNeuroMLDocument' fname = os.path.join(outdir, 'test_morphology_conversion.nml') NeuroMLWriter.write(doc, fname) - print 'Wrote', fname + print('Wrote', fname) if __name__ == '__main__': unittest.main() diff --git a/python/moose/neuroml2/test_hhfit.py b/python/moose/neuroml2/test_hhfit.py index 1e72fde..31156ff 100644 --- a/python/moose/neuroml2/test_hhfit.py +++ b/python/moose/neuroml2/test_hhfit.py @@ -47,6 +47,7 @@ # Code: +from __future__ import print_function import os import numpy as np import uuid @@ -82,9 +83,9 @@ class TestFindRateFn(unittest.TestCase): self.p_dblexp = p_dblexp def test_sigmoid(self): - print 'Testing sigmoid' + print('Testing sigmoid') fn, params = hhfit.find_ratefn(self.v_array, self.sigmoid) - print 'Sigmoid params original:', self.p_sigmoid, 'detected:', params + print('Sigmoid params original:', self.p_sigmoid, 'detected:', params) pylab.plot(self.v_array, self.sigmoid, 'y-', self.v_array, hhfit.sigmoid(self.v_array, *self.p_sigmoid), 'b--', self.v_array, fn(self.v_array, *params), 'r-.') @@ -95,9 +96,9 @@ class TestFindRateFn(unittest.TestCase): self.assertAlmostEqual(rms_error/max(abs(self.sigmoid)), 0.0, places=3) def test_exponential(self): - print 'Testing exponential' + print('Testing exponential') fn, params = hhfit.find_ratefn(self.v_array, self.exp) - print 'Exponential params original:', self.p_exp, 'detected:', params + print('Exponential params original:', self.p_exp, 'detected:', params) fnval = hhfit.exponential(self.v_array, *params) pylab.plot(self.v_array, self.exp, 'y-', self.v_array, hhfit.exponential(self.v_array, *self.p_exp), 'b--', @@ -112,13 +113,13 @@ class TestFindRateFn(unittest.TestCase): # pylab.plot(self.v_array, self.exp, 'b-') # pylab.plot(self.v_array, fnval, 'r-.') # pylab.show() - print rms_error, rms_error/max(self.exp) + print(rms_error, rms_error/max(self.exp)) self.assertAlmostEqual(rms_error/max(self.exp), 0.0, places=3) def test_linoid(self): - print 'Testing linoid' + print('Testing linoid') fn, params = hhfit.find_ratefn(self.v_array, self.linoid) - print 'Linoid params original:', self.p_linoid, 'detected:', params + print('Linoid params original:', self.p_linoid, 'detected:', params) pylab.plot(self.v_array, self.linoid, 'y-', self.v_array, hhfit.linoid(self.v_array, *self.p_linoid), 'b--', self.v_array, fn(self.v_array, *params), 'r-.') @@ -133,7 +134,7 @@ class TestFindRateFn(unittest.TestCase): # self.assertAlmostEqual(abs(err/orig), 0.0, places=2) def test_dblexponential(self): - print 'Testing double exponential' + print('Testing double exponential') fn, params = hhfit.find_ratefn(self.v_array, self.dblexp) fnval = fn(self.v_array, *params) pylab.plot(self.v_array, self.dblexp, 'y-', @@ -143,7 +144,7 @@ class TestFindRateFn(unittest.TestCase): pylab.show() self.assertEqual(hhfit.double_exp, fn) rms_error = np.sqrt(np.mean((self.dblexp - fnval)**2)) - print params, rms_error + print(params, rms_error) self.assertAlmostEqual(rms_error/max(self.dblexp), 0.0, places=3) diff --git a/python/moose/neuroml2/test_reader.py b/python/moose/neuroml2/test_reader.py index 8e68525..7afb232 100644 --- a/python/moose/neuroml2/test_reader.py +++ b/python/moose/neuroml2/test_reader.py @@ -45,6 +45,7 @@ # Code: +from __future__ import print_function import unittest import numpy as np import moose @@ -110,7 +111,7 @@ class TestFullCell(unittest.TestCase): def test_protochans(self): """TODO: verify the prototype cahnnel.""" for chan_id in moose.wildcardFind('/library/##[ISA=HHChannel]'): - print moose.element(chan_id) + print(moose.element(chan_id)) def test_HHChannels(self): """Verify copied channel in membrane properties.""" diff --git a/python/moose/neuroml2/units.py b/python/moose/neuroml2/units.py index 5e4a66d..cd89edf 100644 --- a/python/moose/neuroml2/units.py +++ b/python/moose/neuroml2/units.py @@ -49,6 +49,7 @@ in NeuroMLCoreDimensions.xml) to SI """ +from __future__ import print_function import numpy as np import re from xml.etree import ElementTree @@ -67,7 +68,7 @@ def SI(expression): try: match = magnitude_regex.match(expression) except Exception, e: - print 'Error %s with expression: %s' % (e, expression) + print('Error %s with expression: %s' % (e, expression)) raise(e) magnitude = float(match.group(0)) unitstr = re.split(magnitude_regex, expression)[-1] diff --git a/python/moose/recording.py b/python/moose/recording.py index 1cba449..312d1d9 100644 --- a/python/moose/recording.py +++ b/python/moose/recording.py @@ -1,3 +1,4 @@ +from __future__ import print_function import moose as _moose _tick = 8 @@ -218,7 +219,7 @@ def show( try: from matplotlib import pyplot as plt except ImportError: - print "Warning: recording.show(): Cannot find 'matplotlib'. Not showing plots." + print("Warning: recording.show(): Cannot find 'matplotlib'. Not showing plots.") return plots = _selectedPlots( selected ) @@ -230,7 +231,7 @@ def show( if not combine: plt.figure() - print _label( plot ) + print(_label( plot )) plt.plot( plot.time, plot.values, label = _label( plot ) ) plt.legend() diff --git a/python/moose/utils.py b/python/moose/utils.py index 15e86d9..61d5a2e 100644 --- a/python/moose/utils.py +++ b/python/moose/utils.py @@ -1,6 +1,8 @@ #!/usr/bin/env python """Utility functions for MOOSE """ +from __future__ import print_function + __author__ = 'Subhasis Ray and Aditya Gilra, NCBS' __date__ = '21 November 2012' @@ -61,7 +63,7 @@ def readtable(table, filename, separ... [truncated message content] |
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:12:05
|
/usr/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API..." --- pymoose/ematrix.cpp | 2 ++ pymoose/melement.cpp | 2 ++ pymoose/mfield.cpp | 2 ++ pymoose/moosemodule.cpp | 2 ++ 4 files changed, 8 insertions(+) diff --git a/pymoose/ematrix.cpp b/pymoose/ematrix.cpp index f20931a..726ca05 100644 --- a/pymoose/ematrix.cpp +++ b/pymoose/ematrix.cpp @@ -46,6 +46,8 @@ // Code: +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include <Python.h> #include <structmember.h> // This defines the type id macros like T_STRING #include "numpy/arrayobject.h" diff --git a/pymoose/melement.cpp b/pymoose/melement.cpp index 140a677..bb82df0 100644 --- a/pymoose/melement.cpp +++ b/pymoose/melement.cpp @@ -46,6 +46,8 @@ // Code: +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include <Python.h> #include <structmember.h> // This defines the type id macros like T_STRING #include "numpy/arrayobject.h" diff --git a/pymoose/mfield.cpp b/pymoose/mfield.cpp index e264c7b..676c938 100644 --- a/pymoose/mfield.cpp +++ b/pymoose/mfield.cpp @@ -45,6 +45,8 @@ // Code: +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include <Python.h> #include <structmember.h> // This defines the type id macros like T_STRING #include "numpy/arrayobject.h" diff --git a/pymoose/moosemodule.cpp b/pymoose/moosemodule.cpp index 1bed2d6..6641dd5 100644 --- a/pymoose/moosemodule.cpp +++ b/pymoose/moosemodule.cpp @@ -75,6 +75,8 @@ //////////////////////////// Headers //////////////////////////////// +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include <Python.h> #include <structmember.h> // This defines the type id macros like T_STRING #include "numpy/arrayobject.h" -- 1.8.5.3 |
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:58
|
For the last few years, Python 2 is installed as both
python and python2, so the rules can be simplified. As
defined, INSTALLED_PYTHON was used to define flags which
only make sense on UNIX-y systems, since the paths for
Windows will be completely different. So the whole block
can just be removed.
---
Makefile | 31 +++++++++----------------------
1 file changed, 9 insertions(+), 22 deletions(-)
diff --git a/Makefile b/Makefile
index ded4db2..207592d 100644
--- a/Makefile
+++ b/Makefile
@@ -359,32 +359,19 @@ libmoose.so: libs
$(CXX) -G $(LIBS) -o libmoose.so
@echo "Created dynamic library"
+PYTHON_DEBUG_CFLAGS = -fno-strict-aliasing -fwrapv -Wstrict-prototypes -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security
+PYTHON_DEBUG_LDFLAGS = -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
+
# Get the python version
ifneq ($(OSTYPE),win32)
-ifeq ($(PYTHON),3)
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python3 --version 2>&1)))
-PYTHON_CFLAGS := $(shell pkg-config --cflags python3)
-PYTHON_LDFLAGS := $(shell pkg-config --libs python3)
-else # Python 2.x
-PYTHON_VERSION := $(subst ., ,$(lastword $(shell python --version 2>&1)))
-ifneq ($(BUILD),debug)
-PYTHON_CFLAGS := $(shell pkg-config --cflags python3)
-PYTHON_LDFLAGS := $(shell pkg-config --libs python3)
-else
-PYTHON_CFLAGS := $(shell pkg-config --includes python) -fno-strict-aliasing -fwrapv -Wstrict-prototypes -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security
-PYTHON_LDFLAGS := $(shell pkg-config --libs python) -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
-endif # ifneq ($(BUILD),debug)
-endif # ifeq ($(PYTHON),3)
-PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION})
-PYTHON_VERSION_MINOR := $(word 2,${PYTHON_VERSION})
-INSTALLED_PYTHON := python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
+PYTHON_CFLAGS := $(shell pkg-config --cflags python$(PYTHON))
+PYTHON_LDFLAGS := $(shell pkg-config --libs python$(PYTHON))
+ifeq ($(BUILD),debug)
+PYTHON_CFLAGS += $(PYTHON_DEBUG_CFLAGS)
+PYTHON_LDFLAGS += $(PYTHON_DEBUG_LDFLAGS)
+endif # debug
endif
-ifndef PYTHON_CFLAGS
-PYTHON_CFLAGS := -I/usr/include/$(INSTALLED_PYTHON) -fno-strict-aliasing -fwrapv -Wstrict-prototypes -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security
-PYTHON_LDFLAGS := -L/usr/lib/$(INSTALLED_PYTHON) -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
-endif
-# There are some unix/gcc specific paths here. Should be cleaned up in future.
pymoose: python/moose/_moose.so
pymoose: CXXFLAGS += -DPYMOOSE $(PYTHON_CFLAGS)
pymoose: OBJLIBS += pymoose/_pymoose.o basecode/_basecode_pymoose.o
--
1.8.5.3
|
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:51
|
---
python/moose/moose.py | 4 ++--
python/moose/neuroml2/generated_neuroml.py | 2 +-
python/moose/utils.py | 2 +-
python/moose/xmls_to_network/core/neuroml2_parser.py | 2 +-
python/moose/xmls_to_network/parser/nml_parser.py | 2 +-
5 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/python/moose/moose.py b/python/moose/moose.py
index e995ab6..f0c2f1a 100644
--- a/python/moose/moose.py
+++ b/python/moose/moose.py
@@ -32,7 +32,7 @@
# Code:
from __future__ import print_function
-import cStringIO
+import io
import warnings
import platform
import pydoc
@@ -304,7 +304,7 @@ def getmoosedoc(tokens):
"""
indent = ' '
- docstring = cStringIO.StringIO()
+ docstring = io.StringIO()
if not tokens:
return ""
class_path = '/classes/%s' % (tokens[0])
diff --git a/python/moose/neuroml2/generated_neuroml.py b/python/moose/neuroml2/generated_neuroml.py
index f1870f6..0406ec4 100644
--- a/python/moose/neuroml2/generated_neuroml.py
+++ b/python/moose/neuroml2/generated_neuroml.py
@@ -14197,7 +14197,7 @@ def parseEtree(inFileName):
def parseString(inString):
- from StringIO import StringIO
+ from io import StringIO
doc = parsexml_(StringIO(inString))
rootNode = doc.getroot()
roots = get_root_tag(rootNode)
diff --git a/python/moose/utils.py b/python/moose/utils.py
index 7e1515d..9b1c49a 100644
--- a/python/moose/utils.py
+++ b/python/moose/utils.py
@@ -819,7 +819,7 @@ def connect_CaConc(compartment_list, temperature=None):
import uuid
import unittest
import sys
-from cStringIO import StringIO as _sio
+from io import StringIO as _sio
class _TestMooseUtils(unittest.TestCase):
def test_printtree(self):
diff --git a/python/moose/xmls_to_network/core/neuroml2_parser.py b/python/moose/xmls_to_network/core/neuroml2_parser.py
index 686dec7..40829d6 100644
--- a/python/moose/xmls_to_network/core/neuroml2_parser.py
+++ b/python/moose/xmls_to_network/core/neuroml2_parser.py
@@ -14553,7 +14553,7 @@ def parseEtree(inFileName, silence=False):
def parseString(inString, silence=False):
- from StringIO import StringIO
+ from io import StringIO
doc = parsexml_(StringIO(inString))
rootNode = doc.getroot()
roots = get_root_tag(rootNode)
diff --git a/python/moose/xmls_to_network/parser/nml_parser.py b/python/moose/xmls_to_network/parser/nml_parser.py
index 3e228ee..0966e94 100644
--- a/python/moose/xmls_to_network/parser/nml_parser.py
+++ b/python/moose/xmls_to_network/parser/nml_parser.py
@@ -14549,7 +14549,7 @@ def parseEtree(inFileName, silence=False):
def parseString(inString, silence=False):
- from StringIO import StringIO
+ from io import StringIO
doc = parsexml_(StringIO(inString))
rootNode = doc.getroot()
roots = get_root_tag(rootNode)
--
1.8.5.3
|
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:44
|
Hi, Since this is my first post to the list, let me start with an introduction: I work in the Computational and Experimental Neuroplasticity Laboratory directed by dr. Avrama Blackwell. We are currently using a MOOSE model created in Python to fit model parameters to experimental data registered in the lab, with promising results. Following patches allow the MOOSE module to be used from Python 3. They are based on the buildQ branch. Just the module is modified, the GUI parts are still Python 2 only. The following approach is taken: code is tweaked to use a common subset of Python 2 and 3. More specifically, it is made compatible with Python 2.7 and Python 3.3 or later. In a few unavoidable places, like the module initialization in the C++ code, separate branches in #ifdefs are used. In the Python part, some compatiblity imports (in _compat.py) are used to "wrap" the remaining differences. This (using the exact same code under both Python 2 and 3) seems to be nicest way to do the conversion. I haven't done very extensive testing, but at least our model seems to return identical results under Python 2 and 3. I hope posting patches to the mailing list the proper way to submit changes... If no, please let me know. Regards, Zbigniew Jędrzejewski-Szmek Zbigniew Jędrzejewski-Szmek (19): Add gitignore Declare that deprecated Numpy API will not be used Fix warnings about deprecated cast to char* Use pkg-config for Python compliation flags Makefile: simplify detection of python flags Fix compilation under Python 3 Convert to print() Apply has_key fixer Convert to modern raise syntax Apply except fixer Remove some unnecessary .keys() and list() calls Convert to incremental zip, map, filter Add compatiblity layer for basestr and unicode Remove unused import Apply imports fixer Convert to relative imports Remove old separate Python 3 code Make sure classes have __module__ set Add missing space in output .gitignore | 7 + Makefile | 31 +-- gui/shell.py | 2 +- pymoose/ematrix.cpp | 18 +- pymoose/melement.cpp | 2 + pymoose/mfield.cpp | 2 + pymoose/moosemodule.cpp | 38 +++- pymoose/moosemodule.h | 2 + python/moose/_compat.py | 5 + python/moose/alternate.py | 31 +-- python/moose/graphutil.py | 4 +- python/moose/hdfutil.py | 45 ++-- python/moose/moose.py | 38 ++-- python/moose/moose_py3k.py | 249 --------------------- python/moose/mtypes.py | 5 +- python/moose/multiscale/core/mumbl.py | 14 +- python/moose/multiscale/core/simulator.py | 6 +- python/moose/multiscale/core/stimulus.py | 4 +- python/moose/multiscale/core/types.py | 9 +- python/moose/multiscale/helper/graph_methods.py | 4 +- python/moose/multiscale/helper/moose_methods.py | 9 +- .../neuroml/v1.8/GranuleCell/FvsI_Granule98.py | 5 +- .../models/neuroml/v1.8/GranuleCell/Granule98.py | 7 +- .../neuroml/v1.8/GranuleCell/Granule98_hsolve.py | 9 +- .../moose/multiscale/multi_bhalla/diffusionOnly.py | 21 +- python/moose/multiscale/multi_bhalla/lm2.py | 7 +- python/moose/multiscale/multi_bhalla/loadMulti.py | 53 ++--- python/moose/multiscale/multi_bhalla/minimal.py | 3 +- python/moose/multiscale/multi_bhalla/runcell18.py | 16 +- python/moose/multiscale/multi_bhalla/x_compt.py | 3 +- python/moose/multiscale/parser/ChannelML.py | 12 +- python/moose/multiscale/parser/MorphML.py | 6 +- python/moose/multiscale/parser/NetworkML.py | 9 +- python/moose/multiscale/parser/NeuroML.py | 6 +- python/moose/multiscale/parser/parser.py | 2 +- python/moose/multiscale/parser/utils.py | 3 +- python/moose/neuroml/ChannelML.py | 27 +-- python/moose/neuroml/MorphML.py | 33 +-- python/moose/neuroml/NetworkML.py | 23 +- python/moose/neuroml/NeuroML.py | 13 +- python/moose/neuroml/utils.py | 13 +- python/moose/neuroml2/converter.py | 3 +- python/moose/neuroml2/generated_neuroml.py | 160 ++++++------- python/moose/neuroml2/hhfit.py | 2 +- python/moose/neuroml2/reader.py | 26 ++- python/moose/neuroml2/test_converter.py | 5 +- python/moose/neuroml2/test_hhfit.py | 19 +- python/moose/neuroml2/test_reader.py | 3 +- python/moose/neuroml2/units.py | 5 +- python/moose/recording.py | 10 +- python/moose/utils.py | 58 ++--- python/moose/xmls_to_network/.noweb/main.nw | 6 +- python/moose/xmls_to_network/core/hhfit.py | 2 +- python/moose/xmls_to_network/core/load_multi.py | 49 ++-- python/moose/xmls_to_network/core/multiscale.py | 7 +- .../moose/xmls_to_network/core/neuroml2_parser.py | 174 +++++++------- .../moose/xmls_to_network/core/neuroml_to_moose.py | 31 ++- .../moose/xmls_to_network/helper/graph_methods.py | 4 +- python/moose/xmls_to_network/parser/nml_parser.py | 170 +++++++------- .../generatedNEURON/NEURONUtils/NEURONSimUtils.py | 2 +- .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- .../generatedNEURON/NeuroMLUtils/NetworkMLNet.py | 5 +- .../NeuroMLUtils/NetworkMLSaxHandler.py | 91 ++++---- .../twoNeurons/generatedNEURON/twoNeurons.hoc | 4 +- .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- .../generatedPyNN/NeuroMLUtils/NetworkMLNet.py | 5 +- .../NeuroMLUtils/NetworkMLSaxHandler.py | 85 +++---- .../twoNeurons/generatedPyNN/PyNNUtils/Pop.py | 13 +- .../generatedPyNN/PyNNUtils/PyNNUtils.py | 11 +- 69 files changed, 791 insertions(+), 971 deletions(-) create mode 100644 .gitignore create mode 100644 python/moose/_compat.py delete mode 100644 python/moose/moose_py3k.py -- 1.8.5.3 |
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:37
|
Without this, help() does not work.
---
pymoose/moosemodule.cpp | 24 ++++++++++++++++++------
1 file changed, 18 insertions(+), 6 deletions(-)
diff --git a/pymoose/moosemodule.cpp b/pymoose/moosemodule.cpp
index 2dba27b..646373d 100644
--- a/pymoose/moosemodule.cpp
+++ b/pymoose/moosemodule.cpp
@@ -1923,9 +1923,20 @@ extern "C" {
if (base && !define_class(module_dict, base)){
return 0;
}
+
+ string str = "moose." + class_name;
+
PyTypeObject * new_class =
(PyTypeObject*)PyType_Type.tp_alloc(&PyType_Type, 0);
// Py_TYPE(new_class) = &PyType_Type;
+#ifdef PY3K
+ new_class->tp_flags = Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HEAPTYPE;
+ PyHeapTypeObject* et = (PyHeapTypeObject*)new_class;
+ et->ht_name = PyUnicode_FromString(class_name.c_str());
+ et->ht_qualname = PyUnicode_FromString(str.c_str());
+
+ new_class->tp_name = strdup(class_name.c_str());
+#else
new_class->tp_flags = Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE;
// should we avoid Py_TPFLAGS_HEAPTYPE as it imposes certain
// limitations:
@@ -1944,11 +1955,10 @@ extern "C" {
// to a heaptype object (resulting in an invalid pointer). If
// heaptype is not set it uses tp_name to print the help.
// Py_SIZE(new_class) = sizeof(_ObjId);
- string str = "moose." + class_name;
- new_class->tp_name = (char *)calloc(str.length()+1,
- sizeof(char));
- strncpy(const_cast<char*>(new_class->tp_name), str.c_str(),
- str.length());
+
+ new_class->tp_name = strdup(str.c_str());
+#endif
+
new_class->tp_doc = moose_Class_documentation;
// strncpy(new_class->tp_doc, moose_Class_documentation, strlen(moose_Class_documentation));
map<string, PyTypeObject *>::iterator base_iter =
@@ -1999,7 +2009,9 @@ extern "C" {
}
get_moose_classes().insert(pair<string, PyTypeObject*> (class_name, new_class));
Py_INCREF(new_class);
- // PyDict_SetItemString(new_class->tp_dict, "__module__", PyString_FromString("moose"));
+#ifdef PY3K
+ PyDict_SetItemString(new_class->tp_dict, "__module__", PyUnicode_InternFromString("moose"));
+#endif
// string doc = const_cast<Cinfo*>(cinfo)->getDocs();
// PyDict_SetItemString(new_class->tp_dict, "__doc__", PyString_FromString(" \0"));
// PyDict_SetItemString(module_dict, class_name.c_str(), (PyObject *)new_class);
--
1.8.5.3
|
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:30
|
One interesting error was detected: in mumbl.py a code like
this appears:
raise UserWarning, "Unsupported type or parameter", direction
but it doesn't actually work, even under Python 2:
>>> direction = "in"
>>> raise UserWarning, "Unsupported", direction
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: raise: arg 3 must be a traceback or None
The proper fix is to format the string before passing it to raise.
---
python/moose/multiscale/core/mumbl.py | 12 ++++++------
python/moose/multiscale/core/types.py | 5 +----
python/moose/multiscale/helper/moose_methods.py | 4 ++--
python/moose/multiscale/parser/ChannelML.py | 6 +++---
python/moose/multiscale/parser/parser.py | 2 +-
.../twoNeurons/generatedPyNN/PyNNUtils/PyNNUtils.py | 2 +-
6 files changed, 14 insertions(+), 17 deletions(-)
diff --git a/python/moose/multiscale/core/mumbl.py b/python/moose/multiscale/core/mumbl.py
index 32e5ca1..a33b4f7 100644
--- a/python/moose/multiscale/core/mumbl.py
+++ b/python/moose/multiscale/core/mumbl.py
@@ -157,7 +157,7 @@ class Mumble():
debug.printDebug("TODO"
, "Unsupported model type : {0}".format(modelType)
)
- raise UserWarning, "Unsupported model type"
+ raise UserWarning("Unsupported model type")
return None
def loadElectricalModel(self, modelXml):
@@ -200,7 +200,7 @@ class Mumble():
, "Loading user external script is not supported yet."
, frame = inspect.currentframe()
)
- raise UserWarning, "Unimplemented feature"
+ raise UserWarning("Unimplemented feature")
# Otherwise load the model.
modelFilePath = modelXml.get('file_path', None)
@@ -244,7 +244,7 @@ class Mumble():
comparment ids.
"""
if chemType != "chemical":
- raise UserWarning, "Only chemical models are supported"
+ raise UserWarning("Only chemical models are supported")
compPath = os.path.join(self.chemPath, self.compartmentName)
moose.Neutral(compPath)
@@ -303,7 +303,7 @@ class Mumble():
tgts = adaptor.findall('target')
[self.outTarget(t, moosePath) for t in tgts]
else:
- raise UserWarning, "Unsupported type or parameter", direction
+ raise UserWarning("Unsupported type or parameter: {}".format(direction))
def inTarget(self, src, moosePath):
"""Set up incoming source and target.
@@ -325,7 +325,7 @@ class Mumble():
# in which compartment and which type of pool
compId = src.get('compartment_id')
if compId is None:
- raise UserWarning, "Missing parameter or value: compartment_id"
+ raise UserWarning("Missing parameter or value: compartment_id")
species = src.get('species')
assert species, "Must have species in source"
poolId = os.path.join(self.compartmentName, compId)
@@ -372,7 +372,7 @@ class Mumble():
compId = tgt.get('compartment_id')
if compId is None:
- raise UserWarning, "Missing parameter or value: compartment_id"
+ raise UserWarning("Missing parameter or value: compartment_id")
assert int(compId) >= 0, "Not a valid compartment id: %s" % compId
diff --git a/python/moose/multiscale/core/types.py b/python/moose/multiscale/core/types.py
index 4ae60c1..f8fcfae 100644
--- a/python/moose/multiscale/core/types.py
+++ b/python/moose/multiscale/core/types.py
@@ -28,10 +28,7 @@ class DoubleDict:
if k == self.v[self.k.get(k, None)]:
txt.append(unicode('{} <-> {}'.format(k, self.k[k])))
else:
- raise UserWarning, "Duplicate Entries: {} {}".format(
- self.k
- , self.v
- )
+ raise UserWarning("Duplicate Entries: {0.k} {0.v}".format(self))
return '{' + ', '.join(txt) + '}'
diff --git a/python/moose/multiscale/helper/moose_methods.py b/python/moose/multiscale/helper/moose_methods.py
index b99b4bd..e3e9d68 100644
--- a/python/moose/multiscale/helper/moose_methods.py
+++ b/python/moose/multiscale/helper/moose_methods.py
@@ -58,7 +58,7 @@ def moosePath(baseName, append):
elif len(nameSep) == 2:
return baseName + nameSep[0] + append + nameSep[1]
else:
- raise UserWarning, "Not more than 2 characters are not supported"
+ raise UserWarning("Not more than 2 characters are not supported")
else:
return os.path.join(baseName, append)
@@ -96,7 +96,7 @@ def stringToFloat(text):
val = float(text)
return val
except Exception:
- raise UserWarning, "Failed to convert {0} to float".format(text)
+ raise UserWarning("Failed to convert {0} to float".format(text))
def dumpMoosePaths(pat, isRoot=True):
diff --git a/python/moose/multiscale/parser/ChannelML.py b/python/moose/multiscale/parser/ChannelML.py
index f24d7fa..48f642e 100644
--- a/python/moose/multiscale/parser/ChannelML.py
+++ b/python/moose/multiscale/parser/ChannelML.py
@@ -84,7 +84,7 @@ class ChannelML:
Gfactor = 1.0
else:
debug.printDebug("ERROR", "Wrong units {0}".format(units))
- raise UserWarning, "Wrong value or parameter {0}".format(units)
+ raise UserWarning("Wrong value or parameter {0}".format(units))
# creates /library in MOOSE tree; elif present, wraps
# NOTE: This path is created by NeuroML now in __init__. Disabling,
@@ -139,7 +139,7 @@ class ChannelML:
, "wrong units %s. Existing... " % units
, frame = inspect.currentframe()
)
- raise UserWarning, "Unknown units"
+ raise UserWarning("Unknown units")
# creates /library in MOOSE tree; elif present, wraps
channel_name = channelElement.attrib['name']
@@ -184,7 +184,7 @@ class ChannelML:
msg = "Sorry! Maximum x, y, and z (three) gates are possible in\
MOOSE/Genesis"
debug.printDebug("ERR", msg, frame=inspect.currentframe())
- raise UserWarning, "Bad value or parameter"
+ raise UserWarning("Bad value or parameter")
# These are the names that MOOSE uses to create gates.
gate_full_name = [ 'gateX', 'gateY', 'gateZ' ]
diff --git a/python/moose/multiscale/parser/parser.py b/python/moose/multiscale/parser/parser.py
index 4e0c4aa..0f05f28 100644
--- a/python/moose/multiscale/parser/parser.py
+++ b/python/moose/multiscale/parser/parser.py
@@ -39,7 +39,7 @@ def parseWithoutValidation(modelName, modelPath) :
except Exception as e :
debug.printDebug("ERROR", "Parsing of {0} failed.".format(modelPath))
debug.printDebug("DEBUG", "Error: {0}".format(e))
- raise RuntimeError, "Failed to parse XML"
+ raise RuntimeError("Failed to parse XML")
return xmlRootElem
def parseXMLs(commandLineArgs, validate=False) :
diff --git a/python/moose/xmls_to_network/twoNeurons/generatedPyNN/PyNNUtils/PyNNUtils.py b/python/moose/xmls_to_network/twoNeurons/generatedPyNN/PyNNUtils/PyNNUtils.py
index 915eada..a9c04c0 100644
--- a/python/moose/xmls_to_network/twoNeurons/generatedPyNN/PyNNUtils/PyNNUtils.py
+++ b/python/moose/xmls_to_network/twoNeurons/generatedPyNN/PyNNUtils/PyNNUtils.py
@@ -201,7 +201,7 @@ class NetManagerPyNN(NetworkHandler):
freq = float(inputProps["frequency"])
if (self.maxSimLength<0):
- raise ValueError, "The value of maxSimLength must be set!"
+ raise ValueError("The value of maxSimLength must be set!")
numberExp = int(float(self.maxSimLength)*freq)
--
1.8.5.3
|
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:23
|
---
python/moose/neuroml/ChannelML.py | 2 +-
python/moose/neuroml/MorphML.py | 4 +-
python/moose/neuroml/NetworkML.py | 2 +-
.../NeuroMLUtils/NetworkMLSaxHandler.py | 72 +++++++++++-----------
.../NeuroMLUtils/NetworkMLSaxHandler.py | 72 +++++++++++-----------
5 files changed, 76 insertions(+), 76 deletions(-)
diff --git a/python/moose/neuroml/ChannelML.py b/python/moose/neuroml/ChannelML.py
index 79ca6f9..830ee4b 100644
--- a/python/moose/neuroml/ChannelML.py
+++ b/python/moose/neuroml/ChannelML.py
@@ -405,7 +405,7 @@ class ChannelML():
allowed_locals['temp_adj_'+self.gate_name] = self.q10factor
for i,parameter in enumerate(self.parameters):
allowed_locals[parameter[0]] = self.parameters[i][1]
- if kwargs.has_key('concdep'):
+ if 'concdep' in kwargs:
concdep = kwargs['concdep']
## ca should appear as neuroML defined 'variable_name' to eval()
if concdep is not None:
diff --git a/python/moose/neuroml/MorphML.py b/python/moose/neuroml/MorphML.py
index 6982c87..08a20d4 100644
--- a/python/moose/neuroml/MorphML.py
+++ b/python/moose/neuroml/MorphML.py
@@ -131,7 +131,7 @@ class MorphML():
running_comp = moosecomp
running_diameter = 0.0
running_dia_nums = 0
- if segment.attrib.has_key('parent'):
+ if 'parent' in segment.attrib:
parentid = segment.attrib['parent'] # I assume the parent is created before the child so that I can immediately connect the child.
parent = self.cellDictBySegmentId[cellname][1][parentid]
## It is always assumed that axial of parent is connected to raxial of moosesegment
@@ -282,7 +282,7 @@ class MorphML():
for mechanism in cell.findall(".//{"+self.bio+"}mechanism"):
mechanismname = mechanism.attrib["name"]
passive = False
- if mechanism.attrib.has_key("passive_conductance"):
+ if "passive_conductance" in mechanism.attrib:
if mechanism.attrib['passive_conductance'] in ["true",'True','TRUE']:
passive = True
print("Loading mechanism ", mechanismname)
diff --git a/python/moose/neuroml/NetworkML.py b/python/moose/neuroml/NetworkML.py
index a521ed9..b671d66 100644
--- a/python/moose/neuroml/NetworkML.py
+++ b/python/moose/neuroml/NetworkML.py
@@ -115,7 +115,7 @@ class NetworkML():
population = target.attrib['population']
for site in target.findall(".//{"+nml_ns+"}site"):
cell_id = site.attrib['cell_id']
- if site.attrib.has_key('segment_id'): segment_id = site.attrib['segment_id']
+ if 'segment_id' in site.attrib: segment_id = site.attrib['segment_id']
else: segment_id = 0 # default segment_id is specified to be 0
## population is populationname, self.populationDict[population][0] is cellname
cell_name = self.populationDict[population][0]
diff --git a/python/moose/xmls_to_network/twoNeurons/generatedNEURON/NeuroMLUtils/NetworkMLSaxHandler.py b/python/moose/xmls_to_network/twoNeurons/generatedNEURON/NeuroMLUtils/NetworkMLSaxHandler.py
index 93ce0e0..e73b0b2 100644
--- a/python/moose/xmls_to_network/twoNeurons/generatedNEURON/NeuroMLUtils/NetworkMLSaxHandler.py
+++ b/python/moose/xmls_to_network/twoNeurons/generatedNEURON/NeuroMLUtils/NetworkMLSaxHandler.py
@@ -157,11 +157,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.currentProjectionName = attrs.get('name',"")
self.log.debug("Found projection element: "+ self.currentProjectionName)
- if attrs.has_key('source'):
+ if 'source' in attrs:
self.currentProjectionSource = attrs.get('source',"")
- if attrs.has_key('target'):
+ if 'target' in attrs:
self.currentProjectionTarget = attrs.get('target',"")
self.log.info("Projection: "+ self.currentProjectionName+" is from: "+ self.currentProjectionSource +" to: "+ self.currentProjectionTarget)
@@ -171,7 +171,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.isSourceElement = 1
- elif name == 'target' and not attrs.has_key('cell_group') and not attrs.has_key('population'):
+ elif name == 'target' and 'cell_group' not in attrs and 'population' not in attrs:
if self.currentProjectionName != "":
self.isTargetElement = 1
@@ -197,27 +197,27 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.currentConnId = attrs.get('id',"")
self.log.debug("Found connection element: "+ self.currentConnId)
- if attrs.has_key('pre_cell_id'):
+ if 'pre_cell_id' in attrs:
self.preCellId = attrs.get('pre_cell_id',"")
- if attrs.has_key('pre_segment_id'):
+ if 'pre_segment_id' in attrs:
self.preSegId = attrs.get('pre_segment_id',"")
else:
self.preSegId = 0
- if attrs.has_key('pre_fraction_along'):
+ if 'pre_fraction_along' in attrs:
self.preFract = attrs.get('pre_fraction_along',"")
else:
self.preFract = 0.5
- if attrs.has_key('post_cell_id'):
+ if 'post_cell_id' in attrs:
self.postCellId = attrs.get('post_cell_id',"")
- if attrs.has_key('post_segment_id'):
+ if 'post_segment_id' in attrs:
self.postSegId = attrs.get('post_segment_id',"")
else:
self.postSegId = 0
- if attrs.has_key('post_fraction_along'):
+ if 'post_fraction_along' in attrs:
self.postFract = attrs.get('post_fraction_along',"")
else:
self.postFract = 0.5
@@ -232,11 +232,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'pre':
if self.currentProjectionName != "":
self.preCellId = attrs.get('cell_id',"")
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
self.preSegId = attrs.get('segment_id',"")
else:
self.preSegId = 0
- if attrs.has_key('fraction_along'):
+ if 'fraction_along' in attrs:
self.preFract = attrs.get('fraction_along',"")
else:
self.preFract = 0.5
@@ -246,11 +246,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'post':
if self.currentProjectionName != "":
self.postCellId = attrs.get('cell_id',"")
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
self.postSegId = attrs.get('segment_id',"")
else:
self.postSegId = 0
- if attrs.has_key('fraction_along'):
+ if 'fraction_along' in attrs:
self.postFract = attrs.get('fraction_along',"")
else:
self.postFract = 0.5
@@ -262,22 +262,22 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
if self.currentProjectionName != "":
newSynapseProps = SynapseProperties()
- if attrs.has_key('synapse_type'):
+ if 'synapse_type' in attrs:
self.latestSynapseType = str(attrs.get('synapse_type'))
self.log.debug("synapse_type is: "+self.latestSynapseType)
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
newSynapseProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
newSynapseProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
newSynapseProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
newSynapseProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
newSynapseProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
newSynapseProps.threshold = attrs.get('threshold',"")
self.globalSynapseProps[self.latestSynapseType] = newSynapseProps
@@ -295,17 +295,17 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
if self.currentProjectionName != "":
newSynapseProps = SynapseProperties()
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
newSynapseProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
newSynapseProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
newSynapseProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
newSynapseProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
newSynapseProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
newSynapseProps.threshold = attrs.get('threshold',"")
self.globalSynapseProps[self.latestSynapseType] = newSynapseProps
@@ -319,7 +319,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
synapse_type = ""
- if attrs.has_key('synapse_type'):
+ if 'synapse_type' in attrs:
synapse_type = attrs.get('synapse_type',"")
elif len(self.localSynapseProps) == 1:
synapse_type = self.localSynapseProps.keys()[0]
@@ -328,17 +328,17 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
synProps = self.localSynapseProps[synapse_type]
self.log.debug("Changing values of local syn props of: "+ synapse_type+", was: "+ str(synProps))
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
synProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
synProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
synProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
synProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
synProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
synProps.threshold = attrs.get('threshold',"")
self.log.info("Changed vals of local syn props: "+ synapse_type+": "+ str(synProps))
@@ -367,7 +367,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'sites':
size = -1
- if attrs.has_key('size'):
+ if 'size' in attrs:
size = int(attrs.get('size',""))
@@ -378,10 +378,10 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
cell_id = int(attrs.get('cell_id',""))
segment_id = 0
fract = 0.5
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
segment_id = int(attrs.get('segment_id',""))
- if attrs.has_key('fract'):
+ if 'fract' in attrs:
fract = float(attrs.get('fract',""))
self.netHandler.handleSingleInput(self.currentInputName, cell_id, segment_id, fract)
diff --git a/python/moose/xmls_to_network/twoNeurons/generatedPyNN/NeuroMLUtils/NetworkMLSaxHandler.py b/python/moose/xmls_to_network/twoNeurons/generatedPyNN/NeuroMLUtils/NetworkMLSaxHandler.py
index 93ce0e0..e73b0b2 100644
--- a/python/moose/xmls_to_network/twoNeurons/generatedPyNN/NeuroMLUtils/NetworkMLSaxHandler.py
+++ b/python/moose/xmls_to_network/twoNeurons/generatedPyNN/NeuroMLUtils/NetworkMLSaxHandler.py
@@ -157,11 +157,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.currentProjectionName = attrs.get('name',"")
self.log.debug("Found projection element: "+ self.currentProjectionName)
- if attrs.has_key('source'):
+ if 'source' in attrs:
self.currentProjectionSource = attrs.get('source',"")
- if attrs.has_key('target'):
+ if 'target' in attrs:
self.currentProjectionTarget = attrs.get('target',"")
self.log.info("Projection: "+ self.currentProjectionName+" is from: "+ self.currentProjectionSource +" to: "+ self.currentProjectionTarget)
@@ -171,7 +171,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.isSourceElement = 1
- elif name == 'target' and not attrs.has_key('cell_group') and not attrs.has_key('population'):
+ elif name == 'target' and 'cell_group' not in attrs and 'population' not in attrs:
if self.currentProjectionName != "":
self.isTargetElement = 1
@@ -197,27 +197,27 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
self.currentConnId = attrs.get('id',"")
self.log.debug("Found connection element: "+ self.currentConnId)
- if attrs.has_key('pre_cell_id'):
+ if 'pre_cell_id' in attrs:
self.preCellId = attrs.get('pre_cell_id',"")
- if attrs.has_key('pre_segment_id'):
+ if 'pre_segment_id' in attrs:
self.preSegId = attrs.get('pre_segment_id',"")
else:
self.preSegId = 0
- if attrs.has_key('pre_fraction_along'):
+ if 'pre_fraction_along' in attrs:
self.preFract = attrs.get('pre_fraction_along',"")
else:
self.preFract = 0.5
- if attrs.has_key('post_cell_id'):
+ if 'post_cell_id' in attrs:
self.postCellId = attrs.get('post_cell_id',"")
- if attrs.has_key('post_segment_id'):
+ if 'post_segment_id' in attrs:
self.postSegId = attrs.get('post_segment_id',"")
else:
self.postSegId = 0
- if attrs.has_key('post_fraction_along'):
+ if 'post_fraction_along' in attrs:
self.postFract = attrs.get('post_fraction_along',"")
else:
self.postFract = 0.5
@@ -232,11 +232,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'pre':
if self.currentProjectionName != "":
self.preCellId = attrs.get('cell_id',"")
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
self.preSegId = attrs.get('segment_id',"")
else:
self.preSegId = 0
- if attrs.has_key('fraction_along'):
+ if 'fraction_along' in attrs:
self.preFract = attrs.get('fraction_along',"")
else:
self.preFract = 0.5
@@ -246,11 +246,11 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'post':
if self.currentProjectionName != "":
self.postCellId = attrs.get('cell_id',"")
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
self.postSegId = attrs.get('segment_id',"")
else:
self.postSegId = 0
- if attrs.has_key('fraction_along'):
+ if 'fraction_along' in attrs:
self.postFract = attrs.get('fraction_along',"")
else:
self.postFract = 0.5
@@ -262,22 +262,22 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
if self.currentProjectionName != "":
newSynapseProps = SynapseProperties()
- if attrs.has_key('synapse_type'):
+ if 'synapse_type' in attrs:
self.latestSynapseType = str(attrs.get('synapse_type'))
self.log.debug("synapse_type is: "+self.latestSynapseType)
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
newSynapseProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
newSynapseProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
newSynapseProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
newSynapseProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
newSynapseProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
newSynapseProps.threshold = attrs.get('threshold',"")
self.globalSynapseProps[self.latestSynapseType] = newSynapseProps
@@ -295,17 +295,17 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
if self.currentProjectionName != "":
newSynapseProps = SynapseProperties()
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
newSynapseProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
newSynapseProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
newSynapseProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
newSynapseProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
newSynapseProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
newSynapseProps.threshold = attrs.get('threshold',"")
self.globalSynapseProps[self.latestSynapseType] = newSynapseProps
@@ -319,7 +319,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
synapse_type = ""
- if attrs.has_key('synapse_type'):
+ if 'synapse_type' in attrs:
synapse_type = attrs.get('synapse_type',"")
elif len(self.localSynapseProps) == 1:
synapse_type = self.localSynapseProps.keys()[0]
@@ -328,17 +328,17 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
synProps = self.localSynapseProps[synapse_type]
self.log.debug("Changing values of local syn props of: "+ synapse_type+", was: "+ str(synProps))
- if attrs.has_key('internal_delay'):
+ if 'internal_delay' in attrs:
synProps.internalDelay = attrs.get('internal_delay',"")
- if attrs.has_key('pre_delay'):
+ if 'pre_delay' in attrs:
synProps.preDelay = attrs.get('pre_delay',"")
- if attrs.has_key('post_delay'):
+ if 'post_delay' in attrs:
synProps.postDelay = attrs.get('post_delay',"")
- if attrs.has_key('prop_delay'):
+ if 'prop_delay' in attrs:
synProps.propDelay = attrs.get('prop_delay',"")
- if attrs.has_key('weight'):
+ if 'weight' in attrs:
synProps.weight = attrs.get('weight',"")
- if attrs.has_key('threshold'):
+ if 'threshold' in attrs:
synProps.threshold = attrs.get('threshold',"")
self.log.info("Changed vals of local syn props: "+ synapse_type+": "+ str(synProps))
@@ -367,7 +367,7 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
elif name == 'sites':
size = -1
- if attrs.has_key('size'):
+ if 'size' in attrs:
size = int(attrs.get('size',""))
@@ -378,10 +378,10 @@ class NetworkMLSaxHandler(xml.sax.ContentHandler):
cell_id = int(attrs.get('cell_id',""))
segment_id = 0
fract = 0.5
- if attrs.has_key('segment_id'):
+ if 'segment_id' in attrs:
segment_id = int(attrs.get('segment_id',""))
- if attrs.has_key('fract'):
+ if 'fract' in attrs:
fract = float(attrs.get('fract',""))
self.netHandler.handleSingleInput(self.currentInputName, cell_id, segment_id, fract)
--
1.8.5.3
|
|
From: Zbigniew Jędrzejewski-S. <zb...@in...> - 2014-04-01 21:11:15
|
---
python/moose/_compat.py | 5 +++++
python/moose/multiscale/core/types.py | 2 ++
python/moose/neuroml2/generated_neuroml.py | 2 ++
python/moose/neuroml2/reader.py | 2 +-
python/moose/recording.py | 2 ++
python/moose/utils.py | 2 ++
python/moose/xmls_to_network/core/neuroml2_parser.py | 6 ++++--
python/moose/xmls_to_network/parser/nml_parser.py | 2 ++
8 files changed, 20 insertions(+), 3 deletions(-)
create mode 100644 python/moose/_compat.py
diff --git a/python/moose/_compat.py b/python/moose/_compat.py
new file mode 100644
index 0000000..d672d33
--- /dev/null
+++ b/python/moose/_compat.py
@@ -0,0 +1,5 @@
+try:
+ basestr
+except NameError:
+ basestring = str
+ unicode = str
diff --git a/python/moose/multiscale/core/types.py b/python/moose/multiscale/core/types.py
index f8fcfae..a691c4b 100644
--- a/python/moose/multiscale/core/types.py
+++ b/python/moose/multiscale/core/types.py
@@ -5,6 +5,8 @@
Last modified: Tue Jan 07, 2014 10:58AM
"""
+
+from moose._compat import basestring
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
diff --git a/python/moose/neuroml2/generated_neuroml.py b/python/moose/neuroml2/generated_neuroml.py
index e39161d..f1870f6 100644
--- a/python/moose/neuroml2/generated_neuroml.py
+++ b/python/moose/neuroml2/generated_neuroml.py
@@ -12,6 +12,8 @@ import re as re_
import base64
import datetime as datetime_
+from moose._compat import basestring, unicode
+
etree_ = None
Verbose_import_ = False
XMLParser_import_none, XMLParser_import_lxml, XMLParser_import_elementtree = 0, 1, 2
diff --git a/python/moose/neuroml2/reader.py b/python/moose/neuroml2/reader.py
index 7d51790..2da4aa7 100644
--- a/python/moose/neuroml2/reader.py
+++ b/python/moose/neuroml2/reader.py
@@ -55,13 +55,13 @@ prototype includes.
from __future__ import print_function
from future_builtins import zip, map
import sys, os
-from urllib2 import urlopen
import numpy as np
import moose
import generated_neuroml as nml
from units import SI
import hhfit
import logging
+from moose._compat import from basestring
loglevel = logging.DEBUG
logstream = logging.StreamHandler()
diff --git a/python/moose/recording.py b/python/moose/recording.py
index 066d2e5..21c60a2 100644
--- a/python/moose/recording.py
+++ b/python/moose/recording.py
@@ -2,6 +2,8 @@ from __future__ import print_function
from future_builtins import zip
import moose as _moose
+from _compat import basestr
+
_tick = 8
_base = '/_utils'
_path = _base + '/y{0}'
diff --git a/python/moose/utils.py b/python/moose/utils.py
index 61d5a2e..7e1515d 100644
--- a/python/moose/utils.py
+++ b/python/moose/utils.py
@@ -10,6 +10,8 @@ import types, parser, token, symbol, string, os, math
from datetime import datetime
import _moose
+from _compat import basestring
+
## for Ca Pool
#FARADAY = 96154.0 # Coulombs # from cadecay.mod : 1/(2*96154.0) = 5.2e-6 which is the Book of Genesis / readcell value
FARADAY = 96485.3415 # Coulombs/mol # from Wikipedia
diff --git a/python/moose/xmls_to_network/core/neuroml2_parser.py b/python/moose/xmls_to_network/core/neuroml2_parser.py
index 4e20177..686dec7 100644
--- a/python/moose/xmls_to_network/core/neuroml2_parser.py
+++ b/python/moose/xmls_to_network/core/neuroml2_parser.py
@@ -12,6 +12,8 @@ import re as re_
import base64
import datetime as datetime_
+from moose._compat import basestring
+
etree_ = None
Verbose_import_ = False
XMLParser_import_none, XMLParser_import_lxml, XMLParser_import_elementtree = 0, 1, 2
@@ -387,7 +389,7 @@ def showIndent(outfile, level, pretty_print=True):
def quote_xml(inStr):
if not inStr:
return ''
- s1 = (isinstance(inStr, basestring) and inStr or
+ s1 = (isinstance(inStr, str) and inStr or
'%s' % inStr)
s1 = s1.replace('&', '&')
s1 = s1.replace('<', '<')
@@ -396,7 +398,7 @@ def quote_xml(inStr):
def quote_attrib(inStr):
- s1 = (isinstance(inStr, basestring) and inStr or
+ s1 = (isinstance(inStr, str) and inStr or
'%s' % inStr)
s1 = s1.replace('&', '&')
s1 = s1.replace('<', '<')
diff --git a/python/moose/xmls_to_network/parser/nml_parser.py b/python/moose/xmls_to_network/parser/nml_parser.py
index 16f4186..3e228ee 100644
--- a/python/moose/xmls_to_network/parser/nml_parser.py
+++ b/python/moose/xmls_to_network/parser/nml_parser.py
@@ -12,6 +12,8 @@ import re as re_
import base64
import datetime as datetime_
+from moose._compat import basestring
+
etree_ = None
Verbose_import_ = False
XMLParser_import_none, XMLParser_import_lxml, XMLParser_import_elementtree = 0, 1, 2
--
1.8.5.3
|
3 messages has been excluded from this view by a project administrator.
